@article {1313, title = {Open-source electronic health record systems: A systematic review of most recent advances.}, journal = {Health Informatics J}, volume = {28}, year = {2022}, month = {2022 Apr-Jun}, pages = {14604582221099828}, abstract = {

Open-source Electronic Health Records (OS-EHRs) are of pivotal importance in the management, operations, and administration of any healthcare organization. With the advancement of health informatics, researchers and healthcare practitioners have proposed various frameworks to assess the maturation of Open-source EHRs. The significance of OS-EHRs stems from the fact that vendor-based EHR implementations are becoming financially burdensome, with some vendors raking in more than $1 billion with one contract. Contrarily, the adoption of OS-EHRs suffers from a lack of systematic evaluation from the standpoint of a standard reference model. To this end, the Healthcare Information and Management Systems Society (HIMSS) has presented a strategic road map called EMR Adoption and Maturity (EMRAM). The HIMSS-EMRAM model proposes a stage-wise model approach that is globally recognized and can be essentially applied as a benchmark evaluation criteria for open-source EHRs. This paper offers an applied descriptive methodology over the frequently studied open-source EHRs currently operational worldwide or has the potential of adoption in healthcare settings. Besides, we also present profiling (User Support, Developer{\textquoteright} Support, Customization Support, Technical details, and Diagnostic help) of studied OS-EHRs from developer{\textquoteright}s and user{\textquoteright}s perspectives using updated standard metrics. We carried out multi-aspect objective analysis of studied systems covering EHR functions, software based features and implementation. This review portrays systematic aspects of electronic medical record standards for open-source software implementations. As we observed in the literature, prevalent research and working prototypes lack systematic review of the HIMSS-EMRAM model and do not present evolving software features. Therefore, after the application of our assessment measures, the results obtained indicate that OS-EHRs are yet to acquire standard compliance and implementation. The findings in this paper can be beneficial in the planning and implementation of OS-EHRs projects in the future.

}, keywords = {electronic health records, Humans, Medical Informatics, Publications, Software}, issn = {1741-2811}, doi = {10.1177/14604582221099828}, author = {Shaikh, Mohsin and Vayani, Arshad Hm and Akram, Sabina and Qamar, Nafees} } @article {1312, title = {The case for free and open source software in research and scholarship.}, journal = {Philos Trans A Math Phys Eng Sci}, volume = {379}, year = {2021}, month = {2021 May 17}, pages = {20200079}, abstract = {

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other {\textquoteright}open{\textquoteright} initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability-including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of {\textquoteright}open source{\textquoteright} as {\textquoteright}open code{\textquoteright} is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today. This article is part of the theme issue {\textquoteright}Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification {\textquoteright}.

}, issn = {1471-2962}, doi = {10.1098/rsta.2020.0079}, author = {Fortunato, Laura and Galassi, Mark} } @article {1301, title = {Use of cost-effective technologies for a routine clinical pathology laboratory}, journal = {Lab on a Chip}, year = {2021}, month = {2021}, pages = { - }, abstract = {Classically, the need for highly sophisticated instruments with important economic costs has been a major limiting factor for clinical pathology laboratories, especially in developing countries. With the aim of making clinical pathology more accessible, a wide variety of free or economical technologies have been developed worldwide in the last years. 3D printing and Arduino approaches can provide up to 94\% economical savings in hardware and instrumentation in comparison to commercial alternatives. The vast selection of Point-of-Care-Tests (POCT) currently available also limits the need for specific instruments or personnel, as they can be used almost anywhere and by anyone. Lastly, there are dozens of free and libre digital tools available in health informatics. This review provides an overview of the state-of-the-art on cost-effective alternatives with applications in routine clinical pathology laboratories. In this context, a variety of technologies including 3D printing and Arduino, lateral flow assays, plasmonic biosensors, and microfluidics, as well as laboratory information systems, are discussed. This review aims to serve as an introduction to different technologies that can make clinical pathology more accessible and, therefore, contribute to achieve universal health coverage.}, isbn = {1473-0197}, url = {http://dx.doi.org/10.1039/D1LC00658D}, author = {Vazquez, Mercedes and Anfossi, L. and Ben-Yoav, Hader and Di{\'e}guez, Lorena and Karopka, Thomas and Della Ventura, Bartolomeo and Abalde-Cela, Sara and Minopoli, Antonio and Di Nardo, Fabio and Kumar Shukla, Vikas and Teixeira, Alexandra and Tvarijonaviciute, Asta and Franco, Lorena} } @article {1299, title = {Using Open Source, Open Data, and Civic Technology to Address the COVID-19 Pandemic and Infodemic.}, journal = {Yearb Med Inform}, year = {2021}, month = {2021 Apr 21}, abstract = {

OBJECTIVES: The emerging COVID-19 pandemic has caused one of the world{\textquoteright}s worst health disasters compounded by social confusion with misinformation, the so-called "Infodemic". In this paper, we discuss how open technology approaches - including data sharing, visualization, and tooling - can address the COVID-19 pandemic and infodemic.

METHODS: In response to the call for participation in the 2020 International Medical Informatics Association (IMIA) Yearbook theme issue on Medical Informatics and the Pandemic, the IMIA Open Source Working Group surveyed recent works related to the use of Free/Libre/Open Source Software (FLOSS) for this pandemic.

RESULTS: FLOSS health care projects including GNU Health, OpenMRS, DHIS2, and others, have responded from the early phase of this pandemic. Data related to COVID-19 have been published from health organizations all over the world. Civic Technology, and the collaborative work of FLOSS and open data groups were considered to support collective intelligence on approaches to managing the pandemic.

CONCLUSION: FLOSS and open data have been effectively used to contribute to managing the COVID-19 pandemic, and open approaches to collaboration can improve trust in data.

}, issn = {2364-0502}, doi = {10.1055/s-0041-1726488}, author = {Kobayashi, Shinji and Falc{\'o}n, Luis and Fraser, Hamish and Braa, J{\o}rn and Amarakoon, Pamod and Marcelo, Alvin and Paton, Chris} } @article {1304, title = {iBEX: Modular Open-Source Software for Digital Radiography.}, journal = {J Digit Imaging}, volume = {33}, year = {2020}, month = {2020 06}, pages = {708-721}, abstract = {

A device-independent software package, named iBEX, is developed to accelerate the research and development efforts for X-ray imaging setups such as chest radiography, linear and multidirectional tomography, and dental and skeletal radiography. Its extension mechanism makes the software adaptable for a wide range of digital X-ray imaging hardware combinations and provides capabilities for researchers to develop image processing plug-ins. Independent of the X-ray sensor technology, iBEX could integrate with heterogeneous communication channels of digital detectors. iBEX is a freeware option for preclinical and early clinical testing of radiography devices. It provides tools to calibrate the device, integrate to health information infrastructure, acquire image, store studies on local storage, and send them to Picture Archiving and Communication System (PACS). iBEX is a unique open-source project bringing X-ray imaging devices{\textquoteright} software into the scope of the open-source community to reduce the X-ray scanners{\textquoteright} research effort, potentially increase the image quality, and cut down the production and testing costs of radiography devices.

}, keywords = {Humans, Image Processing, Computer-Assisted, Radiographic Image Enhancement, Radiology Information Systems, Software, Tomography, X-Ray Computed}, issn = {1618-727X}, doi = {10.1007/s10278-019-00304-1}, author = {Brusan, Altay and Durmaz, F Ayta{\c c} and Yaman, Alper and {\"O}zt{\"u}rk, Cengizhan} } @article {1303, title = {Machado: Open source genomics data integration framework.}, journal = {Gigascience}, volume = {9}, year = {2020}, month = {2020 09 14}, abstract = {

BACKGROUND: Genome projects and multiomics experiments generate huge volumes of data that must be stored, mined, and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for more than a decade and have been implementing software and databases to meet this challenge. The GMOD{\textquoteright}s (Generic Model Organism Database) biological relational database schema, known as Chado, is one of the few successful open source initiatives; it is widely adopted and many software packages are able to connect to it.

FINDINGS: We have been developing an open source software package named Machado, a genomics data integration framework implemented in Python, to enable research groups to both store and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on top of already existing databases. It has several data-loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL, and LSTrAP. There is an API to connect to JBrowse, and a web visualization tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a Google-like search, i.e., single auto-complete search box that provides fast results and filters.

CONCLUSION: Machado aims to be a modern object-relational framework that uses the latest Python libraries to produce an effective open source resource for genomics research.

}, issn = {2047-217X}, doi = {10.1093/gigascience/giaa097}, author = {Mudadu, Mauricio de Alvarenga and Zerlotini, Adhemar} } @article {1212, title = {Bangladesh{\textquoteright}s digital health journey: reflections on a decade of quiet revolution.}, journal = {WHO South East Asia J Public Health}, volume = {8}, year = {2019}, month = {2019 09}, pages = {71-76}, abstract = {

Bangladesh has made remarkable progress in digital health in recent years. Through one of the world{\textquoteright}s largest deployments to date of the open-source District Health Information Software 2 (DHIS2), the country now has a national public sector health data warehouse. Information from previously fragmented data systems is now unified in a common data repository, enabling data exchange for health information systems and decision-making. Work is ongoing to create lifetime electronic health records for all citizens that can be transferred between health facilities. Extensive customization of open-source software has laid the foundations for a national digital networking system. Initiatives have focused on producing digital solutions to aid priorities such as strengthening the health system as a whole as well as supporting specific technical interventions, for example improving the civil registration and vital statistics system. Digital solutions have also supported the Bangladesh health workforce strategy through a set of registries that electronically captures and maintains human resource information for the entire public health sector, including monitoring staff attendance through the use of low-cost biometric fingerprint time-attendance machines. Citizens are encouraged to engage in shaping health services via a web-based complaints and suggestions system, and a new system to raise health awareness via public digital displays has started in Dhaka. Strong support at the highest political level has been critical to the success of efforts to introduce these innovations. The endeavour has also generated a cadre of enthusiastic eHealth proponents, who are focused on further strengthening and expanding the existing systems and on harnessing the vast amount of information amassed at the central data repository through big data analysis, artificial intelligence and machine learning.

}, issn = {2304-5272}, doi = {10.4103/2224-3151.264849}, author = {Khan, Muhammad Abdul Hannan and Cruz, Valeria de Oliveira and Azad, Abul Kalam} } @article {1220, title = {CODE STROKE ALERT-Concept and Development of a Novel Open-Source Platform to Streamline Acute Stroke Management.}, journal = {Front Neurol}, volume = {10}, year = {2019}, month = {2019}, pages = {725}, abstract = {

Effective, time-critical intervention in acute stroke is crucial to mitigate mortality rate and morbidity, but delivery of reperfusion treatments is often hampered by pre-, in-, or inter-hospital system level delays. Disjointed, repetitive, and inefficient communication is a consistent contributor to avoidable treatment delay. In the era of rapid reperfusion therapy for ischemic stroke, there is a need for a communication system to synchronize the flow of clinical information across the entire stroke journey. A multi-disciplinary development team designed an electronic communications platform, integrated between web browsers and a mobile application, to link all relevant members of the stroke treatment pathway. The platform uses tiered notifications, geotagging, incorporates multiple clinical score calculators, and is compliant with security regulations. The system safely saves relevant information for audit and research. Code Stroke Alert is a platform that can be accessed by emergency medical services (EMS) and hospital staff, coordinating the flow of information during acute stroke care, reducing duplication, and error in clinical information handover. Electronic data logs provide an auditable trail of relevant quality improvement metrics, facilitating quality improvement, and research. Code Stroke Alert will be freely available to health networks globally. The open-source nature of the software offers valuable potential for future development of plug-ins and add-ons, based on individual institutional needs. Prospective, multi-site implementation, and measurement of clinical impact are underway.

}, issn = {1664-2295}, doi = {10.3389/fneur.2019.00725}, author = {Seah, Huey Ming and Burney, Moe and Phan, Michael and Shell, Daniel and Wu, Jamin and Zhou, Kevin and Brooks, Owen and Coulton, Bronwyn and Maingard, Julian and Tang, Jennifer and Yazdabadi, Gohar and Tahayori, Bahman and Barras, Christen and Kok, Hong Kuan and Chandra, Ronil and Thijs, Vincent and Brooks, Duncan Mark and Asadi, Hamed} } @article {1289, title = {Community-led data collection using Open Data Kit for surveillance of animal African trypanosomiasis in Shimba hills, Kenya.}, journal = {BMC Res Notes}, volume = {12}, year = {2019}, month = {2019 Mar 18}, pages = {151}, abstract = {

OBJECTIVE: In Sub-Saharan Africa, there is an increase in trypanosome non-susceptibility to multiple trypanocides, but limited information on judicious trypanocide use is accessible to smallholder farmers and agricultural stakeholders in disease endemic regions, resulting in widespread multi-drug resistance. Huge economic expenses and the laborious nature of extensive field studies have hindered collection of the requisite large-scale prospective datasets required to inform disease management. We examined the efficacy of community-led data collection strategies using smartphones by smallholder farmers to acquire robust datasets from the trypanosomiasis endemic Shimba hills region in Kenya. We used Open Data Kit, an open-source smartphone application development software, to create a data collection App.

RESULTS: Our study provides proof of concept for the viability of using smartphone Apps to remotely collect reliable large-scale information from smallholder farmers and veterinary health care givers in resource poor settings. We show that these datasets can be reliably collated remotely, analysed, and the findings can inform policies that improve farming practices and economic wellbeing while restricting widespread multi-drug resistance. Moreover, this strategy can be used to monitor and manage other infectious diseases in other rural, resource poor settings.

}, keywords = {Adult, Animals, Cattle, Cattle Diseases, Community-Based Participatory Research, Data Collection, Epidemiological Monitoring, Farmers, Female, Humans, Kenya, Male, Mobile Applications, Pilot Projects, Proof of Concept Study, Trypanosomiasis, African}, issn = {1756-0500}, doi = {10.1186/s13104-019-4198-z}, author = {Wamwenje, Sarah A O and Wangwe, Ibrahim I and Masila, Nicodemus and Mirieri, Caroline K and Wambua, Lillian and Kulohoma, Benard W} } @article {1226, title = {Comparison of Open-Source Electronic Health Record Systems Based on Functional and User Performance Criteria.}, journal = {Healthc Inform Res}, volume = {25}, year = {2019}, month = {2019 Apr}, pages = {89-98}, abstract = {

Objectives: Open-source Electronic Health Record (EHR) systems have gained importance. The main aim of our research is to guide organizational choice by comparing the features, functionality, and user-facing system performance of the five most popular open-source EHR systems.

Methods: We performed qualitative content analysis with a directed approach on recently published literature (2012-2017) to develop an integrated set of criteria to compare the EHR systems. The functional criteria are an integration of the literature, meaningful use criteria, and the Institute of Medicine{\textquoteright}s functional requirements of EHR, whereas the user-facing system performance is based on the time required to perform basic tasks within the EHR system.

Results: Based on the Alexa web ranking and Google Trends, the five most popular EHR systems at the time of our study were OSHERA VistA, GNU Health, the Open Medical Record System (OpenMRS), Open Electronic Medical Record (OpenEMR), and OpenEHR. We also found the trends in popularity of the EHR systems and the locations where they were more popular than others. OpenEMR met all the 32 functional criteria, OSHERA VistA met 28, OpenMRS met 12 fully and 11 partially, OpenEHR-based EHR met 10 fully and 3 partially, and GNU Health met the least with only 10 criteria fully and 2 partially.

Conclusions: Based on our functional criteria, OpenEMR is the most promising EHR system, closely followed by VistA. With regards to user-facing system performance, OpenMRS has superior performance in comparison to OpenEMR.

}, issn = {2093-3681}, doi = {10.4258/hir.2019.25.2.89}, author = {Purkayastha, Saptarshi and Allam, Roshini and Maity, Pallavi and Gichoya, Judy W} } @article {1286, title = {Cytomine: Toward an Open and Collaborative Software Platform for Digital Pathology Bridged to Molecular Investigations.}, journal = {Proteomics Clin Appl}, volume = {13}, year = {2019}, month = {2019 01}, pages = {e1800057}, abstract = {

PURPOSE: Digital histology is being increasingly used in research and clinical applications. In parallel, new tissue imaging methods (e.g., imaging mass spectrometry) are currently regarded as very promising approaches for better molecular diagnosis in pathology. However, these new data sources are still often underexploited because of the lack of collaborative software to share and correlate information for multimodal analysis.

EXPERIMENTAL DESIGN: The open science paradigm is followed to develop new features in the web-based Cytomine software to support next-generation digital pathology bridged to molecular investigations.

RESULTS: New open-source developments allow to explore whole-slide classical histology with Matrix Assisted Laser Desorption Ionisation (MALDI) imaging and to support preprocessing for biomarker discovery using laser microdissection-based microproteomics.

CONCLUSIONS AND CLINICAL RELEVANCE: The updated version of Cytomine is the first open and web-based tool to enable sharing data from classical histology, molecular imaging, and cell counting for proteomics preprocessing. It holds good promise to fulfill imminent needs in molecular histopathology.

}, keywords = {Intersectoral Collaboration, Multimodal Imaging, Pathology, Proteomics, Software, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization}, issn = {1862-8354}, doi = {10.1002/prca.201800057}, author = {Rubens, Ulysse and Hoyoux, Renaud and Vanosmael, Laurent and Ouras, Mehdy and Tasset, Maxime and Hamilton, Christopher and Longuesp{\'e}e, R{\'e}mi and Mar{\'e}e, Rapha{\"e}l} } @article {1230, title = {Data Migration from Operating EMRs to OpenEMR with Mirth Connect.}, journal = {Stud Health Technol Inform}, volume = {257}, year = {2019}, month = {2019}, pages = {288-292}, abstract = {

Electronic medical records (EMR) are integral to the functionality of day to day operations in a clinic. EMRs perform functions like scheduling or hosting medical records used by physicians and other staff [1]. A certain time comes when it is necessary to upgrade or change EMRs to maintain efficiency in a clinic. The most arduous part of changing a clinic{\textquoteright}s EMR is migrating the clinical data from the old EMR to the new. This paper explores the feasibility of data migration between two Electronic Medical Records using open source technologies. This enables smaller clinics to change EMRs when the need arises without incurring huge costs. Using Mirth Connect as a data integration engine and OpenEMR as the new EMR we successfully migrated data from our old EMR to OpenEMR.

}, keywords = {Ambulatory Care Facilities, electronic health records, Humans, Physicians, Software}, issn = {1879-8365}, author = {Lin, Jing and Ranslam, Kyle and Shi, Fang and Figurski, Mike and Liu, Zheng} } @article {1229, title = {Data model harmonization for the All Of Us Research Program: Transforming i2b2 data into the OMOP common data model.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0212463}, abstract = {

BACKGROUND: The All Of Us Research Program (AOU) is building a nationwide cohort of one million patients{\textquoteright} EHR and genomic data. Data interoperability is paramount to the program{\textquoteright}s success. AOU is standardizing its EHR data around the Observational Medical Outcomes Partnership (OMOP) data model. OMOP is one of several standard data models presently used in national-scale initiatives. Each model is unique enough to make interoperability difficult. The i2b2 data warehousing and analytics platform is used at over 200 sites worldwide, which uses a flexible ontology-driven approach for data storage. We previously demonstrated this ontology system can drive data reconfiguration, to transform data into new formats without site-specific programming. We previously implemented this on our 12-site Accessible Research Commons for Health (ARCH) network to transform i2b2 into the Patient Centered Outcomes Research Network model.

METHODS AND RESULTS: Here, we leverage our investment in i2b2 high-performance transformations to support the AOU OMOP data pipeline. Because the ARCH ontology has gained widespread national interest (through the Accrual to Clinical Trials network, other PCORnet networks, and the Nebraska Lexicon), we leveraged sites{\textquoteright} existing investments into this standard ontology. We developed an i2b2-to-OMOP transformation, driven by the ARCH-OMOP ontology and the OMOP concept mapping dictionary. We demonstrated and validated our approach in the AOU New England HPO (NEHPO). First, we transformed into OMOP a fake patient dataset in i2b2 and verified through AOU tools that the data was structurally compliant with OMOP. We then transformed a subset of data in the Partners Healthcare data warehouse into OMOP. We developed a checklist of assessments to ensure the transformed data had self-integrity (e.g., the distributions have an expected shape and required fields are populated), using OMOP{\textquoteright}s visual Achilles data quality tool. This i2b2-to-OMOP transformation is being used to send NEHPO production data to AOU. It is open-source and ready for use by other research projects.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0212463}, author = {Klann, Jeffrey G and Joss, Matthew A H and Embree, Kevin and Murphy, Shawn N} } @article {1222, title = {Data on security requirements in open-source software projects.}, journal = {Data Brief}, volume = {25}, year = {2019}, month = {2019 Aug}, pages = {103590}, abstract = {

The datasets presented in this article are related the research paper entitled "A Linear Classifier Approach for Identifying Security Requirements in Open Source Software Development" Wang et al. (2018) [1]. This article describes requirements collected from three open-source software (OSS) projects and labels of security requirements. The datasets are made available to support automated security requirements analyzing tools development as well as tools{\textquoteright} evaluation.

}, issn = {2352-3409}, doi = {10.1016/j.dib.2018.12.029}, author = {Wang, Wentao and Mahakala, Kavya Reddy and Gupta, Arushi and Hussein, Nesrin and Wang, Yinglin} } @article {1281, title = {Eye injuries in children - incidence and outcomes: An observational study at a dedicated children{\textquoteright}s eye casualty.}, journal = {Eur J Ophthalmol}, volume = {29}, year = {2019}, month = {2019 Sep}, pages = {499-503}, abstract = {

PURPOSE: Trauma is an important cause of visual loss in children and may affect their quality of life. Prevention and legislation can reduce the incidence of trauma, and appropriate and timely treatment can improve prognosis. We aimed to describe incidence of eye injuries in children and the adherence to national and local management guidelines.

METHODS: Retrospective service evaluation at a tertiary hospital (Moorfields Eye Hospital, London, UK) which operates a dedicated children{\textquoteright}s eye casualty. The electronic patient administration system and electronic patient record system (Openeyes) were used to identify children who presented with eye injuries between January 2015 and December 2015.

RESULTS: Of 2397 first-time attendances to our children{\textquoteright}s casualty, 508 were for injuries (estimated incidence 21.1\%, 95\% confidence interval: 19.5\%-22.7\%). Mean age at presentation was 7.51 (standard deviation: 7.97) years; boys were more commonly affected than girls (69\%). The most common injury was corneal abrasion, followed by blunt and chemical injury; severe injuries such as penetrating trauma were rare. Injuries were sustained mostly during play or sports. Two children sustained permanent loss of vision in the affected eye.

CONCLUSION: Our findings are comparable to other published reports. Adherence to management guidelines is high, but documentation of advice given to families can be improved. Regular training of staff and collaboration with organisations outside the hospital can increase awareness of eye injuries in children.

}, keywords = {Adolescent, Child, Child, Preschool, Emergency Service, Hospital, Eye Injuries, Female, Humans, Incidence, Infant, Male, Prognosis, Quality of Life, Retrospective Studies, Treatment Outcome, Vision Disorders, Visual Acuity}, issn = {1724-6016}, doi = {10.1177/1120672118803512}, author = {Jolly, Rohit and Arjunan, Mousindha and Theodorou, Maria and Dahlmann-Noor, Annegret H} } @article {1266, title = {From paper maps to digital maps: enhancing routine immunisation microplanning in Northern Nigeria.}, journal = {BMJ Glob Health}, volume = {4}, year = {2019}, month = {2019}, pages = {e001606}, abstract = {

Geographical information systems (GIS) can be effective decision-support tools. In this paper, we detail a GIS approach implemented by the Bauchi and Sokoto state primary healthcare development agencies in Nigeria to generate and convert routine immunisation (RI) paper maps to digital maps for microplanning. The process involved three stages: primary and secondary data collection and reconciliation, geospatial data processing and analysis, and production and validation of maps. The data collection and reconciliation stage identified a number of challenges with secondary data sources, including the need to standardise and reconcile health facility and settlement names. The study team was unable to apply population estimates generated from the Global Polio Eradication Initiative to RI planning because operational boundaries for polio activities are defined differently from RI activities. Application of open-source GIS software enabled the combination of multiple datasets and analysis of geospatial data to calculate catchment areas for primary health centres (PHCs) and assign vaccination strategies to communities. The activity resulted in the development of PHC catchment area digital maps, and captured next steps and lessons learnt for RI microplanning in the two states. While the digital maps provided input into the microplanning process, more work is needed to build capacity, standardise processes and ensure the quality of data used to generate the maps. RI service providers and communities must be engaged in the process to validate, understand the data, the contextual factors that influence decisions about which vaccination strategies RI microplans include and how resources are allocated.

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2019-001606}, author = {Dougherty, Leanne and Abdulkarim, Masduq and Mikailu, Fiyidi and Tijani, Usman and Owolabi, Kazeem and Gilroy, Kate and Naiya, Ahmed and Abdullahi, Adamu and Bodinga, Hadiza and Olayinka, Folake and Moise, Imelda} } @article {1213, title = {Governance and Sustainability of an Open Source Electronic Health Record: An Interpretive Case Study of OpenDolphin in Japan.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {739-743}, abstract = {

Electronic Health Records (EHRs) are at the heart of reforms aiming for improving the efficiency and quality of citizens healthcare services. Although there is still some skepticism, open source (OS) EHR is a growing phenomenon in health informatics. Given the widespread adoption of OS software (OSS) in several domains, including operating systems, and enterprise systems, the repeated shortfalls faced by healthcare organizations with dominant proprietary EHRs create an opportunity for other alternatives, such as OSS to demonstrate their abilities in addressing these well-documented problems, including inflexibility, high costs, and low interoperability. However, scholars have expressed extensive concerns about the sustainability of OS EHR. Recognizing that OSS project sustainability relies on their governance arrangements, this case study reports on the evolution of the governance and sustainability of a Japanese OS EHR project and provides rich insights to other open source EHR initiative stakeholders, including physicians, developers, researchers, and policymakers.

}, issn = {1879-8365}, doi = {10.3233/SHTI190321}, author = {Poba-Nzaou, Placide and Kume, Naoto and Kobayashi, Shinji} } @article {1223, title = {Health4Afrika - Implementing HL7 FHIR Based Interoperability.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {20-24}, abstract = {

Supported by the European Commission under Horizon 2020, mHealth4Afrika is co-designing and validating a modular, multilingual, state-of-the-art health information system addressing primary healthcare requirements in resource constrained environments. mHealth4Afrika has co-designed a comprehensive range of functionality and medical programs in partnership with Ministries of Health, district health officers, clinic managers and primary healthcare workers from urban, rural and deep rural health facilities in Ethiopia, Kenya, Malawi and South Africa. This paper provides insights into how mHealth4Afrika is leveraging HL7 FHIR to support standards-based data exchange and interoperability between Electronic Medical Records and DHIS2. This work is currently being validated in the field.

}, issn = {1879-8365}, doi = {10.3233/SHTI190175}, author = {Baskaya, Mert and Yuksel, Mustafa and Erturkmen, Gokce Banu Laleci and Cunningham, Miriam and Cunningham, Paul} } @article {1271, title = {The impact of PEPFAR transition on HIV service delivery at health facilities in Uganda.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0223426}, abstract = {

BACKGROUND: Since 2004, the President{\textquoteright}s Emergency Plan for AIDS Relief (PEPFAR) has played a large role in Uganda{\textquoteright}s HIV/AIDS response. To better target resources to high burden regions and facilities, PEPFAR planned to withdraw from 29\% of previously-supported health facilities in Uganda between 2015 and 2017.

METHODS: We conducted a cross-sectional survey of 226 PEPFAR-supported health facilities in Uganda in mid-2017. The survey gathered information on availability, perceived quality, and access to HIV services before and after transition. We compare responses for facilities transitioned to those maintained on PEPFAR, accounting for survey design. We also extracted data from DHIS2 for the period October 2013-December 2017 on the number of HIV tests and counseling (HTC), number of patients on antiretroviral therapy (Current on ART), and retention on first-line ART (Retention) at 12 months. Using mixed effect models, we compare trends in service volume around the transition period.

RESULTS: There were 206 facilities that reported transition and 20 that reported maintenance on PEPFAR. Some facilities reporting transition may have been in a gap between implementing partners. The median transition date was September 2016, nine months prior to the survey. Transition facilities were more likely to discontinue HIV outreach following transition (51.6\% vs. 1.4\%, p<0.001) and to report declines in HIV care access (43.5\% vs. 3.1\%, p<0.001) and quality (35.6\% vs. 0\%, p<0.001). However, transition facilities did not differ in their trends in HIV service volume relative to maintenance facilities.

CONCLUSIONS: Transition from PEPFAR resulted in facilities reporting worsening patient access and service quality for HIV care, but there is insufficient evidence to suggest negative impacts on volume of HIV services. Facility respondents{\textquoteright} perceptions about access and quality may be overly pessimistic, or they may signal forthcoming impacts. Unrelated to transition, declining retention on ART in Uganda is a cause for concern.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0223426}, author = {Wilhelm, Jess Alan and Qiu, Mary and Paina, Ligia and Colantuoni, Elizabeth and Mukuru, Moses and Ssengooba, Freddie and Bennett, Sara} } @article {1278, title = {Large care gaps in primary care management of asthma: a longitudinal practice audit.}, journal = {BMJ Open}, volume = {9}, year = {2019}, month = {2019 01 29}, pages = {e022506}, abstract = {

OBJECTIVES: Care gaps in asthma may be highly prevalent but are poorly characterised. We sought to prospectively measure adherence to key evidence-based adult asthma practices in primary care, and predictors of these behaviours.

DESIGN: One-year prospective cohort study employing an electronic chart audit.

SETTING: Three family health teams (two academic, one community-based) in Ontario, Canada.

PARTICIPANTS: 884 patients (72.1\% female; 46.0{\textpm}17.5 years old) (4199 total visits; 4.8{\textpm}4.8 visits/patient) assigned to 23 physicians (65\% female; practising for 10.0{\textpm}8.6 years).

MAIN OUTCOME MEASURES: The primary outcome was the proportion of visits during which practitioners assessed asthma control according to symptom-based criteria. Secondary outcomes included the proportion of: patients who had asthma control assessed at least once; visits during which a controller medication was initiated or escalated; and patients who received a written asthma action plan. Behavioural predictors were established a priori and tested in a multivariable model.

RESULTS: Primary outcome: Providers assessed asthma control in 4.9\% of visits and 15.4\% of patients. Factors influencing assessment included clinic site (p=0.019) and presenting symptom, with providers assessing control more often during visits for asthma symptoms (35.0\%) or any respiratory symptoms (18.8\%) relative to other visits (1.6\%) (p<0.01).

SECONDARY OUTCOMES: Providers escalated controller therapy in 3.3\% of visits and 15.4\% of patients. Factors influencing escalation included clinic site, presenting symptom and prior objective asthma diagnosis. Escalation occurred more frequently during visits for asthma symptoms (21.0\%) or any respiratory symptoms (11.9\%) relative to other visits (1.5\%) (p<0.01) and in patients without a prior objective asthma diagnosis (3.5\%) relative to those with (1.3\%) (p=0.025). No asthma action plans were delivered.

CONCLUSIONS: Major gaps in evidence-based asthma practice exist in primary care. Targeted knowledge translation interventions are required to address these gaps, and can be tailored by leveraging the identified behavioural predictors.

TRIAL REGISTRATION NUMBER: NCT01070095; Pre-results.

}, issn = {2044-6055}, doi = {10.1136/bmjopen-2018-022506}, author = {Price, Courtney and Agarwal, Gina and Chan, David and Goel, Sanjeev and Kaplan, Alan G and Boulet, Louis-Philippe and Mamdani, Muhammad M and Straus, Sharon E and Lebovic, Gerald and Gupta, Samir} } @article {1275, title = {A national electronic health record for primary care.}, journal = {CMAJ}, volume = {191}, year = {2019}, month = {2019 01 14}, pages = {E28-E29}, keywords = {Canada, Delivery of Health Care, electronic health records, Health Policy, Primary Health Care}, issn = {1488-2329}, doi = {10.1503/cmaj.181647}, author = {Persaud, Nav} } @article {1302, title = {Open source capillary electrophoresis.}, journal = {Electrophoresis}, volume = {40}, year = {2019}, month = {2019 01}, pages = {65-78}, abstract = {

Open source paradigm is becoming widely accepted in scientific communities and open source hardware is finding its steady place in chemistry research. In this review article, we provide the reader with the most up-to-date information on open source hardware and software resources enabling the construction and utilization of an "open source capillary electrophoresis instrument". While CE is still underused as a separation technique, it offers unique flexibility, low-cost, and high efficiency and is particularly suitable for open source instrumental development. We overview the major parts of CE instruments, such as high voltage power supplies, detectors, data acquisition systems, and CE software resources with emphasis on availability of the open source information on the web and in the scientific literature. This review is the first of its kind, revealing accessible blueprints of most parts from which a fully functional open source CE system can be built. By collecting the extensive information on open source capillary electrophoresis in this review article, the authors aim at facilitating the dissemination of knowledge on CE within and outside the scientific community, fosters innovation and inspire other researchers to improve the shared CE blueprints.

}, keywords = {Electronics, Electrophoresis, Capillary, Equipment Design, Software}, issn = {1522-2683}, doi = {10.1002/elps.201800304}, author = {Kub{\'a}{\v n}, Petr and Foret, Franti{\v s}ek and Erny, Guillaume} } @article {1219, title = {Open Source HMIS Enabled Evaluation of Financial Burden of Disease and Patient Coverage in Three University Hospitals in Great Lakes Africa.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {969-973}, abstract = {

Since the eighties, case mix evaluation methods based on diagnosis-related groups (DRG) were gradually introduced in developed countries. These methods of assessing the costs of diseases to measure the productivity of the hospital have been introduced in management softwares that are not accessible to low-income countries. In this study, the authors applied these methods to an open source hospital management information system (HMIS) implemented in three university hospitals in Great Lakes Africa. A comparative study of the financial burden of five major diseases, monitored as part of a universal health coverage (UHC) analysis, was carried out. The level of coverage of patients in the hospitals was evaluated and the impact of UHC policies demonstrated. Although the financial protection of patients treated in the three hospitals had improved, HIV and tuberculosis treatments that ought to be free, remained a considerable financial burden for the patient.

}, issn = {1879-8365}, doi = {10.3233/SHTI190368}, author = {Karara, Gustave and Verbeke, Frank and Byiringiro, Jean-Claude and Nziza, Franck and Buyl, Ronald and Nyssen, Marc} } @article {1210, title = {Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses.}, journal = {JCO Clin Cancer Inform}, volume = {3}, year = {2019}, month = {2019 Aug}, pages = {1-16}, abstract = {

PURPOSE: We have created a cloud-based machine learning system (CLOBNET) that is an open-source, lean infrastructure for electronic health record (EHR) data integration and is capable of extract, transform, and load (ETL) processing. CLOBNET enables comprehensive analysis and visualization of structured EHR data. We demonstrate the utility of CLOBNET by predicting primary therapy outcomes of patients with high-grade serous ovarian cancer (HGSOC) on the basis of EHR data.

MATERIALS AND METHODS: CLOBNET is built using open-source software to make data preprocessing, analysis, and model training user friendly. The source code of CLOBNET is available in GitHub. The HGSOC data set was based on a prospective cohort of 208 patients with HGSOC who were treated at Turku University Hospital, Finland, from 2009 to 2019 for whom comprehensive clinical and EHR data were available.

RESULTS: We trained machine learning (ML) models using clinical data, including a herein developed dissemination score that quantifies the disease burden at the time of diagnosis, to identify patients with progressive disease (PD) or a complete response (CR) on the basis of RECIST (version 1.1). The best performance was achieved with a logistic regression model, which resulted in an area under receiver operating characteristic curve (AUROC) of 0.86, with a specificity of 73\% and a sensitivity of 89\%, when it classified between patients who experienced PD and CR.

CONCLUSION: We have developed an open-source computational infrastructure, CLOBNET, that enables effective and rapid analysis of EHR and other clinical data. Our results demonstrate that CLOBNET allows predictions to be made on the basis of EHR data to address clinically relevant questions.

}, issn = {2473-4276}, doi = {10.1200/CCI.18.00132}, author = {Isoviita, Veli-Matti and Salminen, Liina and Azar, Jimmy and Lehtonen, Rainer and Roering, Pia and Carp{\'e}n, Olli and Hietanen, Sakari and Gr{\'e}nman, Seija and Hynninen, Johanna and F{\"a}rkkil{\"a}, Anniina and Hautaniemi, Sampsa} } @article {1211, title = {Open source software security vulnerability detection based on dynamic behavior features.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0221530}, abstract = {

Open source software has been widely used in various industries due to its openness and flexibility, but it also brings potential security problems. Therefore, security analysis is required before using open source software. The current mainstream open source software vulnerability analysis technology is based on source code, and there are problems such as false positives, false negatives and restatements. In order to solve the problems, based on the further study of behavior feature extraction and vulnerability detection technology, a method of using dynamic behavior features to detect open source software vulnerabilities is proposed. Firstly, the relationship between open source software vulnerability and API call sequence is studied. Then, the behavioral risk vulnerability database of open source software is proposed as a support for vulnerability detection. In addition, the CNN-IndRNN classification model is constructed by improving the Independently Recurrent Neural Net-work (IndRNN) algorithm and applies to open source software security vulnerability detection. The experimental results verify the effectiveness of the proposed open source software security vulnerability detection method based on dynamic behavior features.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0221530}, author = {Li, Yuancheng and Ma, Longqiang and Shen, Liang and Lv, Junfeng and Zhang, Pan} } @article {1228, title = {PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title.}, journal = {Bioinformatics}, year = {2019}, month = {2019 Jun 19}, abstract = {

MOTIVATION: Electronic Health Records (EHR) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.

RESULTS: We present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership Common Data Model (CDM) format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open-source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.

AVAILABILITY: PatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btz409}, author = {Glicksberg, Benjamin S and Oskotsky, Boris and Thangaraj, Phyllis M and Giangreco, Nicholas and Badgeley, Marcus A and Johnson, Kipp W and Datta, Debajyoti and Rudrapatna, Vivek and Rappoport, Nadav and Shervey, Mark M and Miotto, Riccardo and Goldstein, Theodore C and Rutenberg, Eugenia and Frazier, Remi and Lee, Nelson and Israni, Sharat and Larsen, Rick and Percha, Bethany and Li, Li and Dudley, Joel T and Tatonetti, Nicholas P and Butte, Atul J} } @article {1269, title = {Quality of routine facility data for monitoring priority maternal and newborn indicators in DHIS2: A case study from Gombe State, Nigeria.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0211265}, abstract = {

INTRODUCTION: Routine health information systems are critical for monitoring service delivery. District Heath Information System, version 2 (DHIS2) is an open source software platform used in more than 60 countries, on which global initiatives increasingly rely for such monitoring. We used facility-reported data in DHIS2 for Gombe State, north-eastern Nigeria, to present a case study of data quality to monitor priority maternal and neonatal health indicators.

METHODS: For all health facilities in DHIS2 offering antenatal and postnatal care services (n = 497) and labor and delivery services (n = 486), we assessed the quality of data for July 2016-June 2017 according to the World Health Organization data quality review guidance. Using data from DHIS2 as well as external facility-level and population-level household surveys, we reviewed three data quality dimensions-completeness and timeliness, internal consistency, and external consistency-and considered the opportunities for improvement.

RESULTS: Of 14 priority maternal and neonatal health indicators that could be tracked through facility-based data, 12 were included in Gombe{\textquoteright}s DHIS2. During July 2016-June 2017, facility-reported data in DHIS2 were incomplete at least 40\% of the time, under-reported 10\%-60\% of the events documented in facility registers, and showed inconsistencies over time, between related indicators, and with an external data source. The best quality data elements were those that aligned with Gombe{\textquoteright}s health program priorities, particularly older health programs, and those that reflected contact indicators rather than indicators related to the provision of commodities or content of care.

CONCLUSION: This case study from Gombe State, Nigeria, demonstrates the high potential for effective monitoring of maternal and neonatal health using DHIS2. However, coordinated action at multiple levels of the health system is needed to maximize reporting of existing data; rationalize data flow; routinize data quality review, feedback, and supervision; and ensure ongoing maintenance of DHIS2.

}, keywords = {Adolescent, Adult, Female, Guidelines as Topic, Health information systems, Humans, Infant Health, Infant, Newborn, Maternal Health, Middle Aged, Nigeria, Pregnancy, Quality Indicators, Health Care, Young Adult}, issn = {1932-6203}, doi = {10.1371/journal.pone.0211265}, author = {Bhattacharya, Antoinette Alas and Umar, Nasir and Audu, Ahmed and Felix, Habila and Allen, Elizabeth and Schellenberg, Joanna R M and Marchant, Tanya} } @article {1221, title = {RADAR-Base: Open Source Mobile Health Platform for Collecting, Monitoring, and Analyzing Data Using Sensors, Wearables, and Mobile Devices.}, journal = {JMIR Mhealth Uhealth}, volume = {7}, year = {2019}, month = {2019 08 01}, pages = {e11734}, abstract = {

BACKGROUND: With a wide range of use cases in both research and clinical domains, collecting continuous mobile health (mHealth) streaming data from multiple sources in a secure, highly scalable, and extensible platform is of high interest to the open source mHealth community. The European Union Innovative Medicines Initiative Remote Assessment of Disease and Relapse-Central Nervous System (RADAR-CNS) program is an exemplary project with the requirements to support the collection of high-resolution data at scale; as such, the Remote Assessment of Disease and Relapse (RADAR)-base platform is designed to meet these needs and additionally facilitate a new generation of mHealth projects in this nascent field.

OBJECTIVE: Wide-bandwidth networks, smartphone penetrance, and wearable sensors offer new possibilities for collecting near-real-time high-resolution datasets from large numbers of participants. The aim of this study was to build a platform that would cater for large-scale data collection for remote monitoring initiatives. Key criteria are around scalability, extensibility, security, and privacy.

METHODS: RADAR-base is developed as a modular application; the backend is built on a backbone of the highly successful Confluent/Apache Kafka framework for streaming data. To facilitate scaling and ease of deployment, we use Docker containers to package the components of the platform. RADAR-base provides 2 main mobile apps for data collection, a Passive App and an Active App. Other third-Party Apps and sensors are easily integrated into the platform. Management user interfaces to support data collection and enrolment are also provided.

RESULTS: General principles of the platform components and design of RADAR-base are presented here, with examples of the types of data currently being collected from devices used in RADAR-CNS projects: Multiple Sclerosis, Epilepsy, and Depression cohorts.

CONCLUSIONS: RADAR-base is a fully functional, remote data collection platform built around Confluent/Apache Kafka and provides off-the-shelf components for projects interested in collecting mHealth datasets at scale.

}, issn = {2291-5222}, doi = {10.2196/11734}, author = {Ranjan, Yatharth and Rashid, Zulqarnain and Stewart, Callum and Conde, Pauline and Begale, Mark and Verbeeck, Denny and Boettcher, Sebastian and Dobson, Richard and Folarin, Amos} } @article {1234, title = {Secondary Data Use in Rwanda: Leveraging OpenMRS for Global HIV Research.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {1732}, abstract = {

The Rwandan Ministry of Health supports a countrywide installation of the Open Medical Record System (OpenMRS) to improve clinical recordkeeping and patient care. However, electronic medical records also can be a valuable source of data for observational and experimental studies. We describe the challenges and lessons learned when reusing OpenMRS data in Rwanda for global HIV epidemiology research.

}, keywords = {Biomedical Research, electronic health records, Epidemiologic Studies, HIV, Humans, Rwanda}, issn = {1879-8365}, doi = {10.3233/SHTI190620}, author = {Muhoza, Benjamin and Remera, Eric and Shi, Qiuhu and Kabahizi, Jules and Brazier, Ellen and Sinayobye, Jean d{\textquoteright}Amour and Duda, Stephany N} } @article {1217, title = {STEM: An Open Source Tool for Disease Modeling.}, journal = {Health Secur}, volume = {17}, year = {2019}, month = {2019 Jul/Aug}, pages = {291-306}, abstract = {

The Spatiotemporal Epidemiologic Modeler (STEM) is an open source software project supported by the Eclipse Foundation and used by a global community of researchers and public health officials working to track and, when possible, control outbreaks of infectious disease in human and animal populations. STEM is not a model or a tool designed for a specific disease; it is a flexible, modular framework supporting exchange and integration of community models, reusable plug-in components, and denominator data, available to researchers worldwide at www.eclipse.org/stem. A review of multiple projects illustrates its capabilities. STEM has been used to study variations in transmission of seasonal influenza in Israel by strains; evaluate social distancing measures taken to curb the H1N1 epidemic in Mexico City; study measles outbreaks in part of London and inform local policy on immunization; and gain insights into H7N9 avian influenza transmission in China. A multistrain dengue fever model explored the roles of the mosquito vector, cross-strain immunity, and antibody response in the frequency of dengue outbreaks. STEM has also been used to study the impact of variations in climate on malaria incidence. During the Ebola epidemic, a weekly conference call supported the global modeling community; subsequent work modeled the impact of behavioral change and tested disease reintroduction via animal reservoirs. Work in Germany tracked salmonella in pork from farm to fork; and a recent doctoral dissertation used the air travel feature to compare the potential threats posed by weaponizing infectious diseases. Current projects include work in Great Britain to evaluate control strategies for parasitic disease in sheep, and in Germany and Hungary, to validate the model and inform policy decisions for African swine fever. STEM Version 4.0.0, released in early 2019, includes tools used in these projects and updates technical aspects of the framework to ease its use and re-use.

}, issn = {2326-5108}, doi = {10.1089/hs.2019.0018}, author = {Douglas, Judith V and Bianco, Simone and Edlund, Stefan and Engelhardt, Tekla and Filter, Matthias and G{\"u}nther, Taras and Hu, Kun Maggie and Nixon, Emily J and Sevilla, Nereyda L and Swaid, Ahmad and Kaufman, James H} } @article {1214, title = {Towards an Open-Source Oncology Electronic Medical Records System for Low-Resource Settings: Development of Chemotherapy Management in OpenMRS.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {634-638}, abstract = {

Cancer is a major public health challenge in low and middle income countries (LMICs). In this paper, we describe work in progress to develop functionality within an open-source electronic medical records system to support safe and standardized cancer care in low-resource settings. We engaged cancer care providers from LMICs to elicit and prioritize requirement, and following a rapid application development approach we developed chemotherapy prescription and documentation functionality within OpenMRS.

}, issn = {1879-8365}, doi = {10.3233/SHTI190300}, author = {Kabukye, Johnblack K and Casaceli, Alexis M and Ball, Ellen and De Armas, Mario and Cornet, Ronald} } @article {1216, title = {Transforming Two Decades of ePR Data to OMOP CDM for Clinical Research.}, journal = {Stud Health Technol Inform}, volume = {264}, year = {2019}, month = {2019 Aug 21}, pages = {233-237}, abstract = {

This paper presents the extract-transform-and-load (ETL) process from the Electronic Patient Records (ePR) at the Heart Institute (InCor) to the OMOP Common Data Model (CDM) format. We describe the initial database characterization, relational source mappings, selection filters, data transformations and patient de-identification using the open-source OHDSI tools and SQL scripts. We evaluate the resulting InCor-CDM database by recreating the same patient cohort from a previous reference study (over the original data source) and comparing the cohorts{\textquoteright} descriptive statistics and inclusion reports. The results exhibit that up to 91\% of the reference patients were retrieved by our method from the ePR through InCor-CDM, with AUC=0.938. The results indicate that the method that we employed was able to produce a new database that was both consistent with the original data and in accordance to the OMOP CDM standard.

}, issn = {1879-8365}, doi = {10.3233/SHTI190218}, author = {Lima, Daniel M and Rodrigues-Jr, Jose F and Traina, Agma J M and Pires, Fabio A and Gutierrez, Marco A} } @article {1232, title = {Using HL7 FHIR to achieve interoperability in patient health record.}, journal = {J Biomed Inform}, volume = {94}, year = {2019}, month = {2019 Jun}, pages = {103188}, abstract = {

The rapid growth and acceptance of Electronic Health Records (EHRs) and standards to exchange EHRs have improved various aspects of health practices and patient care. However, the data captured in an EHR is only accessible to the providers and specialists within an organization, but not the patient. The concept of a Personal Health Record (PHR) is to allow the patients to record and manage their health data beyond EHR and if possible, see the EHR data in the PHR. Experts agree that bi-directional communication between the PHR and EHR allows the PHR to be more effective and a valuable tool for both the providers and patients. Communicating near real-time patient recorded data in PHR with an EHR will allow the provider(s) to make appropriate clinical decisions and patients can see any changes to his/her diagnostics or treatment plans. This research explores and critically analyzes HL7 FHIR to design and prototype an interoperable mobile PHR that conforms to the HL7 PHR Functional Model and allows bi-directional communication with OpenEMR.

}, issn = {1532-0480}, doi = {10.1016/j.jbi.2019.103188}, author = {Saripalle, Rishi and Runyan, Christopher and Russell, Mitchell} } @article {1268, title = {Census-independent population mapping in northern Nigeria.}, journal = {Remote Sens Environ}, volume = {204}, year = {2018}, month = {2018 Jan}, pages = {786-798}, abstract = {

Although remote sensing has long been used to aid in the estimation of population, it has usually been in the context of spatial disaggregation of national census data, with the census counts serving both as observational data for specifying models and as constraints on model outputs. Here we present a framework for estimating populations from the bottom up, entirely independently of national census data, a critical need in areas without recent and reliable census data. To make observations of population density, we replace national census data with a microcensus, in which we enumerate population for a sample of small areas within the states of Kano and Kaduna in northern Nigeria. Using supervised texture-based classifiers with very high resolution satellite imagery, we produce a binary map of human settlement at 8-meter resolution across the two states and then a more refined classification consisting of 7 residential types and 1 non-residential type. Using the residential types and a model linking them to the population density observations, we produce population estimates across the two states in a gridded raster format, at approximately 90-meter resolution. We also demonstrate a simulation framework for capturing uncertainty and presenting estimates as prediction intervals for any region of interest of any size and composition within the study region. Used in concert with previously published demographic estimates, our population estimates allowed for predictions of the population under 5 in ten administrative wards that fit strongly with reference data collected during polio vaccination campaigns.

}, issn = {0034-4257}, doi = {10.1016/j.rse.2017.09.024}, author = {Weber, Eric M and Seaman, Vincent Y and Stewart, Robert N and Bird, Tomas J and Tatem, Andrew J and McKee, Jacob J and Bhaduri, Budhendra L and Moehl, Jessica J and Reith, Andrew E} } @article {1272, title = {Data for decision making: using a dashboard to strengthen routine immunisation in Nigeria.}, journal = {BMJ Glob Health}, volume = {3}, year = {2018}, month = {2018}, pages = {e000807}, abstract = {

Availability of reliable data has for a long time been a challenge for health programmes in Nigeria. Routine immunisation (RI) data have always been characterised by conflicting coverage figures for the same vaccine across different routine data reporting platforms. Following the adoption of District Health Information System version 2 (DHIS2) as a national electronic data management platform, the DHIS2 RI Dashboard Project was initiated to address the absence of some RI-specific indicators on DHIS2. The project was also intended to improve visibility and monitoring of RI indicators as well as strengthen the broader national health management information system by promoting the use of routine data for decision making at all governance levels. This paper documents the process, challenges and lessons learnt in implementing the project in Nigeria. A multistakeholder technical working group developed an implementation framework with clear preimplementation; implementation and postimplementation activities. Beginning with a pilot in Kano state in 2014, the project has been scaled up countrywide. Nearly 34 000 health workers at all administrative levels were trained on RI data tools and DHIS2 use. The project contributed to the improvement in completeness of reports on DHIS2 from 53 \% in first quarter 2014 to 81 \% in second quarter 2017. The project faced challenges relating to primary healthcare governance structures at the subnational level, infrastructure and human resource capacity. Our experience highlights the need for early and sustained advocacy to stakeholders in a decentralised health system to promote ownership and sustainability of a centrally coordinated systems strengthening initiative.

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2018-000807}, author = {Etamesor, Sulaiman and Ottih, Chibuzo and Salihu, Ismail Ndalami and Okpani, Arnold Ikedichi} } @article {1293, title = {Designing mHealth for maternity services in primary health facilities in a low-income setting - lessons from a partially successful implementation.}, journal = {BMC Med Inform Decis Mak}, volume = {18}, year = {2018}, month = {2018 11 12}, pages = {96}, abstract = {

BACKGROUND: Increasing mobile phone ownership, functionality and access to mobile-broad band internet services has triggered growing interest to harness the potential of mobile phone technology to improve health services in low-income settings. The present project aimed at designing an mHealth system that assists midlevel health workers to provide better maternal health care services by automating the data collection and decision-making process. This paper describes the development process and technical aspects of the system considered critical for possible replication. It also highlights key lessons learned and challenges during implementation.

METHODS: The mHealth system had front-end and back-end components. The front-end component was implemented as a mobile based application while the back-end component was implemented as a web-based application that ran on a central server for data aggregation and report generation. The current mHealth system had four applications; namely, data collection/reporting, electronic health records, decision support, and provider education along the continuum of care including antenatal, delivery and postnatal care. The system was pilot-tested and deployed in selected health centers of North Shewa Zone, Amhara region, Ethiopia.

RESULTS: The system was used in 5 health centers since Jan 2014 and later expanded to additional 10 health centers in June 2016 with a total of 5927 electronic forms submitted to the back-end system. The submissions through the mHealth system were slightly lower compared to the actual number of clients who visited those facilities as verified by record reviews. Regarding timeliness, only 11\% of the electronic forms were submitted on the day of the client visit, while an additional 17\% of the forms were submitted within 10~days of clients{\textquoteright} visit. On average forms were submitted 39~days after the day of clients visit with a range of 0 to 150~days.

CONCLUSIONS: In conclusion, the study illustrated that an effective mHealth intervention can be developed using an open source platform and local resources. The system impacted key health outcomes and contributed to timely and complete data submission. Lessons learned through the process including success factors and challenges are discussed.

}, keywords = {Cell Phone, Delivery of Health Care, electronic health records, Ethiopia, Female, Health Facilities, Humans, Maternal Health Services, Mobile Applications, Poverty, Pregnancy, Telemedicine}, issn = {1472-6947}, doi = {10.1186/s12911-018-0704-9}, author = {Shiferaw, Solomon and Workneh, Andualem and Yirgu, Robel and Dinant, Geert-Jan and Spigt, Mark} } @article {1274, title = {Development and Evaluation of a New Security and Privacy Track in a Health Informatics Graduate Program: Multidisciplinary Collaboration in Education.}, journal = {JMIR Med Educ}, volume = {4}, year = {2018}, month = {2018 Dec 21}, pages = {e19}, abstract = {

BACKGROUND: The widespread application of technologies such as electronic health record systems, mobile health apps, and telemedicine platforms, has made it easy for health care providers to collect relevant data and deliver health care regimens. While efficacious, these new technologies also pose serious security and privacy challenges.

OBJECTIVE: The training program described here aims at preparing well-informed health information security and privacy professionals with enhanced course materials and various approaches.

METHODS: A new educational track has been built within a health informatics graduate program. Several existing graduate courses have been enhanced with new security and privacy modules. New labs and seminars have been created, and students are being encouraged to participate in research projects and obtain real-world experience from industry partners. Students in this track receive both theoretical education and hands-on practice. Evaluations have been performed on this new track by conducting multiple surveys on a sample of students.

RESULTS: We have succeeded in creating a new security track and developing a pertinent curriculum. The newly created security materials have been implemented in multiple courses. Our evaluation indicated that students (N=72) believed that receiving security and privacy training was important for health professionals, the provided security contents were interesting, and having the enhanced security and privacy training in this program was beneficial for their future career.

CONCLUSIONS: The security and privacy education for health information professionals in this new security track has been significantly enhanced.

}, issn = {2369-3762}, doi = {10.2196/mededu.9081}, author = {Zhou, Leming and Parmanto, Bambang and Joshi, James} } @article {1203, title = {The {District} {Health} {Information} {System} ({DHIS}2): {A} literature review and meta-synthesis of its strengths and operational challenges based on the experiences of 11 countries}, journal = {Health Information Management: Journal of the Health Information Management Association of Australia}, year = {2018}, pages = {1833358318777713}, abstract = {BACKGROUND: Health information systems offer many potential benefits for healthcare, including financial benefits and for improving the quality of patient care. The purpose of District Health Information Systems (DHIS) is to document data that are routinely collected in all public health facilities in a country using the system. OBJECTIVE: The aim of this study was to examine the strengths and operational challenges of DHIS2, with a goal to enable decision makers in different counties to more accurately evaluate the outcomes of introducing DHIS2 into their particular country. METHOD: A review of the literature combined with the method of meta-synthesis was used to source information and interpret results relating to the strengths and operational challenges of DHIS2. Databases (Embase, PubMed, Scopus and Google Scholar) were searched for documents related to strengths and operational challenges of DHIS2, with no time limit up to 8 April 2017. The review and evaluation of selected studies was conducted in three stages: title, abstract and full text. Each of the selected studies was reviewed carefully and key concepts extracted. These key concepts were divided into two categories of strengths and operational challenges of DHIS2. Then, each category was grouped based on conceptual similarity to achieve the main themes and sub-themes. Content analysis was used to analyse extracted data. RESULTS: Of 766 identified citations, 20 studies from 11 countries were included and analysed in this study. Identified strengths in the DHIS were represented in seven themes (with 21 categories): technical features of software, proper management of data, application flexibility, networking and increasing the satisfaction of stakeholders, development of data management, increasing access to information and economic benefits. Operational challenges were identified and captured in 11 themes (with 18 categories): funds; appropriate communication infrastructure; the need for the existence of appropriate data; political, cultural, social and structural infrastructure; manpower; senior managers; training; using academic potentials; definition and standardising the deployment processes; neglect to application of criteria and clinical guidelines in the use of system; data security; stakeholder communications challenges and the necessity to establish a pilot system. CONCLUSION: This study highlighted specific strengths in the technical and functional aspects of DHIS2 and also drew attention to particular challenges and concerns. These results provide a sound evidence base for decision makers and policymakers to enable them to make more accurate decisions about whether or not to use the DHIS2 in the health system of their country.}, keywords = {content analysis, District Health Information System, health information system, health information technology, information technology, meta-synthesis, qualitative research}, issn = {1322-4913}, doi = {10.1177/1833358318777713}, author = {Dehnavieh, Reza and Haghdoost, AliAkbar and Khosravi, Ardeshir and Hoseinabadi, Fahime and Rahimi, Hamed and Poursheikhali, Atousa and Khajehpour, Nahid and Khajeh, Zahra and Mirshekari, Nadia and Hasani, Marziyeh and Radmerikhi, Samera and Haghighi, Hajar and Mehrolhassani, Mohammad Hossain and Kazemi, Elaheh and Aghamohamadi, Saeide} } @article {1282, title = {Effect of glycosylated hemoglobin on response to ranibizumab therapy in diabetic macular edema: real-world outcomes in 312 patients.}, journal = {Can J Ophthalmol}, volume = {53}, year = {2018}, month = {2018 08}, pages = {415-419}, abstract = {

OBJECTIVE: To investigate the effect of serum glycosylated hemoglobin (HbA1c) on the outcomes of ranibizumab therapy for diabetic macular edema (DME).

DESIGN: Retrospective cohort study.

PARTICIPANTS: Patients receiving ranibizumab injections for centre-involving DME in a National Health Service setting.

METHODS: The Moorfields OpenEyes database was used to study eyes with DME treated with ranibizumab from October 2013 to November 2015 at the Moorfields City Road, Ealing, Northwick Park, and St George{\textquoteright}s Hospital sites. Only eyes receiving a minimum of 3 injections and completing 12 months of follow-up were included. If both eyes received treatment, the first eye treated was analyzed. When both eyes received initial treatment simultaneously, random number tables were used to select the eye for analysis. HbA1c was tested at the initiation of ranibizumab treatment. Multivariate regression analysis was used to identify relationships between HbA1c and the outcome measures.

OUTCOMES: The primary outcome was change in visual acuity (VA) Early Treatment of Diabetic Retinopathy study (ETDRS) letters. The secondary outcomes were change in central subfield thickness (CSFT) and macular volume (MV), as well as number of injections in year 1.

RESULTS: Three hundred and twelve eyes of 312 patients were included in the analysis. HbA1c was not related to change in VA (p = 0.577), change in CSFT (p = 0.099), change in MV (p = 0.082), or number of injections in year 1 (p = 0.859).

CONCLUSIONS: HbA1c is not related to functional or anatomical outcomes at 1 year in DME treated with ranibizumab.

}, keywords = {Aged, Angiogenesis Inhibitors, Biomarkers, Diabetic Retinopathy, Female, Follow-Up Studies, Glycated Hemoglobin A, Humans, Intravitreal Injections, Macula Lutea, Macular Edema, Male, Middle Aged, Ranibizumab, Retrospective Studies, Tomography, Optical Coherence, Treatment Outcome, Vascular Endothelial Growth Factor A, Visual Acuity}, issn = {1715-3360}, doi = {10.1016/j.jcjo.2017.10.008}, author = {Shalchi, Zaid and Okada, Mali and Bruynseels, Alice and Palethorpe, David and Yusuf, Ammar and Hussain, Rohan and Herrspiegel, Christina and Scazzarriello, Antonio and Habib, Abubakar and Amin, Razia and Rajendram, Ranjan} } @article {1283, title = {How do paper and electronic records compare for completeness? A three centre study.}, journal = {Eye (Lond)}, volume = {32}, year = {2018}, month = {2018 07}, pages = {1232-1236}, abstract = {

OBJECTIVES: Medical records are legal documentation of patients{\textquoteright} care hence must be accurate and complete for both medical and legal purposes. Electronic patient record (EPR) systems aim to improve the accuracy of documentation, provide better organisation and access of data. This study compares the completeness of traditional note records and EPR in glaucoma patients.

METHODS: Using criteria from the April 2009 National Institute for Health and Care Excellence (NICE) guidelines completeness of data entry was compared between EPR and paper notes in three units. Moorfields Eye Hospital (City Road) uses the Openeyes EPR. Bedford Hospital (Moorfields Eye Centre) and Western Eye Hospital use the Medisoft EPR. The standard was set at 100\% compliance for predetermined parameters.

RESULTS: One hundred seventy paper notes and 270 electronic records were analysed. With the exception of central corneal thickness (p = 0.31), all other key parameters were more consistently recorded in the paper records than in the EPR. Intraocular pressure (p = 0.004), anterior chamber configuration and depth assessments using gonioscopy (p < 0.001), fundus examination (p = 0.015), past medical history (p < 0.001), medication including glaucoma medication (p < 0.001) and drug allergies (p < 0.001).

CONCLUSIONS: Our results show that paper records are significantly more complete than EPR. This is the case for two different EPRs and three separate sites. We propose additional training to aid data-collection; improving the design of EPRs by investigating factors such as layout and use of forced choice fields.

}, keywords = {electronic health records, Glaucoma, Humans, Medical Records, Ophthalmology}, issn = {1476-5454}, doi = {10.1038/s41433-018-0065-8}, author = {Wu, Clara Hoi Ka and Luk, Sheila M H and Holder, Richard L and Rodrigues, Zena and Ahmed, Faisal and Murdoch, Ian} } @article {1287, title = {Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach.}, journal = {Sci Rep}, volume = {8}, year = {2018}, month = {2018 01 11}, pages = {538}, abstract = {

The detection of anatomical landmarks in bioimages is a necessary but tedious step for geometric morphometrics studies in many research domains. We propose variants of a multi-resolution tree-based approach to speed-up the detection of landmarks in bioimages. We extensively evaluate our method variants on three different datasets (cephalometric, zebrafish, and drosophila images). We identify the key method parameters (notably the multi-resolution) and report results with respect to human ground truths and existing methods. Our method achieves recognition performances competitive with current existing approaches while being generic and fast. The algorithms are integrated in the open-source Cytomine software and we provide parameter configuration guidelines so that they can be easily exploited by end-users. Finally, datasets are readily available through a Cytomine server to foster future research.

}, keywords = {Algorithms, Animals, Body Weights and Measures, Drosophila, Humans, Image Processing, Computer-Assisted, Software, Zebrafish}, issn = {2045-2322}, doi = {10.1038/s41598-017-18993-5}, author = {Vandaele, R{\'e}my and Aceto, Jessica and Muller, Marc and P{\'e}ronnet, Fr{\'e}d{\'e}rique and Debat, Vincent and Wang, Ching-Wei and Huang, Cheng-Ta and Jodogne, S{\'e}bastien and Martinive, Philippe and Geurts, Pierre and Mar{\'e}e, Rapha{\"e}l} } @article {1290, title = {mLearning in the Democratic Republic of the Congo: A Mixed-Methods Feasibility and Pilot Cluster Randomized Trial Using the Safe Delivery App.}, journal = {Glob Health Sci Pract}, volume = {6}, year = {2018}, month = {2018 12 27}, pages = {693-710}, abstract = {

BACKGROUND: Substandard delivery care has been widely documented as a major cause of maternal mortality in health facilities globally. Health worker learning via mobile devices is increasing rapidly; however, there is little evidence of mLearning effectiveness. This study sought to determine the feasibility, acceptability, and potential effect of the Safe Delivery App (SDA) on health workers{\textquoteright} practices in basic emergency obstetric and newborn care (BEmONC) in the Democratic Republic of the Congo (DRC). The Theoretical Domains Framework was used to guide this research.

METHODS: Eight BEmONC facilities in central DRC were randomized to either an mLearning intervention or to standard practice (control). Maternal and newborn health workers in intervention facilities (n=64) were trained on the use of smartphones and the French version of the SDA. The SDA is an evidence-based BEmONC training resource with visual guidance using animated videos and clinical management instructions developed by the Maternity Foundation and the Universities of Copenhagen and Southern Denmark. Knowledge on postpartum hemorrhage (PPH) and neonatal resuscitation (NR) and self-confidence in performing 12 BEmONC procedures were assessed at baseline and at 3 months post-intervention. Eighteen qualitative interviews were conducted with app users and key stakeholders to assess feasibility and acceptability of mLearning and the use of the SDA. Maternal mortality was compared in intervention and control facilities using a smartphone-based Open Data Kit (ODK) data application. One smartphone with SDA and ODK was entrusted to intervention facilities for the study period, whereas control facilities received smartphones with ODK only.

RESULTS: The analysis included 62 heath workers. Knowledge scores on postpartum hemorrhage and neonatal resuscitation increased significantly from baseline among intervention participants compared with controls at 3 months post-intervention (mean difference for PPH knowledge, 17.4 out of 100; 95\% confidence interval [CI]=10.7 to 24.0 and 19.4 for NR knowledge; 95\% CI=11.4 to 27.4), as did self-confidence scores on 12 essential BEmONC procedures (mean difference, 4.2 out of 48; CI=0.7 to 7.7). Increases were unaffected by health worker cadre and previous smartphone use. Qualitative interviews supported the feasibility and acceptability of the SDA and mLearning, and the potential for it to impact maternal and neonatal mortality in the DRC.

CONCLUSION: Use of the Safe Delivery App supported increased health worker knowledge and self-confidence in the management of obstetric and newborn emergencies after 3 months. SDA and mLearning were found to be feasible and acceptable to health workers and key stakeholders in the DRC.

}, keywords = {Congo, Feasibility Studies, Female, Humans, Infant Care, Infant, Newborn, Interviews as Topic, Male, Maternal Mortality, Mobile Applications, Obstetrics, Pilot Projects, qualitative research, Quality of Health Care}, issn = {2169-575X}, doi = {10.9745/GHSP-D-18-00275}, author = {Bolan, Nancy E and Sthreshley, Larry and Ngoy, Bernard and Ledy, Faustin and Ntayingi, Mano and Makasy, Davis and Mbuyi, Marie-Claude and Lowa, Gisele and Nemeth, Lynne and Newman, Susan} } @article {1204, title = {The mobile sleep lab app: {An} open-source framework for mobile sleep assessment based on consumer-grade wearable devices}, journal = {Computers in Biology and Medicine}, volume = {103}, year = {2018}, pages = {8{\textendash}16}, abstract = {BACKGROUND: Sleep disorders have a prevalence of up to 50\% and are commonly diagnosed using polysomnography. However, polysomnography requires trained staff and specific equipment in a laboratory setting, which are expensive and limited resources are available. Mobile and wearable devices such as fitness wristbands can perform limited sleep monitoring but are not evaluated well. Here, the development and evaluation of a mobile application to record and synchronize data from consumer-grade sensors suitable for sleep monitoring is presented and evaluated for data collection capability in a clinical trial. METHODS: Wearable and ambient consumer-grade sensors were selected to mimic the functionalities of clinical sleep laboratories. Then, a modular application was developed for recording, processing and visualizing the sensor data. A validation was performed in three phases: (1) sensor functionalities were evaluated, (2) self-experiments were performed in full-night experiments, and (3) the application was tested for usability in a clinical trial on primary snoring. RESULTS: The evaluation of the sensors indicated their suitability for assessing basic sleep characteristics. Additionally, the application successfully recorded full-night sleep. The collected data was of sufficient quality to detect and measure body movements, cardiac activity, snoring and brightness. The ongoing clinical trial phase showed the successful deployment of the application by medical professionals. CONCLUSION: The proposed software demonstrated a strong potential for medical usage. With low costs, it can be proposed for screening, long-term monitoring or in resource-austere environments. However, further validations are needed, in particular the comparison to a clinical sleep laboratory.}, keywords = {Mobile sleep laboratory, Sleep screening, Smartphone, Telemedicine, Wearable technology}, issn = {1879-0534}, doi = {10.1016/j.compbiomed.2018.09.025}, author = {Burgdorf, Andreas and G{\"u}the, Inga and Jovanovi{\'c}, Marko and Kutafina, Ekaterina and Kohlschein, Christian and Bitsch, J{\'o} {\'A}gila and Jonas, Stephan M.} } @article {1225, title = {The Orthanc Ecosystem for Medical Imaging.}, journal = {J Digit Imaging}, volume = {31}, year = {2018}, month = {2018 06}, pages = {341-352}, abstract = {

This paper reviews the components of Orthanc, a free and open-source, highly versatile ecosystem for medical imaging. At the core of the Orthanc ecosystem, the Orthanc server is a lightweight vendor neutral archive that provides PACS managers with a powerful environment to automate and optimize the imaging flows that are very specific to each hospital. The Orthanc server can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise-ready databases. It is shown how software developers and research engineers can easily develop external software or Web portals dealing with medical images, with minimal knowledge of the DICOM standard, thanks to the advanced programming interface of the Orthanc server. The paper concludes by introducing the Stone of Orthanc, an innovative toolkit for the cross-platform rendering of medical images.

}, keywords = {Diagnostic Imaging, Humans, Radiology Information Systems}, issn = {1618-727X}, doi = {10.1007/s10278-018-0082-y}, author = {Jodogne, S{\'e}bastien} } @article {1235, title = {A Platform for Innovation and Standards Evaluation: a Case Study from the OpenMRS Open-Source Radiology Information System.}, journal = {J Digit Imaging}, volume = {31}, year = {2018}, month = {2018 06}, pages = {361-370}, abstract = {

Open-source development can provide a platform for innovation by seeking feedback from community members as well as providing tools and infrastructure to test new standards. Vendors of proprietary systems may delay adoption of new standards until there are sufficient incentives such as legal mandates or financial incentives to encourage/mandate adoption. Moreover, open-source systems in healthcare have been widely adopted in low- and middle-income countries and can be used to bridge gaps that exist in global health radiology. Since 2011, the authors, along with a community of open-source contributors, have worked on developing an open-source radiology information system (RIS) across two communities-OpenMRS and LibreHealth. The main purpose of the RIS is to implement core radiology workflows, on which others can build and test new radiology standards. This work has resulted in three major releases of the system, with current architectural changes driven by changing technology, development of new standards in health and imaging informatics, and changing user needs. At their core, both these communities are focused on building general-purpose EHR systems, but based on user contributions from the fringes, we have been able to create an innovative system that has been used by hospitals and clinics in four different countries. We provide an overview of the history of the LibreHealth RIS, the architecture of the system, overview of standards integration, describe challenges of developing an open-source product, and future directions. Our goal is to attract more participation and involvement to further develop the LibreHealth RIS into an Enterprise Imaging System that can be used in other clinical imaging including pathology and dermatology.

}, keywords = {Diagnostic Imaging, Humans, Radiology Information Systems, Software, Systems Integration, Workflow}, issn = {1618-727X}, doi = {10.1007/s10278-018-0088-5}, author = {Gichoya, Judy W and Kohli, Marc and Ivange, Larry and Schmidt, Teri S and Purkayastha, Saptarshi} } @article {1224, title = {Towards Implementation of OMOP in a German University Hospital Consortium.}, journal = {Appl Clin Inform}, volume = {9}, year = {2018}, month = {2018 01}, pages = {54-61}, abstract = {

BACKGROUND: In 2015, the German Federal Ministry of Education and Research initiated a large data integration and data sharing research initiative to improve the reuse of data from patient care and translational research. The Observational Medical Outcomes Partnership (OMOP) common data model and the Observational Health Data Sciences and Informatics (OHDSI) tools could be used as a core element in this initiative for harmonizing the terminologies used as well as facilitating the federation of research analyses across institutions.

OBJECTIVE: To realize an OMOP/OHDSI-based pilot implementation within a consortium of eight German university hospitals, evaluate the applicability to support data harmonization and sharing among them, and identify potential enhancement requirements.

METHODS: The vocabularies and terminological mapping required for importing the fact data were prepared, and the process for importing the data from the source files was designed. For eight German university hospitals, a virtual machine preconfigured with the OMOP database and the OHDSI tools as well as the jobs to import the data and conduct the analysis was provided. Last, a federated/distributed query to test the approach was executed.

RESULTS: While the mapping of ICD-10 German Modification succeeded with a rate of 98.8\% of all terms for diagnoses, the procedures could not be mapped and hence an extension to the OMOP standard terminologies had to be made.Overall, the data of 3 million inpatients with approximately 26 million conditions, 21 million procedures, and 23 million observations have been imported.A federated query to identify a cohort of colorectal cancer patients was successfully executed and yielded 16,701 patient cases visualized in a Sunburst plot.

CONCLUSION: OMOP/OHDSI is a viable open source solution for data integration in a German research consortium. Once the terminology problems can be solved, researchers can build on an active community for further development.

}, keywords = {Cooperative Behavior, Germany, Health Plan Implementation, Hospitals, University, Humans, Outcome Assessment (Health Care), Surveys and Questionnaires, Vocabulary}, issn = {1869-0327}, doi = {10.1055/s-0037-1617452}, author = {Maier, C and Lang, L and Storf, H and Vormstein, P and Bieber, R and Bernarding, J and Herrmann, T and Haverkamp, C and Horki, P and Laufer, J and Berger, F and H{\"o}ning, G and Fritsch, H W and Sch{\"u}ttler, J and Ganslandt, T and Prokosch, H U and Sedlmayr, M} } @article {1277, title = {Barriers and facilitators to Electronic Medical Records usage in the Emergency Centre at Komfo Anokye Teaching Hospital, Kumasi-Ghana.}, journal = {Afr J Emerg Med}, volume = {7}, year = {2017}, month = {2017 Dec}, pages = {177-182}, abstract = {

Introduction: The use of paper for record keeping (or a manual system) has been the order of the day in almost all health care facilities in resource poor countries. This system has presented numerous challenges, which the use of Electronic Medical Records (EMR) seeks to address. The objectives of the study were to identify the facilitators and barriers to EMR implementation in Komfo Anokye Teaching Hospital{\textquoteright}s (KATH) Emergency Centre (EC) and to identify lessons learned. These will help in implementation of EMR in ECs in similar settings.

Methods: This was a non-interventional, descriptive cross-sectional and purely qualitative study using a semi-structured interview guide for a study population of 24. The interviews were manually recorded and analysed thematically. EMR implementation was piloted in the EC. Some of the EC staff doubled as EMR personnel. An open source EMR was freely downloaded and customised to meet the needs of the EC. The EMR database created was a hybrid one comprising of digital bio-data of patients and scanned copies of their paper EC records.

Results: The facilitators for utilising the system included providing training to staff, the availability of some logistics, and the commitment of staff. The project barriers were funding, full-time information technology expertise, and automatic data and power backups. It was observed that with the provision of adequate human and financial resources, the challenges were overcome and the adoption of the EMR improved.

Discussion: The EMR has been a partial success. The facilitators identified in this study, namely training, provision of logistics, and staff commitment represent foundations to work from. The barriers identified could be addressed with additional funding, provision of information technology expertise, and data and power back up. It is acknowledged that lack of funding could substantially limit EMR implementation.

}, issn = {2211-4203}, doi = {10.1016/j.afjem.2017.05.002}, author = {Gyamfi, Adwoa and Mensah, Kofi A and Oduro, George and Donkor, Peter and Mock, Charles N} } @article {1270, title = {Coverage of routine reporting on malaria parasitological testing in Kenya, 2015-2016.}, journal = {Glob Health Action}, volume = {10}, year = {2017}, month = {2017}, pages = {1413266}, abstract = {

BACKGROUND: Following the launch of District Health Information System 2 across facilities in Kenya, more health facilities are now capable of carrying out malaria parasitological testing and reporting data as part of routine health information systems, improving the potential value of routine data for accurate and timely tracking of rapidly changing disease epidemiology at fine spatial resolutions.

OBJECTIVES: This study evaluates the current coverage and completeness of reported malaria parasitological testing data in DHIS2 specifically looking at patterns in geographic coverage of public health facilities in Kenya.

METHODS: Monthly facility level data on malaria parasitological testing were extracted from Kenya DHIS2 between November 2015 and October 2016. DHIS2 public facilities were matched to a geo-coded master facility list to obtain coordinates. Coverage was defined as the geographic distribution of facilities reporting any data by region. Completeness of reporting was defined as the percentage of facilities reporting any data for the whole 12-month period or for 3, 6 and 9 months.

RESULTS: Public health facilities were 5,933 (59\%) of 10,090 extracted. Fifty-nine per Cent of the public facilities did not report any data while 36, 29 and 22\% facilities had data reported at least 3, 6 and 9 months, respectively. Only 8\% of public facilities had data reported for every month. There were proportionately more hospitals (86\%) than health centres (76\%) and dispensaries/clinics (30\%) reporting. There were significant geographic variations in reporting rates. Counties along the malaria endemic coast had the lowest reporting rate with only 1\% of facilities reporting consistently for 12 months.

CONCLUSION: Current coverage and completeness of reporting of malaria parasitological diagnosis across Kenya{\textquoteright}s public health system remains poor. The usefulness of routine data to improve our understanding of sub-national heterogeneity across Kenya would require significant improvements to the consistency and coverage of data captured by DHIS2.

}, keywords = {Health Facilities, Health information systems, Humans, Kenya, Malaria, Mandatory Reporting, Public Health Surveillance}, issn = {1654-9880}, doi = {10.1080/16549716.2017.1413266}, author = {Maina, Joseph K and Macharia, Peter M and Ouma, Paul O and Snow, Robert W and Okiro, Emelda A} } @article {1238, title = {Design and implementation of an affordable, public sector electronic medical record in rural Nepal.}, journal = {J Innov Health Inform}, volume = {24}, year = {2017}, month = {2017 Jun 23}, pages = {862}, abstract = {

INTRODUCTION: Globally, electronic medical records are central to the infrastructure of modern healthcare systems. Yet the vast majority of electronic medical records have been designed for resource-rich environments and are not feasible in settings of poverty. Here we describe the design and implementation of an electronic medical record at a public sector district hospital in rural Nepal, and its subsequent expansion to an additional public sector facility.DevelopmentThe electronic medical record was designed to solve for the following elements of public sector healthcare delivery: 1) integration of the systems across inpatient, surgical, outpatient, emergency, laboratory, radiology, and pharmacy sites of care; 2) effective data extraction for impact evaluation and government regulation; 3) optimization for longitudinal care provision and patient tracking; and 4) effectiveness for quality improvement initiatives.

APPLICATION: For these purposes, we adapted Bahmni, a product built with open-source components for patient tracking, clinical protocols, pharmacy, laboratory, imaging, financial management, and supply logistics. In close partnership with government officials, we deployed the system in February of 2015, added on additional functionality, and iteratively improved the system over the following year. This experience enabled us then to deploy the system at an additional district-level hospital in a different part of the country in under four weeks. We discuss the implementation challenges and the strategies we pursued to build an electronic medical record for the public sector in rural Nepal.DiscussionOver the course of 18 months, we were able to develop, deploy and iterate upon the electronic medical record, and then deploy the refined product at an additional facility within only four weeks. Our experience suggests the feasibility of an integrated electronic medical record for public sector care delivery even in settings of rural poverty.

