@article {1304, title = {iBEX: Modular Open-Source Software for Digital Radiography.}, journal = {J Digit Imaging}, volume = {33}, year = {2020}, month = {2020 06}, pages = {708-721}, abstract = {

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

}, keywords = {Humans, Image Processing, Computer-Assisted, Radiographic Image Enhancement, Radiology Information Systems, Software, Tomography, X-Ray Computed}, issn = {1618-727X}, doi = {10.1007/s10278-019-00304-1}, author = {Brusan, Altay and Durmaz, F Ayta{\c c} and Yaman, Alper and {\"O}zt{\"u}rk, Cengizhan} } @article {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 {1266, title = {From paper maps to digital maps: enhancing routine immunisation microplanning in Northern Nigeria.}, journal = {BMJ Glob Health}, volume = {4}, year = {2019}, month = {2019}, pages = {e001606}, abstract = {

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

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2019-001606}, author = {Dougherty, Leanne and Abdulkarim, Masduq and Mikailu, Fiyidi and Tijani, Usman and Owolabi, Kazeem and Gilroy, Kate and Naiya, Ahmed and Abdullahi, Adamu and Bodinga, Hadiza and Olayinka, Folake and Moise, Imelda} } @article {1228, title = {PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title.}, journal = {Bioinformatics}, year = {2019}, month = {2019 Jun 19}, abstract = {

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

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

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

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btz409}, author = {Glicksberg, Benjamin S and Oskotsky, Boris and Thangaraj, Phyllis M and Giangreco, Nicholas and Badgeley, Marcus A and Johnson, Kipp W and Datta, Debajyoti and Rudrapatna, Vivek and Rappoport, Nadav and Shervey, Mark M and Miotto, Riccardo and Goldstein, Theodore C and Rutenberg, Eugenia and Frazier, Remi and Lee, Nelson and Israni, Sharat and Larsen, Rick and Percha, Bethany and Li, Li and Dudley, Joel T and Tatonetti, Nicholas P and Butte, Atul J} } @article {1272, title = {Data for decision making: using a dashboard to strengthen routine immunisation in Nigeria.}, journal = {BMJ Glob Health}, volume = {3}, year = {2018}, month = {2018}, pages = {e000807}, abstract = {

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

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2018-000807}, author = {Etamesor, Sulaiman and Ottih, Chibuzo and Salihu, Ismail Ndalami and Okpani, Arnold Ikedichi} } @article {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 {1277, title = {Barriers and facilitators to Electronic Medical Records usage in the Emergency Centre at Komfo Anokye Teaching Hospital, Kumasi-Ghana.}, journal = {Afr J Emerg Med}, volume = {7}, year = {2017}, month = {2017 Dec}, pages = {177-182}, abstract = {

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

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

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

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

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

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

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

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

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

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

}, keywords = {Health Facilities, Health information systems, Humans, Kenya, Malaria, Mandatory Reporting, Public Health Surveillance}, issn = {1654-9880}, doi = {10.1080/16549716.2017.1413266}, author = {Maina, Joseph K and Macharia, Peter M and Ouma, Paul O and Snow, Robert W and Okiro, Emelda A} } @article {1236, title = {Development and Deployment of the OpenMRS-Ebola Electronic Health Record System for an Ebola Treatment Center in Sierra Leone.}, journal = {J Med Internet Res}, volume = {19}, year = {2017}, month = {2017 08 21}, pages = {e294}, abstract = {

