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

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

}, keywords = {electronic health records, Humans, Medical Informatics, Publications, Software}, issn = {1741-2811}, doi = {10.1177/14604582221099828}, author = {Shaikh, Mohsin and Vayani, Arshad Hm and Akram, Sabina and Qamar, Nafees} } @article {1301, title = {Use of cost-effective technologies for a routine clinical pathology laboratory}, journal = {Lab on a Chip}, year = {2021}, month = {2021}, pages = { - }, abstract = {Classically, the need for highly sophisticated instruments with important economic costs has been a major limiting factor for clinical pathology laboratories, especially in developing countries. With the aim of making clinical pathology more accessible, a wide variety of free or economical technologies have been developed worldwide in the last years. 3D printing and Arduino approaches can provide up to 94\% economical savings in hardware and instrumentation in comparison to commercial alternatives. The vast selection of Point-of-Care-Tests (POCT) currently available also limits the need for specific instruments or personnel, as they can be used almost anywhere and by anyone. Lastly, there are dozens of free and libre digital tools available in health informatics. This review provides an overview of the state-of-the-art on cost-effective alternatives with applications in routine clinical pathology laboratories. In this context, a variety of technologies including 3D printing and Arduino, lateral flow assays, plasmonic biosensors, and microfluidics, as well as laboratory information systems, are discussed. This review aims to serve as an introduction to different technologies that can make clinical pathology more accessible and, therefore, contribute to achieve universal health coverage.}, isbn = {1473-0197}, url = {http://dx.doi.org/10.1039/D1LC00658D}, author = {Vazquez, Mercedes and Anfossi, L. and Ben-Yoav, Hader and Di{\'e}guez, Lorena and Karopka, Thomas and Della Ventura, Bartolomeo and Abalde-Cela, Sara and Minopoli, Antonio and Di Nardo, Fabio and Kumar Shukla, Vikas and Teixeira, Alexandra and Tvarijonaviciute, Asta and Franco, Lorena} } @article {1299, title = {Using Open Source, Open Data, and Civic Technology to Address the COVID-19 Pandemic and Infodemic.}, journal = {Yearb Med Inform}, year = {2021}, month = {2021 Apr 21}, abstract = {

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

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

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

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

}, issn = {2364-0502}, doi = {10.1055/s-0041-1726488}, author = {Kobayashi, Shinji and Falc{\'o}n, Luis and Fraser, Hamish and Braa, J{\o}rn and Amarakoon, Pamod and Marcelo, Alvin and Paton, Chris} } @article {1212, title = {Bangladesh{\textquoteright}s digital health journey: reflections on a decade of quiet revolution.}, journal = {WHO South East Asia J Public Health}, volume = {8}, year = {2019}, month = {2019 09}, pages = {71-76}, abstract = {

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

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

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

}, issn = {1664-2295}, doi = {10.3389/fneur.2019.00725}, author = {Seah, Huey Ming and Burney, Moe and Phan, Michael and Shell, Daniel and Wu, Jamin and Zhou, Kevin and Brooks, Owen and Coulton, Bronwyn and Maingard, Julian and Tang, Jennifer and Yazdabadi, Gohar and Tahayori, Bahman and Barras, Christen and Kok, Hong Kuan and Chandra, Ronil and Thijs, Vincent and Brooks, Duncan Mark and Asadi, Hamed} } @article {1226, title = {Comparison of Open-Source Electronic Health Record Systems Based on Functional and User Performance Criteria.}, journal = {Healthc Inform Res}, volume = {25}, year = {2019}, month = {2019 Apr}, pages = {89-98}, abstract = {

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

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

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

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

}, issn = {2093-3681}, doi = {10.4258/hir.2019.25.2.89}, author = {Purkayastha, Saptarshi and Allam, Roshini and Maity, Pallavi and Gichoya, Judy W} } @article {1281, title = {Eye injuries in children - incidence and outcomes: An observational study at a dedicated children{\textquoteright}s eye casualty.}, journal = {Eur J Ophthalmol}, volume = {29}, year = {2019}, month = {2019 Sep}, pages = {499-503}, abstract = {

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

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

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

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

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

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

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2019-001606}, author = {Dougherty, Leanne and Abdulkarim, Masduq and Mikailu, Fiyidi and Tijani, Usman and Owolabi, Kazeem and Gilroy, Kate and Naiya, Ahmed and Abdullahi, Adamu and Bodinga, Hadiza and Olayinka, Folake and Moise, Imelda} } @article {1278, title = {Large care gaps in primary care management of asthma: a longitudinal practice audit.}, journal = {BMJ Open}, volume = {9}, year = {2019}, month = {2019 01 29}, pages = {e022506}, abstract = {

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

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

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

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

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

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

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

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

TRIAL REGISTRATION NUMBER: NCT01070095; Pre-results.

}, issn = {2044-6055}, doi = {10.1136/bmjopen-2018-022506}, author = {Price, Courtney and Agarwal, Gina and Chan, David and Goel, Sanjeev and Kaplan, Alan G and Boulet, Louis-Philippe and Mamdani, Muhammad M and Straus, Sharon E and Lebovic, Gerald and Gupta, Samir} } @article {1210, title = {Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses.}, journal = {JCO Clin Cancer Inform}, volume = {3}, year = {2019}, month = {2019 Aug}, pages = {1-16}, abstract = {

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

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

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

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

}, issn = {2473-4276}, doi = {10.1200/CCI.18.00132}, author = {Isoviita, Veli-Matti and Salminen, Liina and Azar, Jimmy and Lehtonen, Rainer and Roering, Pia and Carp{\'e}n, Olli and Hietanen, Sakari and Gr{\'e}nman, Seija and Hynninen, Johanna and F{\"a}rkkil{\"a}, Anniina and Hautaniemi, Sampsa} } @article {1269, title = {Quality of routine facility data for monitoring priority maternal and newborn indicators in DHIS2: A case study from Gombe State, Nigeria.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0211265}, abstract = {

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

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

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

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

}, keywords = {Adolescent, Adult, Female, Guidelines as Topic, Health information systems, Humans, Infant Health, Infant, Newborn, Maternal Health, Middle Aged, Nigeria, Pregnancy, Quality Indicators, Health Care, Young Adult}, issn = {1932-6203}, doi = {10.1371/journal.pone.0211265}, author = {Bhattacharya, Antoinette Alas and Umar, Nasir and Audu, Ahmed and Felix, Habila and Allen, Elizabeth and Schellenberg, Joanna R M and Marchant, Tanya} } @article {1203, title = {The {District} {Health} {Information} {System} ({DHIS}2): {A} literature review and meta-synthesis of its strengths and operational challenges based on the experiences of 11 countries}, journal = {Health Information Management: Journal of the Health Information Management Association of Australia}, year = {2018}, pages = {1833358318777713}, abstract = {BACKGROUND: Health information systems offer many potential benefits for healthcare, including financial benefits and for improving the quality of patient care. The purpose of District Health Information Systems (DHIS) is to document data that are routinely collected in all public health facilities in a country using the system. OBJECTIVE: The aim of this study was to examine the strengths and operational challenges of DHIS2, with a goal to enable decision makers in different counties to more accurately evaluate the outcomes of introducing DHIS2 into their particular country. METHOD: A review of the literature combined with the method of meta-synthesis was used to source information and interpret results relating to the strengths and operational challenges of DHIS2. Databases (Embase, PubMed, Scopus and Google Scholar) were searched for documents related to strengths and operational challenges of DHIS2, with no time limit up to 8 April 2017. The review and evaluation of selected studies was conducted in three stages: title, abstract and full text. Each of the selected studies was reviewed carefully and key concepts extracted. These key concepts were divided into two categories of strengths and operational challenges of DHIS2. Then, each category was grouped based on conceptual similarity to achieve the main themes and sub-themes. Content analysis was used to analyse extracted data. RESULTS: Of 766 identified citations, 20 studies from 11 countries were included and analysed in this study. Identified strengths in the DHIS were represented in seven themes (with 21 categories): technical features of software, proper management of data, application flexibility, networking and increasing the satisfaction of stakeholders, development of data management, increasing access to information and economic benefits. Operational challenges were identified and captured in 11 themes (with 18 categories): funds; appropriate communication infrastructure; the need for the existence of appropriate data; political, cultural, social and structural infrastructure; manpower; senior managers; training; using academic potentials; definition and standardising the deployment processes; neglect to application of criteria and clinical guidelines in the use of system; data security; stakeholder communications challenges and the necessity to establish a pilot system. CONCLUSION: This study highlighted specific strengths in the technical and functional aspects of DHIS2 and also drew attention to particular challenges and concerns. These results provide a sound evidence base for decision makers and policymakers to enable them to make more accurate decisions about whether or not to use the DHIS2 in the health system of their country.}, keywords = {content analysis, District Health Information System, health information system, health information technology, information technology, meta-synthesis, qualitative research}, issn = {1322-4913}, doi = {10.1177/1833358318777713}, author = {Dehnavieh, Reza and Haghdoost, AliAkbar and Khosravi, Ardeshir and Hoseinabadi, Fahime and Rahimi, Hamed and Poursheikhali, Atousa and Khajehpour, Nahid and Khajeh, Zahra and Mirshekari, Nadia and Hasani, Marziyeh and Radmerikhi, Samera and Haghighi, Hajar and Mehrolhassani, Mohammad Hossain and Kazemi, Elaheh and Aghamohamadi, Saeide} } @article {1282, title = {Effect of glycosylated hemoglobin on response to ranibizumab therapy in diabetic macular edema: real-world outcomes in 312 patients.}, journal = {Can J Ophthalmol}, volume = {53}, year = {2018}, month = {2018 08}, pages = {415-419}, abstract = {