}, keywords = {Delivery of Health Care, Integrated, electronic health records, Global Health, Health Plan Implementation, Hospitals, Public, Humans, Nepal, Public Sector, Rural Population}, issn = {2058-4563}, doi = {10.14236/jhi.v24i2.862}, author = {Raut, Anant and Yarbrough, Chase and Singh, Vivek and Gauchan, Bikash and Citrin, David and Verma, Varun and Hawley, Jessica and Schwarz, Dan and Harsha Bangura, Alex and Shrestha, Biplav and Schwarz, Ryan and Adhikari, Mukesh and Maru, Duncan} } @article {1236, title = {Development and Deployment of the OpenMRS-Ebola Electronic Health Record System for an Ebola Treatment Center in Sierra Leone.}, journal = {J Med Internet Res}, volume = {19}, year = {2017}, month = {2017 08 21}, pages = {e294}, abstract = {

BACKGROUND: Stringent infection control requirements at Ebola treatment centers (ETCs), which are specialized facilities for isolating and treating Ebola patients, create substantial challenges for recording and reviewing patient information. During the 2014-2016 West African Ebola epidemic, paper-based data collection systems at ETCs compromised the quality, quantity, and confidentiality of patient data. Electronic health record (EHR) systems have the potential to address such problems, with benefits for patient care, surveillance, and research. However, no suitable software was available for deployment when large-scale ETCs opened as the epidemic escalated in 2014.

OBJECTIVE: We present our work on rapidly developing and deploying OpenMRS-Ebola, an EHR system for the Kerry Town ETC in Sierra Leone. We describe our experience, lessons learned, and recommendations for future health emergencies.

METHODS: We used the OpenMRS platform and Agile software development approaches to build OpenMRS-Ebola. Key features of our work included daily communications between the development team and ground-based operations team, iterative processes, and phased development and implementation. We made design decisions based on the restrictions of the ETC environment and regular user feedback. To evaluate the system, we conducted predeployment user questionnaires and compared the EHR records with duplicate paper records.

RESULTS: We successfully built OpenMRS-Ebola, a modular stand-alone EHR system with a tablet-based application for infectious patient wards and a desktop-based application for noninfectious areas. OpenMRS-Ebola supports patient tracking (registration, bed allocation, and discharge); recording of vital signs and symptoms; medication and intravenous fluid ordering and monitoring; laboratory results; clinician notes; and data export. It displays relevant patient information to clinicians in infectious and noninfectious zones. We implemented phase 1 (patient tracking; drug ordering and monitoring) after 2.5 months of full-time development. OpenMRS-Ebola was used for 112 patient registrations, 569 prescription orders, and 971 medication administration recordings. We were unable to fully implement phases 2 and 3 as the ETC closed because of a decrease in new Ebola cases. The phase 1 evaluation suggested that OpenMRS-Ebola worked well in the context of the rollout, and the user feedback was positive.

CONCLUSIONS: To our knowledge, OpenMRS-Ebola is the most comprehensive adaptable clinical EHR built for a low-resource setting health emergency. It is designed to address the main challenges of data collection in highly infectious environments that require robust infection prevention and control measures and it is interoperable with other electronic health systems. Although we built and deployed OpenMRS-Ebola more rapidly than typical software, our work highlights the challenges of having to develop an appropriate system during an emergency rather than being able to rapidly adapt an existing one. Lessons learned from this and previous emergencies should be used to ensure that a set of well-designed, easy-to-use, pretested health software is ready for quick deployment in future.

}, keywords = {electronic health records, Epidemics, Hemorrhagic Fever, Ebola, Humans, Infection Control, Sierra Leone, Telemedicine}, issn = {1438-8871}, doi = {10.2196/jmir.7881}, author = {Oza, Shefali and Jazayeri, Darius and Teich, Jonathan M and Ball, Ellen and Nankubuge, Patricia Alexandra and Rwebembera, Job and Wing, Kevin and Sesay, Alieu Amara and Kanter, Andrew S and Ramos, Glauber D and Walton, David and Cummings, Rachael and Checchi, Francesco and Fraser, Hamish S} } @article {1160, title = {Donor{\textquoteright}s support tool: {Enabling} informed secondary use of patient{\textquoteright}s biomaterial and personal data}, journal = {International Journal of Medical Informatics}, volume = {97}, year = {2017}, pages = {282{\textendash}292}, abstract = {PURPOSE: Biomedical research is being catalyzed by the vast amount of data rapidly collected through the application of information technologies (IT). Despite IT advances, the methods for involving patients and citizens in biomedical research remain static, paper-based and organized around national boundaries and anachronistic legal frameworks. The purpose of this paper is to study the current practices for obtaining consent for biobanking and the legal requirements for reusing the available biomaterial and data in EU and finally to present a novel tool to this direction enabling the secondary use of data and biomaterial. METHOD: We review existing European legislation for secondary use of patient{\textquoteright}s biomaterial and data for research, identify types and scopes of consent, formal requirements for consent, and consider their implications for implementing electronic consent tools. To this direction, we proceed further to develop a modular tool, named Donor{\textquoteright}s Support Tool (DST), designed to connect researchers with participants, and to promote engagement, informed participation and individual decision making. RESULTS: To identify the advantages of our solution we compare our tool with six other relevant approaches. The results show that our tool scores higher than the other tools in functionality, security and intelligence whereas it is the only one free and open-source. In addition, the potential of our solution is shown by a proof of concept deployment in an existing clinical setting, where it was really appreciated, as streamlining the relevant workflow.}, keywords = {Biobank, Dynamic consent, Electronic consent, Secondary use of biomaterial and personal data}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.10.019}, author = {Kondylakis, Haridimos and Koumakis, Lefteris and H{\"a}nold, Stephanie and Nwankwo, Iheanyi and Forg{\'o}, Nikolaus and Marias, Kostas and Tsiknakis, Manolis and Graf, Norbert} } @article {1175, title = {Easy {Handling} of {Sensors} and {Actuators} over {TCP}/{IP} {Networks} by {Open} {Source} {Hardware}/{Software}}, journal = {Sensors (Basel, Switzerland)}, volume = {17}, year = {2017}, abstract = {There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)-this one designed using the intuitive graphical system of EJS-located on the user{\textquoteright}s computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented.}, keywords = {Arduino, collaborative access, data acquisition, EJS, HMI, Internet-of-Things, Modbus, open source hardware/software, remote access}, issn = {1424-8220}, doi = {10.3390/s17010094}, author = {Mej{\'\i}as, Andr{\'e}s and Herrera, Reyes S. and M{\'a}rquez, Marco A. and Calder{\'o}n, Antonio Jos{\'e} and Gonz{\'a}lez, Isa{\'\i}as and And{\'u}jar, Jos{\'e} Manuel} } @article {1206, title = {Health care consumer{\textquoteright}s perception of the {Electronic} {Medical} {Record} ({EMR}) system within a referral hospital in {Kigali}, {Rwanda}}, journal = {Rwanda Journal}, volume = {4}, year = {2017}, pages = {48{\textendash}53{\textendash}53}, abstract = {Background: Worldwide Electronic Medical Records (EMR) when compared to a paper-based system has been proven to improve service delivering numerous health care facilities. However, no research has been described in the literature regarding the user{\textquoteright}s perception of the clinical electronic medical record (EMR) system in Rwanda. The objective of this study is to evaluate the health care consumer{\textquoteright}s perception of the Electronic Medical Record (EMR) OpenClinic regarding improving the quality of health care delivery within the hospital setting. How does the OpenClinic system affect the patients{\textquoteright} waiting time? How complete is the information obtained from OpenClinic as compared to paper medical records, and the level of satisfaction of the users of OpenClinic.Method: A structured questionnaire was developed, validated and utilized in this quantitative research project. Quantitative data were collected from 170 participants while an interview guide was used to collect qualitative data from 6 key informants at a referral hospital in Kigali. The SPSS version 20.0 was used to analyze the quantitative data. The interviews transcribed verbatim; the data were thematically analyzed and categorized by pre-determined themes. Permission to conduct the study was approved from the ethics committee of the University of Rwanda, College of Health Sciences and the hospital.Results: The majority of the participants were satisfied with OpenClinic, (90\%), while only a few (10\%) did not perceive any advantage of a computer-based EMR and preferred paper based records.Conclusion: Openclinc EMR was seen to be an improvement in the data collection involving health care delivery in Kigali, Rwanda.Keywords: Electronic Medical Records, OpenClinic and Perceptions}, keywords = {Electronic medical records, OpenClinic and Perceptions}, issn = {2305-2678}, doi = {10.4314/rj.v4i1.7F}, url = {https://www.ajol.info/index.php/rj/article/view/156412}, author = {Uwambaye, Peace and Njunwa, Kato and Nuhu, Assouman and Kumurenzi, Anne and Isyagi, Moses and Murererehe, Julienne and Ngarambe, Donart} } @article {1231, title = {Home Behavior Monitoring Module in OpenEMR: Use of home sensors as Patient-Generated Data (PGD) for elderly care.}, journal = {AMIA Annu Symp Proc}, volume = {2017}, year = {2017}, month = {2017}, pages = {2279-2283}, issn = {1942-597X}, author = {Casanova-Perez, Regina A and Padilla-Huamantinco, Pierre G and De Freitas-Vidal, Catharine I and Choi, Yong K} } @article {1294, title = {How the introduction of a human resources information system helped the Democratic Republic of Congo to mobilise domestic resources for an improved health workforce.}, journal = {Health Policy Plan}, volume = {32}, year = {2017}, month = {2017 Nov 01}, pages = {iii25-iii31}, abstract = {

The Democratic Republic of Congo has flagged health workforce management and compensation as issues requiring attention, including the problem of ghost workers (individuals on payroll who do not exist and/or show up at work). Recognising the need for reliable health workforce information, the government has worked to implement iHRIS, an open source human resources information system that facilitates health workforce management. In Kasa{\"\i} Central and Kasa{\"\i} Provinces, health workers brought relevant documentation to data collection points, where trained teams interviewed them and entered contact information, identification, photo, current job, and employment and education history into iHRIS on laptops. After uploading the data, the Ministry of Public Health used the database of over 11 500 verified health worker records to analyse health worker characteristics, density, compensation, and payroll. Both provinces had less than one physician per 10 000 population and a higher urban versus rural health worker density. Most iHRIS-registered health workers (57\% in Kasa{\"\i} Central and 73\% in Kasa{\"\i}) reported receiving no regular government pay of any kind (salaries or risk allowances). Payroll analysis showed that 27\% of the health workers listed as salary recipients in the electronic payroll system were ghost workers, as were 42\% of risk allowance recipients. As a result, the Ministries of Public Health, Public Service, and Finance reallocated funds away from ghost workers to cover salaries (n = 781) and risk allowances (n = 2613) for thousands of health workers who were previously under- or uncompensated due to lack of funds. The reallocation prioritised previously under- or uncompensated mid-level health workers, with 49\% of those receiving salaries and 68\% of those receiving risk allowances representing cadres such as nurses, laboratory technicians, and midwifery cadres. Assembling accurate health worker records can help governments understand health workforce characteristics and use data to direct scarce domestic resources to where they are most needed.

}, keywords = {Democratic Republic of the Congo, Health Personnel, Health Workforce, Humans, Management Information Systems, Personnel Management, Remuneration}, issn = {1460-2237}, doi = {10.1093/heapol/czx113}, author = {Likofata Esanga, Jean-Robert and Viadro, Claire and McManus, Leah and Wesson, Jennifer and Matoko, Nicaise and Ngumbu, Epiphane and Gilroy, Kate E and Trudeau, Daren} } @article {1273, title = {Leveraging the Value of Human Relationships to Improve Health Outcomes. Lessons learned from the OpenMRS Electronic Health Record System.}, journal = {Appl Clin Inform}, volume = {8}, year = {2017}, month = {2017 Feb 01}, pages = {108-121}, abstract = {

OBJECTIVES: Despite significant awareness on the value of leveraging patient relationships across the healthcare continuum, there is no research on the potential of using Electronic Health Record (EHR) systems to store structured patient relationship data, or its impact on enabling better healthcare. We sought to identify which EHR systems supported effective patient relationship data collection, and for systems that do, what types of relationship data is collected, how this data is used, and the perceived value of doing so.

MATERIALS AND METHODS: We performed a literature search to identify EHR systems that supported patient relationship data collection. Based on our results, we defined attributes of an effective patient relationship model. The Open Medical Record System (OpenMRS), an open source medical record platform for underserved settings met our eligibility criteria for effective patient relationship collection. We performed a survey to understand how the OpenMRS patient relationship model was used, and how it brought value to implementers.

RESULTS: The OpenMRS patient relationship model has won widespread adoption across many implementations and is perceived to be valuable in enabling better health care delivery. Patient relationship information is widely used for community health programs and enabling chronic care. Additionally, many OpenMRS implementers were using this feature to collect custom relationship types for implementation specific needs.

CONCLUSIONS: We believe that flexible patient relationship data collection is critical for better healthcare, and can inform community care and chronic care initiatives across the world. Additionally, patient relationship data could also be leveraged for many other initiatives such as patient centric care and in the field of precision medicine.

}, keywords = {Data Collection, Delivery of Health Care, electronic health records, Humans, Interpersonal Relations}, issn = {1869-0327}, doi = {10.4338/ACI-2016-08-RA-0139}, author = {Kasthurirathne, Suranga N and Mamlin, Burke W and Cullen, Theresa} } @article {1285, title = {Long-Term Outcomes of Aflibercept Treatment for Neovascular Age-Related Macular Degeneration in a Clinical Setting.}, journal = {Am J Ophthalmol}, volume = {174}, year = {2017}, month = {2017 Feb}, pages = {160-168}, abstract = {

PURPOSE: To report 2-year treatment outcomes with intravitreal aflibercept for neovascular age-related macular degeneration (nAMD) in routine clinical practice.

DESIGN: Retrospective, nonrandomized, interventional case series.

METHODS: Retrospective analysis of electronic medical record (EMR) notes (OpenEyes) and paper case notes and review of spectral-domain optical coherence tomography (SDOCT) imaging of patients with consecutively treated eyes with previously untreated nAMD. Patients were commenced on aflibercept injections in 1 or both eyes from October 1, 2013 to December 31, 2013. Data including age, sex, visual acuity (VA) measured on Early Treatment Diabetic Retinopathy Study charts, injection episodes, and complications were recorded. Additionally, SDOCT data, including presence or absence of macular fluid and automated central subfield macular thickness (CSMT) at year 1 and 2, were recorded.

RESULTS: Of the 109 eyes of 102 patients treated, data from 94 eyes of 88 patients were available at 2-year follow-up (86\% of patients). In the analysis of 2-year outcomes, there were 58 women (65.9\%); the mean ({\textpm} standard deviation) age was 77.5 {\textpm} 8 years. Over the 2 years, these eyes received a median of 12 (mean, 11.4 {\textpm} 4) injections at a median of 100 (mean, 99.3 {\textpm} 5.3) weeks of follow-up. The mean VA changed from 55.9 {\textpm} 15 letters at baseline to 61.3 {\textpm} 16.9 letters (VA gain 5.4 letters) at 1 year and to 61 {\textpm} 17.1 letters (VA gain 5.1 {\textpm} 14.9 letters) at 2 years. The reduction in CSMT was 79~μm with absence of macular fluid in 72.7\% of the 88 eyes with SDOCT data available at 2-year follow-up.

CONCLUSIONS: The VA and SDOCT results compare favorably with outcomes seen in randomized controlled trials. The results suggest that good long-term outcomes can be achieved using aflibercept for nAMD in clinical settings.

}, keywords = {Aged, Dose-Response Relationship, Drug, Female, Fluorescein Angiography, Follow-Up Studies, Fundus Oculi, Humans, Intravitreal Injections, Macula Lutea, Macular Degeneration, Male, Receptors, Vascular Endothelial Growth Factor, Recombinant Fusion Proteins, Retinal Neovascularization, Retrospective Studies, Time Factors, Tomography, Optical Coherence, Treatment Outcome, Visual Acuity}, issn = {1879-1891}, doi = {10.1016/j.ajo.2016.09.038}, author = {Eleftheriadou, Maria and Vazquez-Alfageme, Clara and Citu, Cristina Maria and Crosby-Nwaobi, Roxanne and Sivaprasad, Sobha and Hykin, Philip and Hamilton, Robin D and Patel, Praveen J} } @article {1267, title = {Mapping for Health in Cameroon: Polio Legacy and Beyond.}, journal = {J Infect Dis}, volume = {216}, year = {2017}, month = {2017 07 01}, pages = {S337-S342}, abstract = {

During the poliovirus outbreak in Cameroon from October 2013 to April 2015, the Ministry of Public Health{\textquoteright}s Expanded Program on Immunization requested technical support to improve mapping of health district boundaries and health facility locations for more effective planning and analysis of polio program data. In December 2015, teams collected data on settlements, health facilities, and other features using smartphones. These data, combined with high-resolution satellite imagery, were used to create new health area and health district boundaries, providing the most accurate health sector administrative boundaries to date for Cameroon. The new maps are useful to and used by the polio program as well as other public health programs within Cameroon such as the District Health Information System and the Emergency Operations Center, demonstrating the value of the Global Polio Eradication Initiative{\textquoteright}s legacy.

}, keywords = {Cameroon, Geographic Information Systems, Humans, Immunization Programs, Poliomyelitis, Public Health, Public Health Surveillance, Smartphone}, issn = {1537-6613}, doi = {10.1093/infdis/jix008}, author = {Rosencrans, Louie C and Sume, Gerald E and Kouontchou, Jean-Christian and Voorman, Arend and Anokwa, Yaw and Fezeu, Maurice and Seaman, Vincent Y} } @article {1276, title = {A Mobile-Based Community Health Management Information System for Community Health Workers and Their Supervisors in 2 Districts of Zambia.}, journal = {Glob Health Sci Pract}, volume = {5}, year = {2017}, month = {2017 09 27}, pages = {486-494}, abstract = {

INTRODUCTION: Effective community health management information systems (C-HMIS) are important in low-resource countries that rely heavily on community-based health care providers. Zambia currently lacks a functioning C-HMIS to provide real-time, community-based health information from community health workers (CHWs) to health center staff and higher levels of the health system.

PROGRAM DESCRIPTION: We developed a C-HMIS mobile platform for use by CHWs providing integrated community case management (iCCM) services and their supervisors to address challenges of frequent stock-outs and inadequate supportive supervision of iCCM-trained CHWs. The platform used simple feature mobile phones on which were loaded the District Health Information System version 2 (DHIS2) software and Java 2 platform micro edition (J2ME) aggregation and tracker applications. This project was implemented in Chipata and Chadiza districts, which supported previous mHealth programs and had cellular coverage from all 3 major network carriers in Zambia. A total of 40 CHWs and 20 CHW supervisors received mobile phones with data bundles and training in the mobile application, after which they implemented the program over a period of 5.5 months, from February to mid-July 2016. CHWs used the mobile phones to submit data on iCCM cases seen, managed, and referred, as well as iCCM medical and diagnostic supplies received and dispensed. Using their mobile phones, the supervisors tracked CHWs{\textquoteright} reported cases with medicine consumption, sent CHWs feedback on their referrals, and received SMS reminders to set up mentorship sessions.

OBSERVATIONS: CHWs were able to use the mobile application to send weekly reports to health center supervisors on disease caseloads and medical commodities consumed, to make drug and supply requisitions, and to send pre-referral notices to health centers. Health center staff used the mobile system to provide feedback to CHWs on the case outcomes of referred patients and to receive automated monthly SMS reminders to invite CHWs to the facility for mentorship. District- and central-level staff were able to access community-level health data in real time using passwords.

LESSONS LEARNED: C-HMIS, using simple feature phones, was feasible and viable for the provision of real-time community-based health information to all levels of the health care system in Zambia, but smartphones, laptops, or desktop computers are needed to perform data analysis and visualization. Ongoing technical support is needed to address the hardware and software challenges CHWs face in their day-to-day interaction with the application on their mobile phones.

}, keywords = {Community Health Services, Community Health Workers, Delivery of Health Care, Health information systems, Humans, Mobile Applications, Referral and Consultation, Zambia}, issn = {2169-575X}, doi = {10.9745/GHSP-D-16-00275}, author = {Biemba, Godfrey and Chiluba, Boniface and Yeboah-Antwi, Kojo and Silavwe, Vichaels and Lunze, Karsten and Mwale, Rodgers K and Russpatrick, Scott and Hamer, Davidson H} } @article {1174, title = {A national standards-based assessment on functionality of electronic medical records systems used in {Kenyan} public-{Sector} health facilities}, journal = {International Journal of Medical Informatics}, volume = {97}, year = {2017}, pages = {68{\textendash}75}, abstract = {BACKGROUND: Variations in the functionality, content and form of electronic medical record systems (EMRs) challenge national roll-out of these systems as part of a national strategy to monitor HIV response. To enforce the EMRs minimum requirements for delivery of quality HIV services, the Kenya Ministry of Health (MoH) developed EMRs standards and guidelines. The standards guided the recommendation of EMRs that met a preset threshold for national roll-out. METHODS: Using a standards-based checklist, six review teams formed by the MoH EMRs Technical Working Group rated a total of 17 unique EMRs in 28 heath facilities selected by individual owners for their optimal EMR implementation. EMRs with an aggregate score of >=60\% against checklist criteria were identified by the MoH as suitable for upgrading and rollout to Kenyan public health facilities. RESULTS: In Kenya, existing EMRs scored highly in health information and reporting (mean score=71.8\%), followed by security, system features, core clinical information, and order entry criteria (mean score=58.1\%-55.9\%), and lowest against clinical decision support (mean score=17.6\%) and interoperability criteria (mean score=14.3\%). Four EMRs met the 60.0\% threshold: OpenMRS, IQ-Care, C-PAD and Funsoft. On the basis of the review, the MoH provided EMRs upgrade plans to owners of all the 17 systems reviewed. CONCLUSION: The standards-based review in Kenya represents an effort to determine level of conformance to the EMRs standards and prioritize EMRs for enhancement and rollout. The results support concentrated use of resources towards development of the four recommended EMRs. Further review should be conducted to determine the effect of the EMR-specific upgrade plans on the other 13 EMRs that participated in the review exercise.}, keywords = {Checklist, EMRs, Review, Standards}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.09.013}, author = {Kang{\textquoteright}a, Samuel and Puttkammer, Nancy and Wanyee, Steven and Kimanga, Davies and Madrano, Jason and Muthee, Veronica and Odawo, Patrick and Sharma, Anjali and Oluoch, Tom and Robinson, Katherine and Kwach, James and Lober, William B.} } @article {1205, title = {Open-{Source} {Electronic} {Health} {Record} {Systems} for {Low}-{Resource} {Settings}: {Systematic} {Review}}, journal = {JMIR Medical Informatics}, volume = {5}, year = {2017}, abstract = {Background Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. Objective The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. Methods First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. Results The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code-based language, (17) development activity, (18) modularity, (19) user interface, (20) community support, and (21) customization. The quality of each feature is discussed for each of the evaluated solutions and a final comparison is presented. Conclusions There is a clear demand for open-source, reliable, and flexible EHR systems in low-resource settings. In this study, we have evaluated and compared five open-source EHR systems following a multidimensional methodology that can provide informed recommendations to other implementers, developers, and health care professionals. We hope that the results of this comparison can guide decision making when needing to adopt, install, and maintain an open-source EHR solution in low-resource settings.}, issn = {2291-9694}, doi = {10.2196/medinform.8131}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703976/}, author = {Syzdykova, Assel and Malta, Andr{\'e} and Zolfo, Maria and Diro, Ermias and Oliveira, Jos{\'e} Lu{\'\i}s} } @article {1192, title = {{OpenICE} medical device interoperability platform overview and requirement analysis}, journal = {Biomedizinische Technik. Biomedical Engineering}, year = {2017}, abstract = {We give an overview of OpenICE, an open source implementation of the ASTM standard F2761 for the Integrated Clinical Environment (ICE) that leverages medical device interoperability, together with an analysis of the clinical and non-functional requirements and community process that inspired its design.}, keywords = {Interoperability, medical applications, patient safety, platform, requirements engineering}, issn = {1862-278X}, doi = {10.1515/bmt-2017-0040}, author = {Arney, David and Plourde, Jeffrey and Goldman, Julian M.} } @article {1202, title = {Open-source mobile digital platform for clinical trial data collection in low-resource settings}, journal = {BMJ innovations}, volume = {3}, year = {2017}, pages = {26{\textendash}31}, abstract = {BACKGROUND: Governments, universities and pan-African research networks are building durable infrastructure and capabilities for biomedical research in Africa. This offers the opportunity to adopt from the outset innovative approaches and technologies that would be challenging to retrofit into fully established research infrastructures such as those regularly found in high-income countries. In this context we piloted the use of a novel mobile digital health platform, designed specifically for low-resource environments, to support high-quality data collection in a clinical research study. OBJECTIVE: Our primary aim was to assess the feasibility of a using a mobile digital platform for clinical trial data collection in a low-resource setting. Secondarily, we sought to explore the potential benefits of such an approach. METHODS: The investigative site was a research institute in Nairobi, Kenya. We integrated an open-source platform for mobile data collection commonly used in the developing world with an open-source, standard platform for electronic data capture in clinical trials. The integration was developed using common data standards (Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model), maximising the potential to extend the approach to other platforms. The system was deployed in a pharmacokinetic study involving healthy human volunteers. RESULTS: The electronic data collection platform successfully supported conduct of the study. Multidisciplinary users reported high levels of satisfaction with the mobile application and highlighted substantial advantages when compared with traditional paper record systems. The new system also demonstrated a potential for expediting data quality review. DISCUSSION AND CONCLUSIONS: This pilot study demonstrated the feasibility of using a mobile digital platform for clinical research data collection in low-resource settings. Sustainable scientific capabilities and infrastructure are essential to attract and support clinical research studies. Since many research structures in Africa are being developed anew, stakeholders should consider implementing innovative technologies and approaches.}, keywords = {clinical research, eSource, Global Health, mHealth, Reverse Innovations}, issn = {2055-642X}, doi = {10.1136/bmjinnov-2016-000164}, author = {van Dam, Joris and Omondi Onyango, Kevin and Midamba, Brian and Groosman, Nele and Hooper, Norman and Spector, Jonathan and Pillai, Goonaseelan Colin and Ogutu, Bernhards} } @article {1189, title = {Orchestrating differential data access for translational research: a pilot implementation}, journal = {BMC Medical Informatics and Decision Making}, volume = {17}, year = {2017}, month = {2017}, pages = {30}, abstract = {BACKGROUND: Translational researchers need robust IT solutions to access a range of data types, varying from public data sets to pseudonymised patient information with restricted access, provided on a case by case basis. The reason for this complication is that managing access policies to sensitive human data must consider issues of data confidentiality, identifiability, extent of consent, and data usage agreements. All these ethical, social and legal aspects must be incorporated into a differential management of restricted access to sensitive data. METHODS: In this paper we present a pilot system that uses several common open source software components in a novel combination to coordinate access to heterogeneous biomedical data repositories containing open data (open access) as well as sensitive data (restricted access) in the domain of biobanking and biosample research. Our approach is based on a digital identity federation and software to manage resource access entitlements. RESULTS: Open source software components were assembled and configured in such a way that they allow for different ways of restricted access according to the protection needs of the data. We have tested the resulting pilot infrastructure and assessed its performance, feasibility and reproducibility. CONCLUSIONS: Common open source software components are sufficient to allow for the creation of a secure system for differential access to sensitive data. The implementation of this system is exemplary for researchers facing similar requirements for restricted access data. Here we report experience and lessons learnt of our pilot implementation, which may be useful for similar use cases. Furthermore, we discuss possible extensions for more complex scenarios.}, isbn = {1472-6947}, doi = {10.1186/s12911-017-0424-6}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363029/}, author = {Brandizi, Marco and Melnichuk, Olga and Bild, Raffael and Kohlmayer, Florian and Rodriguez-Castro, Benedicto and Spengler, Helmut and Kuhn, Klaus A and Kuchinke, Wolfgang and Ohmann, Christian and Mustonen, Timo and Linden, Mikael and Nyr{\"o}nen, Tommi and Lappalainen, Ilkka and Brazma, Alvis and Sarkans, Ugis} } @article {1300, title = {QuPath: Open source software for digital pathology image analysis.}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {2017 12 04}, pages = {16878}, abstract = {

QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath{\textquoteright}s flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.

}, keywords = {Algorithms, Biomarkers, Tumor, Colonic Neoplasms, Humans, Image Interpretation, Computer-Assisted, Kaplan-Meier Estimate, Programmed Cell Death 1 Ligand 2 Protein, User-Computer Interface}, issn = {2045-2322}, doi = {10.1038/s41598-017-17204-5}, author = {Bankhead, Peter and Loughrey, Maurice B and Fern{\'a}ndez, Jos{\'e} A and Dombrowski, Yvonne and McArt, Darragh G and Dunne, Philip D and McQuaid, Stephen and Gray, Ronan T and Murray, Liam J and Coleman, Helen G and James, Jacqueline A and Salto-Tellez, Manuel and Hamilton, Peter W} } @article {1284, title = {Risk of Posterior Capsule Rupture During Cataract Surgery in Eyes With Previous Intravitreal Injections.}, journal = {Am J Ophthalmol}, volume = {177}, year = {2017}, month = {2017 May}, pages = {77-80}, abstract = {

PURPOSE: To investigate the risk of posterior capsular rupture (PCR) during cataract surgery in eyes with previous intravitreal injection (IVI).

DESIGN: Retrospective cohort study.

METHODS: The Moorfields Patient Administrative System and OpenEyes electronic databases were used to study all cataract surgery procedures undertaken between January 1, 2012 and August 31, 2015 in the Moorfields main and satellite sites. Clinical data were anonymized and extracted, including prior occurrence and number of intravitreal injections. Logistic regression was performed with the Hosmer-Lemeshow test for goodness of fit to generate odds ratios for possible risk factors.

RESULTS: In total, 62 994 cataract surgery procedures were undertaken over the study period, of which 1035 (1.64\%) were in eyes with previous intravitreal injection(s). PCR occurred in 650 (1.04\%) eyes. After logistic regression, prior intravitreal injection was associated with an increased risk of PCR (P~= .037), with an odds ratio of 1.66. The number of prior injections, indication for injections, and service undertaking the surgery were not associated with increased risk of PCR (P > .1).

CONCLUSIONS: Eyes with previous IVI have a higher risk of PCR. This is not affected by number of previous injections, indication for injections, or the specialty undertaking the surgery.

}, keywords = {Aged, Cataract Extraction, Female, Follow-Up Studies, Glucocorticoids, Humans, Incidence, Intraoperative Complications, Intravitreal Injections, Lens Capsule, Crystalline, Male, Posterior Capsular Rupture, Ocular, Retrospective Studies, Risk Factors, United Kingdom, Visual Acuity}, issn = {1879-1891}, doi = {10.1016/j.ajo.2017.02.006}, author = {Shalchi, Zaid and Okada, Mali and Whiting, Chris and Hamilton, Robin} } @article {1263, title = {The State of Open Source Electronic Health Record Projects: A Software Anthropology Study.}, journal = {JMIR Med Inform}, volume = {5}, year = {2017}, month = {2017 Feb 24}, pages = {e6}, abstract = {

BACKGROUND: Electronic health records (EHR) are a key tool in managing and storing patients{\textquoteright} information. Currently, there are over 50 open source EHR systems available. Functionality and usability are important factors for determining the success of any system. These factors are often a direct reflection of the domain knowledge and developers{\textquoteright} motivations. However, few published studies have focused on the characteristics of free and open source software (F/OSS) EHR systems and none to date have discussed the motivation, knowledge background, and demographic characteristics of the developers involved in open source EHR projects.

OBJECTIVE: This study analyzed the characteristics of prevailing F/OSS EHR systems and aimed to provide an understanding of the motivation, knowledge background, and characteristics of the developers.

METHODS: This study identified F/OSS EHR projects on SourceForge and other websites from May to July 2014. Projects were classified and characterized by license type, downloads, programming languages, spoken languages, project age, development status, supporting materials, top downloads by country, and whether they were "certified" EHRs. Health care F/OSS developers were also surveyed using an online survey.

RESULTS: At the time of the assessment, we uncovered 54 open source EHR projects, but only four of them had been successfully certified under the Office of the National Coordinator for Health Information Technology (ONC Health IT) Certification Program. In the majority of cases, the open source EHR software was downloaded by users in the United States (64.07\%, 148,666/232,034), underscoring that there is a significant interest in EHR open source applications in the United States. A survey of EHR open source developers was conducted and a total of 103 developers responded to the online questionnaire. The majority of EHR F/OSS developers (65.3\%, 66/101) are participating in F/OSS projects as part of a paid activity and only 25.7\% (26/101) of EHR F/OSS developers are, or have been, health care providers in their careers. In addition, 45\% (45/99) of developers do not work in the health care field.

CONCLUSION: The research presented in this study highlights some challenges that may be hindering the future of health care F/OSS. A minority of developers have been health care professionals, and only 55\% (54/99) work in the health care field. This undoubtedly limits the ability of functional design of F/OSS EHR systems from being a competitive advantage over prevailing commercial EHR systems. Open source software seems to be a significant interest to many; however, given that only four F/OSS EHR systems are ONC-certified, this interest is unlikely to yield significant adoption of these systems in the United States. Although the Health Information Technology for Economic and Clinical Health (HITECH) act was responsible for a substantial infusion of capital into the EHR marketplace, the lack of a corporate entity in most F/OSS EHR projects translates to a marginal capacity to market the respective F/OSS system and to navigate certification. This likely has further disadvantaged F/OSS EHR adoption in the United States.

}, issn = {2291-9694}, doi = {10.2196/medinform.5783}, author = {Alsaffar, Mona and Yellowlees, Peter and Odor, Alberto and Hogarth, Michael} } @article {1176, title = {Three-dimensional image reconstruction with free open-source {OsiriX} software in video-assisted thoracoscopic lobectomy and segmentectomy}, journal = {International Journal of Surgery (London, England)}, year = {2017}, abstract = {OBJECTIVE: The aim of this retrospective study was to evaluate the practice and the feasibility of Osirix, a free and open-source medical imaging software, in performing accurate video-assisted thoracoscopic lobectomy and segmentectomy. METHODS: From July 2014 to April 2016, 63 patients received anatomical video-assisted thoracoscopic surgery (VATS), either lobectomy or segmentectomy, in our department. Three-dimensional (3D) reconstruction images of 61 (96.8\%) patients were preoperatively obtained with contrast-enhanced computed tomography (CT). Preoperative resection simulations were accomplished with patient-individual reconstructed 3D images. For lobectomy, pulmonary lobar veins, arteries and bronchi were identified meticulously by carefully reviewing the 3D images on the display. For segmentectomy, the intrasegmental veins in the affected segment for division and the intersegmental veins to be preserved were identified on the 3D images. Patient preoperative characteristics, surgical outcomes and postoperative data were reviewed from a prospective database. RESULTS: The study cohort of 63 patients included 33 (52.4\%) men and 30 (47.6\%) women, of whom 46 (73.0\%) underwent VATS lobectomy and 17 (37.0\%) underwent VATS segmentectomy. There was 1 conversion from VATS lobectomy to open thoracotomy because of fibrocalcified lymph nodes. A VATS lobectomy was performed in 1 case after completing the segmentectomy because invasive adenocarcinoma was detected by intraoperative frozen-section analysis. There were no 30-day or 90-day operative mortalities CONCLUSIONS: The free, simple, and user-friendly software program Osirix can provide a 3D anatomic structure of pulmonary vessels and a clear vision into the space between the lesion and adjacent tissues, which allows surgeons to make preoperative simulations and improve the accuracy and safety of actual surgery.}, keywords = {Lobectomy, Segmentectomy, Three-dimensional reconstruction technique, Video-assisted thoracoscopic surgery}, issn = {1743-9159}, doi = {10.1016/j.ijsu.2017.01.079}, author = {Yao, Fei and Wang, Jian and Yao, Ju and Hang, Fangrong and Lei, Xu and Cao, Yongke} } @article {1291, title = {Using Android and Open Data Kit Technology in Data Management for Research in Resource-Limited Settings in the Niger Delta Region of Nigeria: Cross-Sectional Household Survey.}, journal = {JMIR Mhealth Uhealth}, volume = {5}, year = {2017}, month = {2017 Nov 30}, pages = {e171}, abstract = {

BACKGROUND: Data collection in Sub-Saharan Africa has traditionally been paper-based. However, the popularization of Android mobile devices and data capture software has brought paperless data management within reach. We used Open Data Kit (ODK) technology on Android mobile devices during a household survey in the Niger Delta region of Nigeria.

OBJECTIVE: The aim of this study was to describe the pros and cons of deploying ODK for data management.

METHODS: A descriptive cross-sectional household survey was carried out by 6 data collectors between April and May 2016. Data were obtained from 1706 persons in 601 households across 6 communities in 3 states in the Niger Delta. The use of Android mobile devices and ODK technology involved form building, testing, collection, aggregation, and download for data analysis. The median duration for data collection per household and per individual was 25.7 and 9.3 min, respectively.

RESULTS: Data entries per device ranged from 33 (33/1706, 1.93\%) to 482 (482/1706, 28.25\%) individuals between 9 (9/601, 1.5\%) and 122 (122/601, 20.3\%) households. The most entries (470) were made by data collector 5. Only 2 respondents had data entry errors (2/1706, 0.12\%). However, 73 (73/601, 12.1\%) households had inaccurate date and time entries for when data collection started and ended. The cost of deploying ODK was estimated at US $206.7 in comparison with the estimated cost of US $466.7 for paper-based data management.

CONCLUSIONS: We found the use of mobile data capture technology to be efficient and cost-effective. As Internet services improve in Africa, we advocate their use as effective tools for health information management.

}, issn = {2291-5222}, doi = {10.2196/mhealth.7827}, author = {Maduka, Omosivie and Akpan, Godwin and Maleghemi, Sylvester} } @article {1123, title = {3D for the people: multi-camera motion capture in the field with consumer-grade cameras and open source software.}, journal = {Biol Open}, year = {2016}, month = {2016 Jul 21}, abstract = {

Ecological, behavioral, and biomechanical studies often need to quantify animal movement and behavior in three dimensions. In laboratory studies, a major tool to accomplish these measurements is the use of multiple, calibrated high-speed cameras. Until very recently, the complexity, weight, and cost of such cameras have made their deployment in field situations risky; furthermore, such cameras are not affordable to many researchers. Here we show how inexpensive, consumer-grade cameras can accomplish these measurements both within the laboratory and in the field. Combined with our methods and open source software, the availability of inexpensive, portable and rugged cameras will open up new areas of biological study by providing precise 3D tracking and quantification of animal and human movement to researchers in a wide variety of field and laboratory contexts.

}, issn = {2046-6390}, doi = {10.1242/bio.018713}, author = {Jackson, Brandon E and Evangelista, Dennis J and Ray, Dylan D and Hedrick, Tyson L} } @article {1134, title = {Assessment of four common underfive children illnesses Routine Health Management Information System data for decision making at Ilemela Municipal Council, Northwest Tanzania: A case series analysis.}, journal = {Int J Med Inform}, volume = {93}, year = {2016}, month = {2016 Sep}, pages = {85-91}, abstract = {

BACKGROUND: In 2012, The Tanzania Ministry Of Health introduced the revised Routine Health Management Information System (RHMIS) modules and registers, and introduced the open source software for data collection at the district council level. Despite a series of data collection tools revisions, the quality of data collated from both public and private primary health care facilities has not been investigated.

METHODS: A case series study design was conducted on underfive children outpatient registers and monthly reports on malaria, acute respiratory infections, acute diarrhoea and pneumonia from 10 randomly selected health facilities. The data was entered into excel software and exported to stata version 11 for analysis. The data was analyzed for completeness, timely report submission and reporting accuracy.

RESULTS: The Study found that 62\% of the expected data was complete. Around 40\% of the facilities submitted reports on time. Private health facilities submitted monthly reports late compared to the public facilities (p-value=0.039). There was 26\% over-reporting of diagnosis. Health centres tended to over-report more diagnoses by 11 times higher than the dispensaries. In addition, private owned health facilities tended to over-report more diagnoses by 6 times higher than public owned health facilities.

CONCLUSION: The RHMIS data collected through out patients department (OPD) registers on four common underfive children{\textquoteright}s illnesses at ilemela municipality were of unsatisfactory quality in light of allocation of resource allocations in the comprehensive council health plan.

}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.06.003}, author = {Kabakama, Severin and Ngallaba, Sospatro and Musto, Richard and Montesanti, Stephanie and Konje, Eveline and Kishamawe, Coleman} } @article {1172, title = {Automated population of an i2b2 clinical data warehouse from an {openEHR}-based data repository}, journal = {Journal of Biomedical Informatics}, volume = {63}, year = {2016}, pages = {277{\textendash}294}, abstract = {BACKGROUND: Detailed Clinical Model (DCM) approaches have recently seen wider adoption. More specifically, openEHR-based application systems are now used in production in several countries, serving diverse fields of application such as health information exchange, clinical registries and electronic medical record systems. However, approaches to efficiently provide openEHR data to researchers for secondary use have not yet been investigated or established. METHODS: We developed an approach to automatically load openEHR data instances into the open source clinical data warehouse i2b2. We evaluated query capabilities and the performance of this approach in the context of the Hanover Medical School Translational Research Framework (HaMSTR), an openEHR-based data repository. RESULTS: Automated creation of i2b2 ontologies from archetypes and templates and the integration of openEHR data instances from 903 patients of a paediatric intensive care unit has been achieved. In total, it took an average of \~{}2527s to create 2.311.624 facts from 141.917 XML documents. Using the imported data, we conducted sample queries to compare the performance with two openEHR systems and to investigate if this representation of data is feasible to support cohort identification and record level data extraction. DISCUSSION: We found the automated population of an i2b2 clinical data warehouse to be a feasible approach to make openEHR data instances available for secondary use. Such an approach can facilitate timely provision of clinical data to researchers. It complements analytics based on the Archetype Query Language by allowing querying on both, legacy clinical data sources and openEHR data instances at the same time and by providing an easy-to-use query interface. However, due to different levels of expressiveness in the data models, not all semantics could be preserved during the ETL process.}, keywords = {Archetypes, Clinical data repository, clinical information systems, Data warehouse, Detailed clinical models, Healthcare analytics, i2b2, openEHR, Secondary use}, issn = {1532-0480}, doi = {10.1016/j.jbi.2016.08.007}, author = {Haarbrandt, Birger and Tute, Erik and Marschollek, Michael} } @article {1237, title = {Automating indicator data reporting from health facility EMR to a national aggregate data system in Kenya: An Interoperability field-test using OpenMRS and DHIS2.}, journal = {Online J Public Health Inform}, volume = {8}, year = {2016}, month = {2016}, pages = {e188}, abstract = {

Developing countries are increasingly strengthening national health information systems (HIS) for evidence-based decision-making. However, the inability to report indicator data automatically from electronic medical record systems (EMR) hinders this process. Data are often printed and manually re-entered into aggregate reporting systems. This affects data completeness, accuracy, reporting timeliness, and burdens staff who support routine indicator reporting from patient-level data. After conducting a feasibility test to exchange indicator data from Open Medical Records System (OpenMRS) to District Health Information System version 2 (DHIS2), we conducted a field test at a health facility in Kenya. We configured a field-test DHIS2 instance, similar to the Kenya Ministry of Health (MOH) DHIS2, to receive HIV care and treatment indicator data and the KenyaEMR, a customized version of OpenMRS, to generate and transmit the data from a health facility. After training facility staff how to send data using DHIS2 reporting module, we compared completeness, accuracy and timeliness of automated indicator reporting with facility monthly reports manually entered into MOH DHIS2. All 45 data values in the automated reporting process were 100\% complete and accurate while in manual entry process, data completeness ranged from 66.7\% to 100\% and accuracy ranged from 33.3\% to 95.6\% for seven months (July 2013-January 2014). Manual tally and entry process required at least one person to perform each of the five reporting activities, generating data from EMR and manual entry required at least one person to perform each of the three reporting activities, while automated reporting process had one activity performed by one person. Manual tally and entry observed in October 2013 took 375 minutes. Average time to generate data and manually enter into DHIS2 was over half an hour (M=32.35 mins, SD=0.29) compared to less than a minute for automated submission (M=0.19 mins, SD=0.15). The results indicate that indicator data sent electronically from OpenMRS-based EMR at a health facility to DHIS2 improves data completeness, eliminates transcription errors and delays in reporting, and reduces the reporting burden on human resources. This increases availability of quality indicator data using available resources to facilitate monitoring service delivery and measuring progress towards set goals.

}, issn = {1947-2579}, doi = {10.5210/ojphi.v8i2.6722}, author = {Kariuki, James M and Manders, Eric-Jan and Richards, Janise and Oluoch, Tom and Kimanga, Davies and Wanyee, Steve and Kwach, James O and Santas, Xenophon} } @article {1157, title = {Benefits, {Challenges} and {Potential} {Strategies} of {Open} {Source} {Health} {Economic} {Models}}, journal = {PharmacoEconomics}, year = {2016}, issn = {1179-2027}, doi = {10.1007/s40273-016-0479-8}, author = {Dunlop, William C. N. and Mason, Nicola and Kenworthy, James and Akehurst, Ron L.} } @inbook {1119, title = {BiobankCloud: A Platform for the Secure Storage, Sharing, and Processing of Large Biomedical Data Sets}, booktitle = {Biomedical Data Management and Graph Online Querying: VLDB 2015 Workshops, Big-O(Q) and DMAH, Waikoloa, HI, USA, August 31 {\textendash} September 4, 2015, Revised Selected Papers}, year = {2016}, pages = {89{\textendash}105}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {Biobanks store and catalog human biological material that is increasingly being digitized using next-generation sequencing (NGS). There is, however, a computational bottleneck, as existing software systems are not scalable and secure enough to store and process the incoming wave of genomic data from NGS machines. In the BiobankCloud project, we are building a Hadoop-based platform for the secure storage, sharing, and parallel processing of genomic data. We extended Hadoop to include support for multi-tenant studies, reduced storage requirements with erasure coding, and added support for extensible and consistent metadata. On top of Hadoop, we built a scalable scientific workflow engine featuring a proper workflow definition language focusing on simple integration and chaining of existing tools, adaptive scheduling on Apache Yarn, and support for iterative dataflows. Our platform also supports the secure sharing of data across different, distributed Hadoop clusters. The software is easily installed and comes with a user-friendly web interface for running, managing, and accessing data sets behind a secure 2-factor authentication. Initial tests have shown that the engine scales well to dozens of nodes. The entire system is open-source and includes pre-defined workflows for popular tasks in biomedical data analysis, such as variant identification, differential transcriptome analysis using RNA-Seq, and analysis of miRNA-Seq and ChIP-Seq data.}, isbn = {978-3-319-41576-5}, doi = {10.1007/978-3-319-41576-5_7}, url = {http://dx.doi.org/10.1007/978-3-319-41576-5_7}, author = {Bessani, Alysson and Brandt, J{\"o}rgen and Bux, Marc and Cogo, Vinicius and Dimitrova, Lora and Dowling, Jim and Gholami, Ali and Hakimzadeh, Kamal and Hummel, Micheal and Ismail, Mahmoud and Laure, Erwin and Leser, Ulf and Litton, Jan-Eric and Martinez, Roxanna and Niazi, Salman and Reichel, Jane and Zimmermann, Karin}, editor = {Wang, Fusheng and Luo, Gang and Weng, Chunhua and Khan, Arijit and Mitra, Prasenjit and Yu, Cong} } @article {1288, title = {Collaborative analysis of multi-gigapixel imaging data using Cytomine.}, journal = {Bioinformatics}, volume = {32}, year = {2016}, month = {2016 05 01}, pages = {1395-401}, abstract = {

MOTIVATION: Collaborative analysis of massive imaging datasets is essential to enable scientific discoveries.

RESULTS: We developed Cytomine to foster active and distributed collaboration of multidisciplinary teams for large-scale image-based studies. It uses web development methodologies and machine learning in order to readily organize, explore, share and analyze (semantically and quantitatively) multi-gigapixel imaging data over the internet. We illustrate how it has been used in several biomedical applications.

AVAILABILITY AND IMPLEMENTATION: Cytomine (http://www.cytomine.be/) is freely available under an open-source license from http://github.com/cytomine/ A documentation wiki (http://doc.cytomine.be) and a demo server (http://demo.cytomine.be) are also available.

CONTACT: info@cytomine.be

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

}, keywords = {Image Interpretation, Computer-Assisted, Internet, Software, Statistics as Topic}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btw013}, author = {Mar{\'e}e, Rapha{\"e}l and Rollus, Lo{\"\i}c and St{\'e}vens, Benjamin and Hoyoux, Renaud and Louppe, Gilles and Vandaele, R{\'e}my and Begon, Jean-Michel and Kainz, Philipp and Geurts, Pierre and Wehenkel, Louis} } @article {1167, title = {{ConoSurf}: {Open}-source 3D scanning system based on a conoscopic holography device for acquiring surgical surfaces}, journal = {The international journal of medical robotics + computer assisted surgery: MRCAS}, year = {2016}, abstract = {BACKGROUND: A difficulty in computer-assisted interventions is acquiring the patient{\textquoteright}s anatomy intraoperatively. Standard modalities have several limitations: low image quality (ultrasound), radiation exposure (computed tomography) or high costs (magnetic resonance imaging). An alternative approach uses a tracked pointer; however, the pointer causes tissue deformation and requires sterilizing. Recent proposals, utilizing a tracked conoscopic holography device, have shown promising results without the previously mentioned drawbacks. METHODS: We have developed an open-source software system that enables real-time surface scanning using a conoscopic holography device and a wide variety of tracking systems, integrated into pre-existing and well-supported software solutions. RESULTS: The mean target registration error of point measurements was 1.46~mm. For a quick guidance scan, surface reconstruction improved the surface registration error compared with point-set registration. CONCLUSIONS: We have presented a system enabling real-time surface scanning using a tracked conoscopic holography device. Results show that it can be useful for acquiring the patient{\textquoteright}s anatomy during surgery.}, issn = {1478-596X}, doi = {10.1002/rcs.1788}, author = {Brudfors, Mikael and Garc{\'\i}a-V{\'a}zquez, Ver{\'o}nica and Ses{\'e}-Lucio, Bego{\~n}a and Marinetto, Eugenio and Desco, Manuel and Pascau, Javier} } @article {1129, title = {Development of an Open Source Educational Resource: "Clinical Procedures for Safer Patient Care".}, journal = {Stud Health Technol Inform}, volume = {225}, year = {2016}, month = {2016}, pages = {979-80}, abstract = {

An Open Education Resource (OER) has been developed by two nurse educators to address inconsistencies in how clinical health care skills are taught and practiced in the clinical setting, and to ensure best practice and quality care based on the latest evidence. A checklist approach aims to provide clear steps and rationale for procedures, standardized processes for clinical skills and to assist nursing schools and clinical practice partners in teaching clinical skills, and keeping procedural practice current. The format is logical, organized and focused on patient safety, and will provide information retrieval opportunities at the point of care to support decisions and plan patient care. This poster discusses the development of this resource, the framework used, and the process from conception to distribution.

}, issn = {0926-9630}, author = {Doyle, Glynda and McCutcheon, Jodie} } @article {1130, title = {Development of an open technology sensor suite for assisted living: a student-led research project.}, journal = {Interface Focus}, volume = {6}, year = {2016}, month = {2016 Aug 6}, pages = {20160018}, abstract = {

Many countries have a rapidly ageing population, placing strain on health services and creating a growing market for assistive technology for older people. We have, through a student-led, 12-week project for 10 students from a variety of science and engineering backgrounds, developed an integrated sensor system to enable older people, or those at risk, to live independently in their own homes for longer, while providing reassurance for their family and carers. We provide details on the design procedure and performance of our sensor system and the management and execution of a short-term, student-led research project. Detailed information on the design and use of our devices, including a door sensor, power monitor, fall detector, general in-house sensor unit and easy-to-use location-aware communications device, is given, with our open designs being contrasted with closed proprietary systems. A case study is presented for the use of our devices in a real-world context, along with a comparison with commercially available systems. We discuss how the system could lead to improvements in the quality of life of older users and increase the effectiveness of their associated care network. We reflect on how recent developments in open source technology and rapid prototyping increase the scope and potential for the development of powerful sensor systems and, finally, conclude with a student perspective on this team effort and highlight learning outcomes, arguing that open technologies will revolutionize the way in which technology will be deployed in academic research in the future.

}, issn = {2042-8898}, doi = {10.1098/rsfs.2016.0018}, author = {Manton, James D and Hughes, Josephine A E and Bonner, Oliver and Amjad, Omar A and Mair, Philip and Miele, Isabella and Wang, Tiesheng and Levdik, Vitaly and Hall, Richard D and Baekelandt, G{\'e}raldine and Vasconcellos, Fernando da Cruz and Hadeler, Oliver and Hutter, Tanya and Kaminski, Clemens F} } @article {1120, title = {Development of an open-source web-based intervention for Brazilian smokers - Viva sem Tabaco.}, journal = {BMC Med Inform Decis Mak}, volume = {16}, year = {2016}, month = {2016}, pages = {103}, abstract = {

BACKGROUND: Web-based interventions for smoking cessation available in Portuguese do not adhere to evidence-based treatment guidelines. Besides, all existing web-based interventions are built on proprietary platforms that developing countries often cannot afford. We aimed to describe the development of "Viva sem Tabaco", an open-source web-based intervention.

RESULTS: The development of the intervention included the selection of content from evidence-based guidelines for smoking cessation, the design of the first layout, conduction of 2 focus groups to identify potential features, refinement of the layout based on focus groups and correction of content based on feedback provided by specialists on smoking cessation. At the end, we released the source-code and intervention on the Internet and translated it into Spanish and English.

CONCLUSIONS: The intervention developed fills gaps in the information available in Portuguese and the lack of open-source interventions for smoking cessation. The open-source licensing format and its translation system may help researchers from different countries deploying evidence-based interventions for smoking cessation.

}, issn = {1472-6947}, doi = {10.1186/s12911-016-0339-7}, author = {Gomide, H P and Bernardino, H S and Richter, K and Martins, L F and Ronzani, T M} } @article {1169, title = {dot-app: a {Graphviz}-{Cytoscape} conversion plug-in}, journal = {F1000Research}, volume = {5}, year = {2016}, pages = {2543}, abstract = {dot-app is a Cytoscape 3 app that allows Cytoscape to import and export Graphviz (*.dot, *.gv) files, also known as DOT files due to the *.dot extension and their conformance to the DOT language syntax. The DOT format was originally created in the early 2000s to represent graph topologies, layouts and formatting. DOT-encoded files are produced and consumed by a number of open-source graph applications, including GraphViz, Gephi, neato, smyrna, and others. While DOT-based graph applications are popular, they emphasize general graph layout and styling over the topological and semantic analysis functions available in domain-focused applications such as Cytoscape. While domain-focused applications have easy access to large networks (10,000 to 100,000 nodes) and advanced analysis and formatting, they do not offer all of the styling options that DOT-based applications (particularly GraphViz) do. dot-app enables the interchange of networks between Cytoscape and DOT-based applications so that users can benefit from the features of both. dot-app was first deployed to the Cytoscape App Store in August 2015, has since registered more than 1,200 downloads, and has been highly rated by more than 20 users.}, keywords = {attribute conversion, Cytoscape, Data visualization, DOT, export, format conversion, GraphViz, import, Network}, doi = {10.12688/f1000research.9751.1}, author = {Fitts, Braxton and Zhang, Ziran and Maher, Massoud and Demchak, Barry} } @article {1127, title = {Evaluating Open-Source Full-Text Search Engines for Matching ICD-10 Codes.}, journal = {Stud Health Technol Inform}, volume = {226}, year = {2016}, month = {2016}, pages = {127-30}, abstract = {

This research presents the results of evaluating multiple free, open-source engines on matching ICD-10 diagnostic codes via full-text searches. The study investigates what it takes to get an accurate match when searching for a specific diagnostic code. For each code the evaluation starts by extracting the words that make up its text and continues with building full-text search queries from the combinations of these words. The queries are then run against all the ICD-10 codes until a match indicates the code in question as a match with the highest relative score. This method identifies the minimum number of words that must be provided in order for the search engines choose the desired entry. The engines analyzed include a popular Java-based full-text search engine, a lightweight engine written in JavaScript which can even execute on the user{\textquoteright}s browser, and two popular open-source relational database management systems.

}, issn = {0926-9630}, author = {Jurc{\u a}u, Daniel-Alexandru and Stoicu-Tivadar, Vasile} } @article {1150, title = {Free and open-source automated 3-D microscope.}, journal = {J Microsc}, year = {2016}, month = {2016 Aug 29}, abstract = {

Open-source technology not only has facilitated the expansion of the greater research community, but by lowering costs it has encouraged innovation and customizable design. The field of automated microscopy has continued to be a challenge in accessibility due the expense and inflexible, noninterchangeable stages. This paper presents a low-cost, open-source microscope 3-D stage. A RepRap 3-D printer was converted to an optical microscope equipped with a customized, 3-D printed holder for a USB microscope. Precision measurements were determined to have an average error of 10 μm at the maximum speed and 27 μm at the minimum recorded speed. Accuracy tests yielded an error of 0.15\%. The machine is a true 3-D stage and thus able to operate with USB microscopes or conventional desktop microscopes. It is larger than all commercial alternatives, and is thus capable of high-depth images over unprecedented areas and complex geometries. The repeatability is below 2-D microscope stages, but testing shows that it is adequate for the majority of scientific applications. The open-source microscope stage costs less than 3-9\% of the closest proprietary commercial stages. This extreme affordability vastly improves accessibility for 3-D microscopy throughout the world.

}, issn = {1365-2818}, doi = {10.1111/jmi.12433}, author = {Wijnen, Bas and Petersen, Emily E and Hunt, Emily J and Pearce, Joshua M} } @article {1136, title = {Full body musculoskeletal model for muscle-driven simulation of human gait.}, journal = {IEEE Trans Biomed Eng}, year = {2016}, month = {2016 Jul 7}, abstract = {

OBJECTIVE: Musculoskeletal models provide a noninvasive means to study human movement and predict the effects of interventions on gait. Our goal was to create an open-source, three-dimensional musculoskeletal model with high-fidelity representations of the lower limb musculature of healthy young individuals that can be used to generate accurate simulations of gait.

METHODS: Our model includes bony geometry for the full body, 37 degrees of freedom to define joint kinematics, Hill-type models of 80 muscle-tendon units actuating the lower limbs, and 17 ideal torque actuators driving the upper body. The model{\textquoteright}s musculotendon parameters are derived from previous anatomical measurements of 21 cadaver specimens and magnetic resonance images of 24 young healthy subjects. We tested the model by evaluating its computational time and accuracy of simulations of healthy walking and running.

RESULTS: Generating muscle-driven simulations of normal walking and running took approximately 10 minutes on a typical desktop computer. The differences between our muscle-generated and inverse dynamics joint moments were within 3\% (RMSE) of the peak inverse dynamics joint moments in both walking and running, and our simulated muscle activity showed qualitative agreement with salient features from experimental electromyography data.

CONCLUSION: These results suggest that our model is suitable for generating muscle-driven simulations of healthy gait. We encourage other researchers to further validate and apply the model to study other motions of the lower-extremity.

SIGNIFICANCE: The model is implemented in the open source software platform OpenSim. The model and data used to create and test the simulations are freely available at https://simtk.org/home/full_body/, allowing others to reproduce these results and create their own simulations.

}, issn = {1558-2531}, doi = {10.1109/TBME.2016.2586891}, author = {Rajagopal, Apoorva and Dembia, Christopher and DeMers, Matthew and Delp, Denny and Hicks, Jennifer and Delp, Scott} } @article {1106, title = {Health figures: an open source JavaScript library for health data visualization.}, journal = {BMC Med Inform Decis Mak}, volume = {16}, year = {2016}, month = {2016}, pages = {38}, abstract = {

BACKGROUND: The way we look at data has a great impact on how we can understand it, particularly when the data is related to health and wellness. Due to the increased use of self-tracking devices and the ongoing shift towards preventive medicine, better understanding of our health data is an important part of improving the general welfare of the citizens. Electronic Health Records, self-tracking devices and mobile applications provide a rich variety of data but it often becomes difficult to understand. We implemented the hFigures library inspired on the hGraph visualization with additional improvements. The purpose of the library is to provide a visual representation of the evolution of health measurements in a complete and useful manner.

RESULTS: We researched the usefulness and usability of the library by building an application for health data visualization in a health coaching program. We performed a user evaluation with Heuristic Evaluation, Controlled User Testing and Usability Questionnaires. In the Heuristics Evaluation the average response was 6.3 out of 7 points and the Cognitive Walkthrough done by usability experts indicated no design or mismatch errors. In the CSUQ usability test the system obtained an average score of 6.13 out of 7, and in the ASQ usability test the overall satisfaction score was 6.64 out of 7.

CONCLUSIONS: We developed hFigures, an open source library for visualizing a complete, accurate and normalized graphical representation of health data. The idea is based on the concept of the hGraph but it provides additional key features, including a comparison of multiple health measurements over time. We conducted a usability evaluation of the library as a key component of an application for health and wellness monitoring. The results indicate that the data visualization library was helpful in assisting users in understanding health data and its evolution over time.

}, keywords = {Data visualization, Health data, Health informatics, Javascript}, issn = {1472-6947}, doi = {10.1186/s12911-016-0275-6}, author = {Ledesma, Andres and Al-Musawi, Mohammed and Nieminen, Hannu} } @article {1137, title = {How open science helps researchers succeed.}, journal = {Elife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Open access, open data, open source and other open scholarship practices are growing in popularity and necessity. However, widespread adoption of these practices has not yet been achieved. One reason is that researchers are uncertain about how sharing their work will affect their careers. We review literature demonstrating that open research is associated with increases in citations, media attention, potential collaborators, job opportunities and funding opportunities. These findings are evidence that open research practices bring significant benefits to researchers relative to more traditional closed practices.

}, issn = {2050-084X}, doi = {10.7554/eLife.16800}, author = {McKiernan, Erin C and Bourne, Philip E and Brown, C Titus and Buck, Stuart and Kenall, Amye and Lin, Jennifer and McDougall, Damon and Nosek, Brian A and Ram, Karthik and Soderberg, Courtney K and Spies, Jeffrey R and Thaney, Kaitlin and Updegrove, Andrew and Woo, Kara H and Yarkoni, Tal} } @article {1146, title = {A HTML5 open source tool to conduct studies based on Libet{\textquoteright}s clock paradigm.}, journal = {Sci Rep}, volume = {6}, year = {2016}, month = {2016}, pages = {32689}, abstract = {

Libet{\textquoteright}s clock is a well-known procedure in experiments in psychology and neuroscience. Examples of its use include experiments exploring the subjective sense of agency, action-effect binding, and subjective timing of conscious decisions and perceptions. However, the technical details of the apparatus used to conduct these types of experiments are complex, and are rarely explained in sufficient detail as to guarantee an exact replication of the procedure. With this in mind, we developed Labclock Web, a web tool designed to conduct online and offline experiments using Libet{\textquoteright}s clock. After describing its technical features, we explain how to configure specific experiments using this tool. Its degree of accuracy and precision in the presentation of stimuli has been technically validated, including the use of two cognitive experiments conducted with voluntary participants who performed the experiment both in our laboratory and via the Internet. Labclock Web is distributed without charge under a free software license (GPLv3) since one of our main objectives is to facilitate the replication of experiments and hence the advancement of knowledge in this area.

}, issn = {2045-2322}, doi = {10.1038/srep32689}, author = {Garaizar, Pablo and Cubillas, Carmelo P and Matute, Helena} } @article {1135, title = {Improving documentation of clinical care within a clinical information network: an essential initial step in efforts to understand and improve care in Kenyan hospitals.}, journal = {BMJ Glob Health}, volume = {1}, year = {2016}, month = {2016 May 24}, pages = {e000028}, abstract = {

In many low income countries health information systems are poorly equipped to provide detailed information on hospital care and outcomes. Information is thus rarely used to support practice improvement. We describe efforts to tackle this challenge and to foster learning concerning collection and use of information. This could improve hospital services in Kenya. We are developing a Clinical Information Network, a collaboration spanning 14 hospitals, policy makers and researchers with the goal of improving information available on the quality of inpatient paediatric care across common childhood illnesses in Kenya. Standardised data from hospitals{\textquoteright} paediatric wards are collected using non-commercial and open source tools. We have implemented procedures for promoting data quality which are performed prior to a process of semi-automated analysis and routine report generation for hospitals in the network. In the first phase of the Clinical Information Network, we collected data on over 65 000 admission episodes. Despite clinicians{\textquoteright} initial unfamiliarity with routine performance reporting, we found that, as an initial focus, both engaging with each hospital and providing them information helped improve the quality of data and therefore reports. The process has involved mutual learning and building of trust in the data and should provide the basis for collaborative efforts to improve care, to understand patient outcome, and to evaluate interventions through shared learning. We have found that hospitals are willing to support the development of a clinically focused but geographically dispersed Clinical Information Network in a low-income setting. Such networks show considerable promise as platforms for collaborative efforts to improve care, to provide better information for decision making, and to enable locally relevant research.

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2016-000028}, author = {Tuti, Timothy and Bitok, Michael and Malla, Lucas and Paton, Chris and Muinga, Naomi and Gathara, David and Gachau, Susan and Mbevi, George and Nyachiro, Wycliffe and Ogero, Morris and Julius, Thomas and Irimu, Grace and English, Mike} } @article {1131, title = {Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.}, journal = {Med Image Anal}, year = {2016}, month = {2016 Jul 7}, abstract = {

The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision.

}, issn = {1361-8423}, doi = {10.1016/j.media.2016.06.035}, author = {Kapur, Tina and Pieper, Steve and Fedorov, Andriy and Fillion-Robin, J-C and Halle, Michael and O{\textquoteright}Donnell, Lauren and Lasso, Andras and Ungi, Tamas and Pinter, Csaba and Finet, Julien and Pujol, Sonia and Jagadeesan, Jayender and Tokuda, Junichi and Norton, Isaiah and Estepar, Raul San Jose and Gering, David and Aerts, Hugo J W L and Jakab, Marianna and Hata, Nobuhiko and Ibanez, Luiz and Blezek, Daniel and Miller, Jim and Aylward, Stephen and Grimson, W Eric L and Fichtinger, Gabor and Wells, William M and Lorensen, William E and Schroeder, Will and Kikinis, Ron} } @article {1133, title = {Integrating Heterogeneous Biomedical Data for Cancer Research: the CARPEM infrastructure.}, journal = {Appl Clin Inform}, volume = {7}, year = {2016}, month = {2016}, pages = {260-74}, abstract = {

Cancer research involves numerous disciplines. The multiplicity of data sources and their heterogeneous nature render the integration and the exploration of the data more and more complex. Translational research platforms are a promising way to assist scientists in these tasks. In this article, we identify a set of scientific and technical principles needed to build a translational research platform compatible with ethical requirements, data protection and data-integration problems. We describe the solution adopted by the CARPEM cancer research program to design and deploy a platform able to integrate retrospective, prospective, and day-to-day care data. We designed a three-layer architecture composed of a data collection layer, a data integration layer and a data access layer. We leverage a set of open-source resources including i2b2 and tranSMART.

}, issn = {1869-0327}, doi = {10.4338/ACI-2015-09-RA-0125}, author = {Rance, Bastien and Canuel, Vincent and Countouris, Hector and Laurent-Puig, Pierre and Burgun, Anita} } @article {1162, title = {Jenkins-{CI}, an {Open}-{Source} {Continuous} {Integration} {System}, as a {Scientific} {Data} and {Image}-{Processing} {Platform}}, journal = {Journal of Biomolecular Screening}, year = {2016}, abstract = {High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.}, keywords = {CellProfiler, continuous integration, high-content screening, high-performance computing}, issn = {1552-454X}, doi = {10.1177/1087057116679993}, author = {Moutsatsos, Ioannis K. and Hossain, Imtiaz and Agarinis, Claudia and Harbinski, Fred and Abraham, Yann and Dobler, Luc and Zhang, Xian and Wilson, Christopher J. and Jenkins, Jeremy L. and Holway, Nicholas and Tallarico, John and Parker, Christian N.} } @article {1151, title = {A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD).}, journal = {J Am Med Inform Assoc}, year = {2016}, month = {2016 Aug 18}, abstract = {

OBJECTIVE: The goal of this study was to develop a practical framework for recognizing and disambiguating clinical abbreviations, thereby improving current clinical natural language processing (NLP) systems{\textquoteright} capability to handle abbreviations in clinical narratives.

METHODS: We developed an open-source framework for clinical abbreviation recognition and disambiguation (CARD) that leverages our previously developed methods, including: (1) machine learning based approaches to recognize abbreviations from a clinical corpus, (2) clustering-based semiautomated methods to generate possible senses of abbreviations, and (3) profile-based word sense disambiguation methods for clinical abbreviations. We applied CARD to clinical corpora from Vanderbilt University Medical Center (VUMC) and generated 2 comprehensive sense inventories for abbreviations in discharge summaries and clinic visit notes. Furthermore, we developed a wrapper that integrates CARD with MetaMap, a widely used general clinical NLP system.Results and Conclusion CARD detected 27 317 and 107 303 distinct abbreviations from discharge summaries and clinic visit notes, respectively. Two sense inventories were constructed for the 1000 most frequent abbreviations in these 2 corpora. Using the sense inventories created from discharge summaries, CARD achieved an F1 score of 0.755 for identifying and disambiguating all abbreviations in a corpus from the VUMC discharge summaries, which is superior to MetaMap and Apache{\textquoteright}s clinical Text Analysis Knowledge Extraction System (cTAKES). Using additional external corpora, we also demonstrated that the MetaMap-CARD wrapper improved MetaMap{\textquoteright}s performance in recognizing disorder entities in clinical notes. The CARD framework, 2 sense inventories, and the wrapper for MetaMap are publicly available at https://sbmi.uth.edu/ccb/resources/abbreviation.htm We believe the CARD framework can be a valuable resource for improving abbreviation identification in clinical NLP systems.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocw109}, author = {Wu, Yonghui and Denny, Joshua C and Rosenbloom, S Trent and Miller, Randolph A and Giuse, Dario A and Wang, Lulu and Blanquicett, Carmelo and Soysal, Ergin and Xu, Jun and Xu, Hua} } @article {1128, title = {A Low Cost/Low Power Open Source Sensor System for Automated Tuberculosis Drug Susceptibility Testing.}, journal = {Sensors (Basel)}, volume = {16}, year = {2016}, month = {2016}, abstract = {

In this research an open source, low power sensor node was developed to check the growth of mycobacteria in a culture bottle with a nitrate reductase assay method for a drug susceptibility test. The sensor system reports the temperature and color sensor output frequency change of the culture bottle when the device is triggered. After the culture process is finished, a nitrite ion detecting solution based on a commercial nitrite ion detection kit is injected into the culture bottle by a syringe pump to check bacterial growth by the formation of a pigment by the reaction between the solution and the color sensor. Sensor status and NRA results are broadcasted via a Bluetooth low energy beacon. An Android application was developed to collect the broadcasted data, classify the status of cultured samples from multiple devices, and visualize the data for the end users, circumventing the need to examine each culture bottle manually during a long culture period. The authors expect that usage of the developed sensor will decrease the cost and required labor for handling large amounts of patient samples in local health centers in developing countries. All 3D-printerable hardware parts, a circuit diagram, and software are available online.

}, issn = {1424-8220}, doi = {10.3390/s16060942}, author = {Kim, Kyukwang and Kim, Hyeong Keun and Lim, Hwijoon and Myung, Hyun} } @article {1168, title = {Methods for {Specifying} {Scientific} {Data} {Standards} and {Modeling} {Relationships} with {Applications} to {Neuroscience}}, journal = {Frontiers in Neuroinformatics}, volume = {10}, year = {2016}, pages = {48}, abstract = {Neuroscience continues to experience a tremendous growth in data; in terms of the volume and variety of data, the velocity at which data is acquired, and in turn the veracity of data. These challenges are a serious impediment to sharing of data, analyses, and tools within and across labs. Here, we introduce BRAINformat, a novel data standardization framework for the design and management of scientific data formats. The BRAINformat library defines application-independent design concepts and modules that together create a general framework for standardization of scientific data. We describe the formal specification of scientific data standards, which facilitates sharing and verification of data and formats. We introduce the concept of Managed Objects, enabling semantic components of data formats to be specified as self-contained units, supporting modular and reusable design of data format components and file storage. We also introduce the novel concept of Relationship Attributes for modeling and use of semantic relationships between data objects. Based on these concepts we demonstrate the application of our framework to design and implement a standard format for electrophysiology data and show how data standardization and relationship-modeling facilitate data analysis and sharing. The format uses HDF5, enabling portable, scalable, and self-describing data storage and integration with modern high-performance computing for data-driven discovery. The BRAINformat library is open source, easy-to-use, and provides detailed user and developer documentation and is freely available at: https://bitbucket.org/oruebel/brainformat.}, keywords = {data format specification, electrophysiology, neuroscience, relationship modeling}, doi = {10.3389/fninf.2016.00048}, author = {R{\"u}bel, Oliver and Dougherty, Max and Prabhat, null and Denes, Peter and Conant, David and Chang, Edward F. and Bouchard, Kristofer} } @article {1111, title = {Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks.}, journal = {J Neurophysiol}, year = {2016}, month = {2016 Apr 20}, pages = {jn.00137.2016}, abstract = {

Neurophysiology requires an extensive workflow of information analysis routines, which often includes incompatible proprietary software, introducing limitations based on financial costs, transfer of data between platforms, and the ability to share. An ecosystem of free open-source software exists to fill these gaps, including 1000{\textquoteright}s of analysis and plotting packages written in Python and R, which can be implemented in a sharable and reproducible format, such as the Jupyter electronic notebook. This tool chain can largely replace current routines by importing data, producing analyses, and generating publication quality graphics. An electronic notebook, like Jupyter, allows these analyses, along with documentation of procedures, to display locally or remotely in an internet browser, which can be saved as an HTML, PDF, or other file format for sharing with team members and the scientific community. The current report illustrates these methods using data from electrophysiological recordings of the musk shrew vagus - a model system to investigate gut-brain communication, for example, cancer chemotherapy-induced emesis. We show methods for spike sorting (including statistical validation), spike train analysis, and analysis of compound action potentials in notebooks. Raw data and code are available from notebooks in Data Supplements or from an executable online version, which replicates all analyses without installing software - an implementation of reproducible research. This demonstrates the promise of combining disparate analyses into one platform, along with the ease of sharing this work. In an age of diverse, high-throughput computational workflows, this methodology can increase efficiency, transparency, and the collaborative potential of neurophysiological research.

}, issn = {1522-1598}, doi = {10.1152/jn.00137.2016}, author = {Rosenberg, David M and Horn, Charles C} } @article {1170, title = {Open {Source} {Drug} {Discovery}: {Highly} {Potent} {Antimalarial} {Compounds} {Derived} from the {Tres} {Cantos} {Arylpyrroles}}, journal = {ACS central science}, volume = {2}, year = {2016}, pages = {687{\textendash}701}, abstract = {The development of new antimalarial compounds remains a pivotal part of the strategy for malaria elimination. Recent large-scale phenotypic screens have provided a wealth of potential starting points for hit-to-lead campaigns. One such public set is explored, employing an open source research mechanism in which all data and ideas were shared in real time, anyone was able to participate, and patents were not sought. One chemical subseries was found to exhibit oral activity but contained a labile ester that could not be replaced without loss of activity, and the original hit exhibited remarkable sensitivity to minor structural change. A second subseries displayed high potency, including activity within gametocyte and liver stage assays, but at the cost of low solubility. As an open source research project, unexplored avenues are clearly identified and may be explored further by the community; new findings may be cumulatively added to the present work.}, issn = {2374-7943}, doi = {10.1021/acscentsci.6b00086}, author = {Williamson, Alice E. and Ylioja, Paul M. and Robertson, Murray N. and Antonova-Koch, Yevgeniya and Avery, Vicky and Baell, Jonathan B. and Batchu, Harikrishna and Batra, Sanjay and Burrows, Jeremy N. and Bhattacharyya, Soumya and Calderon, Felix and Charman, Susan A. and Clark, Julie and Crespo, Benigno and Dean, Matin and Debbert, Stefan L. and Delves, Michael and Dennis, Adelaide S. M. and Deroose, Frederik and Duffy, Sandra and Fletcher, Sabine and Giaever, Guri and Hallyburton, Irene and Gamo, Francisco-Javier and Gebbia, Marinella and Guy, R. Kiplin and Hungerford, Zoe and Kirk, Kiaran and Lafuente-Monasterio, Maria J. and Lee, Anna and Meister, Stephan and Nislow, Corey and Overington, John P. and Papadatos, George and Patiny, Luc and Pham, James and Ralph, Stuart A. and Ruecker, Andrea and Ryan, Eileen and Southan, Christopher and Srivastava, Kumkum and Swain, Chris and Tarnowski, Matthew J. and Thomson, Patrick and Turner, Peter and Wallace, Iain M. and Wells, Timothy N. C. and White, Karen and White, Laura and Willis, Paul and Winzeler, Elizabeth A. and Wittlin, Sergio and Todd, Matthew H.} } @article {1121, title = {Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.}, journal = {PLoS Pathog}, volume = {12}, year = {2016}, month = {2016 Jul}, pages = {e1005763}, abstract = {

A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34\%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal chemistry programs. The data for all of these assays are presented and analyzed to show how outstanding leads for many indications can be selected. These results reveal the immense potential for translating the dispersed expertise in biological assays involving human pathogens into drug discovery starting points, by providing open access to new families of molecules, and emphasize how a small additional investment made to help acquire and distribute compounds, and sharing the data, can catalyze drug discovery for dozens of different indications. Another lesson is that when multiple screens from different groups are run on the same library, results can be integrated quickly to select the most valuable starting points for subsequent medicinal chemistry efforts.

}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1005763}, author = {Van Voorhis, Wesley C and Adams, John H and Adelfio, Roberto and Ahyong, Vida and Akabas, Myles H and Alano, Pietro and Alday, Aintzane and Alem{\'a}n Resto, Yesmalie and Alsibaee, Aishah and Alzualde, Ainhoa and Andrews, Katherine T and Avery, Simon V and Avery, Vicky M and Ayong, Lawrence and Baker, Mark and Baker, Stephen and Ben Mamoun, Choukri and Bhatia, Sangeeta and Bickle, Quentin and Bounaadja, Lotfi and Bowling, Tana and Bosch, J{\"u}rgen and Boucher, Lauren E and Boyom, Fabrice F and Brea, Jose and Brennan, Marian and Burton, Audrey and Caffrey, Conor R and Camarda, Grazia and Carrasquilla, Manuela and Carter, Dee and Belen Cassera, Maria and Chih-Chien Cheng, Ken and Chindaudomsate, Worathad and Chubb, Anthony and Colon, Beatrice L and Col{\'o}n-L{\'o}pez, Daisy D and Corbett, Yolanda and Crowther, Gregory J and Cowan, Noemi and D{\textquoteright}Alessandro, Sarah and Le Dang, Na and Delves, Michael and DeRisi, Joseph L and Du, Alan Y and Duffy, Sandra and Abd El-Salam El-Sayed, Shimaa and Ferdig, Michael T and Fern{\'a}ndez Robledo, Jos{\'e} A and Fidock, David A and Florent, Isabelle and Fokou, Patrick V T and Galstian, Ani and Gamo, Francisco Javier and Gokool, Suzanne and Gold, Ben and Golub, Todd and Goldgof, Gregory M and Guha, Rajarshi and Guiguemde, W Armand and Gural, Nil and Guy, R Kiplin and Hansen, Michael A E and Hanson, Kirsten K and Hemphill, Andrew and Hooft van Huijsduijnen, Rob and Horii, Takaaki and Horrocks, Paul and Hughes, Tyler B and Huston, Christopher and Igarashi, Ikuo and Ingram-Sieber, Katrin and Itoe, Maurice A and Jadhav, Ajit and Naranuntarat Jensen, Amornrat and Jensen, Laran T and Jiang, Rays H Y and Kaiser, Annette and Keiser, Jennifer and Ketas, Thomas and Kicka, Sebastien and Kim, Sunyoung and Kirk, Kiaran and Kumar, Vidya P and Kyle, Dennis E and Lafuente, Maria Jose and Landfear, Scott and Lee, Nathan and Lee, Sukjun and Lehane, Adele M and Li, Fengwu and Little, David and Liu, Liqiong and Llin{\'a}s, Manuel and Loza, Maria I and Lubar, Aristea and Lucantoni, Leonardo and Lucet, Isabelle and Maes, Louis and Mancama, Dalu and Mansour, Nuha R and March, Sandra and McGowan, Sheena and Medina Vera, Iset and Meister, Stephan and Mercer, Luke and Mestres, Jordi and Mfopa, Alvine N and Misra, Raj N and Moon, Seunghyun and Moore, John P and Morais Rodrigues da Costa, Francielly and M{\"u}ller, Joachim and Muriana, Arantza and Nakazawa Hewitt, Stephen and Nare, Bakela and Nathan, Carl and Narraidoo, Nathalie and Nawaratna, Sujeevi and Ojo, Kayode K and Ortiz, Diana and Panic, Gordana and Papadatos, George and Parapini, Silvia and Patra, Kailash and Pham, Ngoc and Prats, Sarah and Plouffe, David M and Poulsen, Sally-Ann and Pradhan, Anupam and Quevedo, Celia and Quinn, Ronald J and Rice, Christopher A and Abdo Rizk, Mohamed and Ruecker, Andrea and St Onge, Robert and Salgado Ferreira, Rafaela and Samra, Jasmeet and Robinett, Natalie G and Schlecht, Ulrich and Schmitt, Marjorie and Silva Villela, Filipe and Silvestrini, Francesco and Sinden, Robert and Smith, Dennis A and Soldati, Thierry and Spitzm{\"u}ller, Andreas and Stamm, Serge Maximilian and Sullivan, David J and Sullivan, William and Suresh, Sundari and Suzuki, Brian M and Suzuki, Yo and Swamidass, S Joshua and Taramelli, Donatella and Tchokouaha, Lauve R Y and Theron, Anjo and Thomas, David and Tonissen, Kathryn F and Townson, Simon and Tripathi, Abhai K and Trofimov, Valentin and Udenze, Kenneth O and Ullah, Imran and Vallieres, Cindy and Vigil, Edgar and Vinetz, Joseph M and Voong Vinh, Phat and Vu, Hoan and Watanabe, Nao-Aki and Weatherby, Kate and White, Pamela M and Wilks, Andrew F and Winzeler, Elizabeth A and Wojcik, Edward and Wree, Melanie and Wu, Wesley and Yokoyama, Naoaki and Zollo, Paul H A and Abla, Nada and Blasco, Benjamin and Burrows, Jeremy and Laleu, Beno{\^\i}t and Leroy, Didier and Spangenberg, Thomas and Wells, Timothy and Willis, Paul A} } @article {1166, title = {Open {Source} {Paradigm}: {A} {Synopsis} of {The} {Cathedral} and the {Bazaar} for {Health} and {Social} {Care}}, journal = {Journal of Innovation in Health Informatics}, volume = {23}, year = {2016}, pages = {488{\textendash}492}, abstract = {BACKGROUND: Open source software (OSS) is becoming more fashionable in health and social care, although the ideas are not new. However progress has been slower than many had expected. OBJECTIVE: The purpose is to summarise the Free/Libre Open Source Software (FLOSS) paradigm in terms of what it is, how it impacts users and software engineers and how it can work as a business model in health and social care sectors. METHOD: Much of this paper is a synopsis of Eric Raymond{\textquoteright}s seminal book The Cathedral and the Bazaar, which was the first comprehensive description of the open source ecosystem, set out in three long essays. Direct quotes from the book are used liberally, without reference to specific passages. The first part contrasts open and closed source approaches to software development and support. The second part describes the culture and practices of the open source movement. The third part considers business models. CONCLUSION: A key benefit of open source is that users can access and collaborate on improving the software if they wish. Closed source code may be regarded as a strategic business risk that that may be unacceptable if there is an open source alternative. The sharing culture of the open source movement fits well with that of health and social care.}, keywords = {Delivery of Health Care., Medical Informatics, Open Access to Information, Software}, issn = {2058-4563}, author = {Benson, Tim} } @article {1149, title = {Open Source Platform for Collaborative Construction of Wearable Sensor Datasets for Human Motion Analysis and an Application for Gait Analysis.}, journal = {J Biomed Inform}, year = {2016}, month = {2016 Sep 1}, abstract = {

Nearly every practical improvement in modelling human motion is well founded in a properly designed collection of data or datasets. These datasets must be made publicly available for the community could validate and accept them. It is reasonable to concede that a collective, guided enterprise could serve to devise solid and substantial datasets, as a result of a collaborative effort, in the same sense as the open software community does. In this way datasets could be complemented, extended and expanded in size with, for example, more individuals, samples and human actions. For this to be possible some commitments must be made by the collaborators, being one of them sharing the same data acquisition platform. In this paper, we offer an affordable open source hardware and software platform based on inertial wearable sensors in a way that several groups could cooperate in the construction of datasets through common software suitable for collaboration. Some experimental results about the throughput of the overall system are reported showing the feasibility of acquiring data from up to 6 sensors with a sampling frequency no less than 118Hz. Also, a proof-of-concept dataset is provided comprising sampled data from 12 subjects suitable for gait analysis.