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

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

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

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

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

}, keywords = {electronic health records, Epidemics, Hemorrhagic Fever, Ebola, Humans, Infection Control, Sierra Leone, Telemedicine}, issn = {1438-8871}, doi = {10.2196/jmir.7881}, author = {Oza, Shefali and Jazayeri, Darius and Teich, Jonathan M and Ball, Ellen and Nankubuge, Patricia Alexandra and Rwebembera, Job and Wing, Kevin and Sesay, Alieu Amara and Kanter, Andrew S and Ramos, Glauber D and Walton, David and Cummings, Rachael and Checchi, Francesco and Fraser, Hamish S} } @article {1174, title = {A national standards-based assessment on functionality of electronic medical records systems used in {Kenyan} public-{Sector} health facilities}, journal = {International Journal of Medical Informatics}, volume = {97}, year = {2017}, pages = {68{\textendash}75}, abstract = {BACKGROUND: Variations in the functionality, content and form of electronic medical record systems (EMRs) challenge national roll-out of these systems as part of a national strategy to monitor HIV response. To enforce the EMRs minimum requirements for delivery of quality HIV services, the Kenya Ministry of Health (MoH) developed EMRs standards and guidelines. The standards guided the recommendation of EMRs that met a preset threshold for national roll-out. METHODS: Using a standards-based checklist, six review teams formed by the MoH EMRs Technical Working Group rated a total of 17 unique EMRs in 28 heath facilities selected by individual owners for their optimal EMR implementation. EMRs with an aggregate score of >=60\% against checklist criteria were identified by the MoH as suitable for upgrading and rollout to Kenyan public health facilities. RESULTS: In Kenya, existing EMRs scored highly in health information and reporting (mean score=71.8\%), followed by security, system features, core clinical information, and order entry criteria (mean score=58.1\%-55.9\%), and lowest against clinical decision support (mean score=17.6\%) and interoperability criteria (mean score=14.3\%). Four EMRs met the 60.0\% threshold: OpenMRS, IQ-Care, C-PAD and Funsoft. On the basis of the review, the MoH provided EMRs upgrade plans to owners of all the 17 systems reviewed. CONCLUSION: The standards-based review in Kenya represents an effort to determine level of conformance to the EMRs standards and prioritize EMRs for enhancement and rollout. The results support concentrated use of resources towards development of the four recommended EMRs. Further review should be conducted to determine the effect of the EMR-specific upgrade plans on the other 13 EMRs that participated in the review exercise.}, keywords = {Checklist, EMRs, Review, Standards}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2016.09.013}, author = {Kang{\textquoteright}a, Samuel and Puttkammer, Nancy and Wanyee, Steven and Kimanga, Davies and Madrano, Jason and Muthee, Veronica and Odawo, Patrick and Sharma, Anjali and Oluoch, Tom and Robinson, Katherine and Kwach, James and Lober, William B.} } @article {1205, title = {Open-{Source} {Electronic} {Health} {Record} {Systems} for {Low}-{Resource} {Settings}: {Systematic} {Review}}, journal = {JMIR Medical Informatics}, volume = {5}, year = {2017}, abstract = {Background Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. Objective The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. Methods First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. Results The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code-based language, (17) development activity, (18) modularity, (19) user interface, (20) community support, and (21) customization. The quality of each feature is discussed for each of the evaluated solutions and a final comparison is presented. Conclusions There is a clear demand for open-source, reliable, and flexible EHR systems in low-resource settings. In this study, we have evaluated and compared five open-source EHR systems following a multidimensional methodology that can provide informed recommendations to other implementers, developers, and health care professionals. We hope that the results of this comparison can guide decision making when needing to adopt, install, and maintain an open-source EHR solution in low-resource settings.}, issn = {2291-9694}, doi = {10.2196/medinform.8131}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703976/}, author = {Syzdykova, Assel and Malta, Andr{\'e} and Zolfo, Maria and Diro, Ermias and Oliveira, Jos{\'e} Lu{\'\i}s} } @article {1202, title = {Open-source mobile digital platform for clinical trial data collection in low-resource settings}, journal = {BMJ innovations}, volume = {3}, year = {2017}, pages = {26{\textendash}31}, abstract = {BACKGROUND: Governments, universities and pan-African research networks are building durable infrastructure and capabilities for biomedical research in Africa. This offers the opportunity to adopt from the outset innovative approaches and technologies that would be challenging to retrofit into fully established research infrastructures such as those regularly found in high-income countries. In this context we piloted the use of a novel mobile digital health platform, designed specifically for low-resource environments, to support high-quality data collection in a clinical research study. OBJECTIVE: Our primary aim was to assess the feasibility of a using a mobile digital platform for clinical trial data collection in a low-resource setting. Secondarily, we sought to explore the potential benefits of such an approach. METHODS: The investigative site was a research institute in Nairobi, Kenya. We integrated an open-source platform for mobile data collection commonly used in the developing world with an open-source, standard platform for electronic data capture in clinical trials. The integration was developed using common data standards (Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model), maximising the potential to extend the approach to other platforms. The system was deployed in a pharmacokinetic study involving healthy human volunteers. RESULTS: The electronic data collection platform successfully supported conduct of the study. Multidisciplinary users reported high levels of satisfaction with the mobile application and highlighted substantial advantages when compared with traditional paper record systems. The new system also demonstrated a potential for expediting data quality review. DISCUSSION AND CONCLUSIONS: This pilot study demonstrated the feasibility of using a mobile digital platform for clinical research data collection in low-resource settings. Sustainable scientific capabilities and infrastructure are essential to attract and support clinical research studies. Since many research structures in Africa are being developed anew, stakeholders should consider implementing innovative technologies and approaches.}, keywords = {clinical research, eSource, Global Health, mHealth, Reverse Innovations}, issn = {2055-642X}, doi = {10.1136/bmjinnov-2016-000164}, author = {van Dam, Joris and Omondi Onyango, Kevin and Midamba, Brian and Groosman, Nele and Hooper, Norman and Spector, Jonathan and Pillai, Goonaseelan Colin and Ogutu, Bernhards} } @article {1189, title = {Orchestrating differential data access for translational research: a pilot implementation}, journal = {BMC Medical Informatics and Decision Making}, volume = {17}, year = {2017}, month = {2017}, pages = {30}, abstract = {BACKGROUND: Translational researchers need robust IT solutions to access a range of data types, varying from public data sets to pseudonymised patient information with restricted access, provided on a case by case basis. The reason for this complication is that managing access policies to sensitive human data must consider issues of data confidentiality, identifiability, extent of consent, and data usage agreements. All these ethical, social and legal aspects must be incorporated into a differential management of restricted access to sensitive data. METHODS: In this paper we present a pilot system that uses several common open source software components in a novel combination to coordinate access to heterogeneous biomedical data repositories containing open data (open access) as well as sensitive data (restricted access) in the domain of biobanking and biosample research. Our approach is based on a digital identity federation and software to manage resource access entitlements. RESULTS: Open source software components were assembled and configured in such a way that they allow for different ways of restricted access according to the protection needs of the data. We have tested the resulting pilot infrastructure and assessed its performance, feasibility and reproducibility. CONCLUSIONS: Common open source software components are sufficient to allow for the creation of a secure system for differential access to sensitive data. The implementation of this system is exemplary for researchers facing similar requirements for restricted access data. Here we report experience and lessons learnt of our pilot implementation, which may be useful for similar use cases. Furthermore, we discuss possible extensions for more complex scenarios.}, isbn = {1472-6947}, doi = {10.1186/s12911-017-0424-6}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363029/}, author = {Brandizi, Marco and Melnichuk, Olga and Bild, Raffael and Kohlmayer, Florian and Rodriguez-Castro, Benedicto and Spengler, Helmut and Kuhn, Klaus A and Kuchinke, Wolfgang and Ohmann, Christian and Mustonen, Timo and Linden, Mikael and Nyr{\"o}nen, Tommi and Lappalainen, Ilkka and Brazma, Alvis and Sarkans, Ugis} } @article {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 {1237, title = {Automating indicator data reporting from health facility EMR to a national aggregate data system in Kenya: An Interoperability field-test using OpenMRS and DHIS2.}, journal = {Online J Public Health Inform}, volume = {8}, year = {2016}, month = {2016}, pages = {e188}, abstract = {

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

}, issn = {1947-2579}, doi = {10.5210/ojphi.v8i2.6722}, author = {Kariuki, James M and Manders, Eric-Jan and Richards, Janise and Oluoch, Tom and Kimanga, Davies and Wanyee, Steve and Kwach, James O and Santas, Xenophon} } @article {1135, title = {Improving documentation of clinical care within a clinical information network: an essential initial step in efforts to understand and improve care in Kenyan hospitals.}, journal = {BMJ Glob Health}, volume = {1}, year = {2016}, month = {2016 May 24}, pages = {e000028}, abstract = {

