bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Smoking on the Association between Long-Term Alcohol Consumption and Dyslipidemia in a Middle-Aged and Older Population
Authors: Lee Kyueun , Kim Jihye 
Published: May 2020

Abstract

Aims
The joint effects of chronic alcohol consumption and smoking on dyslipidemia remain unclear in a prospective design. This study examined the effect of smoking on the association between long-term alcohol consumption and risk of incident dyslipidemia.

Methods
A total of 4467 participants (1866 men and 2601women) aged 40–69 years without dyslipidemia were recruited at baseline. Alcohol consumption was assessed biennially using a questionnaire and classified as light, moderate or heavy drinker. Smoking status was examined at baseline and categorized into non-smokers and current smokers. Dyslipidemia was defined as the presence of one or more of following: hypertriglyceridemia (triglyceride ≥200 mg/dL), hypercholesterolemia (total cholesterol ≥240 mg/dL), low high-density lipoprotein-cholesterol (HDL-C) &lt; 40 mg/dL, or high low-density lipoprotein cholesterol ≥160 mg/dL.

Results
During a follow-up period of 12 years, 2872 (64.3%) participants developed dyslipidemia. In non-smoking men, light or moderate alcohol consumption was associated with a lower risk of incident dyslipidemia such as hypertriglyceridemia and hypercholesterolemia, whereas this association was not observed in current smoking men. Unlike non-smokers, the duration of alcohol drinking &gt; 10 years was associated with a higher risk of hypertriglyceridemia in current smoking men (hazard ratio = 1.57, 95% confidence interval: 1.07–2.30, P = 0.020). In addition, alcohol consumption was inversely associated with low HDL-C regardless of smoking status. In women, alcohol consumption was inversely associated with dyslipidemia hypercholesterolemia and low HDL-C regardless of alcohol amount.

Conclusion
Smoking crucially confounds the association between long-term alcohol consumption and dyslipidemia, particularly in hypertriglyceridemia and hypercholesterolemia.
Parasitologist-level classification of apicomplexan parasites and host cell with deep cycle transfer learning (DCTL)
Authors: Li Sen , Yang Qi , Jiang Hao , Cortés-Vecino Jesús A , Zhang Yang 
Published: May 2020

Abstract

Motivation
Apicomplexan parasites, including Toxoplasma, Plasmodium and Babesia, are important pathogens that affect billions of humans and animals worldwide. Usually a microscope is used to detect these parasites, but it is difficult to use microscopes and clinician requires to be trained. Finding a cost-effective solution to detect these parasites is of particular interest in developing countries, in which infection is more common.

Results
Here, we propose an alternative method, deep cycle transfer learning (DCTL), to detect apicomplexan parasites, by utilizing deep learning-based microscopic image analysis. DCTL is based on observations of parasitologists that Toxoplasma is banana-shaped, Plasmodium is generally ring-shaped, and Babesia is typically pear-shaped. Our approach aims to connect those microscopic objects (Toxoplasma, Plasmodium, Babesia and erythrocyte) with their morphological similar macro ones (banana, ring, pear and apple) through a cycle transfer of knowledge. In the experiments, we conduct DCTL on 24 358 microscopic images of parasites. Results demonstrate high accuracy and effectiveness of DCTL, with an average accuracy of 95.7% and an area under the curve of 0.995 for all parasites types. This article is the first work to apply knowledge from parasitologists to apicomplexan parasite recognition, and it opens new ground for developing AI-powered microscopy image diagnostic systems.

Availability and implementation
Code and dataset available at https://github.com/senli2018/DCTL.