}, issn = {1532-0480}, doi = {10.1016/j.jbi.2016.08.025}, author = {Llamas, C{\'e}sar and Gonz{\'a}lez, Manuel A and Hern{\'a}ndez, C{\'a}rmen and Vegas, Jes{\'u}s} } @article {1138, title = {Open source posturography.}, journal = {Acta Otolaryngol}, year = {2016}, month = {2016 Jul 6}, pages = {1-5}, abstract = {

CONCLUSION: The proposed validation goal of 0.9 in intra-class correlation coefficient was reached with the results of this study. With the obtained results we consider that the developed software (RombergLab) is a validated balance assessment software. The reliability of this software is dependent of the used force platform technical specifications.

OBJECTIVE: Develop and validate a posturography software and share its source code in open source terms.

METHODS: Prospective non-randomized validation study: 20 consecutive adults underwent two balance assessment tests, six condition posturography was performed using a clinical approved software and force platform and the same conditions were measured using the new developed open source software using a low cost force platform. Intra-class correlation index of the sway area obtained from the center of pressure variations in both devices for the six conditions was the main variable used for validation.

RESULTS: Excellent concordance between RombergLab and clinical approved force platform was obtained (intra-class correlation coefficient =0.94). A Bland and Altman graphic concordance plot was also obtained. The source code used to develop RombergLab was published in open source terms.

}, issn = {1651-2251}, doi = {10.1080/00016489.2016.1204665}, author = {Rey-Martinez, Jorge and P{\'e}rez-Fern{\'a}ndez, Nicol{\'a}s} } @article {1147, title = {An open source solution for an in-house built dynamic platform for the validation of stereotactic ablative body radiotherapy for VMAT and IMRT.}, journal = {Australas Phys Eng Sci Med}, year = {2016}, month = {2016 Sep 15}, abstract = {

An in-house solution for the verification of dose delivered to a moving phantom as required for the clinical implementation of lung stereotactic ablative body radiation therapy was developed. The superior-inferior movement required to simulate tumour motion during a normal breathing cycle was achieved via the novel use of an Arduino Uno{\texttrademark}, a low-cost open-source microcontroller board connected to a high torque servo motor. Slow CT imaging was used to acquire the image set and a 4D cone beam CT (4D-CBCT) verified the efficacy of contoured margins before treatment on the moving phantom. Treatment fields were delivered to a section of a CIRS{\texttrademark} anthropomorphic phantom. Dose verification to the dynamic phantom with Gafchromic EBT3 film using 3~\%-1~mm gamma analysis acceptance criteria registered an absolute dose pass rate for IMRT and VMAT of 98 and 96.6~\%, respectively. It was verified that 100~\% of the PTV received the prescribed dose of 12~Gy per fraction using the dynamic phantom, and no major discrepancy between planned and measured results due to interplay between multileaf collimator sequences and target motion was observed. This study confirmed that the use of an in-house solution using open source hardware and software with existing quality assurance equipment was appropriate in validating a new treatment technique.

}, issn = {1879-5447}, doi = {10.1007/s13246-016-0484-4}, author = {Munoz, Luis and Ziebell, Amy and Morton, Jason and Bhat, Madhava} } @article {1110, title = {Open-source hardware for medical devices.}, journal = {BMJ Innov}, volume = {2}, year = {2016}, month = {2016 Apr}, pages = {78-83}, abstract = {

Open-source hardware is hardware whose design is made publicly available so anyone can study, modify, distribute, make and sell the design or the hardware based on that design. Some open-source hardware projects can potentially be used as active medical devices. The open-source approach offers a unique combination of advantages, including reducing costs and faster innovation. This article compares 10 of open-source healthcare projects in terms of how easy it is to obtain the required components and build the device.

}, issn = {2055-642X}, doi = {10.1136/bmjinnov-2015-000080}, author = {Niezen, Gerrit and Eslambolchilar, Parisa and Thimbleby, Harold} } @article {1124, title = {Open-source LIMS in Vietnam: The path toward sustainability and host country ownership.}, journal = {Int J Med Inform}, volume = {93}, year = {2016}, month = {2016 Sep}, pages = {92-102}, abstract = {

OBJECTIVE: The objectives of this case report are as follows: to describe the process of establishing a national laboratory information management system (LIMS) program for clinical and public health laboratories in Vietnam; to evaluate the outcomes and lessons learned; and to present a model for sustainability based on the program outcomes that could be applied to diverse laboratory programs.

METHODS: This case report comprises a review of program documentation and records, including planning and budgetary records of the donor, monthly reports from the implementer, direct observation, and ad-hoc field reports from technical advisors and governmental agencies. Additional data on program efficacy and user acceptance were collected from routine monitoring of laboratory policies and operational practices.

RESULTS: LIMS software was implemented at 38 hospital, public health and HIV testing laboratories in Vietnam. This LIMS was accepted by users and program managers as a useful tool to support laboratory processes. Implementation cost per laboratory and average duration of deployment decreased over time, and project stakeholders initiated transition of financing (from the donor to local institutions) and of system maintenance functions (from the implementer to governmental and site-level staff). Collaboration between the implementer in Vietnam and the global LIMS user community was strongly established, and knowledge was successfully transferred to staff within Vietnam.

CONCLUSION: Implementing open-sourced LIMS with local development and support was a feasible approach towards establishing a sustainable laboratory informatics program that met the needs of health laboratories in Vietnam. Further effort to institutionalize IT support capacity within key government agencies is ongoing.

}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.06.010}, author = {Landgraf, Kenneth M and Kakkar, Reshma and Meigs, Michelle and Jankauskas, Paul T and Phan, Thi Thu Huong and Nguyen, Viet Nga and Nguyen, Duy Thai and Duong, Thanh Tung and Nguyen, Thi Hoa and Bond, Kyle B} } @article {1109, title = {Open-source platforms for navigated image-guided interventions.}, journal = {Med Image Anal}, year = {2016}, month = {2016 Jun 15}, abstract = {

Navigation technology is changing the clinical standards in medical interventions by making existing procedures more accurate, and new procedures possible. Navigation is based on preoperative or intraoperative imaging combined with 3-dimensional position tracking of interventional tools registered to the images. Research of navigation technology in medical interventions requires significant engineering efforts. The difficulty of developing such complex systems has been limiting the clinical translation of new methods and ideas. A key to the future success of this field is to provide researchers with platforms that allow rapid implementation of applications with minimal resources spent on reimplementing existing system features. A number of platforms have been already developed that can share data in real time through standard interfaces. Complete navigation systems can be built using these platforms using a layered software architecture. In this paper, we review the most popular platforms, and show an effective way to take advantage of them through an example surgical navigation application.

}, issn = {1361-8423}, doi = {10.1016/j.media.2016.06.011}, author = {Ungi, Tamas and Lasso, Andras and Fichtinger, Gabor} } @article {1148, title = {Open-source, small-animal magnetic resonance-guided focused ultrasound system.}, journal = {J Ther Ultrasound}, volume = {4}, year = {2016}, month = {2016}, pages = {22}, abstract = {

BACKGROUND: MR-guided focused ultrasound or high-intensity focused ultrasound (MRgFUS/MRgHIFU) is a non-invasive therapeutic modality with many potential applications in areas such as cancer therapy, drug delivery, and blood-brain barrier opening. However, the large financial costs involved in developing preclinical MRgFUS systems represent a barrier to research groups interested in developing new techniques and applications. We aim to mitigate these challenges by detailing a validated, open-source preclinical MRgFUS system capable of delivering thermal and mechanical FUS in a quantifiable and repeatable manner under real-time MRI guidance.

METHODS: A hardware and software package was developed that includes closed-loop feedback controlled thermometry code and CAD drawings for a therapy table designed for a preclinical MRI scanner. For thermal treatments, the modular software uses a proportional integral derivative controller to maintain a precise focal temperature rise in the target given input from MR phase images obtained concurrently. The software computes the required voltage output and transmits it to a FUS transducer that is embedded in the delivery table within the magnet bore. The delivery table holds the FUS transducer, a small animal and its monitoring equipment, and a transmit/receive RF coil. The transducer is coupled to the animal via a water bath and is translatable in two dimensions from outside the magnet. The transducer is driven by a waveform generator and amplifier controlled by real-time software in Matlab. MR acoustic radiation force imaging is also implemented to confirm the position of the focus for mechanical and thermal treatments.

RESULTS: The system was validated in tissue-mimicking phantoms and in vivo during murine tumor hyperthermia treatments. Sonications were successfully controlled over a range of temperatures and thermal doses for up to 20 min with minimal temperature overshoot. MR thermometry was validated with an optical temperature probe, and focus visualization was achieved with acoustic radiation force imaging.

CONCLUSIONS: We developed an MRgFUS platform for small-animal treatments that robustly delivers accurate, precise, and controllable sonications over extended time periods. This system is an open source and could increase the availability of low-cost small-animal systems to interdisciplinary researchers seeking to develop new MRgFUS applications and technology.

}, issn = {2050-5736}, doi = {10.1186/s40349-016-0066-7}, author = {Poorman, Megan E and Chaplin, Vandiver L and Wilkens, Ken and Dockery, Mary D and Giorgio, Todd D and Grissom, William A and Caskey, Charles F} } @article {1113, title = {Open-sourced coding expands UMN{\textquoteright}s StudyFinder to additional CTSA institutions}, year = {2016}, publisher = { AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE}, address = {Washington}, abstract = {Research tool connects patients, healthy participants to translational research.}, url = {http://www.eurekalert.org/pub_releases/2016-04/uoma-oce042616.php}, author = {Erin McHenry} } @article {1122, title = {PACS for Bhutan: a cost effective open source architecture for emerging countries.}, journal = {Insights Imaging}, year = {2016}, month = {2016 Jul 28}, abstract = {

This paper reports the design and implementation of an innovative and cost-effective imaging management infrastructure suitable for radiology centres in emerging countries. It was implemented in the main referring hospital of Bhutan equipped with a CT, an MRI, digital radiology, and a suite of several ultrasound units. They lacked the necessary informatics infrastructure for image archiving and interpretation and needed a system for distribution of images to clinical wards. The solution developed for this project combines several open source software platforms in a robust and versatile archiving and communication system connected to analysis workstations equipped with a FDA-certified version of the highly popular Open-Source software. The whole system was implemented on standard off-the-shelf hardware. The system was installed in three~days, and training of the radiologists as well as the technical and IT staff was provided onsite to ensure full ownership of the system by the local team. Radiologists were rapidly capable of reading and interpreting studies on the diagnostic workstations, which had a significant benefit on their workflow and ability to perform diagnostic tasks more efficiently. Furthermore, images were also made available to several clinical units on standard desktop computers through a web-based viewer.

MESSAGES/TEACHING POINTS: {\textbullet} Open source imaging informatics platforms can provide cost-effective alternatives for PACS {\textbullet} Robust and cost-effective open architecture can provide adequate solutions for emerging countries {\textbullet} Imaging informatics is often lacking in hospitals equipped with digital modalities.

}, issn = {1869-4101}, doi = {10.1007/s13244-016-0512-7}, author = {Ratib, Osman and Roduit, Nicolas and Nidup, Dechen and De Geer, Gerard and Rosset, Antoine and Geissbuhler, Antoine} } @article {1153, title = {Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions.}, journal = {Microsc Microanal}, volume = {22}, year = {2016}, month = {2016 Jul}, pages = {2064-2065}, abstract = {

A challenge in any imaging laboratory, especially one that uses modern techniques, is to achieve a sustainable and productive balance between using open source and commercial software to perform quantitative image acquisition, analysis and visualization. In addition to considering the expense of software licensing, one must consider factors such as the quality and usefulness of the software{\textquoteright}s support, training and documentation. Also, one must consider the reproducibility with which multiple people generate results using the same software to perform the same analysis, how one may distribute their methods to the community using the software and the potential for achieving automation to improve productivity.

}, issn = {1435-8115}, author = {Shenoy, Shailesh M} } @article {1164, title = {Process control charts in infection prevention: {Make} it simple to make it happen}, journal = {American Journal of Infection Control}, year = {2016}, abstract = {BACKGROUND: Quality improvement is central to Infection Prevention and Control (IPC) programs. Challenges may occur when applying quality improvement methodologies like process control charts, often due to the limited exposure of typical IPs. Because of this, our team created an open-source database with a process control chart generator for IPC programs. The objectives of this report are to outline the development of the application and demonstrate application using simulated data. METHODS: We used Research Electronic Data Capture (REDCap Consortium, Vanderbilt University, Nashville, TN), R (R Foundation for Statistical Computing, Vienna, Austria), and R Studio Shiny (R Foundation for Statistical Computing) to create an open source data collection system with automated process control chart generation. We used simulated data to test and visualize both in-control and out-of-control processes for commonly used metrics in IPC programs. RESULTS: The R code for implementing the control charts and Shiny application can be found on our Web site (https://github.com/ul-research-support/spcapp). Screen captures of the workflow and simulated data indicating both common cause and special cause variation are provided. CONCLUSIONS: Process control charts can be easily developed based on individual facility needs using freely available software. Through providing our work free to all interested parties, we hope that others will be able to harness the power and ease of use of the application for improving the quality of care and patient safety in their facilities.}, keywords = {Health care-associated infection, Quality Improvement, Surveillance}, issn = {1527-3296}, doi = {10.1016/j.ajic.2016.09.021}, author = {Wiemken, Timothy L. and Furmanek, Stephen P. and Carrico, Ruth M. and Mattingly, William A. and Persaud, Annuradha K. and Guinn, Brian E. and Kelley, Robert R. and Ramirez, Julio A.} } @article {1163, title = {{RABIX}: {AN} {OPEN}-{SOURCE} {WORKFLOW} {EXECUTOR} {SUPPORTING} {RECOMPUTABILITY} {AND} {INTEROPERABILITY} {OF} {WORKFLOW} {DESCRIPTIONS}}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {22}, year = {2016}, pages = {154{\textendash}165}, abstract = {As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optim1izations to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor, an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions.}, issn = {2335-6936}, author = {Kaushik, Gaurav and Ivkovic, Sinisa and Simonovic, Janko and Tijanic, Nebojsa and Davis-Dusenbery, Brandi and Kural, Deniz} } @article {1152, title = {Real-World Use of Open Source Artificial Pancreas Systems.}, journal = {J Diabetes Sci Technol}, year = {2016}, month = {2016 Aug 10}, issn = {1932-2968}, doi = {10.1177/1932296816665635}, author = {Lewis, Dana and Leibrand, Scott} } @article {1161, title = {Reliability of infarct volumetry: {Its} relevance and the improvement by a software-assisted approach}, journal = {Journal of Cerebral Blood Flow and Metabolism: Official Journal of the International Society of Cerebral Blood Flow and Metabolism}, year = {2016}, abstract = {Despite the efficacy of neuroprotective approaches in animal models of stroke, their translation has so far failed from bench to bedside. One reason is presumed to be a low quality of preclinical study design, leading to bias and a low a priori power. In this study, we propose that the key read-out of experimental stroke studies, the volume of the ischemic damage as commonly measured by free-handed planimetry of TTC-stained brain sections, is subject to an unrecognized low inter-rater and test-retest reliability with strong implications for statistical power and bias. As an alternative approach, we suggest a simple, open-source, software-assisted method, taking advantage of automatic-thresholding techniques. The validity and the improvement of reliability by an automated method to tMCAO infarct volumetry are demonstrated. In addition, we show the probable consequences of increased reliability for precision, p-values, effect inflation, and power calculation, exemplified by a systematic analysis of experimental stroke studies published in the year 2015. Our study reveals an underappreciated quality problem in translational stroke research and suggests that software-assisted infarct volumetry might help to improve reproducibility and therefore the robustness of bench to bedside translation.}, keywords = {experimental stroke, Image analysis, middle cerebral artery occlusion, Neuroprotection, power}, issn = {1559-7016}, doi = {10.1177/0271678X16681311}, author = {Friedl{\"a}nder, Felix and Bohmann, Ferdinand and Brunkhorst, Max and Chae, Ju-Hee and Devraj, Kavi and K{\"o}hler, Yvette and Kraft, Peter and Kuhn, Hannah and Lucaciu, Alexandra and Luger, Sebastian and Pfeilschifter, Waltraud and Sadler, Rebecca and Liesz, Arthur and Scholtyschik, Karolina and Stolz, Leonie and Vutukuri, Rajkumar and Brunkhorst, Robert} } @article {1158, title = {{SCIFIO}: an extensible framework to support scientific image formats}, journal = {BMC bioinformatics}, volume = {17}, year = {2016}, pages = {521}, abstract = {BACKGROUND: No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation. RESULTS: SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats{\textquoteright} OME-TIFF, within a unified environment. CONCLUSIONS: SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.}, keywords = {Bio-Formats, Image analysis, ImageJ, open-source, SCIFIO}, issn = {1471-2105}, doi = {10.1186/s12859-016-1383-0}, author = {Hiner, Mark C. and Rueden, Curtis T. and Eliceiri, Kevin W.} } @article {1156, title = {{SimVascular}: {An} {Open} {Source} {Pipeline} for {Cardiovascular} {Simulation}}, journal = {Annals of Biomedical Engineering}, year = {2016}, abstract = {Patient-specific cardiovascular simulation has become a paradigm in cardiovascular research and is emerging as a powerful tool in basic, translational and clinical research. In this paper we discuss the recent development of a fully open-source SimVascular software package, which provides a complete pipeline from medical image data segmentation to patient-specific blood flow simulation and analysis. This package serves as a research tool for cardiovascular modeling and simulation, and has contributed to numerous advances in personalized medicine, surgical planning and medical device design. The SimVascular software has recently been refactored and expanded to enhance functionality, usability, efficiency and accuracy of image-based patient-specific modeling tools. Moreover, SimVascular previously required several licensed components that hindered new user adoption and code management and our recent developments have replaced these commercial components to create a fully open source pipeline. These developments foster advances in cardiovascular modeling research, increased collaboration, standardization of methods, and a growing developer community.}, keywords = {Hemodynamics, Image-based CFD, open-source, Patient-specific modeling}, issn = {1573-9686}, doi = {10.1007/s10439-016-1762-8}, author = {Updegrove, Adam and Wilson, Nathan M. and Merkow, Jameson and Lan, Hongzhi and Marsden, Alison L. and Shadden, Shawn C.} } @article {1159, title = {{SIproc}: an open-source biomedical data processing platform for large hyperspectral images}, journal = {The Analyst}, year = {2016}, abstract = {There has recently been significant interest within the vibrational spectroscopy community to apply quantitative spectroscopic imaging techniques to histology and clinical diagnosis. However, many of the proposed methods require collecting spectroscopic images that have a similar region size and resolution to the corresponding histological images. Since spectroscopic images contain significantly more spectral samples than traditional histology, the resulting data sets can approach hundreds of gigabytes to terabytes in size. This makes them difficult to store and process, and the tools available to researchers for handling large spectroscopic data sets are limited. Fundamental mathematical tools, such as MATLAB, Octave, and SciPy, are extremely powerful but require that the data be stored in fast memory. This memory limitation becomes impractical for even modestly sized histological images, which can be hundreds of gigabytes in size. In this paper, we propose an open-source toolkit designed to perform out-of-core processing of hyperspectral images. By taking advantage of graphical processing unit (GPU) computing combined with adaptive data streaming, our software alleviates common workstation memory limitations while achieving better performance than existing applications.}, issn = {1364-5528}, doi = {10.1039/c6an02082h}, author = {Berisha, Sebastian and Chang, Shengyuan and Saki, Sam and Daeinejad, Davar and He, Ziqi and Mankar, Rupali and Mayerich, David} } @article {1165, title = {A systematic literature review of open source software quality assessment models}, journal = {SpringerPlus}, volume = {5}, year = {2016}, pages = {1936}, abstract = {BACKGROUND: Many open source software (OSS) quality assessment models are proposed and available in the literature. However, there is little or no adoption of these models in practice. In order to guide the formulation of newer models so they can be acceptable by practitioners, there is need for clear discrimination of the existing models based on their specific properties. Based on this, the aim of this study is to perform a systematic literature review to investigate the properties of the existing OSS quality assessment models by classifying them with respect to their quality characteristics, the methodology they use for assessment, and their domain of application so as to guide the formulation and development of newer models. Searches in IEEE Xplore, ACM, Science Direct, Springer and Google Search is performed so as to retrieve all relevant primary studies in this regard. Journal and conference papers between the year 2003 and 2015 were considered since the first known OSS quality model emerged in 2003. RESULTS: A total of 19 OSS quality assessment model papers were selected. To select these models we have developed assessment criteria to evaluate the quality of the existing studies. Quality assessment models are classified into five categories based on the quality characteristics they possess namely: single-attribute, rounded category, community-only attribute, non-community attribute as well as the non-quality in use models. Our study reflects that software selection based on hierarchical structures is found to be the most popular selection method in the existing OSS quality assessment models. Furthermore, we found that majority (47\%) of the existing models do not specify any domain of application. CONCLUSIONS: In conclusion, our study will be a valuable contribution to the community and helps the quality assessment model developers in formulating newer models and also to the practitioners (software evaluators) in selecting suitable OSS in the midst of alternatives.}, keywords = {Analysis, Community, ISO 25010, open source software, Quality assessment models}, doi = {10.1186/s40064-016-3612-4}, author = {Adewumi, Adewole and Misra, Sanjay and Omoregbe, Nicholas and Crawford, Broderick and Soto, Ricardo} } @article {1112, title = {TACIT: An open-source text analysis, crawling, and interpretation tool.}, journal = {Behav Res Methods}, year = {2016}, month = {2016 Mar 4}, abstract = {

As human activity and interaction increasingly take place online, the digital residues of these activities provide a valuable window into a range of psychological and social processes. A great deal of progress has been made toward utilizing these opportunities; however, the complexity of managing and analyzing the quantities of data currently available has limited both the types of analysis used and the number of researchers able to make use of these data. Although fields such as computer science have developed a range of techniques and methods for handling these difficulties, making use of those tools has often required specialized knowledge and programming experience. The Text Analysis, Crawling, and Interpretation Tool (TACIT) is designed to bridge this gap by providing an intuitive tool and interface for making use of state-of-the-art methods in text analysis and large-scale data management. Furthermore, TACIT is implemented as an open, extensible, plugin-driven architecture, which will allow other researchers to extend and expand these capabilities as new methods become available.

}, issn = {1554-3528}, doi = {10.3758/s13428-016-0722-4}, author = {Dehghani, Morteza and Johnson, Kate M and Garten, Justin and Boghrati, Reihane and Hoover, Joe and Balasubramanian, Vijayan and Singh, Anurag and Shankar, Yuvarani and Pulickal, Linda and Rajkumar, Aswin and Parmar, Niki Jitendra} } @article {1126, title = {TREMOR12: An Open-Source Mobile App for Tremor Quantification.}, journal = {Stereotact Funct Neurosurg}, volume = {94}, year = {2016}, month = {2016}, pages = {182-186}, abstract = {

BACKGROUND: Evaluating the effect of treatment of tremor is mostly performed with clinical rating scales. Mobile applications facilitate a more rapid, objective, and quantitative evaluation of treatment effect. Existing mobile apps do not offer raw data access, which limits algorithm development.

OBJECTIVE: To develop a novel open-source mobile app for tremor quantification.

METHODS: TREMOR12 is an open-source mobile app that samples acceleration, rotation, rotation speed, and gravity, each in 3 axes and time-stamped in a frequency up to 100 Hz. The raw measurement data can be exported as a comma-separated value file for further analysis in the TREMOR12P data processing module. The app was evaluated with 3 patients suffering from essential tremor, who were between 55 and 71 years of age.

RESULTS: This proof-of-concept study shows that the TREMOR12 app is able to detect and register tremor characteristics such as acceleration, rotation, rotation speed, and gravity in a simple and nonburdensome way. The app is compatible with current regulatory oversight by the European Union (MEDDEV regulations) and the Food and Drug Administration (FDA) guidance on mobile medical applications.

CONCLUSION: TREMOR12 offers low-cost tremor quantification for research purposes and algorithm development, and may help to improve treatment evaluation.

}, issn = {1423-0372}, doi = {10.1159/000446610}, author = {Kubben, Pieter L and Kuijf, Mark L and Ackermans, Linda P C M and Leentjes, Albert F G} } @article {1125, title = {TREMOR12: An Open-Source Mobile App for Tremor Quantification.}, journal = {Stereotact Funct Neurosurg}, volume = {94}, year = {2016}, month = {2016}, pages = {182-186}, abstract = {

BACKGROUND: Evaluating the effect of treatment of tremor is mostly performed with clinical rating scales. Mobile applications facilitate a more rapid, objective, and quantitative evaluation of treatment effect. Existing mobile apps do not offer raw data access, which limits algorithm development.

OBJECTIVE: To develop a novel open-source mobile app for tremor quantification.

METHODS: TREMOR12 is an open-source mobile app that samples acceleration, rotation, rotation speed, and gravity, each in 3 axes and time-stamped in a frequency up to 100 Hz. The raw measurement data can be exported as a comma-separated value file for further analysis in the TREMOR12P data processing module. The app was evaluated with 3 patients suffering from essential tremor, who were between 55 and 71 years of age.

RESULTS: This proof-of-concept study shows that the TREMOR12 app is able to detect and register tremor characteristics such as acceleration, rotation, rotation speed, and gravity in a simple and nonburdensome way. The app is compatible with current regulatory oversight by the European Union (MEDDEV regulations) and the Food and Drug Administration (FDA) guidance on mobile medical applications.

CONCLUSION: TREMOR12 offers low-cost tremor quantification for research purposes and algorithm development, and may help to improve treatment evaluation.

}, issn = {1423-0372}, doi = {10.1159/000446610}, author = {Kubben, Pieter L and Kuijf, Mark L and Ackermans, Linda P C M and Leentjes, Albert F G and Temel, Yasin} } @article {1139, title = {VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy.}, journal = {Sci Rep}, volume = {6}, year = {2016}, month = {2016}, pages = {29132}, abstract = {

The nanoscale molecular assembly of mammalian viruses during their infectious life cycle remains poorly understood. Their small dimensions, generally bellow the 300nm diffraction limit of light microscopes, has limited most imaging studies to electron microscopy. The recent development of super-resolution (SR) light microscopy now allows the visualisation of viral structures at resolutions of tens of nanometers. In addition, these techniques provide the added benefit of molecular specific labelling and the capacity to investigate viral structural dynamics using live-cell microscopy. However, there is a lack of robust analytical tools that allow for precise mapping of viral structure within the setting of infection. Here we present an open-source analytical framework that combines super-resolution imaging and na{\"\i}ve single-particle analysis to generate unbiased molecular models. This tool, VirusMapper, is a high-throughput, user-friendly, ImageJ-based software package allowing for automatic statistical mapping of conserved multi-molecular structures, such as viral substructures or intact viruses. We demonstrate the usability of VirusMapper by applying it to SIM and STED images of vaccinia virus in isolation and when engaged with host cells. VirusMapper allows for the generation of accurate, high-content, molecular specific virion models and detection of nanoscale changes in viral architecture.

}, issn = {2045-2322}, doi = {10.1038/srep29132}, author = {Gray, Robert D M and Beerli, Corina and Pereira, Pedro Matos and Scherer, Kathrin Maria and Samolej, Jerzy and Bleck, Christopher Karl Ernst and Mercer, Jason and Henriques, Ricardo} } @article {1132, title = {Web-based GIS for spatial pattern detection: application to malaria incidence in Vietnam.}, journal = {Springerplus}, volume = {5}, year = {2016}, month = {2016}, pages = {1014}, abstract = {

INTRODUCTION: There is a great concern on how to build up an interoperable health information system of public health and health information technology within the development of public information and health surveillance programme. Technically, some major issues remain regarding to health data visualization, spatial processing of health data, health information dissemination, data sharing and the access of local communities to health information. In combination with GIS, we propose a technical framework for web-based health data visualization and spatial analysis.

METHODS: Data was collected from open map-servers and geocoded by open data kit package and data geocoding tools. The Web-based system is designed based on Open-source frameworks and libraries. The system provides Web-based analyst tool for pattern detection through three spatial tests: Nearest neighbour, K function, and Spatial Autocorrelation.

RESULTS: The result is a web-based GIS, through which end users can detect disease patterns via selecting area, spatial test parameters and contribute to managers and decision makers. The end users can be health practitioners, educators, local communities, health sector authorities and decision makers. This web-based system allows for the improvement of health related services to public sector users as well as citizens in a secure manner.

CONCLUSIONS: The combination of spatial statistics and web-based GIS can be a solution that helps empower health practitioners in direct and specific intersectional actions, thus provide for better analysis, control and decision-making.

}, issn = {2193-1801}, doi = {10.1186/s40064-016-2518-5}, author = {Bui, Thanh Quang and Pham, Hai Minh} } @article {1032, title = {Anterior loop of the inferior alveolar nerve: Averages and prevalence based on CT scans.}, journal = {J Prosthet Dent}, year = {2015}, month = {2015 Oct 9}, abstract = {

STATEMENT OF PROBLEM: The treatment of edentulous patients by using a complete implant-supported fixed prosthetic with distal extension has been widely studied; success is mainly dependent upon the placement of the distal implants. The location of the inferior alveolar nerve determines implant placement, but the length, prevalence, and symmetry between the left and right side of the anterior loop of the alveolar nerve are unknown.

PURPOSE: The purpose of this clinical study was to measure the anterior loop of the inferior alveolar nerve, which determines the placement of distal implants, in a group of 55 Mexican participants. The study expected to ascertain the average length, prevalence, and symmetry between left and right side and any sex differences. To differentiate the inferior alveolar nerve path, a new technique was applied using Hounsfield unit (HU) thresholds. The null hypothesis was that no significant differences would be found between the left and right sides or between men and women for the anterior loop of the inferior alveolar nerve.

MATERIAL AND METHODS: Fifty-five computed tomography (CT) scans were made (Somatom Sensation 16; Siemens Healthcare) and were visualized with InVesalius software. Anterior loop measurements were made on 3-dimensional surfaces. To determine statistical differences between the left and right side and between the sexes, the t test was used. The interclass correlation coefficient test was also applied to verify the reliability of the measurements.

RESULTS: Ninety percent of participants showed the anterior loop of the inferior alveolar nerve. The length of the anterior loop ranged between 0 and 6.68 mm, with a mean of 2.19 mm. No significant differences were found between the left and right sides or between men and women.

CONCLUSIONS: The mean length for the anterior loop in the sample was 2.19 mm. As the anterior loop length shows a high degree of variability, these findings suggest that a CT scan for each patient is recommended in order to visualize a safety zone before placing implants close to the mental foramen.

}, issn = {1097-6841}, doi = {10.1016/j.prosdent.2015.06.025}, author = {Juan, Del Valle Lovato and Grageda, Edgar and Crespo, Salvador G{\'o}mez} } @article {1062, title = {Archetype relational mapping - a practical openEHR persistence solution.}, journal = {BMC Med Inform Decis Mak}, volume = {15}, year = {2015}, month = {2015}, pages = {88}, abstract = {

BACKGROUND: One of the primary obstacles to the widespread adoption of openEHR methodology is the lack of practical persistence solutions for future-proof electronic health record (EHR) systems as described by the openEHR specifications. This paper presents an archetype relational mapping (ARM) persistence solution for the archetype-based EHR systems to support healthcare delivery in the clinical environment.

METHODS: First, the data requirements of the EHR systems are analysed and organized into archetype-friendly concepts. The Clinical Knowledge Manager (CKM) is queried for matching archetypes; when necessary, new archetypes are developed to reflect concepts that are not encompassed by existing archetypes. Next, a template is designed for each archetype to apply constraints related to the local EHR context. Finally, a set of rules is designed to map the archetypes to data tables and provide data persistence based on the relational database.

RESULTS: A comparison study was conducted to investigate the differences among the conventional database of an EHR system from a tertiary Class A hospital in China, the generated ARM database, and the Node + Path database. Five data-retrieving tests were designed based on clinical workflow to retrieve exams and laboratory tests. Additionally, two patient-searching tests were designed to identify patients who satisfy certain criteria. The ARM database achieved better performance than the conventional database in three of the five data-retrieving tests, but was less efficient in the remaining two tests. The time difference of query executions conducted by the ARM database and the conventional database is less than 130~\%. The ARM database was approximately 6-50 times more efficient than the conventional database in the patient-searching tests, while the Node + Path database requires far more time than the other two databases to execute both the data-retrieving and the patient-searching tests.

CONCLUSIONS: The ARM approach is capable of generating relational databases using archetypes and templates for archetype-based EHR systems, thus successfully adapting to changes in data requirements. ARM performance is similar to that of conventionally-designed EHR systems, and can be applied in a practical clinical environment. System components such as ARM can greatly facilitate the adoption of openEHR architecture within EHR systems.

}, issn = {1472-6947}, doi = {10.1186/s12911-015-0212-0}, author = {Wang, Li and Min, Lingtong and Wang, Rui and Lu, Xudong and Duan, Huilong} } @article {992, title = {A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Sep 2}, abstract = {

OBJECTIVE: Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management.

MATERIALS AND METHODS: An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software.

RESULTS: Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application ("app"), Blip, to visualize the data. Tidepool{\textquoteright}s software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security.

DISCUSSION: By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use.

CONCLUSION: The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool{\textquoteright}s open source, cloud model for health data interoperability is applicable to other healthcare use cases.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv104}, author = {Neinstein, Aaron and Wong, Jenise and Look, Howard and Arbiter, Brandon and Quirk, Kent and McCanne, Steve and Sun, Yao and Blum, Michael and Adi, Saleh} } @article {1190, title = {caTissue Suite to OpenSpecimen: developing an extensible, open source, web-based biobanking management system}, journal = {Journal of biomedical informatics}, volume = {57}, year = {2015}, month = {2015/10/}, pages = {456 - 464}, abstract = {The National Cancer Institute (NCI) Cancer Biomedical Informatics Grid({\textregistered}) (caBIG({\textregistered})) program established standards and best practices for biorepository data management by creating an infrastructure to propagate biospecimen resource sharing while maintaining data integrity and security. caTissue suite, a biospecimen data management software tool, has evolved from this effort. More recently, the caTissue suite continues to evolve as an open source initiative known as OpenSpecimen. The essential functionality of OpenSpecimen includes the capture and representation of highly granular, hierarchically-structured data for biospecimen processing, quality assurance, tracking, and annotation. Ideal for multi-user and multi-site biorepository environments, OpenSpecimen permits role-based access to specific sets of data operations through a user-interface designed to accommodate varying workflows and unique user needs. The software is interoperable, both syntactically and semantically, with an array of other bioinformatics tools given its integration of standard vocabularies thus enabling research involving biospecimens. End-users are encouraged to share their day-to-day experiences in working with the application, thus providing to the community board insight into the needs and limitations which need be addressed. Users are also requested to review and validate new features through group testing environments and mock screens. Through this user interaction, application flexibility and interoperability have been recognized as necessary developmental focuses essential for accommodating diverse adoption scenarios and biobanking workflows to catalyze advances in biomedical research and operations. Given the diversity of biobanking practices and workforce roles, efforts have been made consistently to maintain robust data granularity while aiding user accessibility, data discoverability, and security within and across applications by providing a lower learning curve in using OpenSpecimen. Iterative development and testing cycles provide continuous maintenance and up-to-date capabilities for this freely available, open-access, web-based software application that is globally-adopted at over 25 institutions.}, isbn = {1532-04641532-0480}, doi = {10.1016/j.jbi.2015.08.020}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772150/}, author = {McIntosh, Leslie D and Sharma, Mukesh K and Mulvihill, David and Gupta, Snehil and Juehne, Anthony and George, Bijoy and Khot, Suhas B and Kaushal, Atul and Watson, Mark A and Nagarajan, Rakesh} } @article {1008, title = {Design and development of an EMR for Ebola Treatment Centers in Sierra Leone using OpenMRS.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {916}, abstract = {

Ebola treatment presents unique challenges for medical records because strict infection control requirements rule out most conventional record-keeping systems. We used the OpenMRS platform to rapidly develop an EMR system for the recently opened Kerry Town, Sierra Leone Ebola Treatment Centre. This system addresses the need for recording patient data and communicating it between the infectious and non-infectious zones, and is specifically designed for maximum usability by staff wearing cumbersome protective equipment. This platform is interoperable with other key eHealth systems in the country, and is extensible to other sites and diseases.

}, issn = {0926-9630}, author = {Jazayeri, Darius and Oza, Shefali and Ramos, Glauber and Fraser, Hamish and Teich, Jonathan M and Kanter, Andrew S and Ball, Ellen} } @article {978, title = {DICOM for Clinical Research: PACS-Integrated Electronic Data Capture in Multi-Center Trials.}, journal = {J Digit Imaging}, year = {2015}, month = {2015 May 23}, abstract = {

Providing surrogate endpoints in clinical trials, medical imaging has become increasingly important in human-centered research. Nowadays, electronic data capture systems (EDCS) are used but binary image data is integrated insufficiently. There exists no structured way, neither to manage digital imaging and communications in medicine (DICOM) data in EDCS nor to interconnect EDCS with picture archiving and communication systems (PACS). Manual detours in the trial workflow yield errors, delays, and costs. In this paper, requirements for a DICOM-based system interconnection of EDCS and research PACS are analysed. Several workflow architectures are compared. Optimized for multi-center trials, we propose an entirely web-based solution integrating EDCS, PACS, and DICOM viewer, which has been implemented using the open source projects OpenClinica, DCM4CHEE, and Weasis, respectively. The EDCS forms the primary access point. EDCS to PACS interchange is integrated seamlessly on the data and the context levels. DICOM data is viewed directly from the electronic case report form (eCRF), while PACS-based management is hidden from the user. Data privacy is ensured by automatic de-identification and re-labelling with study identifiers. Our concept is evaluated on a variety of 13 DICOM modalities and transfer syntaxes. We have implemented the system in an ongoing investigator-initiated trial (IIT), where five centers have recruited 24 patients so far, performing decentralized computed tomography (CT) screening. Using our system, the chief radiologist is reading DICOM data directly from the eCRF. Errors and workflow processing time are reduced. Furthermore, an imaging database is built that may support future research.

}, issn = {1618-727X}, doi = {10.1007/s10278-015-9802-8}, author = {Haak, Daniel and Page, Charles-E and Reinartz, Sebastian and Kr{\"u}ger, Thilo and Deserno, Thomas M} } @article {1022, title = {Digital Imaging and Electronic Data Capture in Multi-Center Clinical Trials.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {930}, abstract = {

While medical image data is managed in picture archiving and communication systems (PACS) via the digital imaging and communications in medicine (DICOM) protocol, electronic data capture systems (EDCS) in clinical trials lack PACS interfacing. This complicates the trial workflow and increases errors, time, and costs. In this work, four system architectures of image integration for multi-center trials are analyzed with respect to data, function, visual, and context integration levels. We propose an open source-based architecture composed of OpenClinica, DCM4CHE, and Weasis for EDCS, PACS, and Viewer, respectively.

}, issn = {0926-9630}, author = {Deserno, Thomas M and Deserno, Verena and Haak, Daniel and Kabino, Klaus} } @article {1030, title = {Do interoperable national information systems enhance availability of data to assess the effect of scale-up of HIV services on health workforce deployment in resource-limited countries?}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {677-81}, abstract = {

Sub-Saharan Africa (SSA) bears the heaviest burden of the HIV epidemic. Health workers play a critical role in the scale-up of HIV programs. SSA also has the weakest information and communication technology (ICT) infrastructure globally. Implementing interoperable national health information systems (HIS) is a challenge, even in developed countries. Countries in resource-limited settings have yet to demonstrate that interoperable systems can be achieved, and can improve quality of healthcare through enhanced data availability and use in the deployment of the health workforce. We established interoperable HIS integrating a Master Facility List (MFL), District Health Information Software (DHIS2), and Human Resources Information Systems (HRIS) through application programmers interfaces (API). We abstracted data on HIV care, health workers deployment, and health facilities geo-coordinates. Over 95\% of data elements were exchanged between the MFL-DHIS and HRIS-DHIS. The correlation between the number of HIV-positive clients and nurses and clinical officers in 2013 was R2=0.251 and R2=0.261 respectively. Wrong MFL codes, data type mis-match and hyphens in legacy data were key causes of data transmission errors. Lack of information exchange standards for aggregate data made programming time-consuming.

}, issn = {0926-9630}, author = {Oluoch, Tom and Muturi, David and Kiriinya, Rose and Waruru, Anthony and Lanyo, Kevin and Nguni, Robert and Ojwang, James and Waters, Keith P and Richards, Janise} } @article {1006, title = {Enabling Better Interoperability for HealthCare: Lessons in Developing a Standards Based Application Programing Interface for Electronic Medical Record Systems.}, journal = {J Med Syst}, volume = {39}, year = {2015}, month = {2015 Nov}, pages = {182}, abstract = {

We sought to enable better interoperability and easy adoption of healthcare applications by developing a standardized domain independent Application Programming Interface (API) for an Electronic Medical Record (EMR) system. We leveraged the modular architecture of the Open Medical Record System (OpenMRS) to build a Fast Healthcare Interoperability Resources (FHIR) based add-on module that could consume FHIR resources and requests made on OpenMRS. The OpenMRS FHIR module supports a subset of FHIR resources that could be used to interact with clinical data persisted in OpenMRS. We demonstrate the ease of connecting healthcare applications using the FHIR API by integrating a third party Substitutable Medical Apps \& Reusable Technology (SMART) application with OpenMRS via FHIR. The OpenMRS FHIR module is an optional component of the OpenMRS platform. The FHIR API significantly reduces the effort required to implement OpenMRS by preventing developers from having to learn or work with a domain specific OpenMRS API. We propose an integration pathway where the domain specific legacy OpenMRS API is gradually retired in favor of the new FHIR API, which would be integrated into the core OpenMRS platform. Our efforts indicate that a domain independent API is a reality for any EMR system. These efforts demonstrate the adoption of an emerging FHIR standard that is seen as a replacement for both Health Level 7 (HL7) Version 2 and Version 3. We propose a gradual integration approach where our FHIR API becomes the preferred method for communicating with the OpenMRS platform.

}, issn = {1573-689X}, doi = {10.1007/s10916-015-0356-6}, author = {Kasthurirathne, Suranga N and Mamlin, Burke and Kumara, Harsha and Grieve, Grahame and Biondich, Paul} } @article {1002, title = {Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.}, journal = {J Biomed Inform}, volume = {53}, year = {2015}, month = {2015 Feb}, pages = {390-404}, abstract = {

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages.

}, issn = {1532-0480}, doi = {10.1016/j.jbi.2014.11.012}, author = {Zaidan, A A and Zaidan, B B and Al-Haiqi, Ahmed and Kiah, M L M and Hussain, Muzammil and Abdulnabi, Mohamed} } @article {1145, title = {A Generic Data Harmonization Process for Cross-linked Research and Network Interaction. Construction and Application for the Lung Cancer Phenotype Database of the German Center for Lung Research.}, journal = {Methods Inf Med}, volume = {54}, year = {2015}, month = {2015}, pages = {455-60}, abstract = {

OBJECTIVE: Joint data analysis is a key requirement in medical research networks. Data are available in heterogeneous formats at each network partner and their harmonization is often rather complex. The objective of our paper is to provide a generic approach for the harmonization process in research networks. We applied the process when harmonizing data from three sites for the Lung Cancer Phenotype Database within the German Center for Lung Research.

METHODS: We developed a spreadsheet-based solution as tool to support the harmonization process for lung cancer data and a data integration procedure based on Talend Open Studio.

RESULTS: The harmonization process consists of eight steps describing a systematic approach for defining and reviewing source data elements and standardizing common data elements. The steps for defining common data elements and harmonizing them with local data definitions are repeated until consensus is reached. Application of this process for building the phenotype database led to a common basic data set on lung cancer with 285 structured parameters. The Lung Cancer Phenotype Database was realized as an i2b2 research data warehouse.

CONCLUSION: Data harmonization is a challenging task requiring informatics skills as well as domain knowledge. Our approach facilitates data harmonization by providing guidance through a uniform process that can be applied in a wide range of projects.

}, issn = {0026-1270}, doi = {10.3414/ME14-02-0030}, author = {Firnkorn, D and Ganzinger, M and Muley, T and Thomas, M and Knaup, P} } @article {981, title = {Going open source: some lessons learned from the development of OpenRecLink.}, journal = {Cad Saude Publica}, volume = {31}, year = {2015}, month = {2015 Feb}, pages = {257-63}, abstract = {

Record linkage is the process of identifying and merging records across different databases belonging to the same entity. The health sector is one of the pioneering areas of record linkage techniques applications. In 1998 we began the development of a software package, called RecLink that implemented probabilistic record linkage techniques. In this article we report the development of a new, open-source version of that program, now named OpenRecLink. The aim of this article is to present the main characteristics of the new version and some of the lessons learned during its development. The new version is a total rewrite of the program, based on three goals: (1) to migrate to a free and open source software (FOSS) platform; (2) to implement a multiplatform version; (3) to implement the support for internationalization. We describe the tools that we adopted, the process of development and some of the problems encountered.

}, keywords = {Databases, Factual, Medical Record Linkage, Software, Software Design}, issn = {1678-4464}, author = {Camargo Jr, Kenneth Rochel de and Coeli, Claudia Medina} } @article {1279, title = {Identifying patients with asthma in primary care electronic medical record systems Chart analysis-based electronic algorithm validation study.}, journal = {Can Fam Physician}, volume = {61}, year = {2015}, month = {2015 Oct}, pages = {e474-83}, abstract = {

OBJECTIVE: To develop and test a variety of electronic medical record (EMR) search algorithms to allow clinicians to accurately identify their patients with asthma in order to enable improved care.

DESIGN: A retrospective chart analysis identified 5 relevant unique EMR information fields (electronic disease registry, cumulative patient profile, billing diagnostic code, medications, and chart notes); asthma-related search terms were designated for each field. The accuracy of each term was tested for its ability to identify the asthma patients among all patients whose charts were reviewed. Increasingly sophisticated search algorithms were then designed and evaluated by serially combining individual searches with Boolean operators.

SETTING: Two large academic primary care clinics in Hamilton, Ont.

PARTICIPANTS: Charts for 600 randomly selected patients aged 16 years and older identified in an initial EMR search as likely having asthma (n = 150), chronic obstructive pulmonary disease (n = 150), other respiratory conditions (n = 150), or nonrespiratory conditions (n = 150) were reviewed until 100 patients per category were identified (or until all available names were exhausted). A total of 398 charts were reviewed in full and included.

MAIN OUTCOME MEASURES: Sensitivity and specificity of each search for asthma diagnosis (against the reference standard of a physician chart review-based diagnosis).

RESULTS: Two physicians reviewed the charts identified in the initial EMR search using a standardized data collection form and ascribed the following diagnoses in 398 patients: 112 (28.1\%) had asthma, 81 (20.4\%) had chronic obstructive pulmonary disease, 104 (26.1\%) had other respiratory conditions, and 101 (25.4\%) had nonrespiratory conditions. Concordance between reviewers in chart abstraction diagnosis was high (κ = 0.89, 95\% CI 0.80 to 0.97). Overall, the algorithm searching for patients who had asthma in their cumulative patient profiles or for whom an asthma billing code had been used was the most accurate (sensitivity of 90.2\%, 95\% CI 87.3\% to 93.1\%; specificity of 83.9\%, 95\% CI 80.3\% to 87.5\%).

CONCLUSION: Usable, practical search algorithms that accurately identify patients with asthma in existing EMRs are presented. Clinicians can apply 1 of these algorithms to generate asthma registries for targeted quality improvement initiatives and outcome measurements. This methodology can be emulated for other diseases.

}, keywords = {Adult, Aged, Algorithms, Asthma, Data Accuracy, electronic health records, Female, Humans, Male, Middle Aged, Ontario, Primary Health Care, Pulmonary Disease, Chronic Obstructive, Registries, Retrospective Studies, Sensitivity and Specificity}, issn = {1715-5258}, author = {Xi, Nancy and Wallace, Rebecca and Agarwal, Gina and Chan, David and Gershon, Andrea and Gupta, Samir} } @article {970, title = {The ImageJ ecosystem: An open platform for biomedical image analysis.}, journal = {Mol Reprod Dev}, year = {2015}, month = {2015 Jul 7}, abstract = {

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software{\textquoteright}s extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. Mol. Reprod. Dev. 2015. {\textcopyright} 2015 Wiley Periodicals, Inc.

}, issn = {1098-2795}, doi = {10.1002/mrd.22489}, author = {Schindelin, Johannes and Rueden, Curtis T and Hiner, Mark C and Eliceiri, Kevin W} } @article {977, title = {Implementation, reliability, and feasibility test of an Open-Source PACS.}, journal = {Radiol Med}, year = {2015}, month = {2015 Jun 19}, abstract = {

PURPOSE: To implement a hardware and software system able to perform the major functions of an Open-Source PACS, and to analyze it in a simulated real-world environment.

MATERIALS AND METHODS: A small home network was implemented, and the Open-Source operating system Ubuntu 11.10 was installed in a laptop containing the Dcm4chee suite with the software devices needed.

RESULTS: The Open-Source PACS implemented is compatible with Linux OS, Microsoft OS, and Mac OS X; furthermore, it was used with operating systems that guarantee the operation in portable devices (smartphone, tablet) Android and iOS.

CONCLUSIONS: An OSS PACS is useful for making tutorials and workshops on post-processing techniques for educational and training purposes.

}, issn = {1826-6983}, doi = {10.1007/s11547-015-0560-y}, author = {Valeri, Gianluca and Zuccaccia, Matteo and Badaloni, Andrea and Ciriaci, Damiano and La Riccia, Luigi and Mazzoni, Giovanni and Maggi, Stefania and Giovagnoni, Andrea} } @article {997, title = {Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Jun 10}, abstract = {

OBJECTIVE: To share approaches and innovations adopted to deliver a relatively inexpensive clinical data management (CDM) framework within a low-income setting that aims to deliver quality pediatric data useful for supporting research, strengthening the information culture and informing improvement efforts in local clinical practice.

MATERIALS AND METHODS: The authors implemented a CDM framework to support a Clinical Information Network (CIN) using Research Electronic Data Capture (REDCap), a noncommercial software solution designed for rapid development and deployment of electronic data capture tools. It was used for collection of standardized data from case records of multiple hospitals{\textquoteright} pediatric wards. R, an open-source statistical language, was used for data quality enhancement, analysis, and report generation for the hospitals.

RESULTS: In the first year of CIN, the authors have developed innovative solutions to support the implementation of a secure, rapid pediatric data collection system spanning 14 hospital sites with stringent data quality checks. Data have been collated on over 37 000 admission episodes, with considerable improvement in clinical documentation of admissions observed. Using meta-programming techniques in R, coupled with branching logic, randomization, data lookup, and Application Programming Interface (API) features offered by REDCap, CDM tasks were configured and automated to ensure quality data was delivered for clinical improvement and research use.

CONCLUSION: A low-cost clinically focused but geographically dispersed quality CDM (Clinical Data Management) in a long-term, multi-site, and real world context can be achieved and sustained and challenges can be overcome through thoughtful design and implementation of open-source tools for handling data and supporting research.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv028}, author = {Tuti, Timothy and Bitok, Michael and Paton, Chris and Makone, Boniface and Malla, Lucas and Muinga, Naomi and Gathara, David and English, Mike} } @article {1292, title = {Innovative Technological Approach to Ebola Virus Disease Outbreak Response in Nigeria Using the Open Data Kit and Form Hub Technology.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0131000}, abstract = {

The recent outbreak of Ebola Virus Disease (EVD) in West Africa has ravaged many lives. Effective containment of this outbreak relies on prompt and effective coordination and communication across various interventions; early detection and response being critical to successful control. The use of information and communications technology (ICT) in active surveillance has proved to be effective but its use in Ebola outbreak response has been limited. Due to the need for timeliness in reporting and communication for early discovery of new EVD cases and promptness in response; it became imperative to empower the response team members with technologies and solutions which would enable smooth and rapid data flow. The Open Data Kit and Form Hub technology were used in combination with the Dashboard technology and ArcGIS mapping for follow up of contacts, identification of cases, case investigation and management and also for strategic planning during the response. A remarkable improvement was recorded in the reporting of daily follow-up of contacts after the deployment of the integrated real time technology. The turnaround time between identification of symptomatic contacts and evacuation to the isolation facility and also for receipt of laboratory results was reduced and informed decisions could be taken by all concerned. Accountability in contact tracing was ensured by the use of a GPS enabled device. The use of innovative technologies in the response of the EVD outbreak in Nigeria contributed significantly to the prompt control of the outbreak and containment of the disease by providing a valuable platform for early warning and guiding early actions.

}, keywords = {Disease Outbreaks, Ebolavirus, Epidemiological Monitoring, Female, Hemorrhagic Fever, Ebola, Humans, Male, Medical Informatics, Nigeria}, issn = {1932-6203}, doi = {10.1371/journal.pone.0131000}, author = {Tom-Aba, Daniel and Olaleye, Adeniyi and Olayinka, Adebola Tolulope and Nguku, Patrick and Waziri, Ndadilnasiya and Adewuyi, Peter and Adeoye, Olawunmi and Oladele, Saliu and Adeseye, Aderonke and Oguntimehin, Olukayode and Shuaib, Faisal} } @article {975, title = {"Just Another Tool for Online Studies" (JATOS): An Easy Solution for Setup and Management of Web Servers Supporting Online Studies.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0130834}, abstract = {

We present here "Just Another Tool for Online Studies" (JATOS): an open source, cross-platform web application with a graphical user interface (GUI) that greatly simplifies setting up and communicating with a web server to host online studies that are written in JavaScript. JATOS is easy to install in all three major platforms (Microsoft Windows, Mac OS X, and Linux), and seamlessly pairs with a database for secure data storage. It can be installed on a server or locally, allowing researchers to try the application and feasibility of their studies within a browser environment, before engaging in setting up a server. All communication with the JATOS server takes place via a GUI (with no need to use a command line interface), making JATOS an especially accessible tool for researchers without a strong IT background. We describe JATOS{\textquoteright} main features and implementation and provide a detailed tutorial along with example studies to help interested researchers to set up their online studies. JATOS can be found under the Internet address: www.jatos.org.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0130834}, author = {Lange, Kristian and K{\"u}hn, Simone and Filevich, Elisa} } @article {979, title = {medplot: a web application for dynamic summary and analysis of longitudinal medical data based on R.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0121760}, abstract = {

In biomedical studies the patients are often evaluated numerous times and a large number of variables are recorded at each time-point. Data entry and manipulation of longitudinal data can be performed using spreadsheet programs, which usually include some data plotting and analysis capabilities and are straightforward to use, but are not designed for the analyses of complex longitudinal data. Specialized statistical software offers more flexibility and capabilities, but first time users with biomedical background often find its use difficult. We developed medplot, an interactive web application that simplifies the exploration and analysis of longitudinal data. The application can be used to summarize, visualize and analyze data by researchers that are not familiar with statistical programs and whose knowledge of statistics is limited. The summary tools produce publication-ready tables and graphs. The analysis tools include features that are seldom available in spreadsheet software, such as correction for multiple testing, repeated measurement analyses and flexible non-linear modeling of the association of the numerical variables with the outcome. medplot is freely available and open source, it has an intuitive graphical user interface (GUI), it is accessible via the Internet and can be used within a web browser, without the need for installing and maintaining programs locally on the user{\textquoteright}s computer. This paper describes the application and gives detailed examples describing how to use the application on real data from a clinical study including patients with early Lyme borreliosis.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0121760}, author = {Ahlin, {\v C}rt and Stupica, Da{\v s}a and Strle, Franc and Lusa, Lara} } @article {972, title = {MzJava: An open source library for mass spectrometry data processing.}, journal = {J Proteomics}, year = {2015}, month = {2015 Jun 30}, abstract = {

Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need for sharing and reuse of code among bioinformaticians working with MS data prompted the design and implementation of MzJava, an open-source Java Application Programming Interface (API) for MS related data processing. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce (hadoop.apache.org) and Apache Spark (spark.apache.org) frameworks for cluster computing was implemented. The library has been developed applying best practices of software engineering. To ensure that MzJava contains code that is correct and easy to use the library{\textquoteright}s API was carefully designed and thoroughly tested. MzJava is an open-source project distributed under the AGPL v3.0 licence. MzJava requires Java 1.7 or higher. Binaries, source code and documentation can be downloaded from http://mzjava.expasy.org and https://bitbucket.org/sib-pig/mzjava.

}, issn = {1876-7737}, doi = {10.1016/j.jprot.2015.06.013}, author = {Horlacher, Oliver and Nikitin, Frederic and Alocci, Davide and Mariethoz, Julien and M{\"u}ller, Markus and Lisacek, Frederique} } @article {974, title = {Omics Metadata Management Software (OMMS).}, journal = {Bioinformation}, volume = {11}, year = {2015}, month = {2015}, pages = {165-72}, abstract = {Next-generation sequencing projects have underappreciated information management tasks requiring detailed attention to specimen curation, nucleic acid sample preparation and sequence production methods required for downstream data processing, comparison, interpretation, sharing and reuse. The few existing metadata management tools for genome-based studies provide weak curatorial frameworks for experimentalists to store and manage idiosyncratic, project-specific information, typically offering no automation supporting unified naming and numbering conventions for sequencing production environments that routinely deal with hundreds, if not thousands of samples at a time. Moreover, existing tools are not readily interfaced with bioinformatics executables, (e.g., BLAST, Bowtie2, custom pipelines). Our application, the Omics Metadata Management Software (OMMS), answers both needs, empowering experimentalists to generate intuitive, consistent metadata, and perform analyses and information management tasks via an intuitive web-based interface. Several use cases with short-read sequence datasets are provided to validate installation and integrated function, and suggest possible methodological road maps for prospective users. Provided examples highlight possible OMMS workflows for metadata curation, multistep analyses, and results management and downloading. The OMMS can be implemented as a stand alone-package for individual laboratories, or can be configured for webbased deployment supporting geographically-dispersed projects. The OMMS was developed using an open-source software base, is flexible, extensible and easily installed and executed. The OMMS can be obtained at http://omms.sandia.gov.

AVAILABILITY: The OMMS can be obtained at http://omms.sandia.gov.

}, issn = {0973-2063}, doi = {10.6026/97320630011165}, author = {Perez-Arriaga, Martha O and Wilson, Susan and Williams, Kelly P and Schoeniger, Joseph and Waymire, Russel L and Powell, Amy Jo} } @article {976, title = {Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field.}, journal = {J Cheminform}, volume = {7}, year = {2015}, month = {2015}, pages = {26}, abstract = {

BACKGROUND: There has been huge progress in the open cheminformatics field in both methods and software development. Unfortunately, there has been little effort to unite those methods and software into one package. We here describe the Open Drug Discovery Toolkit (ODDT), which aims to fulfill the need for comprehensive and open source drug discovery software.

RESULTS: The Open Drug Discovery Toolkit was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. ODDT reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible. Therefore, users are strongly encouraged to extend it and develop new methods. We here present three use cases for ODDT in common tasks in computer-aided drug discovery.

CONCLUSION: Open Drug Discovery Toolkit is released on a permissive 3-clause BSD license for both academic and industrial use. ODDT{\textquoteright}s source code, additional examples and documentation are available on GitHub (https://github.com/oddt/oddt).

}, issn = {1758-2946}, doi = {10.1186/s13321-015-0078-2}, author = {W{\'o}jcikowski, Maciej and Zielenkiewicz, Piotr and Siedlecki, Pawel} } @article {984, title = {An open source business model for malaria.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0117150}, abstract = {

Greater investment is required in developing new drugs and vaccines against malaria in order to eradicate malaria. These precious funds must be carefully managed to achieve the greatest impact. We evaluate existing efforts to discover and develop new drugs and vaccines for malaria to determine how best malaria R\&D can benefit from an enhanced open source approach and how such a business model may operate. We assess research articles, patents, clinical trials and conducted a smaller survey among malaria researchers. Our results demonstrate that the public and philanthropic sectors are financing and performing the majority of malaria drug/vaccine discovery and development, but are then restricting access through patents, {\textquoteright}closed{\textquoteright} publications and hidden away physical specimens. This makes little sense since it is also the public and philanthropic sector that purchases the drugs and vaccines. We recommend that a more "open source" approach is taken by making the entire value chain more efficient through greater transparency which may lead to more extensive collaborations. This can, for example, be achieved by empowering an existing organization like the Medicines for Malaria Venture (MMV) to act as a clearing house for malaria-related data. The malaria researchers that we surveyed indicated that they would utilize such registry data to increase collaboration. Finally, we question the utility of publicly or philanthropically funded patents for malaria medicines, where little to no profits are available. Malaria R\&D benefits from a publicly and philanthropically funded architecture, which starts with academic research institutions, product development partnerships, commercialization assistance through UNITAID and finally procurement through mechanisms like The Global Fund to Fight AIDS, Tuberculosis and Malaria and the U.S.{\textquoteright} President{\textquoteright}s Malaria Initiative. We believe that a fresh look should be taken at the cost/benefit of patents particularly related to new malaria medicines and consider alternative incentives, like WHO prequalification.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0117150}, author = {{\r A}rdal, Christine and R{\o}ttingen, John-Arne} } @article {996, title = {Open source in cachexia?}, journal = {J Cachexia Sarcopenia Muscle}, volume = {6}, year = {2015}, month = {2015 Mar}, pages = {112-3}, issn = {2190-5991}, doi = {10.1002/jcsm.12013}, author = {Stemmler, Britta and Argil{\'e}s, Joseph M} } @article {985, title = {Open source libraries and frameworks for biological data visualisation: a guide for developers.}, journal = {Proteomics}, volume = {15}, year = {2015}, month = {2015 Apr}, pages = {1356-74}, abstract = {

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories.

}, issn = {1615-9861}, doi = {10.1002/pmic.201400377}, author = {Wang, Rui and Perez-Riverol, Yasset and Hermjakob, Henning and Vizca{\'\i}no, Juan Antonio} } @article {993, title = {Open Source Software For Patient Data Management In Critical Care.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {920}, abstract = {

We have previously developed a Patient Data Management System for Intensive Care based on Open Source Software. The aim of this work was to adapt this software to use in Emergency Departments in low resource environments. The new software includes facilities for utilization of the South African Triage Scale and prediction of mortality based on independent predictive factors derived from data from the Tabarre Emergency Trauma Center in Port au Prince, Haiti.

}, issn = {0926-9630}, author = {Massaut, Jacques and Charretk, Nicolas and Gayraud, Olivia and Van Den Bergh, Rafael and Charles, Adelin and Edema, Nathalie} } @article {987, title = {Open source software in a practical approach for post processing of radiologic images.}, journal = {Radiol Med}, volume = {120}, year = {2015}, month = {2015 Mar}, pages = {309-23}, abstract = {

PURPOSE: The purpose of this paper is to evaluate the use of open source software (OSS) to process DICOM images.

MATERIALS AND METHODS: We selected 23 programs for Windows and 20 programs for Mac from 150 possible OSS programs including DICOM viewers and various tools (converters, DICOM header editors, etc.). The programs selected all meet the basic requirements such as free availability, stand-alone application, presence of graphical user interface, ease of installation and advanced features beyond simple display monitor. Capabilities of data import, data export, metadata, 2D viewer, 3D viewer, support platform and usability of each selected program were evaluated on a scale ranging from 1 to 10 points.

RESULTS: Twelve programs received a score higher than or equal to eight. Among them, five obtained a score of 9: 3D Slicer, MedINRIA, MITK 3M3, VolView, VR Render; while OsiriX received 10.

CONCLUSIONS: OsiriX appears to be the only program able to perform all the operations taken into consideration, similar to a workstation equipped with proprietary software, allowing the analysis and interpretation of images in a simple and intuitive way. OsiriX is a DICOM PACS workstation for medical imaging and software for image processing for medical research, functional imaging, 3D imaging, confocal microscopy and molecular imaging. This application is also a good tool for teaching activities because it facilitates the attainment of learning objectives among students and other specialists.

}, keywords = {Diagnostic Imaging, Humans, Image Interpretation, Computer-Assisted, Image Processing, Computer-Assisted, Radiology Information Systems, Reproducibility of Results, Sensitivity and Specificity, Software, Software Validation, User-Computer Interface}, issn = {1826-6983}, doi = {10.1007/s11547-014-0437-5}, author = {Valeri, Gianluca and Mazza, Francesco Antonino and Maggi, Stefania and Aramini, Daniele and La Riccia, Luigi and Mazzoni, Giovanni and Giovagnoni, Andrea} } @article {998, title = {Open source tools for large-scale neuroscience.}, journal = {Curr Opin Neurobiol}, volume = {32}, year = {2015}, month = {2015 Jun}, pages = {156-63}, abstract = {

New technologies for monitoring and manipulating the nervous system promise exciting biology but pose challenges for analysis and computation. Solutions can be found in the form of modern approaches to distributed computing, machine learning, and interactive visualization. But embracing these new technologies will require a cultural shift: away from independent efforts and proprietary methods and toward an open source and collaborative neuroscience.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2015.04.002}, author = {Freeman, Jeremy} } @article {1065, title = {OpenFDA: an innovative platform providing access to a wealth of FDA{\textquoteright}s publicly available data.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Dec 7}, abstract = {

OBJECTIVE: The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs).

MATERIALS AND METHODS: Using cutting-edge technologies deployed on FDA{\textquoteright}s new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges.

RESULTS: Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event.

CONCLUSION: With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv153}, author = {Kass-Hout, Taha A and Xu, Zhiheng and Mohebbi, Matthew and Nelsen, Hans and Baker, Adam and Levine, Jonathan and Johanson, Elaine and Bright, Roselie A} } @article {995, title = {OpenHELP (Heidelberg laparoscopy phantom): development of an open-source surgical evaluation and training tool.}, journal = {Surg Endosc}, year = {2015}, month = {2015 Feb 12}, abstract = {

BACKGROUND: Apart from animal testing and clinical trials, surgical research and laparoscopic training mainly rely on phantoms. The aim of this project was to design a phantom with realistic anatomy and haptic characteristics, modular design and easy reproducibility. The phantom was named open-source Heidelberg laparoscopic phantom (OpenHELP) and serves as an open-source platform.

METHODS: The phantom was based on an anonymized CT scan of a male patient. The anatomical structures were segmented to obtain digital three-dimensional models of the torso and the organs. The digital models were materialized via rapid prototyping. One flexible, using an elastic abdominal wall, and one rigid method, using a plastic shell, to simulate pneumoperitoneum were developed. Artificial organ production was carried out sequentially starting from raw gypsum models to silicone molds to final silicone casts. The reproduction accuracy was exemplarily evaluated for ten silicone rectum models by comparing the digital 3D surface of the original rectum with CT scan by calculating the root mean square error of surface variations. Haptic realism was also evaluated to find the most realistic silicone compositions on a visual analog scale (VAS, 0-10).

RESULTS: The rigid and durable plastic torso and soft silicone organs of the abdominal cavity were successfully produced. A simulation of pneumoperitoneum could be created successfully by both methods. The reproduction accuracy of ten silicone rectum models showed an average root mean square error of 2.26 (0-11.48) mm. Haptic realism revealed an average value on a VAS of 7.25 (5.2-9.6) for the most realistic rectum.

CONCLUSION: The OpenHELP phantom proved to be feasible and accurate. The phantom was consecutively applied frequently in the field of computer-assisted surgery at our institutions and is accessible as an open-source project at www.open-cas.org for the academic community.

}, issn = {1432-2218}, doi = {10.1007/s00464-015-4094-0}, author = {Kenngott, H G and W{\"u}nscher, J J and Wagner, M and Preukschas, A and Wekerle, A L and Neher, P and Suwelack, S and Speidel, S and Nickel, F and Oladokun, D and Maier-Hein, L and Dillmann, R and Meinzer, H P and M{\"u}ller-Stich, B P} } @article {1058, title = {OpenNCP: a novel framework to foster cross-border e-Health services.}, journal = {Stud Health Technol Inform}, volume = {210}, year = {2015}, month = {2015}, pages = {617-21}, abstract = {

The continuity of cross-border health care in the European Union depends on the ability to set up shared practices with respect to patient data exchange across Member States. This flow of data must comply with demanding security, legal and interoperability requirements, as defined by the epSOS project specifications. In this paper, we describe the OpenNCP framework that offers a comprehensive set of interoperability services to enable national and regional e-Health platforms to set up cross-border health information networks compliant with epSOS, with minimal adaptation of the existing infrastructure. The OpenNCP, available as open source software, has been adopted in 10 Member States, allowing them to securely interconnect their eHealth infrastructures.

}, issn = {0926-9630}, author = {Fonseca, Marcelo and Karkaletsis, Kostas and Cruz, Isabel A and Berler, Alexander and Oliveira, Il{\'\i}dio C} } @article {1098, title = {Open-source health information technology: A case study of electronic medical records}, journal = {Health Policy and Technology}, volume = {4}, year = {2015}, pages = {14{\textendash}28}, author = {Safadi, Hani and Chan, David and Dawes, Martin and Roper, Mark and Faraj, Samer} } @article {1067, title = {Open-Source Radiation Exposure Extraction Engine (RE3) with Patient-Specific Outlier Detection.}, journal = {J Digit Imaging}, year = {2015}, month = {2015 Dec 7}, abstract = {

We present an open-source, picture archiving and communication system (PACS)-integrated radiation exposure extraction engine (RE3) that provides study-, series-, and slice-specific data for automated monitoring of computed tomography (CT) radiation exposure. RE3 was built using open-source components and seamlessly integrates with the PACS. RE3 calculations of dose length product (DLP) from the Digital imaging and communications in medicine (DICOM) headers showed high agreement (R (2) = 0.99) with the vendor dose pages. For study-specific outlier detection, RE3 constructs robust, automatically updating multivariable regression models to predict DLP in the context of patient gender and age, scan length, water-equivalent diameter (D w), and scanned body volume (SBV). As proof of concept, the model was trained on 811 CT chest, abdomen + pelvis (CAP) exams and 29 outliers were detected. The continuous variables used in the outlier detection model were scan length (R (2) = 0.45), D w (R (2) = 0.70), SBV (R (2) = 0.80), and age (R (2) = 0.01). The categorical variables were gender (male average 1182.7 {\textpm} 26.3 and female 1047.1 {\textpm} 26.9~mGy~cm) and pediatric status (pediatric average 710.7 {\textpm} 73.6~mGy~cm and adult 1134.5 {\textpm} 19.3~mGy~cm).

}, issn = {1618-727X}, doi = {10.1007/s10278-015-9852-y}, author = {Weisenthal, Samuel J and Folio, Les and Kovacs, William and Seff, Ari and Derderian, Vana and Summers, Ronald M and Yao, Jianhua} } @article {982, title = {Patient Access to Their Health Record Using Open Source EHR.}, journal = {Stud Health Technol Inform}, volume = {208}, year = {2015}, month = {2015}, pages = {104-8}, abstract = {

In both Europe and North America, patients are beginning to gain access to their health records in electronic form. Using the open source cityEHR as an example, we have focussed on the needs of clinical users to gather requirements for patient access and have implemented these requirements in a new application called cityEHR-PA. The development of a separate application for patient access was necessary to address requirements for security and ease of use. The use of open standards throughout the design of the EHR allows the possibility of third parties to develop applications for patient access, consuming the individual patient record extracted from the full EHR.

}, issn = {0926-9630}, author = {Chelsom, John and Dogar, Naveed} } @article {983, title = {A RESTful interface to pseudonymization services in modern web applications.}, journal = {BMC Med Inform Decis Mak}, volume = {15}, year = {2015}, month = {2015}, pages = {2}, abstract = {

BACKGROUND: Medical research networks rely on record linkage and pseudonymization to determine which records from different sources relate to the same patient. To establish informational separation of powers, the required identifying data are redirected to a trusted third party that has, in turn, no access to medical data. This pseudonymization service receives identifying data, compares them with a list of already reported patient records and replies with a (new or existing) pseudonym. We found existing solutions to be technically outdated, complex to implement or not suitable for internet-based research infrastructures. In this article, we propose a new RESTful pseudonymization interface tailored for use in web applications accessed by modern web browsers.

METHODS: The interface is modelled as a resource-oriented architecture, which is based on the representational state transfer (REST) architectural style. We translated typical use-cases into resources to be manipulated with well-known HTTP verbs. Patients can be re-identified in real-time by authorized users{\textquoteright} web browsers using temporary identifiers. We encourage the use of PID strings for pseudonyms and the EpiLink algorithm for record linkage. As a proof of concept, we developed a Java Servlet as reference implementation.

RESULTS: The following resources have been identified: Sessions allow data associated with a client to be stored beyond a single request while still maintaining statelessness. Tokens authorize for a specified action and thus allow the delegation of authentication. Patients are identified by one or more pseudonyms and carry identifying fields. Relying on HTTP calls alone, the interface is firewall-friendly. The reference implementation has proven to be production stable.

CONCLUSION: The RESTful pseudonymization interface fits the requirements of web-based scenarios and allows building applications that make pseudonymization transparent to the user using ordinary web technology. The open-source reference implementation implements the web interface as well as a scientifically grounded algorithm to generate non-speaking pseudonyms.

}, issn = {1472-6947}, doi = {10.1186/s12911-014-0123-5}, author = {Lablans, Martin and Borg, Andreas and {\"U}ckert, Frank} } @article {1115, title = {A RESTful interface to pseudonymization services in modern web applications}, journal = {BMC Medical Informatics and Decision Making}, volume = {15}, year = {2015}, month = {2015}, pages = {2}, abstract = {BACKGROUND: Medical research networks rely on record linkage and pseudonymization to determine which records from different sources relate to the same patient. To establish informational separation of powers, the required identifying data are redirected to a trusted third party that has, in turn, no access to medical data. This pseudonymization service receives identifying data, compares them with a list of already reported patient records and replies with a (new or existing) pseudonym. We found existing solutions to be technically outdated, complex to implement or not suitable for internet-based research infrastructures. In this article, we propose a new RESTful pseudonymization interface tailored for use in web applications accessed by modern web browsers. METHODS: The interface is modelled as a resource-oriented architecture, which is based on the representational state transfer (REST) architectural style. We translated typical use-cases into resources to be manipulated with well-known HTTP verbs. Patients can be re-identified in real-time by authorized users{\textquoteright} web browsers using temporary identifiers. We encourage the use of PID strings for pseudonyms and the EpiLink algorithm for record linkage. As a proof of concept, we developed a Java Servlet as reference implementation. RESULTS: The following resources have been identified: Sessions allow data associated with a client to be stored beyond a single request while still maintaining statelessness. Tokens authorize for a specified action and thus allow the delegation of authentication. Patients are identified by one or more pseudonyms and carry identifying fields. Relying on HTTP calls alone, the interface is firewall-friendly. The reference implementation has proven to be production stable. CONCLUSION: The RESTful pseudonymization interface fits the requirements of web-based scenarios and allows building applications that make pseudonymization transparent to the user using ordinary web technology. The open-source reference implementation implements the web interface as well as a scientifically grounded algorithm to generate non-speaking pseudonyms.}, isbn = {1472-6947}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350982/}, author = {Lablans, Martin and Borg, Andreas and {\"U}ckert, Frank} } @article {1045, title = {The Role of Hospital Information Systems in Universal Health Coverage Monitoring in Rwanda.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {193-7}, abstract = {

In this retrospective study, the authors monitored the patient health coverage in 6 Rwandan hospitals in the period between 2011 and 2014. Among the 6 hospitals, 2 are third level hospitals, 2 district hospitals and 2 private hospitals. Patient insurance and financial data were extracted and analyzed from OpenClinic GA, an open source hospital information system (HIS) used in those 6 hospitals. The percentage of patients who had no health insurer globally decreased from 35\% in 2011 to 15\% in 2014. The rate of health insurance coverage in hospitals varied between 75\% in private hospitals and 84\% in public hospitals. The amounts paid by the patients for health services decreased in private hospitals to 25\% of the total costs in 2014 (-7.4\%) and vary between 14\% and 19\% in public hospitals. Although the number of insured patients has increased and the patient share decreased over the four years of study, the patients{\textquoteright} out-of-pocket payments increased especially for in-patients. This study emphasizes the value of integrated hospital information systems for this kind of health economics research in developing countries.

}, issn = {0926-9630}, author = {Karara, Gustave and Verbeke, Frank and Nyssen, Marc} } @article {999, title = {Role of OpenEHR as an open source solution for the regional modelling of patient data in obstetrics.}, journal = {J Biomed Inform}, volume = {55}, year = {2015}, month = {2015 Jun}, pages = {174-87}, abstract = {

This work investigates, whether openEHR with its reference model, archetypes and templates is suitable for the digital representation of demographic as well as clinical data. Moreover, it elaborates openEHR as a tool for modelling Hospital Information Systems on a regional level based on a national logical infrastructure. OpenEHR is a dual model approach developed for the modelling of Hospital Information Systems enabling semantic interoperability. A holistic solution to this represents the use of dual model based Electronic Healthcare Record systems. Modelling data in the field of obstetrics is a challenge, since different regions demand locally specific information for the process of treatment. Smaller health units in developing countries like Brazil or Malaysia, which until recently handled automatable processes like the storage of sensitive patient data in paper form, start organizational reconstruction processes. This archetype proof-of-concept investigation has tried out some elements of the openEHR methodology in cooperation with a health unit in Colombo, Brazil. Two legal forms provided by the Brazilian Ministry of Health have been analyzed and classified into demographic and clinical data. LinkEHR-Ed editor was used to read, edit and create archetypes. Results show that 33 clinical and demographic concepts, which are necessary to cover data demanded by the Unified National Health System, were identified. Out of the concepts 61\% were reused and 39\% modified to cover domain requirements. The detailed process of reuse, modification and creation of archetypes is shown. We conclude that, although a major part of demographic and clinical patient data were already represented by existing archetypes, a significant part required major modifications. In this study openEHR proved to be a highly suitable tool in the modelling of complex health data. In combination with LinkEHR-Ed software it offers user-friendly and highly applicable tools, although the complexity built by the vast specifications requires expert networks to define generally excepted clinical models. Finally, this project has pointed out main benefits enclosing high coverage of obstetrics data on the Clinical Knowledge Manager, simple modelling, and wide network and support using openEHR. Moreover, barriers described are enclosing the allocation of clinical content to respective archetypes, as well as stagnant adaption of changes on the Clinical Knowledge Manager leading to redundant efforts in data contribution that need to be addressed in future works.