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

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

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

}, issn = {1361-8423}, doi = {10.1016/j.media.2016.06.035}, author = {Kapur, Tina and Pieper, Steve and Fedorov, Andriy and Fillion-Robin, J-C and Halle, Michael and O{\textquoteright}Donnell, Lauren and Lasso, Andras and Ungi, Tamas and Pinter, Csaba and Finet, Julien and Pujol, Sonia and Jagadeesan, Jayender and Tokuda, Junichi and Norton, Isaiah and Estepar, Raul San Jose and Gering, David and Aerts, Hugo J W L and Jakab, Marianna and Hata, Nobuhiko and Ibanez, Luiz and Blezek, Daniel and Miller, Jim and Aylward, Stephen and Grimson, W Eric L and Fichtinger, Gabor and Wells, William M and Lorensen, William E and Schroeder, Will and Kikinis, Ron} } @article {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 {1165, title = {A systematic literature review of open source software quality assessment models}, journal = {SpringerPlus}, volume = {5}, year = {2016}, pages = {1936}, abstract = {BACKGROUND: Many open source software (OSS) quality assessment models are proposed and available in the literature. However, there is little or no adoption of these models in practice. In order to guide the formulation of newer models so they can be acceptable by practitioners, there is need for clear discrimination of the existing models based on their specific properties. Based on this, the aim of this study is to perform a systematic literature review to investigate the properties of the existing OSS quality assessment models by classifying them with respect to their quality characteristics, the methodology they use for assessment, and their domain of application so as to guide the formulation and development of newer models. Searches in IEEE Xplore, ACM, Science Direct, Springer and Google Search is performed so as to retrieve all relevant primary studies in this regard. Journal and conference papers between the year 2003 and 2015 were considered since the first known OSS quality model emerged in 2003. RESULTS: A total of 19 OSS quality assessment model papers were selected. To select these models we have developed assessment criteria to evaluate the quality of the existing studies. Quality assessment models are classified into five categories based on the quality characteristics they possess namely: single-attribute, rounded category, community-only attribute, non-community attribute as well as the non-quality in use models. Our study reflects that software selection based on hierarchical structures is found to be the most popular selection method in the existing OSS quality assessment models. Furthermore, we found that majority (47\%) of the existing models do not specify any domain of application. CONCLUSIONS: In conclusion, our study will be a valuable contribution to the community and helps the quality assessment model developers in formulating newer models and also to the practitioners (software evaluators) in selecting suitable OSS in the midst of alternatives.}, keywords = {Analysis, Community, ISO 25010, open source software, Quality assessment models}, doi = {10.1186/s40064-016-3612-4}, author = {Adewumi, Adewole and Misra, Sanjay and Omoregbe, Nicholas and Crawford, Broderick and Soto, Ricardo} } @article {1008, title = {Design and development of an EMR for Ebola Treatment Centers in Sierra Leone using OpenMRS.}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {916}, abstract = {

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

}, issn = {0926-9630}, author = {Jazayeri, Darius and Oza, Shefali and Ramos, Glauber and Fraser, Hamish and Teich, Jonathan M and Kanter, Andrew S and Ball, Ellen} } @article {1030, title = {Do interoperable national information systems enhance availability of data to assess the effect of scale-up of HIV services on health workforce deployment in resource-limited countries?}, journal = {Stud Health Technol Inform}, volume = {216}, year = {2015}, month = {2015}, pages = {677-81}, abstract = {

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

}, issn = {0926-9630}, author = {Oluoch, Tom and Muturi, David and Kiriinya, Rose and Waruru, Anthony and Lanyo, Kevin and Nguni, Robert and Ojwang, James and Waters, Keith P and Richards, Janise} } @article {1292, title = {Innovative Technological Approach to Ebola Virus Disease Outbreak Response in Nigeria Using the Open Data Kit and Form Hub Technology.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0131000}, abstract = {

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

}, keywords = {Disease Outbreaks, Ebolavirus, Epidemiological Monitoring, Female, Hemorrhagic Fever, Ebola, Humans, Male, Medical Informatics, Nigeria}, issn = {1932-6203}, doi = {10.1371/journal.pone.0131000}, author = {Tom-Aba, Daniel and Olaleye, Adeniyi and Olayinka, Adebola Tolulope and Nguku, Patrick and Waziri, Ndadilnasiya and Adewuyi, Peter and Adeoye, Olawunmi and Oladele, Saliu and Adeseye, Aderonke and Oguntimehin, Olukayode and Shuaib, Faisal} } @article {995, title = {OpenHELP (Heidelberg laparoscopy phantom): development of an open-source surgical evaluation and training tool.}, journal = {Surg Endosc}, year = {2015}, month = {2015 Feb 12}, abstract = {

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

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

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

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

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

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

}, issn = {0926-9630}, author = {Fonseca, Marcelo and Karkaletsis, Kostas and Cruz, Isabel A and Berler, Alexander and Oliveira, Il{\'\i}dio C} } @article {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 {1003, title = {Innovative approaches to clinical data management in resource limited settings using open-source technologies.}, journal = {PLoS Negl Trop Dis}, volume = {8}, year = {2014}, month = {2014 Sep}, pages = {e3134}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0003134}, author = {Omollo, Raymond and Ochieng, Michael and Mutinda, Brian and Omollo, Truphosa and Owiti, Rhoda and Okeyo, Seth and Wasunna, Monique and Edwards, Tansy} } @article {890, title = {Comparison of femoral tunnel widening between outside-in and trans-tibial double-bundle ACL reconstruction.}, journal = {Knee Surg Sports Traumatol Arthrosc}, year = {2013}, month = {2013 Jul 13}, abstract = {

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

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

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

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

LEVEL OF EVIDENCE: Retrospective comparative study, Level III.

}, issn = {1433-7347}, doi = {10.1007/s00167-013-2597-6}, author = {Lee, Yong Seuk and Lee, Beom Koo and Oh, Won Seok and Cho, Yong Kyun} } @article {862, title = {MRIdb: Medical Image Management for Biobank Research.}, journal = {J Digit Imaging}, year = {2013}, month = {2013 Apr 26}, abstract = {

