The Standard Problem

Crafting, adhering to, and maintaining standards is an ongoing challenge. This paper uses a framework based on common models to explore the standard problem: the impossibility of creating, implementing or maintain definitive common models in an open system. The problem arises from uncertainty driven by variations in operating context, standard quality, differences in implementation, and drift over time. Fitting work by conformance services repairs these gaps between a standard and what is required for interoperation, using several strategies: (a) Universal conformance (all agents access the same standard); (b) Mediated conformance (an interoperability layer supports heterogeneous agents) and (c) Localized conformance, (autonomous adaptive agents manage their own needs). Conformance methods include incremental design, modular design, adaptors, and creating interactive and adaptive agents. Machine learning should have a major role in adaptive fitting. Choosing a conformance service depends on the stability and homogeneity of shared tasks, and whether common models are shared ahead of time or are adjusted at task time. This analysis thus decouples interoperability and standardization. While standards facilitate interoperability, interoperability is achievable without standardization.Comment: Keywords: information standard, interoperability, machine learning, technology evaluation 25 Pages Main text word Count: 5108 Abstract word count: 206 Tables: 1 Figures: 7 Boxes: 2 Submitted to JAMI

Towards bioinformatics assisted infectious disease control

BACKGROUND: This paper proposes a novel framework for bioinformatics assisted biosurveillance and early warning to address the inefficiencies in traditional surveillance as well as the need for more timely and comprehensive infection monitoring and control. It leverages on breakthroughs in rapid, high-throughput molecular profiling of microorganisms and text mining. RESULTS: This framework combines the genetic and geographic data of a pathogen to reconstruct its history and to identify the migration routes through which the strains spread regionally and internationally. A pilot study of Salmonella typhimurium genotype clustering and temporospatial outbreak analysis demonstrated better discrimination power than traditional phage typing. Half of the outbreaks were detected in the first half of their duration. CONCLUSION: The microbial profiling and biosurveillance focused text mining tools can enable integrated infectious disease outbreak detection and response environments based upon bioinformatics knowledge models and measured by outcomes including the accuracy and timeliness of outbreak detection.9 page(s

The Effects of Industry Sponsorship on Comparator Selection in Trial Registrations for Neuropsychiatric Conditions in Children

Pediatric populations continue to be understudied in clinical drug trials despite the increasing use of pharmacotherapy in children, particularly with psychotropic drugs. Most pertinent to the clinical selection of drug interventions are trials directly comparing drugs against other drugs. The aim was to measure the prevalence of active drug comparators in neuropsychiatric drug trials in children and identify the effects of funding source on comparator selection. We analyzed the selection of drugs and drug comparisons in clinical trials registered between January 2006 and May 2012. Completed and ongoing interventional trials examining treatments for six neuropsychiatric conditions in children were included. Networks of drug comparisons for each condition were constructed using information about the trial study arms. Of 421 eligible trial registrations, 228 (63,699 participants) were drug trials addressing ADHD (106 trials), autism spectrum disorders (47), unipolar depression (16), seizure disorders (38), migraines and other headaches (15), or schizophrenia (11). Active drug comparators were used in only 11.0% of drug trials while 44.7% used a placebo control and 44.3% no drug or placebo comparator. Even among conditions with well-established pharmacotherapeutic options, almost all drug interventions were compared to a placebo. Active comparisons were more common among trials without industry funding (17% vs. 8%, p=0.04). Trials with industry funding differed from non-industry trials in terms of the drugs studied and the comparators selected. For 73% (61/84) of drugs and 90% (19/21) of unique comparisons, trials were funded exclusively by either industry or non-industry. We found that industry and non-industry differed when choosing comparators and active drug comparators were rare for both groups. This gap in pediatric research activity limits the evidence available to clinicians treating children and suggests a need to reassess the design and funding of pediatric trials in order to optimize the information derived from pediatric participation in clinical trials

Associations between exposure to and expression of negative opinions about Human Papillomavirus vaccines on social media: an observational study