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

DESIGN: Retrospective cohort study.

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

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

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

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

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

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

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

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

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

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

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

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

}, keywords = {Algorithms, Animals, Body Weights and Measures, Drosophila, Humans, Image Processing, Computer-Assisted, Software, Zebrafish}, issn = {2045-2322}, doi = {10.1038/s41598-017-18993-5}, author = {Vandaele, R{\'e}my and Aceto, Jessica and Muller, Marc and P{\'e}ronnet, Fr{\'e}d{\'e}rique and Debat, Vincent and Wang, Ching-Wei and Huang, Cheng-Ta and Jodogne, S{\'e}bastien and Martinive, Philippe and Geurts, Pierre and Mar{\'e}e, Rapha{\"e}l} } @article {1238, title = {Design and implementation of an affordable, public sector electronic medical record in rural Nepal.}, journal = {J Innov Health Inform}, volume = {24}, year = {2017}, month = {2017 Jun 23}, pages = {862}, abstract = {

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

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

}, keywords = {Delivery of Health Care, Integrated, electronic health records, Global Health, Health Plan Implementation, Hospitals, Public, Humans, Nepal, Public Sector, Rural Population}, issn = {2058-4563}, doi = {10.14236/jhi.v24i2.862}, author = {Raut, Anant and Yarbrough, Chase and Singh, Vivek and Gauchan, Bikash and Citrin, David and Verma, Varun and Hawley, Jessica and Schwarz, Dan and Harsha Bangura, Alex and Shrestha, Biplav and Schwarz, Ryan and Adhikari, Mukesh and Maru, Duncan} } @article {1175, title = {Easy {Handling} of {Sensors} and {Actuators} over {TCP}/{IP} {Networks} by {Open} {Source} {Hardware}/{Software}}, journal = {Sensors (Basel, Switzerland)}, volume = {17}, year = {2017}, abstract = {There are several specific solutions for accessing sensors and actuators present in any process or system through a TCP/IP network, either local or a wide area type like the Internet. The usage of sensors and actuators of different nature and diverse interfaces (SPI, I2C, analogue, etc.) makes access to them from a network in a homogeneous and secure way more complex. A framework, including both software and hardware resources, is necessary to simplify and unify networked access to these devices. In this paper, a set of open-source software tools, specifically designed to cover the different issues concerning the access to sensors and actuators, and two proposed low-cost hardware architectures to operate with the abovementioned software tools are presented. They allow integrated and easy access to local or remote sensors and actuators. The software tools, integrated in the free authoring tool Easy Java and Javascript Simulations (EJS) solve the interaction issues between the subsystem that integrates sensors and actuators into the network, called convergence subsystem in this paper, and the Human Machine Interface (HMI)-this one designed using the intuitive graphical system of EJS-located on the user{\textquoteright}s computer. The proposed hardware architectures and software tools are described and experimental implementations with the proposed tools are presented.}, keywords = {Arduino, collaborative access, data acquisition, EJS, HMI, Internet-of-Things, Modbus, open source hardware/software, remote access}, issn = {1424-8220}, doi = {10.3390/s17010094}, author = {Mej{\'\i}as, Andr{\'e}s and Herrera, Reyes S. and M{\'a}rquez, Marco A. and Calder{\'o}n, Antonio Jos{\'e} and Gonz{\'a}lez, Isa{\'\i}as and And{\'u}jar, Jos{\'e} Manuel} } @article {1267, title = {Mapping for Health in Cameroon: Polio Legacy and Beyond.}, journal = {J Infect Dis}, volume = {216}, year = {2017}, month = {2017 07 01}, pages = {S337-S342}, abstract = {

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

}, keywords = {Cameroon, Geographic Information Systems, Humans, Immunization Programs, Poliomyelitis, Public Health, Public Health Surveillance, Smartphone}, issn = {1537-6613}, doi = {10.1093/infdis/jix008}, author = {Rosencrans, Louie C and Sume, Gerald E and Kouontchou, Jean-Christian and Voorman, Arend and Anokwa, Yaw and Fezeu, Maurice and Seaman, Vincent Y} } @article {1192, title = {{OpenICE} medical device interoperability platform overview and requirement analysis}, journal = {Biomedizinische Technik. Biomedical Engineering}, year = {2017}, abstract = {We give an overview of OpenICE, an open source implementation of the ASTM standard F2761 for the Integrated Clinical Environment (ICE) that leverages medical device interoperability, together with an analysis of the clinical and non-functional requirements and community process that inspired its design.}, keywords = {Interoperability, medical applications, patient safety, platform, requirements engineering}, issn = {1862-278X}, doi = {10.1515/bmt-2017-0040}, author = {Arney, David and Plourde, Jeffrey and Goldman, Julian M.} } @article {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 {1291, title = {Using Android and Open Data Kit Technology in Data Management for Research in Resource-Limited Settings in the Niger Delta Region of Nigeria: Cross-Sectional Household Survey.}, journal = {JMIR Mhealth Uhealth}, volume = {5}, year = {2017}, month = {2017 Nov 30}, pages = {e171}, abstract = {

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

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

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

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

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

}, issn = {2291-5222}, doi = {10.2196/mhealth.7827}, author = {Maduka, Omosivie and Akpan, Godwin and Maleghemi, Sylvester} } @article {1157, title = {Benefits, {Challenges} and {Potential} {Strategies} of {Open} {Source} {Health} {Economic} {Models}}, journal = {PharmacoEconomics}, year = {2016}, issn = {1179-2027}, doi = {10.1007/s40273-016-0479-8}, author = {Dunlop, William C. N. and Mason, Nicola and Kenworthy, James and Akehurst, Ron L.} } @article {1130, title = {Development of an open technology sensor suite for assisted living: a student-led research project.}, journal = {Interface Focus}, volume = {6}, year = {2016}, month = {2016 Aug 6}, pages = {20160018}, abstract = {

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

}, issn = {2042-8898}, doi = {10.1098/rsfs.2016.0018}, author = {Manton, James D and Hughes, Josephine A E and Bonner, Oliver and Amjad, Omar A and Mair, Philip and Miele, Isabella and Wang, Tiesheng and Levdik, Vitaly and Hall, Richard D and Baekelandt, G{\'e}raldine and Vasconcellos, Fernando da Cruz and Hadeler, Oliver and Hutter, Tanya and Kaminski, Clemens F} } @article {1106, title = {Health figures: an open source JavaScript library for health data visualization.}, journal = {BMC Med Inform Decis Mak}, volume = {16}, year = {2016}, month = {2016}, pages = {38}, abstract = {

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

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

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

}, keywords = {Data visualization, Health data, Health informatics, Javascript}, issn = {1472-6947}, doi = {10.1186/s12911-016-0275-6}, author = {Ledesma, Andres and Al-Musawi, Mohammed and Nieminen, Hannu} } @article {1131, title = {Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.}, journal = {Med Image Anal}, year = {2016}, month = {2016 Jul 7}, abstract = {

