LIMSI@CLEF eHealth 2017 Task 2: Logistic Regression for Automatic Article Ranking

This paper describes the participation of the LIMSI-MIROR team at CLEF eHealth 2017, task 2. The task addresses the automatic ranking of articles in order to assist with the screening process of Diagnostic Test Accuracy (DTA) Systematic Reviews. We used a logistic regression classifier and handled class imbalance using a combination of class reweighting and undersampling. We also experimented with two strategies for relevance feedback. Our best run obtained an overall Average Precision of 0.179 and Work Saved over Sampling @95% Recall of 0.650. This run uses stochastic gradient descent for training but no feature selection or relevance feedback. We observe high performance variation within the queries in the test set. Nonetheless, our results suggest that automatic assistance is promising for ranking the DTA literature as it could reduce the screening workload for review writer by 65% on average

Cochrane diagnostic test accuracy reviews

In 1996, shortly after the founding of The Cochrane Collaboration, leading figures in test evaluation research established a Methods Group to focus on the relatively new and rapidly evolving methods for the systematic review of studies of diagnostic tests. Seven years later, the Collaboration decided it was time to develop a publication format and methodology for Diagnostic Test Accuracy (DTA) reviews, as well as the software needed to implement these reviews in The Cochrane Library. A meeting hosted by the German Cochrane Centre in 2004 brought together key methodologists in the area, many of whom became closely involved in the subsequent development of the methodological framework for DTA reviews. DTA reviews first appeared in The Cochrane Library in 2008 and are now an integral part of the work of the Collaboration

Hypothalamic-pituitary-adrenal axis and autonomic nervous system reactivity in children prenatally exposed to maternal depression:A systematic review of prospective studies

Depression is a common condition affecting up to 20% of all pregnant women, and is associated with subsequent developmental and behavioral problems in children, such as conduct disorder and ADHD. One proposed mechanism underlying these associations is modification of the fetal hypothalamic pituitary adrenal (HPA)-axis and the autonomic nervous system (ANS), resulting in altered responses to stress. This review examined the evidence regarding altered HPA-axis and ANS reactivity in children prenatally exposed to high maternal depressive symptoms. A systematic search was conducted in the electronic databases MEDLINE, EMBASE and PsycINFO, for studies published till 25 July 2017. A total of 13 studies comprising 2271 mother-infant dyads were included. None of the studies were suitable for meta-analysis. Risk of bias assessment showed low risk for four studies. Only three studies described an independent association between exposure to high maternal prenatal depressive symptoms and altered stress reactivity in children. There is limited evidence of an independent association between prenatal exposure to maternal depression and altered HPA or ANS reactivity in children

Моніторинг розвитку навичок мовлення та аудіювання

Мета цього дослідження є спостереження та аналіз змін якості навичок володіння мовленням і якості володіння навичками аудіювання в процесі навчання. Завдання дослідження полягає у наступному : а) вивчити яким чином сучасні методи моніторингу впливають на поліпшення якості володіння мовленням, б) простежити якісні зміни знань студентів на трьох етапах: стартовому, поточному та підсумковому. Методами моніторингу є анкетування. самостійна робота, тестування

Evaluation of an automatic article selection method for timelier updates of the Comet Core Outcome Set database

Curated databases of scientific literature play an important role in helping researchers find relevant literature, but populating such databases is a labour intensive and time-consuming process. One such database is the freely accessible Comet Core Outcome Set database, which was originally populated using manual screening in an annually updated systematic review. In order to reduce the workload and facilitate more timely updates we are evaluating machine learning methods to reduce the number of references needed to screen. In this study we have evaluated a machine learning approach based on logistic regression to automatically rank the candidate articles. Data from the original systematic review and its four first review updates were used to train the model and evaluate performance. We estimated that using automatic screening would yield a workload reduction of at least 75% while keeping the number of missed references around 2%. We judged this to be an acceptable trade-off for this systematic review, and the method is now being used for the next round of the Comet database update