Background Groups and individuals that seek to negatively influence public opinion about the safety and value of vaccination are active in online and social media and may influence decision making within some communities. Objective We sought to measure whether exposure to negative opinions about human papillomavirus (HPV) vaccines in Twitter communities is associated with the subsequent expression of negative opinions by explicitly measuring potential information exposure over the social structure of Twitter communities. Methods We hypothesized that prior exposure to opinions rejecting the safety or value of HPV vaccines would be associated with an increased risk of posting similar opinions and tested this hypothesis by analyzing temporal sequences of messages posted on Twitter (tweets). The study design was a retrospective analysis of tweets related to HPV vaccines and the social connections between users. Between October 2013 and April 2014, we collected 83,551 English-language tweets that included terms related to HPV vaccines and the 957,865 social connections among 30,621 users posting or reposting the tweets. Tweets were classified as expressing negative or neutral/positive opinions using a machine learning classifier previously trained on a manually labeled sample. Results During the 6-month period, 25.13% (20,994/83,551) of tweets were classified as negative; among the 30,621 users that tweeted about HPV vaccines, 9046 (29.54%) were exposed to a majority of negative tweets. The likelihood of a user posting a negative tweet after exposure to a majority of negative opinions was 37.78% (2780/7361) compared to 10.92% (1234/11,296) for users who were exposed to a majority of positive and neutral tweets corresponding to a relative risk of 3.46 (95% CI 3.25-3.67, P<.001). Conclusions The heterogeneous community structure on Twitter appears to skew the information to which users are exposed in relation to HPV vaccines. We found that among users that tweeted about HPV vaccines, those who were more often exposed to negative opinions were more likely to subsequently post negative opinions. Although this research may be useful for identifying individuals and groups currently at risk of disproportionate exposure to misinformation about HPV vaccines, there is a clear need for studies capable of determining the factors that affect the formation and adoption of beliefs about public health interventions

Delay in reviewing test results prolongs hospital length of stay: a retrospective cohort study

Background: Failure in the timely follow-up of test results has been widely documented, contributing to delayed medical care. Yet, the impact of delay in reviewing test results on hospital length of stay (LOS) has not been studied. We examine the relationship between laboratory tests review time and hospital LOS. Methods: A retrospective cohort study of inpatients admitted to a metropolitan teaching hospital in Sydney, Australia, between 2011 and 2012 (n = 5804). Generalized linear models were developed to examine the relationship between hospital LOS and cumulative clinician read time (CRT), defined as the time taken by clinicians to review laboratory test results performed during an inpatient stay after they were reported in the computerized test reporting system. The models were adjusted for patients’ age, sex, and disease severity (measured by the Charlson Comorbidity index), the number of test panels performed, the number of unreviewed tests pre-discharge, and the cumulative laboratory turnaround time (LTAT) of tests performed during an inpatient stay. Results: Cumulative CRT is significantly associated with prolonged LOS, with each day of delay in reviewing test results increasing the likelihood of prolonged LOS by 13.2% (p < 0.0001). Restricting the analysis to tests with abnormal results strengthened the relationship between cumulative CRT and prolonged LOS, with each day of delay in reviewing test results increasing the likelihood of delayed discharge by 33.6% (p < 0.0001). Increasing age, disease severity and total number of tests were also significantly associated with prolonged LOS. Increasing number of unreviewed tests was negatively associated with prolonged LOS. Conclusions: Reducing unnecessary hospital LOS has become a critical health policy goal as healthcare costs escalate. Preventing delay in reviewing test results represents an important opportunity to address potentially avoidable hospital stays and unnecessary resource utilization. Electronic supplementary material The online version of this article (10.1186/s12913-018-3181-z) contains supplementary material, which is available to authorized users

A PubMed-Wide Associational Study of Infectious Diseases

Background: Computational discovery is playing an ever-greater role in supporting the processes of knowledge synthesis. A significant proportion of the more than 18 million manuscripts indexed in the PubMed database describe infectious disease syndromes and various infectious agents. This study is the first attempt to integrate online repositories of text-based publications and microbial genome databases in order to explore the dynamics of relationships between pathogens and infectious diseases. Methodology/Principal Findings: Herein we demonstrate how the knowledge space of infectious diseases can be computationally represented and quantified, and tracked over time. The knowledge space is explored by mapping of the infectious disease literature, looking at dynamics of literature deposition, zooming in from pathogen to genome level and searching for new associations. Syndromic signatures for different pathogens can be created to enable a new and clinically focussed reclassification of the microbial world. Examples of syndrome and pathogen networks illustrate how multilevel network representations of the relationships between infectious syndromes, pathogens and pathogen genomes can illuminate unexpected biological similarities in disease pathogenesis and epidemiology. Conclusions/Significance: This new approach based on text and data mining can support the discovery of previously hidden associations between diseases and microbial pathogens, clinically relevant reclassification of pathogeni