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

}, issn = {1361-8423}, doi = {10.1016/j.media.2016.06.035}, author = {Kapur, Tina and Pieper, Steve and Fedorov, Andriy and Fillion-Robin, J-C and Halle, Michael and O{\textquoteright}Donnell, Lauren and Lasso, Andras and Ungi, Tamas and Pinter, Csaba and Finet, Julien and Pujol, Sonia and Jagadeesan, Jayender and Tokuda, Junichi and Norton, Isaiah and Estepar, Raul San Jose and Gering, David and Aerts, Hugo J W L and Jakab, Marianna and Hata, Nobuhiko and Ibanez, Luiz and Blezek, Daniel and Miller, Jim and Aylward, Stephen and Grimson, W Eric L and Fichtinger, Gabor and Wells, William M and Lorensen, William E and Schroeder, Will and Kikinis, Ron} } @article {1162, title = {Jenkins-{CI}, an {Open}-{Source} {Continuous} {Integration} {System}, as a {Scientific} {Data} and {Image}-{Processing} {Platform}}, journal = {Journal of Biomolecular Screening}, year = {2016}, abstract = {High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.}, keywords = {CellProfiler, continuous integration, high-content screening, high-performance computing}, issn = {1552-454X}, doi = {10.1177/1087057116679993}, author = {Moutsatsos, Ioannis K. and Hossain, Imtiaz and Agarinis, Claudia and Harbinski, Fred and Abraham, Yann and Dobler, Luc and Zhang, Xian and Wilson, Christopher J. and Jenkins, Jeremy L. and Holway, Nicholas and Tallarico, John and Parker, Christian N.} } @article {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 {1126, title = {TREMOR12: An Open-Source Mobile App for Tremor Quantification.}, journal = {Stereotact Funct Neurosurg}, volume = {94}, year = {2016}, month = {2016}, pages = {182-186}, abstract = {

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

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

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

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

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

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

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

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

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

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

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

}, issn = {1423-0372}, doi = {10.1159/000446610}, author = {Kubben, Pieter L and Kuijf, Mark L and Ackermans, Linda P C M and Leentjes, Albert F G and Temel, Yasin} } @article {992, title = {A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Sep 2}, abstract = {

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

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

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

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

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

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv104}, author = {Neinstein, Aaron and Wong, Jenise and Look, Howard and Arbiter, Brandon and Quirk, Kent and McCanne, Steve and Sun, Yao and Blum, Michael and Adi, Saleh} } @article {1002, title = {Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.}, journal = {J Biomed Inform}, volume = {53}, year = {2015}, month = {2015 Feb}, pages = {390-404}, abstract = {

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

}, issn = {1532-0480}, doi = {10.1016/j.jbi.2014.11.012}, author = {Zaidan, A A and Zaidan, B B and Al-Haiqi, Ahmed and Kiah, M L M and Hussain, Muzammil and Abdulnabi, Mohamed} } @article {1279, title = {Identifying patients with asthma in primary care electronic medical record systems Chart analysis-based electronic algorithm validation study.}, journal = {Can Fam Physician}, volume = {61}, year = {2015}, month = {2015 Oct}, pages = {e474-83}, abstract = {

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

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

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

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

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

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

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

}, keywords = {Adult, Aged, Algorithms, Asthma, Data Accuracy, electronic health records, Female, Humans, Male, Middle Aged, Ontario, Primary Health Care, Pulmonary Disease, Chronic Obstructive, Registries, Retrospective Studies, Sensitivity and Specificity}, issn = {1715-5258}, author = {Xi, Nancy and Wallace, Rebecca and Agarwal, Gina and Chan, David and Gershon, Andrea and Gupta, Samir} } @article {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 {979, title = {medplot: a web application for dynamic summary and analysis of longitudinal medical data based on R.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0121760}, abstract = {

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

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

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

}, issn = {1876-7737}, doi = {10.1016/j.jprot.2015.06.013}, author = {Horlacher, Oliver and Nikitin, Frederic and Alocci, Davide and Mariethoz, Julien and M{\"u}ller, Markus and Lisacek, Frederique} } @article {984, title = {An open source business model for malaria.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0117150}, abstract = {

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

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0117150}, author = {{\r A}rdal, Christine and R{\o}ttingen, John-Arne} } @article {996, title = {Open source in cachexia?}, journal = {J Cachexia Sarcopenia Muscle}, volume = {6}, year = {2015}, month = {2015 Mar}, pages = {112-3}, issn = {2190-5991}, doi = {10.1002/jcsm.12013}, author = {Stemmler, Britta and Argil{\'e}s, Joseph M} } @article {987, title = {Open source software in a practical approach for post processing of radiologic images.}, journal = {Radiol Med}, volume = {120}, year = {2015}, month = {2015 Mar}, pages = {309-23}, abstract = {

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

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

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

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

}, keywords = {Diagnostic Imaging, Humans, Image Interpretation, Computer-Assisted, Image Processing, Computer-Assisted, Radiology Information Systems, Reproducibility of Results, Sensitivity and Specificity, Software, Software Validation, User-Computer Interface}, issn = {1826-6983}, doi = {10.1007/s11547-014-0437-5}, author = {Valeri, Gianluca and Mazza, Francesco Antonino and Maggi, Stefania and Aramini, Daniele and La Riccia, Luigi and Mazzoni, Giovanni and Giovagnoni, Andrea} } @article {1005, title = {A Standards-Based Architecture Proposal for Integrating Patient mHealth Apps to Electronic Health Record Systems.}, journal = {Appl Clin Inform}, volume = {6}, year = {2015}, month = {2015}, pages = {488-505}, abstract = {

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

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

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

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

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

}, issn = {1869-0327}, doi = {10.4338/ACI-2014-12-RA-0115}, author = {Marceglia, S and Fontelo, P and Rossi, E and Ackerman, M J} } @article {1052, title = {Translational research platforms integrating clinical and omics data: a review of publicly available solutions.}, journal = {Brief Bioinform}, volume = {16}, year = {2015}, month = {2015 Mar}, pages = {280-90}, abstract = {

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

}, issn = {1477-4054}, doi = {10.1093/bib/bbu006}, author = {Canuel, Vincent and Rance, Bastien and Avillach, Paul and Degoulet, Patrice and Burgun, Anita} } @article {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 {1031, title = {Evaluation of software maintain ability with open EHR - a comparison of architectures.}, journal = {Int J Med Inform}, volume = {83}, year = {2014}, month = {2014 Nov}, pages = {849-59}, abstract = {

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

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

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

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

}, keywords = {Data Curation, electronic health records, Information Dissemination, Information Storage and Retrieval, Meaningful Use, Software, Software Design}, issn = {1872-8243}, doi = {10.1016/j.ijmedinf.2014.07.006}, author = {Atalag, Koray and Yang, Hong Yul and Tempero, Ewan and Warren, James R} } @article {945, title = {ExpertEyes: Open-source, high-definition eyetracking.}, journal = {Behav Res Methods}, year = {2014}, month = {2014 Jun 17}, abstract = {

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

}, issn = {1554-3528}, doi = {10.3758/s13428-014-0465-z}, author = {Parada, Francisco J and Wyatte, Dean and Yu, Chen and Akavipat, Ruj and Emerick, Brandi and Busey, Thomas} } @article {1033, title = {Making cytological diagnoses on digital images using the iPath network.}, journal = {Acta Cytol}, volume = {58}, year = {2014}, month = {2014}, pages = {453-60}, abstract = {

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

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

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

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

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

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, Computers, Handheld, Cytodiagnosis, Diagnosis, Differential, Female, Humans, Hyperplasia, Infant, Male, Metaplasia, Middle Aged, Neoplasms, Observer Variation, Reproducibility of Results, Sensitivity and Specificity, Telemedicine}, issn = {0001-5547}, doi = {10.1159/000369241}, author = {Dalquen, Peter and Savic Prince, Spasenija and Spieler, Peter and Kunze, Dietmar and Neumann, Heinrich and Eppenberger-Castori, Serenella and Adams, Heiner and Glatz, Katharina and Bubendorf, Lukas} } @article {943, title = {Open-source electronic data capture system offered increased accuracy and cost-effectiveness compared with paper methods in Africa.}, journal = {J Clin Epidemiol}, year = {2014}, month = {2014 Aug 15}, abstract = {