Supplementary information
Supplementary data are available at Bioinformatics online.
TheMacroptilium gracilespecies complex (Fabaceae, Papilionoideae): an integrative taxonomic study based on morphological, molecular and ecological data
Authors: Berlingeri Chiara , Crespo Manuel B , Calles Teodardo 
Published: May 2020

AbstractMacroptilium gracile (Phaseolinae, Fabaceae) sensu lato is an extremely diverse species distributed from Mexico to Argentina. The taxonomic and nomenclatural history of the species is confusing, due to existing contrasting treatments. All 15 names corresponding to 12 taxa that have often been considered akin to M. gracile were selected here to clarify the identity of this taxonomic aggregate, using morphological, molecular and biogeographical analyses. Univariate and multivariate statistical analyses (nMDS and cluster) of 67 morphological traits were performed on a sample of 109 herbarium sheets. Maximum parsimony and Bayesian inference analyses were conducted using plastid (rpl32-trnL(UAG), trnK-matK-trnK) and nuclear (ITS/5.8S) DNA sequence data on a sample of 31 accessions belonging to taxa of the M. gracile complex and other Macroptilium spp., using three members of related genera (Phaseolus and Vigna) as outgroups. A database with plant locations per taxa was used to elaborate a distribution map, and the potential habitats were estimated through nMDS analysis. Our morphological, molecular and biogeographic results suggest that members of the M. gracile complex belong to three taxonomic entities, for which a new arrangement is proposed accepting Macroptilium gracile (with two varieties) and M. campestre, including two new nomenclatural combinations (M. gracile var. subcoriaceum and M. campestre). Types for all cited names are indicated where available (with a new lectotype designation). Morphological, ecological and distributional data are reported for each accepted taxon.
Definitions and classification of malformations of cortical development: practical guidelines
Authors: Severino Mariasavina , Geraldo Ana Filipa , Utz Norbert , Tortora Domenico , Pogledic Ivana , Klonowski Wlodzimierz , Triulzi Fabio , Arrigoni Filippo , Mankad Kshitij , Leventer Richard J , Mancini Grazia M S , Barkovich James A , Lequin Maarten H , Rossi Andrea 
Published: May 2020

AbstractMalformations of cortical development are a group of rare disorders commonly manifesting with developmental delay, cerebral palsy or seizures. The neurological outcome is extremely variable depending on the type, extent and severity of the malformation and the involved genetic pathways of brain development. Neuroimaging plays an essential role in the diagnosis of these malformations, but several issues regarding malformations of cortical development definitions and classification remain unclear. The purpose of this consensus statement is to provide standardized malformations of cortical development terminology and classification for neuroradiological pattern interpretation. A committee of international experts in paediatric neuroradiology prepared systematic literature reviews and formulated neuroimaging recommendations in collaboration with geneticists, paediatric neurologists and pathologists during consensus meetings in the context of the European Network Neuro-MIG initiative on Brain Malformations (https://www.neuro-mig.org/). Malformations of cortical development neuroimaging features and practical recommendations are provided to aid both expert and non-expert radiologists and neurologists who may encounter patients with malformations of cortical development in their practice, with the aim of improving malformations of cortical development diagnosis and imaging interpretation worldwide.
Tuberculosis Infection in Women of Reproductive Age: A Cross-sectional Study at Antenatal Care Clinics in an Ethiopian City
Authors: Walles John , Tesfaye Fregenet , Jansson Marianne , Balcha Taye Tolera , Sturegård Erik , Kefeni Mestawet , Merga Gadissa , Hansson Stefan R , Winqvist Niclas , Björkman Per 
Published: May 2020

Abstract

Background
Knowledge on tuberculosis (TB) infection epidemiology in women of reproductive age living in TB-endemic areas is limited. We used a composite definition of TB infection in a cohort of pregnant women recruited in an Ethiopian city as a model for TB exposure patterns, and to identify factors associated with TB infection.

Methods
Women seeking antenatal care at public health facilities underwent structured interviews, physical examination, and QuantiFERON-TB Gold-Plus (QFT) testing. Women with symptoms compatible with TB disease, and all human immunodeficiency virus (HIV)–positive women, were investigated for active TB by sputum bacteriological testing. TB infection (TB+) was defined as either positive QFT (≥ 0.35 IU/mL), self-reported previous active TB, or current active TB. Associations between TB infection and clinical, demographic, and socioeconomic characteristics were tested in multiple logistic regression analysis.