}, issn = {1532-0480}, doi = {10.1016/j.jbi.2015.04.004}, author = {Pahl, Christina and Zare, Mojtaba and Nilashi, Mehrbakhsh and de Faria Borges, Marco Aur{\'e}lio and Weingaertner, Daniel and Detschew, Vesselin and Supriyanto, Eko and Ibrahim, Othman} } @article {1064, title = {Software to Facilitate Remote Sensing Data Access for Disease Early Warning Systems.}, journal = {Environ Model Softw}, volume = {74}, year = {2015}, month = {2015 Dec 1}, pages = {247-257}, abstract = {

Satellite remote sensing produces an abundance of environmental data that can be used in the study of human health. To support the development of early warning systems for mosquito-borne diseases, we developed an open-source, client based software application to enable the Epidemiological Applications of Spatial Technologies (EASTWeb). Two major design decisions were full automation of the discovery, retrieval and processing of remote sensing data from multiple sources, and making the system easily modifiable in response to changes in data availability and user needs. Key innovations that helped to achieve these goals were the implementation of a software framework for data downloading and the design of a scheduler that tracks the complex dependencies among multiple data processing tasks and makes the system resilient to external errors. EASTWeb has been successfully applied to support forecasting of West Nile virus outbreaks in the United States and malaria epidemics in the Ethiopian highlands.

}, issn = {1364-8152}, doi = {10.1016/j.envsoft.2015.07.006}, author = {Liu, Yi and Hu, Jiameng and Snell-Feikema, Isaiah and VanBemmel, Michael S and Lamsal, Aashis and Wimberly, Michael C} } @article {1063, title = {Solving a Health Information Management Problem. An international success story.}, journal = {World Hosp Health Serv}, volume = {51}, year = {2015}, month = {2015}, pages = {32-5}, abstract = {

The management of health care delivery requires the availability of effective {\textquoteright}information management{\textquoteright} tools based on e-technologies [eHealth]. In developed economies many of these {\textquoteright}tools{\textquoteright} are readily available whereas in Low and Middle Income Countries (LMIC) there is limited access to eHealth technologies and this has been defined as the "digital divide". This paper provides a short introduction to the fundamental understanding of what is meant by information management in health care and how it applies to all social economies. The core of the paper describes the successful implementation of appropriate information management tools in a resource poor environment to manage the HIV/AIDS epidemic and other disease states, in sub-Saharan Africa and how the system has evolved to become the largest open source eHealth project in the world and become the health information infrastructure for several national eHealth economies. The system is known as Open MRS [www.openmrs.org). The continuing successful evolution of the OpenMRS project has permitted its key implementers to define core factors that are the foundations for successful eHealth projects.

}, issn = {1029-0540}, author = {Hannan, Terry J} } @article {1005, title = {A Standards-Based Architecture Proposal for Integrating Patient mHealth Apps to Electronic Health Record Systems.}, journal = {Appl Clin Inform}, volume = {6}, year = {2015}, month = {2015}, pages = {488-505}, abstract = {

BACKGROUND: Mobile health Applications (mHealth Apps) are opening the way to patients{\textquoteright} responsible and active involvement with their own healthcare management. However, apart from Apps allowing patient{\textquoteright}s access to their electronic health records (EHRs), mHealth Apps are currently developed as dedicated "island systems".

OBJECTIVE: Although much work has been done on patient{\textquoteright}s access to EHRs, transfer of information from mHealth Apps to EHR systems is still low. This study proposes a standards-based architecture that can be adopted by mHealth Apps to exchange information with EHRs to support better quality of care.

METHODS: Following the definition of requirements for the EHR/mHealth App information exchange recently proposed, and after reviewing current standards, we designed the architecture for EHR/mHealth App integration. Then, as a case study, we modeled a system based on the proposed architecture aimed to support home monitoring for congestive heart failure patients. We simulated such process using, on the EHR side, OpenMRS, an open source longitudinal EHR and, on the mHealth App side, the iOS platform.

RESULTS: The integration architecture was based on the bi-directional exchange of standard documents (clinical document architecture rel2 - CDA2). In the process, the clinician "prescribes" the home monitoring procedures by creating a CDA2 prescription in the EHR that is sent, encrypted and de-identified, to the mHealth App to create the monitoring calendar. At the scheduled time, the App alerts the patient to start the monitoring. After the measurements are done, the App generates a structured CDA2-compliant monitoring report and sends it to the EHR, thus avoiding local storage.

CONCLUSIONS: The proposed architecture, even if validated only in a simulation environment, represents a step forward in the integration of personal mHealth Apps into the larger health-IT ecosystem, allowing the bi-directional data exchange between patients and healthcare professionals, supporting the patient{\textquoteright}s engagement in self-management and self-care.

}, issn = {1869-0327}, doi = {10.4338/ACI-2014-12-RA-0115}, author = {Marceglia, S and Fontelo, P and Rossi, E and Ackerman, M J} } @article {986, title = {Taking advantage of continuity of care documents to populate a research repository.}, journal = {J Am Med Inform Assoc}, volume = {22}, year = {2015}, month = {2015 Mar}, pages = {370-9}, abstract = {

OBJECTIVE: Clinical data warehouses have accelerated clinical research, but even with available open source tools, there is a high barrier to entry due to the complexity of normalizing and importing data. The Office of the National Coordinator for Health Information Technology{\textquoteright}s Meaningful Use Incentive Program now requires that electronic health record systems produce standardized consolidated clinical document architecture (C-CDA) documents. Here, we leverage this data source to create a low volume standards based import pipeline for the Informatics for Integrating Biology and the Bedside (i2b2) clinical research platform. We validate this approach by creating a small repository at Partners Healthcare automatically from C-CDA documents.

MATERIALS AND METHODS: We designed an i2b2 extension to import C-CDAs into i2b2. It is extensible to other sites with variances in C-CDA format without requiring custom code. We also designed new ontology structures for querying the imported data.

RESULTS: We implemented our methodology at Partners Healthcare, where we developed an adapter to retrieve C-CDAs from Enterprise Services. Our current implementation supports demographics, encounters, problems, and medications. We imported approximately 17 000 clinical observations on 145 patients into i2b2 in about 24 min. We were able to perform i2b2 cohort finding queries and view patient information through SMART apps on the imported data.

DISCUSSION: This low volume import approach can serve small practices with local access to C-CDAs and will allow patient registries to import patient supplied C-CDAs. These components will soon be available open source on the i2b2 wiki.

CONCLUSIONS: Our approach will lower barriers to entry in implementing i2b2 where informatics expertise or data access are limited.

}, keywords = {Biomedical Research, Continuity of Patient Care, Database Management Systems, Databases as Topic, Humans, Information Storage and Retrieval, Meaningful Use, Systems Integration}, issn = {1527-974X}, doi = {10.1136/amiajnl-2014-003040}, author = {Klann, Jeffrey G and Mendis, Michael and Phillips, Lori C and Goodson, Alyssa P and Rocha, Beatriz H and Goldberg, Howard S and Wattanasin, Nich and Murphy, Shawn N} } @article {1007, title = {Towards Standardized Patient Data Exchange: Integrating a FHIR Based API for the Open Medical Record System.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {932}, abstract = {

Interoperability is essential to address limitations caused by the ad hoc implementation of clinical information systems and the distributed nature of modern medical care. The HL7 V2 and V3 standards have played a significant role in ensuring interoperability for healthcare. FHIR is a next generation standard created to address fundamental limitations in HL7 V2 and V3. FHIR is particularly relevant to OpenMRS, an Open Source Medical Record System widely used across emerging economies. FHIR has the potential to allow OpenMRS to move away from a bespoke, application specific API to a standards based API. We describe efforts to design and implement a FHIR based API for the OpenMRS platform. Lessons learned from this effort were used to define long term plans to transition from the legacy OpenMRS API to a FHIR based API that greatly reduces the learning curve for developers and helps enhance adhernce to standards.

}, issn = {0926-9630}, author = {Kasthurirathne, Suranga N and Mamlin, Burke and Grieve, Grahame and Biondich, Paul} } @article {994, title = {Towards the Implementation of an openEHR-based Open Source EHR Platform (a vision paper).}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {45-9}, abstract = {

Healthcare Information Systems are a big business. Currently there is an explosion of EHR/EMR products available on the market, and the best tools are really expensive. Many developing countries and healthcare providers cannot access such tools, and for those who can, there is not a clear strategy for the evolution, scaling, and cost of these electronic health products. The lack of standard-based implementations conduct to the creation of isolated information silos that cannot be exploited (i.e. shared between providers to promote a holistic view of each patient{\textquoteright}s medical history). This paper exposes the main elements behind a Standard-based Open Source EHR Platform that is future-proof and allows to evolve and scale with minimal cost. The proposed EHR Architecture is based on openEHR specifications, adding elements emerged from research and development experiences, leading to a design that can be implemented in any modern technology. Different implementations will be interoperable by design. This Platform will leverage contexts of scarce resources, reusing clinical knowledge, a common set of software components and services.

}, issn = {0926-9630}, author = {Pazos Guti{\'e}rrez, Pablo} } @article {1052, title = {Translational research platforms integrating clinical and omics data: a review of publicly available solutions.}, journal = {Brief Bioinform}, volume = {16}, year = {2015}, month = {2015 Mar}, pages = {280-90}, abstract = {

The rise of personalized medicine and the availability of high-throughput molecular analyses in the context of clinical care have increased the need for adequate tools for translational researchers to manage and explore these data. We reviewed the biomedical literature for translational platforms allowing the management and exploration of clinical and omics data, and identified seven platforms: BRISK, caTRIP, cBio Cancer Portal, G-DOC, iCOD, iDASH and tranSMART. We analyzed these platforms along seven major axes. (1) The community axis regrouped information regarding initiators and funders of the project, as well as availability status and references. (2) We regrouped under the information content axis the nature of the clinical and omics data handled by each system. (3) The privacy management environment axis encompassed functionalities allowing control over data privacy. (4) In the analysis support axis, we detailed the analytical and statistical tools provided by the platforms. We also explored (5) interoperability support and (6) system requirements. The final axis (7) platform support listed the availability of documentation and installation procedures. A large heterogeneity was observed in regard to the capability to manage phenotype information in addition to omics data, their security and interoperability features. The analytical and visualization features strongly depend on the considered platform. Similarly, the availability of the systems is variable. This review aims at providing the reader with the background to choose the platform best suited to their needs. To conclude, we discuss the desiderata for optimal translational research platforms, in terms of privacy, interoperability and technical features.

}, issn = {1477-4054}, doi = {10.1093/bib/bbu006}, author = {Canuel, Vincent and Rance, Bastien and Avillach, Paul and Degoulet, Patrice and Burgun, Anita} } @article {980, title = {Virtualization of Open-Source Secure Web Services to Support Data Exchange in a Pediatric Critical Care Research Network.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Mar 21}, abstract = {

OBJECTIVES: To examine the feasibility of deploying a virtual web service for sharing data within a research network, and to evaluate the impact on data consistency and quality.

MATERIAL AND METHODS: Virtual machines (VMs) encapsulated an open-source, semantically and syntactically interoperable secure web service infrastructure along with a shadow database. The VMs were deployed to 8 Collaborative Pediatric Critical Care Research Network Clinical Centers.

RESULTS: Virtual web services could be deployed in hours. The interoperability of the web services reduced format misalignment from 56\% to 1\% and demonstrated that 99\% of the data consistently transferred using the data dictionary and 1\% needed human curation.

CONCLUSIONS: Use of virtualized open-source secure web service technology could enable direct electronic abstraction of data from hospital databases for research purposes.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv009}, author = {Frey, Lewis J and Sward, Katherine A and Newth, Christopher Jl and Khemani, Robinder G and Cryer, Martin E and Thelen, Julie L and Enriquez, Rene and Shaoyu, Su and Pollack, Murray M and Harrison, Rick E and Meert, Kathleen L and Berg, Robert A and Wessel, David L and Shanley, Thomas P and Dalton, Heidi and Carcillo, Joseph and Jenkins, Tammara L and Dean, J Michael} } @article {1000, title = {Why open source?}, journal = {Cad Saude Publica}, volume = {31}, year = {2015}, month = {2015 Feb}, pages = {221-2}, keywords = {Access to Information, Periodicals as Topic, Reproducibility of Results, Software, Software Design}, issn = {1678-4464}, author = {Carvalho, Marilia S{\'a}} } @article {971, title = {XNAT Central: Open sourcing imaging research data.}, journal = {Neuroimage}, year = {2015}, month = {2015 Jul 2}, abstract = {

XNAT Central is a publicly accessible medical imaging data repository based on the XNAT open-source imaging informatics platform. It hosts a wide variety of research imaging data sets. The primary motivation for creating XNAT Central was to provide a central repository to host and provide access to a wide variety of neuroimaging data. In this capacity, XNAT Central hosts a number of data sets from research labs and investigative efforts from around the world, including the OASIS Brains imaging studies, the NUSDAST study of schizophrenia, and more. Over time, XNAT Central has expanded to include imaging data from many different fields of research, including oncology, orthopedics, cardiology, and animal studies, but continues to emphasize neuroimaging data. Through the use of XNAT{\textquoteright}S DICOM metadata extraction capabilities, XNAT Central provides a searchable repository of imaging data that can be referenced by groups, labs, or individuals working in many different areas of research. The future development of XNAT Central will be geared towards greater ease of use as a reference library of heterogeneous neuroimaging data and associated synthetic data. It will also become a tool for making data available supporting published research and academic articles.

}, issn = {1095-9572}, doi = {10.1016/j.neuroimage.2015.06.076}, author = {Herrick, Rick and Horton, William and Olsen, Timothy and McKay, Michael and Archie, Kevin A and Marcus, Daniel S} } @article {946, title = {An Albanian open source telemedicine platform.}, journal = {Telemed J E Health}, volume = {20}, year = {2014}, month = {2014 Jul}, pages = {673-7}, abstract = {

INTRODUCTION: The use of open source technologies to create collaboration platforms can produce huge advantages with small investment.

MATERIALS AND METHODS: We set up a telemedicine network for a healthcare district with typical centralization issues of developing countries. Our network was built using broadband Internet connection, and the digital divide in rural areas was reduced by means of wireless Internet connection. A software infrastructure was deployed on the network to implement the collaboration platform among different healthcare facilities.

RESULTS: We obtained an integrated platform with modest investment in hardware and operating systems and no costs for application software. Messaging, content management, information sharing, and videoconferencing are among the available services of the infrastructure. Furthermore, open source software is managed and continuously updated by active communities, making it possible to obtain systems similar to commercial ones in terms of quality and reliability.

CONCLUSIONS: As the use of free software in public administration is being widely promoted across the European Union, our experience may provide an example to implement similar infrastructures in the field of healthcare and welfare.

}, issn = {1556-3669}, doi = {10.1089/tmj.2013.0239}, author = {Zangara, Gianluca and Valentino, Francesca and Spinelli, Gaetano and Valenza, Mario and Marcheggiani, Angelo and Di Blasi, Francesco} } @article {932, title = {Automated Detection and Analysis of Ca(2+) Sparks in x-y Image Stacks Using a Thresholding Algorithm Implemented within the Open-Source Image Analysis Platform ImageJ.}, journal = {Biophys J}, volume = {106}, year = {2014}, month = {2014 Feb 4}, pages = {566-76}, abstract = {

Previous studies have used analysis of Ca(2+) sparks extensively to investigate both normal and pathological Ca(2+) regulation in cardiac myocytes. The great majority of these studies used line-scan confocal imaging. In part, this is because the development of open-source software for automatic detection of Ca(2+) sparks in line-scan images has greatly simplified data analysis. A disadvantage of line-scan imaging is that data are collected from a single row of pixels, representing only a small fraction of the cell, and in many instances x-y confocal imaging is preferable. However, the limited availability of software for Ca(2+) spark analysis in two-dimensional x-y image stacks presents an obstacle to its wider application. This study describes the development and characterization of software to enable automatic detection and analysis of Ca(2+) sparks within x-y image stacks, implemented as a plugin within the open-source image analysis platform ImageJ. The program includes methods to enable precise identification of cells within confocal fluorescence images, compensation for changes in background fluorescence, and options that allow exclusion of events based on spatial characteristics.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2013.12.040}, author = {Steele, Elliot M and Steele, Derek S} } @article {1024, title = {CohortExplorer: A Generic Application Programming Interface for Entity Attribute Value Database Schemas.}, journal = {JMIR Med Inform}, volume = {2}, year = {2014}, month = {2014}, pages = {e32}, abstract = {

BACKGROUND: Most electronic data capture (EDC) and electronic data management (EDM) systems developed to collect and store clinical data from participants recruited into studies are based on generic entity-attribute-value (EAV) database schemas which enable rapid and flexible deployment in a range of study designs. The drawback to such schemas is that they are cumbersome to query with structured query language (SQL). The problem increases when researchers involved in multiple studies use multiple electronic data capture and management systems each with variation on the EAV schema.

OBJECTIVE: The aim of this study is to develop a generic application which allows easy and rapid exploration of data and metadata stored under EAV schemas that are organized into a survey format (questionnaires/events, questions, values), in other words, the Clinical Data Interchange Standards Consortium (CDISC) Observational Data Model (ODM).

METHODS: CohortExplorer is written in Perl programming language and uses the concept of SQL abstract which allows the SQL query to be treated like a hash (key-value pairs).

RESULTS: We have developed a tool, CohortExplorer, which once configured for a EAV system will "plug-n-play" with EAV schemas, enabling the easy construction of complex queries through an abstracted interface. To demonstrate the utility of the CohortExplorer system, we show how it can be used with the popular EAV based frameworks; Opal (OBiBa) and REDCap.

CONCLUSIONS: The application is available under a GPL-3+ license at the CPAN website. Currently the application only provides datasource application programming interfaces (APIs) for Opal and REDCap. In the future the application will be available with datasource APIs for all major electronic data capture and management systems such as OpenClinica and LabKey. At present the application is only compatible with EAV systems where the metadata is organized into surveys, questionnaires and events. Further work is needed to make the application compatible with EAV schemas where the metadata is organized into hierarchies such as Informatics for Integrating Biology \& the Bedside (i2b2). A video tutorial demonstrating the application setup, datasource configuration, and search features is available on YouTube. The application source code is available at the GitHub website and the users are encouraged to suggest new features and contribute to the development of APIs for new EAV systems.

}, issn = {2291-9694}, doi = {10.2196/medinform.3339}, author = {Dixit, Abhishek and Dobson, Richard J B} } @article {941, title = {Computational Pathology and Telepathology: SY05-1 TELECYTOLOGY TC AND TELEPATHOLOGY TP IN UNDERSERVED COUNTRIES TOY OR TOOL?}, journal = {Pathology}, volume = {46 Suppl 2}, year = {2014}, month = {2014 Oct}, pages = {S7}, abstract = {

BACKGROUND: Pathologic anatomic practice is an essential part of medical practice even in low-income countries. It is an extraordinarily helpful tool in finding therapeutic decisions, monitoring therapeutic processes and in academic teaching students and residents in understanding aetiology and morphology of infectious and neoplastic diseases. However, all countries worldwide are suffering from a shortage of experienced surgical pathologists providing an adequate service to the clinics. Training pathologists is a time-consuming procedure and it takes more than one decade. Therefore new techniques have to be utilized to overcome the gap of human resources in medical fields in these countries. Telepathology and telecytology may be effective tools to transfer both knowledge and experience to any place in the world with simple technical equipment using the Internet. We evaluate the benefit of TP and TC on three projects, with different educational levels of the local pathologists.

MATERIAL AND APPROACH: In 2002 Cambodian pathologists started off with telepathology using iPath Network as an open-source system. Up to now more than 5600 cases have been submitted to experts. In 2007 a Tanzanian hospital started telepathology and solved more than 3600 cases. In 2010 an Afghan group of medical experts started using TP and submitted more than 1600 cases. The latest 100 cases of each group were analysed with respect to (1) the organs concerned; (2) the diagnostic techniques used such as histology vs cytology; (3) complexity of the diagnostic question; (4) information quality and quantity; (5) diagnostic concordance between primary diagnosis and the experts opinion; and (6) diagnostic accuracy of the experts diagnoses in order to evaluate the benefit of the projects.

RESULTS AND CONCLUSION: Telepathology services are ranging from a triage of diagnostic assessment of benign vs malignant to academic-scientific services including teaching and research facilities. Breast pathology is predominant in Afghanistan, whereas cervix pathology is the leading issue in Tanzania, and in Cambodia soft tissue/bone pathology plays the major role. In more than 50\% cytology was applied in Afghanistan and only 10\% and 5\% in Cambodia and Tanzania respectively. The complexity of diagnostic questions differs from Cambodia using TP for confirmation in most cases, to Tanzania and Afghanistan using TP mostly for primary diagnosis. Diagnostic concordance depending on both the experience of local pathologists and the technical facilities of the laboratory was high in Cambodia, followed by Tanzania and Afghanistan. Diagnostic accuracy corresponding with the quantity and quality of information followed the same pattern. The success of TP projects can be measured by the number of TP sessions and by the sustainability of projects. Our TP/TC projects in those countries with limited resources are effective tools in improving medical health care.

}, keywords = {iPath, open source software, telepathology}, issn = {1465-3931}, doi = {10.1097/01.PAT.0000454068.32934.09}, author = {Stauch, Gerhard and Miringa, Angelica and Raoufi, Rokai and Vathana, Cchut Serey and Hetzmann, Sophia and Hinsch, Nora and Dalquen, Peter and Voelker, Ullrich and Kunze, Dietmar} } @mastersthesis {1197, title = {Design and Development of a Web-Based Clinical Trial Management System}, year = {2014}, month = {05/2014}, school = {Graz University of Technology}, abstract = {Clinical trials represent a compulsory and labour-intensive part in the course of the approval process of new diagnostic or therapeutic measures. Trials are conducted by specialized staff at trial sites such as the Clinical Research Center (CRC), a dedicated facility for Phase I and II clinical trials of the Medical University of Graz. Clinical Trial Management System (CTMS) is a term for enterprise applications, which map the particular processes of trial sites. This work introduces the Phoenix CTMS, a tailored Java web application of medium size, which covers all major processes at the CRC. Its mutli-tiered architecture is based on a Spring/Hibernate/JSF technology stack. While a model-driven approach is used for backend layers, generated artefacts are avoided for the extensive Rich Internet Application (RIA) presentation layer, which utilizes a state-of-the-art JSF component suite. Elaborated user requirements are implemented in multiple modules and range from group-ware features such as web calendars, document management and creation up to complete Electronic Data Capture (EDC) capabilities with input form composition and scripting plus editors for ad-hoc queries, allowing to formulate subject eligibility criteria. Compliance with relevant regulations (Good Clinical Practice, Data Privacy Act) is considered by an exceptional number of data security measures, including: subject de-identification and application-level encryption of data at rest, audit trail and digital signatures, configurable user privileges and host-based access restriction. It is shown how this business-critical application was designed, implemeted and rolled out at the level of commercial software products, while keeping costs minimal. The Phoenix CTMS is realeased under LGPLv2.1, www.phoenixctms.org, ISBN 978-3-200-04054-0. Design and Development of a Web-Based Clinical Trial Management System (PDF Download Available). Available from: https://www.researchgate.net/publication/263412137_Design_and_Development_of_a_Web-Based_Clinical_Trial_Management_System [accessed Nov 05 2017].}, doi = {10.13140/2.1.4306.2723 }, url = {https://www.researchgate.net/publication/263412137_Design_and_Development_of_a_Web-Based_Clinical_Trial_Management_System}, author = {Krenn, Rene} } @article {1044, title = {The development of an application for data privacy by applying an audit repository based on IHE ATNA.}, journal = {Stud Health Technol Inform}, volume = {198}, year = {2014}, month = {2014}, pages = {219-25}, abstract = {

It is necessary to optimize workflows and communication between institutions involved in patients{\textquoteright} treatment to improve quality and efficiency of the German healthcare. To achieve these in the Metropolregion Rhein-Neckar, a personal, cross-institutional patient record (PEPA) is used. Given the immense sensitivity of health-related information saved in the PEPA, it is imperative to obey the data protection regulations in Germany. One important aspect is the logging of access to personal health data and all other safety-related events. For gathering audit information, the IHE profile ATNA can be used, because it provides a flexible and standardized infrastructure. There are already existing solutions for gathering the audit information based on ATNA. In this article one solution (OpenATNA) is evaluated, which uses the method of evaluation defined by Peter Baumgartner. In addition, a user interface for a privacy officer is necessary to support the examination of the audit information. Therefore, we will describe a method to develop an application in Liferay (an OpenSource enterprise portal project) which supports examinations on the gathered audit information.

}, keywords = {Computer Security, Confidentiality, Data Curation, Databases, Factual, electronic health records, Guideline Adherence, Guidelines as Topic, Information Storage and Retrieval, Internationality, Medical Audit, Medical Record Linkage, Software, Software Design}, issn = {0926-9630}, author = {Bresser, Laura and K{\"o}hler, Steffen and Schwaab, Christoph} } @article {1031, title = {Evaluation of software maintain ability with open EHR - a comparison of architectures.}, journal = {Int J Med Inform}, volume = {83}, year = {2014}, month = {2014 Nov}, pages = {849-59}, abstract = {

PURPOSE: To assess whether it is easier to maintain a clinical information system developed using open EHR model driven development versus mainstream methods.

METHODS: A new open source application (GastrOS) has been developed following open EHR{\textquoteright}s multi-level modelling approach using .Net/C$\#$ based on the same requirements of an existing clinically used application developed using Microsoft Visual Basic and Access database. Almost all the domain knowledge was embedded into the software code and data model in the latter. The same domain knowledge has been expressed as a set of open EHR Archetypes in GastrOS. We then introduced eight real-world change requests that had accumulated during live clinical usage, and implemented these in both systems while measuring time for various development tasks and change in software size for each change request.

RESULTS: Overall it took half the time to implement changes in GastrOS. However it was the more difficult application to modify for one change request, suggesting the nature of change is also important. It was not possible to implement changes by modelling only. Comparison of relative measures of time and software size change within each application highlights how architectural differences affected maintain ability across change requests.

CONCLUSIONS: The use of open EHR model driven development can result in better software maintain ability. The degree to which open EHR affects software maintain ability depends on the extent and nature of domain knowledge involved in changes. Although we used relative measures for time and software size, confounding factors could not be totally excluded as a controlled study design was not feasible.

}, keywords = {Data Curation, electronic health records, Information Dissemination, Information Storage and Retrieval, Meaningful Use, Software, Software Design}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2014.07.006}, author = {Atalag, Koray and Yang, Hong Yul and Tempero, Ewan and Warren, James R} } @article {1025, title = {Experience of using an open source clinical trials data management software system in Kenya.}, journal = {BMC Res Notes}, volume = {7}, year = {2014}, month = {2014}, pages = {845}, abstract = {

BACKGROUND: Clinical trials data management (CTDM) remains one of the many challenges in running state of the art trials in resource-poor settings since most trials do not allocate, or have available, sufficient resources for CTDM and because of poor internet connectivity. Open-source software like OpenClinica could be a solution in such scenarios.

FINDINGS: In 2007, the KEMRI-Wellcome Trust Research Programme (KWTRP) adopted OpenClinica (OC) community edition, an open-source software system and we share our experience and lessons learnt since its adoption. We have used OC in three different modes; direct remote data entry from sites through Global System for Mobile Communications (GSM) modems, a centralized data centre approach where all data from paper records were entered at a central location and an off-line approach where data entry was done from a copy of database hosted on a field-site server laptop, then data uploaded to a centralized server later. We have used OC in eleven trials/studies with a cumulative number of participants in excess of 6000. These include large and complex trials, with multiple sites recruiting in different regions of East Africa. In the process, we have developed substantial local capacity through hands-on training and mentorship, which we have now begun to share with other institutions in the region.

CONCLUSIONS: Our experience demonstrates that an open source data management system to manage trials{\textquoteright} data can be utilized to international industry standards in resource-poor countries.

}, issn = {1756-0500}, doi = {10.1186/1756-0500-7-845}, author = {Ngari, Moses M and Waithira, Naomi and Chilengi, Roma and Njuguna, Patricia and Lang, Trudie and Fegan, Greg} } @article {945, title = {ExpertEyes: Open-source, high-definition eyetracking.}, journal = {Behav Res Methods}, year = {2014}, month = {2014 Jun 17}, abstract = {

ExpertEyes is a low-cost, open-source package of hardware and software that is designed to provide portable high-definition eyetracking. The project involves several technological innovations, including portability, high-definition video recording, and multiplatform software support. It was designed for challenging recording environments, and all processing is done offline to allow for optimization of parameter estimation. The pupil and corneal reflection are estimated using a novel forward eye model that simultaneously fits both the pupil and the corneal reflection with full ellipses, addressing a common situation in which the corneal reflection sits at the edge of the pupil and therefore breaks the contour of the ellipse. The accuracy and precision of the system are comparable to or better than what is available in commercial eyetracking systems, with a typical accuracy of less than 0.4{\textdegree} and best accuracy below 0.3{\textdegree}, and with a typical precision (SD method) around 0.3{\textdegree} and best precision below 0.2{\textdegree}. Part of the success of the system comes from a high-resolution eye image. The high image quality results from uncasing common digital camcorders and recording directly to SD cards, which avoids the limitations of the analog NTSC format. The software is freely downloadable, and complete hardware plans are available, along with sources for custom parts.

}, issn = {1554-3528}, doi = {10.3758/s13428-014-0465-z}, author = {Parada, Francisco J and Wyatte, Dean and Yu, Chen and Akavipat, Ruj and Emerick, Brandi and Busey, Thomas} } @article {1023, title = {A framework for integration of heterogeneous medical imaging networks.}, journal = {Open Med Inform J}, volume = {8}, year = {2014}, month = {2014}, pages = {20-32}, abstract = {

Medical imaging is increasing its importance in matters of medical diagnosis and in treatment support. Much is due to computers that have revolutionized medical imaging not only in acquisition process but also in the way it is visualized, stored, exchanged and managed. Picture Archiving and Communication Systems (PACS) is an example of how medical imaging takes advantage of computers. To solve problems of interoperability of PACS and medical imaging equipment, the Digital Imaging and Communications in Medicine (DICOM) standard was defined and widely implemented in current solutions. More recently, the need to exchange medical data between distinct institutions resulted in Integrating the Healthcare Enterprise (IHE) initiative that contains a content profile especially conceived for medical imaging exchange: Cross Enterprise Document Sharing for imaging (XDS-i). Moreover, due to application requirements, many solutions developed private networks to support their services. For instance, some applications support enhanced query and retrieve over DICOM objects metadata. This paper proposes anintegration framework to medical imaging networks that provides protocols interoperability and data federation services. It is an extensible plugin system that supports standard approaches (DICOM and XDS-I), but is also capable of supporting private protocols. The framework is being used in the Dicoogle Open Source PACS.

}, issn = {1874-4311}, doi = {10.2174/1874431101408010020}, author = {Viana-Ferreira, Carlos and Ribeiro, Lu{\'\i}s S and Costa, Carlos} } @article {954, title = {Free/Libre open source software in health care: a review.}, journal = {Healthc Inform Res}, volume = {20}, year = {2014}, month = {2014 Jan}, pages = {11-22}, abstract = {

OBJECTIVES: To assess the current state of the art and the contribution of Free/Libre Open Source Software in health care (FLOSS-HC).

METHODS: The review is based on a narrative review of the scientific literature as well as sources in the context of FLOSS-HC available through the Internet. All relevant available sources have been integrated into the MedFLOSS database and are freely available to the community.

RESULTS: The literature review reveals that publications about FLOSS-HC are scarce. The largest part of information about FLOSS-HC is available on dedicated websites and not in the academic literature. There are currently FLOSS alternatives available for nearly every specialty in health care. Maturity and quality varies considerably and there is little information available on the percentage of systems that are actually used in health care delivery.

CONCLUSIONS: The global impact of FLOSS-HC is still very limited and no figures on the penetration and usage of FLOSS-HC are available. However, there has been a considerable growth in the last 5 to 10 years. While there where only few systems available a decade ago, in the meantime many systems got available (e.g., more than 300 in the MedFLOSS database). While FLOSS concepts play an important role in most IT related sectors (e.g., telecommunications, embedded devices) the healthcare industry is lagging behind this trend.

}, issn = {2093-3681}, doi = {10.4258/hir.2014.20.1.11}, author = {Karopka, Thomas and Schmuhl, Holger and Demski, Hans} } @article {1051, title = {High dimensional biological data retrieval optimization with NoSQL technology.}, journal = {BMC Genomics}, volume = {15 Suppl 8}, year = {2014}, month = {2014}, pages = {S3}, abstract = {

BACKGROUND: High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is supported in data warehouses such as tranSMART, when querying relational databases for hundreds of different patient gene expression records queries are slow due to poor performance. Non-relational data models, such as the key-value model implemented in NoSQL databases, hold promise to be more performant solutions. Our motivation is to improve the performance of the tranSMART data warehouse with a view to supporting Next Generation Sequencing data.

RESULTS: In this paper we introduce a new data model better suited for high-dimensional data storage and querying, optimized for database scalability and performance. We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google{\textquoteright}s BigTable storage system. An experimental performance comparison was carried out against the traditional relational data model implemented in both MySQL Cluster and MongoDB, using a large publicly available transcriptomic data set taken from NCBI GEO concerning Multiple Myeloma. Our new key-value data model implemented on HBase exhibits an average 5.24-fold increase in high-dimensional biological data query performance compared to the relational model implemented on MySQL Cluster, and an average 6.47-fold increase on query performance on MongoDB.

CONCLUSIONS: The performance evaluation found that the new key-value data model, in particular its implementation in HBase, outperforms the relational model currently implemented in tranSMART. We propose that NoSQL technology holds great promise for large-scale data management, in particular for high-dimensional biological data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new data model as a basis for migrating tranSMART{\textquoteright}s implementation to a more scalable solution for Big Data.

}, keywords = {Database Management Systems, Databases, Genetic, High-Throughput Nucleotide Sequencing, Humans, Information Storage and Retrieval, Medical Informatics, Multiple Myeloma, Oligonucleotide Array Sequence Analysis, Transcriptome}, issn = {1471-2164}, doi = {10.1186/1471-2164-15-S8-S3}, author = {Wang, Shicai and Pandis, Ioannis and Wu, Chao and He, Sijin and Johnson, David and Emam, Ibrahim and Guitton, Florian and Guo, Yike} } @article {1003, title = {Innovative approaches to clinical data management in resource limited settings using open-source technologies.}, journal = {PLoS Negl Trop Dis}, volume = {8}, year = {2014}, month = {2014 Sep}, pages = {e3134}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0003134}, author = {Omollo, Raymond and Ochieng, Michael and Mutinda, Brian and Omollo, Truphosa and Owiti, Rhoda and Okeyo, Seth and Wasunna, Monique and Edwards, Tansy} } @article {1033, title = {Making cytological diagnoses on digital images using the iPath network.}, journal = {Acta Cytol}, volume = {58}, year = {2014}, month = {2014}, pages = {453-60}, abstract = {

BACKGROUND: The iPath telemedicine platform Basel is mainly used for histological and cytological consultations, but also serves as a valuable learning tool.

AIM: To study the level of accuracy in making diagnoses based on still images achieved by experienced cytopathologists, to identify limiting factors, and to provide a cytological image series as a learning set.

METHOD: Images from 167 consecutive cytological specimens of different origin were uploaded on the iPath platform and evaluated by four cytopathologists. Only wet-fixed and well-stained specimens were used. The consultants made specific diagnoses and categorized each as benign, suspicious or malignant.

RESULTS: For all consultants, specificity and sensitivity regarding categorized diagnoses were 83-92 and 85-93\%, respectively; the overall accuracy was 88-90\%. The interobserver agreement was substantial (κ = 0.791). The lowest rate of concordance was achieved in urine and bladder washings and in the identification of benign lesions.

CONCLUSION: Using a digital image set for diagnostic purposes implies that even under optimal conditions the accuracy rate will not exceed to 80-90\%, mainly because of lacking supportive immunocytochemical or molecular tests. This limitation does not disqualify digital images for teleconsulting or as a learning aid. The series of images used for the study are open to the public at http://pathorama.wordpress.com/extragenital-cytology-2013/.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, Computers, Handheld, Cytodiagnosis, Diagnosis, Differential, Female, Humans, Hyperplasia, Infant, Male, Metaplasia, Middle Aged, Neoplasms, Observer Variation, Reproducibility of Results, Sensitivity and Specificity, Telemedicine}, issn = {0001-5547}, doi = {10.1159/000369241}, author = {Dalquen, Peter and Savic Prince, Spasenija and Spieler, Peter and Kunze, Dietmar and Neumann, Heinrich and Eppenberger-Castori, Serenella and Adams, Heiner and Glatz, Katharina and Bubendorf, Lukas} } @article {931, title = {Managing multicentre clinical trials with open source.}, journal = {Inform Health Soc Care}, volume = {39}, year = {2014}, month = {2014 Mar}, pages = {67-80}, abstract = {

Background: Multicentre clinical trials are challenged by high administrative burden, data management pitfalls and costs. This leads to a reduced enthusiasm and commitment of the physicians involved and thus to a reluctance in conducting multicentre clinical trials. Objective: The purpose of this study was to develop a web-based open source platform to support a multi-centre clinical trial. Methods: We developed on Drupal, an open source software distributed under the terms of the General Public License, a web-based, multi-centre clinical trial management system with the design science research approach. Results: This system was evaluated by user-testing and well supported several completed and on-going clinical trials and is available for free download. Conclusion: Open source clinical trial management systems are capable in supporting multi-centre clinical trials by enhancing efficiency, quality of data management and collaboration.

}, issn = {1753-8165}, doi = {10.3109/17538157.2013.812647}, author = {Raptis, Dimitri Aristotle and Mettler, Tobias and Fischer, Michael Alexander and Patak, Michael and Lesurtel, Mickael and Eshmuminov, Dilmurodjon and de Rougemont, Olivier and Graf, Rolf and Clavien, Pierre-Alain and Breitenstein, Stefan} } @article {1096, title = {Medical Subject Headings (MeSH) for indexing and retrieving open-source healthcare data.}, journal = {Stud Health Technol Inform}, volume = {202}, year = {2014}, month = {2014}, pages = {157-60}, abstract = {

The US federal government initiated the Open Government Directive where federal agencies are required to publish high value datasets so that they are available to the public. Data.gov and the community site Healthdata.gov were initiated to disperse such datasets. However, data searches and retrieval for these sites are keyword driven and severely limited in performance. The purpose of this paper is to address the issue of extracting relevant open-source data by proposing a method of adopting the MeSH framework for indexing and data retrieval. A pilot study was conducted to compare the performance of traditional keywords to MeSH terms for retrieving relevant open-source datasets related to "mortality". The MeSH framework resulted in greater sensitivity with comparable specificity to the keyword search. MeSH showed promise as a method for indexing and retrieving data, yet future research should conduct a larger scale evaluation of the performance of the MeSH framework for retrieving relevant open-source healthcare datasets.

}, issn = {0926-9630}, author = {Marc, David T and Khairat, Saif S} } @article {944, title = {Open source EMR software: Profiling, insights and hands-on analysis.}, journal = {Comput Methods Programs Biomed}, year = {2014}, month = {2014 Jul 17}, abstract = {

BACKGROUND: The use of open source software in health informatics is increasingly advocated by authors in the literature. Although there is no clear evidence of the superiority of the current open source applications in the healthcare field, the number of available open source applications online is growing and they are gaining greater prominence. This repertoire of open source options is of a great value for any future-planner interested in adopting an electronic medical/health record system, whether selecting an existent application or building a new one. The following questions arise. How do the available open source options compare to each other with respect to functionality, usability and security? Can an implementer of an open source application find sufficient support both as a user and as a developer, and to what extent? Does the available literature provide adequate answers to such questions? This review attempts to shed some light on these aspects.

OBJECTIVE: The objective of this study is to provide more comprehensive guidance from an implementer perspective toward the available alternatives of open source healthcare software, particularly in the field of electronic medical/health records.

METHODS: The design of this study is twofold. In the first part, we profile the published literature on a sample of existent and active open source software in the healthcare area. The purpose of this part is to provide a summary of the available guides and studies relative to the sampled systems, and to identify any gaps in the published literature with respect to our research questions. In the second part, we investigate those alternative systems relative to a set of metrics, by actually installing the software and reporting a hands-on experience of the installation process, usability, as well as other factors.

RESULTS: The literature covers many aspects of open source software implementation and utilization in healthcare practice. Roughly, those aspects could be distilled into a basic taxonomy, making the literature landscape more perceivable. Nevertheless, the surveyed articles fall short of fulfilling the targeted objective of providing clear reference to potential implementers. The hands-on study contributed a more detailed comparative guide relative to our set of assessment measures. Overall, no system seems to satisfy an industry-standard measure, particularly in security and interoperability. The systems, as software applications, feel similar from a usability perspective and share a common set of functionality, though they vary considerably in community support and activity.

CONCLUSION: More detailed analysis of popular open source software can benefit the potential implementers of electronic health/medical records systems. The number of examined systems and the measures by which to compare them vary across studies, but still rewarding insights start to emerge. Our work is one step toward that goal. Our overall conclusion is that open source options in the medical field are still far behind the highly acknowledged open source products in other domains, e.g. operating systems market share.

}, issn = {1872-7565}, doi = {10.1016/j.cmpb.2014.07.002}, author = {Kiah, M L M and Haiqi, Ahmed and Zaidan, B B and Zaidan, A A} } @article {943, title = {Open-source electronic data capture system offered increased accuracy and cost-effectiveness compared with paper methods in Africa.}, journal = {J Clin Epidemiol}, year = {2014}, month = {2014 Aug 15}, abstract = {

OBJECTIVES: Existing electronic data capture options are often financially unfeasible in resource-poor settings or difficult to support technically in the field. To help facilitate large-scale multicenter studies in sub-Saharan Africa, the African Partnership for Chronic Disease Research (APCDR) has developed an open-source electronic questionnaire (EQ).

STUDY DESIGN AND SETTING: To assess its relative validity, we compared the EQ against traditional pen-and-paper methods using 200 randomized interviews conducted in an ongoing type 2 diabetes case-control study in South Africa.

RESULTS: During its 3-month validation, the EQ had a lower frequency of errors (EQ, 0.17 errors per 100 questions; paper, 0.73 errors per 100 questions; P-value <=0.001), and a lower monetary cost per correctly entered question, compared with the pen-and-paper method. We found no marked difference in the average duration of the interview between methods (EQ, 5.4~minutes; paper, 5.6~minutes).

CONCLUSION: This validation study suggests that the EQ may offer increased accuracy, similar interview duration, and increased cost-effectiveness compared with paper-based data collection methods. The APCDR EQ software is freely available (https://github.com/apcdr/questionnaire).

}, issn = {1878-5921}, doi = {10.1016/j.jclinepi.2014.06.012}, author = {Dillon, David G and Pirie, Fraser and Pomilla, Cristina and Sandhu, Manjinder S and Motala, Ayesha A and Young, Elizabeth H} } @article {1004, title = {An open-source, mobile-friendly search engine for public medical knowledge.}, journal = {Stud Health Technol Inform}, volume = {205}, year = {2014}, month = {2014}, pages = {358-62}, abstract = {

The World Wide Web has become an important source of information for medical practitioners. To complement the capabilities of currently available web search engines we developed FindMeEvidence, an open-source, mobile-friendly medical search engine. In a preliminary evaluation, the quality of results from FindMeEvidence proved to be competitive with those from TRIP Database, an established, closed-source search engine for evidence-based medicine.

}, keywords = {Computers, Handheld, Consumer Health Information, Data Mining, Evidence-Based Medicine, Information Dissemination, Internet, Search Engine, Software, Software Design, User-Computer Interface}, issn = {0926-9630}, author = {Samwald, Matthias and Hanbury, Allan} } @article {942, title = {Plug-and-play Integration of dual-model based Knowledge Artefacts into an Open Source Ehr System.}, journal = {Stud Health Technol Inform}, volume = {205}, year = {2014}, month = {2014}, pages = {101-5}, abstract = {

In this paper we present our experiences with extending an existing approach for an archetype-compliant collection and export of data according to the openEHR specifications within the open source EHR system OpenMRS. It allows an automatic generation of forms from templates, which were introduced by openEHR as an extension of the dual-model approach. Data entered in these forms can be exported in form of standardized EHR extracts. The use of templates allowed us to solve problems reported for the original archetype-based version of the approach, which were caused by the high optionality within archetypes.

}, issn = {0926-9630}, author = {Krexner, Rabea and Duftschmid, Georg} } @article {1027, title = {Possible combinations of electronic data capture and randomization systems. principles and the realization with RANDI2 and OpenClinica.}, journal = {Methods Inf Med}, volume = {53}, year = {2014}, month = {2014}, pages = {202-7}, abstract = {

BACKGROUND: Clinical trials (CT) are in a wider sense experiments to prove and establish clinical benefit of treatments. Nowadays electronic data capture systems (EDCS) are used more often bringing a better data management and higher data quality into clinical practice. Also electronic systems for the randomization are used to assign the patients to the treatments.

OBJECTIVES: If the mentioned randomization system (RS) and EDCS are used, possibly identical data are collected in both, especially by stratified randomization. This separated data storage may lead to data inconsistency and in general data samples have to be aligned. The article discusses solutions to combine RS and EDCS. In detail one approach is realized and introduced.

METHODS: Different possible settings of combination of EDCS and RS are determined and the pros and cons for each solution are worked out. For the combination of two independent applications the necessary interfaces for the communication are defined. Thereby, existing standards are considered. An example realization is implemented with the help of open-source applications and state-of-the-art software development procedures.

RESULTS: Three possibilities of separate usage or combination of EDCS and RS are presented and assessed: i) the complete independent usage of both systems; ii) realization of one system with both functions; and iii) two separate systems, which communicate via defined interfaces. In addition a realization of our preferred approach, the combination of both systems, is introduced using the open source tools RANDI2 and OpenClinica.

CONCLUSION: The advantage of a flexible independent development of EDCS and RS is shown based on the fact that these tool are very different featured. In our opinion the combination of both systems via defined interfaces fulfills the requirements of randomization and electronic data capture and is feasible in practice. In addition, the use of such a setting can reduce the training costs and the error-prone duplicated data entry.

}, keywords = {Automatic Data Processing, Computer Communication Networks, Humans, Medical Informatics Computing, Medical Records Systems, Computerized, Random Allocation, Randomized Controlled Trials as Topic, Software Design}, issn = {0026-1270}, doi = {10.3414/ME13-01-0074}, author = {Schrimpf, D and Haag, M and Pilz, L R} } @article {1026, title = {Simplifying electronic data capture in clinical trials: workflow embedded image and biosignal file integration and analysis via web services.}, journal = {J Digit Imaging}, volume = {27}, year = {2014}, month = {2014 Oct}, pages = {571-80}, abstract = {

To improve data quality and save cost, clinical trials are nowadays performed using electronic data capture systems (EDCS) providing electronic case report forms (eCRF) instead of paper-based CRFs. However, such EDCS are insufficiently integrated into the medical workflow and lack in interfacing with other study-related systems. In addition, most EDCS are unable to handle image and biosignal data, although electrocardiography (EGC, as example for one-dimensional (1D) data), ultrasound (2D data), or magnetic resonance imaging (3D data) have been established as surrogate endpoints in clinical trials. In this paper, an integrated workflow based on OpenClinica, one of the world{\textquoteright}s largest EDCS, is presented. Our approach consists of three components for (i) sharing of study metadata, (ii) integration of large volume data into eCRFs, and (iii) automatic image and biosignal analysis. In all components, metadata is transferred between systems using web services and JavaScript, and binary large objects (BLOBs) are sent via the secure file transfer protocol and hypertext transfer protocol. We applied the close-looped workflow in a multicenter study, where long term (7~days/24~h) Holter ECG monitoring is acquired on subjects with diabetes. Study metadata is automatically transferred into OpenClinica, the 4~GB BLOBs are seamlessly integrated into the eCRF, automatically processed, and the results of signal analysis are written back into the eCRF immediately.

}, keywords = {Algorithms, Automatic Data Processing, Clinical Trials as Topic, Database Management Systems, Humans, Image Processing, Computer-Assisted, Information Storage and Retrieval, Internet, Medical Records Systems, Computerized, Systems Integration, Workflow}, issn = {1618-727X}, doi = {10.1007/s10278-014-9694-z}, author = {Haak, Daniel and Samsel, Christian and Gehlen, Johan and Jonas, Stephan and Deserno, Thomas M} } @article {1019, title = {Strengthening district-based health reporting through the district health management information software system: the Ugandan experience.}, journal = {BMC Med Inform Decis Mak}, volume = {14}, year = {2014}, month = {2014}, pages = {40}, abstract = {

BACKGROUND: Untimely, incomplete and inaccurate data are common challenges in planning, monitoring and evaluation of health sector performance, and health service delivery in many sub-Saharan African settings. We document Uganda{\textquoteright}s experience in strengthening routine health data reporting through the roll-out of the District Health Management Information Software System version 2 (DHIS2).

METHODS: DHIS2 was adopted at the national level in January 2011. The system was initially piloted in 4 districts, before it was rolled out to all the 112 districts by July 2012. As part of the roll-out process, 35 training workshops targeting 972 users were conducted throughout the country. Those trained included Records Assistants (168, 17.3\%), District Health Officers (112, 11.5\%), Health Management Information System Focal Persons (HMIS-FPs) (112, 11.5\%), District Biostatisticians (107, 11\%) and other health workers (473, 48.7\%). To assess improvements in health reporting, we compared data on completeness and timeliness of outpatient and inpatient reporting for the period before (2011/12) and after (2012/13) the introduction of DHIS2. We reviewed data on the reporting of selected health service coverage indicators as a proxy for improved health reporting, and documented implementation challenges and lessons learned during the DHIS2 roll-out process.

RESULTS: Completeness of outpatient reporting increased from 36.3\% in 2011/12 to 85.3\% in 2012/13 while timeliness of outpatient reporting increased from 22.4\% to 77.6\%. Similarly, completeness of inpatient reporting increased from 20.6\% to 57.9\% while timeliness of inpatient reporting increased from 22.5\% to 75.6\%. There was increased reporting on selected health coverage indicators (e.g. the reporting of one-year old children who were immunized with three doses of pentavelent vaccine increased from 57\% in 2011/12 to 87\% in 2012/13). Implementation challenges included limited access to computers and internet (34\%), inadequate technical support (23\%) and limited worker force (18\%).

CONCLUSION: Implementation of DHIS2 resulted in improved timeliness and completeness in reporting of routine outpatient, inpatient and health service usage data from the district to the national level. Continued onsite support supervision and mentorship and additional system/infrastructure enhancements, including internet connectivity, are needed to further enhance the performance of DHIS2.

}, keywords = {Health Information Management, Health information systems, Health Services, Humans, Inpatients, Outpatients, Uganda}, issn = {1472-6947}, doi = {10.1186/1472-6947-14-40}, author = {Kiberu, Vincent Micheal and Matovu, Joseph K B and Makumbi, Fredrick and Kyozira, Carol and Mukooyo, Eddie and Wanyenze, Rhoda K} } @article {949, title = {Surgical planning of Isshiki type I thyroplasty using an open-source Digital Imaging and Communication in Medicine viewer OsiriX.}, journal = {Acta Otolaryngol}, volume = {134}, year = {2014}, month = {2014 Jun}, pages = {620-5}, abstract = {

CONCLUSION: Preoperative surgical planning of Isshiki type I thyroplasty with the Digital Imaging and Communication in Medicine (DICOM) viewer OsiriX can be used for strategic and predictable type I thyroplasty.

OBJECTIVES: The aim of this study was to determine the efficacy of the preoperative planning of type I thyroplasty using the DICOM viewer OsiriX.

METHODS: Five patients with unilateral vocal cord paralysis and severe breathy dysphonia were included in this study. Multidetector computed tomography (CT) DICOM data were obtained and breath holding was performed during image acquisition. Using three-dimensional multiplanar reconstruction, we outlined the optimal location for a window. Type I thyroplasty was performed using Isshiki{\textquoteright}s original method, and only the placement of the window was decided according to the preoperative simulation point. To verify the advantages of this method, we compared our data with the previous data for total operation time and voice quality at 3 months after the operation without the DICOM viewer planning.

RESULTS: All patients are free from dysphonia and their glottic closures have resolved satisfactorily. Postoperative CT revealed that appropriate implant positioning resulted in successful surgical intervention. The comparison of total operation time showed that with the new method, operation duration was shortened by 12 min.

}, issn = {1651-2251}, doi = {10.3109/00016489.2014.880796}, author = {Hara, Hirotaka and Hori, Takeshi and Sugahara, Kazuma and Yamashita, Hiroshi} } @article {1034, title = {Telecytological diagnosis of space-occupying lesions of the liver.}, journal = {Acta Cytol}, volume = {58}, year = {2014}, month = {2014}, pages = {174-81}, abstract = {

OBJECTIVE: In this study, the efficiency of telemedical consulting with regard to fine needle aspirates from space-occupying lesions (SOLs) of the liver is investigated for the first time.

STUDY DESIGN: The study includes fine needle aspirations from 62 patients, 33 with hepatocellular carcinoma (HCC) and 29 with non-hepatic tumors. Using the Internet-based iPath system, the initial pathologist submitted 1-8 images from smears and cell block sections. One consultant assessed the cytological and another one the histological images. Both made their diagnoses independent of each other. A final diagnosis was made by immunochemistry of cell block sections. The cytological images were analyzed retrospectively for the occurrence of the most typical HCC indicators. The number of these indicators was related to the initial diagnoses of the three pathologists, and possible reasons for diagnostic errors were analyzed based on this analysis.

RESULTS: The accuracy of the preliminary telemedical diagnoses regarding HCC was 82.0\% for the cytological images and 87.7\% for the histological images. Most of the false diagnoses occurred in tumors with unusual cytological and histological patterns.

CONCLUSIONS: Telemedical consulting is a valuable tool to obtain a second opinion. However, for improvement of the diagnosis of HCC, supplementary immunochemical tests are necessary.

}, keywords = {Adult, Aged, Aged, 80 and over, Carcinoma, Hepatocellular, Female, Humans, Image-Guided Biopsy, Liver, Liver Neoplasms, Male, Middle Aged, Retrospective Studies, Telemedicine}, issn = {0001-5547}, doi = {10.1159/000357195}, author = {Mostafa, Mohammad Golam and Dalquen, Peter and Kunze, Dietmar and Terracciano, Luigi} } @article {1020, title = {Towards an intelligent decision support system for public health surveillance - a qualitative analysis of information needs.}, journal = {Stud Health Technol Inform}, volume = {202}, year = {2014}, month = {2014}, pages = {44-7}, abstract = {

Public health information systems are often implemented considering the functionalities and requirements established by administrative staff or researchers, but sometimes ignoring the particular needs of decision makers. This paper describes a proposal to support the design of a Decision Support System for Public Health Surveillance in Colombia, by conducting a qualitative study to identify the real needs of people involved in decision making processes. Based on the study results, an intelligent computational component that supports Data Analysis Automation, Prediction of future scenarios and the identification of new Behavioral Patterns is proposed. The component will be implemented using the Case Based Reasoning methodology, which will be integrated as a new component of the Open Source DHIS2 Platform, enabling public health decision-making.

}, issn = {0926-9630}, author = {Mera, Maritza and Gonz{\'a}lez, Carolina and L{\'o}pez, Diego M} } @article {1001, title = {tranSMART: An Open Source Knowledge Management and High Content Data Analytics Platform.}, journal = {AMIA Jt Summits Transl Sci Proc}, volume = {2014}, year = {2014}, month = {2014}, pages = {96-101}, abstract = {

The tranSMART knowledge management and high-content analysis platform is a flexible software framework featuring novel research capabilities. It enables analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research. tranSMART bridges the prolific world of basic science and clinical practice data at the point of care by merging multiple types of data from disparate sources into a common environment. The application supports data harmonization and integration with analytical pipelines. The application code was released into the open source community in January 2012, with 32 instances in operation. tranSMART{\textquoteright}s extensible data model and corresponding data integration processes, rapid data analysis features, and open source nature make it an indispensable tool in translational or clinical research.

}, issn = {2153-4063}, author = {Scheufele, Elisabeth and Aronzon, Dina and Coopersmith, Robert and McDuffie, Michael T and Kapoor, Manish and Uhrich, Christopher A and Avitabile, Jean E and Liu, Jinlei and Housman, Dan and Palchuk, Matvey B} } @article {947, title = {A user-friendly, open-source tool to project impact and cost of diagnostic tests for tuberculosis.}, journal = {Elife}, year = {2014}, month = {2014 Jun 4}, pages = {e02565}, abstract = {

Most existing models of infectious diseases, including tuberculosis (TB), do not allow end-users to customize results to local conditions. We created a dynamic transmission model to project TB incidence, TB mortality, multidrug-resistant (MDR) TB prevalence, and incremental costs over five years after scale-up of nine alternative diagnostic strategies including combinations of sputum smear microscopy, Xpert MTB/RIF, microcolony-based culture, and same-day diagnosis. We developed a corresponding web-based interface that allows users to specify local costs and epidemiology. Full model code - including the ability to change any input parameter - is also included. The impact of improved diagnostic testing was greater for mortality and MDR-TB prevalence than TB incidence, and was maximized in high-incidence, low-HIV settings. More costly interventions generally had greater impact. In settings with little capacity for up-front investment, same-day microscopy had greatest impact on TB incidence and became cost-saving within five years if feasible to deliver at $10/test. In settings where more initial investment was possible, population-level scale-up of either Xpert MTB/RIF or microcolony-based culture offered substantially greater benefits, often averting ten times more TB cases than narrowly-targeted diagnostic strategies at minimal incremental long-term cost. Where containing MDR-TB is the overriding concern, Xpert for smear-positives has reasonable impact on MDR-TB incidence, but at substantial price and little impact on overall TB incidence and mortality. This novel, user-friendly modeling framework improves decision-makers{\textquoteright} ability to evaluate the impact of TB diagnostic strategies, accounting for local conditions.

}, issn = {2050-084X}, doi = {10.7554/eLife.02565}, author = {Dowdy, David W and Andrews, Jason R and Dodd, Peter J and Gilman, Robert H} } @article {948, title = {Utilization of open source electronic health record around the world: A systematic review.}, journal = {J Res Med Sci}, volume = {19}, year = {2014}, month = {2014 Jan}, pages = {57-64}, abstract = {

Many projects on developing Electronic Health Record (EHR) systems have been carried out in many countries. The current study was conducted to review the published data on the utilization of open source EHR systems in different countries all over the world. Using free text and keyword search techniques, six bibliographic databases were searched for related articles. The identified papers were screened and reviewed during a string of stages for the irrelevancy and validity. The findings showed that open source EHRs have been wildly used by source limited regions in all continents, especially in Sub-Saharan Africa and South America. It would create opportunities to improve national healthcare level especially in developing countries with minimal financial resources. Open source technology is a solution to overcome the problems of high-costs and inflexibility associated with the proprietary health information systems.

}, issn = {1735-1995}, author = {Aminpour, Farzaneh and Sadoughi, Farahnaz and Ahamdi, Maryam} } @article {1009, title = {AccessMRS: integrating OpenMRS with smart forms on Android.}, journal = {Stud Health Technol Inform}, volume = {192}, year = {2013}, month = {2013}, pages = {866-70}, abstract = {

We present a new open-source Android application, AccessMRS, for interfacing with an electronic medical record system (OpenMRS) and loading {\textquoteright}Smart Forms{\textquoteright} on a mobile device. AccessMRS functions as a patient-centered interface for viewing OpenMRS data; managing patient information in reminders, task lists, and previous encounters; and launching patient-specific {\textquoteright}Smart Forms{\textquoteright} for electronic data collection and dissemination of health information. We present AccessMRS in the context of related software applications we developed to serve Community Health Workers, including AccessInfo, AccessAdmin, AccessMaps, and AccessForms. The specific features and design of AccessMRS are detailed in relationship to the requirements that drove development: the workflows of the Kenyan Ministry of Health Community Health Volunteers (CHVs) supported by the AMPATH Primary Health Care Program. Specifically, AccessMRS was designed to improve the quality of community-based Maternal and Child Health services delivered by CHVs in Kosirai Division. AccessMRS is currently in use by more than 80 CHVs in Kenya and undergoing formal assessment of acceptability, effectiveness, and cost.

}, keywords = {electronic health records, Forms and Records Control, Information Storage and Retrieval, Medical Record Linkage, Mobile Applications, Programming Languages, Software Design, Systems Integration, User-Computer Interface}, issn = {0926-9630}, author = {Fazen, Louis E and Chemwolo, Benjamin T and Songok, Julia J and Ruhl, Laura J and Kipkoech, Carolyne and Green, James M and Ikemeri, Justus E and Christoffersen-Deb, Astrid} } @conference {1081, title = {Analyzing open-source and commercial EHR solutions from an international perspective}, booktitle = {e-Health Networking, Applications Services (Healthcom), 2013 IEEE 15th International Conference on}, year = {2013}, month = {Oct}, keywords = {African continent, Allscripts Professional, Asia, CareTracker, commercial, commercial EHR solutions, commercial electronic health records, Companies, eclinicalworks, economic resources, EHR, electronic health records systems market, Electronic medical records, healthcare systems, Hospitals, HOSxp, implementation, international barrier, international perspective, interoperable EHR platform, Latin America, medical information systems, open source software, open systems, open-source, open-source EHR systems, open-source electronic health records, open-source solutions, OpenEMR, OpenVistA, public domain software, search engines, US companies, wealthiest countries}, doi = {10.1109/HealthCom.2013.6720708}, author = {de la Torre, I. and Martinez, B. and Lopez-Coronado, M.} } @article {860, title = {A case study of private{\textendash}public collaboration for humanitarian free and open source disaster management software deployment}, journal = {Decision Support Systems}, volume = {55}, year = {2013}, pages = {1 - 11}, abstract = {Abstract Free and open source software (FOSS) has been increasingly adopted for humanitarian purpose worldwide, yet the factors for successful deployment of humanitarian \{FOSS\} in a disaster situation remain largely unexplored. Drawing upon the Technology{\textendash}Organization{\textendash}Environment (TOE) framework, this study identifies the key issues in collaborative deployment of \{FOSS\} for humanitarian relief operations. The research further elaborates the key research issues by adopting a case study approach in which qualitative data were gathered from key informants from both private and public sectors. The results suggest that task{\textendash}technology fit, expertise management, and inter-organizational relationship management play critical roles in humanitarian \{FOSS\} deployment.}, keywords = {Private{\textendash}public partnership}, issn = {0167-9236}, doi = {http://dx.doi.org/10.1016/j.dss.2012.10.030}, url = {http://www.sciencedirect.com/science/article/pii/S0167923612002850}, author = {Jessica P. Li and Rui Chen and JinKyu Lee and H. Raghav Rao} } @article {856, title = {Clinician-led development of electronic health records systems.}, journal = {Stud Health Technol Inform}, volume = {183}, year = {2013}, month = {2013}, pages = {3-8}, abstract = {

The open source cityEHR system was evaluated as a toolkit for clinician-led development of an Electronic Health Record for management of patients in the Ponseti clinic of a major London hospital. As a toolkit, it was found that the ontology-driven approach of cityEHR was too complex for clinicians to use. The toolkit was refined to use more familiar spreadsheet s to represent the ontology and was then used successfully to create an effective clinical system, generated automatically from the information model.

}, issn = {0926-9630}, author = {Chelsom, John and Ahluwalia, Raju and Dogar, Naveed} } @article {848, title = {A common type system for clinical natural language processing.}, journal = {J Biomed Semantics}, volume = {4}, year = {2013}, month = {2013}, pages = {1}, abstract = {

UNLABELLED:

BACKGROUND: One challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information in clinical text to a standard representation that is comparable and interoperable. Information may be processed and shared when a type system specifies the allowable data structures. Therefore, we aim to define a common type system for clinical NLP that enables interoperability between structured and unstructured data generated in different clinical settings.

RESULTS: We describe a common type system for clinical NLP that has an end target of deep semantics based on Clinical Element Models (CEMs), thus interoperating with structured data and accommodating diverse NLP approaches. The type system has been implemented in UIMA (Unstructured Information Management Architecture) and is fully functional in a popular open-source clinical NLP system, cTAKES (clinical Text Analysis and Knowledge Extraction System) versions 2.0 and later.

CONCLUSIONS: We have created a type system that targets deep semantics, thereby allowing for NLP systems to encapsulate knowledge from text and share it alongside heterogenous clinical data sources. Rather than surface semantics that are typically the end product of NLP algorithms, CEM-based semantics explicitly build in deep clinical semantics as the point of interoperability with more structured data types.

}, issn = {2041-1480}, doi = {10.1186/2041-1480-4-1}, author = {Wu, Stephen T and Kaggal, Vinod C and Dligach, Dmitriy and Masanz, James J and Chen, Pei and Becker, Lee and Chapman, Wendy W and Savova, Guergana K and Liu, Hongfang and Chute, Christopher G} } @article {890, title = {Comparison of femoral tunnel widening between outside-in and trans-tibial double-bundle ACL reconstruction.}, journal = {Knee Surg Sports Traumatol Arthrosc}, year = {2013}, month = {2013 Jul 13}, abstract = {

PURPOSE: The objectives of this study were to compare (1) the degree of widening by comparing the diameter at the most widened area and the site of widening by measuring the distance from the tunnel entrance to the most widened area in two femoral tunnels (anteromedial and posterolateral), and (2) the morphologic change at the tunnel entrance between outside-in and trans-tibial double-bundle anterior cruciate ligament (ACL) reconstruction.

METHODS: A retrospective study that included 17 trans-tibial and 19 outside-in double-bundle ACL reconstructed patients was conducted for evaluation of serial computed tomography (CT) scan (immediate post-operation and post-operative 1~year). Digital image communication in medicine (DICOM) data was extracted from the PiViewSTAR and imported into OsiriX({\textregistered}), which was installed on a Macbook Pro laptop computer. Diameter of the most widened area and distance from the entrance to this point were measured from each of two perpendicular (sagittal and coronal) planes that were accurately realigned parallel to the tunnel direction. Change in the morphology of the tunnel entrance between immediate post-operation and 1-year post-operation was evaluated.

RESULTS: Widening was observed in both planes of both tunnels in the two techniques. However, no statistical significances in the diameter of most widened area and distance from the tunnel entrance to the most widened point were observed between the both techniques (n.s.). Distances from the centre point to each four sections showed an increase in all four sections of all both tunnels in both techniques. However, no statistical significance was observed between the two techniques (n.s.).

CONCLUSION: Widening was observed in all tunnels using both techniques and degrees, and sites of the widening did not differ between groups. Morphologic change at the tunnel entrance was not limited to the specific direction and occurred in all directions without significant difference between groups.

LEVEL OF EVIDENCE: Retrospective comparative study, Level III.

}, issn = {1433-7347}, doi = {10.1007/s00167-013-2597-6}, author = {Lee, Yong Seuk and Lee, Beom Koo and Oh, Won Seok and Cho, Yong Kyun} } @article {874, title = {Customising DHIS2 for Maternal and Child Health Information Management in Sri Lanka}, journal = {Sri Lanka Journal of Bio-Medical Informatics}, volume = {3}, year = {2013}, abstract = {Maternal and Child Health (MCH) is an important component of the primary health care system. MCH systems are developed incorporated with health information systems. Electronic MCH Information Management Systems are emerging and they have proven to improve the quality, efficiency and the cost of medical care. Vendor neutral open source software, such as DHIS2, provides the resources to develop most of the Health Information Management systems. By following open standards; quality, productivity, cost management and data safety can be improved.DOi: http://dx.doi.org/10.4038/sljbmi.v3i2.2496 Sri Lanka Journal of Biomedical Informatics 2012; 3:47-54}, keywords = {DHIS2, Information Systems, Maternal and Child Health, open source}, url = {http://www.sljol.info/index.php/SLJBMI/article/view/2496}, author = {M. Manoj} } @inbook {1091, title = {Designing Sustainable Open Source Systems: The Cuban National Health Care Network and Portal (INFOMED)}, booktitle = {Grand Successes and Failures in IT. Public and Private Sectors}, series = {IFIP Advances in Information and Communication Technology}, volume = {402}, year = {2013}, pages = {451-466}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, keywords = {Cuba, INFOMED, national health care systems, open source software, qualitative research methods, virtual infrastructures}, isbn = {978-3-642-38861-3}, doi = {10.1007/978-3-642-38862-0_28}, url = {http://dx.doi.org/10.1007/978-3-642-38862-0_28}, author = {S{\'e}ror, Ann}, editor = {Dwivedi, YogeshK. and Henriksen, HelleZinner and Wastell, David and De{\textquoteright}, Rahul} } @article {863, title = {DICOM RIS/PACS Telemedicine Network Implementation using Free Open Source Software}, journal = {Latin America Transactions, IEEE (Revista IEEE America Latina)}, volume = {11}, year = {2013}, pages = {168-171}, abstract = {The increasing incorporation of modern medical imaging equipment requires the operation of systems that store, transmit and display images, PACS (Picture Archiving and Communication System) via digital networks to provide health services with higher quality. These revolutionized radiology systems based on digital techniques, communications, visualization and information technologies. One of the major problems that arise in institutions working with Imaging Diagnosis (Dx) in the interconnection network or equipment, are the "bottlenecks" caused by the high flow of network data. This flux is given by the transfer of images in DICOM (Digital Imaging and Communications in Medicine) to the various devices that make up a DICOM network, called Service Class Users (SCU) and Service Class Providers (SCP). This paper describes the development and implementation of a network of medical images using free software and its compatibility with its own data network of a RIS (Radiology Information System). Describes techniques used for the interconnection of local nodes on a LAN (Local Area Network) remote WAN Wide Area Network) via Internet and WLAN (Wireless Area Network.}, keywords = {DICOM, Free Software, Medical Imaging, Telemedicine}, issn = {1548-0992}, doi = {10.1109/TLA.2013.6502797}, author = {Alvarez, Luis R. and Vargas Solis, Roberto} } @article {1010, title = {E-health systems for management of MDR-TB in resource-poor environments: a decade of experience and recommendations for future work.}, journal = {Stud Health Technol Inform}, volume = {192}, year = {2013}, month = {2013}, pages = {627-31}, abstract = {

INTRODUCTION: Multi-drug resistant TB (MDR-TB) is a complex infectious disease that is a growing threat to global health. It requires lengthy treatment with multiple drugs and specialized laboratory testing. To effectively scale up treatment to thousands of patients requires good information systems to support clinical care, reporting, drug forecasting, supply chain management and monitoring.

METHODS: Over the last decade we have developed the PIH-EMR electronic medical record system, and subsequently OpenMRS-TB, to support the treatment of MDR-TB in Peru, Haiti, Pakistan, and other resource-poor environments.

RESULTS: We describe here the experience with implementing these systems and evaluating many aspects of their performance, and review other systems for MDR-TB management.

CONCLUSIONS: We recommend a new approach to information systems to address the barriers to scale up MDR-TB treatment, particularly access to the appropriate drugs and lab data. We propose moving away from fragmented, vertical systems to focus on common platforms, addressing all stages of TB care, support for open data standards and interoperability, care for a wide range of diseases including HIV, integration with mHealth applications, and ability to function in resource-poor environments.

}, keywords = {Developing Countries, electronic health records, Electronic Prescribing, Extensively Drug-Resistant Tuberculosis, Haiti, Health Information Management, Humans, Medication Systems, Hospital, Pakistan, Remote Consultation}, issn = {0926-9630}, author = {Fraser, Hamish S F and Habib, Ali and Goodrich, Mark and Thomas, David and Blaya, Joaquin A and Fils-Aime, Joseph Reginald and Jazayeri, Darius and Seaton, Michael and Khan, Aamir J and Choi, Sharon S and Kerrison, Foster and Falzon, Dennis and Becerra, Mercedes C} } @article {840, title = {The Evolving Role of Open Source Software in Medicine and Health Services}, journal = {Technology Innovation Management Review}, year = {2013}, month = {01/2013}, pages = {32-39}, abstract = {The past five decades have witnessed immense coevolution of methods and tools of information technology, and their practical and experimental application within the medical and healthcare domain. Healthcare itself continues to evolve in response to change in healthcare needs, progress in the scientific foundations of treatments, and in professional and managerial organization of affordable and effective services, in which patients and their families and carers increasingly participate. Taken together, these trends impose highly complex underlying challenges for the design, development, and sustainability of the quality of supporting information services and software infrastructure that are needed. The challenges are multidisciplinary and multiprofessional in scope, and they require deeper study and learning to inform policy and promote public awareness of the problems health services have faced in this area for many years. The repeating pattern of failure to live up to expectations of policy-driven national health IT initiatives has proved very costly and remains frustrating and unproductive for all involved. In this article, we highlight the barriers to progress and discuss the dangers of pursuing a standardization framework devoid of empirical testing and iterative development. We give the example of the openEHR Foundation, which was established at University College London (UCL) in London, England, with members in 80 countries. The Foundation is a not-for-profit company providing open specifications and working for generic standards for electronic records, informed directly by a wide range of implementation experience. We also introduce the Opereffa open source framework, which was developed at UCL based on these specifications and which has been downloaded in some 70 countries. We argue that such an approach is now essential to support good discipline, innovation, and governance at the heart of medicine and health services, in line with the new mandate for health commissioning in the United Kingdom{\textquoteright}s National Health Service (NHS), which emphasizes patient participation, innovation, transparency, and accountability.}, keywords = {electronic health care record, information retrieval, open source framework, openEHR Foundation, persistence, standards based}, issn = {1927-0321}, author = {David Ingram and Sevket Seref Arikan} } @article {891, title = {Fundus image diagnostic agreement in uveitis utilizing free and open source software.}, journal = {Can J Ophthalmol}, volume = {48}, year = {2013}, month = {2013 Aug}, pages = {227-34}, abstract = {

OBJECTIVE: To assess the adequacy of image agreement regarding uveitis based on color fundus and fluorescein angiography images alone, and to use free and open source applications to conduct an image agreement study.

DESIGN: Cross-sectional agreement study.

PARTICIPANTS: Baseline fundus and fluorescein images of patients with panuveitis, posterior, or intermediate uveitis enrolled in the Multi-center Uveitis Steroid Treatment (MUST) trial.

METHODS: Three fellowship-trained specialists in uveitis independently reviewed patient images using ClearCanvas{\texttrademark} and responded using Epi Info{\texttrademark}. The diagnoses of the 3 reviewers were compared with the MUST clinician as a gold standard. A rank transformation adjusted for the possible variation in number of responses per patient. Chance-corrected interobserver agreement among the 3 reviewers was estimated with the ι coefficient. Confidence interval (CI) and SE were bootstrapped.

RESULTS: Agreement between the diagnoses of the respondents and the baseline MUST clinician{\textquoteright}s diagnosis was poor across all diagnostic categories, ι = 0.09 (95\% CI, 0.07-0.11). The agreement among respondents alone also was poor, ι = 0.11 {\textpm} 0.02 (95\% CI, 0.08-0.13). The specialists requested more patient historical and clinical information to make a diagnosis on all patients.

CONCLUSIONS: The role in distinguishing the multiple conditions in uveitis appears to be limited when based on fundus imaging alone. Future studies should investigate different categories of clinical data to supplement image data. Freely available applications have excellent utility in ophthalmic imaging agreement studies.

}, issn = {0008-4182}, doi = {10.1016/j.jcjo.2013.02.010}, author = {Hsieh, Jane and Honda, Andrea F and Su{\'a}rez-Fari{\~n}as, Mayte and Samson, C Michael and Kedhar, Sanjay and Mauro, John and Francis, Jasmine and Badamo, Jason and Diaz, Vicente A and Kempen, John H and Latkany, Paul A} } @article {865, title = {GBM volumetry using the 3D Slicer medical image computing platform.}, journal = {Sci Rep}, volume = {3}, year = {2013}, month = {2013}, pages = {1364}, abstract = {

Volumetric change in glioblastoma multiforme (GBM) over time is a critical factor in treatment decisions. Typically, the tumor volume is computed on a slice-by-slice basis using MRI scans obtained at regular intervals. (3D)Slicer - a free platform for biomedical research - provides an alternative to this manual slice-by-slice segmentation process, which is significantly faster and requires less user interaction. In this study, 4 physicians segmented GBMs in 10 patients, once using the competitive region-growing based GrowCut segmentation module of Slicer, and once purely by drawing boundaries completely manually on a slice-by-slice basis. Furthermore, we provide a variability analysis for three physicians for 12 GBMs. The time required for GrowCut segmentation was on an average 61\% of the time required for a pure manual segmentation. A comparison of Slicer-based segmentation with manual slice-by-slice segmentation resulted in a Dice Similarity Coefficient of 88.43 {\textpm} 5.23\% and a Hausdorff Distance of 2.32 {\textpm} 5.23 mm.

}, issn = {2045-2322}, doi = {10.1038/srep01364}, author = {Egger, Jan and Kapur, Tina and Fedorov, Andriy and Pieper, Steve and Miller, James V and Veeraraghavan, Harini and Freisleben, Bernd and Golby, Alexandra J and Nimsky, Christopher and Kikinis, Ron} } @article {855, title = {Health care transformation through collaboration on open-source informatics projects: integrating a medical applications platform, research data repository, and patient summarization.}, journal = {Interact J Med Res}, volume = {2}, year = {2013}, month = {2013}, pages = {e11}, abstract = {

BACKGROUND: The Strategic Health IT Advanced Research Projects (SHARP) program seeks to conquer well-understood challenges in medical informatics through breakthrough research. Two SHARP centers have found alignment in their methodological needs: (1) members of the National Center for Cognitive Informatics and Decision-making (NCCD) have developed knowledge bases to support problem-oriented summarizations of patient data, and (2) Substitutable Medical Apps, Reusable Technologies (SMART), which is a platform for reusable medical apps that can run on participating platforms connected to various electronic health records (EHR). Combining the work of these two centers will ensure wide dissemination of new methods for synthesized views of patient data. Informatics for Integrating Biology and the Bedside (i2b2) is an NIH-funded clinical research data repository platform in use at over 100 sites worldwide. By also working with a co-occurring initiative to SMART-enabling i2b2, we can confidently write one app that can be used extremely broadly.

OBJECTIVE: Our goal was to facilitate development of intuitive, problem-oriented views of the patient record using NCCD knowledge bases that would run in any EHR. To do this, we developed a collaboration between the two SHARPs and an NIH center, i2b2.

METHODS: First, we implemented collaborative tools to connect researchers at three institutions. Next, we developed a patient summarization app using the SMART platform and a previously validated NCCD problem-medication linkage knowledge base derived from the National Drug File-Reference Terminology (NDF-RT). Finally, to SMART-enable i2b2, we implemented two new Web service "cells" that expose the SMART application programming interface (API), and we made changes to the Web interface of i2b2 to host a "carousel" of SMART apps.

RESULTS: We deployed our SMART-based, NDF-RT-derived patient summarization app in this SMART-i2b2 container. It displays a problem-oriented view of medications and presents a line-graph display of laboratory results.

CONCLUSIONS: This summarization app can be run in any EHR environment that either supports SMART or runs SMART-enabled i2b2. This i2b2 "clinical bridge" demonstrates a pathway for reusable app development that does not require EHR vendors to immediately adopt the SMART API. Apps can be developed in SMART and run by clinicians in the i2b2 repository, reusing clinical data extracted from EHRs. This may encourage the adoption of SMART by supporting SMART app development until EHRs adopt the platform. It also allows a new variety of clinical SMART apps, fueled by the broad aggregation of data types available in research repositories. The app (including its knowledge base) and SMART-i2b2 are open-source and freely available for download.