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

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

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

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

}, issn = {1878-5921}, doi = {10.1016/j.jclinepi.2014.06.012}, author = {Dillon, David G and Pirie, Fraser and Pomilla, Cristina and Sandhu, Manjinder S and Motala, Ayesha A and Young, Elizabeth H} } @article {1001, title = {tranSMART: An Open Source Knowledge Management and High Content Data Analytics Platform.}, journal = {AMIA Jt Summits Transl Sci Proc}, volume = {2014}, year = {2014}, month = {2014}, pages = {96-101}, abstract = {

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

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

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

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

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

}, issn = {1735-1995}, author = {Aminpour, Farzaneh and Sadoughi, Farahnaz and Ahamdi, Maryam} } @article {856, title = {Clinician-led development of electronic health records systems.}, journal = {Stud Health Technol Inform}, volume = {183}, year = {2013}, month = {2013}, pages = {3-8}, abstract = {

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

}, issn = {0926-9630}, author = {Chelsom, John and Ahluwalia, Raju and Dogar, Naveed} } @article {863, title = {DICOM RIS/PACS Telemedicine Network Implementation using Free Open Source Software}, journal = {Latin America Transactions, IEEE (Revista IEEE America Latina)}, volume = {11}, year = {2013}, pages = {168-171}, abstract = {The increasing incorporation of modern medical imaging equipment requires the operation of systems that store, transmit and display images, PACS (Picture Archiving and Communication System) via digital networks to provide health services with higher quality. These revolutionized radiology systems based on digital techniques, communications, visualization and information technologies. One of the major problems that arise in institutions working with Imaging Diagnosis (Dx) in the interconnection network or equipment, are the "bottlenecks" caused by the high flow of network data. This flux is given by the transfer of images in DICOM (Digital Imaging and Communications in Medicine) to the various devices that make up a DICOM network, called Service Class Users (SCU) and Service Class Providers (SCP). This paper describes the development and implementation of a network of medical images using free software and its compatibility with its own data network of a RIS (Radiology Information System). Describes techniques used for the interconnection of local nodes on a LAN (Local Area Network) remote WAN Wide Area Network) via Internet and WLAN (Wireless Area Network.}, keywords = {DICOM, Free Software, Medical Imaging, Telemedicine}, issn = {1548-0992}, doi = {10.1109/TLA.2013.6502797}, author = {Alvarez, Luis R. and Vargas Solis, Roberto} } @article {840, title = {The Evolving Role of Open Source Software in Medicine and Health Services}, journal = {Technology Innovation Management Review}, year = {2013}, month = {01/2013}, pages = {32-39}, abstract = {The past five decades have witnessed immense coevolution of methods and tools of information technology, and their practical and experimental application within the medical and healthcare domain. Healthcare itself continues to evolve in response to change in healthcare needs, progress in the scientific foundations of treatments, and in professional and managerial organization of affordable and effective services, in which patients and their families and carers increasingly participate. Taken together, these trends impose highly complex underlying challenges for the design, development, and sustainability of the quality of supporting information services and software infrastructure that are needed. The challenges are multidisciplinary and multiprofessional in scope, and they require deeper study and learning to inform policy and promote public awareness of the problems health services have faced in this area for many years. The repeating pattern of failure to live up to expectations of policy-driven national health IT initiatives has proved very costly and remains frustrating and unproductive for all involved. In this article, we highlight the barriers to progress and discuss the dangers of pursuing a standardization framework devoid of empirical testing and iterative development. We give the example of the openEHR Foundation, which was established at University College London (UCL) in London, England, with members in 80 countries. The Foundation is a not-for-profit company providing open specifications and working for generic standards for electronic records, informed directly by a wide range of implementation experience. We also introduce the Opereffa open source framework, which was developed at UCL based on these specifications and which has been downloaded in some 70 countries. We argue that such an approach is now essential to support good discipline, innovation, and governance at the heart of medicine and health services, in line with the new mandate for health commissioning in the United Kingdom{\textquoteright}s National Health Service (NHS), which emphasizes patient participation, innovation, transparency, and accountability.}, keywords = {electronic health care record, information retrieval, open source framework, openEHR Foundation, persistence, standards based}, issn = {1927-0321}, author = {David Ingram and Sevket Seref Arikan} } @article {892, title = {Integration of advanced 3D SPECT modeling into the open-source STIR framework}, journal = {Medical Physics}, volume = {40}, year = {2013}, pages = {092502}, keywords = {C++ language, image reconstruction, medical image processing, object-oriented programming, public domain software, single photon emission computed tomography, software libraries, software packages}, doi = {10.1118/1.4816676}, url = {http://link.aip.org/link/?MPH/40/092502/1}, author = {Berta Marti Fuster and Carles Falcon and Charalampos Tsoumpas and Lefteris Livieratos and Pablo Aguiar and Albert Cot and Domenec Ros and Kris Thielemans} } @article {1053, title = {tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research.}, journal = {AMIA Jt Summits Transl Sci Proc}, volume = {2013}, year = {2013}, month = {2013}, pages = {6-8}, abstract = {

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

}, issn = {2153-4063}, author = {Athey, Brian D and Braxenthaler, Michael and Haas, Magali and Guo, Yike} } @article {896, title = {Utility of an open-source DICOM viewer software (OsiriX) to assess pulmonary fibrosis in systemic sclerosis: preliminary results.}, journal = {Rheumatol Int}, year = {2013}, month = {2013 Aug 15}, abstract = {