Results
Among 1834 participants, 679 (37.0%) met criteria for TB+ (80 [4.4%] previous active TB, 5 [0.3%] current active TB, and 594 [32.4%] QFT-positive without previous or current active TB). Age (annual adjusted odds ratio [AOR], 1.069 [95% confidence interval {CI}, 1.045–1.093]) and HIV infection (AOR, 1.43 [95% CI, 1.033–1.988]) were independently associated with TB+. The relationship with increasing age was only observed in HIV-negative women, and translated to an estimated annual risk of TB infection of 2.1% in HIV-negative women.

Conclusions
TB infection in women of reproductive age in Ethiopia was independently associated with HIV infection and increasing age, suggesting exposure to contagious TB and continuous acquisition of TB infection in this population.
Risk Factors for Severe Disease and Efficacy of Treatment in Patients Infected With COVID-19: A Systematic Review, Meta-Analysis, and Meta-Regression Analysis
Authors: Zhang John J Y , Lee Keng Siang , Ang Li Wei , Leo Yee Sin , Young Barnaby Edward 
Published: May 2020

Abstract
The coronavirus disease 2019 (COVID-19) pandemic spread globally in the beginning of 2020. At present, predictors of severe disease and the efficacy of different treatments are not well understood. We conducted a systematic review and meta-analysis of all published studies up to 15 March 2020, which reported COVID-19 clinical features and/or treatment outcomes. Forty-five studies reporting 4203 patients were included. Pooled rates of intensive care unit (ICU) admission, mortality, and acute respiratory distress syndrome (ARDS) were 10.9%, 4.3%, and 18.4%, respectively. On meta-regression, ICU admission was predicted by increased leukocyte count (P &lt; .0001), alanine aminotransferase (P = .024), and aspartate transaminase (P = .0040); elevated lactate dehydrogenase (LDH) (P &lt; .0001); and increased procalcitonin (P &lt; .0001). ARDS was predicted by elevated LDH (P &lt; .0001), while mortality was predicted by increased leukocyte count (P = .0005) and elevated LDH (P &lt; .0001). Treatment with lopinavir-ritonavir showed no significant benefit in mortality and ARDS rates. Corticosteroids were associated with a higher rate of ARDS (P = .0003).
Opportunities in the cloud or pie in the sky? Current status and future perspectives of telemedicine in nephrology
Authors: Stauss Madelena , Floyd Lauren , Becker Stefan , Ponnusamy Arvind , Woywodt Alexander 
Published: May 2020

AbstractThe use of telehealth to support, enhance or substitute traditional methods of delivering healthcare is becoming increasingly common in many specialties, such as stroke care, radiology and oncology. There is reason to believe that this approach remains underutilized within nephrology, which is somewhat surprising given the fact that nephrologists have always driven technological change in developing dialysis technology. Despite the obvious benefits that telehealth may provide, robust evidence remains lacking and many of the studies are anecdotal, limited to small numbers or without conclusive proof of benefit. More worryingly, quite a few studies report unexpected obstacles, pitfalls or patient dissatisfaction. However, with increasing global threats such as climate change and infectious disease, a change in approach to delivery of healthcare is needed. The current pandemic with coronavirus disease 2019 (COVID-19) has prompted the renal community to embrace telehealth to an unprecedented extent and at speed. In that sense the pandemic has already served as a disruptor, changed clinical practice and shown immense transformative potential. Here, we provide an update on current evidence and use of telehealth within various areas of nephrology globally, including the fields of dialysis, inpatient care, virtual consultation and patient empowerment. We also provide a brief primer on the use of artificial intelligence in this context and speculate about future implications. We also highlight legal aspects and pitfalls and discuss the ‘digital divide’ as a key concept that healthcare providers need to be mindful of when providing telemedicine-based approaches. Finally, we briefly discuss the immediate use of telenephrology at the onset of the COVID-19 pandemic. We hope to provide clinical nephrologists with an overview of what is currently available, as well as a glimpse into what may be expected in the future.
Basal tolerance but not plasticity gives invasive springtails the advantage in an assemblage setting
Authors: Phillips Laura M , Aitkenhead Ian , Janion-Scheepers Charlene , King Catherine K , McGeoch Melodie A , Nielsen Uffe N , Terauds Aleks , Liu W P Amy , Chown Steven L 
Published: May 2020