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

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

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

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

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

}, issn = {1472-684X}, doi = {10.1186/1472-684X-12-31}, author = {Shah, Kamal G and Slough, Tara Lyn and Yeh, Ping Teresa and Gombwa, Suave and Kiromera, Athanase and Oden, Z Maria and Richards-Kortum, Rebecca R} } @article {899, title = {SIVIC: Open-source, standards-based software for DICOM MR spectroscopy workflows}, journal = {International Journal of Biomedical Imaging}, volume = {2013}, year = {2013}, abstract = {Quantitative analysis of magnetic resonance spectroscopic imaging (MRSI) data provides maps of metabolic parameters that show promise for improving medical diagnosis and therapeutic monitoring. While anatomical images are routinely reconstructed on the scanner, formatted using the DICOM standard, and interpreted using PACS workstations, this is not the case for MRSI data. The evaluation of MRSI data is made more complex because files are typically encoded with vendor-specific file formats and there is a lack of standardized tools for reconstruction, processing, and visualization. SIVIC is a flexible open-source software framework and application suite that enables a complete scanner-to-PACS workflow for evaluation and interpretation of MRSI data. It supports conversion of vendor-specific formats into the DICOM MR spectroscopy (MRS) standard, provides modular and extensible reconstruction and analysis pipelines, and provides tools to support the unique visualization requirements associated with such data. Workflows are presented which demonstrate the routine use of SIVIC to support the acquisition, analysis, and delivery to PACS of clinical 1H MRSI datasets at UCSF. {\textcopyright} 2013 Jason C. Crane et al.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84881398824\&partnerID=40\&md5=dbbc0d09b4153fd2609d0bb01b37bb30}, author = {Crane, J C and Olson, M P and Nelson, S J} } @article {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} } @inbook {1080, title = {Development of an mHealth Open Source Platform for Diabetic Foot Ulcers Tele-consultations}, booktitle = {Wireless Mobile Communication and Healthcare}, series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering}, volume = {83}, year = {2012}, pages = {158-164}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, keywords = {diabetic foot ulcers, m-health, Telemedicine}, isbn = {978-3-642-29733-5}, doi = {10.1007/978-3-642-29734-2_22}, url = {http://dx.doi.org/10.1007/978-3-642-29734-2_22}, author = {Dafoulas, GeorgeE. and Koutsias, Stylianos and Behar, Joachim and Osorio, Juan and Malley, Brian and Gruentzig, Alexander and Celi, LeoAnthony and Angelidis, Pantelis and Theodorou, Kyriaki and Giannoukas, Athanasios}, editor = {Nikita, KonstantinaS. and Lin, JamesC. and Fotiadis, DimitriosI. and Arredondo Waldmeyer, Maria-Teresa} } @inbook {851, title = {Development of an mHealth Open Source Platform for Diabetic Foot Ulcers Tele-consultations}, booktitle = {Wireless Mobile Communication and Healthcare}, series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering}, volume = {83}, year = {2012}, pages = {158-164}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Diabetes is one of the foremost causes of death in many countries and a leading cause of blindness, renal failure, and non-traumatic amputation. Therefore, diabetic foot ulceration and amputation cause extensive burden on individuals and health care systems in developed and developing countries. Due to the multi-disciplinary requirements for the treatment of diabetic foot ulceration, telemedicine has been introduced to facilitate the access of the patients to specialized health professionals. In this paper the development of an open source mobile health platform is presented, able to support diagnostic algorithms, with the use of a smartphone.}, keywords = {diabetic foot ulcers, m-health, Telemedicine}, isbn = {978-3-642-29733-5}, doi = {10.1007/978-3-642-29734-2_22}, url = {http://dx.doi.org/10.1007/978-3-642-29734-2_22}, author = {Dafoulas, GeorgeE. and Koutsias, Stylianos and Behar, Joachim and Osorio, Juan and Malley, Brian and Gruentzig, Alexander and Celi, LeoAnthony and Angelidis, Pantelis and Theodorou, Kyriaki and Giannoukas, Athanasios}, editor = {Nikita, KonstantinaS. and Lin, JamesC. and Fotiadis, DimitriosI. and Arredondo Waldmeyer, Maria-Teresa} } @article {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 {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 {1055, title = {The NIH National Center for Integrative Biomedical Informatics (NCIBI).}, journal = {J Am Med Inform Assoc}, volume = {19}, year = {2012}, month = {2012 Mar-Apr}, pages = {166-70}, abstract = {

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

}, keywords = {Biomedical Research, Databases as Topic, Forecasting, Goals, Information Dissemination, Integrative Medicine, Medical Informatics, National Institutes of Health (U.S.), United States}, issn = {1527-974X}, doi = {10.1136/amiajnl-2011-000552}, author = {Athey, Brian D and Cavalcoli, James D and Jagadish, H V and Omenn, Gilbert S and Mirel, Barbara and Kretzler, Matthias and Burant, Charles and Isokpehi, Raphael D and DeLisi, Charles} } @article {1036, title = {A static-image telepathology system for dermatopathology consultation in East Africa: the Massachusetts General Hospital Experience.}, journal = {J Am Acad Dermatol}, volume = {67}, year = {2012}, month = {2012 Nov}, pages = {997-1007}, abstract = {

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

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

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

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

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

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

}, keywords = {Africa, Eastern, Cost-Benefit Analysis, Feasibility Studies, Hospitals, General, Humans, Massachusetts, Microscopy, Observer Variation, Pathology, Clinical, Remote Consultation, Skin Diseases, Skin Neoplasms, telepathology}, issn = {1097-6787}, doi = {10.1016/j.jaad.2011.12.036}, author = {Gimbel, Devon C and Sohani, Aliyah R and Prasad Busarla, Satya Vara and Kirimi, Jesca Muthoni and Sayed, Shahin and Okiro, Patricia and Nazarian, Rosalynn M} } @article {1012, title = {Use of Electronic Health Records in sub-Saharan Africa: Progress and challenges.}, journal = {J Med Trop}, volume = {14}, year = {2012}, month = {2012}, pages = {1-6}, abstract = {

