The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

Implementation of XpertMalTyph: An Expert System for Medical Diagnosis of the Complications of Malaria and Typhoid

The dearth of medical experts in the developing world has subjected a large percentage of its populace to preventable ailments and deaths. Also, because of the predominant rural communities, the few medical experts that are available always opt for practice in the few urban cities. This consequently puts the rural communities at a disadvantage with respect to access to quality health care services. In this work, we designed and implemented XpertMalTyph; a novel medical diagnostic expert system for the various kinds of malaria and typhoid complications. A medical diagnostic expert system uses computer(s) to simulate medical doctor skills in diagnosis of ailments and prescription of treatments, hence can be used to provide the same service in the absence of the experts. XpertMalTyph is based on JESS (Java Expert System Shell) programming because of its robust inference engine and rules for implementing expert system

Ensemble methods for meningitis aetiology diagnosis

In this work, we explore data-driven techniques for the fast and early diagnosis concerning the etiological origin of meningitis, more specifically with regard to differentiating between viral and bacterial meningitis. We study how machine learning can be used to predict meningitis aetiology once a patient has been diagnosed with this disease. We have a dataset of 26,228 patients described by 19 attributes, mainly about the patient's observable symptoms and the early results of the cerebrospinal fluid analysis. Using this dataset, we have explored several techniques of dataset sampling, feature selection and classification models based both on ensemble methods and on simple techniques (mainly, decision trees). Experiments with 27 classification models (19 of them involving ensemble methods) have been conducted for this paper. Our main finding is that the combination of ensemble methods with decision trees leads to the best meningitis aetiology classifiers. The best performance indicator values (precision, recall and f-measure of 89% and an AUC value of 95%) have been achieved by the synergy between bagging and NBTrees. Nonetheless, our results also suggest that the combination of ensemble methods with certain decision tree clearly improves the performance of diagnosis in comparison with those obtained with only the corresponding decision tree.This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. We would like to thank the Health Department of the Brazilian Government for providing the dataset and for authorizing its use in this study. We would also like to express our gratitude to the reviewers for their thoughtful comments and efforts towards improving our manuscript. Funding for open access charge: Universidad de Málaga / CBUA

Methodologies of Legacy Clinical Decision Support System -A Review

Information technology playing a prominent role in the field of medical by incorporating the Clinical Decision Support System(CDSS) in their routine practices. CDSS is a computer based interactive program to assist the physician to make the right decision at the right time. Now a day's Clinical decision support system is a dynamic research area in the field of computer, but the lack of the knowledge of the understanding as well as the functioning of the system ,make the adoption slow by the physician and patient. The literature review of this paper will focus on the overview of legacy CDSS, the kind of methodologies and classifier employed to prepare such decision support system using a non-technical approach to the physician and the strategy- makers . This study will provide the scope of understanding the clinical decision support along with the gateway to physician ,policy-makers to develop and deploy the decision support system as a healthcare service to make the quick, agile and right decision. Future direction to handle the uncertainties along with the challenges of clinical decision support system are also enlightened in this study

Analysing Spatio-Temporal Clustering of Meningococcal Meningitis Outbreaks in Niger Reveals Opportunities for Improved Disease Control

Meningococcal meningitis (MM) is an infection of the meninges caused by a bacterium, Neisseria meningitidis, transmitted through respiratory and throat secretions. It can cause brain damage and results in death in 5–15% of cases. Large epidemics of MM occur almost every year in sub-Saharan Africa during the hot, dry season. Understanding how epidemics emerge and spread in time and space would help public health authorities to develop more efficient strategies for the prevention and the control of meningitis. We studied the spatio-temporal distribution of MM cases in Niger from 2002 to 2009 at the scale of the health centre catchment areas (HCCAs). We found that spatial clusters of cases most frequently occurred within nine districts out of 42, which can assist public health authorities to better adjust allocation of resources such as antibiotics or rapid diagnostic tests. We also showed that the epidemics break out in different HCCAs from year to year and did not follow a systematic geographical direction. Finally, this analysis showed that surveillance at a finer spatial scale (health centre catchment area rather than district) would be more efficient for public health response: outbreaks would be detected earlier and reactive vaccination would be better targeted