}, issn = {1929-073X}, doi = {10.2196/ijmr.2454}, author = {Klann, Jeffrey G and McCoy, Allison B and Wright, Adam and Wattanasin, Nich and Sittig, Dean F and Murphy, Shawn N} } @article {1035, title = {A hybrid approach to telepathology in Cambodia.}, journal = {J Telemed Telecare}, volume = {19}, year = {2013}, month = {2013 Dec}, pages = {475-8}, abstract = {

We established a hybrid telepathology network at the Children{\textquoteright}s Surgical Centre (CSC) in Cambodia, based on store-and-forward communication using iPATH and videoconferencing using Skype. We retrospectively analysed all data from the CSC stored on the iPATH server and reviewed the patient notes over an 8-month period. Of 115 patients for histopathology diagnosis during the study period, 38 cases were uploaded onto iPATH for further telemedicine discussion. The median number of days it took a specialist, other than the local one, to comment on the case on iPATH was 5 days (range 0-15). In three cases (8\%) there was no reply from a specialist on iPATH. During the study period, seven clinical conferences were held, with an average of 6 cases (range 4-7) discussed at each conference. All 38 cases discussed had a final agreed diagnosis and firm management plans were made. Of the 24 cases where proactive management was advised, 17 patients followed through with the recommendations. Although the combination of video consultations and store-and-forward communication has not been used much before in the developing world, it has benefited patient care and outcomes at the CSC.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Cambodia, Child, Child, Preschool, Female, Humans, Internet, Male, Middle Aged, Remote Consultation, Retrospective Studies, Surgical Procedures, Operative, telepathology, Videoconferencing, Young Adult}, issn = {1758-1109}, doi = {10.1177/1357633X13512071}, author = {Kadaba, Varsha and Ly, Tho and Noor, Saqib and Chhut, Serey V and Hinsch, Nora and Stauch, Gerhard and Gollogly, James} } @article {1011, title = {Informatics lessons from using a novel immunization information system.}, journal = {Stud Health Technol Inform}, volume = {192}, year = {2013}, month = {2013}, pages = {589-93}, abstract = {

In the 1990s, NewYork-Presbyterian Hospital began developing a comprehensive, standards-based immunization information system. The system, known as EzVac, has been operational since 1998 and now includes information on 2 million immunizations administered to more than 260,000 individuals. The system exchanges data with multiple electronic health records, a public health immunization registry, and a standalone personal health record. EzVac modules have recently been incorporated into the OpenMRS application and are being used to enhance immunization efforts in developing nations. We report on our experience with developing and using the EzVac system for 1) clinical care, both in local and global settings, 2) public health reporting, 3) consumer engagement, and 4) clinical and informatics research. We emphasize the advantages of using health IT standards to facilitate immunization information exchange in each of these domains.

}, keywords = {electronic health records, Health Information Management, Immunization, Internet, Medical Record Linkage, New York, Registries, Software}, issn = {0926-9630}, author = {Vawdrey, David K and Natarajan, Karthik and Kanter, Andrew S and Hripcsak, George and Kuperman, Gilad J and Stockwell, Melissa S} } @article {900, title = {Innovative low-cost telemonitoring: A versatile system using generic hardware, open source software and free data brokering services}, journal = {Health Care and Informatics Review Online}, volume = {17}, year = {2013}, pages = {2{\textendash}10}, abstract = {Improving access to vital medical information by telemonitoring has been shown to improve patient health, prevent admissions and shorten hospital length of stay [1,2]. Telemonitoring systems are costly and not in widespread use. This paper investigates the feasibility of creating a low-cost, versatile telemonitoring system through the use of generic hardware, open source software (OSS) and free data brokering services, by creating a working prototype. A low-cost, user friendly, widely available system could address the barriers that prevent widespread uptake of telemonitoring in healthcare.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84877107346\&partnerID=40\&md5=eb58b3030333d55f7624d0b54cabe051}, author = {Kok, K.a}, editor = {Lang, D.b} } @article {892, title = {Integration of advanced 3D SPECT modeling into the open-source STIR framework}, journal = {Medical Physics}, volume = {40}, year = {2013}, pages = {092502}, keywords = {C++ language, image reconstruction, medical image processing, object-oriented programming, public domain software, single photon emission computed tomography, software libraries, software packages}, doi = {10.1118/1.4816676}, url = {http://link.aip.org/link/?MPH/40/092502/1}, author = {Berta Marti Fuster and Carles Falcon and Charalampos Tsoumpas and Lefteris Livieratos and Pablo Aguiar and Albert Cot and Domenec Ros and Kris Thielemans} } @article {864, title = {Integration of PACS and CAD systems using DICOMDIR and open-source tools}, year = {2013}, pages = {86740V-86740V-6}, abstract = {The advancements of the last 30 years have made picture archiving and communication system (PACS) an indispensable technology to improve the delivery and management of clinical imaging services. Similarly, the maturation of algorithms and computer aided detection (CAD) systems has enhanced the interpretation and diagnosis of radiographical images. However, the lack of integration between the two systems inhibits the rate of development and application of these recent innovations in reaching the clinical users of PACS. We aim to enhance the clinical efficiency of CAD systems by developing an accessible, fully automated, user-friendly, and integrated linkage of CAD and PACS systems. This is the first integration initiative to take advantage of DICOMDIR file and its ability to index DICOM files, allowing images outside of PACS to be viewed within PACS. In this demonstration, the CAD system evaluates CT chest exams to detect lesions in the ribs and produces whole rib map images, screenshots, and detection report. A script executes the rib CAD system and creates a DICOMDIR file using {\quotedblbase}DCMTK", an open-source DICOM toolkit. We evaluated our system on thirty 5mm slice thickness and thirty 2mm slice thickness image studies and demonstrated a time saving efficiency of 93s{\textpm}14s and 221s{\textpm}17s per exam, respectively, compared to the current non-integrated workflow of using CAD systems. The advantages of this system are that it is easy to implement, requires no additional workstation and training, and allows CAD results to be viewed in PACS without disrupting radiology workflow, while maintaining the independence of both technologies. {\textcopyright} (2013) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).}, doi = {10.1117/12.2001560}, url = {+ http://dx.doi.org/10.1117/12.2001560}, author = {Huang, Jiaxin and Ling, Alexander and Summers, Ronald M. and Yao, Jianhua} } @article {933, title = {International data-sharing for radiotherapy research: An open-source based infrastructure for multicentric clinical data mining.}, journal = {Radiother Oncol}, year = {2013}, month = {2013 Dec 2}, abstract = {

Extensive, multifactorial data sharing is a crucial prerequisite for current and future (radiotherapy) research. However, the cost, time and effort to achieve this are often a roadblock. We present an open-source based data-sharing infrastructure between two radiotherapy departments, allowing seamless exchange of de-identified, automatically translated clinical and biomedical treatment data.

}, issn = {1879-0887}, doi = {10.1016/j.radonc.2013.11.001}, author = {Roelofs, Erik and Dekker, Andr{\'e} and Meldolesi, Elisa and van Stiphout, Ruud G P M and Valentini, Vincenzo and Lambin, Philippe} } @article {852, title = {The Medical Imaging Interaction Toolkit: challenges and advances : 10 years of open-source development.}, journal = {Int J Comput Assist Radiol Surg}, year = {2013}, month = {2013 Apr 16}, abstract = {

PURPOSE: ~~~The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. METHODS: ~~~MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. RESULTS: ~~~MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. CONCLUSIONS: ~~~MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today{\textquoteright}s and tomorrow{\textquoteright}s clinically motivated research.

}, issn = {1861-6429}, doi = {10.1007/s11548-013-0840-8}, author = {Nolden, Marco and Zelzer, Sascha and Seitel, Alexander and Wald, Diana and M{\"u}ller, Michael and Franz, Alfred M and Maleike, Daniel and Fangerau, Markus and Baumhauer, Matthias and Maier-Hein, Lena and Maier-Hein, Klaus H and Meinzer, Hans -Peter and Wolf, Ivo} } @inbook {866, title = {MITK-US: Echtzeitverarbeitung von Ultraschallbildern in MITK}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2013}, series = {Informatik aktuell}, year = {2013}, pages = {302-307}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Ultraschall (US) als bildgebendes Verfahren in der Medizin ist nicht invasiv, schnell, vielerorts verf{\"u}gbar, kommt ohne Strahlenbelastung aus und liefert kontinuierlich Daten in Echtzeit. Die Nutzung von US f{\"u}r computerassistierte Interventionen (CAI) stellt jedoch nicht nur extrem hohe Anforderungen an die Methoden zur Bildverarbeitung aufgrund der beschr{\"a}nkten Bildqualit{\"a}t, sondern bedeutet auch einen betr{\"a}chtlichen Integrationsaufwand wenn die Daten in Echtzeit weiterverarbeitet werden sollen. Mit MITK-US stellen wir in dieser Arbeit ein neues Modul f{\"u}r das Open Source verf{\"u}gbare Medical Imaging Interaction Toolkit (MITK) vor, welches die einheitliche Einbindung und Weiterverarbeitung von Echtzeitultraschalldaten erm{\"o}glicht und somit den Aufwand f{\"u}r die Integration von US in CAI Systeme verringert. Da die Verwendung von Echtzeitdaten insbesondere im Bereich der CAI zahlreiche neue M{\"o}glichkeiten bietet, erwarten wir einen hohen Nutzen dieses Moduls f{\"u}r k{\"u}nftige Projekte.}, isbn = {978-3-642-36479-2}, doi = {10.1007/978-3-642-36480-8_53}, url = {http://dx.doi.org/10.1007/978-3-642-36480-8_53}, author = {Franz, AlfredMichael and M{\"a}rz, Keno and Seitel, Alexander and M{\"u}ller, Michael and Zelzer, Sascha and Nodeln, Marco and Meinzer, Hans-Peter and Maier-Hein, Lena}, editor = {Meinzer, Hans-Peter and Deserno, Thomas Martin and Handels, Heinz and Tolxdorff, Thomas} } @article {862, title = {MRIdb: Medical Image Management for Biobank Research.}, journal = {J Digit Imaging}, year = {2013}, month = {2013 Apr 26}, abstract = {

Clinical picture archiving and communications systems provide convenient, efficient access to digital medical images from multiple modalities but can prove challenging to deploy, configure and use. MRIdb is a self-contained image database, particularly suited to the storage and management of magnetic resonance imaging data sets for population phenotyping. It integrates a mature image archival system with an intuitive web-based user interface that provides visualisation and export functionality. In addition, utilities for auditing, data migration and system monitoring are included in a virtual machine image that is easily deployed with minimal configuration. The result is a freely available turnkey solution, designed to support epidemiological and imaging genetics research. It allows the management of patient data sets in a secure, scalable manner without requiring the installation of any bespoke software on end users{\textquoteright} workstations. MRIdb is an open-source software, available for download at http://www3.imperial.ac.uk/bioinfsupport/resources/software/mridb .

}, issn = {1618-727X}, doi = {10.1007/s10278-013-9604-9}, author = {Woodbridge, Mark and Fagiolo, Gianlorenzo and O{\textquoteright}Regan, Declan P} } @article {894, title = {Novel open-source electronic medical records system for palliative care in low-resource settings.}, journal = {BMC Palliat Care}, volume = {12}, year = {2013}, month = {2013}, pages = {31}, abstract = {

BACKGROUND: The need for palliative care in sub-Saharan Africa is staggering: this region shoulders over 67\% of the global burden of HIV/AIDS and cancer. However, provisions for these essential services remain limited and poorly integrated with national health systems in most nations. Moreover, the evidence base for palliative care in the region remains scarce. This study chronicles the development and evaluation of DataPall, an open-source electronic medical records system that can be used to track patients, manage data, and generate reports for palliative care providers in these settings.DataPall was developed using design criteria encompassing both functional and technical objectives articulated by hospital leaders and palliative care staff at a leading palliative care center in Malawi. The database can be used with computers that run Windows XP SP 2 or newer, and does not require an internet connection for use. Subsequent to its development and implementation in two hospitals, DataPall was tested among both trained and untrained hospital staff populations on the basis of its usability with comparison to existing paper records systems as well as on the speed at which users could perform basic database functions. Additionally, all participants evaluated this program on a standard system usability scale.

RESULTS: In a study of health professionals in a Malawian hospital, DataPall enabled palliative care providers to find patients{\textquoteright} appointments, on average, in less than half the time required to locate the same record in current paper records. Moreover, participants generated customizable reports documenting patient records and comprehensive reports on providers{\textquoteright} activities with little training necessary. Participants affirmed this ease of use on the system usability scale.

CONCLUSIONS: DataPall is a simple, effective electronic medical records system that can assist in developing an evidence base of clinical data for palliative care in low resource settings. The system is available at no cost, is specifically designed to chronicle care in the region, and is catered to meet the technical needs and user specifications of such facilities.

}, issn = {1472-684X}, doi = {10.1186/1472-684X-12-31}, author = {Shah, Kamal G and Slough, Tara Lyn and Yeh, Ping Teresa and Gombwa, Suave and Kiromera, Athanase and Oden, Z Maria and Richards-Kortum, Rebecca R} } @article {858, title = {Open source electronic health records and chronic disease management.}, journal = {J Am Med Inform Assoc}, year = {2013}, month = {2013 Jun 29}, abstract = {

OBJECTIVE: To study and report on the use of open source electronic health records (EHR) to assist with chronic care management within safety net medical settings, such as community health centers (CHC).

METHODS AND MATERIALS: The study was conducted by NORC at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to CHC that currently use an open source EHR.

RESULTS: Two of the sites chosen by NORC were actively using an open source EHR to assist in the redesign of their care delivery system to support more effective chronic disease management. This included incorporating the chronic care model into an CHC and using the EHR to help facilitate its elements, such as care teams for patients, in addition to maintaining health records on indigent populations, such as tuberculosis status on homeless patients.

DISCUSSION: The ability to modify the open-source EHR to adapt to the CHC environment and leverage the ecosystem of providers and users to assist in this process provided significant advantages in chronic care management. Improvements in diabetes management, controlled hypertension and increases in tuberculosis vaccinations were assisted through the use of these open source systems.

CONCLUSIONS: The flexibility and adaptability of open source EHR demonstrated its utility and viability in the provision of necessary and needed chronic disease care among populations served by CHC.

}, issn = {1527-974X}, doi = {10.1136/amiajnl-2013-001672}, author = {Goldwater, Jason C and Kwon, Nancy J and Nathanson, Ashley and Muckle, Alison E and Brown, Alexa and Cornejo, Kerri} } @article {919, title = {Physiological states and functional relation between thyrotropin and free thyroxine in thyroid health and disease: in vivo and in silico data suggest a hierarchical model.}, journal = {J Clin Pathol}, volume = {66}, year = {2013}, month = {2013 Apr}, pages = {335-42}, abstract = {

AIMS: Understanding the exact relationship between serum thyrotropin/thyroid stimulating hormone (TSH) and free thyroxine (FT(4)) is a prerequisite for improving diagnostic reliability and clinical decision making.

METHODS: We (1) retrospectively studied the relationship between TSH and FT(4) in a large unselected clinical sample (n=6641) of primary hypothyroid, euthyroid and hyperthyroid subjects, and (2) applied a mathematical model of thyroid hormone feedback control to assess the relation between structural parameters and TSH levels in the different functional states.

RESULTS: When separately analysing total sample and untreated subjects, the correlation slope for logTSH versus FT(4) for hypothyroid subjects was significantly different from that of the euthyroid panel and hyperthyroid subjects (the latter being compromised by reaching the TSH assay{\textquoteright}s lower detection limit). As trends between functional states changed, each functional segment appeared to become differently regulated. Theoretical modelling and sensitivity analysis revealed that the influence of various structural parameters on TSH levels also depends on the overall function of the feedback loop.

CONCLUSIONS: Our data suggest that the states of hypothyroidism, euthyroidism and hyperthyroidism can be regarded as differently regulated entities. The apparent complexity could be replicated by mathematical modelling suggesting a hierarchical type of feedback regulation involving patterns of operative mechanisms unique to each condition. For clinical purposes and assay evaluation, neither the standard model relating logTSH with FT(4), nor an alternative model based on non-competitive inhibition can be reliably represented by a single correlation comparing all samples for both hormones in one all-inclusive group.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Autoantibodies, Autoantigens, Biological Markers, Computer Simulation, Feedback, Physiological, Humans, Hyperthyroidism, Hypothyroidism, Iodide Peroxidase, Iron-Binding Proteins, Linear Models, Middle Aged, Models, Biological, Multivariate Analysis, Nonlinear Dynamics, Predictive Value of Tests, Retrospective Studies, Thyroid Diseases, Thyroid Function Tests, Thyroid Gland, Thyrotropin, Thyroxine, Young Adult}, issn = {1472-4146}, doi = {10.1136/jclinpath-2012-201213}, author = {Midgley, John E M and Hoermann, Rudolf and Larisch, Rolf and Dietrich, Johannes W} } @article {918, title = {Is pituitary TSH an adequate measure of thyroid hormone-controlled homoeostasis during thyroxine treatment?}, journal = {Eur J Endocrinol}, volume = {168}, year = {2013}, month = {2013 Feb}, pages = {271-80}, abstract = {

OBJECTIVE: In recognition of its primary role in pituitary-thyroid feedback, TSH determination has become a key parameter for clinical decision-making. This study examines the value of TSH as a measure of thyroid hormone homoeostasis under thyroxine (T(4)) therapy.

DESIGN AND METHODS: We have examined the interrelationships between free triiodothyronine (FT(3)), free T(4) (FT(4)) and pituitary TSH by means of i) a retrospective analysis of a large clinical sample comprising 1994 patients either untreated or on varying doses of l-T(4) and ii) independent mathematical simulation applying a model of thyroid homoeostasis, together with a sensitivity analysis.

RESULTS: Over a euthyroid to mildly hyperthyroid functional range, we found markedly different correlation slopes of log TSH vs FT(3) and FT(4) between untreated patients and l-T(4) groups. Total deiodinase activity (G(D)) was positively correlated with TSH in untreated subjects. However, G(D) was significantly altered and the correlation was lost under increasing l-T(4) doses. Ninety-five per cent confidence intervals for FT(3) and FT(4), when assessed in defined TSH concentration bands, differed significantly for l-T(4)-treated compared with untreated patients. Higher doses were often needed to restore FT(3) levels within its reference range. Sensitivity analysis revealed the influence of various structural parameters on pituitary TSH secretion including an important role of pituitary deiodinase type 2.

CONCLUSION: The data reveal disjoints between FT(4)-TSH feedback and T(3) production that persist even when sufficient T(4) apparently restores euthyroidism. T(4) treatment displays a compensatory adaptation but does not completely re-enact normal euthyroid physiology. This invites a study of the clinical consequences of this disparity.

}, keywords = {Adult, Female, Homeostasis, Humans, Hypothyroidism, Male, Pituitary Gland, Retrospective Studies, Thyrotropin, Thyroxine, Triiodothyronine}, issn = {1479-683X}, doi = {10.1530/EJE-12-0819}, author = {Hoermann, Rudolf and Midgley, John E M and Larisch, Rolf and Dietrich, Johannes W} } @article {895, title = {Revolutionizing patient control of health information.}, journal = {Can Fam Physician}, volume = {59}, year = {2013}, month = {2013 Aug}, pages = {823-4}, issn = {1715-5258}, author = {Chan, David and Howard, Michelle and Dolovich, Lisa and Bartlett, Gillian and Price, David} } @article {899, title = {SIVIC: Open-source, standards-based software for DICOM MR spectroscopy workflows}, journal = {International Journal of Biomedical Imaging}, volume = {2013}, year = {2013}, abstract = {Quantitative analysis of magnetic resonance spectroscopic imaging (MRSI) data provides maps of metabolic parameters that show promise for improving medical diagnosis and therapeutic monitoring. While anatomical images are routinely reconstructed on the scanner, formatted using the DICOM standard, and interpreted using PACS workstations, this is not the case for MRSI data. The evaluation of MRSI data is made more complex because files are typically encoded with vendor-specific file formats and there is a lack of standardized tools for reconstruction, processing, and visualization. SIVIC is a flexible open-source software framework and application suite that enables a complete scanner-to-PACS workflow for evaluation and interpretation of MRSI data. It supports conversion of vendor-specific formats into the DICOM MR spectroscopy (MRS) standard, provides modular and extensible reconstruction and analysis pipelines, and provides tools to support the unique visualization requirements associated with such data. Workflows are presented which demonstrate the routine use of SIVIC to support the acquisition, analysis, and delivery to PACS of clinical 1H MRSI datasets at UCSF. {\textcopyright} 2013 Jason C. Crane et al.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84881398824\&partnerID=40\&md5=dbbc0d09b4153fd2609d0bb01b37bb30}, author = {Crane, J C and Olson, M P and Nelson, S J} } @article {875, title = {Three-dimensional volumetric rendition of cannon ball pulmonary metastases by the use of 3D Slicer, an open source free software package.}, journal = {BMJ Case Rep}, volume = {2013}, year = {2013}, month = {2013}, issn = {1757-790X}, doi = {10.1136/bcr-2012-008248}, author = {Revannasiddaiah, Swaroop and Susheela, Sridhar Papaiah and Madhusudhan, N and Mallarajapatna, Govindarajan J} } @article {1053, title = {tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research.}, journal = {AMIA Jt Summits Transl Sci Proc}, volume = {2013}, year = {2013}, month = {2013}, pages = {6-8}, abstract = {

tranSMART is an emerging global open source public private partnership community developing a comprehensive informatics-based analysis and data-sharing cloud platform for clinical and translational research. The tranSMART consortium includes pharmaceutical and other companies, not-for-profits, academic entities, patient advocacy groups, and government stakeholders. The tranSMART value proposition relies on the concept that the global community of users, developers, and stakeholders are the best source of innovation for applications and for useful data. Continued development and use of the tranSMART platform will create a means to enable "pre-competitive" data sharing broadly, saving money and, potentially accelerating research translation to cures. Significant transformative effects of tranSMART includes 1) allowing for all its user community to benefit from experts globally, 2) capturing the best of innovation in analytic tools, 3) a growing {\textquoteright}big data{\textquoteright} resource, 4) convergent standards, and 5) new informatics-enabled translational science in the pharma, academic, and not-for-profit sectors.

}, issn = {2153-4063}, author = {Athey, Brian D and Braxenthaler, Michael and Haas, Magali and Guo, Yike} } @article {859, title = {The use of open source electronic health records within the federal safety net.}, journal = {J Am Med Inform Assoc}, year = {2013}, month = {2013 Jun 6}, abstract = {

OBJECTIVE: To conduct a federally funded study that examines the acquisition, implementation and operation of open source electronic health records (EHR) within safety net medical settings, such as federally qualified health centers (FQHC). METHODS AND MATERIALS: The study was conducted by the National Opinion Research Center (NORC) at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to West Virginia, California and Arizona FQHC that were currently using an open source EHR. RESULTS: Five of the six sites that were chosen as part of the study found a number of advantages in the use of their open source EHR system, such as utilizing a large community of users and developers to modify their EHR to fit the needs of their provider and patient communities, and lower acquisition and implementation costs as compared to a commercial system. DISCUSSION: Despite these advantages, many of the informants and site visit participants felt that widespread dissemination and use of open source was restrained due to a negative connotation regarding this type of software. In addition, a number of participants stated that there is a necessary level of technical acumen needed within the FQHC to make an open source EHR effective. CONCLUSIONS: An open source EHR provides advantages for FQHC that have limited resources to acquire and implement an EHR, but additional study is needed to evaluate its overall effectiveness.

}, issn = {1527-974X}, doi = {10.1136/amiajnl-2013-001671}, author = {Goldwater, Jason C and Kwon, Nancy J and Nathanson, Ashley and Muckle, Alison E and Brown, Alexa and Cornejo, Kerri} } @article {887, title = {Use of Open Source Software in Health Care Delivery - Results of a Qualitative Field Study. Contribution of the EFMI LIFOSS Working Group.}, journal = {Yearb Med Inform}, volume = {8}, year = {2013}, month = {2013}, pages = {107-13}, abstract = {

OBJECTIVES: To assess and analyze the attitude of health IT executives towards the utilization of specialized medical Open Source software (OSS) in Germany{\textquoteright}s and other European countries{\textquoteright} health care delivery.

METHODS: After an initial literature review a field study was carried out based on semi-structured expert interviews. Eight German and 11 other European health IT executives were surveyed. The results were qualitatively analyzed using the grounded theory approach. Identified concepts were reviewed using SWOT analysis.

RESULTS: In total, 13 strengths, 11 weaknesses, 3 opportunities, and 8 threats of the utilization of OSS in a clinical setting could be identified. Additionally, closely related aspects like general software procurement criteria, the overall attitude of health IT executives, users, and management towards OSS and its current and future use could as well be assessed.

CONCLUSIONS: Medical OSS is rarely used in health care delivery. In order to capitalize the unique advantages of OSS in a clinical setting, complex requirements need to be addressed. Shortcomings of OSS describe an attractive breeding ground for new commercial offerings and services that need yet to be seen.

}, issn = {0943-4747}, author = {Schmuhl, H and Heinze, O and Bergh, B} } @article {896, title = {Utility of an open-source DICOM viewer software (OsiriX) to assess pulmonary fibrosis in systemic sclerosis: preliminary results.}, journal = {Rheumatol Int}, year = {2013}, month = {2013 Aug 15}, abstract = {

To investigate the utility of an open-source Digital Imaging and Communication in Medicine viewer software-OsiriX-to assess pulmonary fibrosis (PF) in patients with systemic sclerosis (SSc). Chest high-resolution computed tomography (HRCT) examinations obtained from 10 patients with diagnosis of SSc were analysed by two radiologists adopting a standard semiquantitative scoring for PF. Pulmonary involvement was evaluated in three sections (superior, middle and inferior). For the assessment of the extension of PF, the adopted semiquantitative HRCT score ranged from 0 to 3 (0~=~absence of PF; 1~=~1-20~\% of lung section involvement; 2~=~21-40~\% of lung section involvement; 3~=~41-100~\% of lung section involvement). Further, a quantitative assessment (i.e. parameters of distribution of lung attenuation such as kurtosis and mean lung attenuation) of PF was independently performed on the same sections by a rheumatologist, independently and blinded to radiologists{\textquoteright} scoring, using OsiriX. The results obtained were compared with those of HRCT semiquantitative analysis. Intra-reader reliability of HRCT findings and feasibility of OsiriX quantitative segmentation was recorded. A significant association between the median values of kurtosis by both the quantitative OsiriX assessment and the HRCT semiquantitative analysis was found (p~<~0.0001). Moreover, kurtosis correlated significantly with the mean lung attenuation (Spearman{\textquoteright}s rho~=~0.885; p~=~0.0001). An excellent intra-reader reliability of HRCT findings among both readers was obtained. A significant difference between the mean time spent on the OsiriX quantitative analysis (mean 1.85~{\textpm}~SD 1.3~min) and the mean time spent by the radiologist for the HRCT semiquantitative assessment (mean 8.5~{\textpm}~SD 4.5~min, p~<~0.00001) was noted. The study provides the new working hypothesis that OsiriX may be a useful and feasible tool to achieve a quantitative evaluation of PF in SSc patients.

}, issn = {1437-160X}, doi = {10.1007/s00296-013-2845-6}, author = {Ariani, Alarico and Carotti, Marina and Gutierrez, Marwin and Bichisecchi, Elisabetta and Grassi, Walter and Giuseppetti, Gian Marco and Salaffi, Fausto} } @article {1280, title = {What do electronic health record vendors reveal about their products: an analysis of vendor websites.}, journal = {J Med Internet Res}, volume = {15}, year = {2013}, month = {2013 Feb 19}, pages = {e36}, abstract = {

BACKGROUND: Purchasing electronic health records (EHRs) typically follows a process in which potential adopters actively seek information, compare alternatives, and form attitudes towards the product. A potential source of information on EHRs that can be used in the process is vendor websites. It is unclear how much product information is presented on EHR vendor websites or the extent of its value during EHR purchasing decisions.

OBJECTIVE: To explore what features of EHR systems are presented by vendors in Ontario, Canada, on their websites, and the persuasive means they use to market such systems; to compare the online information available about primary care EHR systems with that about hospital EHR systems, and with data compiled by OntarioMD, a regional certifying agency.

METHODS: A list of EHR systems available in Ontario was created. The contents of vendor websites were analyzed. A template for data collection and organization was developed and used to collect and organize information on the vendor, website content, and EHR features. First, we mapped information on system features to categories based on a framework from the Institute of Medicine (IOM). Second, we used a grounded theory-like approach to explore information for building consumer confidence in the vendor and product, and the various persuasive strategies employed on vendor websites. All data were first coded by one researcher. A peer reviewer independently analyzed a randomly chosen subset of the websites (10 of 21; 48\%) and provided feedback towards a unified coding scheme. All data were then re-coded and categorized into themes. Finally, we compared information from vendor websites and data gathered by OntarioMD.

RESULTS: Vendors provided little specific product information on their websites. Only two of five acute care EHR websites (40\%) and nine of 16 websites for primary care systems (56\%) featured seven or all eight of the IOM components. Several vendor websites included system interface demonstrations: screenshots (six websites), public videos or slideshows (four websites), or for registered viewers only (three websites). Persuasive means used by vendors included testimonials on 14/21 (67\%) websites, and directional language. Except for one free system, trial EHR versions were not available. OntarioMD provided more comprehensive information about primary care systems than the vendors{\textquoteright} websites. Of 14 points of comparison, only the inclusion of templates and bilingual interfaces were fully represented in both data sources. For all other categories, the vendor websites were less complete than the OntarioMD site.

CONCLUSIONS: EHR vendor websites employ various persuasive means, but lack product-specific information and do not provide options for trying systems on a limited basis. This may impede the ability of potential adopters to form perceptions and compare various offerings. Both vendors and clients could benefit from greater transparency and more specific product information on the Web.

TRIAL REGISTRATION: N/A.

}, keywords = {Commerce, electronic health records, Humans, Internet, Marketing of Health Services, Ontario, Telemedicine}, issn = {1438-8871}, doi = {10.2196/jmir.2312}, author = {Yeung, Natalie K and Jadad, Alejandro R and Shachak, Aviv} } @article {721, title = {Accuracy and Reliability of Length Measurements on Three-Dimensional Computed Tomography Using Open-Source OsiriX Software.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, year = {2012}, month = {2012 Jan 20}, abstract = {There is a growing interest in three-dimensional computed tomography (3D-CT) as a research tool for the study of bone, joint anatomy, and kinematics. However, when CT data are processed and handled manually using image processing programs to yield 3D image and coordinate value, systematic and random errors should be validated. We evaluated the accuracy and reliability of length measurement on CT with OsiriX software. 3D-CT scans were made of 14 frozen pig knees with five transosseous holes in the metaphyseal portion of femur. The lengths between tunnel orifices were measured using Mitutoyo Digimatic digital calipers to establish the gold standard, and with the OsiriX program in 3D multi-planar reformatting mode for comparison. All measurements were recorded by a principal (replicate 1, trial 1) and a secondary observer (replicate 2, trial 1) and were repeated once by each observer (trial 2). The mean differences between OsiriX and real measurements were less than 0.1~mm in both replicates, and maximum differences were less than 0.3~mm. There were no significant differences between the replicates and real measurements (p = 0.544 and 0.622 for replicates 1 and 2, respectively). The intraclass correlation coefficients (ICC) were very high between trials and between replicates (ICC = 0.998 and 0.999, respectively). For kinematic analysis of the knees, length measurements on 3D-CT using OsiriX program can be used as alternatives to real measurements with less than 0.3-mm accuracy and very high reliability.}, issn = {1618-727X}, doi = {10.1007/s10278-012-9458-6}, author = {Kim, Gihyeon and Jung, Ho-Joong and Lee, Han-Jun and Lee, Jae-Sung and Koo, Seungbum and Chang, Seung-Hwan} } @article {837, title = {Adaptation of a web-based, open source electronic medical record system platform to support a large study of tuberculosis epidemiology.}, journal = {BMC Med Inform Decis Mak}, volume = {12}, year = {2012}, month = {2012}, pages = {125}, abstract = {UNLABELLED: ABSTRACT: BACKGROUND: In 2006, we were funded by the US National Institutes of Health to implement a study of tuberculosis epidemiology in Peru. The study required a secure information system to manage data from a target goal of 16,000 subjects who needed to be followed for at least one year. With previous experience in the development and deployment of web-based medical record systems for TB treatment in Peru, we chose to use the OpenMRS open source electronic medical record system platform to develop the study information system. Supported by a core technical and management team and a large and growing worldwide community, OpenMRS is now being used in more than 40 developing countries. We adapted the OpenMRS platform to better support foreign languages. We added a new module to support double data entry, linkage to an existing laboratory information system, automatic upload of GPS data from handheld devices, and better security and auditing of data changes. We added new reports for study managers, and developed data extraction tools for research staff and statisticians. Further adaptation to handle direct entry of laboratory data occurred after the study was launched. RESULTS: Data collection in the OpenMRS system began in September 2009. By August 2011 a total of 9,256 participants had been enrolled, 102,274 forms and 13,829 laboratory results had been entered, and there were 208 users. The system is now entirely supported by the Peruvian study staff and programmers. CONCLUSIONS: The information system served the study objectives well despite requiring some significant adaptations mid-stream. OpenMRS has more tools and capabilities than it did in 2008, and requires less adaptations for future projects. OpenMRS can be an effective research data system in resource poor environments, especially for organizations using or considering it for clinical care as well as research.}, issn = {1472-6947}, doi = {10.1186/1472-6947-12-125}, author = {Fraser, Hamish S F and Thomas, David and Tomaylla, Juan and Garcia, Nadia and Lecca, Leonid and Murray, Megan and Becerra, Mercedes C} } @article {813, title = {ADDIS: a decision support system for evidence-based medicine}, journal = {Decision Support Systems}, volume = {in press}, year = {2012}, abstract = {Clinical trials are the main source of information for the efficacy and safety evaluation of medical treatments. Al- though they are of pivotal importance in evidence-based medicine, there is a lack of usable information systems providing data-analysis and decision support capabilities for aggregate clinical trial results. This is partly caused by unavailability (i) of trial data in a structured format suitable for re-analysis, and (ii) of a complete data model for ag- gregate level results. In this paper, we develop a unifying data model that enables the development of evidence-based decision support in the absence of a complete data model. We describe the supported decision processes and show how these are implemented in the open source ADDIS software. ADDIS enables semi-automated construction of meta-analyses, network meta-analyses and benefit-risk decision models, and provides visualization of all results.}, keywords = {clinicaltrial, datamodel, decisionanalysis, Evidence-basedmedicine, evidencesynthesis}, doi = {10.1016/j.dss.2012.10.005}, author = {van Valkenhoef, G. and Tervonen, T. and Zwinkels, T. and de Brock, B. and Hillege, H.} } @booklet {814, title = {ADDIS: an automated way to do network meta-analysis}, year = {2012}, author = {Zhao, J. and van Valkenhoef, G. and de Brock, B. and Hillege, H.} } @article {1021, title = {ARDEN2BYTECODE: a one-pass Arden Syntax compiler for service-oriented decision support systems based on the OSGi platform.}, journal = {Comput Methods Programs Biomed}, volume = {106}, year = {2012}, month = {2012 May}, pages = {114-25}, abstract = {

Patient empowerment might be one key to reduce the pressure on health care systems challenged by the expected demographic changes. Knowledge based systems can, in combination with automated sensor measurements, improve the patients{\textquoteright} ability to review their state of health and make informed decisions. The Arden Syntax as a standardized language to represent medical knowledge can be used to express the corresponding decision rules. In this paper we introduce ARDEN2BYTECODE, a newly developed open source compiler for the Arden Syntax. ARDEN2BYTECODE runs on Java Virtual Machines (JVM) and translates Arden Syntax directly to Java Bytecode (JBC) executable on JVMs. ARDEN2BYTECODE easily integrates into service oriented architectures, like the Open Services Gateway Initiative (OSGi) platform. Apart from an evaluation of compilation performance and execution times, ARDEN2BYTECODE was integrated into an existing knowledge supported exercise training system and recorded training sessions have been used to check the implementation.

}, keywords = {Decision Support Systems, Management, Programming Languages}, issn = {1872-7565}, doi = {10.1016/j.cmpb.2011.11.003}, author = {Gietzelt, Matthias and Goltz, Ursula and Grunwald, Daniel and Lochau, Malte and Marschollek, Michael and Song, Bianying and Wolf, Klaus-Hendrik} } @article {795, title = {BioImageXD: an open, general-purpose and high-throughput image-processing platform.}, journal = {Nat Methods}, volume = {9}, year = {2012}, month = {2012}, pages = {683-9}, abstract = {BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.}, issn = {1548-7105}, doi = {10.1038/nmeth.2047}, author = {Kankaanp{\"a}{\"a}, Pasi and Paavolainen, Lassi and Tiitta, Silja and Karjalainen, Mikko and P{\"a}iv{\"a}rinne, Joacim and Nieminen, Jonna and Marjom{\"a}ki, Varpu and Heino, Jyrki and White, Daniel J} } @article {776, title = {Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: The SHARPn project.}, journal = {J Biomed Inform}, year = {2012}, month = {2012 Feb 4}, abstract = {The Strategic Health IT Advanced Research Projects (SHARP) Program, established by the Office of the National Coordinator for Health Information Technology in 2010 supports research findings that remove barriers for increased adoption of health IT. The improvements envisioned by the SHARP Area 4 Consortium (SHARPn) will enable the use of the electronic health record (EHR) for secondary purposes, such as care process and outcomes improvement, biomedical research and epidemiologic monitoring of the nation{\textquoteright}s health. One of the primary informatics problem areas in this endeavor is the standardization of disparate health data from the nation{\textquoteright}s many health care organizations and providers. The SHARPn team is developing open source services and components to support the ubiquitous exchange, sharing and reuse or {\textquoteright}liquidity{\textquoteright} of operational clinical data stored in electronic health records. One year into the design and development of the SHARPn framework, we demonstrated end to end data flow and a prototype SHARPn platform, using thousands of patient electronic records sourced from two large healthcare organizations: Mayo Clinic and Intermountain Healthcare. The platform was deployed to (1) receive source EHR data in several formats, (2) generate structured data from EHR narrative text, and (3) normalize the EHR data using common detailed clinical models and Consolidated Health Informatics standard terminologies, which were (4) accessed by a phenotyping service using normalized data specifications. The architecture of this prototype SHARPn platform is presented. The EHR data throughput demonstration showed success in normalizing native EHR data, both structured and narrative, from two independent organizations and EHR systems. Based on the demonstration, observed challenges for standardization of EHR data for interoperable secondary use are discussed.}, issn = {1532-0480}, doi = {10.1016/j.jbi.2012.01.009}, author = {Rea, Susan and Pathak, Jyotishman and Savova, Guergana and Oniki, Thomas A and Westberg, Les and Beebe, Calvin E and Tao, Cui and Parker, Craig G and Haug, Peter J and Huff, Stanley M and Chute, Christopher G} } @article {827, title = {Code Sharing is Associated with Research Impact in Image Processing}, journal = {IEEE Computing in Science and Engineering}, year = {2012}, month = {April}, abstract = {In computational sciences such as image processing, the publication itself is often not enough to allow other researchers to verify the results by repeating the described experiments. In many cases, supplementary material such as source code and measurement data are required, or can at least be very helpful. Still, only approximately 10\% of recently published papers in image processing have code available online. One of the arguments for not making code available is the extra time required to prepare the material. In this paper, we claim that this additional time may be well spent, as the availability of code for a publication is associated with an increase in the expected number of citations. We show this with exploratory analyses of the relationship between code availability and the number of citations for image processing papers.}, url = {http://rr.epfl.ch/37/}, author = {Patrick Vandewalle} } @article {797, title = {Deformable three-dimensional model architecture for interactive augmented reality in minimally invasive surgery.}, journal = {Surg Endosc}, year = {2012}, month = {2012 Jun 27}, abstract = {BACKGROUND: Surgical procedures have undergone considerable advancement during the last few decades. More recently, the availability of some imaging methods intraoperatively has added a new dimension to minimally invasive techniques. Augmented reality in surgery has been a topic of intense interest and research. METHODS: Augmented reality involves usage of computer vision algorithms on video from endoscopic cameras or cameras mounted in the operating room to provide the surgeon additional information that he or she otherwise would have to recognize intuitively. One of the techniques combines a virtual preoperative model of the patient with the endoscope camera using natural or artificial landmarks to provide an augmented reality view in the operating room. The authors{\textquoteright} approach is to provide this with the least number of changes to the operating room. Software architecture is presented to provide interactive adjustment in the registration of a three-dimensional (3D) model and endoscope video. RESULTS: Augmented reality including adrenalectomy, ureteropelvic junction obstruction, and retrocaval ureter and pancreas was used to perform 12 surgeries. The general feedback from the surgeons has been very positive not only in terms of deciding the positions for inserting points but also in knowing the least change in anatomy. CONCLUSIONS: The approach involves providing a deformable 3D model architecture and its application to the operating room. A 3D model with a deformable structure is needed to show the shape change of soft tissue during the surgery. The software architecture to provide interactive adjustment in registration of the 3D model and endoscope video with adjustability of every 3D model is presented.}, issn = {1432-2218}, doi = {10.1007/s00464-012-2395-0}, author = {Vemuri, Anant S and Wu, Jungle Chi-Hsiang and Liu, Kai-Che and Wu, Hurng-Sheng} } @article {1049, title = {Designing and Implementing an Innovative SMS-based alert system (RapidSMS-MCH) to monitor pregnancy and reduce maternal and child deaths in Rwanda.}, journal = {Pan Afr Med J}, volume = {13}, year = {2012}, month = {2012}, pages = {31}, abstract = {

INTRODUCTION: With the continuous growth of mobile network coverage and unprecedented penetration of mobile devices in the developing world, several mHealth initiatives are being implemented in developing countries. This paper aims to describe requirements for designing and implementing a mobile phone-based communication system aiming at monitoring pregnancy and reducing bottlenecks in communication associated with maternal and newborn deaths; and document challenges and lessons learned.

METHODS: An SMS-based system was developed to improve maternal and child health (MCH) using RapidSMS({\textregistered}), a free and open-sourced software development framework. To achieve the expected results, the RapidSMS-MCH system was customized to allow interactive communication between a community health worker (CHW)following mother-infant pairs in their community, a national centralized database, the health facility and in case of an emergency alert, the ambulance driver. The RapidSMS-MCH system was piloted in Musanze district, Nothern province of Rwanda over a 12-month period.

RESULTS: A total of 432 CHW were trained and equipped with mobile phones. A total of 35,734 SMS were sent by 432 CHW from May 2010 to April 2011. A total of 11,502 pregnancies were monitored. A total of 362 SMS alerts for urgent and life threatening events were registered. We registered a 27\% increase in facility based delivery from 72\% twelve months before to 92\% at the end of the twelve months pilot phase. Major challenges were telephone maintenance and replacement. Disctrict heath team capacity to manage and supervise the system was strengthened by the end of pilot phase. Highly committed CHWs and effective coordination by the District health team were critical enablers.

CONCLUSION: We successully designed and implemented a mobile phone SMS-based system to track pregnancy and maternal and child outcomes in limited resources setting. Implementation of mobile-phone systems at community level could contribute to improving emergency obstetric and neonatal care, yet it requires a well-organized community health structure in limited resource settings.

}, keywords = {Cell Phones, Child Mortality, Child, Preschool, Emergency Medical Services, Female, Fetal Death, Health Plan Implementation, Humans, Infant, Newborn, Maternal Death, Maternal Health Services, Maternal-Child Health Centers, Monitoring, Physiologic, Pregnancy, Prenatal Care, Program Development, Rwanda, Telemedicine}, issn = {1937-8688}, author = {Ngabo, Fidele and Nguimfack, Judith and Nwaigwe, Friday and Mugeni, Catherine and Muhoza, Denis and Wilson, David R and Kalach, John and Gakuba, Richard and Karema, Corrine and Binagwaho, Agnes} } @article {816, title = {Developing open source, self-contained disease surveillance software applications for use in resource-limited settings.}, journal = {BMC Med Inform Decis Mak}, volume = {12}, year = {2012}, month = {2012}, pages = {99}, abstract = {UNLABELLED: ABSTRACT: BACKGROUND: Emerging public health threats often originate in resource-limited countries. In recognition of this fact, the World Health Organization issued revised International Health Regulations in 2005, which call for significantly increased reporting and response capabilities for all signatory nations. Electronic biosurveillance systems can improve the timeliness of public health data collection, aid in the early detection of and response to disease outbreaks, and enhance situational awareness. METHODS: As components of its Suite for Automated Global bioSurveillance (SAGES) program, The Johns Hopkins University Applied Physics Laboratory developed two open-source, electronic biosurveillance systems for use in resource-limited settings. OpenESSENCE provides web-based data entry, analysis, and reporting. ESSENCE Desktop Edition provides similar capabilities for settings without internet access. Both systems may be configured to collect data using locally available cell phone technologies. RESULTS: ESSENCE Desktop Edition has been deployed for two years in the Republic of the Philippines. Local health clinics have rapidly adopted the new technology to provide daily reporting, thus eliminating the two-to-three week data lag of the previous paper-based system. CONCLUSIONS: OpenESSENCE and ESSENCE Desktop Edition are two open-source software products with the capability of significantly improving disease surveillance in a wide range of resource-limited settings. These products, and other emerging surveillance technologies, can assist resource-limited countries compliance with the revised International Health Regulations.}, issn = {1472-6947}, doi = {10.1186/1472-6947-12-99}, author = {Campbell, Timothy C and Hodanics, Charles J and Babin, Steven M and Poku, Adjoa M and Wojcik, Richard A and Skora, Joseph F and Coberly, Jacqueline S and Mistry, Zarna S and Lewis, Sheri H} } @inbook {792, title = {Development of a Laparoscopic Surgical Training System with Simulation Open Framework Architecture (SOFA)}, booktitle = {Computer Aided Surgery}, series = {Proceedings in Information and Communications Technology}, volume = {3}, year = {2012}, pages = {83-91}, publisher = {Springer Japan}, organization = {Springer Japan}, abstract = {With a number of advantages over traditional laparotomy, laparoscopic surgery is a successful minimally invasive surgical procedure. However, laparoscopy demands high surgical skill. For efficient and safe training, virtual surgery simulation systems have been developed recently. In this paper, we describe the development of a laparoscopic surgery training system using Simulation Open Framework Architecture (SOFA). The simulation software was integrated with a two-hand haptic device specially developed for laparoscopic surgical training. As an example, we focused on the simulation of gallbladder removal surgery using laparoscopic instruments. Gallbladder removal was successfully simulated by the proposed methods. We expect this training system to be similarly successful in simulating a number of other surgical procedures.}, isbn = {978-4-431-54094-6}, url = {http://dx.doi.org/10.1007/978-4-431-54094-6_10}, author = {Kim, Youngjun and Kim, Kyunghwan and Roy, Fr{\'e}d{\'e}rick and Park, Sehyung}, editor = {Dohi, Takeyoshi and Liao, Hongen} } @article {804, title = {Development of a Next-Generation Automated DICOM Processing System in a PACS-Less Research Environment.}, journal = {J Digit Imaging}, year = {2012}, month = {2012 May 1}, abstract = {The use of clinical imaging modalities within the pharmaceutical research space provides value and challenges. Typical clinical settings will utilize a Picture Archive and Communication System (PACS) to transmit and manage Digital Imaging and Communications in Medicine (DICOM) images generated by clinical imaging systems. However, a PACS is complex and provides many features that are not required within a research setting, making it difficult to generate a business case and determine the return on investment. We have developed a next-generation DICOM processing system using open-source software, commodity server hardware such as Apple Xserve{\textregistered}, high-performance network-attached storage (NAS), and in-house-developed preprocessing programs. DICOM-transmitted files are arranged in a flat file folder hierarchy easily accessible via our downstream analysis tools and a standard file browser. This next-generation system had a minimal construction cost due to the reuse of all the components from our first-generation system with the addition of a second server for a few thousand dollars. Performance metrics were gathered and the system was found to be highly scalable, performed significantly better than the first-generation system, is modular, has satisfactory image integrity, and is easier to maintain than the first-generation system. The resulting system is also portable across platforms and utilizes minimal hardware resources, allowing for easier upgrades and migration to smaller form factors at the hardware end-of-life. This system has been in production successfully for 8~months and services five clinical instruments and three pre-clinical instruments. This system has provided us with the necessary DICOM C-Store functionality, eliminating the need for a clinical PACS for day-to-day image processing.}, issn = {1618-727X}, doi = {10.1007/s10278-012-9482-6}, author = {Ziegler, Scott E} } @inbook {1080, title = {Development of an mHealth Open Source Platform for Diabetic Foot Ulcers Tele-consultations}, booktitle = {Wireless Mobile Communication and Healthcare}, series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering}, volume = {83}, year = {2012}, pages = {158-164}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, keywords = {diabetic foot ulcers, m-health, Telemedicine}, isbn = {978-3-642-29733-5}, doi = {10.1007/978-3-642-29734-2_22}, url = {http://dx.doi.org/10.1007/978-3-642-29734-2_22}, author = {Dafoulas, GeorgeE. and Koutsias, Stylianos and Behar, Joachim and Osorio, Juan and Malley, Brian and Gruentzig, Alexander and Celi, LeoAnthony and Angelidis, Pantelis and Theodorou, Kyriaki and Giannoukas, Athanasios}, editor = {Nikita, KonstantinaS. and Lin, JamesC. and Fotiadis, DimitriosI. and Arredondo Waldmeyer, Maria-Teresa} } @inbook {851, title = {Development of an mHealth Open Source Platform for Diabetic Foot Ulcers Tele-consultations}, booktitle = {Wireless Mobile Communication and Healthcare}, series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering}, volume = {83}, year = {2012}, pages = {158-164}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Diabetes is one of the foremost causes of death in many countries and a leading cause of blindness, renal failure, and non-traumatic amputation. Therefore, diabetic foot ulceration and amputation cause extensive burden on individuals and health care systems in developed and developing countries. Due to the multi-disciplinary requirements for the treatment of diabetic foot ulceration, telemedicine has been introduced to facilitate the access of the patients to specialized health professionals. In this paper the development of an open source mobile health platform is presented, able to support diagnostic algorithms, with the use of a smartphone.}, keywords = {diabetic foot ulcers, m-health, Telemedicine}, isbn = {978-3-642-29733-5}, doi = {10.1007/978-3-642-29734-2_22}, url = {http://dx.doi.org/10.1007/978-3-642-29734-2_22}, author = {Dafoulas, GeorgeE. and Koutsias, Stylianos and Behar, Joachim and Osorio, Juan and Malley, Brian and Gruentzig, Alexander and Celi, LeoAnthony and Angelidis, Pantelis and Theodorou, Kyriaki and Giannoukas, Athanasios}, editor = {Nikita, KonstantinaS. and Lin, JamesC. and Fotiadis, DimitriosI. and Arredondo Waldmeyer, Maria-Teresa} } @article {784, title = {DicomBrowser: Software for Viewing and Modifying DICOM Metadata.}, journal = {J Digit Imaging}, year = {2012}, month = {2012 Feb 15}, abstract = {Digital Imaging and Communications in Medicine (DICOM) is the dominant standard for medical imaging data. DICOM-compliant devices and the data they produce are generally designed for clinical use and often do not match the needs of users in research or clinical trial settings. DicomBrowser is software designed to ease the transition between clinically oriented DICOM tools and the specialized workflows of research imaging. It supports interactive loading and viewing of DICOM images and metadata across multiple studies and provides a rich and flexible system for modifying DICOM metadata. Users can make ad hoc changes in a graphical user interface, write metadata modification scripts for batch operations, use partly automated methods that guide users to modify specific attributes, or combine any of these approaches. DicomBrowser can save modified objects as local files or send them to a DICOM storage service using the C-STORE network protocol. DicomBrowser is open-source software, available for download at http://nrg.wustl.edu/software/dicom-browser .}, issn = {1618-727X}, doi = {10.1007/s10278-012-9462-x}, author = {Archie, Kevin A and Marcus, Daniel S} } @article {799, title = {A framework for mapping, visualisation and automatic model creation of signal-transduction networks.}, journal = {Mol Syst Biol}, volume = {8}, year = {2012}, month = {2012}, pages = {578}, abstract = {Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal-transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system.}, issn = {1744-4292}, doi = {10.1038/msb.2012.12}, author = {Tiger, Carl-Fredrik and Krause, Falko and Cedersund, Gunnar and Palm{\'e}r, Robert and Klipp, Edda and Hohmann, Stefan and Kitano, Hiroaki and Krantz, Marcus} } @article {815, title = {Free and open-source software application for the evaluation of coronary computed tomography angiography images.}, journal = {Arq Bras Cardiol}, year = {2012}, month = {2012 Oct 2}, abstract = {BACKGROUND: The standardization of images used in Medicine in 1993 was performed using the DICOM (Digital Imaging and Communications in Medicine) standard. Several tests use this standard and it is increasingly necessary to design software applications capable of handling this type of image; however, these software applications are not usually free and open-source, and this fact hinders their adjustment to most diverse interests. OBJECTIVE: To develop and validate a free and open-source software application capable of handling DICOM coronary computed tomography angiography images. METHODS: We developed and tested the ImageLab software in the evaluation of 100 tests randomly selected from a database. We carried out 600 tests divided between two observers using ImageLab and another software sold with Philips Brilliance computed tomography appliances in the evaluation of coronary lesions and plaques around the left main coronary artery (LMCA) and the anterior descending artery (ADA). To evaluate intraobserver, interobserver and intersoftware agreements, we used simple and kappa statistics agreements. RESULTS: The agreements observed between software applications were generally classified as substantial or almost perfect in most comparisons. CONCLUSION: The ImageLab software agreed with the Philips software in the evaluation of coronary computed tomography angiography tests, especially in patients without lesions, with lesions < 50\% in the LMCA and < 70\% in the ADA. The agreement for lesions > 70\% in the ADA was lower, but this is also observed when the anatomical reference standard is used.}, issn = {1678-4170}, author = {Hadlich, Marcelo Souza and Oliveira, Gl{\'a}ucia Maria Moraes and Feij{\'o}o, Ra{\'u}l A and Azevedo, Clerio F and Tura, Bernardo Rangel and Ziemer, Paulo Gustavo Portela and Blanco, Pablo Javier and Pina, Gustavo and Meira, M{\'a}rcio and Souza E Silva, Nelson Albuquerque de} } @conference {811, title = {Implementing a Personal Health Record Cloud Platform Using Ciphertext-Policy Attribute-Based Encryption}, booktitle = {Intelligent Networking and Collaborative Systems (INCoS), 2012 4th International Conference on}, year = {2012}, month = {sept.}, abstract = {Work on designing and implementing a patient-centric, personal health record cloud platform based on open-source Indivo X system. We adopt cipher text-policy attribute-based encryption to provide privacy protection and fine-grained access control.}, doi = {10.1109/iNCoS.2012.65}, author = {Wang, Changji and Liu, Xuan and Li, Wentao} } @article {805, title = {The Importance of Using Open Source Technologies and Common Standards for Interoperability within eHealth: Perspectives from the Millennium Villages Project}, journal = {Advances in Health Care Management}, volume = {Advances in Health Care Management}, year = {2012}, pages = {189{\textendash}204}, abstract = {Purpose {\textendash} The purpose of this chapter is to illustrate the importance of using open source technologies and common standards for interoperability when implementing eHealth systems, and to illustrate this through case studies, where possible. Design/methodology/approach {\textendash} The sources used to inform this chapter draw from the implementation and evaluation of the eHealth Program in the context of the Millennium Villages Project (MVP). Findings {\textendash} As the eHealth Team was tasked to deploy an eHealth architecture, the Millennium Villages Global-Network (MVG-Net), across all 14 of the MVP sites in sub-Saharan Africa, the team not only recognized the need for standards and uniformity but also realized that context would be an important factor. Therefore, the team decided to utilize open source solutions. Practical implications {\textendash} The MVP implementation of MVG-Net provides a model for those looking to implement informatics solutions across disciplines and countries. Furthermore, there are valuable lessons learned that the eHealth community can benefit from. Originality/value {\textendash} By sharing lessons learned and developing an accessible, open source eHealth platform, we believe that we can more efficiently and rapidly achieve the health-related and collaborative Millennium Development Goals.}, issn = {978-1-78052-858-8}, doi = {10.1108/S1474-8231(2012)0000012013}, author = {Andrew S. Kanter, Rob Borland, Mourice Barasa, Casey Iiams-Hauser, Olivia Velez, Nadi Nina Kaonga, Matt Berg} } @article {796, title = {Improving quality and use of data through data-use workshops: Zanzibar, United Republic of Tanzania.}, journal = {Bull World Health Organ}, volume = {90}, year = {2012}, month = {2012 May 1}, pages = {379-84}, abstract = {PROBLEM: In Zanzibar, United Republic of Tanzania, as in many developing countries, health managers lack faith in the national Health Management Information System (HMIS). The establishment of parallel data collection systems generates a vicious cycle: national health data are used little because they are of poor quality, and their relative lack of use, in turn, makes their quality remain poor. APPROACH: An action research approach was applied to strengthen the use of information and improve data quality in Zanzibar. The underlying premise was that encouraging use in small incremental steps could help to break the vicious cycle and improve the HMIS. LOCAL SETTING: To test the hypothesis at the national and district levels a project to strengthen the HMIS was established in Zanzibar. The project included quarterly data-use workshops during which district staff assessed their own routine data and critiqued their colleagues{\textquoteright} data. RELEVANT CHANGES: The data-use workshops generated inputs that were used by District Health Information Software developers to improve the tool. The HMIS, which initially covered only primary care outpatients and antenatal care, eventually grew to encompass all major health programmes and district and referral hospitals. The workshops directly contributed to improvements in data coverage, data set quality and rationalization, and local use of target indicators. LESSONS LEARNT: Data-use workshops with active engagement of data users themselves can improve health information systems overall and enhance staff capacity for information use, presentation and analysis for decision-making.}, issn = {1564-0604}, doi = {10.2471/BLT.11.099580}, author = {Braa, J{\o}rn and Heywood, Arthur and Sahay, Sundeep} } @article {905, title = {Informatics in radiology: An open-source and open-access cancer Biomedical Informatics Grid Annotation and Image Markup Template Builder}, journal = {Radiographics}, volume = {32}, year = {2012}, pages = {1223{\textendash}1232}, abstract = {In a routine clinical environment or clinical trial, a case report form or structured reporting template can be used to quickly generate uniform and consistent reports. Annotation and Image Markup (AIM), a project supported by the National Cancer Institute{\textquoteright}s cancer Biomedical Informatics Grid, can be used to collect information for a case report form or structured reporting template. AIM is designed to store, in a single information source, (a) the description of pixel data with use of markups or graphical drawings placed on the image, (b) calculation results (which may or may not be directly related to the markups), and (c) supplemental information. To facilitate the creation of AIM annotations with data entry templates, an AIM template schema and an open-source template creation application were developed to assist clinicians, image researchers, and designers of clinical trials to quickly create a set of data collection items, thereby ultimately making image information more readily accessible. {\textcopyright} RSNA, 2012.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84863860787\&partnerID=40\&md5=154429b57f255f957ea8a13055866456}, author = {Mongkolwat, P.a and Channin, D.S.b and Kleper, V.a and Rubin, D.L.c} } @article {793, title = {Integrating clinical practice and public health surveillance using electronic medical record systems.}, journal = {Am J Prev Med}, volume = {42}, year = {2012}, month = {2012 Jun}, pages = {S154-62}, abstract = {Electronic medical record (EMR) systems have rich potential to improve integration between primary care and the public health system at the point of care. EMRs make it possible for clinicians to contribute timely, clinically detailed surveillance data to public health practitioners without changing their existing workflows or incurring extra work. New surveillance systems can extract raw data from providers{\textquoteright} EMRs, analyze them for conditions of public health interest, and automatically communicate results to health departments. The current paper describes a model EMR-based public health surveillance platform called Electronic Medical Record Support for Public Health (ESP). The ESP platform provides live, automated surveillance for notifiable diseases, influenza-like illness, and diabetes prevalence, care, and complications. Results are automatically transmitted to state health departments.}, issn = {1873-2607}, doi = {10.1016/j.amepre.2012.04.005}, author = {Klompas, Michael and McVetta, Jason and Lazarus, Ross and Eggleston, Emma and Haney, Gillian and Kruskal, Benjamin A and Yih, W Katherine and Daly, Patricia and Oppedisano, Paul and Beagan, Brianne and Lee, Michael and Kirby, Chaim and Heisey-Grove, Dawn and DeMaria, Alfred and Platt, Richard} } @article {801, title = {Integration of the Image-Guided Surgery Toolkit (IGSTK) into the Medical Imaging Interaction Toolkit (MITK).}, journal = {J Digit Imaging}, year = {2012}, month = {2012 Apr 26}, abstract = {The development cycle of an image-guided surgery navigation system is too long to meet current clinical needs. This paper presents an integrated system developed by the integration of two open-source software (IGSTK and MITK) to shorten the development cycle of the image-guided surgery navigation system and save human resources simultaneously. An image-guided surgery navigation system was established by connecting the two aforementioned open-source software libraries. It used the Medical Imaging Interaction Toolkit (MITK) as a framework providing image processing tools for the image-guided surgery navigation system of medical imaging software with a high degree of interaction and used the Image-Guided Surgery Toolkit (IGSTK) as a library that provided the basic components of the system for location, tracking, and registration. The electromagnetic tracking device was used to measure the real-time position of surgical tools and fiducials attached to the patient{\textquoteright}s anatomy. IGSTK was integrated into MITK; at the same time, the compatibility and the stability of this system were emphasized. Experiments showed that an integrated system of the image-guided surgery navigation system could be developed in 2~months. The integration of IGSTK into MITK is feasible. Several techniques for 3D reconstruction, geometric analysis, mesh generation, and surface data analysis for medical image analysis of MITK can connect with the techniques for location, tracking, and registration of IGSTK. This integration of advanced modalities can decrease software development time and emphasize the precision, safety, and robustness of the image-guided surgery navigation system.}, issn = {1618-727X}, doi = {10.1007/s10278-012-9477-3}, author = {Lu, Tong and Liang, Ping and Wu, Wen-Bo and Xue, Jin and Lei, Cheng-Long and Li, Yin-Yan and Sun, Yun-Na and Liu, Fang-Yi} } @conference {838, title = {Interactive Electromechanical Model of the Heart for Patient-Specific Therapy Planning and Training using SOFA}, booktitle = {VPH 2012}, year = {2012}, address = {Londres, United Kingdom}, abstract = {The contributions of this work are twofold. First, we developed an electrophysiological training simulator in SOFA which tackles the interactive issue in the context of cardiac arrhythmias. Coupled with this electrophysiology, we developed a mechanical model of the heart that can be personalized from MRI datasets. Our simulations are based on the SOFA platform. SOFA is an open-source framework targeted at real-time simulation with an emphasis on medical simulation, mainly developed at Inria. A large choice of efficient solvers, hyperelastic or viscous material laws are already implemented in SOFA. Moreover, it enables interactivity during the simulation (pacing, surgery planning, ...) and gives a good trade-off between accuracy and computational efficiency.}, url = {http://hal.inria.fr/hal-00751537}, author = {Talbot, Hugo and Marchesseau, St{\'e}phanie and Duriez, Christian and Courtecuisse, Hadrien and Relan, Jatin and Sermesant, Maxime and Cotin, St{\'e}phane and Delingette, Herv{\'e}} } @article {820, title = {MITK Diffusion Imaging.}, journal = {Methods Inf Med}, volume = {51}, year = {2012}, month = {2012 Oct 11}, pages = {441-8}, abstract = {Background: Diffusion-MRI provides a unique window on brain anatomy and insights into aspects of tissue structure in living humans that could not be studied previously. There is a major effort in this rapidly evolving field of research to develop the algorithmic tools necessary to cope with the complexity of the datasets. Objectives: This work illustrates our strategy that encompasses the development of a modularized and open software tool for data processing, visualization and interactive exploration in diffusion imaging research and aims at reinforcing sustainable evaluation and progress in the field. Methods: In this paper, the usability and capabilities of a new application and toolkit component of the Medical Imaging and Interaction Toolkit (MITK, www.mitk.org), MITK-DI, are demonstrated using in-vivo datasets. Results: MITK-DI provides a comprehensive software framework for high-performance data processing, analysis and interactive data exploration, which is designed in a modular, extensible fashion (using CTK) and in adherence to widely accepted coding standards (e.g. ITK, VTK). MITK-DI is available both as an open source software development toolkit and as a ready-to-use installable application. Conclusions: The open source release of the modular MITK-DI tools will increase verifiability and comparability within the research community and will also be an important step towards bringing many of the current techniques towards clinical application.}, issn = {0026-1270}, doi = {10.3414/ME11-02-0031}, author = {Fritzsche, K H and Neher, P F and Reicht, I and van Bruggen, T and Goch, C and Reisert, M and Nolden, M and Zelzer, S and Meinzer, H-P and Stieltjes, B} } @conference {785, title = {MITK global tractography}, booktitle = {Medical Imaging 2012: Image Processing}, year = {2012}, publisher = {SPIE}, organization = {SPIE}, abstract = {Fiber tracking algorithms yield valuable information for neurosurgery as well as automated diagnostic approaches. However, they have not yet arrived in the daily clinical practice. In this paper we present an open source integration of the global tractography algorithm proposed by Reisert et.al.1 into the open source Medical Imaging Interaction Toolkit (MITK) developed and maintained by the Division of Medical and Biological Informatics at the German Cancer Research Center (DKFZ). The integration of this algorithm into a standardized and open development environment like MITK enriches accessibility of tractography algorithms for the science community and is an important step towards bringing neuronal tractography closer to a clinical application. The MITK diffusion imaging application, downloadable from www.mitk.org, combines all the steps necessary for a successful tractography: preprocessing, reconstruction of the images, the actual tracking, live monitoring of intermediate results, postprocessing and visualization of the final tracking results. This paper presents typical tracking results and demonstrates the steps for pre- and post-processing of the images.}, doi = {10.1117/12.911215}, url = {http://link.aip.org/link/?PSI/8314/83144D/1}, author = {Peter F. Neher and Bram Stieltjes and Marco Reisert and Ignaz Reicht and Meinzer, Hans-Peter and Klaus H. Fritzsche}, editor = {David R. Haynor and Sebastien Ourselin} } @article {908, title = {The National Alliance for Medical Image Computing, a roadmap initiative to build a free and open source software infrastructure for translational research in medical image analysis}, journal = {Journal of the American Medical Informatics Association}, volume = {19}, year = {2012}, pages = {176{\textendash}180}, abstract = {The National Alliance for Medical Image Computing (NA-MIC), is a multi-institutional, interdisciplinary community of researchers, who share the recognition that modern health care demands improved technologies to ease suffering and prolong productive life. Organized under the National Centers for Biomedical Computing 7 years ago, the mission of NA-MIC is to implement a robust and flexible open-source infrastructure for developing and applying advanced imaging technologies across a range of important biomedical research disciplines. A measure of its success, NA-MIC is now applying this technology to diseases that have immense impact on the duration and quality of life: cancer, heart disease, trauma, and degenerative genetic diseases. The targets of this technology range from group comparisons to subject-specific analysis.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84857161947\&partnerID=40\&md5=c7d7cbab9304114a219812cb7c5091ee}, author = {Kapur, T.a and Pieper, S.b and Whitaker, R.c and Aylward, S.d and Jakab, M.a and Schroeder, W.d and Kikinis, R.a} } @article {791, title = {Navigated laparoscopy - liver shift and deformation due to pneumoperitoneum in an animal model.}, journal = {Minim Invasive Ther Allied Technol}, volume = {21}, year = {2012}, month = {2012 May}, pages = {241-8}, abstract = {Abstract Background: Precise laparoscopic liver resection requires accurate planning and visualization of important anatomy such as vessels and tumors. Combining laparoscopic ultrasound with navigation technology could provide this. Preoperative images are valuable for planning and overview of the procedure, while intraoperative images provide an updated view of the surgical field. Purpose: To validate the accuracy of navigation technology based on preoperative images, we need to understand how much the liver shifts and deforms due to heartbeat, breathing, surgical manipulation and pneumoperitoneum. In this study, we evaluated liver tumor shift and deformation due to pneumoperitoneum in an animal model. Methods: Tumor models were injected into the liver of the animal, and 3D CT images were acquired before and after insufflation. Tumor shifts and deformation were determined. Results: The results showed significant tumor position shift due to pneumoperitoneum, with a maximum of 28 mm in cranio-caudal direction. No significant tumor deformation was detected. Small standard deviations suggest rigid body transformation of the liver as a whole, but this needs further investigation. Conclusion: The findings indicate a need for anatomic shift correction of preoperative images before they are used in combination with LUS guidance during a laparoscopic liver resection procedure.}, issn = {1365-2931}, doi = {10.3109/13645706.2012.665805}, author = {Zijlmans, Mariken and Lang{\o}, Thomas and Hofstad, Erlend Fagertun and Van Swol, Christiaan F P and Rethy, Anna} } @conference {819, title = {Net4Care: Towards a Mission-Critical Software Ecosystem}, booktitle = {Software Architecture (WICSA) and European Conference on Software Architecture (ECSA), 2012 Joint Working IEEE/IFIP Conference on}, year = {2012}, month = {aug.}, abstract = {The demographics of the western world is changing: people are getting older and as a partial consequence get an increasing number of chronic diseases such as diabetes, chronic obstructive pulmonary disease (COPD), and coronary disease. At the same time, healthcare systems are stressed for resources, health centers are getting larger and more distributed, and the number of healthcare professionals does not follow the trend in chronic diseases. All of this leads to a need for telemedical and mobile health applications. In a Danish context, these applications are often developed through local (innovative) initiatives with little regards for national and global (standardization) initiatives. A reason for this discrepancy is that the software architecture for national (and global) systems and standards are hard to understand, hard to develop systems based on, and hard to deploy. To counter this, we propose a software ecosystem approach for telemedicine applications, providing a framework, Net4Care, encapsulating national/global design decisions with respect to standardization while allowing for local innovation. This paper presents an analysis of existing systems, of requirements for a software ecosystem for telemedicine, and a summary of initial design decisions for the Net4Care framework.}, doi = {10.1109/WICSA-ECSA.212.34}, author = {Christensen, Henrik Baerbak and Hansen, Klaus Marius} } @article {1055, title = {The NIH National Center for Integrative Biomedical Informatics (NCIBI).}, journal = {J Am Med Inform Assoc}, volume = {19}, year = {2012}, month = {2012 Mar-Apr}, pages = {166-70}, abstract = {

The National Center for Integrative and Biomedical Informatics (NCIBI) is one of the eight NCBCs. NCIBI supports information access and data analysis for biomedical researchers, enabling them to build computational and knowledge models of biological systems to address the Driving Biological Problems (DBPs). The NCIBI DBPs have included prostate cancer progression, organ-specific complications of type 1 and 2 diabetes, bipolar disorder, and metabolic analysis of obesity syndrome. Collaborating with these and other partners, NCIBI has developed a series of software tools for exploratory analysis, concept visualization, and literature searches, as well as core database and web services resources. Many of our training and outreach initiatives have been in collaboration with the Research Centers at Minority Institutions (RCMI), integrating NCIBI and RCMI faculty and students, culminating each year in an annual workshop. Our future directions include focusing on the TranSMART data sharing and analysis initiative.

}, keywords = {Biomedical Research, Databases as Topic, Forecasting, Goals, Information Dissemination, Integrative Medicine, Medical Informatics, National Institutes of Health (U.S.), United States}, issn = {1527-974X}, doi = {10.1136/amiajnl-2011-000552}, author = {Athey, Brian D and Cavalcoli, James D and Jagadish, H V and Omenn, Gilbert S and Mirel, Barbara and Kretzler, Matthias and Burant, Charles and Isokpehi, Raphael D and DeLisi, Charles} } @article {772, title = {Open Sourse Software Development on Medical Domain}, year = {2012}, publisher = {InTech}, edition = {Christos Kalloniatis}, issn = {978-953-51-0647-0}, doi = {10.5772/38117}, url = {http://www.intechopen.com/books/modern-information-systems/open-source-software-in-medicine}, author = {Shinji Kobayashi} } @article {817, title = {Open-source point-of-care electronic medical records for use in resource-limited settings: systematic review and questionnaire surveys.}, journal = {BMJ Open}, volume = {2}, year = {2012}, month = {2012}, abstract = {BACKGROUND: Point-of-care electronic medical records (EMRs) are a key tool to manage chronic illness. Several EMRs have been developed for use in treating HIV and tuberculosis, but their applicability to primary care, technical requirements and clinical functionalities are largely unknown. OBJECTIVES: This study aimed to address the needs of clinicians from resource-limited settings without reliable internet access who are considering adopting an open-source EMR. STUDY ELIGIBILITY CRITERIA: Open-source point-of-care EMRs suitable for use in areas without reliable internet access. STUDY APPRAISAL AND SYNTHESIS METHODS: The authors conducted a comprehensive search of all open-source EMRs suitable for sites without reliable internet access. The authors surveyed clinician users and technical implementers from a single site and technical developers of each software product. The authors evaluated availability, cost and technical requirements. RESULTS: The hardware and software for all six systems is easily available, but they vary considerably in proprietary components, installation requirements and customisability. LIMITATIONS: This study relied solely on self-report from informants who developed and who actively use the included products. CONCLUSIONS AND IMPLICATIONS OF KEY FINDINGS: Clinical functionalities vary greatly among the systems, and none of the systems yet meet minimum requirements for effective implementation in a primary care resource-limited setting. The safe prescribing of medications is a particular concern with current tools. The dearth of fully functional EMR systems indicates a need for a greater emphasis by global funding agencies to move beyond disease-specific EMR systems and develop a universal open-source health informatics platform.}, issn = {2044-6055}, doi = {10.1136/bmjopen-2011-000690}, author = {Millard, Peter S and Bru, Juan and Berger, Christopher A} } @article {898, title = {Opportunities and Challenges of Open Source Software Integration in Developing Countries: Case of Zanzibar Health Sector}, journal = {Journal of Health Informatics in Developing Countries}, volume = {6}, year = {2012}, abstract = {This paper describes the opportunities and related challenges of integrating Open Source Software process in organization. It focuses on technical and organizational part of the integration practice in Open Source Software philosophy. Thus, several issues about opportunities and challenges of integration have been identified, including the homogeneity of the systems in place and cooperation nature of integration. In essence, integration has proved to be the solution to several technical and administrative capacity problems that face health sector in Zanzibar.}, keywords = {heterogeneous., homogeneous, ntegration process, open source software}, author = {BAKAR, Abubakar and SHEIKH, Yahya and SULTAN, Bakar} } @inbook {794, title = {Overview of the Most Important Open Source Software: Analysis of the Benefits of OpenMRS, OpenEMR, and VistA}, booktitle = {Telemedicine and E-Health Services, Policies, and Applications: Advancements and Developments}, year = {2012}, pages = {315{\textendash}346}, publisher = {IGI Global}, organization = {IGI Global}, address = {Hershey, PA, USA}, abstract = {In this chapter, the authors review software that enables the proper management of EHR. The different types of software share the feature of being open source and offer the best opportunity in health care to developing countries{\textemdash}an overall integrated approach. The authors analyze the main free software programs (technical features, programming languages, places for introduction, etc.). Then they focus on the description and the comparison of the three most important open source software programs EHR (OpenMRS, OpenVistA, and OpenEMR) that are installed on two operating systems (Linux Ubuntu and Windows). Finally, the authors show the results of the various parameters measured in these systems after using different Web browsers. The results show us how the three main EHR applications work depending on which operating system is installed and which web browser is used.}, isbn = {9781466608887}, doi = {10.4018/978-1-4666-0888-7.ch012}, url = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/978-1-4666-0888-7.ch012}, author = {Sainz de Abajo, Beatriz and Agust{\'\i}n Llamas Ballestero} } @article {828, title = {A quick guide to software licensing for the scientist-programmer.}, journal = {PLoS Comput Biol}, volume = {8}, year = {2012}, month = {2012}, pages = {e1002598}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002598}, author = {Morin, Andrew and Urban, Jennifer and Sliz, Piotr} } @conference {774, title = {Research and implementation of Electronic Medical Records Editing System based on CDA}, booktitle = {Consumer Electronics, Communications and Networks (CECNet), 2012 2nd International Conference on}, year = {2012}, month = {april}, abstract = {It is difficult to exchange information between heterogeneous Hospital Information Systems (HIS). It becomes the obstacle of regional medical system establishment. The coming forth of HL7 (Health Level 7) CDA (Clinical Document Architecture) standard provides the technical basic conditions. This paper describes CDA standards and CDA document structure. Through a complete analysis of Electronic Medical Record (EMR), the model of Electronic Medical Records Editing Subsystem is given. Based on this model, functional modules of Electronic Medical Records Editing Subsystem are designed and implemented. Through Electronic Medical Records Editing Subsystem, clinical documents can effectively produce, parse, validate and view. It provides a technical support for exchanges of medical and health information.}, keywords = {CDA document structure, CDA standards, clinical document architecture, document handling, electronic medical records editing system, EMR, health level 7, HIS, HL7, hospital information systems, information exchange, medical information systems, regional medical system establishment}, doi = {10.1109/CECNet.2012.6201451}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=\&arnumber=6201451\&contentType=Conference+Publications\&queryText\%3DResearch+and+implementation+of+Electronic+Medical+Records+Editing+System+based+on+CDA}, author = {Lu Xiaoqi and Yu Ning and Gu Yu and Jia Weitao} } @article {1050, title = {S2DIA: a diagnostic system for Diabetes mellitus using SANA platform.}, journal = {Conf Proc IEEE Eng Med Biol Soc}, volume = {2012}, year = {2012}, month = {2012}, pages = {6078-81}, abstract = {

Currently, Diabetes is a very common disease around the world, and with an increase in sedentary lifestyles, obesity and an aging population the number of people with Diabetes worldwide will increase by more than 50\%. In this context, the MIT (Massachusetts Institute of Technology) developed the SANA platform, which brings the benefits of information technology to the field of healthcare. It offers healthcare delivery in remote areas, improves patient access to medical specialists for faster, higher quality, and more cost effective diagnosis and intervention. For these reasons, we developed a system for diagnosis of Diabetes using the SANA platform, called S2DIA. It is the first step towards knowing the risks for type 2 Diabetes, and it will be evaluated, especially, in remote/poor areas of Brazil.