Establishment of Valid Laboratory Case Definition for Human Leptospirosis

Laboratory case definition of leptospirosis is scarcely de ned by a solid evaluation that determines cut-off values in the tests that are applied. This study describes the process of determining optimal cut-off titers of laboratory tests for leptospirosis for a valid case definition of leptospirosis. In this case the tests are the microscopic agglutination test (MAT) and an in-house IgM enzyme-linked immunosorbent assay (ELISA) both on single serum and paired samples using a positive culture as the reference test in the Dutch population. The specificity was assessed using panels of sera from healthy donors, cases with known other diseases and non-leptospirosis cases with symptoms compatible with leptospirosis. Cases were divided into three periods corroborating the acute phase (1-10 days post onset of illness (DPO)), the early convalescent (11-20 DPO) and the late convalescent phase (>20 DPO). Cut-off titers for MAT and IgM ELISA were determined as 1:160 and 1:80 respectively for all three periods. These cut-off titers combined 100% specificity with a sensitivity that changed according to the stage of disease for both tests. The low sensitivities in the early acute phase are consistent with the dynamics of the humoral immune response. IgM ELISA yielded higher sensitivities compared to MAT in the acute and early convalescent stages. Moreover, the optimal sensitivity of MAT, the gold standard was < 82%, implying that a significant part of global cases is missed by this recommended test. MAT and IgM ELISA manifested partly complementary, resulting in a higher sensitivity when combining the results of these two tests. The availability of paired samples and of adequate clinical and epidemiological data are other parameters that

Prediction models for hospital readmissions in patients with heart disease: a systematic review and meta-analysis

Objective: To describe the discrimination and calibration of clinical prediction models, identify characteristics that contribute to better predictions and investigate predictors that are associated with unplanned hospital readmissions. Design: Systematic review and meta-analysis. Data source: Medline, EMBASE, ICTPR (for study protocols) and Web of Science (for conference proceedings) were searched up to 25 August 2020. Eligibility criteria for selecting studies: Studies were eligible if they reported on (1) hospitalised adult patients with acute heart disease; (2) a clinical presentation of prediction models with c-statistic; (3) unplanned hospital readmission within 6 months. Primary and secondary outcome measures: Model discrimination for unplanned hospital readmission within 6 months measured using concordance (c) statistics and model calibration. Meta-regression and subgroup analyses were performed to investigate predefined sources of heterogeneity. Outcome measures from models reported in multiple independent cohorts and similarly defined risk predictors were pooled. Results: Sixty studies describing 81 models were included: 43 models were newly developed, and 38 were externally validated. Included populations were mainly patients with heart failure (HF) (n=29). The average age ranged between 56.5 and 84 years. The incidence of readmission ranged from 3% to 43%. Risk of bias (RoB) was high in almost all studies. The c-statistic was 0.8 in 5 models. The study population, data source and number of predictors were significant moderators for the discrimination. Calibration was reported for 27 models. Only the GRACE (Global Registration of Acute Coronary Events) score had adequate discrimination in independent cohorts (0.78, 95% CI 0.63 to 0.86). Eighteen predictors were pooled. Conclusion: Some promising models require updating and validation before use in clinical practice. The lack of independent validation studies, high RoB and low consistency in measured predictors limit their applicability. Prospero registration number: CRD42020159839. Keywords: adverse events; cardiology; risk management

Systematic review and meta-analysis: rapid diagnostic tests versus placental histology, microscopy and PCR for malaria in pregnant women

