Medical Image Data and Datasets in the Era of Machine Learning-Whitepaper from the 2016 C-MIMI Meeting Dataset Session.

At the first annual Conference on Machine Intelligence in Medical Imaging (C-MIMI), held in September 2016, a conference session on medical image data and datasets for machine learning identified multiple issues. The common theme from attendees was that everyone participating in medical image evaluation with machine learning is data starved. There is an urgent need to find better ways to collect, annotate, and reuse medical imaging data. Unique domain issues with medical image datasets require further study, development, and dissemination of best practices and standards, and a coordinated effort among medical imaging domain experts, medical imaging informaticists, government and industry data scientists, and interested commercial, academic, and government entities. High-level attributes of reusable medical image datasets suitable to train, test, validate, verify, and regulate ML products should be better described. NIH and other government agencies should promote and, where applicable, enforce, access to medical image datasets. We should improve communication among medical imaging domain experts, medical imaging informaticists, academic clinical and basic science researchers, government and industry data scientists, and interested commercial entities

The Human Studies Database Project: Federating Human Studies Design Data Using the Ontology of Clinical Research

Human studies, encompassing interventional and observational studies, are the most important source of evidence for advancing our understanding of health, disease, and treatment options. To promote discovery, the design and results of these studies should be made machine-readable for large-scale data mining, synthesis, and re-analysis. The Human Studies Database Project aims to define and implement an informatics infrastructure for institutions to share the design of their human studies. We have developed the Ontology of Clinical Research (OCRe) to model study features such as design type, interventions, and outcomes to support scientific query and analysis. We are using OCRe as the reference semantics for federated data sharing of human studies over caGrid, and are piloting this implementation with several Clinical and Translational Science Award (CTSA) institutions

Large Scale In Silico Screening on Grid Infrastructures

Large-scale grid infrastructures for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale in silico docking within the framework of the WISDOM initiative against Malaria and Avian Flu requiring about 105 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated the relevance of large-scale grid infrastructures for the virtual screening by molecular docking. This also allowed evaluating the performances of the grid infrastructures and to identify specific issues raised by large-scale deployment.Comment: 14 pages, 2 figures, 2 tables, The Third International Life Science Grid Workshop, LSGrid 2006, Yokohama, Japan, 13-14 october 2006, to appear in the proceeding

Prevalence and Characterization of Salmonella Isolates from Poultry Farms in Ilorin, Nigeria

Poultry birds are very important source of essential proteins in developing countries, but also play an important role in transmission of Salmonella to human and nonhuman. Exposure to this pathogen also occurs through use of poultry droppings as manure for crop and vegetable production. This study investigated prevalence of Salmonella in feces of poultry farms in Ilorin, Nigeria. Salmonella isolated were further characterized by molecular method. Fecal samples were cultured in pre-enrichment medium, Selenite F medium and finally sub-cultured on Salmonella-Shigella agar. None lactose fermenting colonies with black center were picked for presumptive identification using biochemical tests and confirmed by serological test by method previously described. Molecular characterization was carried out using 16S rRNA gene sequencing following standard procedure. Out of 170 samples collected and examined, 8 (4.7%) gave biochemical characteristics that resembled Salmonella, but only 6 (3.5%) were confirmed as Salmonella by polyvalent antisera. Molecular characterization revealed that serovars isolated were Salmonella Enteritidis 3 (1.8%) and Salmonella Paratyphi 3 (1.8%). Phylogenetic tree constructed by neighbor-joining method as derived from analysis of the 16S rRNA gene sequences showed close relationship to Salmonella Paratyphi strain FB0015 16S ribosoma RNA gene partial sequence to our Salmonella Paratyphi isolates. The detection of 3.5% prevalence rate of Salmonella serovar from feces of laying poultry birds my serve as potential source of transmission of this pathogen to human through chicken meat, egg or use of poultry dropping as manure in crop or vegetable production

Virtual Screening on Large Scale Grids

PCSV, article in press in Parallel ComputingLarge scale grids for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale virtual docking within the framework of the WISDOM initiative against malaria and avian influenza requiring about 100 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated the relevance of large scale grids for the virtual screening by molecular docking. This also allowed evaluating the performances of the grid infrastructures and to identify specific issues raised by large scale deployment

Resource Control or Terrorism: Competing Perspectives on the Conflict in the Niger Delta Region, Nigeria.