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

}, issn = {1437-160X}, doi = {10.1007/s00296-013-2845-6}, author = {Ariani, Alarico and Carotti, Marina and Gutierrez, Marwin and Bichisecchi, Elisabetta and Grassi, Walter and Giuseppetti, Gian Marco and Salaffi, Fausto} } @inbook {1080, title = {Development of an mHealth Open Source Platform for Diabetic Foot Ulcers Tele-consultations}, booktitle = {Wireless Mobile Communication and Healthcare}, series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering}, volume = {83}, year = {2012}, pages = {158-164}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, keywords = {diabetic foot ulcers, m-health, Telemedicine}, isbn = {978-3-642-29733-5}, doi = {10.1007/978-3-642-29734-2_22}, url = {http://dx.doi.org/10.1007/978-3-642-29734-2_22}, author = {Dafoulas, GeorgeE. and Koutsias, Stylianos and Behar, Joachim and Osorio, Juan and Malley, Brian and Gruentzig, Alexander and Celi, LeoAnthony and Angelidis, Pantelis and Theodorou, Kyriaki and Giannoukas, Athanasios}, editor = {Nikita, KonstantinaS. and Lin, JamesC. and Fotiadis, DimitriosI. and Arredondo Waldmeyer, Maria-Teresa} } @inbook {851, title = {Development of an mHealth Open Source Platform for Diabetic Foot Ulcers Tele-consultations}, booktitle = {Wireless Mobile Communication and Healthcare}, series = {Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering}, volume = {83}, year = {2012}, pages = {158-164}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Diabetes is one of the foremost causes of death in many countries and a leading cause of blindness, renal failure, and non-traumatic amputation. Therefore, diabetic foot ulceration and amputation cause extensive burden on individuals and health care systems in developed and developing countries. Due to the multi-disciplinary requirements for the treatment of diabetic foot ulceration, telemedicine has been introduced to facilitate the access of the patients to specialized health professionals. In this paper the development of an open source mobile health platform is presented, able to support diagnostic algorithms, with the use of a smartphone.}, keywords = {diabetic foot ulcers, m-health, Telemedicine}, isbn = {978-3-642-29733-5}, doi = {10.1007/978-3-642-29734-2_22}, url = {http://dx.doi.org/10.1007/978-3-642-29734-2_22}, author = {Dafoulas, GeorgeE. and Koutsias, Stylianos and Behar, Joachim and Osorio, Juan and Malley, Brian and Gruentzig, Alexander and Celi, LeoAnthony and Angelidis, Pantelis and Theodorou, Kyriaki and Giannoukas, Athanasios}, editor = {Nikita, KonstantinaS. and Lin, JamesC. and Fotiadis, DimitriosI. and Arredondo Waldmeyer, Maria-Teresa} } @article {784, title = {DicomBrowser: Software for Viewing and Modifying DICOM Metadata.}, journal = {J Digit Imaging}, year = {2012}, month = {2012 Feb 15}, abstract = {Digital Imaging and Communications in Medicine (DICOM) is the dominant standard for medical imaging data. DICOM-compliant devices and the data they produce are generally designed for clinical use and often do not match the needs of users in research or clinical trial settings. DicomBrowser is software designed to ease the transition between clinically oriented DICOM tools and the specialized workflows of research imaging. It supports interactive loading and viewing of DICOM images and metadata across multiple studies and provides a rich and flexible system for modifying DICOM metadata. Users can make ad hoc changes in a graphical user interface, write metadata modification scripts for batch operations, use partly automated methods that guide users to modify specific attributes, or combine any of these approaches. DicomBrowser can save modified objects as local files or send them to a DICOM storage service using the C-STORE network protocol. DicomBrowser is open-source software, available for download at http://nrg.wustl.edu/software/dicom-browser .}, issn = {1618-727X}, doi = {10.1007/s10278-012-9462-x}, author = {Archie, Kevin A and Marcus, Daniel S} } @article {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 {805, title = {The Importance of Using Open Source Technologies and Common Standards for Interoperability within eHealth: Perspectives from the Millennium Villages Project}, journal = {Advances in Health Care Management}, volume = {Advances in Health Care Management}, year = {2012}, pages = {189{\textendash}204}, abstract = {Purpose {\textendash} The purpose of this chapter is to illustrate the importance of using open source technologies and common standards for interoperability when implementing eHealth systems, and to illustrate this through case studies, where possible. Design/methodology/approach {\textendash} The sources used to inform this chapter draw from the implementation and evaluation of the eHealth Program in the context of the Millennium Villages Project (MVP). Findings {\textendash} As the eHealth Team was tasked to deploy an eHealth architecture, the Millennium Villages Global-Network (MVG-Net), across all 14 of the MVP sites in sub-Saharan Africa, the team not only recognized the need for standards and uniformity but also realized that context would be an important factor. Therefore, the team decided to utilize open source solutions. Practical implications {\textendash} The MVP implementation of MVG-Net provides a model for those looking to implement informatics solutions across disciplines and countries. Furthermore, there are valuable lessons learned that the eHealth community can benefit from. Originality/value {\textendash} By sharing lessons learned and developing an accessible, open source eHealth platform, we believe that we can more efficiently and rapidly achieve the health-related and collaborative Millennium Development Goals.}, issn = {978-1-78052-858-8}, doi = {10.1108/S1474-8231(2012)0000012013}, author = {Andrew S. Kanter, Rob Borland, Mourice Barasa, Casey Iiams-Hauser, Olivia Velez, Nadi Nina Kaonga, Matt Berg} } @article {908, title = {The National Alliance for Medical Image Computing, a roadmap initiative to build a free and open source software infrastructure for translational research in medical image analysis}, journal = {Journal of the American Medical Informatics Association}, volume = {19}, year = {2012}, pages = {176{\textendash}180}, abstract = {The National Alliance for Medical Image Computing (NA-MIC), is a multi-institutional, interdisciplinary community of researchers, who share the recognition that modern health care demands improved technologies to ease suffering and prolong productive life. Organized under the National Centers for Biomedical Computing 7 years ago, the mission of NA-MIC is to implement a robust and flexible open-source infrastructure for developing and applying advanced imaging technologies across a range of important biomedical research disciplines. A measure of its success, NA-MIC is now applying this technology to diseases that have immense impact on the duration and quality of life: cancer, heart disease, trauma, and degenerative genetic diseases. The targets of this technology range from group comparisons to subject-specific analysis.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84857161947\&partnerID=40\&md5=c7d7cbab9304114a219812cb7c5091ee}, author = {Kapur, T.a and Pieper, S.b and Whitaker, R.c and Aylward, S.d and Jakab, M.a and Schroeder, W.d and Kikinis, R.a} } @article {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 {788, title = {The SMART Platform: early experience enabling substitutable applications for electronic health records.}, journal = {J Am Med Inform Assoc}, year = {2012}, month = {2012 Mar 17}, abstract = {ObjectiveThe Substitutable Medical Applications, Reusable Technologies (SMART) Platforms project seeks to develop a health information technology platform with substitutable applications (apps) constructed around core services. The authors believe this is a promising approach to driving down healthcare costs, supporting standards evolution, accommodating differences in care workflow, fostering competition in the market, and accelerating innovation.Materials and methodsThe Office of the National Coordinator for Health Information Technology, through the Strategic Health IT Advanced Research Projects (SHARP) Program, funds the project. The SMART team has focused on enabling the property of substitutability through an app programming interface leveraging web standards, presenting predictable data payloads, and abstracting away many details of enterprise health information technology systems. Containers-health information technology systems, such as electronic health records (EHR), personally controlled health records, and health information exchanges that use the SMART app programming interface or a portion of it-marshal data sources and present data simply, reliably, and consistently to apps.ResultsThe SMART team has completed the first phase of the project (a) defining an app programming interface, (b) developing containers, and (c) producing a set of charter apps that showcase the system capabilities. A focal point of this phase was the SMART Apps Challenge, publicized by the White House, using http://www.challenge.gov website, and generating 15 app submissions with diverse functionality.ConclusionKey strategic decisions must be made about the most effective market for further disseminating SMART: existing market-leading EHR vendors, new entrants into the EHR market, or other stakeholders such as health information exchanges.}, issn = {1527-974X}, doi = {10.1136/amiajnl-2011-000622}, author = {Mandl, Kenneth D and Mandel, Joshua C and Murphy, Shawn N and Bernstam, Elmer Victor and Ramoni, Rachel L and Kreda, David A and McCoy, J Michael and Adida, Ben and Kohane, Isaac S.} } @inbook {789, title = {SOFA: A Multi-Model Framework for Interactive Physical Simulation}, booktitle = {Soft Tissue Biomechanical Modeling for Computer Assisted Surgery}, series = {Studies in Mechanobiology, Tissue Engineering and Biomaterials}, volume = {11}, year = {2012}, pages = {283-321}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Simulation Open Framework Architecture (SOFA) is an open-source C++ library primarily targeted at interactive computational medical simulation. SOFA facilitates collaborations between specialists from various domains, by decomposing complex simulators into components designed independently and organized in a scenegraph data structure. Each component encapsulates one of the aspects of a simulation, such as the degrees of freedom, the forces and constraints, the differential equations, the main loop algorithms, the linear solvers, the collision detection algorithms or the interaction devices. The simulated objects can be represented using several models, each of them optimized for a different task such as the computation of internal forces, collision detection, haptics or visual display. These models are synchronized during the simulation using a mapping mechanism. CPU and GPU implementations can be transparently combined to exploit the computational power of modern hardware architectures. Thanks to this flexible yet efficient architecture, SOFA can be used as a test-bed to compare models and algorithms, or as a basis for the development of complex, high-performance simulators.}, isbn = {978-3-642-29013-8}, doi = {10.1007/8415_2012_125}, url = {http://dx.doi.org/10.1007/8415_2012_125}, author = {Faure, Fran{\c c}ois and Duriez, Christian and Delingette, Herv{\'e} and Allard, J{\'e}r{\'e}mie and Gilles, Benjamin and Marchesseau, St{\'e}phanie and Talbot, Hugo and Courtecuisse, Hadrien and Bousquet, Guillaume and Peterlik, Igor and Cotin, St{\'e}phane}, editor = {Payan, Yohan} } @article {779, title = {STIR: software for tomographic image reconstruction release 2.