<p>Abstract</p> <p>Background</p> <p>During pregnancy, malaria infection with <it>Plasmodium falciparum </it>or <it>Plasmodium vivax </it>is related to adverse maternal health and poor birth outcomes. Diagnosis of malaria, during pregnancy, is complicated by the absence or low parasite densities in peripheral blood. Diagnostic methods, other than microscopy, are needed for detection of placental malaria. Therefore, the diagnostic accuracy of rapid diagnostic tests (RDTs), detecting antigen, and molecular techniques (PCR), detecting DNA, for the diagnosis of <it>Plasmodium </it>infections in pregnancy was systematically reviewed.</p> <p>Methods</p> <p>MEDLINE, EMBASE and Web of Science were searched for studies assessing the diagnostic accuracy of RDTs, PCR, microscopy of peripheral and placental blood and placental histology for the detection of malaria infection (all species) in pregnant women.</p> <p>Results</p> <p>The results of 49 studies were analysed in metandi (Stata), of which the majority described <it>P. falciparum </it>infections. Although both placental and peripheral blood microscopy cannot reliably replace histology as a reference standard for placental <it>P. falciparum </it>infection, many studies compared RDTs and PCR to these tests. The proportion of microscopy positives in placental blood (sensitivity) detected by peripheral blood microscopy, RDTs and PCR are respectively 72% [95% CI 62-80], 81% [95% CI 55-93] and 94% [95% CI 86-98]. The proportion of placental blood microscopy negative women that were negative in peripheral blood microscopy, RDTs and PCR (specificity) are 98% [95% CI 95-99], 94% [95% CI 76-99] and 77% [95% CI 71-82]. Based on the current data, it was not possible to determine if the false positives in RDTs and PCR are caused by sequestered parasites in the placenta that are not detected by placental microscopy.</p> <p>Conclusion</p> <p>The findings suggest that RDTs and PCR may have good performance characteristics to serve as alternatives for the diagnosis of malaria in pregnancy, besides any other limitations and practical considerations concerning the use of these tests. Nevertheless, more studies with placental histology as reference test are urgently required to reliably determine the accuracy of RDTs and PCR for the diagnosis of placental malaria. <it>P. vivax</it>-infections have been neglected in diagnostic test accuracy studies of malaria in pregnancy.</p

Benefit-Harm Analysis for Informed Decision Making on Participating in Colorectal Cancer Screening: A Modeling Study

OBJECTIVES To facilitate informed decision making on participating in colorectal cancer (CRC) screening, we assessed the benefit-harm balance of CRC screening for a wide range of subgroups over different time horizons. METHODS The study combined incidence proportions of benefits and harms of (not) participating in CRC screening estimated by the Adenoma and Serrated pathway to CAncer microsimulation model, a preference eliciting survey, and benefit-harm balance modeling combining all outcomes to determine the net health benefit of CRC screening over 10, 20, and 30 years. Probability of net health benefit was estimated for 210 different subgroups based on age, sex, previous participation in CRC screening, and lifestyle. RESULTS CRC screening was net beneficial in 183 of 210 subgroups over 30 years (median probability [MP] of 0.79, interquartile range [IQR] of 0.69-0.85) across subgroups. Net health benefit was greater for men (MP 0.82; IQR 0.69-0.89) than women (MP 0.76; IQR 0.67-0.83) and for those without history of participation in previous screenings (MP 0.84; IQR 0.80-0.89) compared with those with (MP 0.69; IQR 0.59-0.75). Net health benefit decreased with increasing age, from MP of 0.84 (IQR 0.80-0.86) at age 55 to 0.61 (IQR 0.56-0.71) at age 75. Shorter time horizons led to lower benefit, with MP of 0.70 (IQR 0.62-0.80) over 20 years and 0.54 (IQR 0.48-0.67) over 10 years. CONCLUSIONS Our benefit-harm analysis provides information about net health benefit of screening participation, based on important characteristics and preferences of individuals, which could assist screening invitees in making informed decisions on screening participation

Самоподобие массивов сетевых публикаций по компьютерной вирусологии

Описан подход к организации анализа потока тематических публикаций по компьютерной вирусологии, представленных в web-пространстве. Обоснована фрактальная природа информационных потоков, описаны основные алгоритмы, применяемые в процессе исследований, а также приведены прогнозные выводы на основе свойств персистентности временных рядов.Описано підхід до організації аналізу потоку тематичних публікацій з комп’ютерної вірусології, які наведені у web-просторі. Обґрунтовано фрактальну природу інформаційних потоків, описано основні алгоритми, що застосовуються в процесі досліджень, а також наведено прогнозні висновки на базі властивостей персистентності часових рядів.An approach to the organization of the analysis of a thematic publications stream on computer virology, submitted in web-space, is described. The fractal nature of information streams is proved, the basic algorithms used during researches are described and forecasts conclusions on the basis of persistent properties of time series are given