A state of conflict has existed in the Niger Delta for fifty years. The nature of the conflict, whether it is terrorism or civil insurrection, has not been resolved by the respective legislative entities. This qualitative case study was designed to explore the nature of the Niger Delta conflict from the perspective of several members of the Nigerian National Assembly and determine whether terrorism in Nigeria is related to the general conflict. Social conflict theory provided the basis for the exploration. An ancillary question explored whether antiterrorism legislation in 2006 alleviated the Niger Delta conflict. Interview data were collected from 1 senator and 5 representatives of the Nigerian National Assembly. These data were inductively coded and manually analyzed for major themes, and then triangulated with a review of internal and public documents pertaining to the relevant legislation. The study established that the root causes of the Niger Delta conflict were economic inequities. Three conclusions were drawn from the case study and data regarding legislative attempts to address the conflict: (1) the antiterrorism legislation of 2006 did not criminalize the Niger Delta conflict, (2) the legislation did not have an impact on fiscal resource allocations to the region, and (3) no link between the conflict and current terrorism activities in Nigeria was evident. Recommendations are given for the Nigerian state to engage in fiscal federalism as a means of equitable allocations of resources to the region, thereby contributing to positive social change

A general practice provider federation in a mixed health economy in England – a case study examination

For over 70 years GP practices have existed within the NHS as independent contractors playing a significant role in the equitable delivery of primary health care. The traditional model of general practice has developed over time, but features such as independent contractor status, the professional partnership business model, and professional autonomy remain as key characteristics. The profession is faced with significant challenges, including increased demand on services with more complex multiple morbidities prevalent in an ageing population, workforce shortages precipitating the need to introduce new disciplines of staff, and the long-term sustainability of the partnership business model. The cumulative effect of these factors challenge the existing model of general practice, and practices are being encouraged to move from what has been termed a small cottage industry (Digby, 1999; Mathers & Lester, 2011; Mathers, 2012) to larger organisational group arrangements. General practice is the empirical setting for this research which adopts pragmatism as a research philosophy within a mixed methods single organisational case study. The study is an example of a GP Federation established as a corporate venture by a group of entrepreneurial GPs. The study examined what insights business theory could offer in explaining how a group of GP practices developed their venture and what advantages and challenges this offered. A mixed methods approach to data collection included interviews and surveys with the executive team who led the venture, GPs, managers and nurses from the member practices, and other senior personnel in the health economy. The activities pursued over an eight-year period (2011-2019) that contributed to strategy were identified, with some aspects of strategy more successful than others. Benefits were realised through activities that all practices participated in, including education, training, research, and quality improvement. A lack of commercial opportunities within the health economy limited the ability to develop a portfolio of services which ended up taking several years to establish. Purpose and vision were identified as important features to ensure continued engagement from practices as sponsors, and the level of investment in leadership and management to dedicate to the venture should not be underestimated. At the beginning of the study in 2011 health policy was focussing on implementation of the Health and Social Care Act (2012) with significant changes introduced in the commissioning landscape. After a period of eight years in 2019, national health policy introduced initiatives to support the ailing sector of general practice through the establishment of Primary Care Networks, and this study reflects on the learning from federated working between 2011-2019 as practices prepared to establish a Primary Care Network though a formal contractual arrangement (NHS England, 2018)

New Advanced Technologies to Provide Decentralised and Secure Access to Medical Records: Case Studies in Oncology

The main problem for health professionals and patients in accessing information is that this information is very often distributed over many medical records and locations. This problem is particularly acute in cancerology because patients may be treated for many years and undergo a variety of examinations. Recent advances in technology make it feasible to gain access to medical records anywhere and anytime, allowing the physician or the patient to gather information from an “ephemeral electronic patient record”. However, this easy access to data is accompanied by the requirement for improved security (confidentiality, traceability, integrity, ...) and this issue needs to be addressed. In this paper we propose and discuss a decentralised approach based on recent advances in information sharing and protection: Grid technologies and watermarking methodologies. The potential impact of these technologies for oncology is illustrated by the examples of two experimental cases: a cancer surveillance network and a radiotherapy treatment plan. It is expected that the proposed approach will constitute the basis of a future secure “google-like” access to medical records

AMUSE: autonomic management of ubiquitous e-Health systems

Future e-Health systems will consist of low-power on-body wireless sensors attached to mobile users that interact with an ubiquitous computing environment to monitor the health and well being of patients in hospitals or at home. Patients or health practitioners have very little technical computing expertise so these systems need to be self-configuring and self-managing with little or no user input. More importantly, they should adapt autonomously to changes resulting from user activity, device failure, and the addition or loss of services. We propose the Self-Managed Cell (SMC) as an architectural pattern for all such types of ubiquitous computing applications and use an e-Health application in which on-body sensors are used to monitor a patient living in their home as an exemplar. We describe the services comprising the SMC and discuss cross-SMC interactions as well as the composition of SMCs into larger structures

Building the Future Internet through FIRE

The Internet as we know it today is the result of a continuous activity for improving network communications, end user services, computational processes and also information technology infrastructures. The Internet has become a critical infrastructure for the human-being by offering complex networking services and end-user applications that all together have transformed all aspects, mainly economical, of our lives. Recently, with the advent of new paradigms and the progress in wireless technology, sensor networks and information systems and also the inexorable shift towards everything connected paradigm, first as known as the Internet of Things and lately envisioning into the Internet of Everything, a data-driven society has been created. In a data-driven society, productivity, knowledge, and experience are dependent on increasingly open, dynamic, interdependent and complex Internet services. The challenge for the Internet of the Future design is to build robust enabling technologies, implement and deploy adaptive systems, to create business opportunities considering increasing uncertainties and emergent systemic behaviors where humans and machines seamlessly cooperate