Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease

<p>Abstract</p> <p>Background</p> <p>Natural Language Processing (NLP) systems can be used for specific Information Extraction (IE) tasks such as extracting phenotypic data from the electronic medical record (EMR). These data are useful for translational research and are often found only in free text clinical notes. A key required step for IE is the manual annotation of clinical corpora and the creation of a reference standard for (1) training and validation tasks and (2) to focus and clarify NLP system requirements. These tasks are time consuming, expensive, and require considerable effort on the part of human reviewers.</p> <p>Methods</p> <p>Using a set of clinical documents from the VA EMR for a particular use case of interest we identify specific challenges and present several opportunities for annotation tasks. We demonstrate specific methods using an open source annotation tool, a customized annotation schema, and a corpus of clinical documents for patients known to have a diagnosis of Inflammatory Bowel Disease (IBD). We report clinician annotator agreement at the document, concept, and concept attribute level. We estimate concept yield in terms of annotated concepts within specific note sections and document types.</p> <p>Results</p> <p>Annotator agreement at the document level for documents that contained concepts of interest for IBD using estimated Kappa statistic (95% CI) was very high at 0.87 (0.82, 0.93). At the concept level, F-measure ranged from 0.61 to 0.83. However, agreement varied greatly at the specific concept attribute level. For this particular use case (IBD), clinical documents producing the highest concept yield per document included GI clinic notes and primary care notes. Within the various types of notes, the highest concept yield was in sections representing patient assessment and history of presenting illness. Ancillary service documents and family history and plan note sections produced the lowest concept yield.</p> <p>Conclusion</p> <p>Challenges include defining and building appropriate annotation schemas, adequately training clinician annotators, and determining the appropriate level of information to be annotated. Opportunities include narrowing the focus of information extraction to use case specific note types and sections, especially in cases where NLP systems will be used to extract information from large repositories of electronic clinical note documents.</p

Enrolling adolescents in HIV vaccine trials: reflections on legal complexities from South Africa

<p>Abstract</p> <p>Background</p> <p>South Africa is likely to be the first country in the world to host an adolescent HIV vaccine trial. Adolescents may be enrolled in late 2007. In the development and review of adolescent HIV vaccine trial protocols there are many complexities to consider, and much work to be done if these important trials are to become a reality.</p> <p>Discussion</p> <p>This article sets out essential requirements for the lawful conduct of adolescent research in South Africa including compliance with consent requirements, child protection laws, and processes for the ethical and regulatory approval of research.</p> <p>Summary</p> <p>This article outlines likely complexities for researchers and research ethics committees, including determining that trial interventions meet current risk standards for child research. Explicit recommendations are made for role-players in other jurisdictions who may also be planning such trials. This article concludes with concrete steps for implementing these important trials in South Africa and other jurisdictions, including planning for consent processes; delineating privacy rights; compiling information necessary for ethics committees to assess risks to child participants; training trial site staff to recognize when disclosures trig mandatory reporting response; networking among relevant ethics commitees; and lobbying the National Regulatory Authority for guidance.</p

Fitting censored quantile regression by variable neighborhood search

Quantile regression is an increasingly important topic in statistical analysis. However, fitting censored quantile regression is hard to solve numerically because the objective function to be minimized is not convex nor concave in regressors. Performance of standard methods is not satisfactory, particularly if a high degree of censoring is present. The usual approach is to simplify (linearize) estimator function, and to show theoretically that such approximation converges to optimal values. In this paper, we suggest a new approach, to solve optimization problem (nonlinear, nonconvex, and nondifferentiable) directly. Our method is based on variable neighborhood search approach, a recent successful technique for solving global optimization problems. The presented results indicate that our method can improve quality of censored quantizing regressors estimator considerably

Why don't some women attend antenatal and postnatal care services?: a qualitative study of community members' perspectives in Garut, Sukabumi and Ciamis districts of West Java Province, Indonesia