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

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

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

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

}, issn = {2276-7096}, author = {Akanbi, Maxwell O and Ocheke, Amaka N and Agaba, Patricia A and Daniyam, Comfort A and Agaba, Emmanuel I and Okeke, Edith N and Ukoli, Christiana O} } @inbook {786, title = {VURTIGO: Visualization Platform for Real-Time, MRI-Guided Cardiac Electroanatomic Mapping}, booktitle = {Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges}, series = {Lecture Notes in Computer Science}, volume = {7085}, year = {2012}, pages = {244-253}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Guidance of electrophysiological (EP) procedures by magnetic resonance imaging (MRI) has significant advantages over x-ray fluoroscopy. Display of electroanatomic mapping (EAM) during an intervention fused with a prior MR volume and DE-MRI derived tissue classification should improve the accuracy of cardiac resynchronization therapy (CRT) for ventricular arrhythmias. Improved accuracy in the spatial localization of recorded EP points will produce an EAM to constrain and customize patient-specific cardiac electroanatomic models being developed for understanding the patterns of arrhythmogenic slow conduction zones causing reentry circuits and treatment planning. The Vurtigo software presented here is a four dimensional (3D+time) real-time visualization application for guiding interventions capable of displaying prior volumes, real-time MRI scan planes, EAM (voltage or activation times), segmented models, and tracked catheters. This paper will describe the architecture and features of Vurtigo followed by the application example of guiding percutaneous cardiac electroanatomic mapping in porcine models.}, isbn = {978-3-642-28325-3}, url = {http://dx.doi.org/10.1007/978-3-642-28326-0_25}, author = {Radau, Perry and Pintilie, Stefan and Flor, Roey and Biswas, Labonny and Oduneye, Samuel and Ramanan, Venkat and Anderson, Kevan and Wright, Graham}, editor = {Camara, Oscar and Konukoglu, Ender and Pop, Mihaela and Rhode, Kawal and Sermesant, Maxime and Young, Alistair} } @article {660, title = {Dicoogle - an Open Source Peer-to-Peer PACS.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {24}, year = {2011}, month = {2011 Oct}, pages = {848-56}, abstract = {Picture Archiving and Communication Systems (PACS) have been widely deployed in healthcare institutions, and they now constitute a normal commodity for practitioners. However, its installation, maintenance, and utilization are still a burden due to their heavy structures, typically supported by centralized computational solutions. In this paper, we present Dicoogle, a PACS archive supported by a document-based indexing system and by peer-to-peer (P2P) protocols. Replacing the traditional database storage (RDBMS) by a documental organization permits gathering and indexing data from file-based repositories, which allows searching the archive through free text queries. As a direct result of this strategy, more information can be extracted from medical imaging repositories, which clearly increases flexibility when compared with current query and retrieval DICOM services. The inclusion of P2P features allows PACS internetworking without the need for a central management framework. Moreover, Dicoogle is easy to install, manage, and use, and it maintains full interoperability with standard DICOM services.}, issn = {1618-727X}, doi = {10.1007/s10278-010-9347-9}, author = {Costa, Carlos and Ferreira, Carlos and Basti{\~a}o, Lu{\'\i}s and Ribeiro, Lu{\'\i}s and Silva, Augusto and Oliveira, Jos{\'e} Lu{\'\i}s} } @article {589, title = {FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.}, journal = {Computational intelligence and neuroscience}, volume = {2011}, year = {2011}, month = {2011}, pages = {156869}, abstract = {This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.}, keywords = {Electroencephalography, Electrophysiological Phenomena, Humans, Magnetoencephalography, Numerical Analysis, Computer-Assisted, Software, User-Computer Interface}, issn = {1687-5273}, author = {Oostenveld, Robert and Fries, Pascal and Maris, Eric and Schoffelen, Jan-Mathijs} } @article {597, title = {Forward field computation with OpenMEEG.}, journal = {Computational intelligence and neuroscience}, volume = {2011}, year = {2011}, month = {2011}, pages = {923703}, abstract = {To recover the sources giving rise to electro- and magnetoencephalography in individual measurements, realistic physiological modeling is required, and accurate numerical solutions must be computed. We present OpenMEEG, which solves the electromagnetic forward problem in the quasistatic regime, for head models with piecewise constant conductivity. The core of OpenMEEG consists of the symmetric Boundary Element Method, which is based on an extended Green Representation theorem. OpenMEEG is able to provide lead fields for four different electromagnetic forward problems: Electroencephalography (EEG), Magnetoencephalography (MEG), Electrical Impedance Tomography (EIT), and intracranial electric potentials (IPs). OpenMEEG is open source and multiplatform. It can be used from Python and Matlab in conjunction with toolboxes that solve the inverse problem; its integration within FieldTrip is operational since release 2.0.}, issn = {1687-5273}, author = {Gramfort, Alexandre and Papadopoulo, Th{\'e}odore and Olivi, Emmanuel and Clerc, Maureen} } @inbook {springerlink:10.1007/978-1-4419-7046-6_68, title = {Open Source Clinical Portals: A Model for Healthcare Information Systems to Support Care Processes and Feed Clinical Research}, booktitle = {Software Tools and Algorithms for Biological Systems}, series = {Advances in Experimental Medicine and Biology}, volume = {696}, year = {2011}, note = {10.1007/978-1-4419-7046-6_68}, pages = {667-677}, publisher = {Springer New York}, organization = {Springer New York}, abstract = {Open source is a still unexploited chance for healthcare organizations and technology providers to answer to a growing demand for innovation and to join economical benefits with a new way of managing hospital information systems. This chapter will present the case of the web enterprise clinical portal developed in Italy by Niguarda Hospital in Milan with the support of Fondazione Politecnico di Milano, to enable a paperless environment for clinical and administrative activities in the ward. This represents also one rare case of open source technology and reuse in the healthcare sector, as the system{\textquoteright}s porting is now taking place at Besta Neurological Institute in Milan. This institute is customizing the portal to feed researchers with structured clinical data collected in its portal{\textquoteright}s patient records, so that they can be analyzed, e.g., through business intelligence tools. Both organizational and clinical advantages are investigated, from process monitoring, to semantic data structuring, to recognition of common patterns in care processes.}, isbn = {978-1-4419-7046-6}, url = {http://dx.doi.org/10.1007/978-1-4419-7046-6_68}, author = {Locatelli, Paolo and Baj, Emanuele and Restifo, Nicola and Origgi, Gianni and Bragagia, Silvia}, editor = {Arabnia, Hamid R. R. and Tran, Quoc-Nam} } @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 {529, title = {AngioLab: Integrated technology for patient-specific management of intracranial aneurysms.}, journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference}, volume = {1}, year = {2010}, month = {2010}, pages = {6801-4}, abstract = {AngioLab is a software tool developed within the GIMIAS framework and is part of a more ambitious pipeline for the integrated management of cerebral aneurysms. AngioLab currently includes three plug-ins: angio segmentation, angio morphology and stenting, as well as supports advanced rendering techniques for the visualization of virtual angiographies. In December 2009, 23 clinicians completed an evaluation questionnaire about AngioLab. This activity was part of a teaching course held during the 2(nd) European Society for Minimally Invasive Neurovascular Treatment (ESMINT) Teaching Course held at the Universitat Pompeu Fabra, Barcelona, Spain. The Automated Morphological Analysis (angio morphology plug-in) and the Endovascular Treatment Planning (stenting plug-in) were evaluated. In general, the results provided by these tools were considered as relevant and as an emerging need in their clinical field.}, issn = {1557-170X}, author = {Villa-Uriol, M C and Larrabide, I and Geers, A J and Pozo, J and Bogunovic, H and Mazzeo, M and Omedas, P and Barbarito, V and Carotenuto, L and Riccobene, C and Planes, X and Martelli, Y and Frangi, A F} } @article {531, title = {Building a open source framework for virtual medical training.}, journal = {Journal of digital imaging : the official journal of the Society for Computer Applications in Radiology}, volume = {23}, year = {2010}, month = {2010 Dec}, pages = {706-20}, abstract = {This paper presents a framework to build medical training applications by using virtual reality and a tool that helps the class instantiation of this framework. The main purpose is to make easier the building of virtual reality applications in the medical training area, considering systems to simulate biopsy exams and make available deformation, collision detection, and stereoscopy functionalities. The instantiation of the classes allows quick implementation of the tools for such a purpose, thus reducing errors and offering low cost due to the use of open source tools. Using the instantiation tool, the process of building applications is fast and easy. Therefore, computer programmers can obtain an initial application and adapt it to their needs. This tool allows the user to include, delete, and edit parameters in the functionalities chosen as well as storing these parameters for future use. In order to verify the efficiency of the framework, some case studies are presented.}, issn = {1618-727X}, author = {de Oliveira, Ana Cl{\'a}udia Melo Tiessi Gomes and Nunes, F{\'a}tima de Lourdes dos Santos} } @article {1013, title = {Combining vital events registration, verbal autopsy and electronic medical records in rural Ghana for improved health services delivery.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {416-20}, abstract = {