}, keywords = {Diabetes Mellitus, Type 2, Diagnosis, Computer-Assisted, Humans, Risk Factors}, issn = {1557-170X}, doi = {10.1109/EMBC.2012.6347380}, author = {Costa, Clayton M and Gondim, Dikson D and Gondim, Dibson D and Soares, Heliana B and Ribeiro, Anna G C D and Silva, Ikaro and Winkler, Erick and Celi, Leo and Guerreiro, Ana M G and Leite, Cic{\'\i}lia R M} } @article {788, title = {The SMART Platform: early experience enabling substitutable applications for electronic health records.}, journal = {J Am Med Inform Assoc}, year = {2012}, month = {2012 Mar 17}, abstract = {ObjectiveThe Substitutable Medical Applications, Reusable Technologies (SMART) Platforms project seeks to develop a health information technology platform with substitutable applications (apps) constructed around core services. The authors believe this is a promising approach to driving down healthcare costs, supporting standards evolution, accommodating differences in care workflow, fostering competition in the market, and accelerating innovation.Materials and methodsThe Office of the National Coordinator for Health Information Technology, through the Strategic Health IT Advanced Research Projects (SHARP) Program, funds the project. The SMART team has focused on enabling the property of substitutability through an app programming interface leveraging web standards, presenting predictable data payloads, and abstracting away many details of enterprise health information technology systems. Containers-health information technology systems, such as electronic health records (EHR), personally controlled health records, and health information exchanges that use the SMART app programming interface or a portion of it-marshal data sources and present data simply, reliably, and consistently to apps.ResultsThe SMART team has completed the first phase of the project (a) defining an app programming interface, (b) developing containers, and (c) producing a set of charter apps that showcase the system capabilities. A focal point of this phase was the SMART Apps Challenge, publicized by the White House, using http://www.challenge.gov website, and generating 15 app submissions with diverse functionality.ConclusionKey strategic decisions must be made about the most effective market for further disseminating SMART: existing market-leading EHR vendors, new entrants into the EHR market, or other stakeholders such as health information exchanges.}, issn = {1527-974X}, doi = {10.1136/amiajnl-2011-000622}, author = {Mandl, Kenneth D and Mandel, Joshua C and Murphy, Shawn N and Bernstam, Elmer Victor and Ramoni, Rachel L and Kreda, David A and McCoy, J Michael and Adida, Ben and Kohane, Isaac S.} } @inbook {789, title = {SOFA: A Multi-Model Framework for Interactive Physical Simulation}, booktitle = {Soft Tissue Biomechanical Modeling for Computer Assisted Surgery}, series = {Studies in Mechanobiology, Tissue Engineering and Biomaterials}, volume = {11}, year = {2012}, pages = {283-321}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Simulation Open Framework Architecture (SOFA) is an open-source C++ library primarily targeted at interactive computational medical simulation. SOFA facilitates collaborations between specialists from various domains, by decomposing complex simulators into components designed independently and organized in a scenegraph data structure. Each component encapsulates one of the aspects of a simulation, such as the degrees of freedom, the forces and constraints, the differential equations, the main loop algorithms, the linear solvers, the collision detection algorithms or the interaction devices. The simulated objects can be represented using several models, each of them optimized for a different task such as the computation of internal forces, collision detection, haptics or visual display. These models are synchronized during the simulation using a mapping mechanism. CPU and GPU implementations can be transparently combined to exploit the computational power of modern hardware architectures. Thanks to this flexible yet efficient architecture, SOFA can be used as a test-bed to compare models and algorithms, or as a basis for the development of complex, high-performance simulators.}, isbn = {978-3-642-29013-8}, doi = {10.1007/8415_2012_125}, url = {http://dx.doi.org/10.1007/8415_2012_125}, author = {Faure, Fran{\c c}ois and Duriez, Christian and Delingette, Herv{\'e} and Allard, J{\'e}r{\'e}mie and Gilles, Benjamin and Marchesseau, St{\'e}phanie and Talbot, Hugo and Courtecuisse, Hadrien and Bousquet, Guillaume and Peterlik, Igor and Cotin, St{\'e}phane}, editor = {Payan, Yohan} } @article {790, title = {Standardized volumetric 3D-analysis of SPECT/CT imaging in orthopaedics: overcoming the limitations of qualitative 2D analysis.}, journal = {BMC Med Imaging}, volume = {12}, year = {2012}, month = {2012}, pages = {5}, abstract = {UNLABELLED: ABSTRACT: BACKGROUND: SPECT/CT combines high resolution anatomical 3D computerized tomography (CT) and single photon emission computerized tomography (SPECT) as functional imaging, which provides 3D information about biological processes into a single imaging modality. The clinical utility of SPECT/CT imaging has been recognized in a variety of medical fields and most recently in orthopaedics; however, clinical adoption has been limited due to shortcomings of analytical tools available. Specifically, SPECT analyses are mainly qualitative due to variation in overall metabolic uptake among patients. Furthermore, most analyses are done in 2D, although rich 3D data are available. Consequently, it is difficult to quantitatively compare the position, size, and intensity of SPECT uptake regions among patients, and therefore difficult to draw meaningful clinical conclusions. METHODS: We propose a method for normalizing orthopaedic SPECT/CT data that enables standardised 3D volumetric quantitative measurements and comparison among patients. Our method is based on 3D localisation using clinically relevant anatomical landmarks and frames of reference, along with intensity value normalisation using clinically relevant reference regions. Using the normalised data, we describe a thresholding technique to distinguish clinically relevant hot spots from background activity. RESULTS: Using an exemplar comparison of two patients, we demonstrate how the normalised, 3D-rendered data can provide a richer source of clinical information and allow quantitative comparison of SPECT/CT measurements across patients. Specifically, we demonstrate how non-normalized SPECT/CT analysis can lead to different clinical conclusions than the normalized SPECT/CT analysis, and that normalized quantitative analysis can be a more accurate indicator of pathology. CONCLUSIONS: Conventional orthopaedic frames of reference, 3D volumetric data analysis and thresholding are used to distinguish clinically relevant hot spots from background activity. Our goal is to facilitate a standardised approach to quantitative data collection and comparison of clinical studies using SPECT/CT, enabling more widespread clinical use of this powerful imaging tool.}, issn = {1471-2342}, doi = {10.1186/1471-2342-12-5}, author = {Hirschmann, Michael T and Wagner, Christopher R and Rasch, Helmut and Henckel, Johann} } @conference {829, title = {A Standards-Based Open Source Application to Gather Health Assessment Data in Developing Countries}, booktitle = {Global Humanitarian Technology Conference (GHTC), 2012 IEEE}, year = {2012}, month = {oct.}, abstract = {Many organizations are working in developing coun- tries to support local health care organizations and infrastructure to provide sustainable, community-based health care. This requires not only the influx of medical staff and supplies, but also requires maintaining individual health care records and enabling the ability to collect, analyze and aggregate data in the field to customize care to the local needs of the community, and to provide continuity of care to its citizens. The recent rise of adoption of standards for electronic health records(EHR) provides an alternative to using paper forms in mobile health clinics that often serve these countries. In this paper, we describe an open-source, standards-based health assessment software application developed by the non-profit organization Health Records For Everyone (HR4E) and field tested in a mobile health clinic in rural Ethiopia in the fall of 2011. The application allows mobile health clinic staff to quickly deploy medical clinics and collect patient data electronically in the face of various environmental challenges. In addition to producing electronic patient records which are validated in-field using HL7{\textquoteright}s Clinical Document Architecture standard, the application allows medical practitioners to view and summarize patient data for in-field analysis.}, keywords = {and Telemedicine, Ash, Communities, Computers, Health, Medical services, Medical Technology, Mobile communication, Software, Standards}, doi = {10.1109/GHTC.2012.78}, author = {Gainer, Alex and Roth, Mary and Strong, Phil and Davis, James} } @article {1036, title = {A static-image telepathology system for dermatopathology consultation in East Africa: the Massachusetts General Hospital Experience.}, journal = {J Am Acad Dermatol}, volume = {67}, year = {2012}, month = {2012 Nov}, pages = {997-1007}, abstract = {

BACKGROUND: The histologic diagnosis of skin lesions in the developing world is complicated by the shortage of pathologists with subspecialty training in dermatopathology, limited access to ancillary diagnostic testing, and costly referrals for expert glass slide consultation in challenging cases.

OBJECTIVE: In this study we evaluate the feasibility of a static-image telepathology platform in Africa for performing accurate dermatopathology consultations.

METHODS: A static-image telepathology platform using the iPath server was utilized by referring pathologists in 4 African hospitals. Diagnostic interpretations were provided by Massachusetts General Hospital dermatopathologists at no cost. The diagnostic accuracy and interobserver correlation was evaluated.

RESULTS: The static histopathologic images were diagnostic in 22 of 29 (76\%) cases. Diagnostic accuracy between static image and glass slide diagnosis in 22 cases was 91\%, ranging from 86\% to 95\% according to years of dermatopathology subspecialty expertise. Comparison with the glass slides showed that the telepathology diagnosis was limited by inappropriate field selection in only one case. Interobserver concordance between two pathologists was high (K = 0.86) suggesting that this platform is easy to use with minimal training of both referring and consulting pathologists.

LIMITATIONS: Concordance between conventional microscopy and static image telepathology was performed in 22 of 29 cases for which glass slides were received. Interobserver concordance was performed for two pathologists.

CONCLUSION: Static-image telepathology is a feasible means of rendering diagnoses on dermatopathology cases and is a cost-effective technology for obtaining much-needed second opinions in resource-poor settings.

}, keywords = {Africa, Eastern, Cost-Benefit Analysis, Feasibility Studies, Hospitals, General, Humans, Massachusetts, Microscopy, Observer Variation, Pathology, Clinical, Remote Consultation, Skin Diseases, Skin Neoplasms, telepathology}, issn = {1097-6787}, doi = {10.1016/j.jaad.2011.12.036}, author = {Gimbel, Devon C and Sohani, Aliyah R and Prasad Busarla, Satya Vara and Kirimi, Jesca Muthoni and Sayed, Shahin and Okiro, Patricia and Nazarian, Rosalynn M} } @article {779, title = {STIR: software for tomographic image reconstruction release 2.}, journal = {Phys Med Biol}, volume = {57}, year = {2012}, month = {2012 Feb 21}, pages = {867-83}, abstract = {We present a new version of STIR (Software for Tomographic Image Reconstruction), an open source object-oriented library implemented in C++~for 3D positron emission tomography reconstruction. This library has been designed such that it can be used for many algorithms and scanner geometries, while being portable to various computing platforms. This second release enhances its flexibility and modular design and includes additional features such as Compton scatter simulation, an additional iterative reconstruction algorithm and parametric image reconstruction (both indirect and direct). We discuss the new features in this release and present example results. STIR can be downloaded from http://stir.sourceforge.net.}, keywords = {Algorithms, Animals, Computers, Image Processing, Computer-Assisted, Mice, Software, Tomography}, issn = {1361-6560}, doi = {10.1088/0031-9155/57/4/867}, author = {Thielemans, Kris and Tsoumpas, Charalampos and Mustafovic, Sanida and Beisel, Tobias and Aguiar, Pablo and Dikaios, Nikolaos and Jacobson, Matthew W} } @article {1037, title = {A telemedicine network to support paediatric care in small hospitals in rural Tanzania.}, journal = {J Telemed Telecare}, volume = {18}, year = {2012}, month = {2012 Jan}, pages = {59-62}, abstract = {

We reviewed our experience with the Tanzanian Telemedicine Network in supporting paediatric care at 40 small, rural hospitals in the country. The network began operating in 2008. Store and forward telemedicine was provided via the open source software iPath. The 33 volunteer consultants were based in several countries, although most of them had practical experience in Tanzania. During the first three years of network operation there were 533 referrals. There were 159 paediatric cases (median age five years). Three paediatric specialists provided most consultations (64\%), but other specialists provided recommendations when required. The response time was usually less than two days (median 6 h; inter-quartile range 2-24 h). A precise recommendation was not always provided, but since all consultants had an intimate knowledge of the state of health services in Tanzania, their advice was usually well adapted to the local circumstances of the hospitals. Referral to a higher level of care was recommended in 26 cases (16\%). A simple web-based telemedicine system combined with email alerts is feasible in remote locations in Tanzania, even where fast Internet connections are not available.

}, keywords = {Child, Child, Preschool, Electronic Mail, Female, Hospitals, Rural, Humans, Internet, Male, Pediatrics, Physician{\textquoteright}s Practice Patterns, Referral and Consultation, Retrospective Studies, Rural Health Services, Tanzania, Telemedicine}, issn = {1758-1109}, doi = {10.1258/jtt.2011.110312}, author = {Kr{\"u}ger, Carsten and Niemi, Mauri} } @article {826, title = {Ten simple rules for the open development of scientific software.}, journal = {PLoS Comput Biol}, volume = {8}, year = {2012}, month = {2012 Dec}, pages = {e1002802}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002802}, author = {Prli{\'c}, Andreas and Procter, James B} } @article {921, title = {[Thyroid storm].}, journal = {Med Klin Intensivmed Notfmed}, volume = {107}, year = {2012}, month = {2012 Sep}, pages = {448-53}, abstract = {

Thyroid storm is a complicated, life-threatening form of thyrotoxicosis. The causes are multifactorial and elevated iodothyronine levels are only one of many components. Usually, the transition from thyrotoxicosis to thyroid storm is ignited by non-thyroidal triggers. This is a rare condition observed with an incidence between 0.8 and 1.4 cases per 100,000 inhabitants. Diagnosis relies primarily on clinical criteria. Multimodal therapy aims at disrupting positive feedback loops between elevated levels of free T3 or T4 and their effects on target tissues and organs. Timely diagnosis and therapy help to reduce mortality to below 35\%.

}, keywords = {Antithyroid Agents, Cross-Sectional Studies, Diagnosis, Differential, Humans, Intensive Care Units, Prognosis, Risk Factors, Survival Rate, Thyroid Crisis, Thyroxine, Triiodothyronine}, issn = {2193-6226}, doi = {10.1007/s00063-012-0113-2}, author = {Dietrich, J W} } @article {844, title = {Towards an international electronic repository and virtual laboratory of open data and open-source software for telehealth research: comparison of international, Australian and finnish privacy policies.}, journal = {Stud Health Technol Inform}, volume = {182}, year = {2012}, month = {2012}, pages = {153-60}, abstract = {

Health data includes all content related to health in all data formats, document types, information systems, publication media and languages from all specialties, organisations, regions, states and countries. Capabilities to share, integrate and compare these data contents, clinical trial results and other evaluation outcomes together with telehealth applications for data processing are critical to accelerate discovery and its diffusion to clinical practice. However, the same ethical and legal frameworks that protect privacy hinder this open data and open-source code approach and the issues accumulate if moving data across national, regional or organisational borders. This can be seen as one of the reasons why many telehealth applications and health-research findings tend to be limited to very narrow domains and global results are lacking. The aim of this paper is to take steps towards establishing an international electronic repository and virtual laboratory of open data and open-source code for research purposes by comparing international, Australian and Finnish frameworks. The frameworks seem to be fundamentally similar; they apply the principles of accountability and adequacy to using and disclosing personal data. Their requirements to inform data subjects about the purposes of data collection and use before the dataset is collected, assure that individuals are no longer identifiable and to destruct data when the research activities are finished make sharing data and even secondary data difficult. Using the Internet or cloud services for sharing without proper approvals by ethics committees is technically not allowed if the data are stored in another country. The research community needs to overcome these barriers and develop a virtual laboratory, which operates on distributed data repositories. This empowers the community by enabling systematic evaluations of new technologies and research hypotheses on a rich variety of data and against existing applications, and subsequent tracking of quality improvements in time.

}, issn = {0926-9630}, author = {Suominen, Hanna} } @article {775, title = {Towards the Adoption of Open Source and Open Access Electronic Health Record Systems}, journal = {Journal of Healthcare Engineering}, volume = {3}, year = {2012}, month = {03}, pages = {141{\textendash}162}, abstract = {As the Electronic Health Record (EHR) systems constantly expand to support more clinical activities and their implementations in healthcare organizations become more widespread, several communities have been working intensively for several years to develop open access and open source EHR software, aiming at reducing the costs of EHR deployment and maintenance. In this paper, we describe and evaluate the most popular open source electronic medical records such as openEMR, openMRS and patientOS, providing their technical features and potentials. These systems are considered quite important due to their prevalence. The article presents the key features of each system and outlines the advantages and problems of Open Source Software (OSS) Systems through a review of the literature, in order to demonstrate the possibility of their adoption in modern electronic healthcare systems. Also discussed are the future trends of OS EHRs in the context of the Personal Health Records and mobile computing paradigm.}, doi = {10.1260/2040-2295.3.1.141}, url = {http://dx.doi.org/10.1260/2040-2295.3.1.141}, author = {Maglogiannis, Ilias} } @article {917, title = {TSH and Thyrotropic Agonists: Key Actors in Thyroid Homeostasis.}, journal = {J Thyroid Res}, volume = {2012}, year = {2012}, month = {2012}, pages = {351864}, abstract = {

This paper provides the reader with an overview of our current knowledge of hypothalamic-pituitary-thyroid feedback from a cybernetic standpoint. Over the past decades we have gained a plethora of information from biochemical, clinical, and epidemiological investigation, especially on the role of TSH and other thyrotropic agonists as critical components of this complex relationship. Integrating these data into a systems perspective delivers new insights into static and dynamic behaviour of thyroid homeostasis. Explicit usage of this information with mathematical methods promises to deliver a better understanding of thyrotropic feedback control and new options for personalised diagnosis of thyroid dysfunction and targeted therapy, also by permitting a new perspective on the conundrum of the TSH reference range.

}, issn = {2042-0072}, doi = {10.1155/2012/351864}, author = {Dietrich, Johannes W and Landgrafe, Gabi and Fotiadou, Elisavet H} } @article {888, title = {The use and role of open source software applications in public and not-for-profit hospitals in the United States.}, journal = {Health Care Manage Rev}, year = {2012}, month = {2012 Oct 31}, abstract = {

BACKGROUND:: The potential cost savings and customizability of open source software (OSS) may be particularly attractive for hospitals. However, numerous health-care-specific OSS applications exist, the adoption of OSS health information technology (HIT) applications is not widespread in the United States. PURPOSE:: This disconnect between the availability of promising software and low adoption raises the basic question: If OSS HIT is so advantageous, why are more health care organizations not using it? METHODOLOGY:: We interviewed the chief information officer, or equivalent position, at 17 not-for-profit and public hospitals across the United States. Through targeted recruitment, our sample included nine hospitals using OSS HIT and eight hospitals not using OSS HIT. The open-ended interview questions were guided by domains included in the fit-viability theory, an organizational-level innovation adoption framework, and those suggested by a review of the literature. Transcripts were analyzed using an inductive and comparative approach, which involved an open coding for relevant themes. FINDINGS:: Interviews described the state of OSS use in hospitals. Specifically, general OSS applications were widely used by IT professionals. In addition, hospitals using OSS HIT still relied heavily on vendor support. In terms of why decisions arose to use OSS HIT, several hospitals using OSS HIT noted the cost advantages. In contrast, hospitals avoiding OSS HIT were clear, OSS as a class did not fit with clinical work and posed too much risk. PRACTICE IMPLICATIONS:: Perceptions of OSS HIT ranged from enthusiastic embracement to resigned adoption, to refusal, to abandonment. Some organizations were achieving success with their OSS HIT choices, but they still relied on vendors for significant support. The decision to adopt OSS HIT was not uniform but contingent upon views of the risk posed by the technology, economic factors, and the hospital{\textquoteright}s existing capabilities.

}, issn = {1550-5030}, doi = {10.1097/HMR.0b013e318276f9ed}, author = {Vest, Joshua R and Stephens, James H} } @article {1012, title = {Use of Electronic Health Records in sub-Saharan Africa: Progress and challenges.}, journal = {J Med Trop}, volume = {14}, year = {2012}, month = {2012}, pages = {1-6}, abstract = {

BACKGROUND: The Electronic Health Record (EHR) is a key component of medical informatics that is increasingly being utilized in industrialized nations to improve healthcare. There is limited information on the use of EHR in sub-Saharan Africa. This paper reviews availability of EHRs in sub-Saharan Africa.

METHODS: Searches were performed on PubMed and Google Scholar databases using the terms {\textquoteright}Electronic Health Records OR Electronic Medical Records OR e-Health and Africa{\textquoteright}. References from identified publications were reviewed. Inclusion criterion was documented use of EHR in Africa.

RESULTS: The search yielded 147 publications of which 21papers from 15 sub-Saharan African countries documented the use of EHR in Africa and were reviewed. About 91\% reported use of Open Source healthcare software, with OpenMRS being the most widely used. Most reports were from HIV related health centers. Barriers to adoption of EHRs include high cost of procurement and maintenance, poor network infrastructure and lack of comfort among health workers with electronic medical records.

CONCLUSION: There has been an increase in the use of EHRs in sub-Saharan Africa, largely driven by utilization by HIV treatment programs. Penetration is still however very low.

}, issn = {2276-7096}, author = {Akanbi, Maxwell O and Ocheke, Amaka N and Agaba, Patricia A and Daniyam, Comfort A and Agaba, Emmanuel I and Okeke, Edith N and Ukoli, Christiana O} } @inbook {786, title = {VURTIGO: Visualization Platform for Real-Time, MRI-Guided Cardiac Electroanatomic Mapping}, booktitle = {Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges}, series = {Lecture Notes in Computer Science}, volume = {7085}, year = {2012}, pages = {244-253}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Guidance of electrophysiological (EP) procedures by magnetic resonance imaging (MRI) has significant advantages over x-ray fluoroscopy. Display of electroanatomic mapping (EAM) during an intervention fused with a prior MR volume and DE-MRI derived tissue classification should improve the accuracy of cardiac resynchronization therapy (CRT) for ventricular arrhythmias. Improved accuracy in the spatial localization of recorded EP points will produce an EAM to constrain and customize patient-specific cardiac electroanatomic models being developed for understanding the patterns of arrhythmogenic slow conduction zones causing reentry circuits and treatment planning. The Vurtigo software presented here is a four dimensional (3D+time) real-time visualization application for guiding interventions capable of displaying prior volumes, real-time MRI scan planes, EAM (voltage or activation times), segmented models, and tracked catheters. This paper will describe the architecture and features of Vurtigo followed by the application example of guiding percutaneous cardiac electroanatomic mapping in porcine models.}, isbn = {978-3-642-28325-3}, url = {http://dx.doi.org/10.1007/978-3-642-28326-0_25}, author = {Radau, Perry and Pintilie, Stefan and Flor, Roey and Biswas, Labonny and Oduneye, Samuel and Ramanan, Venkat and Anderson, Kevan and Wright, Graham}, editor = {Camara, Oscar and Konukoglu, Ender and Pop, Mihaela and Rhode, Kawal and Sermesant, Maxime and Young, Alistair} } @article {810, title = {Arden2ByteCode: A one-pass Arden Syntax compiler for service-oriented decision support systems based on the OSGi platform.}, journal = {Comput Methods Programs Biomed}, year = {2011}, doi = {10.1016/j.cmpb.2011.11.003}, url = {http://dx.doi.org/10.1016/j.cmpb.2011.11.003} note = {Epub ahead of print}, author = {Gietzelt, Matthias and Goltz, Ursula and Grunwald, Daniel and Lochau, Malte and Marschollek, Michael and Song, Bianying and Wolf, Klaus-Hendrik} } @article {696, title = {ATOM - an OMERO add-on for automated import of image data.}, journal = {BMC research notes}, volume = {4}, year = {2011}, month = {2011}, pages = {382}, abstract = {UNLABELLED: ABSTRACT: BACKGROUND: Modern microscope platforms are able to generate multiple gigabytes of image data in a single experimental session. In a routine research laboratory workflow, these data are initially stored on the local acquisition computer from which files need to be transferred to the experimenter{\textquoteright}s (remote) image repository (e.g., DVDs, portable hard discs or server-based storage) because of limited local data storage. Although manual solutions for this migration, such as OMERO - a client-server software for visualising and managing large amounts of image data - exist, this import process may be a time-consuming and tedious task. FINDINGS: We have developed ATOM, a Java-based and thus platform-independent add-on for OMERO enabling automated transfer of image data from a wide variety of acquisition software packages into OMERO. ATOM provides a graphical user interface and allows pre-organisation of experimental data for the transfer. CONCLUSIONS: ATOM is a convenient extension of the OMERO software system. An automated interface to OMERO will be a useful tool for scientists working with file formats supported by the Bio-Formats file format library, a platform-independent library for reading the most common file formats of microscope images.}, issn = {1756-0500}, doi = {10.1186/1756-0500-4-382}, author = {M{\"u}ller, Oliver and Lipp, Peter and Kaestner, Lars} } @article {575, title = {Brainstorm: A User-Friendly Application for MEG/EEG Analysis}, journal = {Computational Intelligence and Neuroscience}, volume = {2011}, year = {2011}, month = {01/2011}, abstract = {Brainstorm is a collaborative open-source application dedicated to magnetoencephalography (MEG) and electroencephalography (EEG) data visualization and processing, with an emphasis on cortical source estimation techniques and their integration with anatomical magnetic resonance imaging (MRI) data. The primary objective of the software is to connect MEG/EEG neuroscience investigators with both the best-established and cutting-edge methods through a simple and intuitive graphical user interface (GUI).}, doi = {10.1155/2011/879716}, url = {http://www.hindawi.com/journals/cin/2011/879716/}, author = {Fran{\c c}ois Tadel and Sylvain Baillet and John C. Mosher and Dimitrios Pantazis} } @article {868, title = {The caBIG{\textregistered} Life Science Business Architecture Model.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 May 15}, pages = {1429-35}, abstract = {

MOTIVATION: Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG{\textregistered}) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research.

RESULTS: LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model{\textquoteright}s current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. Availability and Implementation: The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ).

}, keywords = {Biomedical Research, Computational Biology, Computer Systems, National Cancer Institute (U.S.), Neoplasms, Software, United States, Vocabulary, Controlled}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr141}, author = {Boyd, Lauren Becnel and Hunicke-Smith, Scott P and Stafford, Grace A and Freund, Elaine T and Ehlman, Michele and Chandran, Uma and Dennis, Robert and Fernandez, Anna T and Goldstein, Stephen and Steffen, David and Tycko, Benjamin and Klemm, Juli D} } @article {1047, title = {[Central online quality assurance in radiology: an IT solution exemplified by the German Breast Cancer Screening Program].}, journal = {Rofo}, volume = {183}, year = {2011}, month = {2011 Sep}, pages = {849-54}, abstract = {

PURPOSE: Physical-technical quality assurance is one of the essential tasks of the National Reference Centers in the German Breast Cancer Screening Program. For this purpose the mammography units are required to transfer the measured values of the constancy tests on a daily basis and all phantom images created for this purpose on a weekly basis to the reference centers. This is a serious logistical challenge. To meet these requirements, we developed an innovative software tool.

MATERIALS AND METHODS: By the end of 2005, we had already developed web-based software (MammoControl) allowing the transmission of constancy test results via entry forms. For automatic analysis and transmission of the phantom images, we then introduced an extension (MammoControl DIANA). This was based on Java, Java Web Start, the NetBeans Rich Client Platform, the Pixelmed Java DICOM Toolkit and the ImageJ library.

RESULTS: MammoControl DIANA was designed to run locally in the mammography units. This allows automated on-site image analysis. Both results and compressed images can then be transmitted to the reference center. We developed analysis modules for the daily and monthly consistency tests and additionally for a homogeneity test.

CONCLUSION: The software we developed facilitates the immediate availability of measurement results, phantom images, and DICOM header data in all reference centers. This allows both targeted guidance and short response time in the case of errors. We achieved a consistent IT-based evaluation with standardized tools for the entire screening program in Germany.

}, keywords = {Data Compression, Female, Germany, Guideline Adherence, Humans, Image Processing, Computer-Assisted, Mammography, Mass Screening, Online Systems, Phantoms, Imaging, Quality Assurance, Health Care, Radiology Information Systems, Reference Standards, Software}, issn = {1438-9010}, doi = {10.1055/s-0031-1281599}, author = {Czwoydzinski, J and Girnus, R and Sommer, A and Heindel, W and Lenzen, H} } @article {909, title = {Common characteristics of open source software development and applicability for drug discovery: A systematic review}, journal = {Health Research Policy and Systems}, volume = {9}, year = {2011}, abstract = {Background: Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for researchers, business leaders and government officials who may be interested in utilizing open source innovation in other contexts and with an emphasis on drug discovery.Methods: A systematic review was performed by searching relevant, multidisciplinary databases to extract empirical research regarding the common characteristics and barriers of initiating and maintaining an open source software development project.Results: Common characteristics to open source software development pertinent to open source drug discovery were extracted. The characteristics were then grouped into the areas of participant attraction, management of volunteers, control mechanisms, legal framework and physical constraints. Lastly, their applicability to drug discovery was examined.Conclusions: We believe that the open source model is viable for drug discovery, although it is unlikely that it will exactly follow the form used in software development. Hybrids will likely develop that suit the unique characteristics of drug discovery. We suggest potential motivations for organizations to join an open source drug discovery project. We also examine specific differences between software and medicines, specifically how the need for laboratories and physical goods will impact the model as well as the effect of patents. {\textcopyright} 2011 {\r A}rdal et al; licensee BioMed Central Ltd.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-80053368637\&partnerID=40\&md5=758353a8f6509a3198a8d06164bdec37}, author = {{\r A}rdal, C.a and Alstads{\ae} ter, A.b and R{\o}ttingen, J.-A.b} } @article {869, title = {DDN: a caBIG{\textregistered} analytical tool for differential network analysis.}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011 Apr 1}, pages = {1036-8}, abstract = {

UNLABELLED: Differential dependency network (DDN) is a caBIG{\textregistered} (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks representing two biological conditions. Developed under caBIG{\textregistered}{\textquoteright}s In Silico Research Centers of Excellence (ISRCE) Program, DDN enables differential network analysis and provides an alternative way for defining network biomarkers predictive of phenotypes. DDN also serves as a useful systems biology tool for users across biomedical research communities to infer how genetic, epigenetic or environment variables may affect biological networks and clinical phenotypes. Besides the standalone Java application, we have also developed a Cytoscape plug-in, CytoDDN, to integrate network analysis and visualization seamlessly.

AVAILABILITY: The Java and MATLAB source code can be downloaded at the authors{\textquoteright} web site http://www.cbil.ece.vt.edu/software.htm.

}, keywords = {Animals, Computational Biology, Epigenesis, Genetic, Female, Gene Regulatory Networks, Mammary Glands, Animal, Rats, Software, Systems Biology}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btr052}, author = {Zhang, Bai and Tian, Ye and Jin, Lu and Li, Huai and Shih, Ie-Ming and Madhavan, Subha and Clarke, Robert and Hoffman, Eric P and Xuan, Jianhua and Hilakivi-Clarke, Leena and Wang, Yue} } @article {Ferranti23092011, title = {The design and implementation of an open-source, data-driven cohort recruitment system: the Duke Integrated Subject Cohort and Enrollment Research Network (DISCERN)}, journal = {Journal of the American Medical Informatics Association}, year = {2011}, abstract = {Objective Failure to reach research subject recruitment goals is a significant impediment to the success of many clinical trials. Implementation of health-information technology has allowed retrospective analysis of data for cohort identification and recruitment, but few institutions have also leveraged real-time streams to support such activities.Design Duke Medicine has deployed a hybrid solution, The Duke Integrated Subject Cohort and Enrollment Research Network (DISCERN), that combines both retrospective warehouse data and clinical events contained in prospective Health Level 7 (HL7) messages to immediately alert study personnel of potential recruits as they become eligible.Results DISCERN analyzes more than 500{\quotesinglbase}{\"A}{\`a}000 messages daily in service of 12 projects. Users may receive results via email, text pages, or on-demand reports. Preliminary results suggest DISCERN{\textquoteright}s unique ability to reason over both retrospective and real-time data increases study enrollment rates while reducing the time required to complete recruitment-related tasks. The authors have introduced a preconfigured DISCERN function as a self-service feature for users.Limitations The DISCERN framework is adoptable primarily by organizations using both HL7 message streams and a data warehouse. More efficient recruitment may exacerbate competition for research subjects, and investigators uncomfortable with new technology may find themselves at a competitive disadvantage in recruitment.Conclusion DISCERN{\textquoteright}s hybrid framework for identifying real-time clinical events housed in HL7 messages complements the traditional approach of using retrospective warehoused data. DISCERN is helpful in instances when the required clinical data may not be loaded into the warehouse and thus must be captured contemporaneously during patient care. Use of an open-source tool supports generalizability to other institutions at minimal cost.}, doi = {10.1136/amiajnl-2011-000115}, url = {http://jamia.bmj.com/content/early/2011/09/23/amiajnl-2011-000115.abstract}, author = {Ferranti, Jeffrey M and Gilbert, William and McCall, Jonathan and Shang, Howard and Barros, Tanya and Horvath, Monica M} } @article {660, title = {Dicoogle - an Open Source Peer-to-Peer PACS.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {24}, year = {2011}, month = {2011 Oct}, pages = {848-56}, abstract = {Picture Archiving and Communication Systems (PACS) have been widely deployed in healthcare institutions, and they now constitute a normal commodity for practitioners. However, its installation, maintenance, and utilization are still a burden due to their heavy structures, typically supported by centralized computational solutions. In this paper, we present Dicoogle, a PACS archive supported by a document-based indexing system and by peer-to-peer (P2P) protocols. Replacing the traditional database storage (RDBMS) by a documental organization permits gathering and indexing data from file-based repositories, which allows searching the archive through free text queries. As a direct result of this strategy, more information can be extracted from medical imaging repositories, which clearly increases flexibility when compared with current query and retrieval DICOM services. The inclusion of P2P features allows PACS internetworking without the need for a central management framework. Moreover, Dicoogle is easy to install, manage, and use, and it maintains full interoperability with standard DICOM services.}, issn = {1618-727X}, doi = {10.1007/s10278-010-9347-9}, author = {Costa, Carlos and Ferreira, Carlos and Basti{\~a}o, Lu{\'\i}s and Ribeiro, Lu{\'\i}s and Silva, Augusto and Oliveira, Jos{\'e} Lu{\'\i}s} } @article {1746-1596-6-S1-S16, title = {Distributed computing in image analysis using open source frameworks and application to image sharpness assessment of histological whole slide images}, journal = {Diagnostic Pathology}, volume = {6}, number = {Suppl 1}, year = {2011}, pages = {S16}, abstract = {BACKGROUND:Automated image analysis on virtual slides is evolving rapidly and will play an important role in the future of digital pathology. Due to the image size, the computational cost of processing whole slide images (WSIs) in full resolution is immense. Moreover, image analysis requires well focused images in high magnification.METHODS:We present a system that merges virtual microscopy techniques, open source image analysis software, and distributed parallel processing. We have integrated the parallel processing framework JPPF, so batch processing can be performed distributed and in parallel. All resulting meta data and image data are collected and merged. As an example the system is applied to the specific task of image sharpness assessment. ImageJ is an open source image editing and processing framework developed at the NIH having a large user community that contributes image processing algorithms wrapped as plug-ins in a wide field of life science applications. We developed an ImageJ plug-in that supports both basic interactive virtual microscope and batch processing functionality. For the application of sharpness inspection we employ an approach with non-overlapping tiles. Compute nodes retrieve image tiles of moderate size from the streaming server and compute the focus measure. Each tile is divided into small sub images to calculate an edge based sharpness criterion which is used for classification. The results are aggregated in a sharpness map.RESULTS:Based on the system we calculate a sharpness measure and classify virtual slides into one of the following categories - excellent, okay, review and defective. Generating a scaled sharpness map enables the user to evaluate sharpness of WSIs and shows overall quality at a glance thus reducing tedious assessment work.CONCLUSIONS:Using sharpness assessment as an example, the introduced system can be used to process, analyze and parallelize analysis of whole slide images based on open source software.}, issn = {1746-1596}, doi = {10.1186/1746-1596-6-S1-S16}, url = {http://www.diagnosticpathology.org/content/6/S1/S16}, author = {Zerbe, Norman and Hufnagl, Peter and Schluns, Karsten} } @conference {Helms:2011:EAC:1987993.1988006, title = {Evaluating access control of open source electronic health record systems}, booktitle = {Proceeding of the 3rd workshop on Software engineering in health care}, series = {SEHC {\textquoteright}11}, year = {2011}, pages = {63{\textendash}70}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Incentives and penalties for healthcare providers as laid out in the American Recovery and Reinvestment Act of 2009 have caused tremendous growth in the development and installation of electronic health record (EHR) systems in the US. For the benefit of protecting patient privacy, regulations and certification criteria related to EHR systems stipulate the use of access control of protected health information. The goal of this research is to guide development teams, regulators, and certification bodies by assessing the state of the practice in EHR access control. In this paper, we present a compilation of 25 criteria relative to access control in EHR systems found in the Health Insurance Portability and Accountability Act (HIPAA) regulation, meaningful use certification criteria, best practices embodied in the National Institute for Standards and Technology (NIST) role-based access control standard, and other best practices found in the literature. We then examine the state of the practice in access control by evaluating four open source EHR systems using these 25 evaluation criteria. Our research indicates that the NIST Meaningful Use criteria provide HIPAA compliance, but none of the regulatory and certification criteria address the implementation standards, and best practices related to access control. Additionally, our results indicate that open source EHR system designers are not implementing robust access control mechanisms for the adequate protection of patient data.}, keywords = {access control, electronic health records, health it, healthcare, privacy, role-based access control}, isbn = {978-1-4503-0585-3}, doi = {http://doi.acm.org/10.1145/1987993.1988006}, author = {Helms, Eric and Williams, Laurie} } @article {589, title = {FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.}, journal = {Computational intelligence and neuroscience}, volume = {2011}, year = {2011}, month = {2011}, pages = {156869}, abstract = {This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.}, keywords = {Electroencephalography, Electrophysiological Phenomena, Humans, Magnetoencephalography, Numerical Analysis, Computer-Assisted, Software, User-Computer Interface}, issn = {1687-5273}, author = {Oostenveld, Robert and Fries, Pascal and Maris, Eric and Schoffelen, Jan-Mathijs} } @article {597, title = {Forward field computation with OpenMEEG.}, journal = {Computational intelligence and neuroscience}, volume = {2011}, year = {2011}, month = {2011}, pages = {923703}, abstract = {To recover the sources giving rise to electro- and magnetoencephalography in individual measurements, realistic physiological modeling is required, and accurate numerical solutions must be computed. We present OpenMEEG, which solves the electromagnetic forward problem in the quasistatic regime, for head models with piecewise constant conductivity. The core of OpenMEEG consists of the symmetric Boundary Element Method, which is based on an extended Green Representation theorem. OpenMEEG is able to provide lead fields for four different electromagnetic forward problems: Electroencephalography (EEG), Magnetoencephalography (MEG), Electrical Impedance Tomography (EIT), and intracranial electric potentials (IPs). OpenMEEG is open source and multiplatform. It can be used from Python and Matlab in conjunction with toolboxes that solve the inverse problem; its integration within FieldTrip is operational since release 2.0.}, issn = {1687-5273}, author = {Gramfort, Alexandre and Papadopoulo, Th{\'e}odore and Olivi, Emmanuel and Clerc, Maureen} } @article {1039, title = {The future of telepathology for the developing world.}, journal = {Arch Pathol Lab Med}, volume = {135}, year = {2011}, month = {2011 Feb}, pages = {211-4}, abstract = {

Physician shortages are acute in developing countries, where disease burden is the greatest and resources for health care are very limited. A lack of pathologists in these countries has lead to delays in diagnosis and misdiagnoses that adversely affect patient care and survival. The introduction of telepathology into countries with limited resources for health care is but one of multiple approaches that can be used to alleviate the problem. Telepathology is the electronic transmission of digital images that can be used for education and diagnostic consultation. A basic system consists of a microscope with a mounted digital camera linked to a computer. The ability to produce histologic slides, to repair and maintain equipment, and to provide training are also needed for the successful use of this technology. iPath is a Web-based, open platform, software application which was developed at the University of Basel, Switzerland, for telepathology and which brings together pathologists from around the world to provide telepathology support for diagnostic consultation and provides education to centers with limited resources. The use of virtual-slide technology to provide a digital image of an entire glass slide is another technology for diagnostic consultation and pathology education. This technology requires more costly resources to support it, which may limit its utility in many areas. Telepathology can generate collections of digital images and virtual slides needed for training indigenous pathologists in their countries to become self-sufficient. Thus, the long-term goal of this technology is to improve patient care and survival.

}, keywords = {Developing Countries, Humans, Pathology, Clinical, Software, telepathology}, issn = {1543-2165}, doi = {10.1043/1543-2165-135.2.211}, author = {Hitchcock, Charles L} } @inbook {springerlink:10.1007/978-3-642-24418-6_29, title = {Health Informatics: The Relevance of Open Source and Multilevel Modeling}, booktitle = {Open Source Systems: Grounding Research}, series = {IFIP Advances in Information and Communication Technology}, volume = {365}, year = {2011}, note = {10.1007/978-3-642-24418-6_29}, pages = {338-347}, publisher = {Springer Boston}, organization = {Springer Boston}, abstract = {Health information features significant spatial-temporal and domain complexities, which brings challenges to the implementation of patient-centered, interoperable and semantically coherent healthcare information systems. This position paper supports the idea that the multilevel modeling approach is essential to ensure interoperability at the semantic level, but true interoperability is only achieved by the adoption of open standards, and open source implementations are needed for promote competition based on software quality. The Multilevel Healthcare Information Modelling (MLHIM) specifications are presented as the fully open source multilevel modeling reference implementation, and best practices for the development of multilevel-based open source healthcare applications are suggested.}, isbn = {978-3-642-24417-9}, url = {http://dx.doi.org/10.1007/978-3-642-24418-6_29}, author = {Cavalini, Luciana and Cook, Timothy}, editor = {Hissam, Scott and Russo, Barbara and de Mendon{\c c}a Neto, Manoel and Kon, Fabio} } @article {867, title = {Impact of caBIG on the European cancer community.}, journal = {Ecancermedicalscience}, volume = {5}, year = {2011}, month = {2011}, pages = {225}, abstract = {

The cancer Biomedical Informatics Grid (caBIG) was launched in 2003 by the US National Cancer Institute with the aim of connecting research teams through the use of shared infrastructure and software to collect, analyse and share data. It was an ambitious project, and the issue it aimed to address was huge and far-reaching. With such developments as the mapping of the human genome and the advancement of new technologies for the analysis of genes and proteins, cancer researchers have never produced so much complex data, nor have they understood so much about cancer on a molecular level. This new {\textquoteright}molecular understanding{\textquoteright} of cancer, according to the caBIG 2007 {\textquoteright}Pilot Report{\textquoteright}[1], leads to molecular or {\textquoteright}personalised{\textquoteright} medicine being the way forward in cancer research and treatment, and connects basic research to clinical care in an unprecedented way. But the former {\textquoteright}silo-like{\textquoteright} nature of research does not lend itself to this brave new world of molecular medicine-individual labs and institutes working in isolation, "in effect, as cottage industries, each collecting and interpreting data using a unique language of their own"[2] will not advance cancer research as it should be advanced. The solution proposed by the NCI in caBIG was to produce an integrated informatics grid ({\textquoteright}caGrid{\textquoteright}) to incorporate open source, open access tools to collect, analyse and share data, enabling everyone to use the same methods and language for these tasks.caBIG is primarily a US-based endeavour, and though the tools are openly available for users worldwide, it is in US NCI-funded cancer centres that they have been actively introduced and promoted with the eventual hope, according to the pilot report, of being able to do the same worldwide. caBIG also has a collaboration in place with the UK organisation NCRI to exchange technologies and research data. The European Association for Cancer Research, a member association for cancer researchers, conducted an online survey in January 2011 to identify the penetration of the ambitious caBIG project into European laboratories. The survey was sent to 6396 researchers based in Europe, with 764 respondents, a total response rate of 11.94\%.

}, issn = {1754-6605}, doi = {10.3332/ecancer.2011.225}, author = {Warden, R} } @article {642, title = {Implementation of an open source provider organization registry service.}, journal = {Studies in health technology and informatics}, volume = {169}, year = {2011}, month = {2011}, pages = {265-9}, abstract = {Healthcare Information Exchange Networks (HIEN) enables the exchange of medical information between different institutions. One of the biggest problems running a HIEN is the unique identification of the care providers. The provider and organisation registry service (PORS) has to provide a unique identifier for care providers. The concept and the implementation of PORS will be described in this article. Finally the PORS implementation will be compared with the Integrating the Healthcare Enterprise (IHE) profile for a Healthcare Provider Directory (HPD).}, issn = {0926-9630}, author = {Birkle, Markus and Schneider, Benjamin and Beck, Tobias and Deuster, Thomas and Fischer, Markus and Flatow, Florian and Heinrich, Robert and Kapp, Christian and Riemer, Jasmin and Simon, Michael and Bergh, Bj{\"o}rn} } @article {594, title = {Implementation of the Zambia electronic perinatal record system for comprehensive prenatal and delivery care.}, journal = {International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics}, volume = {113}, year = {2011}, month = {2011 May}, pages = {131-6}, abstract = {OBJECTIVE: To characterize prenatal and delivery care in an urban African setting. METHODS: The Zambia Electronic Perinatal Record System (ZEPRS) was implemented to record demographic characteristics, past medical and obstetric history, prenatal care, and delivery and newborn care for pregnant women across 25 facilities in the Lusaka public health sector. RESULTS: From June 1, 2007, to January 31, 2010, 115552 pregnant women had prenatal and delivery information recorded in ZEPRS. Median gestation age at first prenatal visit was 23weeks (interquartile range [IQR] 19-26). Syphilis screening was documented in 95663 (83\%) pregnancies: 2449 (2.6\%) women tested positive, of whom 1589 (64.9\%) were treated appropriately. 111108 (96\%) women agreed to HIV testing, of whom 22\% were diagnosed with HIV. Overall, 112813 (98\%) of recorded pregnancies resulted in a live birth, and 2739 (2\%) in a stillbirth. The median gestational age was 38weeks (IQR 35-40) at delivery; the median birth weight of newborns was 3000g (IQR 2700-3300g). CONCLUSION: The results demonstrate the feasibility of using a comprehensive electronic medical record in an urban African setting, and highlight its important role in ongoing efforts to improve clinical care.}, issn = {1879-3479}, author = {Chi, Benjamin H and Vwalika, Bellington and Killam, William P and Wamalume, Chibesa and Giganti, Mark J and Mbewe, Reuben and Stringer, Elizabeth M and Chintu, Namwinga T and Putta, Nande B and Liu, Katherine C and Chibwesha, Carla J and Rouse, Dwight J and Stringer, Jeffrey S A} } @article {538, title = {Integration of 3D anatomical data obtained by CT imaging and 3D optical scanning for Computer Aided Implant Surgery.}, journal = {BMC medical imaging}, volume = {11}, year = {2011}, month = {2011 Feb 21}, pages = {5}, abstract = {ABSTRACT: BACKGROUND: A precise placement of dental implants is a crucial step to optimize both prosthetic aspects and functional constraints. In this context, the use of virtual guiding systems has been recognized as a fundamental tool to control the ideal implant position. In particular, complex periodontal surgeries can be performed using preoperative planning based on CT data. The critical point of the procedure relies on the lack of accuracy in transferring CT planning information to surgical field through custom-made stereo-lithographic surgical guides. METHODS: In this work, a novel methodology is proposed for monitoring loss of accuracy in transferring CT dental information into periodontal surgical field. The methodology is based on integrating 3D data of anatomical (impression and cast) and preoperative (radiographic template) models, obtained by both CT and optical scanning processes. RESULTS: A clinical case, relative to a fully edentulous jaw patient, has been used as test case to assess the accuracy of the various steps concurring in manufacturing surgical guides. In particular, a surgical guide has been designed to place implants in the bone structure of the patient. The analysis of the results has allowed the clinician to monitor all the errors, which have been occurring step by step manufacturing the physical templates. CONCLUSIONS: The use of an optical scanner, which has a higher resolution and accuracy than CT scanning, has demonstrated to be a valid support to control the precision of the various physical models adopted and to point out possible error sources. A case study regarding a fully edentulous patient has confirmed the feasibility of the proposed methodology.}, issn = {1471-2342}, author = {Frisardi, Gianni and Chessa, Giacomo and Barone, Sandro and Paoli, Alessandro and Razionale, Armando and Frisardi, Flavio} } @conference {MEJIA:2011:INRIA-00567598:1, title = {Invasive composition for the evolution of a health information system}, booktitle = {Variability \& Composition (VariComp)}, year = {2011}, note = {{ACM} 978-1-4503-0646-1/11/03 {D}.: {S}oftware/{D}.3: {PROGRAMMING} {LANGUAGES}/{D}.3.3: {L}anguage {C}onstructs and {F}eatures}, month = {03}, address = {Pernambuco Brazil}, abstract = {{I}n this paper we show that some of the evolution tasks in {O}pen{MRS}, a health information system, may require the invasive modification of interfaces and implementations in order to offer an appropriate modularization. {W}e introduce a new composition framework in {J}ava that supports the definition of expressive pattern-based invasive compositions. {F}ur thermore, we show that the composition framework allows us to concisely define an evolution scenario of {O}pen{MRS} that supports the consolidation of patient data from differ- ent remote instances.}, keywords = {Aspect-oriented programming, Distributed systems, Health information systems, Invasive software composition}, url = {http://hal.inria.fr/inria-00567598/PDF/mejia-sudholt-benavides_varicomp-AOSD2011.pdf}, author = {Mejia, Ismael and S{\"u}dholt, Mario and Benavides Navarro, Luis Daniel} } @inbook {springerlink:10.1007/978-3-642-24418-6_15, title = {Libre Software as an Innovation Enabler in India Experiences of a Bangalorian Software SME}, booktitle = {Open Source Systems: Grounding Research}, series = {IFIP Advances in Information and Communication Technology}, volume = {365}, year = {2011}, note = {10.1007/978-3-642-24418-6_15}, pages = {220-232}, publisher = {Springer Boston}, organization = {Springer Boston}, abstract = {Free/Libre and open source software (FLOSS) has been advocated for its presumed capacity to support native software industries in developing countries. It is said to create new spaces for exploration and to lower entry barriers to mature software markets, for example. However, little empirical research has been conducted concerning FLOSS business in a developing country setting and, thus, there is not much evidence to support or refute these claims. This paper presents a business case study conducted in India, a country branded as a {\textquoteright}software powerhouse{\textquoteright} of the developing world. The findings show how FLOSS has opened up significant opportunities for the case company, especially in terms of improving its innovative capability and upgrading in the software value chain. On the other hand, they also highlight some challenges to FLOSS involvement that rise specifically from the Indian context.}, isbn = {978-3-642-24417-9}, url = {http://dx.doi.org/10.1007/978-3-642-24418-6_15}, author = {Henttonen, Katja}, editor = {Hissam, Scott and Russo, Barbara and de Mendon{\c c}a Neto, Manoel and Kon, Fabio} } @article {573, title = {mantisGRID: A Grid Platform for DICOM Medical Images Management in Colombia and Latin America.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {24}, year = {2011}, month = {2011 Apr}, pages = {271-83}, abstract = {This paper presents the mantisGRID project, an interinstitutional initiative from Colombian medical and academic centers aiming to provide medical grid services for Colombia and Latin America. The mantisGRID is a GRID platform, based on open source grid infrastructure that provides the necessary services to access and exchange medical images and associated information following digital imaging and communications in medicine (DICOM) and health level 7 standards. The paper focuses first on the data abstraction architecture, which is achieved via Open Grid Services Architecture Data Access and Integration (OGSA-DAI) services and supported by the Globus Toolkit. The grid currently uses a 30-Mb bandwidth of the Colombian High Technology Academic Network, RENATA, connected to Internet 2. It also includes a discussion on the relational database created to handle the DICOM objects that were represented using Extensible Markup Language Schema documents, as well as other features implemented such as data security, user authentication, and patient confidentiality. Grid performance was tested using the three current operative nodes and the results demonstrated comparable query times between the mantisGRID (OGSA-DAI) and Distributed mySQL databases, especially for a large number of records.}, issn = {1618-727X}, author = {Garcia Ruiz, Manuel and Garcia Chaves, Alvin and Ruiz Iba{\~n}ez, Carlos and Gutierrez Mazo, Jorge Mario and Ramirez Giraldo, Juan Carlos and Pelaez Echavarria, Alejandro and Valencia Diaz, Edison and Pelaez Restrepo, Gustavo and Montoya Munera, Edwin Nelson and Garcia Loaiza, Bernardo and Gomez Gonzalez, Sebastian} } @inbook {springerlink:10.1007/978-1-4419-8204-9_9, title = {Medical Image Registration}, booktitle = {Multi Modality State-of-the-Art Medical Image Segmentation and Registration Methodologies}, year = {2011}, note = {10.1007/978-1-4419-8204-9_9}, pages = {227-245}, publisher = {Springer New York}, organization = {Springer New York}, abstract = {In this chapter, we cover the necessary background information required to understand medical image registration, the basic tools required to implement registration algorithms, and demonstrate a complete application for various types of registration between different modalities using freely available and maintained software.}, isbn = {978-1-4419-8204-9}, url = {http://dx.doi.org/10.1007/978-1-4419-8204-9_9}, author = {Aladl, Usaf E. and Peters, Terry}, editor = {El-Baz, Ayman S. and Acharya U, Rajendra and Laine, Andrew F. and Suri, Jasjit S.} } @article {591, title = {MITK-ToF-Range data within MITK.}, journal = {International journal of computer assisted radiology and surgery}, year = {2011}, month = {2011 May 31}, abstract = {PURPOSE: The time-of-flight (ToF) technique is an emerging technique for rapidly acquiring distance information and is becoming increasingly popular for intra-operative surface acquisition. Using the ToF technique as an intra-operative imaging modality requires seamless integration into the clinical workflow. We thus aim to integrate ToF support in an existing framework for medical image processing. METHODS: MITK-ToF was implemented as an extension of the open-source C++ Medical Imaging Interaction Toolkit (MITK) and provides the basic functionality needed for rapid prototyping and development of image-guided therapy (IGT) applications that utilize range data for intra-operative surface acquisition. This framework was designed with a module-based architecture separating the hardware-dependent image acquisition task from the processing of the range data. RESULTS: The first version of MITK-ToF has been released as an open-source toolkit and supports several ToF cameras and basic processing algorithms. The toolkit, a sample application, and a tutorial are available from http://mitk.org . CONCLUSIONS: With the increased popularity of time-of-flight cameras for intra-operative surface acquisition, integration of range data supports into medical image processing toolkits such as MITK is a necessary step. Handling acquisition of range data from different cameras and processing of the data requires the establishment and use of software design principles that emphasize flexibility, extendibility, robustness, performance, and portability. The open-source toolkit MITK-ToF satisfies these requirements for the image-guided therapy community and was already used in several research projects.}, issn = {1861-6429}, author = {Seitel, Alexander and Yung, Kwong and Mersmann, Sven and Kilgus, Thomas and Groch, Anja and Dos Santos, Thiago R and Franz, Alfred M and Nolden, Marco and Meinzer, Hans-Peter and Maier-Hein, Lena} } @article {doi:10.3109/17538157.2011.590257, title = {A novel open-source web-based platform promoting collaboration of healthcare professionals and biostatisticians: A design science approach}, journal = {Informatics for Health and Social Care}, year = {2011}, pages = {1-15}, abstract = {Collaboration among clinicians and statisticians is relatively poor, with many cases leading to poor quality research, reflected by low level of evidence studies published in the literature, thus affecting the overall quality of healthcare. We have developed a novel open-source web-based platform aiming in reinforcing the clinician{\textendash}statistician relationship, using an iterative design research process by involving all end-users. Evaluation of this platform by healthcare professionals and biostatisticians was highly positive, as we first identified the pitfalls of their relationship and overcame them through the use of this platform. We are hoping that this will strengthen the clinician{\textendash}statistician relationship in the short term and ultimately improve the quality of research and hence the quality of healthcare in the long term.}, keywords = {clinician, collaboration, design science research, open source, quality of research, relationship, statisticians, user-centred}, doi = {10.3109/17538157.2011.590257}, url = {http://informahealthcare.com/doi/abs/10.3109/17538157.2011.590257}, author = {Raptis, Dimitri A. and Mettler, Tobias and Tzanas, Kostas and Graf, Rolf} } @article {1038, title = {An online method for diagnosis of difficult TB cases for developing countries.}, journal = {Stud Health Technol Inform}, volume = {164}, year = {2011}, month = {2011}, pages = {168-73}, abstract = {

Optimal use of limited human, technical and financial resources is a major concern for tuberculosis (TB) control in developing nations. Further impediments include a lack of trained physicians, and logistical difficulties in arranging face-to-face (f-2-f) TB Diagnostic Committee (TBDC) consultations. Use of e-Health for virtual TBDCs (Internet and "iPath"), to address such issues is being studied in the Philippines and Pakistan. In Pakistan, radiological diagnosis of 88 sputum smear negative but suspected TB patients has been compared with the {\textquoteright}gold standards{\textquoteright} (TB culture, and 2-month clinical follow up). Of 88 diagnostic decisions made by primary physicians at the spoke site and electronic TBDC (e-TBDC) at hub site, there was agreement in 71 cases and disagreement on 17 cases. The turn-around time (TAT; patient registration at spoke site for f-2-f diagnosis to receiving the electronic diagnosis), averaged 34.6 hours; ranging 9 minutes to 289.2 hours. Average TAT at the rural site (59.15 hours) was more than the urban site (15.9 hours). Comparison of e-TBDC and f-2-f diagnosis with the gold standards showed only slight differences. Using culture as the gold standard, e-TBDC decisions showed greater accuracy (sensitivity - 32.4\%) as compared to f-2-f (27.6\%); using 2-month clinical follow-up as the gold standard, f-2-f diagnosis showed slightly better improvement in patient symptoms and weight as compared to e-TBDC. In Philippines "iPath" was trialed and demonstrated that e-TBDCs have potential. Such groups could review cases, diagnose, and write comments remotely, reducing the diagnosis and treatment delay compared to usual care.

}, keywords = {Adult, Developing Countries, Diagnostic Techniques and Procedures, Female, Humans, Internet, Male, Middle Aged, Mycobacterium Infections, Nontuberculous, Pakistan, Philippines, Telemedicine, Tuberculosis, Pulmonary}, issn = {0926-9630}, author = {Marcelo, Alvin and Fatmi, Zafar and Firaza, Paul Nimrod and Shaikh, Shiraz and Dandan, Alvin Joseph and Irfan, Muhammad and Bari, Vaqar and Scott, Richard E} } @article {10.1371/journal.pone.0027372, title = {An Open Environment CT-US Fusion for Tissue Segmentation during Interventional Guidance}, journal = {PLoS ONE}, volume = {6}, number = {11}, year = {2011}, month = {11}, pages = {e27372}, publisher = {Public Library of Science}, abstract = {

Therapeutic ultrasound (US) can be noninvasively focused to activate drugs, ablate tumors and deliver drugs beyond the blood brain barrier. However, well-controlled guidance of US therapy requires fusion with a navigational modality, such as magnetic resonance imaging (MRI) or X-ray computed tomography (CT). Here, we developed and validated tissue characterization using a fusion between US and CT. The performance of the CT/US fusion was quantified by the calibration error, target registration error and fiducial registration error. Met-1 tumors in the fat pads of 12 female FVB mice provided a model of developing breast cancer with which to evaluate CT-based tissue segmentation. Hounsfield units (HU) within the tumor and surrounding fat pad were quantified, validated with histology and segmented for parametric analysis (fat: -300 to 0 HU, protein-rich: 1 to 300 HU, and bone: HU\>300). Our open source CT/US fusion system differentiated soft tissue, bone and fat with a spatial accuracy of \~{}1 mm. Region of interest (ROI) analysis of the tumor and surrounding fat pad using a 1 mm2 ROI resulted in mean HU of 68{\textpm}44 within the tumor and -97{\textpm}52 within the fat pad adjacent to the tumor (p\<0.005). The tumor area measured by CT and histology was correlated (r2 = 0.92), while the area designated as fat decreased with increasing tumor size (r2 = 0.51). Analysis of CT and histology images of the tumor and surrounding fat pad revealed an average percentage of fat of 65.3\% vs. 75.2\%, 36.5\% vs. 48.4\%, and 31.6\% vs. 38.5\% for tumors \<75 mm3, 75{\textendash}150 mm3 and \>150 mm3, respectively. Further, CT mapped bone-soft tissue interfaces near the acoustic beam during real-time imaging. Combined CT/US is a feasible method for guiding interventions by tracking the acoustic focus within a pre-acquired CT image volume and characterizing tissues proximal to and surrounding the acoustic focus.

}, doi = {10.1371/journal.pone.0027372}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0027372}, author = {Caskey, , Charles F. and Hlawitschka, , Mario and Qin, , Shengping and Mahakian, , Lisa M. and Cardiff, , Robert D. and Boone, , John M. and Ferrara, , Katherine W.} } @inbook {springerlink:10.1007/978-1-4419-7046-6_68, title = {Open Source Clinical Portals: A Model for Healthcare Information Systems to Support Care Processes and Feed Clinical Research}, booktitle = {Software Tools and Algorithms for Biological Systems}, series = {Advances in Experimental Medicine and Biology}, volume = {696}, year = {2011}, note = {10.1007/978-1-4419-7046-6_68}, pages = {667-677}, publisher = {Springer New York}, organization = {Springer New York}, abstract = {Open source is a still unexploited chance for healthcare organizations and technology providers to answer to a growing demand for innovation and to join economical benefits with a new way of managing hospital information systems. This chapter will present the case of the web enterprise clinical portal developed in Italy by Niguarda Hospital in Milan with the support of Fondazione Politecnico di Milano, to enable a paperless environment for clinical and administrative activities in the ward. This represents also one rare case of open source technology and reuse in the healthcare sector, as the system{\textquoteright}s porting is now taking place at Besta Neurological Institute in Milan. This institute is customizing the portal to feed researchers with structured clinical data collected in its portal{\textquoteright}s patient records, so that they can be analyzed, e.g., through business intelligence tools. Both organizational and clinical advantages are investigated, from process monitoring, to semantic data structuring, to recognition of common patterns in care processes.}, isbn = {978-1-4419-7046-6}, url = {http://dx.doi.org/10.1007/978-1-4419-7046-6_68}, author = {Locatelli, Paolo and Baj, Emanuele and Restifo, Nicola and Origgi, Gianni and Bragagia, Silvia}, editor = {Arabnia, Hamid R. R. and Tran, Quoc-Nam} } @article {info:doi/10.2196/jmir.1521, title = {Open Source, Open Standards, and Health Care Information Systems}, journal = {J Med Internet Res}, volume = {13}, number = {1}, year = {2011}, month = {Feb}, pages = {e24}, keywords = {Health Care Information Systems}, doi = {10.2196/jmir.1521}, url = {http://www.jmir.org/2011/1/e24/}, author = {Reynolds, J. Carl and Wyatt, C. Jeremy} } @conference {lien:79670M, title = {Open source tools for standardized privacy protection of medical images}, booktitle = {Medical Imaging 2011: Advanced PACS-based Imaging Informatics and Therapeutic Applications}, volume = {7967}, number = {1}, year = {2011}, pages = {79670M}, publisher = {SPIE}, organization = {SPIE}, abstract = {In addition to the primary care context, medical images are often useful for research projects and community healthcare networks, so-called "secondary use". Patient privacy becomes an issue in such scenarios since the disclosure of personal health information (PHI) has to be prevented in a sharing environment. In general, most PHIs should be completely removed from the images according to the respective privacy regulations, but some basic and alleviated data is usually required for accurate image interpretation. Our objective is to utilize and enhance these specifications in order to provide reliable software implementations for de- and re-identification of medical images suitable for online and offline delivery. DICOM (Digital Imaging and Communications in Medicine) images are de-identified by replacing PHI-specific information with values still being reasonable for imaging diagnosis and patient indexing. In this paper, this approach is evaluated based on a prototype implementation built on top of the open source framework DCMTK (DICOM Toolkit) utilizing standardized de- and re-identification mechanisms. A set of tools has been developed for DICOM de-identification that meets privacy requirements of an offline and online sharing environment and fully relies on standard-based methods.}, doi = {10.1117/12.877989}, url = {http://link.aip.org/link/?PSI/7967/79670M/1}, author = {Chung-Yueh Lien and Onken, Michael and Marco Eichelberg and Tsair Kao and Andreas Hein}, editor = {William W. Boonn and Brent J. Liu} } @article {720, title = {OpenMRS, A Global Medical Records System Collaborative: Factors Influencing Successful Implementation.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, volume = {2011}, year = {2011}, month = {2011}, pages = {960-968}, abstract = {OpenMRS is an open-source, robust electronic health record (EHR) platform that is supported by a large global network and used in over forty countries. We explored what factors lead to successful implementation of OpenMRS in resource constrained settings. Data sources included in-person and telephone key informant interviews, focus groups and responses to an electronic survey from 10 sites in 7 countries. Qualitative data was coded through independent coding, discussion and consensus. The most common perceived benefits of implementation were for providing clinical care, reporting to funders, managing operations and research. Successful implementation factors include securing adequate infrastructure, and sociotechnical system factors, particularly adequate staffing, computers, and ability to use software. Strategic and tactical planning were successful strategies, including understanding and addressing the infrastructure and human costs involved, training or hiring personnel technically capable of modifying the software and integrating it into the daily work flow to meet clinicians{\textquoteright} needs.}, issn = {1942-597X}, author = {Mohammed-Rajput, Nareesa A and Smith, Dawn C and Mamlin, Burke and Biondich, Paul and Doebbeling, Brad N} } @article {1029, title = {A partnership approach for Electronic Data Capture in small-scale clinical trials.}, journal = {J Biomed Inform}, volume = {44 Suppl 1}, year = {2011}, month = {2011 Dec}, pages = {S103-8}, abstract = {

Amid researchers{\textquoteright} growing need for study data management, the CTSA-funded Institute for Translational Health Sciences developed an approach to combine technical and scientific resources with small-scale clinical trials researchers in order to make Electronic Data Capture more efficient. In a 2-year qualitative evaluation we found that the importance of ease of use and training materials outweighed number of features and functionality. EDC systems we evaluated were Catalyst Web Tools, OpenClinica and REDCap. We also found that two other systems, Caisis and LabKey, did not meet the specific user needs of the study group.

}, keywords = {Clinical Trials as Topic, Data Collection, Humans, Internet, Medical Informatics}, issn = {1532-0480}, doi = {10.1016/j.jbi.2011.05.008}, author = {Franklin, Joshua D and Guidry, Alicia and Brinkley, James F} } @article {1048, title = {PopHealth primer. ONC funds open-source software to streamline clinical quality measures reporting for meaningful use program.}, journal = {J AHIMA}, volume = {82}, year = {2011}, month = {2011 Sep}, pages = {48-50}, keywords = {Benchmarking, Financing, Government, Government Agencies, Mandatory Reporting, Organizational Case Studies, Quality Assurance, Health Care, Reimbursement, Incentive, Software, United States, User-Computer Interface}, issn = {1060-5487}, author = {Cottington, Sarah} } @article {10.1109/ESEM.2011.11, title = {A Qualitative Study of Open Source Software Development: The Open EMR Project}, journal = {Empirical Software Engineering and Measurement, International Symposium on}, year = {2011}, pages = {30-39}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Open Source software is competing successfully in many areas. The commercial sector is recognizing the benefits offered by Open Source development methods that lead to high quality software. Can these benefits be realized in specialized domains where expertise is rare? This study examined discussion forums of an Open Source project in a particular specialized application domain -- electronic medical records -- to see how development roles are carried out, and by whom. We found through a qualitative analysis that the core developers in this system include doctors and clinicians who also use the product. We also found that the size of the community associated with the project is an order of magnitude smaller than predicted, yet still maintains a high degree of responsiveness to issues raised by users. The implication is that a few experts and a small core of dedicated programmers can achieve success using an Open Source approach in a specialized domain.}, isbn = {978-0-7695-4604-9}, doi = {http://doi.ieeecomputersociety.org/10.1109/ESEM.2011.11}, author = {John Noll and Sarah Beecham and Dominik Seichter} } @article {902, title = {The rise of open-source electronic health records}, journal = {The Lancet}, volume = {377}, year = {2011}, pages = {1641{\textendash}1642}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79955885166\&partnerID=40\&md5=f959756cb7de6e24377a57a4e54117b0}, author = {Webster, P C} } @article {1082, title = {The rise of open-source electronic health records}, journal = {The LancetThe Lancet}, volume = {377}, year = {2011}, pages = {1641 - 1642}, isbn = {0140-6736}, url = {http://dx.doi.org/10.1016/S0140-6736(11)60659-4}, author = {Webster, Paul C} } @article {1028, title = {On selecting a clinical trial management system for large scale, multi-centre, multi-modal clinical research study.}, journal = {Stud Health Technol Inform}, volume = {168}, year = {2011}, month = {2011}, pages = {89-95}, abstract = {

Clinical research studies offer many challenges for their supporting information systems. AIBL assembled 1112 participants who volunteered crucial information for a comprehensive study on neurodegenerative diseases. This paper discusses the shortcomings of the clinical trial management system chosen to record the results of the study. A set of guidelines was devised and a critique of five systems ensued. OpenClinica was selected as the most appropriate option. The main contribution of this paper is: (i) proposing a set of guidelines to determine the appropriateness of Clinical Trial Management Systems (CTMS) solution; (ii) providing a brief critique of existing commercial and open-sourced CTMS; and (iii) alluding to some data migration issues and providing cues on how to address them. We conclude that open-source CTMS are viable alternatives to the more expensive commercial systems to conduct, record and manage clinical studies.

}, keywords = {Australia, Checklist, Choice Behavior, Clinical Trials as Topic, Decision Support Systems, Clinical, Medical Informatics, Multicenter Studies as Topic}, issn = {0926-9630}, author = {Leroux, Hugo and McBride, Simon and Gibson, Simon} } @article {1155, title = {The {SHARPn} project on secondary use of {Electronic} {Medical} {Record} data: progress, plans, and possibilities}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2011}, year = {2011}, pages = {248{\textendash}256}, abstract = {SHARPn is a collaboration among 16 academic and industry partners committed to the production and distribution of high-quality software artifacts that support the secondary use of EMR data. Areas of emphasis are data normalization, natural language processing, high-throughput phenotyping, and data quality metrics. Our work avails the industrial scalability afforded by the Unstructured Information Management Architecture (UIMA) from IBM Watson Research labs, the same framework which underpins the Watson Jeopardy demonstration. This descriptive paper outlines our present work and achievements, and presages our trajectory for the remainder of the funding period. The project is one of the four Strategic Health IT Advanced Research Projects (SHARP) projects funded by the Office of the National Coordinator in 2010.}, keywords = {Algorithms, Biomedical Research, Cooperative Behavior, Data Mining, electronic health records, Natural Language Processing, Software}, issn = {1942-597X}, author = {Chute, Christopher G. and Pathak, Jyotishman and Savova, Guergana K. and Bailey, Kent R. and Schor, Marshall I. and Hart, Lacey A. and Beebe, Calvin E. and Huff, Stanley M.} } @article {910, title = {Staying open. Open-source health IT gets boost from foundation.}, journal = {Modern healthcare}, volume = {41}, year = {2011}, pages = {10{\textendash}11}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79958716512\&partnerID=40\&md5=034fdbb492b4a355ae02dfa560abe1cd}, author = {Conn, J} } @booklet {10.1118/1.3611983, title = {SU-E-T-33: Pydicom: An Open Source DICOM Library}, volume = {38}, number = {6}, year = {2011}, pages = {3493-3493}, publisher = {AAPM}, issn = {00942405}, doi = {DOI:10.1118/1.3611983}, url = {http://dx.doi.org/doi/10.1118/1.3611983}, author = {D Mason} } @article {640, title = {Towards Open Collaborative Health Informatics - The Role of Free/Libre Open Source Principles. Contribution of the IMIA Open Source Health Informatics Working Group.}, journal = {Yearbook of medical informatics}, volume = {6}, year = {2011}, month = {2011}, pages = {63-72}, abstract = {OBJECTIVES: : To analyze the contribution of Free/Libre Open Source Software in health care (FLOSS-HC) and to give perspectives for future developments. METHODS: The paper summarizes FLOSS-related trends in health care as anticipated by members of the IMIA Open Source Working Group. Data were obtained through literature review and personal experience and observations of the authors in the last two decades. A status quo is given by a frequency analysis of the database of Medfloss.org, one of the world{\textquoteright}s largest platforms dedicated to FLOSS-HC. The authors discuss current problems in the field of health care and finally give a prospective roadmap, a projection of the potential influences of FLOSS in health care. RESULTS: FLOSS-HC already exists for more than 2 decades. Several projects have shown that FLOSS may produce highly competitive alternatives to proprietary solutions that are at least equivalent in usability and have a better total cost of ownership ratio. The Medfloss.org database currently lists 221 projects of diverse application types. CONCLUSIONS: FLOSS principles hold a great potential for addressing several of the most critical problems in health care IT. The authors argue that an ecosystem perspective is relevant and that FLOSS principles are best suited to create health IT systems that are able to evolve over time as medical knowledge, technologies, insights, workflows etc. continuously change. All these factors that inherently influence the development of health IT systems are changing at an ever growing pace. Traditional models of software engineering are not able to follow these changes and provide up-to-date systems for an acceptable cost/value ratio. To allow FLOSS to positively influence Health IT in the future a "FLOSS-friendly" environment has to be provided. Policy makers should resolve uncertainties in the legal framework that disfavor FLOSS. Certification procedures should be specified in a way that they do not raise additional barriers for FLOSS.}, issn = {0943-4747}, author = {Karopka, T and Schmuhl, H and Marcelo, A and Molin, J Dal and Wright, G} } @article {536, title = {Tracking and monitoring the health workforce: a new human resources information system (HRIS) in Uganda.}, journal = {Human resources for health}, volume = {9}, year = {2011}, month = {2011 Feb 17}, pages = {6}, abstract = {ABSTRACT: BACKGROUND: Health workforce planning is important in ensuring that the recruitment, training and deployment of health workers are conducted in the most efficient way possible. However, in many developing countries, human resources for health data are limited, inconsistent, out-dated, or unavailable. Consequently, policy-makers are unable to use reliable data to make informed decisions about the health workforce. Computerized human resources information systems (HRIS) enable countries to collect, maintain, and analyze health workforce data. METHODS: The purpose of this article is twofold. First, we describe Uganda{\textquoteright}s transition from a paper filing system to an electronic HRIS capable of providing information about country-specific health workforce questions. We examine the ongoing five-step HRIS strengthening process used to implement an HRIS that tracks health worker data at the Uganda Nurses and Midwives Council (UNMC). Secondly, we describe how HRIS data can be used to address workforce planning questions via an initial analysis of the UNMC training, licensure and registration records from 1970 through May 2009. RESULTS: The data indicate that, for the 25 482 nurses and midwives who entered training before 2006, 72\% graduated, 66\% obtained a council registration, and 28\% obtained a license to practice. Of the 17 405 nurses and midwives who obtained a council registration as of May 2009, 96\% are of Ugandan nationality and just 3\% received their training outside of the country. Thirteen per cent obtained a registration for more than one type of training. Most (34\%) trainings with a council registration are for the enrolled nurse training, followed by enrolled midwife (25\%), registered (more advanced) nurse (21\%), registered midwife (11\%), and more specialized trainings (9\%). CONCLUSION: The UNMC database is valuable in monitoring and reviewing information about nurses and midwives. However, information obtained from this system is also important in improving strategic planning for the greater health care system in Uganda. We hope that the use of a real-world example of HRIS strengthening provides guidance for the implementation of similar projects in other countries or contexts.}, issn = {1478-4491}, author = {Spero, Julie C and McQuide, Pamela A and Matte, Rita} } @article {906, title = {Tracking PACS usage with open source tools}, journal = {Journal of Digital Imaging}, volume = {24}, year = {2011}, pages = {719{\textendash}723}, abstract = {A typical choice faced by Picture Archiving and Communication System (PACS) administrators is deciding how many PACS workstations are needed and where they should be sited. Oftentimes, the social consequences of having too few are severe enough to encourage oversupply and underutilization. This is costly, at best in terms of hardware and electricity, and at worst (depending on the PACS licensing and support model) in capital costs and maintenance fees. The PACS administrator needs tools to asses accurately the use to which her fleet is being subjected, and thus make informed choices before buying more workstations. Lacking a vended solution for this challenge, we developed our own. {\textcopyright} Society for Imaging Informatics in Medicine 2010.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-80053899930\&partnerID=40\&md5=f823f24d383b58b1b55de9638c3bc0c2}, author = {French, T L}, editor = {Langer, S G} } @article {606, title = {Use of an innovative, affordable, and open-source short message service-based tool to monitor malaria in remote areas of Uganda.}, journal = {The American journal of tropical medicine and hygiene}, volume = {85}, year = {2011}, month = {2011 Jul}, pages = {26-33}, abstract = {Abstract. Quality health management requires timely and accurate data, and paper-based reporting does not fill this role adequately. The introduction of malaria rapid diagnostic tests and the availability of wireless communications present an opportunity to open direct data transmission and feedback between peripheral health workers and central managers. In November 2009, the Uganda Ministry of Health deployed a short message service-based reporting system in two districts. At a set-up cost of $100/health facility, local technician support of $ 400 per month, and a cost of $0.53/week/clinic, the SMS reporting system was started at more than 140 clinics. Positivity rates for rapid diagnostic tests and artemisinin combination therapy stock outs were 48\% and 54\% in Kabale and 71\% and 54\% in Gulu, among other reports, at more than 85\% health facilities reporting weekly and without monetary incentives or additional supervision. The SMS-based reporting systems have potential to improve timeliness in reporting of specific, time-sensitive metrics at modest cost, while by-passing current bottlenecks in the flow of data. With the development of specific capacity to manage stock data at district level, the availability of timely data offers potential to address commodity distribution problems and reduce stock-outs.}, issn = {1476-1645}, author = {Asiimwe, Caroline and Gelvin, David and Lee, Evan and Ben Amor, Yanis and Quinto, Ebony and Katureebe, Charles and Sundaram, Lakshmi and Bell, David and Berg, Matt} } @article {599, title = {Wikipedia: a key tool for global public health promotion.}, journal = {Journal of medical Internet research}, volume = {13}, year = {2011}, month = {2011}, pages = {e14}, abstract = {The Internet has become an important health information resource for patients and the general public. Wikipedia, a collaboratively written Web-based encyclopedia, has become the dominant online reference work. It is usually among the top results of search engine queries, including when medical information is sought. Since April 2004, editors have formed a group called WikiProject Medicine to coordinate and discuss the English-language Wikipedia{\textquoteright}s medical content. This paper, written by members of the WikiProject Medicine, discusses the intricacies, strengths, and weaknesses of Wikipedia as a source of health information and compares it with other medical wikis. Medical professionals, their societies, patient groups, and institutions can help improve Wikipedia{\textquoteright}s health-related entries. Several examples of partnerships already show that there is enthusiasm to strengthen Wikipedia{\textquoteright}s biomedical content. Given its unique global reach, we believe its possibilities for use as a tool for worldwide health promotion are underestimated. We invite the medical community to join in editing Wikipedia, with the goal of providing people with free access to reliable, understandable, and up-to-date health information.}, keywords = {Consumer Health Information, Encyclopedias as Topic, Health Promotion, Humans, Information Dissemination, Information Services, Internet, Patient Education as Topic, Public Health, World Health}, issn = {1438-8871}, author = {Heilman, James M and Kemmann, Eckhard and Bonert, Michael and Chatterjee, Anwesh and Ragar, Brent and Beards, Graham M and Iberri, David J and Harvey, Matthew and Thomas, Brendan and Stomp, Wouter and Martone, Michael F and Lodge, Daniel J and Vondracek, Andrea and de Wolff, Jacob F and Liber, Casimir and Grover, Samir C and Vickers, Tim J and Mesk{\'o}, Bertalan and Laurent, Micha{\"e}l R} } @article {600, title = {WikiProject Medicine.}, journal = {BMJ (Clinical research ed.)}, volume = {342}, year = {2011}, month = {2011}, pages = {d3387}, issn = {1468-5833}, doi = {10.1136/bmj.d3387}, author = {Trevena, Lyndal} } @conference {558, title = {xDAuth: A Scalable and Lightweight Framework for Cross Domain Access Control and Delegation}, booktitle = {SACMAT{\textquoteright}11}, year = {2011}, publisher = {ACM}, organization = {ACM}, address = {Innsbruck, Austria}, abstract = {Cross domain resource sharing and collaborations have be- come pervasive in today{\textquoteright}s service oriented organizations. Existing approaches for the realization of cross domain ac- cess control are either focused on the model level only with- out concrete implementation mechanisms, or not general enough to provide a exible framework for enterprise web applications. In this paper, we present xDAuth, a frame- work for the realization of cross domain access control and delegation with RESTful web service architecture. While focusing on real issues under the context of cross domain access scenarios such as no prede ned trust relationship be- tween a service provider domain and service requestor do- main, xDAuth leverages existing web technologies to real- ize desired security requirements while supporting exible and scalable security policies and privacy protection with low performance overhead. We have implemented xDAuth in a medical module in OpenERP, an open source ERP sys- tem. Our evaluation demonstrates that xDAuth is a feasible framework towards general cross domain access control for service oriented architectures.}, url = {http://profsandhu.com/zhang/pub/sacmat11-xdauth.pdf}, author = {Masoom Alam and Xinwen Zhang and Kamran H Khan and Gohar Ali} } @article {849, title = {The Yale cTAKES extensions for document classification: architecture and application.}, journal = {J Am Med Inform Assoc}, volume = {18}, year = {2011}, month = {2011 Sep-Oct}, pages = {614-20}, abstract = {

BACKGROUND: Open-source clinical natural-language-processing (NLP) systems have lowered the barrier to the development of effective clinical document classification systems. Clinical natural-language-processing systems annotate the syntax and semantics of clinical text; however, feature extraction and representation for document classification pose technical challenges.

METHODS: The authors developed extensions to the clinical Text Analysis and Knowledge Extraction System (cTAKES) that simplify feature extraction, experimentation with various feature representations, and the development of both rule and machine-learning based document classifiers. The authors describe and evaluate their system, the Yale cTAKES Extensions (YTEX), on the classification of radiology reports that contain findings suggestive of hepatic decompensation.

RESULTS AND DISCUSSION: The F(1)-Score of the system for the retrieval of abdominal radiology reports was 96\%, and was 79\%, 91\%, and 95\% for the presence of liver masses, ascites, and varices, respectively. The authors released YTEX as open source, available at http://code.google.com/p/ytex.