Abstract
As global climates change, alien species are anticipated to have a growing advantage relative to their indigenous counterparts, mediated through consistent trait differences between the groups. These insights have largely been developed based on interspecific comparisons using multiple species examined from different locations. Whether such consistent physiological trait differences are present within assemblages is not well understood, especially for animals. Yet, it is at the assemblage level that interactions play out. Here, we examine whether physiological trait differences observed at the interspecific level are also applicable to assemblages. We focus on the Collembola, an important component of the soil fauna characterized by invasions globally, and five traits related to fitness: critical thermal maximum, minimum and range, desiccation resistance and egg development rate. We test the predictions that the alien component of a local assemblage has greater basal physiological tolerances or higher rates, and more pronounced phenotypic plasticity than the indigenous component. Basal critical thermal maximum, thermal tolerance range, desiccation resistance, optimum temperature for egg development, the rate of development at that optimum and the upper temperature limiting egg hatching success are all significantly higher, on average, for the alien than the indigenous components of the assemblage. Outcomes for critical thermal minimum are variable. No significant differences in phenotypic plasticity exist between the alien and indigenous components of the assemblage. These results are consistent with previous interspecific studies investigating basal thermal tolerance limits and development rates and their phenotypic plasticity, in arthropods, but are inconsistent with results from previous work on desiccation resistance. Thus, for the Collembola, the anticipated advantage of alien over indigenous species under warming and drying is likely to be manifest in local assemblages, globally.
The Health Toll of Import Competition
Authors: Adda Jérôme , Fawaz Yarine 
Published: May 2020

AbstractThis paper assesses the effect of import competition on the labour market and health outcomes of US workers. We first show that import shocks affect employment and income, but only in areas where jobs are more intense in routine tasks. Exploiting over 40 million individual observations on health and mortality, we find that import had a detrimental effect on physical and mental health that is concentrated in those areas and exhibits strong persistence. It decreased healthcare utilisation and increased hospitalisation for a large set of conditions, more difficult to treat. The mortality hazard of workers in manufacturing increased by up to 6% per billion-dollar import increase.
Elucidating the child’s perspective in health promotion: children’s experiences of child-centred health dialogue in Sweden
Authors: Derwig Mariette , Tiberg Irén , Hallström Inger 
Published: May 2020

SummaryPromoting young children’s health through health promotion activities is an investment for the future. In the Child Health Services in the south of Sweden a structured Child-Centred Health Dialogue (CCHD) directed to all 4-year-old children was developed using illustrations based on the most important health messages associated with the promotion of healthy lifestyle in preschool children. The aim of this study was to explore the experiences of children participating in CCHD using 21 non-participant observations during their 4-year health visit and additionally 16 individual interviews 0–7 days after their visit, conducted in the child’s home in the presence of a caregiver. Children participated as social actors when guided to express their views based upon their own understanding was the overall main category generated from the qualitative content analysis. The children showed that they liked to participate actively but could influence their choice to participate. They expressed their views based on their daily life and wanted to understand the meaning of the information with which they interacted. The study revealed that 4-year-old children given the opportunity to speak for themselves—elucidating the child’s perspective—interpreted the health messages in a different way than the intended meaning of the illustrations developed by adults. These findings are important for the improvement of CCHD and underline the utmost importance of including children in research on health promotion. This study supports the view that 4-year-old children can take an active role in their health and are capable of making health information meaningful.
Fold-stratified cross-validation for unbiased and privacy-preserving federated learning
Authors: Bey Romain , Goussault Romain , Grolleau François , Benchoufi Mehdi , Porcher Raphaël 
Published: May 2020

Abstract

Objective
We introduce fold-stratified cross-validation, a validation methodology that is compatible with privacy-preserving federated learning and that prevents data leakage caused by duplicates of electronic health records (EHRs).