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

}, keywords = {Cause of Death, Database Management Systems, Delivery of Health Care, electronic health records, Ghana, Medical Record Linkage, Quality Assurance, Health Care, Quality Improvement, Registries, Rural Health Services, Vital Statistics}, issn = {0926-9630}, author = {Ohemeng-Dapaah, Seth and Pronyk, Paul and Akosa, Eric and Nemser, Bennett and Kanter, Andrew S} } @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 {847, title = {Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.}, journal = {J Am Med Inform Assoc}, volume = {17}, year = {2010}, month = {2010 Sep-Oct}, pages = {507-13}, abstract = {

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

}, keywords = {Biomedical Research, electronic health records, Information Storage and Retrieval, Natural Language Processing}, issn = {1527-974X}, doi = {10.1136/jamia.2009.001560}, author = {Savova, Guergana K and Masanz, James J and Ogren, Philip V and Zheng, Jiaping and Sohn, Sunghwan and Kipper-Schuler, Karin C and Chute, Christopher G} } @article {596, title = {OpenMEEG: opensource software for quasistatic bioelectromagnetics.}, journal = {Biomedical engineering online}, volume = {9}, year = {2010}, month = {2010}, pages = {45}, abstract = {Interpreting and controlling bioelectromagnetic phenomena require realistic physiological models and accurate numerical solvers. A semi-realistic model often used in practise is the piecewise constant conductivity model, for which only the interfaces have to be meshed. This simplified model makes it possible to use Boundary Element Methods. Unfortunately, most Boundary Element solutions are confronted with accuracy issues when the conductivity ratio between neighboring tissues is high, as for instance the scalp/skull conductivity ratio in electro-encephalography. To overcome this difficulty, we proposed a new method called the symmetric BEM, which is implemented in the OpenMEEG software. The aim of this paper is to present OpenMEEG, both from the theoretical and the practical point of view, and to compare its performances with other competing software packages.}, keywords = {Benchmarking, Computers, Electric Impedance, Electricity, Electroencephalography, Electromagnetic Phenomena, Licensure, Magnetics, Magnetoencephalography, Models, Theoretical, Quality Control, Software, Time Factors, Tomography}, issn = {1475-925X}, author = {Gramfort, Alexandre and Papadopoulo, Th{\'e}odore and Olivi, Emmanuel and Clerc, Maureen} } @article {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} } @inbook {springerlink:10.1007/978-3-642-01932-6_45, title = {GIMIAS: An Open Source Framework for Efficient Development of Research Tools and Clinical Prototypes}, booktitle = {Functional Imaging and Modeling of the Heart}, series = {Lecture Notes in Computer Science}, volume = {5528}, year = {2009}, note = {10.1007/978-3-642-01932-6_45}, pages = {417-426}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {GIMIAS is a workflow-oriented environment for addressing advanced biomedical image computing and build personalized computational models, which is extensible through the development of application-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Virtual Physiological Human community while allowing business-friendly technology transfer and commercial product development. This framework has been fully developed in ANSI-C++ on top of well known open source libraries like VTK, ITK and wxWidgets among others. Based on GIMIAS, in this paper is presented a workflow for medical image analysis and simulation of the heart.}, url = {http://dx.doi.org/10.1007/978-3-642-01932-6_45}, author = {Larrabide, Ignacio and Omedas, Pedro and Martelli, Yves and Planes, Xavier and Nieber, Maarten and Moya, Juan and Butakoff, Constantine and Sebasti{\'a}n, Rafael and Camara, Oscar and De Craene, Mathieu and Bijnens, Bart and Frangi, Alejandro}, editor = {Ayache, Nicholas and Delingette, Herv{\'e} and Sermesant, Maxime} } @article {1017, title = {Millennium Global Village-Net: bringing together Millennium Villages throughout sub-Saharan Africa.}, journal = {Int J Med Inform}, volume = {78}, year = {2009}, month = {2009 Dec}, pages = {802-7}, abstract = {