}, keywords = {Connecticut, Data Mining, Decision Support Systems, Clinical, electronic health records, Humans, Liver Failure, Natural Language Processing, Pattern Recognition, Automated, Radiology Information Systems}, issn = {1527-974X}, doi = {10.1136/amiajnl-2011-000093}, author = {Garla, Vijay and Lo Re, Vincent and Dorey-Stein, Zachariah and Kidwai, Farah and Scotch, Matthew and Womack, Julie and Justice, Amy and Brandt, Cynthia} } @article {610, title = {Adaptive radiotherapy based on contrast enhanced cone beam CT imaging.}, journal = {Acta oncologica (Stockholm, Sweden)}, volume = {49}, year = {2010}, month = {2010 Oct}, pages = {972-7}, abstract = {Cone beam CT (CBCT) imaging has become an integral part of radiation therapy, with images typically used for offline or online patient setup corrections based on bony anatomy co-registration. Ideally, the co-registration should be based on tumor localization. However, soft tissue contrast in CBCT images may be limited. In the present work, contrast enhanced CBCT (CECBCT) images were used for tumor visualization and treatment adaptation. Material and methods. A spontaneous canine maxillary tumor was subjected to repeated cone beam CT imaging during fractionated radiotherapy (10 fractions in total). At five of the treatment fractions, CECBCT images, employing an iodinated contrast agent, were acquired, as well as pre-contrast CBCT images. The tumor was clearly visible in post-contrast minus pre-contrast subtraction images, and these contrast images were used to delineate gross tumor volumes. IMRT dose plans were subsequently generated. Four different strategies were explored: 1) fully adapted planning based on each CECBCT image series, 2) planning based on images acquired at the first treatment fraction and patient repositioning following bony anatomy co-registration, 3) as for 2), but with patient repositioning based on co-registering contrast images, and 4) a strategy with no patient repositioning or treatment adaptation. The equivalent uniform dose (EUD) and tumor control probability (TCP) calculations to estimate treatment outcome for each strategy. Results. Similar translation vectors were found when bony anatomy and contrast enhancement co-registration were compared. Strategy 1 gave EUDs closest to the prescription dose and the highest TCP. Strategies 2 and 3 gave EUDs and TCPs close to that of strategy 1, with strategy 3 being slightly better than strategy 2. Even greater benefits from strategies 1 and 3 are expected with increasing tumor movement or deformation during treatment. The non-adaptive strategy 4 was clearly inferior to all three adaptive strategies. Conclusion. CECBCT may prove useful for adaptive radiotherapy.}, keywords = {Animals, Carcinoma, Cone-Beam Computed Tomography, Contrast Media, Dog Diseases, Dogs, Female, Maxillary Neoplasms, Patient Positioning, Radiographic Image Enhancement, Radiotherapy Planning, Computer-Assisted}, issn = {1651-226X}, author = {S{\o}vik, Aste and R{\o}dal, Jan and Skogmo, Hege K and Lerv{\r a}g, Christoffer and Eilertsen, Karsten and Malinen, Eirik} } @article {529, title = {AngioLab: Integrated technology for patient-specific management of intracranial aneurysms.}, journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference}, volume = {1}, year = {2010}, month = {2010}, pages = {6801-4}, abstract = {AngioLab is a software tool developed within the GIMIAS framework and is part of a more ambitious pipeline for the integrated management of cerebral aneurysms. AngioLab currently includes three plug-ins: angio segmentation, angio morphology and stenting, as well as supports advanced rendering techniques for the visualization of virtual angiographies. In December 2009, 23 clinicians completed an evaluation questionnaire about AngioLab. This activity was part of a teaching course held during the 2(nd) European Society for Minimally Invasive Neurovascular Treatment (ESMINT) Teaching Course held at the Universitat Pompeu Fabra, Barcelona, Spain. The Automated Morphological Analysis (angio morphology plug-in) and the Endovascular Treatment Planning (stenting plug-in) were evaluated. In general, the results provided by these tools were considered as relevant and as an emerging need in their clinical field.}, issn = {1557-170X}, author = {Villa-Uriol, M C and Larrabide, I and Geers, A J and Pozo, J and Bogunovic, H and Mazzeo, M and Omedas, P and Barbarito, V and Carotenuto, L and Riccobene, C and Planes, X and Martelli, Y and Frangi, A F} } @article {531, title = {Building a open source framework for virtual medical training.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {23}, year = {2010}, month = {2010 Dec}, pages = {706-20}, abstract = {This paper presents a framework to build medical training applications by using virtual reality and a tool that helps the class instantiation of this framework. The main purpose is to make easier the building of virtual reality applications in the medical training area, considering systems to simulate biopsy exams and make available deformation, collision detection, and stereoscopy functionalities. The instantiation of the classes allows quick implementation of the tools for such a purpose, thus reducing errors and offering low cost due to the use of open source tools. Using the instantiation tool, the process of building applications is fast and easy. Therefore, computer programmers can obtain an initial application and adapt it to their needs. This tool allows the user to include, delete, and edit parameters in the functionalities chosen as well as storing these parameters for future use. In order to verify the efficiency of the framework, some case studies are presented.}, issn = {1618-727X}, author = {de Oliveira, Ana Cl{\'a}udia Melo Tiessi Gomes and Nunes, F{\'a}tima de Lourdes dos Santos} } @article {871, title = {The caBIG annotation and image Markup project.}, journal = {J Digit Imaging}, volume = {23}, year = {2010}, month = {2010 Apr}, pages = {217-25}, abstract = {

Image annotation and markup are at the core of medical interpretation in both the clinical and the research setting. Digital medical images are managed with the DICOM standard format. While DICOM contains a large amount of meta-data about whom, where, and how the image was acquired, DICOM says little about the content or meaning of the pixel data. An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human or machine observer. An image markup is the graphical symbols placed over the image to depict an annotation. While DICOM is the standard for medical image acquisition, manipulation, transmission, storage, and display, there are no standards for image annotation and markup. Many systems expect annotation to be reported verbally, while markups are stored in graphical overlays or proprietary formats. This makes it difficult to extract and compute with both of them. The goal of the Annotation and Image Markup (AIM) project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community. The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM.

}, keywords = {Computational Biology, Computer Communication Networks, Databases, Factual, Diagnostic Imaging, Humans, Interdisciplinary Communication, Medical Records Systems, Computerized, National Cancer Institute (U.S.), National Institutes of Health (U.S.), Neoplasms, Program Evaluation, Quality of Health Care, Radiographic Image Enhancement, Radiology Information Systems, Software, Systems Integration, United States, User-Computer Interface}, issn = {1618-727X}, doi = {10.1007/s10278-009-9193-9}, author = {Channin, David S and Mongkolwat, Pattanasak and Kleper, Vladimir and Sepukar, Kastubh and Rubin, Daniel L} } @article {20226035, title = {CASE: a framework for computer supported outbreak detection.}, journal = {BMC medical informatics and decision making}, volume = {10}, year = {2010}, month = {2010}, pages = {14}, abstract = {BACKGROUND: In computer supported outbreak detection, a statistical method is applied to a collection of cases to detect any excess cases for a particular disease. Whether a detected aberration is a true outbreak is decided by a human expert. We present a technical framework designed and implemented at the Swedish Institute for Infectious Disease Control for computer supported outbreak detection, where a database of case reports for a large number of infectious diseases can be processed using one or more statistical methods selected by the user. RESULTS: Based on case information, such as diagnosis and date, different statistical algorithms for detecting outbreaks can be applied, both on the disease level and the subtype level. The parameter settings for the algorithms can be configured independently for different diagnoses using the provided graphical interface. Input generators and output parsers are also provided for all supported algorithms. If an outbreak signal is detected, an email notification is sent to the persons listed as receivers for that particular disease. CONCLUSIONS: The framework is available as open source software, licensed under GNU General Public License Version 3. By making the code open source, we wish to encourage others to contribute to the future development of computer supported outbreak detection systems, and in particular to the development of the CASE framework.}, author = {Cakici, Baki and Hebing, Kenneth and Gr{\"u}newald, Maria and Saretok, Paul and Hulth, Anette} } @article {1013, title = {Combining vital events registration, verbal autopsy and electronic medical records in rural Ghana for improved health services delivery.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {416-20}, abstract = {

This paper describes the process of implementing a low-cost {\textquoteright}real-time{\textquoteright} vital registration and verbal autopsy system integrated within an electronic medical record within the Millennium Village cluster in rural Ghana. Using MGV-Net, an open source health information architecture built around the OpenMRS platform, a total of 2378 births were registered between January 2007 and June 2009. The percentage of births registered in the health facility under supervision of a skilled attendant increased substantially over the course of the project from median of 35\% in 2007 to 64\% in 2008 and 85\% midway through 2009. Building additional clinics to reduce distance to facility and using the CHEWs to refer women for delivery in the clinics are possible explanations for the success in the vital registration. The integration of vital registration and verbal autopsies with the MGV-Net information system makes it possible for rapid assessment of effectiveness and provides important feedback to local providers and the Millennium Villages Project.

}, keywords = {Cause of Death, Database Management Systems, Delivery of Health Care, electronic health records, Ghana, Medical Record Linkage, Quality Assurance, Health Care, Quality Improvement, Registries, Rural Health Services, Vital Statistics}, issn = {0926-9630}, author = {Ohemeng-Dapaah, Seth and Pronyk, Paul and Akosa, Eric and Nemser, Bennett and Kanter, Andrew S} } @proceedings {513, title = {Comprehensive Yet Scalable Health Information Systems for Low Resource Settings: A Collaborative Effort in Sierra Leone}, year = {2010}, month = {11/2010}, abstract = {We address the problem of how to integrate health informa- tion systems in low-income African countries in which techni- cal infrastructure and human resources vary wildly within countries. We describe a set of tools to meet the needs of dif- ferent service areas including managing aggregate indicators, patient level record systems, and mobile tools for community outreach. We present the case of Sierra Leone and use this case to motivate and illustrate an architecture that allows us to provide services at each level of the health system (na- tional, regional, facility and community) and provide different configurations of the tools as appropriate for the individual area. Finally, we present a, collaborative implementation of this approach in Sierra Leone.}, url = {http://proceedings.amia.org/127frh}, author = {Braaa, J{\o}rn and Kanterb, Andrew S. and Leshc, Neal and Crichtond, Ryan and Jolliffea, Bob and S{\ae}b{\o}e, Johan and Kossia, Edem and Seebregts, Christopher J} } @article {20118730, title = {Computer-aided volumetric comparison of reconstructed orbits for blow-out fractures with nonpreformed versus 3-dimensionally preformed titanium mesh plates: a preliminary study.}, journal = {Journal of computer assisted tomography}, volume = {34}, year = {2010}, month = {2010 Jan}, pages = {98-104}, abstract = {OBJECTIVES: To compare and evaluate, using computer-aided volumetric measurements, the accuracy and reliability of nonpreformed mesh plates (NPMPs) versus 3-dimensionally preformed titanium mesh plates (PMPs) in posttraumatic orbital volume restoration. PATIENTS AND METHODS: Facial coronal computed tomographic scan slices from 20 patients (10 in the NPMP and 10 in the PMP group) were used to measure bony orbital volume using OsiriX Medical Image software (version 3.3.2, www.osirix-viewer.com). The procedure was performed on both orbits; thereafter, the volume of the contralateral health orbit was used as a control for comparison in the 2 groups of patients. The difference in orbital volume between the 2 groups and between the reconstructed versus uninjured side in both groups have been statistically correlated. RESULTS: The mean orbital volume between the reconstructed (19.215 mL in NPMP and 21.791 mL in PMP) and the contralateral uninjured side (18.955 mL in NPMP and 21.710 mL in PMP) was not statistically significant (P > 0.05). The mean orbital volumes of the reconstructed orbits were 19.215 mL in the NPMP and 21.791 mL in the PMP group, with no statistically significant difference (P > 0.05). The volume data of the reconstructed orbit fitted that of the contralateral uninjured orbit with an accuracy of a maximum of 1.85 mL in the NPMP group and 2.5 mL in the PMP group. CONCLUSIONS: The current study demonstrated that there were no significant differences in the orbital volume restoration using either technique. In fact, both techniques allow for close reproduction of natural orbital volume and shape, and its use in posttraumatic orbital wall reconstruction was successful.}, author = {Scolozzi, Paolo and Momjian, Armen and Heuberger, Joris} } @article {20335647, title = {The development and design of an electronic patient record using open source web-based technology.}, journal = {The HIM journal}, volume = {39}, year = {2010}, month = {2010}, pages = {30-5}, abstract = {This paper describes the method used to develop the One Stop Crisis Centre (OSCC) Portal, an open source web-based electronic patient record system (EPR) for the One Stop Crisis Center, Hospital Universiti Sains Malaysia (HUSM) in Kelantan, Malaysia. Features and functionalities of the system are presented to demonstrate the workflow. Use of the OSCC Portal improved data integration and data communication and contributed to improvements in care management. With implementation of the OSCC portal, improved coordination between disciplines and standardisation of data in HUSM were noticed. It is expected that this will in turn result in improved data confidentiality and data integrity. The collected data will also be useful for quality assessment and research. Other low-resource centers with limited computer hardware and access to open-source software could benefit from this endeavour.}, author = {Syed-Mohamad, Sharifa Mastura and Ali, Siti Hawa and Mat-Husin, Mohd Nazri} } @article {20517664, title = {E-health integration and interoperability based on open-source information technology.}, journal = {Wiener klinische Wochenschrift}, volume = {122 Suppl 2}, year = {2010}, month = {2010 May}, pages = {3-10}, author = {Dinevski, Dejan and Poli, Andrea and Krajnc, Ivan and Sustersic, Olga and Arh, Tanja} } @article {904, title = {Electronic data capture for registries and clinical trials in orthopaedic surgery: Open source versus commercial systems}, journal = {Clinical Orthopaedics and Related Research}, volume = {468}, year = {2010}, pages = {2664{\textendash}2671}, abstract = {Background: Collection and analysis of clinical data can help orthopaedic surgeons to practice evidence based medicine. Spreadsheets and offline relational databases are prevalent, but not flexible, secure, workflow friendly and do not support the generation of standardized and interoperable data. Additionally these data collection applications usually do not follow a structured and planned approach which may result in failure to achieve the intended goal. Questions/purposes: Our purposes are (1) to provide a brief overview of EDC systems, their types, and related pros and cons as well as to describe commonly used EDC platforms and their features; and (2) describe simple steps involved in designing a registry/clinical study in DADOS P, an open source EDC system. Where are we now?: Electronic data capture systems aimed at addressing these issues are widely being adopted at an institutional/national/ international level but are lacking at an individual level. A wide array of features, relative pros and cons and different business models cause confusion and indecision among orthopaedic surgeons interested in implementing EDC systems. Where do we need to go?: To answer clinical questions and actively participate in clinical studies, orthopaedic surgeons should collect data in parallel to their clinical activities. Adopting a simple, user-friendly, and robust EDC system can facilitate the data collection process. How do we get there?: Conducting a balanced evaluation of available options and comparing them with intended goals and requirements can help orthopaedic surgeons to make an informed choice. {\textcopyright} 2010 The Association of Bone and Joint Surgeons{\textregistered}.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-77957336660\&partnerID=40\&md5=dec3706be86215e9656a06f82265cb28}, author = {Shah, J.a b and Rajgor, D.a b and Pradhan, S.a b and McCready, M.c and Zaveri, A.a d and Pietrobon, R.c} } @article {611, title = {Evaluation of adaptive radiotherapy of bladder cancer by image-based tumour control probability modelling.}, journal = {Acta oncologica (Stockholm, Sweden)}, volume = {49}, year = {2010}, month = {2010 Oct}, pages = {1045-51}, abstract = {Clinical implementation of adaptive radiotherapy strategies could benefit from extended tools for plan evaluation and selection. For this purpose we investigated the feasibility of image-based tumour control probability (TCP) modelling using the bladder as example of a tumour site with potential benefit from adaptive strategies.}, keywords = {Carcinoma, Computer Simulation, Humans, Image Processing, Computer-Assisted, Models, Statistical, Probability, Radiotherapy Dosage, Radiotherapy Planning, Computer-Assisted, Radiotherapy, Conformal, Tumor Burden, Urinary Bladder, Urinary Bladder Neoplasms}, issn = {1651-226X}, author = {Wright, Pauliina and Muren, Ludvig P and H{\o}yer, Morten and Malinen, Eirik} } @article {1016, title = {Experience implementing a point-of-care electronic medical record system for primary care in Malawi.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {96-100}, abstract = {

Due to the fact that health care professionals in Malawi are often overstretched, the use and quality of health data can be compromised. The Malawi Health Management Information System (HMIS) has streamlined data collection and reporting and increased the use of data to improve care. Obstacles remain, including incomplete reporting and low staff morale. With the Baobab Health Trust and the Malawi Ministry of Health, Partners In Health piloted an innovative point-of-care data system for primary care that functions alongside OpenMRS, an open source medical record platform. The system has given access to a patient-level primary care dataset in real time. Initial results highlight some of the benefits of a point-of-care system such as improved data quality, emphasize the importance of sharing data with clinical practitioners, and shed light on how this approach could strengthen HMIS.

}, keywords = {Database Management Systems, electronic health records, Equipment Design, Information Storage and Retrieval, Malawi, Point-of-Care Systems, Primary Health Care, Software}, issn = {0926-9630}, author = {Waters, Evan and Rafter, Jeff and Douglas, Gerald P and Bwanali, Mwatha and Jazayeri, Darius and Fraser, Hamish S F} } @article {1015, title = {Experience implementing OpenMRS to support maternal and reproductive health in Northern Nigeria.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {332-6}, abstract = {

In Northern Nigeria a deteriorating health system has resulted in one of the World{\textquoteright}s highest rates of maternal and infant deaths. The dire situation in Northern Nigeria is only amplified by the lack of an effective health information system, leaving hospitals and clinics to make decisions about patient care with only uninformed guesses about medical history and access to unreliable and unintelligible patient registers and summary reports. In 2009 we implemented an electronic medical records system using OpenMRS for the Family Health Unit of the Shehu Idris College. The three-month process resulted in electronic forms for all clinical areas, greatly reduced data duplication and a monthly reporting process that takes minutes instead of days. This system provides not only access to the first patient-based health indicators in Nigeria (as opposed to previously error-prone aggregate data) but is also an example of the potential to overcome the harsh computing environment in Nigeria to implement eHealth systems that will improve the quality of patient care.

}, keywords = {Delivery of Health Care, electronic health records, Maternal Health Services, Maternal Welfare, Models, Organizational, Needs Assessment, Nigeria, Reproductive Medicine, Utilization Review}, issn = {0926-9630}, author = {Thompson, Adam and Castle, Evelyn and Lubeck, Paul and Makarfi, Provost Shehu} } @article {586, title = {The extensible open-source rigid and affine image registration module of the Medical Imaging Interaction Toolkit (MITK).}, journal = {Computer methods and programs in biomedicine}, volume = {100}, year = {2010}, month = {2010 Oct}, pages = {79-86}, abstract = {Although non-rigid registration methods are available or under development for many specific problems in medicine, rigid and affine registration is an important task that is often performed for pre-aligning images before using non-rigid registration. In this paper, we present a free and open-source application for rigid and affine image registration, which is designed both for developers and for end-users. The application is based on the Medical Imaging Interaction Toolkit (MITK) and allows for inter-modality and intra-modality rigid 2D-2D and 3D-3D registration of medical images such as CT, MRI, or ultrasound. The framework as well as the application can be easily extended by adding new transforms, metrics and optimizers. Thus, developers of new algorithms are enabled to test and use their algorithms more quickly, spending less work on user interfaces. Additionally, the framework provides the possibility to use image masks to restrict the evaluation of metric values by the optimizer on certain areas of the images.}, keywords = {Computers, Diagnostic Imaging, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Software, User-Computer Interface}, issn = {1872-7565}, author = {Stein, D and Fritzsche, K H and Nolden, M and Meinzer, H P and Wolf, I} } @article {20409608, title = {The extensible open-source rigid and affine image registration module of the Medical Imaging Interaction Toolkit (MITK).}, journal = {Computer methods and programs in biomedicine}, year = {2010}, month = {2010 Apr 19}, abstract = {Although non-rigid registration methods are available or under development for many specific problems in medicine, rigid and affine registration is an important task that is often performed for pre-aligning images before using non-rigid registration. In this paper, we present a free and open-source application for rigid and affine image registration, which is designed both for developers and for end-users. The application is based on the Medical Imaging Interaction Toolkit (MITK) and allows for inter-modality and intra-modality rigid 2D-2D and 3D-3D registration of medical images such as CT, MRI, or ultrasound. The framework as well as the application can be easily extended by adding new transforms, metrics and optimizers. Thus, developers of new algorithms are enabled to test and use their algorithms more quickly, spending less work on user interfaces. Additionally, the framework provides the possibility to use image masks to restrict the evaluation of metric values by the optimizer on certain areas of the images.}, author = {Stein, D and Fritzsche, K H and Nolden, M and Meinzer, H P and Wolf, I} } @article {1046, title = {Facilitating secondary use of medical data by using openEHR archetypes.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {1117-21}, abstract = {

Clinical trials are of high importance for medical progress. But even though more and more clinical data is available in electronic patient records (EPRs) and more and more electronic data capture (EDC) systems are used in trials, there is still a gap which makes EPR / EDC interoperability difficult and hampers secondary use of medical routine data. The openEHR architecture for Electronic Health Records is based on a two level modeling approach which makes use of {\textquoteright}archetypes{\textquoteright}. We want to analyze whether archetypes can help to bridge this gap by building an integrated EPR / EDC system based on openEHR archetypes. We used the {\textquoteright}openEHR Reference Framework and Application{\textquoteright} (Opereffa) and existing archetypes for medical data. Furthermore, we developed dedicated archetypes to document study meta data. We developed a first prototype implementation of an archetype based integrated EPR / EDC system. Next steps will be the evaluation of an extended prototype in a real clinical trial scenario. Opereffa was a good starting point for our work. OpenEHR archetypes proved useful for secondary use of health data.

}, keywords = {Clinical Trials as Topic, Feasibility Studies, Humans, Medical Record Linkage, Medical Records Systems, Computerized, Semantics, Systems Integration}, issn = {0926-9630}, author = {Kohl, Christian D and Garde, Sebastian and Knaup, Petra} } @article {901, title = {Free as in freedom: open source software{\textquoteright}s role in remaking healthcare in the twenty-first century.}, journal = {Annals of health law / Loyola University Chicago, School of Law, Institute for Health Law}, volume = {19}, year = {2010}, pages = {259{\textendash}263}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79959513549\&partnerID=40\&md5=d95a66f5d3c54586adda1675dda72e1a}, author = {Loiterman, J} } @article {20974022, title = {Functionalities of free and open electronic health record systems.}, journal = {International journal of technology assessment in health care}, volume = {26}, year = {2010}, month = {2010 Oct}, pages = {382-9}, abstract = {Objectives: The aim of this study was to examine open-source electronic health record (EHR) software to determine their level of functionalities according to the International Organization for Standardization (ISO) standards.Methods: ISO standards were used as a guideline to determine and describe the reference architecture and functionalities of a standard electronic health record system as well the environmental context for which the software has been built. Twelve open-source EHR systems were selected and evaluated according to two-dimensional criteria based on ISO/TS 18308:2004 functional requirements and ISO/TR 20514:2005 context of the EHR system.Results: Open EHR software programs mostly fulfill structural, procedural, evolutional, and medicolegal requirements at the minimal and full functionality levels. Communication, privacy, and security requirements are accomplished in less than 23 percent of the cases, mainly at minimal functional level. Ethical, cultural, and consumer requirements still need to be fulfilled by free and open-source EHR applications.Conclusions: Most analyzed systems had several functional limitations. Nevertheless, especially for clinicians and decision makers in developing countries, open-source EHR systems are an option. The limited functionalities are likely to become requirements for further releases of open-source EHR systems.}, author = {Flores Zuniga, Alejandro Enrique and Win, Khin Than and Susilo, Willy} } @article {20663165, title = {Heterogeneity prevails: the state of clinical trial data management in Europe - results of a survey of ECRIN centres.}, journal = {Trials}, volume = {11}, year = {2010}, month = {2010 Jul 21}, pages = {79}, abstract = {ABSTRACT: BACKGROUND: The use of Clinical Data Management Systems (CDMS) has become essential in clinical trials to handle the increasing amount of data that must be collected and analyzed. With a CDMS trial data are captured at investigator sites with "electronic Case Report Forms". Although more and more of these electronic data management systems are used in academic research centres an overview of CDMS products and of available data management and quality management resources for academic clinical trials in Europe is missing. METHODS: The ECRIN (European Clinical Research Infrastructure Network) data management working group conducted a two-part standardized survey on data management, software tools, and quality management for clinical trials. The questionnaires were answered by nearly 80 centres / units (with an overall response rate of 47\% and 43\%) from 12 European countries and EORTC. RESULTS: Our survey shows that about 90\% of centres have a CDMS in routine use. Of these CDMS nearly 50\% are commercial systems; Open Source solutions don{\textquoteright}t play a major role. In general, solutions used for clinical data management are very heterogeneous: 20 different commercial CDMS products (7 Open Source solutions) in addition to 17/18 proprietary systems are in use. The most widely employed CDMS products are MACRO TM and Capture System TM, followed by solutions that are used in at least 3 centres: eResearch Network TM, CleanWeb TM, GCP Base TM and SAS TM. Although quality management systems for data management are in place in most centres / units, there exist some deficits in the area of system validation. CONCLUSIONS: Because the considerable heterogeneity of data management software solutions may be a hindrance to cooperation based on trial data exchange, standards like CDISC (Clinical Data Interchange Standard Consortium) should be implemented more widely. In a heterogeneous environment the use of data standards can simplify data exchange, increase the quality of data and prepare centres for new developments (e.g. the use of EHR for clinical research). Because data management and the use of electronic data capture systems in clinical trials are characterized by the impact of regulations and guidelines, ethical concerns are discussed. In this context quality management becomes an important part of compliant data management. To address these issues ECRIN will establish certified data centres to support electronic data management and associated compliance needs of clinical trial centres in Europe.}, url = {http://www.trialsjournal.com/content/11/1/79}, author = {Kuchinke, Wolfgang and Ohmann, Christian and Yang, Qin and Salas, Nader and Lauritsen, Jens and Gueyffier, Francois and Leizorovicz, Alan and Schade-Brittinger, Carmen and Wittenberg, Michael and Voko, Zoltan and Gaynor, Siobhan and Cooney, Margaret and Doran, Peter and Maggioni, Aldo and Lorimer, Andrea and Torres, Ferran and McPherson, Gladys and Charvill, Jim and Hellstrom, Mats and Lejeune, Stephane} } @article {1054, title = {How informatics can potentiate precompetitive open-source collaboration to jump-start drug discovery and development.}, journal = {Clin Pharmacol Ther}, volume = {87}, year = {2010}, month = {2010 May}, pages = {614-6}, keywords = {Animals, Cooperative Behavior, Drug Discovery, Drug Industry, Economic Competition, Humans, Informatics, Information Dissemination}, issn = {1532-6535}, doi = {10.1038/clpt.2010.21}, author = {Perakslis, E D and Van Dam, J and Szalma, S} } @article {20663194, title = {ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67.}, journal = {Breast cancer research : BCR}, volume = {12}, year = {2010}, month = {2010 Jul 27}, pages = {R56}, abstract = {ABSTRACT: INTRODUCTION: Accurate assessment of estrogen receptor (ER), progesterone receptor (PR), and Ki-67 is essential in the histopathologic diagnostics of breast cancer. Commercially available image analysis systems are usually bundled with dedicated analysis hardware and, to our knowledge, no easily installable, free software for immunostained slide scoring has been described. In this study, we describe a free, Internet-based web application for quantitative image analysis of ER, PR, and Ki-67 immunohistochemistry in breast cancer tissue sections. METHODS: The application, named ImmunoRatio, calculates the percentage of positively stained nuclear area (labeling index) by using a color deconvolution algorithm for separating the staining components (diaminobenzidine and hematoxylin) and adaptive thresholding for nuclear area segmentation. ImmunoRatio was calibrated using cell counts defined visually as the gold standard (training set, n=50). Validation was done using a separate set of 50 ER, PR, and Ki-67 stained slides (test set, n=50). In addition, Ki-67 labeling indexes determined by ImmunoRatio were studied for their prognostic value in a retrospective cohort of 123 breast cancer patients. RESULTS: The labeling indexes by calibrated ImmunoRatio analyses correlated well with those defined visually in the test set (correlation coefficient r=0.98). Using the median Ki-67 labeling index (20\%) as a cutoff, a hazard ratio of 2.2 was obtained in the survival analysis (n=123, P=0.01). ImmunoRatio was shown to adapt to various staining protocols, microscope setups, digital camera models, and image acquisition settings. The application can be used directly with web browsers running on modern operating systems (e.g., Microsoft Windows, Linux distributions, and Mac OS). No software downloads or installations are required. ImmunoRatio is open source software, and the web application is publicly accessible on our website. CONCLUSIONS: We anticipate that free web applications, such as ImmunoRatio, will make the quantitative image analysis of ER, PR, and Ki-67 easy and straightforward in the diagnostic assessment of breast cancer specimens.}, author = {Tuominen, Vilppu J and Ruotoistenmaki, Sanna and Viitanen, Arttu and Jumppanen, Mervi and Isola, Jorma} } @article {541, title = {Implementing medical information systems in developing countries, what works and what doesn{\textquoteright}t.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, volume = {2010}, year = {2010}, month = {2010}, pages = {232-6}, abstract = {Global Health Informatics is an emerging field, as demonstrated by several substantial and widely used electronic medical record (EMR) systems along with the emergence of mobile based or"mhealth" systems. We describe here many of the practical lessons we have learned from implementing systems in a wide range of challenging environments over the last decade. Some requirements, like data backups, skilled staff and local leadership are universally important. Others, such as limited power, poor network access and distributed populations, require different designs and strategies in resource poor environments.}, issn = {1942-597X}, author = {Fraser, Hamish S F and Blaya, Joaquin} } @article {1014, title = {Implementing OpenMRS for patient monitoring in an HIV/AIDS care and treatment program in rural Mozambique.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {411-5}, abstract = {

We have adopted the Open Medical Record System (OpenMRS) framework to implement an electronic patient monitoring system for an HIV care and treatment program in Mozambique. The program provides technical assistance to the Ministry of Health supporting the scale up of integrated HIV care and support services in health facilities in rural resource limited settings. The implementation is in use for adult and pediatric programs, with ongoing roll-out to cover all supported sites. We describe early experiences in adapting the system to the program needs, addressing infrastructure challenges, creating a regional support team, training data entry staff, migrating a legacy database, deployment, and current use. We find that OpenMRS offers excellent prospects for in-country development of health information systems, even in severely resource limited settings. However, it also requires considerable organizational infrastructure investment and technical capacity building to ensure continued local support.

}, keywords = {Database Management Systems, Delivery of Health Care, electronic health records, HIV Infections, Information Storage and Retrieval, Medical Record Linkage, Mozambique, Population Surveillance, Rural Health Services}, issn = {0926-9630}, author = {Manders, Eric-Jan and Jos{\'e}, Eurico and Solis, Manuel and Burlison, Janeen and Nhampossa, Jos{\'e} Leopoldo and Moon, Troy} } @proceedings {512, title = {Indivo X: Developing a Fully Substitutable Personally Controlled Health Record Platform}, year = {2010}, month = {11/2010}, abstract = {To support a rich ecosystem of third-party applications around a personally controlled health record (PCHR), we have redesigned Indivo, the original PCHR, as a web- based platform with feature-level substitutability. Core to this new release is the Indivo X Application Program- ming Interface (API), the contract between the PCHR platform and the end-user apps. Using rapid iterative de- velopment to build a minimal feature set from real-world requirements, the resulting Indivo X API, now in public stable beta, is enabling developers, including third-party contributors, to quickly create and integrate novel fea- tures into patients{\textquoteright} online records, ultimately building a fully customizable experience for diverse patient needs.}, url = {http://proceedings.amia.org/127eoo}, author = {Adida, Ben and Sanyal, Arjun and Zabak, Steve and Kohane, Isaac S. and Mandl, Kenneth D} } @article {10.1371/journal.pone.0014094, title = {JULIDE: A Software Tool for 3D Reconstruction and Statistical Analysis of Autoradiographic Mouse Brain Sections}, journal = {PLoS ONE}, volume = {5}, number = {11}, year = {2010}, month = {11}, pages = {e14094}, publisher = {Public Library of Science}, abstract = {

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

}, doi = {10.1371/journal.pone.0014094}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0014094}, author = {Ribes, Delphine and Parafita, Julia and Charrier, R{\'e}mi and Magara, Fulvio and Magistretti, Pierre J. and Thiran, Jean-Philippe} } @article {1042, title = {JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.}, journal = {PLoS One}, volume = {5}, year = {2010}, month = {2010}, pages = {e14094}, abstract = {

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

}, keywords = {Animals, Autoradiography, Brain, Carbon Radioisotopes, Deoxyglucose, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Male, Maze Learning, Mice, Mice, Inbred C57BL, Reproducibility of Results, Software}, issn = {1932-6203}, doi = {10.1371/journal.pone.0014094}, author = {Ribes, Delphine and Parafita, Julia and Charrier, R{\'e}mi and Magara, Fulvio and Magistretti, Pierre J and Thiran, Jean-Philippe} } @article {20646816, title = {Mandibular reconstruction with fibula free flap. Experience of virtual reconstruction using Osirix((R)), a free and open source software for medical imagery.}, journal = {Annales de chirurgie plastique et esthetique}, year = {2010}, month = {2010 Jun 18}, abstract = {The techniques of free tissue transfers are mainly used for mandibular reconstruction by specialized surgical teams. This type of reconstruction is mostly realized in matters of head and neck cancers affecting mandibular bone and requiring a wide surgical resection and interruption of the mandible. To decrease the duration of the operation, surgical procedure involves generally two teams, one devoted to cancer resection and the other one to raise the fibular flap and making the reconstruction. For a better preparation of this surgical procedure, we propose here the use of a medical imaging software enabling mandibular reconstructions in three dimensions using the CT-scan done during the initial disease-staging checkup. The software used is Osirix((R)), developed since 2004 by a team of radiologists from Geneva and UCLA, working on Apple((R)) computers and downloadable free of charge in its basic version. We report here our experience of this software in 17 patients, with a preoperative modelling in three dimensions of the mandible, of the segment of mandible to be removed. It also forecasts the numbers of fragments of fibula needed and the location of osteotomies.}, author = {Albert, S and Cristofari, J-P and Cox, A and Bensimon, J-L and Guedon, C and Barry, B} } @article {847, title = {Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.}, journal = {J Am Med Inform Assoc}, volume = {17}, year = {2010}, month = {2010 Sep-Oct}, pages = {507-13}, abstract = {

We aim to build and evaluate an open-source natural language processing system for information extraction from electronic medical record clinical free-text. We describe and evaluate our system, the clinical Text Analysis and Knowledge Extraction System (cTAKES), released open-source at http://www.ohnlp.org. The cTAKES builds on existing open-source technologies-the Unstructured Information Management Architecture framework and OpenNLP natural language processing toolkit. Its components, specifically trained for the clinical domain, create rich linguistic and semantic annotations. Performance of individual components: sentence boundary detector accuracy=0.949; tokenizer accuracy=0.949; part-of-speech tagger accuracy=0.936; shallow parser F-score=0.924; named entity recognizer and system-level evaluation F-score=0.715 for exact and 0.824 for overlapping spans, and accuracy for concept mapping, negation, and status attributes for exact and overlapping spans of 0.957, 0.943, 0.859, and 0.580, 0.939, and 0.839, respectively. Overall performance is discussed against five applications. The cTAKES annotations are the foundation for methods and modules for higher-level semantic processing of clinical free-text.

}, keywords = {Biomedical Research, electronic health records, Information Storage and Retrieval, Natural Language Processing}, issn = {1527-974X}, doi = {10.1136/jamia.2009.001560}, author = {Savova, Guergana K and Masanz, James J and Ogren, Philip V and Zheng, Jiaping and Sohn, Sunghwan and Kipper-Schuler, Karin C and Chute, Christopher G} } @article {19910667, title = {The medical exploration toolkit: an efficient support for visual computing in surgical planning and training.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {16}, year = {2010}, month = {2010 Jan-Feb}, pages = {133-46}, abstract = {Application development is often guided by the usage of software libraries and toolkits. For medical applications, the toolkits currently available focus on image analysis and volume rendering. Advance interactive visualizations and user interface issues are not adequately supported. Hence, we present a toolkit for application development in the field of medical intervention planning, training, and presentation--the MEDICALEXPLORATIONTOOLKIT (METK). The METK is based on the rapid prototyping platform MeVisLab and offers a large variety of facilities for an easy and efficient application development process. We present dedicated techniques for advanced medical visualizations, exploration, standardized documentation, adn interface widgets for common tasks. These include, e.g., advanced animation facilities, viewpoint selection, several illustrative rendering techniques, and new techniques for object selection in 3D surface models. No extended programming skills are needed for application building, since a graphical programming approach can be used. the toolkit is freely available and well documented to facilitate the use and extension of the toolkit.}, author = {M{\"u}hler, Konrad and Tietjen, Christian and Ritter, Felix and Preim, Bernhard} } @article {20348080, title = {Need for open-source electronic health records.}, journal = {Health affairs (Project Hope)}, volume = {29}, year = {2010}, month = {2010 Feb}, pages = {332-4; author reply 332}, author = {Wilder, Bruce} } @article {20398366, title = {Open source challenges for hospital information system (HIS) in developing countries: a pilot project in Mali.}, journal = {BMC medical informatics and decision making}, volume = {10}, year = {2010}, month = {2010}, pages = {22}, abstract = {BACKGROUND: We are currently witnessing a significant increase in use of Open Source tools in the field of health. Our study aims to research the potential of these software packages for developing countries. Our experiment was conducted at the Centre Hospitalier Mere Enfant in Mali. METHODS: After reviewing several Open Source tools in the field of hospital information systems, Mediboard software was chosen for our study. To ensure the completeness of Mediboard in relation to the functionality required for a hospital information system, its features were compared to those of a well-defined comprehensive record management tool set up at the University Hospital "La Timone" of Marseilles in France. It was then installed on two Linux servers: a first server for testing and validation of different modules, and a second one for the deployed full implementation. After several months of use, we have evaluated the usability aspects of the system including feedback from end-users through a questionnaire. RESULTS: Initial results showed the potential of Open Source in the field of health IT for developing countries like Mali.Five main modules have been fully implemented: patient administrative and medical records management of hospital activities, tracking of practitioners{\textquoteright} activities, infrastructure management and the billing system. This last component of the system has been fully developed by the local Mali team.The evaluation showed that the system is broadly accepted by all the users who participated in the study. 77\% of the participants found the system useful; 85\% found it easy; 100\% of them believe the system increases the reliability of data. The same proportion encourages the continuation of the experiment and its expansion throughout the hospital. CONCLUSIONS: In light of the results, we can conclude that the objective of our study was reached. However, it is important to take into account the recommendations and the challenges discussed here to avoid several potential pitfalls specific to the context of Africa.Our future work will target the full integration of the billing module in Mediboard and an expanded implementation throughout the hospital.}, doi = {10.1186/1472-6947-10-22}, url = {http://www.biomedcentral.com/1472-6947/10/22}, author = {Bagayoko, Cheick-Oumar and Dufour, Jean-Charles and Chaacho, Saad and Bouhaddou, Omar and Fieschi, Marius} } @article {487, title = {An open source software project for obstetrical procedure scheduling and occupancy analysis.}, journal = {Health care management science}, year = {2010}, month = {2010 Oct 27}, abstract = {Increases in the rate of births via cesarean section and induced labor have led to challenging scheduling and capacity planning problems for hospital inpatient obstetrical units. We present occupancy and patient scheduling models to help address these challenges. These patient flow models can be used to explore the relationship between procedure scheduling practices and the resulting occupancy on inpatient obstetrical units such as labor and delivery and postpartum. The models capture numerous important characteristics of inpatient obstetrical patient flow such as time of day and day of week dependent arrivals and length of stay, multiple patient types and clinical interventions, and multiple patient care units with inter-unit patient transfers. We have used these models in several projects at different hospitals involving design of procedure scheduling templates and analysis of inpatient obstetrical capacity. In the development of these models, we made heavy use of open source software tools and have released the entire project as a free and open source model and software toolkit.}, issn = {1386-9620}, author = {Isken, Mark W and Ward, Timothy J and Littig, Steven J} } @article {596, title = {OpenMEEG: opensource software for quasistatic bioelectromagnetics.}, journal = {Biomedical engineering online}, volume = {9}, year = {2010}, month = {2010}, pages = {45}, abstract = {Interpreting and controlling bioelectromagnetic phenomena require realistic physiological models and accurate numerical solvers. A semi-realistic model often used in practise is the piecewise constant conductivity model, for which only the interfaces have to be meshed. This simplified model makes it possible to use Boundary Element Methods. Unfortunately, most Boundary Element solutions are confronted with accuracy issues when the conductivity ratio between neighboring tissues is high, as for instance the scalp/skull conductivity ratio in electro-encephalography. To overcome this difficulty, we proposed a new method called the symmetric BEM, which is implemented in the OpenMEEG software. The aim of this paper is to present OpenMEEG, both from the theoretical and the practical point of view, and to compare its performances with other competing software packages.}, keywords = {Benchmarking, Computers, Electric Impedance, Electricity, Electroencephalography, Electromagnetic Phenomena, Licensure, Magnetics, Magnetoencephalography, Models, Theoretical, Quality Control, Software, Time Factors, Tomography}, issn = {1475-925X}, author = {Gramfort, Alexandre and Papadopoulo, Th{\'e}odore and Olivi, Emmanuel and Clerc, Maureen} } @article {20013373, title = {OpenMS and TOPP: open source software for LC-MS data analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {604}, year = {2010}, month = {2010}, pages = {201-11}, abstract = {The automatic analysis of mass spectrometry data is becoming more and more important since increasingly larger datasets are readily available that cannot be evaluated manually. This has triggered the development of several open-source software libraries for the automatic analysis of such data. Among those is OpenMS together with TOPP (The OpenMS Proteomics Pipeline). OpenMS is a C++ library for rapid prototyping of complex algorithms for the analysis of mass spectrometry data. Based on the OpenMS library, TOPP provides a collection of tools for the most important tasks in proteomics analysis. The tight coupling of OpenMS and TOPP makes it easy to extend TOPP by adding new tools to the OpenMS library. We describe the overall concepts behind the software and illustrate its use with several examples.}, author = {Reinert, Knut and Kohlbacher, Oliver} } @article {1043, title = {An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging.}, journal = {BMC Med Imaging}, volume = {10}, year = {2010}, month = {2010}, pages = {16}, abstract = {

BACKGROUND: In magnetic resonance (MR) imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization.

RESULTS: After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/TOMROP T1; modified Look-Locker (MOLLI) T1; single-echo T2/T2*; and multi-echo T2/T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data.

CONCLUSIONS: MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet.

}, keywords = {Algorithms, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Programming Languages, Reproducibility of Results, Sensitivity and Specificity, Software}, issn = {1471-2342}, doi = {10.1186/1471-2342-10-16}, author = {Messroghli, Daniel R and Rudolph, Andre and Abdel-Aty, Hassan and Wassmuth, Ralf and Kuhne, Titus and Dietz, Rainer and Schulz-Menger, Jeanette} } @article {1471-2342-10-16, title = {An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging}, journal = {BMC Medical Imaging}, volume = {10}, number = {1}, year = {2010}, pages = {16}, abstract = {BACKGROUND:In magnetic resonance (MR) imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization. RESULTS:After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/ TOMROP T1; modified Look-Locker inversion recovery (MOLLI) T1; single-echo T2/ T2*; and multi-echo T2/ T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data. CONCLUSIONS:MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet. }, issn = {1471-2342}, doi = {10.1186/1471-2342-10-16}, url = {http://www.biomedcentral.com/1471-2342/10/16}, author = {Messroghli, Daniel and Rudolph, Andre and Abdel-Aty, Hassan and Wassmuth, Ralf and Kuhne, Titus and Dietz, Rainer and Schulz-Menger, Jeanette} } @booklet {UCAM-CL-TR-768, title = {Report on existing open-source electronic medical records}, number = {UCAM-CL-TR-768}, year = {2010}, publisher = {University of Cambridge, Computer Laboratory}, abstract = {In this report we provide an overview of existing open-source electronic medical records and assess them against the criteria established by the EViDence group.}, issn = {1476-2986}, url = {http://www.cl.cam.ac.uk/techreports/UCAM-CL-TR-768.pdf}, author = {Morrison, Cecily and Iosif, Adona and Danka, Miklos} } @proceedings {508, title = {The Role of Workarounds during an Open Source Electronic Medical Record System Implementation}, year = {2010}, abstract = {A significant degree of customization of medical information technology is required to effectively integrate the promise of IT with the diversity and complexity of medical work. In the absence of such customizations, dissatisfaction and resistance toward the system arise. Indeed, the complexity of the medical work and the inability of software to tailor to the diverse medical practices may explain the limited diffusion of health information systems especially in North America. We study the role of workarounds during an open-source Electronic Medical Record System (EMR) implementation at a medium-size urgent care clinic in a major Canadian city. We found that the technology appropriation process involved the evolving of number of non-trivial workarounds in order to match the EMR to medical work. The emergence of workarounds is conceptualized as a knowledge creation and integration process. This perspective allows us to look at the antecedents and the change dynamics of workarounds in the clinic. Furthermore diverging from the negative view toward workarounds, we discuss the importance of incorporating workarounds during and following system development. The workaround perspective shed the light on how users{\textquoteright} behavior can be channeled into a constructive development effort. This paper contributes by examining the workaround of medical practitioners using an open-source electronic medical record system as well as offering a knowledge perspective for the study of EMR appropriation.}, url = {http://aisel.aisnet.org/icis2010_submissions/47}, author = {Safadi, Hani and Faraj, Samer} } @conference {1099, title = {The Role of workarounds during an OpenSource Electronic Medical Record System Implementation.}, booktitle = {ICIS}, year = {2010}, author = {Safadi, Hani and Faraj, Samer} } @inbook {springerlink:10.1007/978-3-642-12197-5_85, title = {rtMEG: A Real-Time Software Toolbox for Brain-Machine Interfaces Using Magnetoencephelography}, booktitle = {17th International Conference on Biomagnetism Advances in Biomagnetism {\textendash} Biomag2010}, series = {IFMBE Proceedings}, volume = {28}, year = {2010}, note = {10.1007/978-3-642-12197-5_85}, pages = {362-365}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, isbn = {978-3-642-12197-5}, url = {http://dx.doi.org/10.1007/978-3-642-12197-5_85}, author = {Sudre, Gustavo and Wang, Wei and Song, Tao and Kajola, Matti and Vinjamuri, Ramana and Collinger, Jennifer and Degenhart, Alan and Bagic, Anto and Weber, Doug J.}, editor = {Magjarevic, R. and Nagel, J. H. and Supek, Selma and Su{\v s}ac, Ana} } @article {20482787, title = {Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.}, journal = {BMC bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {260}, abstract = {BACKGROUND: Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. RESULTS: We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. CONCLUSIONS: The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.}, author = {Tolopko, Andrew N and Sullivan, John P and Erickson, Sean D and Wrobel, David and Chiang, Su L and Rudnicki, Katrina and Rudnicki, Stewart and Nale, Jennifer and Selfors, Laura M and Greenhouse, Dara and Muhlich, Jeremy L and Shamu, Caroline E} } @conference {panchal:3245, title = {SU-GG-T-260: Dicompyler: An Open Source Radiation Therapy Research Platform with a Plugin Architecture}, volume = {37}, number = {6}, year = {2010}, pages = {3245-3245}, publisher = {AAPM}, organization = {AAPM}, doi = {10.1118/1.3468652}, url = {http://link.aip.org/link/?MPH/37/3245/2}, author = {A Panchal and R Keyes} } @article {612, title = {Target Contour Testing/Instructional Computer Software (TaCTICS): A Novel Training and Evaluation Platform for Radiotherapy Target Delineation.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, volume = {2010}, year = {2010}, month = {2010}, pages = {361-5}, abstract = {Target volume delineation is a critical step in the creation of treatment plans in radiation therapy. However, intra-observer and inter-observer variability in target volume definitions can introduce substantial differences in resulting doses between treatments plans from different users and institutions Consequently, there is a need for tools that allow quantitative metrics to be collected and reported regarding inter-and intra-user performance in target volume delineation. We describe TaCTICS, a web-based educational training software application targeted towards residents and non-expert users. TaCTICS allows users to delineate target structures in DICOM-RT compatible formats using their preferred treatment planning system. After uploading the resulting structure file, users are provided a scoring of their structures based on comparison to reference sets derived from expert users using a variety of metrics for volume overlap and surface distances.}, issn = {1942-597X}, author = {Kalpathy-Cramer, Jayashree and Fuller, Clifton David} } @article {1056, title = {TriSano: Collaborating for the Good of Global Public Health}, journal = {Open Source Business Resource}, year = {2010}, month = {12/2010}, type = {Articles}, abstract = {Healthcare and public health continue to experience significant changes, driven primarily due to new legislation and economic challenges. These changes mean that those in healthcare and public health are under pressure to respond differently in order to meet the health needs of the population. Additionally, public health is collaborative, by nature. Epidemiologists, informaticians, public health officials, nurses, and doctors fluidly come together to prevent disease and protect the health of the global citizens. This article explores how collaboration and open source software helps healthcare and public health address their challenges across the globe. It is based on the experiences of the TriSano project from the past three years. It traces the history of the project and the refinement of its business model and product offerings to illustrate how collaboration based on a shared business vision with industry thought leaders leads to sustainable software and communities. Finally, insights are shared from working at the intersection of a humanitarian open source project and the business world.}, issn = {1913-6102}, url = {http://timreview.ca/article/405}, author = {Mike Herrick} } @article {20001786, title = {Using ImageJ for the quantitative analysis of flow-based adhesion assays in real-time under physiologic flow conditions.}, journal = {Platelets}, volume = {21}, year = {2010}, month = {2010 Feb}, pages = {60-6}, abstract = {This article intends to close the gap between the abundance of regular articles focusing on adhesive mechanisms of cells in a flow field and purely technical reports confined to the description of newly developed algorithms, not yet ready to be used by users without programming skills. A simple and robust method is presented for analysing raw videomicroscopic data of flow-based adhesion assays using the freely available public domain software ImageJ. We describe in detail the image processing routines used to rapidly and reliably evaluate the number of adherent and translocating platelets in videomicroscopic recordings. The depicted procedures were exemplified by analysing platelet interaction with immobilized von Willebrand factor and fibrinogen in flowing blood under physiological wall shear rates. Neutralizing GPIbalpha function reduced shear-dependent platelet translocation on von Willebrand factor and abolished firm platelet adhesion. Abciximab, Tirofiban and Eptifibatide completely inhibited GPIIb/IIIa-dependent stable platelet deposition on fibrinogen. The presented method to analyse videomicroscopic recordings from flow-based adhesion assays offers the advantage of providing a simple and reliable way to quantify flow-based adhesion assays, which is completely based on ImageJ and can easily be applied to study adhesion mechanisms of cells in non-fluorescent modes without the need to deviate from the presented protocol.}, author = {Meyer dos Santos, Sascha and Klinkhardt, Ute and Schneppenheim, Reinhard and Harder, Sebastian} } @article {19403467, title = {Acceptability of a personally controlled health record in a community-based setting: implications for policy and design.}, journal = {Journal of medical Internet research}, volume = {11}, year = {2009}, month = {2009}, pages = {e14}, abstract = {BACKGROUND: Consumer-centered health information systems that address problems related to fragmented health records and disengaged and disempowered patients are needed, as are information systems that support public health monitoring and research. Personally controlled health records (PCHRs) represent one response to these needs. PCHRs are a special class of personal health records (PHRs) distinguished by the extent to which users control record access and contents. Recently launched PCHR platforms include Google Health, Microsoft{\textquoteright}s HealthVault, and the Dossia platform, based on Indivo. OBJECTIVE: To understand the acceptability, early impacts, policy, and design requirements of PCHRs in a community-based setting. METHODS: Observational and narrative data relating to acceptability, adoption, and use of a personally controlled health record were collected and analyzed within a formative evaluation of a PCHR demonstration. Subjects were affiliates of a managed care organization run by an urban university in the northeastern United States. Data were collected using focus groups, semi-structured individual interviews, and content review of email communications. Subjects included: n = 20 administrators, clinicians, and institutional stakeholders who participated in pre-deployment group or individual interviews; n = 52 community members who participated in usability testing and/or pre-deployment piloting; and n = 250 subjects who participated in the full demonstration of which n = 81 initiated email communications to troubleshoot problems or provide feedback. All data were formatted as narrative text and coded thematically by two independent analysts using a shared rubric of a priori defined major codes. Sub-themes were identified by analysts using an iterative inductive process. Themes were reviewed within and across research activities (ie, focus group, usability testing, email content review) and triangulated to identify patterns. RESULTS: Low levels of familiarity with PCHRs were found as were high expectations for capabilities of nascent systems. Perceived value for PCHRs was highest around abilities to co-locate, view, update, and share health information with providers. Expectations were lowest for opportunities to participate in research. Early adopters perceived that PCHR benefits outweighed perceived risks, including those related to inadvertent or intentional information disclosure. Barriers and facilitators at institutional, interpersonal, and individual levels were identified. Endorsement of a dynamic platform model PCHR was evidenced by preferences for embedded searching, linking, and messaging capabilities in PCHRs; by high expectations for within-system tailored communications; and by expectation of linkages between self-report and clinical data. CONCLUSIONS: Low levels of awareness/preparedness and high expectations for PCHRs exist as a potentially problematic pairing. Educational and technical assistance for lay users and providers are critical to meet challenges related to: access to PCHRs, especially among older cohorts; workflow demands and resistance to change among providers; inadequate health and technology literacy; clarification of boundaries and responsibility for ensuring accuracy and integrity of health information across distributed data systems; and understanding confidentiality and privacy risks. Continued demonstration and evaluation of PCHRs is essential to advancing their use.}, author = {Weitzman, Elissa R and Kaci, Liljana and Mandl, Kenneth D} } @article {523, title = {Barriers to open source software adoption in Quebec{\textquoteright}s health care organizations.}, journal = {Journal of medical systems}, volume = {33}, year = {2009}, month = {2009 Feb}, pages = {1-7}, abstract = {We conducted in-depth interviews with 15 CIOs to identify the principal impediments to adoption of open source software in the Quebec health sector. We found that key factors for not adopting an open source solution were closely linked to the orientations of ministry level policy makers and a seeming lack of information on the part of operational level IT managers concerning commercially oriented open source providers. We use the case of recent changes in the structure of Quebec{\textquoteright}s health care organizations and a change in the commercial policies of a key vendor to illustrate our conclusions regarding barriers to adoption of open source products.}, keywords = {Attitude of Health Personnel, Delivery of Health Care, Health Facility Administrators, Health Policy, Humans, Medical Informatics, Organizational Innovation, Quebec, Software, Systems Integration, Technology Transfer}, issn = {0148-5598}, author = {Par{\'e}, Guy and Wybo, Michael D and Delannoy, Charles} } @article {499, title = {Bayesian analysis of neuroimaging data in FSL.}, journal = {NeuroImage}, volume = {45}, year = {2009}, month = {2009 Mar}, pages = {S173-86}, abstract = {Typically in neuroimaging we are looking to extract some pertinent information from imperfect, noisy images of the brain. This might be the inference of percent changes in blood flow in perfusion FMRI data, segmentation of subcortical structures from structural MRI, or inference of the probability of an anatomical connection between an area of cortex and a subthalamic nucleus using diffusion MRI. In this article we will describe how Bayesian techniques have made a significant impact in tackling problems such as these, particularly in regards to the analysis tools in the FMRIB Software Library (FSL). We shall see how Bayes provides a framework within which we can attempt to infer on models of neuroimaging data, while allowing us to incorporate our prior belief about the brain and the neuroimaging equipment in the form of biophysically informed or regularising priors. It allows us to extract probabilistic information from the data, and to probabilistically combine information from multiple modalities. Bayes can also be used to not only compare and select between models of different complexity, but also to infer on data using committees of models. Finally, we mention some analysis scenarios where Bayesian methods are impractical, and briefly discuss some practical approaches that we have taken in these cases.}, keywords = {Bayes Theorem, Brain, Diffusion Magnetic Resonance Imaging, Humans, Image Interpretation, Computer-Assisted, Software}, issn = {1095-9572}, author = {Woolrich, Mark W and Jbabdi, Saad and Patenaude, Brian and Chappell, Michael and Makni, Salima and Behrens, Timothy and Beckmann, Christian and Jenkinson, Mark and Smith, Stephen M} } @conference {1084, title = {Building the Free/Libre Open Source Health Care (FLOSS-HC) Community: A Strategy for Pushing Free/Libre Open Source in European Health Care}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001828100030007}, author = {Thomas Karopka} } @article {873, title = {The caBIG terminology review process.}, journal = {J Biomed Inform}, volume = {42}, year = {2009}, month = {2009 Jun}, pages = {571-80}, abstract = {

The National Cancer Institute (NCI) is developing an integrated biomedical informatics infrastructure, the cancer Biomedical Informatics Grid (caBIG), to support collaboration within the cancer research community. A key part of the caBIG architecture is the establishment of terminology standards for representing data. In order to evaluate the suitability of existing controlled terminologies, the caBIG Vocabulary and Data Elements Workspace (VCDE WS) working group has developed a set of criteria that serve to assess a terminology{\textquoteright}s structure, content, documentation, and editorial process. This paper describes the evolution of these criteria and the results of their use in evaluating four standard terminologies: the Gene Ontology (GO), the NCI Thesaurus (NCIt), the Common Terminology for Adverse Events (known as CTCAE), and the laboratory portion of the Logical Objects, Identifiers, Names and Codes (LOINC). The resulting caBIG criteria are presented as a matrix that may be applicable to any terminology standardization effort.

}, keywords = {Medical Informatics, National Institutes of Health (U.S.), Terminology as Topic, United States}, issn = {1532-0480}, doi = {10.1016/j.jbi.2008.12.003}, author = {Cimino, James J and Hayamizu, Terry F and Bodenreider, Olivier and Davis, Brian and Stafford, Grace A and Ringwald, Martin} } @conference {1086, title = {Commercial Open Source RIS/PACS: The ClearCanvas Experience}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001827400220027}, author = {Norman Young and Clinton Chau and John Adziovsky} } @conference {1088, title = {Concept Matching between OpenEHR and SONHO}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001828400450053}, author = {Ricardo Cruz-Correia and Carla {\'A}vila and Rong Chen} } @article {19352444, title = {DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool.}, journal = {Frontiers in neuroinformatics}, volume = {3}, year = {2009}, month = {2009}, pages = {9}, abstract = {Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK{\textquoteright}s low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user{\textquoteright}s operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data.}, author = {Gouws, Andr{\'e} and Woods, Will and Millman, Rebecca and Morland, Antony and Green, Gary} } @article {19230726, title = {Demonstration of the Adamkiewicz artery by multidetector computed tomography angiography analysed with the open-source software OsiriX.}, journal = {European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery}, volume = {37}, year = {2009}, month = {2009 Apr}, pages = {395-400}, abstract = {OBJECTIVE: To evaluate the feasibility of the Adamkiewicz artery (AKA) detection by multidetector computed tomography (CT) data analysis without the need of a dedicated workstation, using low-cost hardware and the freeware OsiriX. METHODS: CT scans of 67 patients undergoing a thoracic or thoraco-abdominal aortic procedure between April 2006 and August 2008 were evaluated with respect to detection rate and AKA level and side using the OsiriX software version 3.2 on Mac OS X computer and compared to results obtained by standard workstation analysis, in a fully blinded analysis. The results were also compared with data compiled from a review of the English-language literature on this topic. RESULTS: (1) AKA identification showed a substantial agreement of 85.07\% between the methods (k=0.636). (2) The comparison of AKA level showed a substantial agreement (weighted k=0.661), with consensus in 70.14\%. (3) From the literature review, we found that recognition of the AKA was achieved in 466 of 555 cases (83.96\%). (4) In 384 (83.3\%) cases the AKA originated from a left intercostal artery. (5) The proposed method and literature-compiled data showed a similar AKA level distribution. CONCLUSIONS: Noninvasive AKA location with open-source software and low-cost hardware is feasible. The OsiriX software allows to effectively navigate through CT data not only to study the aorta, but also to detect the AKA, as in the case of the standard method and the literature data. Its availability and ease of use may contribute to make identification of the AKA part of the routine evaluation of CT scans in patients with aortic disease, even where dedicated workstations are not available, with potential benefits for planning therapeutic procedures.}, author = {Melissano, G and Bertoglio, L and Civelli, V and Amato, A C Moraes and Coppi, G and Civilini, E and Calori, G and De Cobelli, F and Del Maschio, A and Chiesa, R} } @article {19056288, title = {Dimensional error of selective laser sintering, three-dimensional printing and PolyJet models in the reproduction of mandibular anatomy.}, journal = {Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery}, volume = {37}, year = {2009}, month = {2009 Apr}, pages = {167-73}, abstract = {BACKGROUND: Selective laser sintering (SLS), three-dimensional printing (3DP) and PolyJet are rapid prototyping (RP) techniques to fabricate prototypes from virtual biomedical images. To be used in maxillofacial surgery, these models must accurately reproduce the craniofacial skeleton. PURPOSE: To analyze the capacity of SLS, 3DP and PolyJet models to reproduce mandibular anatomy and their dimensional error. MATERIAL: Dry mandible, helical CT images, SLS, 3DP and PolyJet prototypes, and digital electronic caliper. METHODS: Helical CT images were acquired from a dry mandible (criterion standard) and manipulated with the InVesalius software. Prototypes were produced using SLS, 3DP and PolyJet techniques. Thirteen linear measurements of each prototype were made and compared with the dry mandible measurements. RESULTS: The results showed a dimensional error of 1.79\%, 3.14\% and 2.14\% for SLS, 3DP and PolyJet models, respectively. The models satisfactorily reproduced anatomic details and the SLS and PolyJet prototypes showed greater dimensional precision and reproduced mandibular anatomy more accurately than the 3DP model. CONCLUSIONS: The SLS prototype had a greater dimensional accuracy than the PolyJet and 3DP models. The PolyJet technique reproduced anatomic details of the mandible more accurately.}, author = {Ibrahim, Danilo and Broilo, Tiago Leonardo and Heitz, Claiton and Gerhardt de Oliveira, Mar{\'\i}lia and de Oliveira, Helena Willhelm and Nobre, Stella Maris Wanderlei and Dos Santos Filho, Jos{\'e} Henrique Gomes and Silva, Daniela Nascimento} } @article {18952940, title = {Electronic Support for Public Health: validated case finding and reporting for notifiable diseases using electronic medical data.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {16}, year = {2009}, month = {2009 Jan-Feb}, pages = {18-24}, abstract = {Health care providers are legally obliged to report cases of specified diseases to public health authorities, but existing manual, provider-initiated reporting systems generally result in incomplete, error-prone, and tardy information flow. Automated laboratory-based reports are more likely accurate and timely, but lack clinical information and treatment details. Here, we describe the Electronic Support for Public Health (ESP) application, a robust, automated, secure, portable public health detection and messaging system for cases of notifiable diseases. The ESP application applies disease specific logic to any complete source of electronic medical data in a fully automated process, and supports an optional case management workflow system for case notification control. All relevant clinical, laboratory and demographic details are securely transferred to the local health authority as an HL7 message. The ESP application has operated continuously in production mode since January 2007, applying rigorously validated case identification logic to ambulatory EMR data from more than 600,000 patients. Source code for this highly interoperable application is freely available under an approved open-source license at http://esphealth.org.}, author = {Lazarus, Ross and Klompas, Michael and Campion, Francis X and McNabb, Scott J N and Hou, Xuanlin and Daniel, James and Haney, Gillian and DeMaria, Alfred and Lenert, Leslie and Platt, Richard} } @article {496, title = {Establishing a personal electronic health record in the Rhine-Neckar region.}, journal = {Studies in health technology and informatics}, volume = {150}, year = {2009}, month = {2009}, pages = {119}, abstract = {We present an approach to establish a personal and electronic health record (PEHR) system in our region, and describe the underlying vision, the technical aspects, the current status as well as the gained experiences. Applied are international standards (HL7, DICOM) and technologies existing today. Obstacles to overcome during the implementation have been the management of access rights, data privacy as well as the integration of the primary systems.}, keywords = {Germany, Medical Records Systems, Computerized, Organizational Case Studies, Program Development, Regional Health Planning}, issn = {0926-9630}, author = {Heinze, Oliver and Brandner, Antje and Bergh, Bj{\"o}rn} } @conference {1083, title = {Free and Open Source in Healthcare: Enough Waste}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001827800080017}, author = {Nuno Rua} } @article {19457798, title = {Free and open source software for the manipulation of digital images.}, journal = {AJR. American journal of roentgenology}, volume = {192}, year = {2009}, month = {2009 Jun}, pages = {W330-4}, abstract = {OBJECTIVE: Free and open source software is a type of software that is nearly as powerful as commercial software but is freely downloadable. This software can do almost everything that the expensive programs can. GIMP (gnu image manipulation program) is the free program that is comparable to Photoshop, and versions are available for Windows, Macintosh, and Linux platforms. This article briefly describes how GIMP can be installed and used to manipulate radiology images. CONCLUSION: It is no longer necessary to budget large amounts of money for high-quality software to achieve the goals of image processing and document creation because free and open source software is available for the user to download at will.}, author = {Solomon, Robert W} } @article {20124747, title = {Fundamental of medical image processing with personal computer system--Image processing of computed tomography with imageJ}, journal = {Nippon Hoshasen Gijutsu Gakkai zasshi}, volume = {65}, year = {2009}, month = {2009 Dec 20}, pages = {1680-2}, author = {Yamamoto, Shuji} } @inbook {springerlink:10.1007/978-3-642-01932-6_45, title = {GIMIAS: An Open Source Framework for Efficient Development of Research Tools and Clinical Prototypes}, booktitle = {Functional Imaging and Modeling of the Heart}, series = {Lecture Notes in Computer Science}, volume = {5528}, year = {2009}, note = {10.1007/978-3-642-01932-6_45}, pages = {417-426}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {GIMIAS is a workflow-oriented environment for addressing advanced biomedical image computing and build personalized computational models, which is extensible through the development of application-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Virtual Physiological Human community while allowing business-friendly technology transfer and commercial product development. This framework has been fully developed in ANSI-C++ on top of well known open source libraries like VTK, ITK and wxWidgets among others. Based on GIMIAS, in this paper is presented a workflow for medical image analysis and simulation of the heart.}, url = {http://dx.doi.org/10.1007/978-3-642-01932-6_45}, author = {Larrabide, Ignacio and Omedas, Pedro and Martelli, Yves and Planes, Xavier and Nieber, Maarten and Moya, Juan and Butakoff, Constantine and Sebasti{\'a}n, Rafael and Camara, Oscar and De Craene, Mathieu and Bijnens, Bart and Frangi, Alejandro}, editor = {Ayache, Nicholas and Delingette, Herv{\'e} and Sermesant, Maxime} } @article {907, title = {A glass slipper? For cash-strapped organizations with EMR dreams, open-source software may be a perfect fit.}, journal = {Healthcare informatics : the business magazine for information and communication systems}, volume = {26}, year = {2009}, pages = {32{\textendash}36}, abstract = {Open-source EMR software is a potential, and relatively economical, option for hospital organizations that can{\textquoteright}t afford proprietary commercial EMR software, or whose leaders want a non-commercial option. While access to VistA{\textquoteright}s source code is free, any hospital organization seeking to implement commercialized VistA will need assistance from one of the vendors supporting that software. Implementing open-source is a bit closer to self-development than to implementing proprietary, commercial EMR software. CCHIT recently announced it will introduce new channels for certification of open-source EMR software, addressing the concerns of those in healthcare who want to pursue the open-source option while also applying for funding under ARRA-HITECH.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79958156637\&partnerID=40\&md5=8657014eaf815ec3c47c548544084909}, author = {Hagland, M} } @article {20044607, title = {Image analysis of breast cancer immunohistochemistry-stained sections using ImageJ: an RGB-based model.}, journal = {Anticancer research}, volume = {29}, year = {2009}, month = {2009 Dec}, pages = {4995-8}, abstract = {BACKGROUND: Image analysis of tissue sections using RGB image profiling is a modern accepted technique. MATERIALS AND METHODS: A new method of RGB analysis, using the freeware ImageJ, is presented which can be applied to sections with either nuclear or cytoplasmic staining. The step-by-step process is presented and the method is tested using breast cancer specimens immunostained for CK-19 and estrogen receptors. RESULTS: This image analysis easily discriminates CK-19 and estrogen receptor positivity in prepared breast cancer specimens. The method is easy to perform, without the need for previous image transformations. CONCLUSION: Compared to previous methods, this method proved more accurate in estimating the actual colours that an observer recognizes as positive after immunostaining. Further studies are needed to evaluate whether this method is efficient enough to be applied in clinical practice.}, author = {Vrekoussis, T and Chaniotis, V and Navrozoglou, I and Dousias, V and Pavlakis, K and Stathopoulos, E N and Zoras, O} } @article {870, title = {Infrastructure for a learning health care system: CaBIG.}, journal = {Health Aff (Millwood)}, volume = {28}, year = {2009}, month = {2009 May-Jun}, pages = {923-4; author reply 924-5}, keywords = {Cooperative Behavior, Delivery of Health Care, Diffusion of Innovation, Humans, Medical Informatics Applications, Medical Informatics Computing, National Cancer Institute (U.S.), United States, United States Food and Drug Administration}, issn = {1544-5208}, doi = {10.1377/hlthaff.28.3.923-a}, author = {Buetow, Kenneth H and Niederhuber, John} } @article {19439392, title = {Interactive segmentation framework of the Medical Imaging Interaction Toolkit.}, journal = {Computer methods and programs in biomedicine}, volume = {96}, year = {2009}, month = {2009 Oct}, pages = {72-83}, abstract = {Interactive methods are indispensable for real world applications of segmentation in medicine, at least to allow for convenient and fast verification and correction of automated techniques. Besides traditional interactive tasks such as adding or removing parts of a segmentation, adjustment of contours or the placement of seed points, the relatively recent Graph Cut and Random Walker segmentation methods demonstrate an interest in advanced interactive strategies for segmentation. Though the value of toolkits and extensible applications is generally accepted for the development of new segmentation algorithms, the topic of interactive segmentation applications is rarely addressed by current toolkits and applications. In this paper, we present the extension of the Medical Imaging Interaction Toolkit (MITK) with a framework for the development of interactive applications for image segmentation. The framework provides a clear structure for the development of new applications and offers a plugin mechanism to easily extend existing applications with additional segmentation tools. In addition, the framework supports shape-based interpolation and multi-level undo/redo of modifications to binary images. To demonstrate the value of the framework, we also present a free, open-source application named InteractiveSegmentation for manual segmentation of medical images (including 3D+t), which is built based on the extended MITK framework. The application includes several features to effectively support manual segmentation, which are not found in comparable freely available applications. InteractiveSegmentation is fully developed and successfully and regularly used in several projects. Using the plugin mechanism, the application enables developers of new algorithms to begin algorithmic work more quickly.}, author = {Maleike, D and Nolden, M and Meinzer, H-P and Wolf, I} } @conference {1085, title = {MediGrid {\textendash} Facilitating Semantic-Based processing of Biomedical Data and Knowledge}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001828500180021}, author = {Jan Vejvalka and Petr Lesn{\'y} and Tom{\'a}{\v s} Hole{\v c}ek and Kry{\v s}tof Slab{\'y} and Ad{\'e}la Jarol{\'\i}mkov{\'a} and Helena Bouzkov{\'a}} } @article {872, title = {Metadata mapping and reuse in caBIG.}, journal = {BMC Bioinformatics}, volume = {10 Suppl 2}, year = {2009}, month = {2009}, pages = {S4}, abstract = {

BACKGROUND: This paper proposes that interoperability across biomedical databases can be improved by utilizing a repository of Common Data Elements (CDEs), UML model class-attributes and simple lexical algorithms to facilitate the building domain models. This is examined in the context of an existing system, the National Cancer Institute (NCI){\textquoteright}s cancer Biomedical Informatics Grid (caBIG). The goal is to demonstrate the deployment of open source tools that can be used to effectively map models and enable the reuse of existing information objects and CDEs in the development of new models for translational research applications. This effort is intended to help developers reuse appropriate CDEs to enable interoperability of their systems when developing within the caBIG framework or other frameworks that use metadata repositories.

RESULTS: The Dice (di-grams) and Dynamic algorithms are compared and both algorithms have similar performance matching UML model class-attributes to CDE class object-property pairs. With algorithms used, the baselines for automatically finding the matches are reasonable for the data models examined. It suggests that automatic mapping of UML models and CDEs is feasible within the caBIG framework and potentially any framework that uses a metadata repository.

CONCLUSION: This work opens up the possibility of using mapping algorithms to reduce cost and time required to map local data models to a reference data model such as those used within caBIG. This effort contributes to facilitating the development of interoperable systems within caBIG as well as other metadata frameworks. Such efforts are critical to address the need to develop systems to handle enormous amounts of diverse data that can be leveraged from new biomedical methodologies.

}, keywords = {Algorithms, Computational Biology, Database Management Systems, Databases, Factual, Medical Informatics, Software, User-Computer Interface}, issn = {1471-2105}, doi = {10.1186/1471-2105-10-S2-S4}, author = {Kunz, Isaac and Lin, Ming-Chin and Frey, Lewis} } @article {1017, title = {Millennium Global Village-Net: bringing together Millennium Villages throughout sub-Saharan Africa.}, journal = {Int J Med Inform}, volume = {78}, year = {2009}, month = {2009 Dec}, pages = {802-7}, abstract = {

The Millennium Villages Project (MVP), based at The Earth Institute at Columbia University, is a bottom-up, community led approach to show how villages in developing countries can get out of the poverty trap that afflicts more than a billion people worldwide. With well-targeted, practical inputs can help the community invest in a path leading to self-sustaining development. There are 80 Millennium Villages clustered in 10 countries throughout sub-Saharan Africa. MVP is an important development process for empowering communities to invest in a package of integrated interventions aiming to increase food production, improve access to safe water, health care, education and infrastructure. The process benefits from synergies of the integrated approach and relies on community leadership as empowered by proven technological inputs. MVP is committed to a science-based approach to assess and monitor the progress of the communities towards clear objectives; the Millennium Development Goals (MDGs) and to do so with mechanisms that are scalable and sustainable. This approach offers much more than simply collecting and analyzing data since the mechanism used for recording progress would provide a bridge over the divide which separates the haves and the have-nots (by facilitating the sharing of solutions from one community to another bidirectionally). By so doing, it allows people to enhance their own futures in a sustainable manner. Solutions found in one community are transferable to similar communities in other MVP villages. To achieve this goal, the MVP requires an information and communication system which can provide both necessary infrastructure for monitoring and evaluation, and tools for communicating among the villages, cities and countries. This system is called the Millennium Global Village-Net (MGV-Net). It takes advantage of the latest in open source software (OpenMRS), databases (MySQL), interface terminology, a centralized concept dictionary, and uses appropriate technology locally for data entry.

}, keywords = {Africa South of the Sahara, Community Health Services, Developing Countries, Healthy People Programs, Humans, Poverty}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2009.08.002}, author = {Kanter, Andrew S and Negin, Joel and Olayo, Bernard and Bukachi, Frederick and Johnson, Edward and Sachs, Sonia Ehrlich} } @article {1018, title = {Mobile Care (Moca) for Remote Diagnosis and Screening.}, journal = {J Health Inform Dev Ctries}, volume = {3}, year = {2009}, month = {2009 Jan 1}, pages = {17-21}, abstract = {

Moca is a cell phone-facilitated clinical information system to improve diagnostic, screening and therapeutic capabilities in remote resource-poor settings. The software allows transmission of any medical file, whether a photo, x-ray, audio or video file, through a cell phone to (1) a central server for archiving and incorporation into an electronic medical record (to facilitate longitudinal care, quality control, and data mining), and (2) a remote specialist for real-time decision support (to leverage expertise). The open source software is designed as an end-to-end clinical information system that seamlessly connects health care workers to medical professionals. It is integrated with OpenMRS, an existing open source medical records system commonly used in developing countries.