Materials and Methods
Fold-stratified cross-validation complements cross-validation with an initial stratification of EHRs in folds containing patients with similar characteristics, thus ensuring that duplicates of a record are jointly present either in training or in validation folds. Monte Carlo simulations are performed to investigate the properties of fold-stratified cross-validation in the case of a model data analysis using both synthetic data and MIMIC-III (Medical Information Mart for Intensive Care-III) medical records.

Results
In situations in which duplicated EHRs could induce overoptimistic estimations of accuracy, applying fold-stratified cross-validation prevented this bias, while not requiring full deduplication. However, a pessimistic bias might appear if the covariate used for the stratification was strongly associated with the outcome.

Discussion
Although fold-stratified cross-validation presents low computational overhead, to be efficient it requires the preliminary identification of a covariate that is both shared by duplicated records and weakly associated with the outcome. When available, the hash of a personal identifier or a patient’s date of birth provides such a covariate. On the contrary, pseudonymization interferes with fold-stratified cross-validation, as it may break the equality of the stratifying covariate among duplicates.

Conclusion
Fold-stratified cross-validation is an easy-to-implement methodology that prevents data leakage when a model is trained on distributed EHRs that contain duplicates, while preserving privacy.
BRCA1Promoter Methylation and Clinical Outcomes in Ovarian Cancer: An Individual Patient Data Meta-Analysis
Authors: Kalachand Roshni D , Stordal Britta , Madden Stephen , Chandler Benjamin , Cunningham Julie , Goode Ellen L , Ruscito Ilary , Braicu Elena I , Sehouli Jalid , Ignatov Atanas , Yu Herbert , Katsaros Dionyssios , Mills Gordon B , Lu Karen H , Carey Mark S , Timms Kirsten M , Kupryjanczyk Jolanta , Rzepecka Iwona K , Podgorska Agnieszka , McAlpine Jessica N , Swisher Elizabeth M , Bernards Sarah S , O’Riain Ciaran , O’Toole Sharon , O’Leary John J , Bowtell David D , Thomas David M , Prieske Katharina , Joosse Simon A , Woelber Linn , Chaudhry Parvesh , Häfner Norman , Runnebaum Ingo B , Hennessy Bryan T 
Published: May 2020

AbstractBackgroundBRCA1 methylation has been associated with homologous recombination deficiency, a biomarker of platinum sensitivity. Studies evaluating BRCA1-methylated tubal and ovarian cancer (OC) do not consistently support improved survival following platinum chemotherapy. We examine the characteristics of BRCA1-methylated OC in a meta-analysis of individual participant data.MethodsData of 2636 participants across 15 studies were analyzed. BRCA1-methylated tumors were defined according to their original study. Associations between BRCA1 methylation and clinicopathological characteristics were evaluated. The effects of methylation on overall survival (OS) and progression-free survival (PFS) were examined using mixed-effects models. All statistical tests were 2-sided.Results430 (16.3%) tumors were BRCA1-methylated. BRCA1 methylation was associated with younger age and advanced-stage, high-grade serous OC. There were no survival differences between BRCA1-methylated and non–BRCA1-methylated OC (median PFS = 20.0 vs 18.5 months, hazard ratio [HR] = 1.01, 95% CI = 0.87 to 1.16; P = .98; median OS = 46.6 vs 48.0 months, HR = 1.02, 95% CI = 0.87 to 1.18; P = .96). Where BRCA1/2 mutations were evaluated (n = 1248), BRCA1 methylation displayed no survival advantage over BRCA1/2-intact (BRCA1/2 wild-type non–BRCA1-methylated) OC. Studies used different methods to define BRCA1 methylation. Where BRCA1 methylation was determined using methylation-specific polymerase chain reaction and gel electrophoresis (n = 834), it was associated with improved survival (PFS: HR = 0.80, 95% CI = 0.66 to 0.97; P = .02; OS: HR = 0.80, 95% CI = 0.63 to 1.00; P = .05) on mixed-effects modeling.ConclusionBRCA1-methylated OC displays similar clinicopathological features to BRCA1-mutated OC but is not associated with survival. Heterogeneity within BRCA1 methylation assays influences associations. Refining these assays may better identify cases with silenced BRCA1 function and improved patient outcomes.