}, journal = {Phys Med Biol}, volume = {57}, year = {2012}, month = {2012 Feb 21}, pages = {867-83}, abstract = {We present a new version of STIR (Software for Tomographic Image Reconstruction), an open source object-oriented library implemented in C++~for 3D positron emission tomography reconstruction. This library has been designed such that it can be used for many algorithms and scanner geometries, while being portable to various computing platforms. This second release enhances its flexibility and modular design and includes additional features such as Compton scatter simulation, an additional iterative reconstruction algorithm and parametric image reconstruction (both indirect and direct). We discuss the new features in this release and present example results. STIR can be downloaded from http://stir.sourceforge.net.}, keywords = {Algorithms, Animals, Computers, Image Processing, Computer-Assisted, Mice, Software, Tomography}, issn = {1361-6560}, doi = {10.1088/0031-9155/57/4/867}, author = {Thielemans, Kris and Tsoumpas, Charalampos and Mustafovic, Sanida and Beisel, Tobias and Aguiar, Pablo and Dikaios, Nikolaos and Jacobson, Matthew W} } @article {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} } @inbook {springerlink:10.1007/978-1-4419-8204-9_9, title = {Medical Image Registration}, booktitle = {Multi Modality State-of-the-Art Medical Image Segmentation and Registration Methodologies}, year = {2011}, note = {10.1007/978-1-4419-8204-9_9}, pages = {227-245}, publisher = {Springer New York}, organization = {Springer New York}, abstract = {In this chapter, we cover the necessary background information required to understand medical image registration, the basic tools required to implement registration algorithms, and demonstrate a complete application for various types of registration between different modalities using freely available and maintained software.}, isbn = {978-1-4419-8204-9}, url = {http://dx.doi.org/10.1007/978-1-4419-8204-9_9}, author = {Aladl, Usaf E. and Peters, Terry}, editor = {El-Baz, Ayman S. and Acharya U, Rajendra and Laine, Andrew F. and Suri, Jasjit S.} } @inbook {springerlink:10.1007/978-1-4419-7046-6_68, title = {Open Source Clinical Portals: A Model for Healthcare Information Systems to Support Care Processes and Feed Clinical Research}, booktitle = {Software Tools and Algorithms for Biological Systems}, series = {Advances in Experimental Medicine and Biology}, volume = {696}, year = {2011}, note = {10.1007/978-1-4419-7046-6_68}, pages = {667-677}, publisher = {Springer New York}, organization = {Springer New York}, abstract = {Open source is a still unexploited chance for healthcare organizations and technology providers to answer to a growing demand for innovation and to join economical benefits with a new way of managing hospital information systems. This chapter will present the case of the web enterprise clinical portal developed in Italy by Niguarda Hospital in Milan with the support of Fondazione Politecnico di Milano, to enable a paperless environment for clinical and administrative activities in the ward. This represents also one rare case of open source technology and reuse in the healthcare sector, as the system{\textquoteright}s porting is now taking place at Besta Neurological Institute in Milan. This institute is customizing the portal to feed researchers with structured clinical data collected in its portal{\textquoteright}s patient records, so that they can be analyzed, e.g., through business intelligence tools. Both organizational and clinical advantages are investigated, from process monitoring, to semantic data structuring, to recognition of common patterns in care processes.}, isbn = {978-1-4419-7046-6}, url = {http://dx.doi.org/10.1007/978-1-4419-7046-6_68}, author = {Locatelli, Paolo and Baj, Emanuele and Restifo, Nicola and Origgi, Gianni and Bragagia, Silvia}, editor = {Arabnia, Hamid R. R. and Tran, Quoc-Nam} } @article {606, title = {Use of an innovative, affordable, and open-source short message service-based tool to monitor malaria in remote areas of Uganda.}, journal = {The American journal of tropical medicine and hygiene}, volume = {85}, year = {2011}, month = {2011 Jul}, pages = {26-33}, abstract = {Abstract. Quality health management requires timely and accurate data, and paper-based reporting does not fill this role adequately. The introduction of malaria rapid diagnostic tests and the availability of wireless communications present an opportunity to open direct data transmission and feedback between peripheral health workers and central managers. In November 2009, the Uganda Ministry of Health deployed a short message service-based reporting system in two districts. At a set-up cost of $100/health facility, local technician support of $ 400 per month, and a cost of $0.53/week/clinic, the SMS reporting system was started at more than 140 clinics. Positivity rates for rapid diagnostic tests and artemisinin combination therapy stock outs were 48\% and 54\% in Kabale and 71\% and 54\% in Gulu, among other reports, at more than 85\% health facilities reporting weekly and without monetary incentives or additional supervision. The SMS-based reporting systems have potential to improve timeliness in reporting of specific, time-sensitive metrics at modest cost, while by-passing current bottlenecks in the flow of data. With the development of specific capacity to manage stock data at district level, the availability of timely data offers potential to address commodity distribution problems and reduce stock-outs.}, issn = {1476-1645}, author = {Asiimwe, Caroline and Gelvin, David and Lee, Evan and Ben Amor, Yanis and Quinto, Ebony and Katureebe, Charles and Sundaram, Lakshmi and Bell, David and Berg, Matt} } @conference {558, title = {xDAuth: A Scalable and Lightweight Framework for Cross Domain Access Control and Delegation}, booktitle = {SACMAT{\textquoteright}11}, year = {2011}, publisher = {ACM}, organization = {ACM}, address = {Innsbruck, Austria}, abstract = {Cross domain resource sharing and collaborations have be- come pervasive in today{\textquoteright}s service oriented organizations. Existing approaches for the realization of cross domain ac- cess control are either focused on the model level only with- out concrete implementation mechanisms, or not general enough to provide a exible framework for enterprise web applications. In this paper, we present xDAuth, a frame- work for the realization of cross domain access control and delegation with RESTful web service architecture. While focusing on real issues under the context of cross domain access scenarios such as no prede ned trust relationship be- tween a service provider domain and service requestor do- main, xDAuth leverages existing web technologies to real- ize desired security requirements while supporting exible and scalable security policies and privacy protection with low performance overhead. We have implemented xDAuth in a medical module in OpenERP, an open source ERP sys- tem. Our evaluation demonstrates that xDAuth is a feasible framework towards general cross domain access control for service oriented architectures.}, url = {http://profsandhu.com/zhang/pub/sacmat11-xdauth.pdf}, author = {Masoom Alam and Xinwen Zhang and Kamran H Khan and Gohar Ali} } @article {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 {20335647, title = {The development and design of an electronic patient record using open source web-based technology.}, journal = {The HIM journal}, volume = {39}, year = {2010}, month = {2010}, pages = {30-5}, abstract = {This paper describes the method used to develop the One Stop Crisis Centre (OSCC) Portal, an open source web-based electronic patient record system (EPR) for the One Stop Crisis Center, Hospital Universiti Sains Malaysia (HUSM) in Kelantan, Malaysia. Features and functionalities of the system are presented to demonstrate the workflow. Use of the OSCC Portal improved data integration and data communication and contributed to improvements in care management. With implementation of the OSCC portal, improved coordination between disciplines and standardisation of data in HUSM were noticed. It is expected that this will in turn result in improved data confidentiality and data integrity. The collected data will also be useful for quality assessment and research. Other low-resource centers with limited computer hardware and access to open-source software could benefit from this endeavour.}, author = {Syed-Mohamad, Sharifa Mastura and Ali, Siti Hawa and Mat-Husin, Mohd Nazri} } @article {20517664, title = {E-health integration and interoperability based on open-source information technology.}, journal = {Wiener klinische Wochenschrift}, volume = {122 Suppl 2}, year = {2010}, month = {2010 May}, pages = {3-10}, author = {Dinevski, Dejan and Poli, Andrea and Krajnc, Ivan and Sustersic, Olga and Arh, Tanja} } @proceedings {512, title = {Indivo X: Developing a Fully Substitutable Personally Controlled Health Record Platform}, year = {2010}, month = {11/2010}, abstract = {To support a rich ecosystem of third-party applications around a personally controlled health record (PCHR), we have redesigned Indivo, the original PCHR, as a web- based platform with feature-level substitutability. Core to this new release is the Indivo X Application Program- ming Interface (API), the contract between the PCHR platform and the end-user apps. Using rapid iterative de- velopment to build a minimal feature set from real-world requirements, the resulting Indivo X API, now in public stable beta, is enabling developers, including third-party contributors, to quickly create and integrate novel fea- tures into patients{\textquoteright} online records, ultimately building a fully customizable experience for diverse patient needs.}, url = {http://proceedings.amia.org/127eoo}, author = {Adida, Ben and Sanyal, Arjun and Zabak, Steve and Kohane, Isaac S. and Mandl, Kenneth D} } @article {20646816, title = {Mandibular reconstruction with fibula free flap. Experience of virtual reconstruction using Osirix((R)), a free and open source software for medical imagery.}, journal = {Annales de chirurgie plastique et esthetique}, year = {2010}, month = {2010 Jun 18}, abstract = {The techniques of free tissue transfers are mainly used for mandibular reconstruction by specialized surgical teams. This type of reconstruction is mostly realized in matters of head and neck cancers affecting mandibular bone and requiring a wide surgical resection and interruption of the mandible. To decrease the duration of the operation, surgical procedure involves generally two teams, one devoted to cancer resection and the other one to raise the fibular flap and making the reconstruction. For a better preparation of this surgical procedure, we propose here the use of a medical imaging software enabling mandibular reconstructions in three dimensions using the CT-scan done during the initial disease-staging checkup. The software used is Osirix((R)), developed since 2004 by a team of radiologists from Geneva and UCLA, working on Apple((R)) computers and downloadable free of charge in its basic version. We report here our experience of this software in 17 patients, with a preoperative modelling in three dimensions of the mandible, of the segment of mandible to be removed. It also forecasts the numbers of fragments of fibula needed and the location of osteotomies.}, author = {Albert, S and Cristofari, J-P and Cox, A and Bensimon, J-L and Guedon, C and Barry, B} } @article {1043, title = {An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging.}, journal = {BMC Med Imaging}, volume = {10}, year = {2010}, month = {2010}, pages = {16}, abstract = {