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

}, keywords = {Africa South of the Sahara, Community Health Services, Developing Countries, Healthy People Programs, Humans, Poverty}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2009.08.002}, author = {Kanter, Andrew S and Negin, Joel and Olayo, Bernard and Bukachi, Frederick and Johnson, Edward and Sachs, Sonia Ehrlich} } @conference {1087, title = {Open Source: A Lever for Enhancing Opportunities of Healthcare Information Systems - An Italian Case Study}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001828700280037}, author = {Emanuele Baj and Paolo Locatelli and Stefano Gatti and Nicola Restifo and Gianni Origgi and Silvia Bragagia} } @article {19745456, title = {Open source and healthcare in Europe - time to put leading edge ideas into practice.}, journal = {Studies in health technology and informatics}, volume = {150}, year = {2009}, month = {2009}, pages = {963-7}, abstract = {Free/Libre and Open Source Software (FLOSS) is a process of software development, a method of licensing and a philosophy. Although FLOSS plays a significant role in several market areas, the impact in the health care arena is still limited. FLOSS is promoted as one of the most effective means for overcoming fragmentation in the health care sector and providing a basis for more efficient, timely and cost effective health care provision. The 2008 European Federation for Medical Informatics (EFMI) Special Topic Conference (STC) explored a range of current and future issues related to FLOSS in healthcare (FLOSS-HC). In particular, there was a focus on health records, ubiquitous computing, knowledge sharing, and current and future applications. Discussions resulted in a list of main barriers and challenges for use of FLOSS-HC. Based on the outputs of this event, the 2004 Open Steps events and subsequent workshops at OSEHC2009 and Med-e-Tel 2009, a four-step strategy has been proposed for FLOSS-HC: 1) a FLOSS-HC inventory; 2) a FLOSS-HC collaboration platform, use case database and knowledge base; 3) a worldwide FLOSS-HC network; and 4) FLOSS-HC dissemination activities. The workshop will further refine this strategy and elaborate avenues for FLOSS-HC from scientific, business and end-user perspectives. To gain acceptance by different stakeholders in the health care industry, different activities have to be conducted in collaboration. The workshop will focus on the scientific challenges in developing methodologies and criteria to support FLOSS-HC in becoming a viable alternative to commercial and proprietary software development and deployment.}, author = {Murray, Peter J and Wright, Graham and Karopka, Thomas and Betts, Helen and Orel, Andrej} } @article {19157968, title = {The OpenMRS Implementers Network.}, journal = {International journal of medical informatics}, volume = {78}, year = {2009}, month = {2009 Nov}, pages = {711-20}, abstract = {OBJECTIVE: OpenMRS (www.openmrs.org) is a configurable open source electronic medical record application developed and maintained by a large network of open source developers coordinated by the Regenstrief Institute and Partners in Health and mainly used for HIV patient and treatment information management in Africa. Our objective is to develop an open Implementers Network for OpenMRS to provide regional support for the growing number of OpenMRS implementations in Africa and to include African developers and implementers in the future growth of OpenMRS. METHODS: We have developed the OpenMRS Implementers Network using a dedicated Wiki site and e-mail server. We have also organized annual meetings in South Africa and regional training courses at African locations where OpenMRS is being implemented. An OpenMRS Internship program has been initiated and we have started collaborating with similar networks and projects working in Africa. To evaluate its potential, OpenMRS was implemented initially at one site in South Africa by a single implementer using a downloadable OpenMRS application and only the OpenMRS Implementers Network for support. RESULTS: The OpenMRS Implementers Network Wiki and list server have grown into effective means of providing implementation support and forums for exchange of implementation experiences. The annual OpenMRS Implementers meeting has been held in South Africa for the past three years and is attracting successively larger numbers of participants with almost 200 implementers and developers attending the 2008 meeting in Durban, South Africa. Six African developers are presently registered on the first intake of the OpenMRS Internship program. Successful collaborations have been started with several African developer groups and projects initiated to develop interoperability between OpenMRS and various applications. The South African OpenMRS Implementer group successfully configured, installed and maintained an integrated HIV/TB OpenMRS application without significant programming support. Since then, this model has been replicated in several other African sites. The OpenMRS Implementers Network has contributed substantially to the growth and sustainability of OpenMRS in Africa and has become a useful way of including Africans in the development and implementation of OpenMRS in developing countries. The Network provides valuable support and enables a basic OpenMRS application to be implemented in the absence of onsite programmers.}, url = {http://www.healthware.org/openmrs/openmrs.pdf}, author = {Seebregts, Christopher J and Mamlin, Burke W and Biondich, Paul G and Fraser, Hamish S F and Wolfe, Benjamin A and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Baker, Elaine and Musinguzi, Nicholas and Kayiwa, Daniel and Fourie, Carl and Lesh, Neal and Kanter, Andrew and Yiannoutsos, Constantin T and Bailey, Christopher} } @conference {903, title = {PESCA: Developing an open source platform to bring eHealth to latin america and the caribbean}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe, OSEHC 2009 In Conjunction with BIOSTEC 2009 and the EFMI LIFOSS WG}, year = {2009}, abstract = {Nowadays the society needs to communicate and the technologies are revolutionizing the information systems, especially for the health; where an effective use of the technologies is used to favor the needs of the persons. These technologies can contribute to the development of the local economies. Open source software (OSS) can be an useful strategy to bring information and communication technologies to developing countries. However, specially in Latin America and the Caribbean, there are some barriers in adopting OSS for health: the need for open standards, heterogeneous OSS developed without normalization and metrics, English predominance as top OSS language, lack of initiatives to evaluate existing health OSS and needs for quality control and functional validation. The Open Source Platform for eHealth (PESCA) has been designed as a set of interoperable modules that can solve either: simple problems on health management and communication in primary care or complex problems in healthcare systems, including telehealth communications between heterogeneous institutions.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-67650527704\&partnerID=40\&md5=cb5a91f3ccf525ed19857b1e3354a61d}, author = {Orcero, D.S.a}, editor = {L{\'o}pez, D.L.b} } @article {19212459, title = {PyMVPA: A Unifying Approach to the Analysis of Neuroscientific Data.}, journal = {Frontiers in neuroinformatics}, volume = {3}, year = {2009}, month = {2009}, pages = {3}, abstract = {The Python programming language is steadily increasing in popularity as the language of choice for scientific computing. The ability of this scripting environment to access a huge code base in various languages, combined with its syntactical simplicity, make it the ideal tool for implementing and sharing ideas among scientists from numerous fields and with heterogeneous methodological backgrounds. The recent rise of reciprocal interest between the machine learning (ML) and neuroscience communities is an example of the desire for an inter-disciplinary transfer of computational methods that can benefit from a Python-based framework. For many years, a large fraction of both research communities have addressed, almost independently, very high-dimensional problems with almost completely non-overlapping methods. However, a number of recently published studies that applied ML methods to neuroscience research questions attracted a lot of attention from researchers from both fields, as well as the general public, and showed that this approach can provide novel and fruitful insights into the functioning of the brain. In this article we show how PyMVPA, a specialized Python framework for machine learning based data analysis, can help to facilitate this inter-disciplinary technology transfer by providing a single interface to a wide array of machine learning libraries and neural data-processing methods. We demonstrate the general applicability and power of PyMVPA via analyses of a number of neural data modalities, including fMRI, EEG, MEG, and extracellular recordings.