<p>Abstract</p> <p>Background</p> <p>Antenatal, delivery and postnatal care services are amongst the recommended interventions aimed at preventing maternal and newborn deaths worldwide. West Java is one of the provinces of Java Island in Indonesia with a high proportion of home deliveries, a low attendance of four antenatal services and a low postnatal care uptake. This paper aims to explore community members' perspectives on antenatal and postnatal care services, including reasons for using or not using these services, the services received during antenatal and postnatal care, and cultural practices during antenatal and postnatal periods in Garut, Sukabumi and Ciamis districts of West Java province.</p> <p>Methods</p> <p>A qualitative study was conducted from March to July 2009 in six villages in three districts of West Java province. Twenty focus group discussions (FGDs) and 165 in-depth interviews were carried out involving a total of 295 respondents. The guidelines for FGDs and in-depth interviews included the topics of community experiences with antenatal and postnatal care services, reasons for not attending the services, and cultural practices during antenatal and postnatal periods.</p> <p>Results</p> <p>Our study found that the main reason women attended antenatal and postnatal care services was to ensure the safe health of both mother and infant. Financial difficulty emerged as the major issue among women who did not fulfil the minimum requirements of four antenatal care services or two postnatal care services within the first month after delivery. This was related to the cost of health services, transportation costs, or both. In remote areas, the limited availability of health services was also a problem, especially if the village midwife frequently travelled out of the village. The distances from health facilities, in addition to poor road conditions were major concerns, particularly for those living in remote areas. Lack of community awareness about the importance of these services was also found, as some community members perceived health services to be necessary only if obstetric complications occurred. The services of traditional birth attendants for antenatal, delivery, and postnatal care were widely used, and their roles in maternal and child care were considered vital by some community members.</p> <p>Conclusions</p> <p>It is important that public health strategies take into account the availability, affordability and accessibility of health services. Poverty alleviation strategies will help financially deprived communities to use antenatal and postnatal health services. This study also demonstrated the importance of health promotion programs for increasing community awareness about the necessity of antenatal and postnatal services.</p

Women convicted for violent offenses: Adverse childhood experiences, low level of education and poor mental health

<p>Abstract</p> <p>Background</p> <p>In past years, the female offender population has grown, leading to an increased interest in the characteristics of female offenders. The aim of this study was to assess the prevalence of female violent offending in a Swiss offender population and to compare possible socio-demographic and offense-related gender differences.</p> <p>Methods</p> <p>Descriptive and bivariate logistic regression analyses were performed for a representative sample of N = 203 violent offenders convicted in Zurich, Switzerland.</p> <p>Results</p> <p>7.9% (N = 16) of the sample were female. Significant gender differences were found: Female offenders were more likely to be married, less educated, to have suffered from adverse childhood experiences and to be in poor mental health. Female violent offending was less heterogeneous than male violent offending, in fact there were only three types of violent offenses females were convicted for in our sample: One third were convicted of murder, one third for arson and only one woman was convicted of a sex offense.</p> <p>Conclusions</p> <p>The results of our study point toward a gender-specific theory of female offending, as well as toward the importance of developing models for explaining female criminal behavior, which need to be implemented in treatment plans and intervention strategies regarding female offenders.</p

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Measurement of the cross-section of high transverse momentum vector bosons reconstructed as single jets and studies of jet substructure in pp collisions at √s = 7 TeV with the ATLAS detector

This paper presents a measurement of the cross-section for high transverse momentum W and Z bosons produced in pp collisions and decaying to all-hadronic final states. The data used in the analysis were recorded by the ATLAS detector at the CERN Large Hadron Collider at a centre-of-mass energy of √s = 7 TeV;{\rm Te}{\rm V}$and correspond to an integrated luminosity of$4.6\;{\rm f}{{{\rm b}}^{-1}}$. The measurement is performed by reconstructing the boosted W or Z bosons in single jets. The reconstructed jet mass is used to identify the W and Z bosons, and a jet substructure method based on energy cluster information in the jet centre-of-mass frame is used to suppress the large multi-jet background. The cross-section for events with a hadronically decaying W or Z boson, with transverse momentum${{p}_{{\rm T}}}\gt 320\;{\rm Ge}{\rm V}$and pseudorapidity$|\eta |\lt 1.9$, is measured to be${{\sigma }_{W+Z}}=8.5\pm 1.7$ pb and is compared to next-to-leading-order calculations. The selected events are further used to study jet grooming techniques

Search for the neutral Higgs bosons of the minimal supersymmetric standard model in pp collisions at root s=7 TeV with the ATLAS detector

A search for neutral Higgs bosons of the Minimal Supersymmetric Standard Model (MSSM) is reported. The analysis is based on a sample of proton-proton collisions at a centre-of-mass energy of 7TeV recorded with the ATLAS detector at the Large Hadron Collider. The data were recorded in 2011 and correspond to an integrated luminosity of 4.7 fb-1 to 4.8 fb-1. Higgs boson decays into oppositely-charged muon or τ lepton pairs are considered for final states requiring either the presence or absence of b-jets. No statistically significant excess over the expected background is observed and exclusion limits at the 95% confidence level are derived. The exclusion limits are for the production cross-section of a generic neutral Higgs boson, φ, as a function of the Higgs boson mass and for h/A/H production in the MSSM as a function of the parameters mA and tan β in the mhmax scenario for mA in the range of 90GeV to 500 GeV. Copyright CERN