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

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

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

}, keywords = {Algorithms, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Programming Languages, Reproducibility of Results, Sensitivity and Specificity, Software}, issn = {1471-2342}, doi = {10.1186/1471-2342-10-16}, author = {Messroghli, Daniel R and Rudolph, Andre and Abdel-Aty, Hassan and Wassmuth, Ralf and Kuhne, Titus and Dietz, Rainer and Schulz-Menger, Jeanette} } @article {1471-2342-10-16, title = {An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging}, journal = {BMC Medical Imaging}, volume = {10}, number = {1}, year = {2010}, pages = {16}, abstract = {BACKGROUND:In magnetic resonance (MR) imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization. RESULTS:After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/ TOMROP T1; modified Look-Locker inversion recovery (MOLLI) T1; single-echo T2/ T2*; and multi-echo T2/ T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data. CONCLUSIONS:MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet. }, issn = {1471-2342}, doi = {10.1186/1471-2342-10-16}, url = {http://www.biomedcentral.com/1471-2342/10/16}, author = {Messroghli, Daniel and Rudolph, Andre and Abdel-Aty, Hassan and Wassmuth, Ralf and Kuhne, Titus and Dietz, Rainer and Schulz-Menger, Jeanette} } @conference {1086, title = {Commercial Open Source RIS/PACS: The ClearCanvas Experience}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001827400220027}, author = {Norman Young and Clinton Chau and John Adziovsky} } @conference {1088, title = {Concept Matching between OpenEHR and SONHO}, booktitle = {Proceedings of the 1st International Workshop on Open Source in European Health Care: The Time is Ripe (BIOSTEC 2009)}, year = {2009}, isbn = {978-989-8111-79-1}, doi = {10.5220/0001828400450053}, author = {Ricardo Cruz-Correia and Carla {\'A}vila and Rong Chen} } @article {19230726, title = {Demonstration of the Adamkiewicz artery by multidetector computed tomography angiography analysed with the open-source software OsiriX.}, journal = {European journal of vascular and endovascular surgery : the official journal of the European Society for Vascular Surgery}, volume = {37}, year = {2009}, month = {2009 Apr}, pages = {395-400}, abstract = {OBJECTIVE: To evaluate the feasibility of the Adamkiewicz artery (AKA) detection by multidetector computed tomography (CT) data analysis without the need of a dedicated workstation, using low-cost hardware and the freeware OsiriX. METHODS: CT scans of 67 patients undergoing a thoracic or thoraco-abdominal aortic procedure between April 2006 and August 2008 were evaluated with respect to detection rate and AKA level and side using the OsiriX software version 3.2 on Mac OS X computer and compared to results obtained by standard workstation analysis, in a fully blinded analysis. The results were also compared with data compiled from a review of the English-language literature on this topic. RESULTS: (1) AKA identification showed a substantial agreement of 85.07\% between the methods (k=0.636). (2) The comparison of AKA level showed a substantial agreement (weighted k=0.661), with consensus in 70.14\%. (3) From the literature review, we found that recognition of the AKA was achieved in 466 of 555 cases (83.96\%). (4) In 384 (83.3\%) cases the AKA originated from a left intercostal artery. (5) The proposed method and literature-compiled data showed a similar AKA level distribution. CONCLUSIONS: Noninvasive AKA location with open-source software and low-cost hardware is feasible. The OsiriX software allows to effectively navigate through CT data not only to study the aorta, but also to detect the AKA, as in the case of the standard method and the literature data. Its availability and ease of use may contribute to make identification of the AKA part of the routine evaluation of CT scans in patients with aortic disease, even where dedicated workstations are not available, with potential benefits for planning therapeutic procedures.}, author = {Melissano, G and Bertoglio, L and Civelli, V and Amato, A C Moraes and Coppi, G and Civilini, E and Calori, G and De Cobelli, F and Del Maschio, A and Chiesa, R} } @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 {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 {444, title = {Visualization Software for Real-time, Image-guided Therapeutics in Cardiovascular Interventions}, year = {2009}, publisher = {CCSd/HAL : e-articles server (based on gBUS) [http://hal.ccsd.cnrs.fr/oai/oai.php] (France)}, abstract = {This paper introduces RtViewer, a four-dimensional (3D + time) real-time visualization software for guiding cardiovascular interventions that is open source and freely available. RtViewer was designed to be part of a pipeline that can connect it to a magnetic resonance imaging (MRI) scanner, actively tracked catheters, and navigational devices. The architecture and features of RtViewer will be described with examples of guiding percutaneous cardiovascular interventions. The paper concludes with a brief description of the work in progress on the next generation of this platform, named Vurtigo.}, keywords = {Computer Science/Medical Imaging}, url = {http://hal.archives-ouvertes.fr/inria-00417831/en/}, author = {Pintilie, Stefan and Biswas, Labonny and Anderson, Kevan and Dick, Sandy and Wright, Graham and Radau, Perry} } @article {920, title = {The AQUA-FONTIS study: protocol of a multidisciplinary, cross-sectional and prospective longitudinal study for developing standardized diagnostics and classification of non-thyroidal illness syndrome.}, journal = {BMC Endocr Disord}, volume = {8}, year = {2008}, month = {2008}, pages = {13}, abstract = {

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

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

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

TRIAL REGISTRATION: ClinicalTrials.gov NCT00591032.

