@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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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} } @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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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 {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} } @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 {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 {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 {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 {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 {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} } @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 {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 {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 {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 {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} } @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 {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 {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 {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 {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 {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 {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} } @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} } @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 {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} } @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 {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 {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} } @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 {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 {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 {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 {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} } @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 {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.} } @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 {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 {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 {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 {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 {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 {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 {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 {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} } @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} } @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} } @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 {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} } @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 {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 {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 {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 {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 {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 {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} } @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 {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 {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 {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 {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 {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 {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} }