Characterizing the Information Needs of Rural Healthcare Practitioners with Language Agnostic Automated Text Analysis

Objectives – Previous research has characterized urban healthcare providers\u27 information needs, using various qualitative methods. However, little is known about the needs of rural primary care practitioners in Brazil. Communication exchanged during tele-consultations presents a unique data source for the study of these information needs. In this study, I characterize rural healthcare providers\u27 information needs expressed electronically, using automated methods. Methods – I applied automated methods to categorize messages obtained from the telehealth system from two regions in Brazil. A subset of these messages, annotated with top-level categories in the DeCS terminology (the regional equivalent of MeSH), was used to train text categorization models, which were then applied to a larger, unannotated data set. On account of their more granular nature, I focused on answers provided to the queries sent by rural healthcare providers. I studied these answers, as surrogates for the information needs they met. Message representations were generated using methods of distributional semantics, permitting the application of k-Nearest Neighbor classification for category assignment. The resulting category assignments were analyzed to determine differences across regions, and healthcare providers. Results – Analysis of the assigned categories revealed differences in information needs across regions, corresponding to known differences in the distributions of diseases and tele-consultant expertise across these regions. Furthermore, information needs of rural nurses were observed to be different from those documented in qualitative studies of their urban counterparts, and the distribution of expressed information needs categories differed across types of providers (e.g. nurses vs. physicians). Discussion – The automated analysis of large amounts of digitally-captured tele-consultation data suggests that rural healthcare providers\u27 information needs in Brazil are different than those of their urban counterparts in developed countries. The observed disparities in information needs correspond to known differences in the distribution of illness and expertise in these regions, supporting the applicability of my methods in this context. In addition, these methods have the potential to mediate near real-time monitoring of information needs, without imposing a direct burden upon healthcare providers. Potential applications include automated delivery of needed information at the point of care, needs-based deployment of tele-consultation resources and syndromic surveillance. Conclusion – I used automated text categorization methods to assess the information needs expressed at the point of care in rural Brazil. My findings reveal differences in information needs across regions, and across practitioner types, demonstrating the utility of these methods and data as a means to characterize information needs

Impact of HIV-Associated Conditions on Mortality in People Commencing Anti-Retroviral Therapy in Resource Limited Settings

To identify associations between specific WHO stage 3 and 4 conditions diagnosed after ART initiation and all cause mortality for patients in resource-limited settings (RLS). DESIGN, SETTING: Analysis of routine program data collected prospectively from 25 programs in eight countries between 2002 and 2010

Knowledge gaps and research priorities in tuberculous meningitis.

Tuberculous meningitis (TBM) is the most severe and disabling form of tuberculosis (TB), accounting for around 1-5% of the global TB caseload, with mortality of approximately 20% in children and up to 60% in persons co-infected with human immunodeficiency virus even in those treated. Relatively few centres of excellence in TBM research exist and the field would therefore benefit from greater co-ordination, advocacy, collaboration and early data sharing. To this end, in 2009, 2015 and 2019 we convened the TBM International Research Consortium, bringing together approximately 50 researchers from five continents. The most recent meeting took place on 1 st and 2 nd March 2019 in Lucknow, India. During the meeting, researchers and clinicians presented updates in their areas of expertise, and additionally presented on the knowledge gaps and research priorities in that field. Discussion during the meeting was followed by the development, by a core writing group, of a synthesis of knowledge gaps and research priorities within seven domains, namely epidemiology, pathogenesis, diagnosis, antimicrobial therapy, host-directed therapy, critical care and implementation science. These were circulated to the whole consortium for written input and feedback. Further cycles of discussion between the writing group took place to arrive at a consensus series of priorities. This article summarises the consensus reached by the consortium concerning the unmet needs and priorities for future research for this neglected and often fatal disease