}, issn = {1472-6823}, doi = {10.1186/1472-6823-8-13}, author = {Dietrich, Johannes W and Stachon, Axel and Antic, Biljana and Klein, Harald H and Hering, Steffen} } @article {802, title = {The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.}, journal = {J Digit Imaging}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {21-33}, abstract = {This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers{\textquoteright} mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.}, keywords = {Computer Systems, Data Display, Database Management Systems, Humans, Information Dissemination, Information Storage and Retrieval, Safety, Software, Software Design, Software Validation, Surgery, Computer-Assisted, Systems Integration, User-Computer Interface}, issn = {0897-1889}, doi = {10.1007/s10278-007-9054-3}, author = {Enquobahrie, Andinet and Cheng, Patrick and Gary, Kevin and Ibanez, Luis and Gobbi, David and Lindseth, Frank and Yaniv, Ziv and Aylward, Stephen and Jomier, Julien and Cleary, Kevin} } @article {17850667, title = {Indivo: a personally controlled health record for health information exchange and communication.}, journal = {BMC medical informatics and decision making}, volume = {7}, year = {2007}, month = {2007}, pages = {25}, abstract = {BACKGROUND: Personally controlled health records (PCHRs), a subset of personal health records (PHRs), enable a patient to assemble, maintain and manage a secure copy of his or her medical data. Indivo (formerly PING) is an open source, open standards PCHR with an open application programming interface (API). RESULTS: We describe how the PCHR platform can provide standard building blocks for networked PHR applications. Indivo allows the ready integration of diverse sources of medical data under a patient{\textquoteright}s control through the use of standards-based communication protocols and APIs for connecting PCHRs to existing and future health information systems. CONCLUSION: The strict and transparent personal control model is designed to encourage widespread participation by patients, healthcare providers and institutions, thus creating the ecosystem for development of innovative, consumer-focused healthcare applications.}, url = {http://www.biomedcentral.com/1472-6947/7/25/}, author = {Mandl, Kenneth D and Simons, William W and Crawford, William C R and Abbett, Jonathan M} } @article {18074196, title = {Open-source, low-cost, high-reliability solutions for digital imaging systems: example of a "dicom router".}, journal = {La Radiologia medica}, volume = {112}, year = {2007}, month = {2007 Dec}, pages = {1252-9}, abstract = {PURPOSE: The purpose of this article is to illustrate a case where acquisition of digital imaging know-how by a modern radiotherapy division has helped to solve a technical problem while allowing substantial savings through the use of free and open-source resources. The problem was related to the necessity to route, with complex policies, the images produced by different digital imaging and communications in medicine (DICOM) sources within the department or in other divisions and/or hospitals. MATERIALS AND METHODS: The problem was solved by using completely free, well-tested and stable technologies (PHP, Apache, MySQL, DCMTK OFFIS, Red Hat Linux 9A and Linux Fedora Core 4) and low-cost hardware to contain costs. In the development, we also considered integration of the routed images with the existing electronic clinical records. RESULTS: The system developed, called the dicom router, implemented two kinds of routing: manual and automatic, both oriented to link the images acquired with the existing electronic clinical records. System stability was enhanced in a second phase by using a low-cost hardware redundancy solution. The system has now been operating for 1 year and has proved the value of the technologies used. CONCLUSIONS: The need to operate with more than one provider creates a series of integration issues, so that it becomes economically appealing to acquire internally the knowledge needed to interact more precisely with providers of big information technology (IT) solutions. This need is well catered for by open-source technologies, which are well documented and available to everyone. By using them, in-house IT technicians are able to implement valuable technical solutions for small-to medium-sized informatization problems, which would otherwise remain unsolved except with great economic efforts.}, author = {Gatta, R and Abeni, F and Buglione, M and Peveri, A and Barbera, F and Tonoli, S and Fratta, P and Magrini, S M} } @article {17249408, title = {OpenSourcePACS: an extensible infrastructure for medical image management.}, journal = {IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society}, volume = {11}, year = {2007}, month = {2007 Jan}, pages = {94-109}, abstract = {The development of comprehensive picture archive and communication systems (PACS) has mainly been limited to proprietary developments by vendors, though a number of freely available software projects have addressed specific image management tasks. The openSourcePACS project aims to provide an open source, common foundation upon which not only can a basic PACS be readily implemented, but to also support the evolution of new PACS functionality through the development of novel imaging applications and services. openSourcePACS consists of four main software modules: 1) image order entry, which enables the ordering and tracking of structured image requisitions; 2) an agent-based image server framework that coordinates distributed image services including routing, image processing, and querying beyond the present digital image and communications in medicine (DICOM) capabilities; 3) an image viewer, supporting standard display and image manipulation tools, DICOM presentation states, and structured reporting; and 4) reporting and result dissemination, supplying web-based widgets for creating integrated reports. All components are implemented using Java to encourage cross-platform deployment. To demonstrate the usage of openSourcePACS, a preliminary application supporting primary care/specialist communication was developed and is described herein. Ultimately, the goal of openSourcePACS is to promote the wide-scale development and usage of PACS and imaging applications within academic and research communities.}, url = {http://escholarship.org/uc/item/186368fv}, author = {Bui, Alex A T and Morioka, Craig and Dionisio, John David N and Johnson, David B and Sinha, Usha and Ardekani, Siamak and Taira, Ricky K and Aberle, Denise R and El-Saden, Suzie and Kangarloo, Hooshang} } @conference {SOFA07, title = {SOFA - an Open Source Framework for Medical Simulation}, booktitle = {Medicine Meets Virtual Reality (MMVR{\textquoteright}15)}, year = {2007}, month = {February}, address = {Long Beach, USA}, url = {http://www.sofa-framework.org/docs/SOFA_MMVR07.pdf}, author = {Allard, J{\'e}r{\'e}mie and Cotin, St{\'e}phane and Faure, Fran{\c c}ois and Bensoussan, Pierre-Jean and Poyer, Fran{\c c}ois and Duriez, Christian and Delingette, Herv{\'e} and Grisoni, Laurent} } @article {17238397, title = {Cooking up an open source EMR for developing countries: OpenMRS - a recipe for successful collaboration.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2006}, month = {2006}, pages = {529-33}, abstract = {Millions of people are continue to die each year from HIV/AIDS. The majority of infected persons (>95\%) live in the developing world. A worthy response to this pandemic will require coordinated, scalable, and flexible information systems. We describe the OpenMRS system, an open source, collaborative effort that can serve as a foundation for EMR development in developing countries. We report our progress to date, lessons learned, and future directions.}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1839638}, author = {Mamlin, Burke W and Biondich, Paul G and Wolfe, Ben A and Fraser, Hamish and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Tierney, William M} } @article {17238765, title = {The OpenMRS system: collaborating toward an open source EMR for developing countries.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, year = {2006}, month = {2006}, pages = {1146}, abstract = {OpenMRS is an open source infrastructure for the creation of medical record systems in developing countries. Produced and maintained collaboratively across multiple institutions, this framework consists of an open source data model, a set of core application functions, and a default implementation. The goal of this implementation is to provide the beginnings of an EMR that is suitable for all groups involved with healthcare in developing countries.}, author = {Wolfe, Benjamin A and Mamlin, Burke W and Biondich, Paul G and Fraser, Hamish S F and Jazayeri, Darius and Allen, Christian and Miranda, Justin and Tierney, William M} } @conference {782, title = {Remote Large Data Visualization in the ParaView Framework.}, booktitle = {EGPGV}, year = {2006}, publisher = {Eurographics Association}, organization = {Eurographics Association}, keywords = {dblp}, isbn = {3-905673-40-1}, url = {http://dblp.uni-trier.de/db/conf/egpgv/egpgv2006.html$\#$CedilnikGMAF06}, author = {Cedilnik, Andy and Geveci, Berk and Moreland, Kenneth and Ahrens, James P. and Favre, Jean M.}, editor = {Heirich, Alan and Raffin, Bruno and dos Santos, Lu{\'\i}s Paulo Peixoto} } @article {1041, title = {Static telepathology in cancer institute of Tehran university: report of the first academic experience in Iran.}, journal = {Diagn Pathol}, volume = {1}, year = {2006}, month = {2006}, pages = {33}, abstract = {

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

}, issn = {1746-1596}, doi = {10.1186/1746-1596-1-33}, author = {Abdirad, Afshin and Sarrafpour, Babak and Ghaderi-Sohi, Siavash} } @article {16257947, title = {Information technology as a tool to improve the quality of American Indian health care.}, journal = {American journal of public health}, volume = {95}, year = {2005}, month = {2005 Dec}, pages = {2173-9}, abstract = {The American Indian/Alaska Native population experiences a disproportionate burden of disease across a spectrum of conditions. While the recent National Healthcare Disparities Report highlighted differences in quality of care among racial and ethnic groups, there was only very limited information available for American Indians. The Indian Health Service (IHS) is currently enhancing its information systems to improve the measurement of health care quality as well as to support quality improvement initiatives. We summarize current knowledge regarding health care quality for American Indians, highlighting the variation in reported measures in the existing literature. We then discuss how the IHS is using information systems to produce standardized performance measures and present future directions for improving American Indian health care quality.}, author = {Sequist, Thomas D and Cullen, Theresa and Ayanian, John Z} } @article {781, title = {ParaView : An End-User Tool for Large Data Visualization}, journal = {Energy}, volume = {836}, year = {2005}, pages = {717{\textendash}732}, url = {http://scholar.google.com/scholar?hl=en\&btnG=Search\&q=intitle:ParaView:+An+end-user+tool+for+large+data+visualization$\#$0}, author = {Ahrens, James and Geveci, Berk and Law, Charles}, editor = {Hansen, C R and Johnson, C DEditors} } @article {11522765, title = {An integrated software suite for surface-based analyses of cerebral cortex.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {8}, year = {2001}, month = {2001 Sep-Oct}, pages = {443-59}, abstract = {The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.}, author = {Van Essen, D C and Drury, H A and Dickson, J and Harwell, J and Hanlon, D and Anderson, C H} }