}, issn = {1178-4407}, author = {Celi, Leo Anthony and Sarmenta, Luis and Rotberg, Jhonathan and Marcelo, Alvin and Clifford, Gari} } @article {20351824, title = {Mychildren{\textquoteright}s: integration of a personally controlled health record with a tethered patient portal for a pediatric and adolescent population.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, volume = {2009}, year = {2009}, month = {2009}, pages = {65-9}, abstract = {Personally controlled health records (PCHRs) and patient portals are increasingly being offered by healthcare institutions, employers, insurance companies and commercial entities to allow patients access to their health information. Both applications offer unique services to provide patients with tools to manage their health. While PCHRs allow users ubiquitous, portable, patient controlled access to their health information, traditional patient portals provide provider-tethered applications allowing patients access, but not control of, certain healthcare information, as well as communication and administrative functions, such as secure messaging, appointment management and prescription refill requests, facilitating care at a specific healthcare facility.We describe our approach for the design, content creation, policy development, and implementation of MyChildren{\textquoteright}s, a unique web-based application leveraging the advantages of both a provider-tethered patient portal and a PCHR to allow patients and their guardians access to the functionality and convenience of a traditional patient portal, as well as the portability and flexibility of a PCHR.}, author = {Bourgeois, Fabienne C and Mandl, Kenneth D and Shaw, Danny and Flemming, Daisy and Nigrin, Daniel J} } @conference {1087, title = {Open Source: A Lever for Enhancing Opportunities of Healthcare Information Systems - An Italian Case Study}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001828700280037}, author = {Emanuele Baj and Paolo Locatelli and Stefano Gatti and Nicola Restifo and Gianni Origgi and Silvia Bragagia} } @article {19745456, title = {Open source and healthcare in Europe - time to put leading edge ideas into practice.}, journal = {Studies in health technology and informatics}, volume = {150}, year = {2009}, month = {2009}, pages = {963-7}, abstract = {Free/Libre and Open Source Software (FLOSS) is a process of software development, a method of licensing and a philosophy. Although FLOSS plays a significant role in several market areas, the impact in the health care arena is still limited. FLOSS is promoted as one of the most effective means for overcoming fragmentation in the health care sector and providing a basis for more efficient, timely and cost effective health care provision. The 2008 European Federation for Medical Informatics (EFMI) Special Topic Conference (STC) explored a range of current and future issues related to FLOSS in healthcare (FLOSS-HC). In particular, there was a focus on health records, ubiquitous computing, knowledge sharing, and current and future applications. Discussions resulted in a list of main barriers and challenges for use of FLOSS-HC. Based on the outputs of this event, the 2004 Open Steps events and subsequent workshops at OSEHC2009 and Med-e-Tel 2009, a four-step strategy has been proposed for FLOSS-HC: 1) a FLOSS-HC inventory; 2) a FLOSS-HC collaboration platform, use case database and knowledge base; 3) a worldwide FLOSS-HC network; and 4) FLOSS-HC dissemination activities. The workshop will further refine this strategy and elaborate avenues for FLOSS-HC from scientific, business and end-user perspectives. To gain acceptance by different stakeholders in the health care industry, different activities have to be conducted in collaboration. The workshop will focus on the scientific challenges in developing methodologies and criteria to support FLOSS-HC in becoming a viable alternative to commercial and proprietary software development and deployment.}, author = {Murray, Peter J and Wright, Graham and Karopka, Thomas and Betts, Helen and Orel, Andrej} } @article {19157968, title = {The OpenMRS Implementers Network.}, journal = {International journal of medical informatics}, volume = {78}, year = {2009}, month = {2009 Nov}, pages = {711-20}, abstract = {OBJECTIVE: OpenMRS (www.openmrs.org) is a configurable open source electronic medical record application developed and maintained by a large network of open source developers coordinated by the Regenstrief Institute and Partners in Health and mainly used for HIV patient and treatment information management in Africa. Our objective is to develop an open Implementers Network for OpenMRS to provide regional support for the growing number of OpenMRS implementations in Africa and to include African developers and implementers in the future growth of OpenMRS. METHODS: We have developed the OpenMRS Implementers Network using a dedicated Wiki site and e-mail server. We have also organized annual meetings in South Africa and regional training courses at African locations where OpenMRS is being implemented. An OpenMRS Internship program has been initiated and we have started collaborating with similar networks and projects working in Africa. To evaluate its potential, OpenMRS was implemented initially at one site in South Africa by a single implementer using a downloadable OpenMRS application and only the OpenMRS Implementers Network for support. RESULTS: The OpenMRS Implementers Network Wiki and list server have grown into effective means of providing implementation support and forums for exchange of implementation experiences. The annual OpenMRS Implementers meeting has been held in South Africa for the past three years and is attracting successively larger numbers of participants with almost 200 implementers and developers attending the 2008 meeting in Durban, South Africa. Six African developers are presently registered on the first intake of the OpenMRS Internship program. Successful collaborations have been started with several African developer groups and projects initiated to develop interoperability between OpenMRS and various applications. The South African OpenMRS Implementer group successfully configured, installed and maintained an integrated HIV/TB OpenMRS application without significant programming support. Since then, this model has been replicated in several other African sites. The OpenMRS Implementers Network has contributed substantially to the growth and sustainability of OpenMRS in Africa and has become a useful way of including Africans in the development and implementation of OpenMRS in developing countries. The Network provides valuable support and enables a basic OpenMRS application to be implemented in the absence of onsite programmers.}, url = {http://www.healthware.org/openmrs/openmrs.pdf}, author = {Seebregts, Christopher J and Mamlin, Burke W and Biondich, Paul G and Fraser, Hamish S F and Wolfe, Benjamin A and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Baker, Elaine and Musinguzi, Nicholas and Kayiwa, Daniel and Fourie, Carl and Lesh, Neal and Kanter, Andrew and Yiannoutsos, Constantin T and Bailey, Christopher} } @article {19534858, title = {OsiriX, a useful tool for processing tomographic images in patients with facial fracture}, journal = {Cirugia y cirujanos}, volume = {77}, year = {2009}, month = {2009 Mar-Apr}, pages = {95-9}, abstract = {BACKGROUND: OsiriX, a Mac OS X-based open source program, is presented as a useful tool to process tomographic images for diagnosis and preoperative planning in patients with facial fractures. METHODS: CT scans were performed on 124 patients with facial fractures treated at the Department of Maxillofacial and Reconstructive Surgery of the Hospital de Traumatolog{\'\i}a y Ortopedia "Lomas Verdes" in Mexico City. Information obtained was recorded in DICOM format in CDs and processed in a Macintosh laptop with OsiriX software, doing multiplanar and 3D reconstructions. Surgical findings were compared to the images obtained by the software. RESULTS: Of the surgical findings, 96.5\% matched with the OsiriX images. Only 3.5\% of the OsiriX images were not consistent because of distortion or artifacts in the CT due to firearm projectiles and Erich arch bars near the involved area. CONCLUSIONS: Based on the results obtained, the authors consider that the OsiriX software is a useful tool for diagnosis and preoperative planning in patients with facial fractures. Furthermore, it prevents the loss of information due to the process of image selection by the radiology staff.}, author = {Sierra-Mart{\'\i}nez, Eduardo and Cienfuegos-Monroy, Ricardo and Fern{\'a}ndez-Sobrino, Gerardo} } @conference {903, title = {PESCA: Developing an open source platform to bring eHealth to latin america and the caribbean}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe, OSEHC 2009 In Conjunction with BIOSTEC 2009 and the EFMI LIFOSS WG}, year = {2009}, abstract = {Nowadays the society needs to communicate and the technologies are revolutionizing the information systems, especially for the health; where an effective use of the technologies is used to favor the needs of the persons. These technologies can contribute to the development of the local economies. Open source software (OSS) can be an useful strategy to bring information and communication technologies to developing countries. However, specially in Latin America and the Caribbean, there are some barriers in adopting OSS for health: the need for open standards, heterogeneous OSS developed without normalization and metrics, English predominance as top OSS language, lack of initiatives to evaluate existing health OSS and needs for quality control and functional validation. The Open Source Platform for eHealth (PESCA) has been designed as a set of interoperable modules that can solve either: simple problems on health management and communication in primary care or complex problems in healthcare systems, including telehealth communications between heterogeneous institutions.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-67650527704\&partnerID=40\&md5=cb5a91f3ccf525ed19857b1e3354a61d}, author = {Orcero, D.S.a}, editor = {L{\'o}pez, D.L.b} } @article {19184561, title = {PyMVPA: A python toolbox for multivariate pattern analysis of fMRI data.}, journal = {Neuroinformatics}, volume = {7}, year = {2009}, month = {2009 Spring}, pages = {37-53}, abstract = {Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python{\textquoteright}s ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability.}, author = {Hanke, Michael and Halchenko, Yaroslav O and Sederberg, Per B and Hanson, Stephen Jos{\'e} and Haxby, James V and Pollmann, Stefan} } @article {19212459, title = {PyMVPA: A Unifying Approach to the Analysis of Neuroscientific Data.}, journal = {Frontiers in neuroinformatics}, volume = {3}, year = {2009}, month = {2009}, pages = {3}, abstract = {The Python programming language is steadily increasing in popularity as the language of choice for scientific computing. The ability of this scripting environment to access a huge code base in various languages, combined with its syntactical simplicity, make it the ideal tool for implementing and sharing ideas among scientists from numerous fields and with heterogeneous methodological backgrounds. The recent rise of reciprocal interest between the machine learning (ML) and neuroscience communities is an example of the desire for an inter-disciplinary transfer of computational methods that can benefit from a Python-based framework. For many years, a large fraction of both research communities have addressed, almost independently, very high-dimensional problems with almost completely non-overlapping methods. However, a number of recently published studies that applied ML methods to neuroscience research questions attracted a lot of attention from researchers from both fields, as well as the general public, and showed that this approach can provide novel and fruitful insights into the functioning of the brain. In this article we show how PyMVPA, a specialized Python framework for machine learning based data analysis, can help to facilitate this inter-disciplinary technology transfer by providing a single interface to a wide array of machine learning libraries and neural data-processing methods. We demonstrate the general applicability and power of PyMVPA via analyses of a number of neural data modalities, including fMRI, EEG, MEG, and extracellular recordings.}, author = {Hanke, Michael and Halchenko, Yaroslav O and Sederberg, Per B and Olivetti, Emanuele and Fr{\"u}nd, Ingo and Rieger, Jochem W and Herrmann, Christoph S and Haxby, James V and Hanson, Stephen Jos{\'e} and Pollmann, Stefan} } @article {19806300, title = {Recent advances in visualization, imaging, and navigation in hepatobiliary and pancreatic sciences.}, journal = {Journal of hepato-biliary-pancreatic surgery}, year = {2009}, month = {2009 Oct 6}, abstract = {BACKGROUND/PURPOSE: Recent introduction of multi-detector CT (MDCT) and high-speed magnetic resonance (MR) imaging have dramatically advanced visualization and imaging technology in diagnostic and therapeutic strategy in hepatobiliary pancreatic disease. However, image diagnostics have progressed with a background of the essence of anatomy, pathology, and physiology. It is important to object the reflection of the patient{\textquoteright}s condition and pathology of each disease and remove pattern recognition in what they were depicted as an image. Visualization plays another important role in various medical diagnostics. Trends in scientific visualization will depend on advancements in molecular technology and computer hardware as well as trends in engineering disciplines. METHODS: In this special issue, the recent advances in visualization and imaging in the field of hepatobiliary and pancreatic sciences are featured including application of advanced visualization techniques, data management, data compression, feature extraction. RESULTS: We discuss the potential benefits of new technologies and procedures in hepatobiliary and pancreatic areas, that are circulating tumor cells, MR imaging for hepatocellular carcinoma, indocyanine green using fluorescence under infrared light observation, carbon dioxide enhanced MDCT virtual cholangiopancreatography, endoscopic ultrasonography-guided biliary drainage, natural orifice translumenal endoscopic surgery, MR-laparoscopy, and image overlay navigation surgery by OsiriX. CONCLUSION: Some of the recent trends are discussed in terms of visualization and imaging in hapatobiliary and pancreatic sciences. The goal in using visualization is to assist existing scientific procedures by providing new insight through visual representation.}, author = {Sugimoto, Maki} } @conference {1089, title = {Repositories of Reusable Auxological (Growth) Algorithms for eHealth}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001827900540058}, author = {Petr Lesn{\'y} and Hana Kr{\'a}sni{\v c}anov{\'a} and Tom{\'a}{\v s} Hole{\v c}ek and Kry{\v s}tof Slab{\'y} and Jan Vejvalka} } @article {19745435, title = {Reversible anonymization of DICOM images using automatically generated policies.}, journal = {Studies in health technology and informatics}, volume = {150}, year = {2009}, month = {2009}, pages = {861-5}, abstract = {Many real-world applications in the area of medical imaging like case study databases require separation of identifying (IDATA) and non-identifying (MDATA) data, specifically those offering Internet-based data access. These kinds of projects also must provide a role-based access system, controlling, how patient data must be organized and how it can be accessed. On DICOM image level, different image types support different kind of information, intermixing IDATA and MDATA in a single object. To separate them, it is possible to reversibly anonymize DICOM objects by substituting IDATA by a unique anonymous token. In case that later an authenticated user needs full access to an image, this token can be used for re-linking formerly separated IDATA and MDATA, thus resulting in a dynamically generated, exact copy of the original image. The approach described in this paper is based on the automatic generation of anonymization policies from the DICOM standard text, providing specific support for all kinds of DICOM images. The policies are executed by a newly developed framework based on the DICOM toolkit DCMTK and offer a reliable approach to reversible anonymization. The implementation is evaluated in a German BMBF-supported expert network in the area of skeletal dysplasias, SKELNET, but may generally be applicable to related projects, enormously improving quality and integrity of diagnostics in a field focused on images. It performs effectively and efficiently on real-world test images from the project and other kind of DICOM images.}, author = {Onken, Michael and Riesmeier, J{\"o}rg and Engel, Marcel and Yabanci, Adem and Zabel, Bernhard and Despr{\'e}s, Stefan} } @article {19321384, title = {The state and profile of open source software projects in health and medical informatics.}, journal = {International journal of medical informatics}, volume = {78}, year = {2009}, month = {2009 Jul}, pages = {457-72}, abstract = {PURPOSE: Little has been published about the application profiles and development patterns of open source software (OSS) in health and medical informatics. This study explores these issues with an analysis of health and medical informatics related OSS projects on SourceForge, a large repository of open source projects. METHODOLOGY: A search was conducted on the SourceForge website during the period from May 1 to 15, 2007, to identify health and medical informatics OSS projects. This search resulted in a sample of 174 projects. A Java-based parser was written to extract data for several of the key variables of each project. Several visually descriptive statistics were generated to analyze the profiles of the OSS projects. RESULTS: Many of the projects have sponsors, implying a growing interest in OSS among organizations. Sponsorship, we discovered, has a significant impact on project success metrics. Nearly two-thirds of the projects have a restrictive license type. Restrictive licensing may indicate tighter control over the development process. Our sample includes a wide range of projects that are at various stages of development (status). Projects targeted towards the advanced end user are primarily focused on bio-informatics, data formats, database and medical science applications. CONCLUSION: We conclude that there exists an active and thriving OSS development community that is focusing on health and medical informatics. A wide range of OSS applications are in development, from bio-informatics to hospital information systems. A profile of OSS in health and medical informatics emerges that is distinct and unique to the health care field. Future research can focus on OSS acceptance and diffusion and impact on cost, efficiency and quality of health care.}, author = {Janamanchi, Balaji and Katsamakas, Evangelos and Raghupathi, Wullianallur and Gao, Wei} } @article {19425593, title = {TOPPView: an open-source viewer for mass spectrometry data.}, journal = {Journal of proteome research}, volume = {8}, year = {2009}, month = {2009 Jul}, pages = {3760-3}, abstract = {Visualization of complex mass spectrometric data sets is becoming increasingly important in proteomics and metabolomics. We present TOPPView, an integrated data visualization and analysis tool for mass spectrometric data sets. TOPPView allows the visualization and comparison of individual mass spectra, two-dimensional LC-MS data sets and their accompanying metadata. By supporting standardized XML-based data exchange formats, data import is possible from any type of mass spectrometer. The integrated analysis tools of the OpenMS Proteomics Pipeline (TOPP) allow efficient data analysis from within TOPPView through a convenient graphical user interface. TOPPView runs on all major operating systems and is available free of charge under an open-source license at http://www.openms.de.}, author = {Sturm, Marc and Kohlbacher, Oliver} } @article {444, title = {Visualization Software for Real-time, Image-guided Therapeutics in Cardiovascular Interventions}, year = {2009}, publisher = {CCSd/HAL : e-articles server (based on gBUS) [http://hal.ccsd.cnrs.fr/oai/oai.php] (France)}, abstract = {This paper introduces RtViewer, a four-dimensional (3D + time) real-time visualization software for guiding cardiovascular interventions that is open source and freely available. RtViewer was designed to be part of a pipeline that can connect it to a magnetic resonance imaging (MRI) scanner, actively tracked catheters, and navigational devices. The architecture and features of RtViewer will be described with examples of guiding percutaneous cardiovascular interventions. The paper concludes with a brief description of the work in progress on the next generation of this platform, named Vurtigo.}, keywords = {Computer Science/Medical Imaging}, url = {http://hal.archives-ouvertes.fr/inria-00417831/en/}, author = {Pintilie, Stefan and Biswas, Labonny and Anderson, Kevan and Dick, Sandy and Wright, Graham and Radau, Perry} } @conference {1090, title = {Writing Open Source SunXACML Access Control in Electronic Health Record with Acceptable Performances}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001813400590068}, author = {Snezana Sucurovic and Dejan Simic} } @article {920, title = {The AQUA-FONTIS study: protocol of a multidisciplinary, cross-sectional and prospective longitudinal study for developing standardized diagnostics and classification of non-thyroidal illness syndrome.}, journal = {BMC Endocr Disord}, volume = {8}, year = {2008}, month = {2008}, pages = {13}, abstract = {

BACKGROUND: Non-thyroidal illness syndrome (NTIS) is a characteristic functional constellation of thyrotropic feedback control that frequently occurs in critically ill patients. Although this condition is associated with significantly increased morbidity and mortality, there is still controversy on whether NTIS is caused by artefacts, is a form of beneficial adaptation, or is a disorder requiring treatment. Trials investigating substitution therapy of NTIS revealed contradictory results. The comparison of heterogeneous patient cohorts may be the cause for those inconsistencies.

OBJECTIVES: Primary objective of this study is the identification and differentiation of different functional states of thyrotropic feedback control in order to define relevant evaluation criteria for the prognosis of affected patients. Furthermore, we intend to assess the significance of an innovative physiological index approach (SPINA) in differential diagnosis between NTIS and latent (so-called "sub-clinical") thyrotoxicosis.Secondary objective is observation of variables that quantify distinct components of NTIS in the context of independent predictors of evolution, survival or pathophysiological condition and influencing or disturbing factors like medication.

DESIGN: The approach to a quantitative follow-up of non-thyroidal illness syndrome (AQUA FONTIS study) is designed as both a cross-sectional and prospective longitudinal observation trial in critically ill patients. Patients are observed in at least two evaluation points with consecutive assessments of thyroid status, physiological and clinical data in additional weekly observations up to discharge. A second part of the study investigates the neuropsychological impact of NTIS and medium-term outcomes.The study design incorporates a two-module structure that covers a reduced protocol in form of an observation trial before patients give informed consent. Additional investigations are performed if and after patients agree in participation.

TRIAL REGISTRATION: ClinicalTrials.gov NCT00591032.

}, issn = {1472-6823}, doi = {10.1186/1472-6823-8-13}, author = {Dietrich, Johannes W and Stachon, Axel and Antic, Biljana and Klein, Harald H and Hering, Steffen} } @article {18612462, title = {Automated identification of acute hepatitis B using electronic medical record data to facilitate public health surveillance.}, journal = {PloS one}, volume = {3}, year = {2008}, month = {2008}, pages = {e2626}, abstract = {BACKGROUND: Automatic identification of notifiable diseases from electronic medical records can potentially improve the timeliness and completeness of public health surveillance. We describe the development and implementation of an algorithm for prospective surveillance of patients with acute hepatitis B using electronic medical record data. METHODS: Initial algorithms were created by adapting Centers for Disease Control and Prevention diagnostic criteria for acute hepatitis B into electronic terms. The algorithms were tested by applying them to ambulatory electronic medical record data spanning 1990 to May 2006. A physician reviewer classified each case identified as acute or chronic infection. Additional criteria were added to algorithms in serial fashion to improve accuracy. The best algorithm was validated by applying it to prospective electronic medical record data from June 2006 through April 2008. Completeness of case capture was assessed by comparison with state health department records. FINDINGS: A final algorithm including a positive hepatitis B specific test, elevated transaminases and bilirubin, absence of prior positive hepatitis B tests, and absence of an ICD9 code for chronic hepatitis B identified 112/113 patients with acute hepatitis B (sensitivity 97.4\%, 95\% confidence interval 94-100\%; specificity 93.8\%, 95\% confidence interval 87-100\%). Application of this algorithm to prospective electronic medical record data identified 8 cases without false positives. These included 4 patients that had not been reported to the health department. There were no known cases of acute hepatitis B missed by the algorithm. CONCLUSIONS: An algorithm using codified electronic medical record data can reliably detect acute hepatitis B. The completeness of public health surveillance may be improved by automatically identifying notifiable diseases from electronic medical record data.}, author = {Klompas, Michael and Haney, Gillian and Church, Daniel and Lazarus, Ross and Hou, Xuanlin and Platt, Richard} } @article {18999296, title = {caBIG compatibility review system: software to support the evaluation of applications using defined interoperability criteria.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2008}, month = {2008}, pages = {197-201}, abstract = {The caBIG Compatibility Review System (CRS) is a web-based application to support compatibility reviews, which certify that software applications that pass the review meet a specific set of criteria that allow them to interoperate. The CRS contains workflows that support both semantic and syntactic reviews, which are performed by the caBIG Vocabularies and Common Data Elements (VCDE) and Architecture workspaces, respectively. The CRS increases the efficiency of compatibility reviews by reducing administrative overhead and it improves uniformity by ensuring that each review is conducted according to a standard process. The CRS provides metrics that allow the review team to evaluate the level of data element reuse in an application, a first step towards quantifying the extent of harmonization between applications. Finally, functionality is being added that will provide automated validation of checklist criteria, which will further simplify the review process.}, author = {Freimuth, Robert R and Schauer, Michael W and Lodha, Preeti and Govindrao, Poornima and Nagarajan, Rakesh and Chute, Christopher G} } @article {18096909, title = {caGrid 1.0: an enterprise Grid infrastructure for biomedical research.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {15}, year = {2008}, month = {2008 Mar-Apr}, pages = {138-49}, abstract = {OBJECTIVE: To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. DESIGN: An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including 1) discovery, 2) integrated and large-scale data analysis, and 3) coordinated study. MEASUREMENTS: The caGrid is built as a Grid software infrastructure and leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. RESULTS: The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid. CONCLUSIONS: While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields. In this respect, caGrid 1.0 is the realization of a framework that can benefit the entire biomedical community.}, author = {Oster, Scott and Langella, Stephen and Hastings, Shannon and Ervin, David and Madduri, Ravi and Phillips, Joshua and Kurc, Tahsin and Siebenlist, Frank and Covitz, Peter and Shanbhag, Krishnakant and Foster, Ian and Saltz, Joel} } @article {18318594, title = {Could an open-source clinical trial data-management system be what we have all been looking for?}, journal = {PLoS medicine}, volume = {5}, year = {2008}, month = {2008 Mar 4}, pages = {e6}, doi = {10.1371/journal.pmed.0050006}, url = {http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0050006}, author = {Fegan, Greg W and Lang, Trudie A} } @article {803, title = {Designing Tracking Software for Image-Guided Surgery Applications: IGSTK Experience.}, journal = {Int J Comput Assist Radiol Surg}, volume = {3}, year = {2008}, month = {2008 Nov 1}, pages = {395-403}, abstract = {OBJECTIVE: Many image-guided surgery applications require tracking devices as part of their core functionality. The Image-Guided Surgery Toolkit (IGSTK) was designed and developed to interface tracking devices with software applications incorporating medical images. METHODS: IGSTK was designed as an open source C++ library that provides the basic components needed for fast prototyping and development of image-guided surgery applications. This library follows a component-based architecture with several components designed for specific sets of image-guided surgery functions. At the core of the toolkit is the tracker component that handles communication between a control computer and navigation device to gather pose measurements of surgical instruments present in the surgical scene. The representations of the tracked instruments are superimposed on anatomical images to provide visual feedback to the clinician during surgical procedures. RESULTS: The initial version of the IGSTK toolkit has been released in the public domain and several trackers are supported. The toolkit and related information are available at www.igstk.org. CONCLUSION: With the increased popularity of minimally invasive procedures in health care, several tracking devices have been developed for medical applications. Designing and implementing high-quality and safe software to handle these different types of trackers in a common framework is a challenging task. It requires establishing key software design principles that emphasize abstraction, extensibility, reusability, fault-tolerance, and portability. IGSTK is an open source library that satisfies these needs for the image-guided surgery community.}, issn = {1861-6429}, doi = {10.1007/s11548-008-0243-4}, author = {Enquobahrie, Andinet and Gobbi, David and Turek, Matt and Cheng, Patrick and Yaniv, Ziv and Lindseth, Frank and Cleary, Kevin} } @article {17947615, title = {Early experiences with personal health records.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {15}, year = {2008}, month = {2008 Jan-Feb}, pages = {1-7}, abstract = {Over the past year, several payers, employers, and commercial vendors have announced personal health record projects. Few of these are widely deployed and few are fully integrated into ambulatory or hospital-based electronic record systems. The earliest adopters of personal health records have many lessons learned that can inform these new initiatives. We present three case studies--MyChart at Palo Alto Medical Foundation, PatientSite at Beth Israel Deaconess Medical Center, and Indivo at Children{\textquoteright}s Hospital Boston. We describe our implementation challenges from 1999 to 2007 and postulate the evolving challenges we will face over the next five years.}, author = {Halamka, John D and Mandl, Kenneth D and Tang, Paul C} } @article {18302744, title = {Epigrass: a tool to study disease spread in complex networks.}, journal = {Source code for biology and medicine}, volume = {3}, year = {2008}, month = {2008}, pages = {3}, abstract = {BACKGROUND: The construction of complex spatial simulation models such as those used in network epidemiology, is a daunting task due to the large amount of data involved in their parameterization. Such data, which frequently resides on large geo-referenced databases, has to be processed and assigned to the various components of the model. All this just to construct the model, then it still has to be simulated and analyzed under different epidemiological scenarios. This workflow can only be achieved efficiently by computational tools that can automate most, if not all, these time-consuming tasks. In this paper, we present a simulation software, Epigrass, aimed to help designing and simulating network-epidemic models with any kind of node behavior. RESULTS: A Network epidemiological model representing the spread of a directly transmitted disease through a bus-transportation network connecting mid-size cities in Brazil. Results show that the topological context of the starting point of the epidemic is of great importance from both control and preventive perspectives. CONCLUSION: Epigrass is shown to facilitate greatly the construction, simulation and analysis of complex network models. The output of model results in standard GIS file formats facilitate the post-processing and analysis of results by means of sophisticated GIS software.}, author = {Coelho, Fl{\'a}vio C and Cruz, Oswaldo G and Code{\c c}o, Cl{\'a}udia T} } @article {547, title = {Free and Open Source Software in Healthcare 1.0}, year = {2008}, publisher = {American Medical Informatics Association Open Source Working Group}, type = {White Paper}, abstract = {The possible benefits of widespread adoption of Electronic Health Record/Electronic Medical Record (EHR/EMR) technologies are widely documented, yet progress is slow and few propose a viable mechanism to achieve shared goals. Multiple problems of cost, interoperability, vendor lock-in, standardization and longevity have been identified and have persisted. Even {\textquotedblleft}successes{\textquotedblright} have problems. While multiple initiatives and much money is spent on finding answers, Free/Open Source Software (FOSS) licensing holds promise for solving these problems or at least making them more tractable. Multiple deployments, novel applications, and multiple companies offering support appear to be occurring. Interoperability and connectivity may be an area of particular proliferation. By vendor and site self-report there are a substantial number of patient records, 3,959,065 in 898 non-Federal government sites and 24,442,000 patient records in 1607 Federal government sites that use FOSS or public domain software EHR/EMR{\textquoteright}s. To date, 232 Open Source titled works on various aspects are listed in PubMed. Local and national education is needed to ensure that equal attention be given to FOSS licensed EHR/EMR software.}, keywords = {Electronic Health Record, Electronic Medical Record, Free and Open Source}, url = {https://www.amia.org/files/Final-OS-WG\%20White\%20Paper_11_19_08_0.pdf}, author = {Ignacio Valdes} } @article {19198666, title = {Generating Stimuli for Neuroscience Using PsychoPy.}, journal = {Frontiers in neuroinformatics}, volume = {2}, year = {2008}, month = {2008}, pages = {10}, abstract = {PsychoPy is a software library written in Python, using OpenGL to generate very precise visual stimuli on standard personal computers. It is designed to allow the construction of as wide a variety of neuroscience experiments as possible, with the least effort. By writing scripts in standard Python syntax users can generate an enormous variety of visual and auditory stimuli and can interact with a wide range of external hardware (enabling its use in fMRI, EEG, MEG etc.). The structure of scripts is simple and intuitive. As a result, new experiments can be written very quickly, and trying to understand a previously written script is easy, even with minimal code comments. PsychoPy can also generate movies and image sequences to be used in demos or simulated neuroscience experiments. This paper describes the range of tools and stimuli that it provides and the environment in which experiments are conducted.}, author = {Peirce, Jonathan W} } @article {19068935, title = {Implementation of the Veterans Health Administration VistA clinical information system around the world.}, journal = {Healthcare quarterly (Toronto, Ont.)}, volume = {11}, year = {2008}, month = {2008}, pages = {83-9}, abstract = {The success story of the Veterans Health Administration (VHA) within the US Department of Veterans Affairs has been well documented and is generally well known. What is generally not known is that the VHA{\textquoteright}s clinical information system, known as VistA, and the computerized patient record system clinical user interface front end have been successfully transported and implemented to a number of non-VHA healthcare organizations across the United States. Moreover, VistA software modules have been installed, or are being considered for installation, in healthcare institutions around the world in countries such as Mexico, Finland, Jordan, Germany, Nigeria, Egypt, Malaysia, India, Brazil, Pakistan and Samoa.}, author = {Protti, Denis and Groen, Peter} } @article {18276143, title = {iPath: interactive exploration of biochemical pathways and networks.}, journal = {Trends in biochemical sciences}, volume = {33}, year = {2008}, month = {2008 Mar}, pages = {101-3}, abstract = {iPath is an open-access online tool (http://pathways.embl.de) for visualizing and analyzing metabolic pathways. An interactive viewer provides straightforward navigation through various pathways and enables easy access to the underlying chemicals and enzymes. Customized pathway maps can be generated and annotated using various external data. For example, by merging human genome data with two important gut commensals, iPath can pinpoint the complementarity of the host-symbiont metabolic capacities.}, author = {Letunic, Ivica and Yamada, Takuji and Kanehisa, Minoru and Bork, Peer} } @article {10.1109/HICSS.2008.26, title = {A Light-Weight Component for Adding Decision Support to Electronic Medical Records}, journal = {Hawaii International Conference on System Sciences}, year = {2008}, pages = {251}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, issn = {1530-1605}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2008.26}, author = {Jens H. Weber-Jahnke and Glen McCallum} } @article {Jahnke-weber_makingavailable, title = {Making available Clinical Decision Support in Service-Oriented Architectures}, journal = {Journal on Information Technology in Healthcare}, volume = {6}, year = {2008}, pages = {54}, chapter = {42}, abstract = {Computer-based clinical decision support (CDS) has great potential for cost savings and for increasing patient safety and quality of care. The cost of owning and particularly maintaining CDS systems is significant. Therefore, it makes good economic sense to share a CDS service installation among a larger set of client systems. The emerging paradigm of serviceoriented architectures (SOAs) embraces the idea of sharing and interaction between loosely coupled, co-operative services. Canada has based its planned architecture for realizing the electronic medical record (EMR) on the SOA paradigm. While CDS components are currently not in the set of services to be constructed for Canada{\textquoteright}s health information infrastructure, they seems to be growing interest in adding them in the future, after the more essential services have been implemented. In this paper, we discuss the status of clinical decision support systems today and some challenges of making them available in SOA-based infrastructures. We report on design choices and solutions we have selected during the construction of the EGADSS (Electronic Guideline and Decision Support System) component. Our design decisions are based on domainspecific challenges such as knowledge, data and workflow interoperability as well as on technical considerations about construction high quality services for SOA-based infrastructures. EGADSS has been released under open-source license and is freely available.}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.88.5385\&rep=rep1\&type=pdf}, author = {Jens H. Jahnke-Weber and Morgan Price and Glen McCallum} } @article {18953134, title = {Open source electronic health record and patient data management system for intensive care.}, journal = {Studies in health technology and informatics}, volume = {141}, year = {2008}, month = {2008}, pages = {139-45}, abstract = {BACKGROUND AND OBJECTIVES: In Intensive Care Units, the amount of data to be processed for patients care, the turn over of the patients, the necessity for reliability and for review processes indicate the use of Patient Data Management Systems (PDMS) and electronic health records (EHR). To respond to the needs of an Intensive Care Unit and not to be locked with proprietary software, we developed a PDMS and EHR based on open source software and components. METHODS: The software was designed as a client-server architecture running on the Linux operating system and powered by the PostgreSQL data base system. The client software was developed in C using GTK interface library. The application offers to the users the following functions: medical notes captures, observations and treatments, nursing charts with administration of medications, scoring systems for classification, and possibilities to encode medical activities for billing processes. RESULTS: Since his deployment in February 2004, the PDMS was used to care more than three thousands patients with the expected software reliability and facilitated data management and review processes. Communications with other medical software were not developed from the start, and are realized by the use of the Mirth HL7 communication engine. Further upgrade of the system will include multi-platform support, use of typed language with static analysis, and configurable interface. CONCLUSION: The developed system based on open source software components was able to respond to the medical needs of the local ICU environment. The use of OSS for development allowed us to customize the software to the preexisting organization and contributed to the acceptability of the whole system.}, author = {Massaut, Jacques and Reper, Pascal} } @article {18366760, title = {OpenMS - an open-source software framework for mass spectrometry.}, journal = {BMC bioinformatics}, volume = {9}, year = {2008}, month = {2008}, pages = {163}, abstract = {BACKGROUND: Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data. Consequently, analysis of the data is currently often the bottleneck for experimental studies. Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow. RESULTS: We present OpenMS, a software framework for rapid application development in mass spectrometry. OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis. This has already been demonstrated in several studies. CONCLUSION: OpenMS is available under the Lesser GNU Public License (LGPL) from the project website at http://www.openms.de.}, url = {http://www.biomedcentral.com/1471-2105/9/163}, author = {Sturm, Marc and Bertsch, Andreas and Gr{\"o}pl, Clemens and Hildebrandt, Andreas and Hussong, Rene and Lange, Eva and Pfeifer, Nico and Schulz-Trieglaff, Ole and Zerck, Alexandra and Reinert, Knut and Kohlbacher, Oliver} } @article {18570637, title = {OSPACS: Ultrasound image management system.}, journal = {Source code for biology and medicine}, volume = {3}, year = {2008}, month = {2008}, pages = {11}, abstract = {ABSTRACT: BACKGROUND: Ultrasound scanning uses the medical imaging format, DICOM, for electronically storing the images and data associated with a particular scan. Large health care facilities typically use a picture archiving and communication system (PACS) for storing and retrieving such images. However, these systems are usually not suitable for managing large collections of anonymized ultrasound images gathered during a clinical screening trial. RESULTS: We have developed a system enabling the accurate archiving and management of ultrasound images gathered during a clinical screening trial. It is based upon a Windows application utilizing an open-source DICOM image viewer and a relational database. The system automates the bulk import of DICOM files from removable media by cross-validating the patient information against an external database, anonymizing the data as well as the image, and then storing the contents of the file as a field in a database record. These image records may then be retrieved from the database and presented in a tree-view control so that the user can select particular images for display in a DICOM viewer or export them to external media. CONCLUSION: This system provides error-free automation of ultrasound image archiving and management, suitable for use in a clinical trial. An open-source project has been established to promote continued development of the system.}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442597/}, author = {Stott, Will and Ryan, Andy and Jacobs, Ian J and Menon, Usha and Bessant, Conrad and Jones, Christopher} } @article {18570554, title = {Standards-based, open-source electronic health record systems: a desirable future for the U.S. health industry.}, journal = {Telemedicine journal and e-health : the official journal of the American Telemedicine Association}, volume = {14}, year = {2008}, month = {2008 Apr}, pages = {284-8}, abstract = {Many healthcare systems are moving toward a fully electronic health record (EHR) in order to better manage patient care. Unfortunately, in the United States, many current EHR systems leave much to be desired. Among well-documented criticisms are that they tend to be inflexible, proprietary, nonintuitive, expensive, difficult to maintain and rarely interoperable across health systems. From the clinician{\textquoteright}s perspective, these flaws sometimes make having an EHR system seem no better than retaining a paper-based system. Open-source software, a great success in other information-intensive industries, is one possible solution to these problems, and may help integrate a functional EHR system into, and across, more health systems and clinics because of the greater potential for local customization. We believe that the advantages of an open-source EHR system outweigh the costs of a more traditional, proprietary EHR system, and recommend that more work be done to advance an interoperable open-source EHR system in the United States. Open-source EHR systems have the potential to improve healthcare in the United States as they have done in many other areas around the world.}, author = {Yellowlees, Peter M and Marks, Shayna L and Hogarth, Michael and Turner, Stuart} } @article {18755989, title = {Whose personal control? Creating private, personally controlled health records for pediatric and adolescent patients.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {15}, year = {2008}, month = {2008 Nov-Dec}, pages = {737-43}, abstract = {Personally controlled health records (PCHRs) enable patients to store, manage, and share their own health data, and promise unprecedented consumer access to medical information. To deploy a PCHR in the pediatric population requires crafting of access and security policies, tailored to a record that is not only under patient control, but one that may also be accessed by parents, guardians, and third-party entities. Such hybrid control of health information requires careful consideration of both the PCHR vendor{\textquoteright}s access policies, as well as institutional policies regulating data feeds to the PCHR, to ensure that the privacy and confidentiality of each user is preserved. Such policies must ensure compliance with legal mandates to prevent unintended disclosures and must preserve the complex interactions of the patient-provider relationship. Informed by our own operational involvement in the implementation of the Indivo PCHR, we provide a framework for understanding and addressing the challenges posed by child, adolescent, and family access to PCHRs.}, author = {Bourgeois, Fabienne C and Taylor, Patrick L and Emans, S Jean and Nigrin, Daniel J and Mandl, Kenneth D} } @article {17917780, title = {Benefits of using the DCM4CHE DICOM archive.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {125-9}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2039778}, author = {Warnock, Max J and Toland, Christopher and Evans, Damien and Wallace, Bill and Nagy, Paul} } @article {17356215, title = {Comparison of four freely available frameworks for image processing and visualization that use ITK.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {13}, year = {2007}, month = {2007 May-Jun}, pages = {483-93}, abstract = {Most image processing and visualization applications allow users to configure computation parameters and manipulate the resulting visualizations. SCIRun, VolView, MeVisLab, and the Medical Interaction Toolkit (MITK) are four image processing and visualization frameworks that were built for these purposes. All frameworks are freely available and all allow the use of the ITK C++ library. In this paper, the benefits and limitations of each visualization framework are presented to aid both application developers and users in the decision of which framework may be best to use for their application. The analysis is based on more than 50 evaluation criteria, functionalities, and example applications. We report implementation times for various steps in the creation of a reference application in each of the compared frameworks. The data-flow programming frameworks, SCIRun and MeVisLab, were determined to be best for developing application prototypes, while VolView was advantageous for nonautomatic end-user applications based on existing ITK functionalities, and MITK was preferable for automated end-user applications that might include new ITK classes specifically designed for the application.}, author = {Bitter, Ingmar and Van Uitert, Robert and Wolf, Ivo and Ib{\'a}{\~n}ez, Luis and Kuhnigk, Jan-Martin} } @mastersthesis {889, title = {An empirical investigation into the adoption of open source software in hospitals}, year = {2007}, school = {University of Maryland at Baltimore County}, type = {phd}, address = {Catonsville, MD, USA}, abstract = {Information technology holds great promise for reducing cost and improving quality in health care. Open source software (OSS) has emerged as a potential alternative to commercial and closed-source products in many domains. OSS has gained considerable attention recently in the health care arena, and proponents claim that it overcomes many of the obstacles to IT adoption that health care organizations face. Yet, how and why OSS is being adopted and implemented within hospitals in particular remains a poorly understood issue. This research attempts to further this understanding so that hospitals may make better informed decisions about adoption of IT, and OSS in particular, in the future. We use a qualitative grounded theory approach in order to explore the extent of OSS adoption in hospitals as well as the factors facilitating and inhibiting adoption. Surveys and interviews are used to acquire both breadth and depth of understanding. First, a survey was used to explore and characterize the types of OSS products adopted in hospitals and the extent to which they have been adopted. For methodological reasons, we focused on Baltimore, Washington and Northern Virginia area hospitals. Following the survey, semi-structured interviews were conducted with hospital IT managers in order to attain a deeper understanding of the factors that are facilitating and inhibiting the adoption of OSS in hospitals. The findings suggest a very limited adoption of OSS in hospitals. Adopters tend to be very large hospitals, with IT budgets of less than 3\% of the total budget and a large number of IT support staff. The results also show that hospitals tend to adopt general-purpose instead of domain-specific OSS. We also found that hospital software vendors are the critical factor facilitating the adoption of OSS in hospitals. Conversely, lack of in-house development, as well as a perceived lack of security, quality, and accountability of OSS products were factors found to be inhibiting adoption. An empirical model describing the adoption of OSS in hospitals, based upon our findings, is presented to illustrate the factors facilitating and inhibiting the adoption of OSS in hospitals.}, isbn = {978-0-549-35501-4}, author = {Munoz-Cornejo, Gilberto} } @article {17700908, title = {Free and open source enabling technologies for patient-centric, guideline-based clinical decision support: a survey.}, journal = {Yearbook of medical informatics}, year = {2007}, month = {2007}, pages = {74-86}, abstract = {OBJECTIVES: Guideline-based clinical decision support is an emerging paradigm to help reduce error, lower cost, and improve quality in evidence-based medicine. The free and open source (FOS) approach is a promising alternative for delivering cost-effective information technology (IT) solutions in health care. In this paper, we survey the current FOS enabling technologies for patient-centric, guideline-based care, and discuss the current trends and future directions of their role in clinical decision support. METHODS: We searched PubMed, major biomedical informatics websites, and the web in general for papers and links related to FOS health care IT systems. We also relied on our background and knowledge for specific subtopics. We focused on the functionalities of guideline modeling tools, and briefly examined the supporting technologies for terminology, data exchange and electronic health record (EHR) standards. RESULTS: To effectively support patient-centric, guideline-based care, the computerized guidelines and protocols need to be integrated with existing clinical information systems or EHRs. Technologies that enable such integration should be accessible, interoperable, and scalable. A plethora of FOS tools and techniques for supporting different knowledge management and quality assurance tasks involved are available. Many challenges, however, remain in their implementation. CONCLUSIONS: There are active and growing trends of deploying FOS enabling technologies for integrating clinical guidelines, protocols, and pathways into the main care processes. The continuing development and maturation of such technologies are likely to make increasingly significant contributions to patient-centric, guideline-based clinical decision support.}, author = {Leong, T Y and Kaiser, K and Miksch, S} } @article {802, title = {The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.}, journal = {J Digit Imaging}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {21-33}, abstract = {This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers{\textquoteright} mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.}, keywords = {Computer Systems, Data Display, Database Management Systems, Humans, Information Dissemination, Information Storage and Retrieval, Safety, Software, Software Design, Software Validation, Surgery, Computer-Assisted, Systems Integration, User-Computer Interface}, issn = {0897-1889}, doi = {10.1007/s10278-007-9054-3}, author = {Enquobahrie, Andinet and Cheng, Patrick and Gary, Kevin and Ibanez, Luis and Gobbi, David and Lindseth, Frank and Yaniv, Ziv and Aylward, Stephen and Jomier, Julien and Cleary, Kevin} } @article {17850667, title = {Indivo: a personally controlled health record for health information exchange and communication.}, journal = {BMC medical informatics and decision making}, volume = {7}, year = {2007}, month = {2007}, pages = {25}, abstract = {BACKGROUND: Personally controlled health records (PCHRs), a subset of personal health records (PHRs), enable a patient to assemble, maintain and manage a secure copy of his or her medical data. Indivo (formerly PING) is an open source, open standards PCHR with an open application programming interface (API). RESULTS: We describe how the PCHR platform can provide standard building blocks for networked PHR applications. Indivo allows the ready integration of diverse sources of medical data under a patient{\textquoteright}s control through the use of standards-based communication protocols and APIs for connecting PCHRs to existing and future health information systems. CONCLUSION: The strict and transparent personal control model is designed to encourage widespread participation by patients, healthcare providers and institutions, thus creating the ecosystem for development of innovative, consumer-focused healthcare applications.}, url = {http://www.biomedcentral.com/1472-6947/7/25/}, author = {Mandl, Kenneth D and Simons, William W and Crawford, William C R and Abbett, Jonathan M} } @article {17680308, title = {Mastering DICOM with DVTk.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {47-62}, abstract = {The Digital Imaging and Communications in Medicine (DICOM) Validation Toolkit (DVTk) is an open-source framework with potential value for anyone working with the DICOM standard. DICOM{\textquoteright}s flexibility requires hands-on experience in understanding ways in which the standard{\textquoteright}s interpretation may vary among vendors. DVTk was developed as a clinical engineering tool to aid and accelerate DICOM integration at clinical sites. DVTk is used to provide an independent measurement of the accuracy of a product{\textquoteright}s DICOM interface, according to both the DICOM standard and the product{\textquoteright}s conformance statement. DVTk has stand-alone tools and a framework with which developers can create new tools. We provide an overview of the architecture of the toolkit, sample scenarios of its utility, and evidence of its relative ease of use. Our goal is to encourage involvement in this open-source project and attract developers to build off and further enrich this platform for DICOM integration testing.}, url = {http://www.springerlink.com/content/r17t75244k2376n0/}, author = {Potter, Glenn and Busbridge, Rick and Toland, Michael and Nagy, Paul} } @inbook {springerlink:10.1007/978-3-540-73044-6_189, title = {O3-RWS: a Java-based, IHE-compliant open-source radiology workstation}, booktitle = {11th Mediterranean Conference on Medical and Biomedical Engineering and Computing 2007}, series = {IFMBE Proceedings}, volume = {16}, year = {2007}, note = {10.1007/978-3-540-73044-6_189}, pages = {727-731}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Within the Open Three Consortium (O3) an open source radiological reporting workstation, called O3- RWS, has been studied, developed and experimented in the routine of European and US hospitals. The O3 Consortium is an international open-source project constituted in 2005 by Higher Education in Clinical Engineering (HECE) of the University of Trieste; it deals with the multi-centric integration of hospitals, RHIOs and citizen (care at home and on the move, and ambient assisted living). O3-RWS has been studied and developed with the goal to give a solution for the needs of the physician, who wants to have an easy-to-use, light and complete solution for the radiology reporting and report creation. O3-RWS, a very versatile platform-independent radiology workstation, providing user authentication and being easy to use also for private users, is able to retrieve, visualize and manage medical images; in an universal version, it is going to be able to deal with vital signs like ECG, hemodynamical and pneumological data.}, isbn = {978-3-540-73044-6}, url = {http://dx.doi.org/10.1007/978-3-540-73044-6_189}, author = {Faustini, Giorgio and Inchingolo, P.}, editor = {Magjarevic, Ratko and Jarm, Tomaz and Kramar, Peter and Zupanic, Anze} } @article {17674101, title = {Open source in imaging informatics.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {1-10}, abstract = {The open source community within radiology is a vibrant collection of developers and users working on scores of collaborative projects with the goal of promoting the use of information technology within radiology for education, clinical, and research purposes. This community, which includes many commercial partners, has a rich history in supporting the success of the digital imaging and communication in medicine (DICOM) standard and today is pioneering interoperability limits by embracing the Integrating the Healthcare Enterprise. This article describes only a small portion of the more successful open source applications and is written to help end users see these projects as practical aids for the imaging informaticist and picture archiving and communication system (PACS) administrator.}, url = {http://www.springerlink.com/content/ux777t47g638k402/}, author = {Nagy, Paul} } @article {17846835, title = {Open source software projects of the caBIG In Vivo Imaging Workspace Software special interest group.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {94-100}, abstract = {The Cancer Bioinformatics Grid (caBIG) program was created by the National Cancer Institute to facilitate sharing of IT infrastructure, data, and applications among the National Cancer Institute-sponsored cancer research centers. The program was launched in February 2004 and now links more than 50 cancer centers. In April 2005, the In Vivo Imaging Workspace was added to promote the use of imaging in cancer clinical trials. At the inaugural meeting, four special interest groups (SIGs) were established. The Software SIG was charged with identifying projects that focus on open-source software for image visualization and analysis. To date, two projects have been defined by the Software SIG. The eXtensible Imaging Platform project has produced a rapid application development environment that researchers may use to create targeted workflows customized for specific research projects. The Algorithm Validation Tools project will provide a set of tools and data structures that will be used to capture measurement information and associated needed to allow a gold standard to be defined for the given database against which change analysis algorithms can be tested. Through these and future efforts, the caBIG In Vivo Imaging Workspace Software SIG endeavors to advance imaging informatics and provide new open-source software tools to advance cancer research.}, author = {Prior, Fred W and Erickson, Bradley J and Tarbox, Lawrence} } @article {18074196, title = {Open-source, low-cost, high-reliability solutions for digital imaging systems: example of a "dicom router".}, journal = {La Radiologia medica}, volume = {112}, year = {2007}, month = {2007 Dec}, pages = {1252-9}, abstract = {PURPOSE: The purpose of this article is to illustrate a case where acquisition of digital imaging know-how by a modern radiotherapy division has helped to solve a technical problem while allowing substantial savings through the use of free and open-source resources. The problem was related to the necessity to route, with complex policies, the images produced by different digital imaging and communications in medicine (DICOM) sources within the department or in other divisions and/or hospitals. MATERIALS AND METHODS: The problem was solved by using completely free, well-tested and stable technologies (PHP, Apache, MySQL, DCMTK OFFIS, Red Hat Linux 9A and Linux Fedora Core 4) and low-cost hardware to contain costs. In the development, we also considered integration of the routed images with the existing electronic clinical records. RESULTS: The system developed, called the dicom router, implemented two kinds of routing: manual and automatic, both oriented to link the images acquired with the existing electronic clinical records. System stability was enhanced in a second phase by using a low-cost hardware redundancy solution. The system has now been operating for 1 year and has proved the value of the technologies used. CONCLUSIONS: The need to operate with more than one provider creates a series of integration issues, so that it becomes economically appealing to acquire internally the knowledge needed to interact more precisely with providers of big information technology (IT) solutions. This need is well catered for by open-source technologies, which are well documented and available to everyone. By using them, in-house IT technicians are able to implement valuable technical solutions for small-to medium-sized informatization problems, which would otherwise remain unsolved except with great economic efforts.}, author = {Gatta, R and Abeni, F and Buglione, M and Peveri, A and Barbera, F and Tonoli, S and Fratta, P and Magrini, S M} } @article {17249408, title = {OpenSourcePACS: an extensible infrastructure for medical image management.}, journal = {IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society}, volume = {11}, year = {2007}, month = {2007 Jan}, pages = {94-109}, abstract = {The development of comprehensive picture archive and communication systems (PACS) has mainly been limited to proprietary developments by vendors, though a number of freely available software projects have addressed specific image management tasks. The openSourcePACS project aims to provide an open source, common foundation upon which not only can a basic PACS be readily implemented, but to also support the evolution of new PACS functionality through the development of novel imaging applications and services. openSourcePACS consists of four main software modules: 1) image order entry, which enables the ordering and tracking of structured image requisitions; 2) an agent-based image server framework that coordinates distributed image services including routing, image processing, and querying beyond the present digital image and communications in medicine (DICOM) capabilities; 3) an image viewer, supporting standard display and image manipulation tools, DICOM presentation states, and structured reporting; and 4) reporting and result dissemination, supplying web-based widgets for creating integrated reports. All components are implemented using Java to encourage cross-platform deployment. To demonstrate the usage of openSourcePACS, a preliminary application supporting primary care/specialist communication was developed and is described herein. Ultimately, the goal of openSourcePACS is to promote the wide-scale development and usage of PACS and imaging applications within academic and research communities.}, url = {http://escholarship.org/uc/item/186368fv}, author = {Bui, Alex A T and Morioka, Craig and Dionisio, John David N and Johnson, David B and Sinha, Usha and Ardekani, Siamak and Taira, Ricky K and Aberle, Denise R and El-Saden, Suzie and Kangarloo, Hooshang} } @article {17254636, title = {PsychoPy--Psychophysics software in Python.}, journal = {Journal of neuroscience methods}, volume = {162}, year = {2007}, month = {2007 May 15}, pages = {8-13}, abstract = {The vast majority of studies into visual processing are conducted using computer display technology. The current paper describes a new free suite of software tools designed to make this task easier, using the latest advances in hardware and software. PsychoPy is a platform-independent experimental control system written in the Python interpreted language using entirely free libraries. PsychoPy scripts are designed to be extremely easy to read and write, while retaining complete power for the user to customize the stimuli and environment. Tools are provided within the package to allow everything from stimulus presentation and response collection (from a wide range of devices) to simple data analysis such as psychometric function fitting. Most importantly, PsychoPy is highly extensible and the whole system can evolve via user contributions. If a user wants to add support for a particular stimulus, analysis or hardware device they can look at the code for existing examples, modify them and submit the modifications back into the package so that the whole community benefits.}, author = {Peirce, Jonathan W} } @article {18183912, title = {PyEPL: a cross-platform experiment-programming library.}, journal = {Behavior research methods}, volume = {39}, year = {2007}, month = {2007 Nov}, pages = {950-8}, abstract = {PyEPL (the Python Experiment-Programming Library) is a Python library which allows cross-platform and object-oriented coding of behavioral experiments. It provides functions for displaying text and images onscreen, as well as playing and recording sound, and is capable of rendering 3-D virtual environments forspatial-navigation tasks. It is currently tested for Mac OS X and Linux. It interfaces with Activewire USB cards (on Mac OS X) and the parallel port (on Linux) for synchronization of experimental events with physiological recordings. In this article, we first present two sample programs which illustrate core PyEPL features. The examples demonstrate visual stimulus presentation, keyboard input, and simulation and exploration of a simple 3-D environment. We then describe the components and strategies used in implementing PyEPL.}, author = {Geller, Aaron S and Schlefer, Ian K and Sederberg, Per B and Jacobs, Joshua and Kahana, Michael J} } @article {1040, title = {The RAFT network: 5 years of distance continuing medical education and tele-consultations over the Internet in French-speaking Africa.}, journal = {Int J Med Inform}, volume = {76}, year = {2007}, month = {2007 May-Jun}, pages = {351-6}, abstract = {

Continuing education of healthcare professionals is a key element for the quality and efficiency of a health system. In developing countries, this activity is usually limited to capitals, and delocalized professionals do not have access to such opportunities, or to didactic material adapted to their needs. This limits the interest of such professionals to remain active in the periphery, where they are most needed to implement effective strategies for prevention and first-line healthcare. Telemedicine tools enable the communication and sharing of medical information in electronic form, and thus facilitate access to remote expertise. A physician located far from a reference center can consult its colleagues remotely in order to resolve a difficult case, follow a continuous education course over the Internet, or access medical information from digital libraries or knowledge bases. These same tools can also be used to facilitate exchanges between centers of medical expertise: health institutions of a same country as well as across borders. Since 2000, the Geneva University Hospitals have been involved in coordinating the development of a network for eHealth in Africa (the RAFT, R{\'e}seau en Afrique Francophone pour la T{\'e}l{\'e}m{\'e}decine), first in Mali, and now extending to 10 French-speaking African countries. The core activity of the RAFT is the webcasting of interactive courses. These sessions put the emphasis on knowledge sharing across care professionals, usually in the form of presentations and dialogs between experts in different countries. The technology used for the webcasting works with a slow (25 kbits/s) internet connection. Other activities of the RAFT network include visioconferences, teleconsultations based on the iPath system, collaborative knowledge bases development, support for medical laboratories quality control, and the evaluation of the use of telemedicine in rural areas (via satellite connections) in the context of multisectorial development. Finally, a strong emphasis is put on the development of capacities for the creation, maintenance, and publication of quality medical didactic contents. Specific courses are organized for the national coordinators of the network to develop these competencies, with the help of the Health-On-the-Net Foundation. The richness of the plurality of knowledge and know-how must be steered towards emulation and sharing, respectful of each partner{\textquoteright}s identity and culture. Collaborations with UNESCO and WHO have been initiated to address these challenges.

}, keywords = {Africa, Computer Simulation, Computer-Assisted Instruction, Curriculum, Education, Distance, Education, Medical, Continuing, Educational Technology, Humans, Internationality, Language, Referral and Consultation, Remote Consultation}, issn = {1386-5056}, doi = {10.1016/j.ijmedinf.2007.01.012}, author = {Geissbuhler, Antoine and Bagayoko, Cheick Oumar and Ly, Ousmane} } @article {17700904, title = {Reflections on the role of open source in health information system interoperability.}, journal = {Yearbook of medical informatics}, year = {2007}, month = {2007}, pages = {50-60}, abstract = {OBJECTIVES: This paper reflects on the role of open source in health information system interoperability. Open source is a driving force in computer science research and the development of information systems. It facilitates the sharing of information and ideas, enables evolutionary development and open collaborative testing of code, and broadens the adoption of interoperability standards. In health care, information systems have been developed largely ad hoc following proprietary specifications and customized design. However, the wide deployment of integrated services such as Electronic Health Records (EHRs) over regional health information networks (RHINs) relies on interoperability of the underlying information systems and medical devices. METHODS: This reflection is built on the experiences of the PICNIC project that developed shared software infrastructure components in open source for RHINs and the OpenECG network that offers open source components to lower the implementation cost of interoperability standards such as SCP-ECG, in electrocardiography. RESULTS: Open source components implementing standards and a community providing feedback from real-world use are key enablers of health care information system interoperability. CONCLUSIONS: Investing in open source is investing in interoperability and a vital aspect of a long term strategy towards comprehensive health services and clinical research.}, author = {Sfakianakis, S and Chronaki, C E and Chiarugi, F and Conforti, F and Katehakis, D G} } @article {17375973, title = {RT_Image: an open-source tool for investigating PET in radiation oncology.}, journal = {Technology in cancer research \& treatment}, volume = {6}, year = {2007}, month = {2007 Apr}, pages = {111-21}, abstract = {Positron emission tomography (PET) has emerged as a valuable imaging modality for the diagnosis and staging of cancer. However, despite evidence that PET may be useful for defining target volumes for radiation therapy, no standardized methodology for accomplishing this task exists. To facilitate the investigation of the utility of PET imaging in radiotherapy treatment planning and accelerate its integration into clinical radiation oncology, we have developed software for exploratory analysis and segmentation of functional imaging datasets. The application, RT_Image, allows display of multiple imaging datasets and associated three-dimensional regions-of-interest (ROIs) at arbitrary view angles and fields of view. It also includes semi-automated image segmentation tools for defining metabolically active tumor volumes that may aid creation of target volumes for treatment planning. RT_Image is DICOM compliant, permitting the transfer of imaging data and DICOM-RT structure sets between the application and treatment planning software. RT_Image has been used by radiation oncologists, nuclear medicine physicians, and radiation physicists to analyze over 200 PET datasets. Novel segmentation techniques have been implemented within this programming framework for therapy planning and for evaluation of molecular imaging-derived parameters as prognostic indicators. RT_Image represents a freely-available software base on which further investigations of the utlity of PET and molecular imaging in radiation oncology may be built. The development of tools such as this is critical in order to realize the potential of molecular imaging-guided radiation therapy.}, author = {Graves, Edward E and Quon, Andrew and Loo, Billy W} } @conference {SOFA07, title = {SOFA - an Open Source Framework for Medical Simulation}, booktitle = {Medicine Meets Virtual Reality (MMVR{\textquoteright}15)}, year = {2007}, month = {February}, address = {Long Beach, USA}, url = {http://www.sofa-framework.org/docs/SOFA_MMVR07.pdf}, author = {Allard, J{\'e}r{\'e}mie and Cotin, St{\'e}phane and Faure, Fran{\c c}ois and Bensoussan, Pierre-Jean and Poyer, Fran{\c c}ois and Duriez, Christian and Delingette, Herv{\'e} and Grisoni, Laurent} } @article {17238397, title = {Cooking up an open source EMR for developing countries: OpenMRS - a recipe for successful collaboration.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2006}, month = {2006}, pages = {529-33}, abstract = {Millions of people are continue to die each year from HIV/AIDS. The majority of infected persons (>95\%) live in the developing world. A worthy response to this pandemic will require coordinated, scalable, and flexible information systems. We describe the OpenMRS system, an open source, collaborative effort that can serve as a foundation for EMR development in developing countries. We report our progress to date, lessons learned, and future directions.}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1839638}, author = {Mamlin, Burke W and Biondich, Paul G and Wolfe, Ben A and Fraser, Hamish and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Tierney, William M} } @article {17018156, title = {Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow.}, journal = {BMC bioinformatics}, volume = {7}, year = {2006}, month = {2006}, pages = {430}, abstract = {BACKGROUND: In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. RESULTS: We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. CONCLUSION: Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved.}, author = {Morisawa, Hiraku and Hirota, Mikako and Toda, Tosifusa} } @article {566, title = {O3-DPACS Open-Source Image-Data Manager/Archiver and HDW2 Image-Data Display: an IHE-compliant project pushing the e-health integration in the world.}, journal = {Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society}, volume = {30}, year = {2006}, month = {2006 Sep-Oct}, pages = {391-406}, abstract = {After many years of study, development and experimentation of open PACS and Image workstation solutions including management of medical data and signals (DPACS project), the research and development at the University of Trieste have recently been directed towards Java-based, IHE compliant and multi-purpose servers and clients. In this paper an original Image-Data Manager/Archiver (O3-DPACS) and a universal Image-Data Display (HDW2) are described. O3-DPACS is also part of a new project called Open Three (O3) Consortium, promoting Open Source adoption in e-health at European and world-wide levels. This project aims to give a contribution to the development of e-health through the study of Healthcare Information Systems and the contemporary proposal of new concepts, designs and solutions for the management of health data in an integrated environment: hospitals, Regional Health Information Organizations and citizens (home-care, mobile-care and ambient assisted living).}, keywords = {Data Display, Database Management Systems, Diagnostic Imaging, Equipment Design, Equipment Failure Analysis, Guidelines as Topic, Information Storage and Retrieval, Internationality, Medical Records Systems, Computerized, Programming Languages, Radiology Information Systems, Systems Integration, User-Computer Interface}, issn = {0895-6111}, author = {Inchingolo, Paolo and Beltrame, Marco and Bosazzi, Pierpaolo and Cicuta, Davide and Faustini, Giorgio and Mininel, Stefano and Poli, Andrea and Vatta, Federica} } @article {17238765, title = {The OpenMRS system: collaborating toward an open source EMR for developing countries.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2006}, month = {2006}, pages = {1146}, abstract = {OpenMRS is an open source infrastructure for the creation of medical record systems in developing countries. Produced and maintained collaboratively across multiple institutions, this framework consists of an open source data model, a set of core application functions, and a default implementation. The goal of this implementation is to provide the beginnings of an EMR that is suitable for all groups involved with healthcare in developing countries.}, author = {Wolfe, Benjamin A and Mamlin, Burke W and Biondich, Paul G and Fraser, Hamish S F and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Tierney, William M} } @conference {782, title = {Remote Large Data Visualization in the ParaView Framework.}, booktitle = {EGPGV}, year = {2006}, publisher = {Eurographics Association}, organization = {Eurographics Association}, keywords = {dblp}, isbn = {3-905673-40-1}, url = {http://dblp.uni-trier.de/db/conf/egpgv/egpgv2006.html$\#$CedilnikGMAF06}, author = {Cedilnik, Andy and Geveci, Berk and Moreland, Kenneth and Ahrens, James P. and Favre, Jean M.}, editor = {Heirich, Alan and Raffin, Bruno and dos Santos, Lu{\'\i}s Paulo Peixoto} } @article {1041, title = {Static telepathology in cancer institute of Tehran university: report of the first academic experience in Iran.}, journal = {Diagn Pathol}, volume = {1}, year = {2006}, month = {2006}, pages = {33}, abstract = {

Telepathology is the practice of pathology, which allows quick and timely access to an expert opinion at a distance. We analyzed our new experience in cancer Institute of Tehran University of Medical Sciences with the iPath telepathology server of Basel University. One hundred sixty one cases in a period of 32 months were consulted. These cases received for second evaluation but the definite diagnosis could not be made in this centre. The number of images per case ranged from 3 to 32 (mean: 8). Except one case all cases were evaluated by consultants. Definite final diagnosis was achieved in 88/160 (54.7\%). Recommendations for further evaluation were offered in 42/160 cases (26\%). Major discrepancies were encountered in 30/160 cases (19\%). Thirty-nine of the cases (24.3\%) were reported within 1 day. The rate of achieving final diagnosis was higher in histological group rather than cytological ones. Increase in number of H\&E images had no significant effect on achieving a definite final diagnosis. The rate of achieving final diagnosis in this study is much lower than other similar studies, which could be due to inappropriate sampling images, a potential cause of misdiagnosis in static telepathology. The other possible reason is that all of the cases in this study were problematic cases that a definite diagnosis could not be made for them even in primary consultation. The mean time for achieving a final diagnosis was also more than other studies, which could be for the reasons mentioned above.

}, issn = {1746-1596}, doi = {10.1186/1746-1596-1-33}, author = {Abdirad, Afshin and Sarrafpour, Babak and Ghaderi-Sohi, Siavash} } @article {16545965, title = {User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability.}, journal = {NeuroImage}, volume = {31}, year = {2006}, month = {2006 Jul 1}, pages = {1116-28}, abstract = {Active contour segmentation and its robust implementation using level set methods are well-established theoretical approaches that have been studied thoroughly in the image analysis literature. Despite the existence of these powerful segmentation methods, the needs of clinical research continue to be fulfilled, to a large extent, using slice-by-slice manual tracing. To bridge the gap between methodological advances and clinical routine, we developed an open source application called ITK-SNAP, which is intended to make level set segmentation easily accessible to a wide range of users, including those with little or no mathematical expertise. This paper describes the methods and software engineering philosophy behind this new tool and provides the results of validation experiments performed in the context of an ongoing child autism neuroimaging study. The validation establishes SNAP intrarater and interrater reliability and overlap error statistics for the caudate nucleus and finds that SNAP is a highly reliable and efficient alternative to manual tracing. Analogous results for lateral ventricle segmentation are provided.}, author = {Yushkevich, Paul A and Piven, Joseph and Hazlett, Heather Cody and Smith, Rachel Gimpel and Ho, Sean and Gee, James C and Gerig, Guido} } @article {10.1109/HICSS.2005.166, title = {Contrasting Community Building in Sponsored and Community Founded Open Source Projects}, journal = {Hawaii International Conference on System Sciences}, volume = {7}, year = {2005}, pages = {196c}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, issn = {1530-1605}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2005.166}, author = {Joel West and Siobh{\'a}n O{\textquoteright}Mahony} } @article {15924271, title = {Establishing a Web-based DICOM teaching file authoring tool using open-source public software.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {18}, year = {2005}, month = {2005 Sep}, pages = {169-75}, abstract = {Online teaching files are an important source of educational and referential materials in the radiology community. The commonly used Digital Imaging and Communications in Medicine (DICOM) file format of the radiology community is not natively supported by common Web browsers. The ability of the Web server to convert and parse DICOM is important when the DICOM-converting tools are not available. In this paper, we describe our approach to develop a Web-based teaching file authoring tool. Our server is built using Apache Web server running on FreeBSD operating system. The dynamic page content is produced by Hypertext Preprocessor (PHP). Digital Imaging and Communications in Medicine images are converted by ImageMagick into Joint Photographic Experts Group (JPEG) format. Digital Imaging and Communications in Medicine attributes are parsed by dicom3tools and stored in PostgreSQL database. Using free software available from the Internet, we build a Web service that allows radiologists to create their own online teaching file cases with a common Web browser.}, author = {Lee, Wen-Jeng and Yang, Chung-Yi and Liu, Kao-Lang and Liu, Hon-Man and Ching, Yu-Tai and Chen, Shyh-Jye} } @article {16284146, title = {Informatics in radiology (infoRAD): an open source framework for modification and communication of DICOM objects.}, journal = {Radiographics : a review publication of the Radiological Society of North America, Inc}, volume = {25}, year = {2005}, month = {2005 Nov-Dec}, pages = {1709-21}, abstract = {A configurable framework has been developed that can receive, modify, and export images in different picture archiving and communication system scenarios. The framework has three main components: a receiver for Digital Imaging and Communications in Medicine (DICOM) objects, a processing pipeline to apply one or more modifications to these objects, and one or more senders to send the processed objects to predefined addresses. The toolbox programming was implemented as an open source project in Java. The processing pipeline uses the concept of configurable plug-ins. One plug-in is user programmable by means of extensible stylesheet language files and allows conversion of DICOM objects to extensible markup language documents or other file types. Input and output channels are the DICOM Storage service, DICOM compact disks-read-only memory (CD-ROMs), and the local file system. The toolbox has been successfully applied to different clinical scenarios, including the correction of DICOM objects from non-Integrating the Healthcare Enterprise (IHE) conform modalities, pseudonaming of DICOM images, and use of the IHE Portable Data for Imaging profile with import and export of CD-ROMs. The toolbox has proved reliability in the clinical routine. Because of the open programming interfaces, the functionality can easily be adapted to future applications.}, author = {Hackl{\"a}nder, Thomas and Martin, Jens and Kleber, Klaus} } @article {16257947, title = {Information technology as a tool to improve the quality of American Indian health care.}, journal = {American journal of public health}, volume = {95}, year = {2005}, month = {2005 Dec}, pages = {2173-9}, abstract = {The American Indian/Alaska Native population experiences a disproportionate burden of disease across a spectrum of conditions. While the recent National Healthcare Disparities Report highlighted differences in quality of care among racial and ethnic groups, there was only very limited information available for American Indians. The Indian Health Service (IHS) is currently enhancing its information systems to improve the measurement of health care quality as well as to support quality improvement initiatives. We summarize current knowledge regarding health care quality for American Indians, highlighting the variation in reported measures in the existing literature. We then discuss how the IHS is using information systems to produce standardized performance measures and present future directions for improving American Indian health care quality.}, author = {Sequist, Thomas D and Cullen, Theresa and Ayanian, John Z} } @article {15923755, title = {iPath - a Telemedicine Platform to Support Health Providers in Low Resource Settings.}, journal = {Studies in health technology and informatics}, volume = {114}, year = {2005}, month = {2005}, pages = {11-7}, abstract = {In many developing countries there is an acute shortage of medical specialists. The specialists and services that are available are usually concentrated in cities and health workers in rural health care, who serve most of the population, are isolated from specialist support [1]. Besides, the few remaining specialist are often isolated from colleagues. With the recent development in information and communication technologies, new option for telemedicine and generally for sharing knowledge at a distance are becoming increasingly accessible to health workers also in developing countries. Since 2001 the Department of Pathology in Basel, Switzerland is operating an Internet based telemedicine platform to assist health workers in developing countries. Over 1800 consultation have been performed since. This paper will give an introduction to iPath - the telemedicine platform developed for this project - and analyse two case studies: a teledermatology project from South Africa and a telepathology project from Solomon Islands.}, author = {Brauchli, K and O{\textquoteright}mahony, D and Banach, L and Oberholzer, M} } @article {16375782, title = {The iPath telemedicine platform.}, journal = {Journal of telemedicine and telecare}, volume = {11 Suppl 2}, year = {2005}, month = {2005}, pages = {S3-7}, abstract = {An early, point-to-point telepathology system at the University of Basel developed into an open-source, Internet-based platform for telemedicine in 2001. The Internet Pathology Suite (iPath) is a Web-based telepathology platform that permits the online presentation and discussion of cases within user groups. It also allows realtime telemicroscopy across firewalls. After four years, the telepathology network has over 700 active users. More than 6,300 cases with a total of about 39,000 images have been diagnosed. The diagnostic workload of all these cases is not exclusively handled by the Department of Pathology in Basel, but by a growing number of independent groups who also use the server simply as a case repository. What started as a small project for hospitals in Switzerland has become a global network.}, author = {Brauchli, Kurt and Oberholzer, Martin} } @article {16160381, title = {Linking primary care information systems and public health information networks: lessons from the Philippines.}, journal = {Studies in health technology and informatics}, volume = {116}, year = {2005}, month = {2005}, pages = {955-60}, abstract = {Community-based primary care information systems are one of the building blocks for national health information systems. In the Philippines, after the devolution of health care to local governments, we observed "health information system islands" connected to national vertical programs being implemented in devolved health units. These structures lead to a huge amount of "information work" in the transformation of health information at the community level. This paper describes work done to develop and implement the open-source Community Based Health Information Tracking System (CHITS) Project, which was implemented to address this information management problem and its outcomes. Several lessons learned from the field as well as software development strategies are highlighted in building community level information systems that link to national level health information systems.}, author = {Tolentino, Herman and Marcelo, Alvin and Marcelo, Portia and Maramba, Inocencio} } @article {16779052, title = {Linking primary care information systems and public health vertical programs in the Philippines: an open-source experience.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2005}, month = {2005}, pages = {311-5}, abstract = {Community-based primary care information systems are one of the building blocks for national health information systems. In the Philippines, after the devolution of health care to local governments, we observed "health information system islands" connected to national vertical programs being implemented in devolved health units. These structures lead to a huge amount of "information work" in the transformation of health information at the community level. This paper describes work done to develop and implement the open-source Community Based Health Information Tracking System (CHITS) Project, which was implemented to address this information management problem and its outcomes. Several lessons learned from the field as well as software development strategies are highlighted in building community level information systems that link to national level health information systems.}, author = {Herman, Tolentino and Marcelo, Alvin and Marcelo, Portia and Maramba, Inocencio} } @article {587, title = {The medical imaging interaction toolkit.}, journal = {Medical image analysis}, volume = {9}, year = {2005}, month = {2005 Dec}, pages = {594-604}, abstract = {Thoroughly designed, open-source toolkits emerge to boost progress in medical imaging. The Insight Toolkit (ITK) provides this for the algorithmic scope of medical imaging, especially for segmentation and registration. But medical imaging algorithms have to be clinically applied to be useful, which additionally requires visualization and interaction. The Visualization Toolkit (VTK) has powerful visualization capabilities, but only low-level support for interaction. In this paper, we present the Medical Imaging Interaction Toolkit (MITK). The goal of MITK is to significantly reduce the effort required to construct specifically tailored, interactive applications for medical image analysis. MITK allows an easy combination of algorithms developed by ITK with visualizations created by VTK and extends these two toolkits with those features, which are outside the scope of both. MITK adds support for complex interactions with multiple states as well as undo-capabilities, a very important prerequisite for convenient user interfaces. Furthermore, MITK facilitates the realization of multiple, different views of the same data (as a multiplanar reconstruction and a 3D rendering) and supports the visualization of 3D+t data, whereas VTK is only designed to create one kind of view of 2D or 3D data. MITK reuses virtually everything from ITK and VTK. Thus, it is not at all a competitor to ITK or VTK, but an extension, which eases the combination of both and adds the features required for interactive, convenient to use medical imaging software. MITK is an open-source project (www.mitk.org).}, keywords = {Algorithms, Artificial Intelligence, Computer Graphics, Diagnostic Imaging, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated, Software, User-Computer Interface}, issn = {1361-8415}, author = {Wolf, Ivo and Vetter, Marcus and Wegner, Ingmar and B{\"o}ttger, Thomas and Nolden, Marco and Sch{\"o}binger, Max and Hastenteufel, Mark and Kunert, Tobias and Meinzer, Hans-Peter} } @article {16300164, title = {Open source approaches to health information systems in Kenya.}, journal = {World hospitals and health services : the official journal of the International Hospital Federation}, volume = {41}, year = {2005}, month = {2005}, pages = {36-9}, abstract = {This paper focuses on the experience to date of an installation of a Free Open Source Software (FOSS) product, Care2X, at a church hospital in Kenya. The FOSS movement has been maturing rapidly. In developed countries, its benefits relative to proprietary software have been extensively discussed and ways of quantifying the total costs of the development have been developed. Nevertheless, empirical data on the impact of FOSS, particularly in the developing world, concerning its use and development is still quite limited, although the possibilities of FOSS are becoming increasingly attractive.}, author = {Drury, Peter and Dahlman, Bruce} } @article {781, title = {ParaView : An End-User Tool for Large Data Visualization}, journal = {Energy}, volume = {836}, year = {2005}, pages = {717{\textendash}732}, url = {http://scholar.google.com/scholar?hl=en\&btnG=Search\&q=intitle:ParaView:+An+end-user+tool+for+large+data+visualization$\#$0}, author = {Ahrens, James and Geveci, Berk and Law, Charles}, editor = {Hansen, C R and Johnson, C DEditors} } @article {850, title = {SQL Clinic: the open-source alternative for electronic medical records.}, journal = {Psychiatr Serv}, volume = {56}, year = {2005}, month = {2005 Mar}, pages = {269-71}, keywords = {Humans, Medical Records Systems, Computerized, Psychiatry, Software}, issn = {1075-2730}, doi = {10.1176/appi.ps.56.3.269}, author = {Good, Thomas and DiTommaso, Marianne} } @article {1262, title = {A study of clinically related open source software projects.}, journal = {AMIA Annu Symp Proc}, year = {2005}, month = {2005}, pages = {330-4}, abstract = {

Open source software development has recently gained significant interest due to several successful mainstream open source projects. This methodology has been proposed as being similarly viable and beneficial in the clinical application domain as well. However, the clinical software development venue differs significantly from the mainstream software venue. Existing clinical open source projects have not been well characterized nor formally studied so the {\textquoteright}fit{\textquoteright} of open source in this domain is largely unknown. In order to better understand the open source movement in the clinical application domain, we undertook a study of existing open source clinical projects. In this study we sought to characterize and classify existing clinical open source projects and to determine metrics for their viability. This study revealed several findings which we believe could guide the healthcare community in its quest for successful open source clinical software projects.

}, keywords = {Clinical Medicine, Information Dissemination, Intellectual Property, Software}, issn = {1942-597X}, author = {Hogarth, Michael A and Turner, Stuart} } @article {500, title = {Advances in functional and structural MR image analysis and implementation as FSL.}, journal = {NeuroImage}, volume = {23 Suppl 1}, year = {2004}, month = {2004}, pages = {S208-19}, abstract = {The techniques available for the interrogation and analysis of neuroimaging data have a large influence in determining the flexibility, sensitivity, and scope of neuroimaging experiments. The development of such methodologies has allowed investigators to address scientific questions that could not previously be answered and, as such, has become an important research area in its own right. In this paper, we present a review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB). This research has focussed on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data. The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB{\textquoteright}s Software Library (FSL).}, keywords = {Bayes Theorem, Brain, Databases, Factual, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Models, Neurological, Models, Statistical, Software}, issn = {1053-8119}, author = {Smith, Stephen M and Jenkinson, Mark and Woolrich, Mark W and Beckmann, Christian F and Behrens, Timothy E J and Johansen-Berg, Heidi and Bannister, Peter R and De Luca, Marilena and Drobnjak, Ivana and Flitney, David E and Niazy, Rami K and Saunders, James and Vickers, John and Zhang, Yongyue and De Stefano, Nicola and Brady, J Michael and Matthews, Paul M} } @article {762, title = {A flexible registration framework for multimodal image data.}, journal = {Conf Proc IEEE Eng Med Biol Soc}, volume = {3}, year = {2004}, month = {2004}, pages = {1755-8}, abstract = {This paper describes a registration framework based on the insight segmentation and registration toolkit (ITK) which can be used for matching multimodal image data. Different target groups with individual needs and precognition are addressed. The framework offers tools for supporting different matching tasks in a clinical environment. A setup editor defines specific rigid or non rigid matching approaches and the appropriate parameters. Different metrics including a correlation metric, a difference metric and mutual information based metrics are available. Furthermore, a test series editor can be used to evaluate the selected setup. The evaluation results, which are expressed in statistical figures, trends and performance measures, can be visualized and used for an optimal adapted setup configuration. Tests for matching precision, quality and parameter adjustments are offered. For export and import of image data, the most frequently used file formats of clinical environments like DICOM and ANALYZE are supported. We demonstrate some registration examples which frequently occur in the neurosurgical routine of a University Hospital.}, issn = {1557-170X}, doi = {10.1109/IEMBS.2004.1403526}, author = {Dickhaus, H and Floca, R and Eisenmann, U and Metzner, R and Wirtz, C R} } @article {15361001, title = {The RODS Open Source Project: removing a barrier to syndromic surveillance.}, journal = {Studies in health technology and informatics}, volume = {107}, year = {2004}, month = {2004}, pages = {1192-6}, abstract = {The goal of the Real-time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate deployment of computer-based syndromic surveillance. To this end, the project has released the RODS software under the GNU General Public License and created an organizational structure to catalyze its development. This paper describes the design of the software, requested extensions, and the structure of the development effort.}, author = {Espino, Jeremy U and Wagner, Michael M and Tsui, Fu-Chang and Su, Hoah-Der and Olszewski, Robert T and Lie, Zhen and Chapman, Wendy and Zeng, Xiaoming and Ma, Lili and Lu, Zhong Wei and Dara, Jagan} } @article {18238234, title = {BioSig: an imaging bioinformatics system for phenotypic analysis.}, journal = {IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society}, volume = {33}, year = {2003}, month = {2003}, pages = {814-24}, abstract = {Organisms express their genomes in a cell-specific manner, resulting in a variety of cellular phenotypes or phenomes. Mapping cell phenomes under a variety of experimental conditions is necessary in order to understand the responses of organisms to stimuli. Representing such data requires an integrated view of experimental and informatic protocols. The proposed system, named BioSig, provides the foundation for cataloging cellular responses as a function of specific conditioning, treatment, staining, etc., for either fixed tissue or living cell studies. A data model has been developed to capture experimental variables and map them to image collections and their computed representation. This representation is hierarchical and spans across sample tissues, cells, and organelles, which are imaged with light microscopy. At each layer, content is represented with an attributed graph, which contains information about cellular morphology, protein localization, and cellular organization in tissue or cell culture. The Web-based multilayer informatics architecture uses the data model to provide guided workflow access for content exploration.}, author = {Parvin, B and Yang, Qing and Fontenay, G and Barcellos-Hoff, M H} } @article {12810121, title = {Open Source software in medical informatics--why, how and what.}, journal = {International journal of medical informatics}, volume = {69}, year = {2003}, month = {2003 Mar}, pages = {175-84}, abstract = {{\textquoteright}Open Source{\textquoteright} is a 20-40 year old approach to licensing and distributing software that has recently burst into public view. Against conventional wisdom this approach has been wildly successful in the general software market--probably because the openness lets programmers the world over obtain, critique, use, and build upon the source code without licensing fees. Linux, a UNIX-like operating system, is the best known success. But computer scientists at the University of California, Berkeley began the tradition of software sharing in the mid 1970s with BSD UNIX and distributed the major internet network protocols as source code without a fee. Medical informatics has its own history of Open Source distribution: Massachusetts General{\textquoteright}s COSTAR and the Veterans Administration{\textquoteright}s VISTA software have been distributed as source code at no cost for decades. Bioinformatics, our sister field, has embraced the Open Source movement and developed rich libraries of open-source software. Open Source has now gained a tiny foothold in health care (OSCAR GEHR, OpenEMed). Medical informatics researchers and funding agencies should support and nurture this movement. In a world where open-source modules were integrated into operational health care systems, informatics researchers would have real world niches into which they could engraft and test their software inventions. This could produce a burst of innovation that would help solve the many problems of the health care system. We at the Regenstrief Institute are doing our part by moving all of our development to the open-source model.}, author = {McDonald, Clement J and Schadow, Gunther and Barnes, Michael and Dexter, Paul and Overhage, J Marc and Mamlin, Burke and McCoy, J Michael} } @article {12925540, title = {Open-source software and the primary care EMR.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {10}, year = {2003}, month = {2003 Nov-Dec}, pages = {616; author reply 617}, author = {Kantor, Gareth S and Wilson, Wayne D and Midgley, Adrian} } @article {494, title = {PropeR: a multi disciplinary EPR system.}, journal = {International journal of medical informatics}, volume = {70}, year = {2003}, month = {2003 Jul}, pages = {149-60}, abstract = {This article describes the architecture of an EPR system developed for the PropeR project. This EPR system not only aims at supporting home care of stroke patients, but is also designed in such a way that it can be ported to other medical services without much effort. We will briefly describe the Stroke Service and the related PropeR project. Starting from a list of requirements to construct a generic EPR system we will outline the architecture and describe the standards and methods used. Subsequently we describe the implementation and the problems encountered. In the discussion, we will go into the advantages and disadvantages of the tools and techniques we have used.}, keywords = {Computer Systems, Delivery of Health Care, Integrated, Humans, Interprofessional Relations, Medical Records Systems, Computerized, Stroke}, issn = {1386-5056}, author = {van der Linden, Helma and Boers, Gerrit and Tange, Huibert and Talmon, Jan and Hasman, Arie} } @article {12807803, title = {Technical description of RODS: a real-time public health surveillance system.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {10}, year = {2003}, month = {2003 Sep-Oct}, pages = {399-408}, abstract = {This report describes the design and implementation of the Real-time Outbreak and Disease Surveillance (RODS) system, a computer-based public health surveillance system for early detection of disease outbreaks. Hospitals send RODS data from clinical encounters over virtual private networks and leased lines using the Health Level 7 (HL7) message protocol. The data are sent in real time. RODS automatically classifies the registration chief complaint from the visit into one of seven syndrome categories using Bayesian classifiers. It stores the data in a relational database, aggregates the data for analysis using data warehousing techniques, applies univariate and multivariate statistical detection algorithms to the data, and alerts users of when the algorithms identify anomalous patterns in the syndrome counts. RODS also has a Web-based user interface that supports temporal and spatial analyses. RODS processes sales of over-the-counter health care products in a similar manner but receives such data in batch mode on a daily basis. RODS was used during the 2002 Winter Olympics and currently operates in two states-Pennsylvania and Utah. It has been and continues to be a resource for implementing, evaluating, and applying new methods of public health surveillance.}, author = {Tsui, Fu-Chiang and Espino, Jeremy U and Dato, Virginia M and Gesteland, Per H and Hutman, Judith and Wagner, Michael M} } @article {11522765, title = {An integrated software suite for surface-based analyses of cerebral cortex.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {8}, year = {2001}, month = {2001 Sep-Oct}, pages = {443-59}, abstract = {The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.}, author = {Van Essen, D C and Drury, H A and Dickson, J and Harwell, J and Hanlon, D and Anderson, C H} } @article {11679206, title = {LIPSIA - a new software system for the evaluation of functional magnetic resonance images of the human brain.}, journal = {Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society}, volume = {25}, year = {2001}, month = {2001 Nov-Dec}, pages = {449-57}, abstract = {This paper describes the non-commercial software system LIPSIA that was developed for the processing of functional magnetic resonance images (fMRI) of the human brain. The analysis of fMRI data comprises various aspects including filtering, spatial transformation, statistical evaluation as well as segmentation and visualization. In LIPSIA, particular emphasis was placed on the development of new visualization and segmentation techniques that support visualizations of individual brain anatomy so that experts can assess the exact location of activation patterns in individual brains. As the amount of data that must be handled is enormous, another important aspect in the development LIPSIA was the efficiency of the software implementation. Well established statistical techniques were used whenever possible.}, author = {Lohmann, G and M{\"u}ller, K and Bosch, V and Mentzel, H and Hessler, S and Chen, L and Zysset, S and von Cramon, D Y} }