}, author = {Hanke, Michael and Halchenko, Yaroslav O and Sederberg, Per B and Olivetti, Emanuele and Fr{\"u}nd, Ingo and Rieger, Jochem W and Herrmann, Christoph S and Haxby, James V and Hanson, Stephen Jos{\'e} and Pollmann, Stefan} } @article {19745435, title = {Reversible anonymization of DICOM images using automatically generated policies.}, journal = {Studies in health technology and informatics}, volume = {150}, year = {2009}, month = {2009}, pages = {861-5}, abstract = {Many real-world applications in the area of medical imaging like case study databases require separation of identifying (IDATA) and non-identifying (MDATA) data, specifically those offering Internet-based data access. These kinds of projects also must provide a role-based access system, controlling, how patient data must be organized and how it can be accessed. On DICOM image level, different image types support different kind of information, intermixing IDATA and MDATA in a single object. To separate them, it is possible to reversibly anonymize DICOM objects by substituting IDATA by a unique anonymous token. In case that later an authenticated user needs full access to an image, this token can be used for re-linking formerly separated IDATA and MDATA, thus resulting in a dynamically generated, exact copy of the original image. The approach described in this paper is based on the automatic generation of anonymization policies from the DICOM standard text, providing specific support for all kinds of DICOM images. The policies are executed by a newly developed framework based on the DICOM toolkit DCMTK and offer a reliable approach to reversible anonymization. The implementation is evaluated in a German BMBF-supported expert network in the area of skeletal dysplasias, SKELNET, but may generally be applicable to related projects, enormously improving quality and integrity of diagnostics in a field focused on images. It performs effectively and efficiently on real-world test images from the project and other kind of DICOM images.}, author = {Onken, Michael and Riesmeier, J{\"o}rg and Engel, Marcel and Yabanci, Adem and Zabel, Bernhard and Despr{\'e}s, Stefan} } @article {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 {10.1109/HICSS.2005.166, title = {Contrasting Community Building in Sponsored and Community Founded Open Source Projects}, journal = {Hawaii International Conference on System Sciences}, volume = {7}, year = {2005}, pages = {196c}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, issn = {1530-1605}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2005.166}, author = {Joel West and Siobh{\'a}n O{\textquoteright}Mahony} } @article {15923755, title = {iPath - a Telemedicine Platform to Support Health Providers in Low Resource Settings.}, journal = {Studies in health technology and informatics}, volume = {114}, year = {2005}, month = {2005}, pages = {11-7}, abstract = {In many developing countries there is an acute shortage of medical specialists. The specialists and services that are available are usually concentrated in cities and health workers in rural health care, who serve most of the population, are isolated from specialist support [1]. Besides, the few remaining specialist are often isolated from colleagues. With the recent development in information and communication technologies, new option for telemedicine and generally for sharing knowledge at a distance are becoming increasingly accessible to health workers also in developing countries. Since 2001 the Department of Pathology in Basel, Switzerland is operating an Internet based telemedicine platform to assist health workers in developing countries. Over 1800 consultation have been performed since. This paper will give an introduction to iPath - the telemedicine platform developed for this project - and analyse two case studies: a teledermatology project from South Africa and a telepathology project from Solomon Islands.}, author = {Brauchli, K and O{\textquoteright}mahony, D and Banach, L and Oberholzer, M} } @article {16375782, title = {The iPath telemedicine platform.}, journal = {Journal of telemedicine and telecare}, volume = {11 Suppl 2}, year = {2005}, month = {2005}, pages = {S3-7}, abstract = {An early, point-to-point telepathology system at the University of Basel developed into an open-source, Internet-based platform for telemedicine in 2001. The Internet Pathology Suite (iPath) is a Web-based telepathology platform that permits the online presentation and discussion of cases within user groups. It also allows realtime telemicroscopy across firewalls. After four years, the telepathology network has over 700 active users. More than 6,300 cases with a total of about 39,000 images have been diagnosed. The diagnostic workload of all these cases is not exclusively handled by the Department of Pathology in Basel, but by a growing number of independent groups who also use the server simply as a case repository. What started as a small project for hospitals in Switzerland has become a global network.}, author = {Brauchli, Kurt and Oberholzer, Martin} } @article {15361001, title = {The RODS Open Source Project: removing a barrier to syndromic surveillance.}, journal = {Studies in health technology and informatics}, volume = {107}, year = {2004}, month = {2004}, pages = {1192-6}, abstract = {The goal of the Real-time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate deployment of computer-based syndromic surveillance. To this end, the project has released the RODS software under the GNU General Public License and created an organizational structure to catalyze its development. This paper describes the design of the software, requested extensions, and the structure of the development effort.}, author = {Espino, Jeremy U and Wagner, Michael M and Tsui, Fu-Chang and Su, Hoah-Der and Olszewski, Robert T and Lie, Zhen and Chapman, Wendy and Zeng, Xiaoming and Ma, Lili and Lu, Zhong Wei and Dara, Jagan} } @article {12810121, title = {Open Source software in medical informatics--why, how and what.}, journal = {International journal of medical informatics}, volume = {69}, year = {2003}, month = {2003 Mar}, pages = {175-84}, abstract = {{\textquoteright}Open Source{\textquoteright} is a 20-40 year old approach to licensing and distributing software that has recently burst into public view. Against conventional wisdom this approach has been wildly successful in the general software market--probably because the openness lets programmers the world over obtain, critique, use, and build upon the source code without licensing fees. Linux, a UNIX-like operating system, is the best known success. But computer scientists at the University of California, Berkeley began the tradition of software sharing in the mid 1970s with BSD UNIX and distributed the major internet network protocols as source code without a fee. Medical informatics has its own history of Open Source distribution: Massachusetts General{\textquoteright}s COSTAR and the Veterans Administration{\textquoteright}s VISTA software have been distributed as source code at no cost for decades. Bioinformatics, our sister field, has embraced the Open Source movement and developed rich libraries of open-source software. Open Source has now gained a tiny foothold in health care (OSCAR GEHR, OpenEMed). Medical informatics researchers and funding agencies should support and nurture this movement. In a world where open-source modules were integrated into operational health care systems, informatics researchers would have real world niches into which they could engraft and test their software inventions. This could produce a burst of innovation that would help solve the many problems of the health care system. We at the Regenstrief Institute are doing our part by moving all of our development to the open-source model.}, author = {McDonald, Clement J and Schadow, Gunther and Barnes, Michael and Dexter, Paul and Overhage, J Marc and Mamlin, Burke and McCoy, J Michael} }