bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study design and baseline characteristics of a population-based prospective cohort study of dementia in Japan: the Japan Prospective Studies Collaboration for Aging and Dementia (JPSC-AD)
Authors:   on behalf of the JPSFC-AD Study Group, Ninomiya Toshiharu , Nakaji Shigeyuki , Maeda Tetsuya , Yamada Masahito , Mimura Masaru , Nakashima Kenji , Mori Takaaki , Takebayashi Minoru , Ohara Tomoyuki , Hata Jun , Kokubo Yoshihiro , Uchida Kazuhiro , Taki Yasuyuki , Kumagai Shuzo , Yonemoto Koji , Yoshida Hisako , Muto Kaori , Momozawa Yukihide , Akiyama Masato , Kubo Michiaki , Ikeda Manabu , Kanba Shigenobu , Kiyohara Yutaka 
Published: October 2020

Abstract

Background
The burden of dementia is growing rapidly and has become a medical and social problem in Japan. Prospective cohort studies have been considered an effective methodology to clarify the risk factors and the etiology of dementia. We aimed to perform a large-scale dementia cohort study to elucidate environmental and genetic risk factors for dementia, as well as their interaction.

Methods
The Japan Prospective Studies Collaboration for Aging and Dementia (JPSC-AD) is a multisite, population-based prospective cohort study of dementia, which was designed to enroll approximately 10,000 community-dwelling residents aged 65 years or older from 8 sites in Japan and to follow them up prospectively for at least 5 years. Baseline exposure data, including lifestyles, medical information, diets, physical activities, blood pressure, cognitive function, blood test, brain magnetic resonance imaging (MRI), and DNA samples, were collected with a pre-specified protocol and standardized measurement methods. The primary outcome was the development of dementia and its subtypes. The diagnosis of dementia was adjudicated by an endpoint adjudication committee using standard criteria and clinical information according to the Diagnostic and Statistical Manual of Mental Disorders, 3rd Revised Edition. For brain MRI, three-dimensional acquisition of T1-weighted images was performed. Individual participant data were pooled for data analyses.

Results
The baseline survey was conducted from 2016 to 2018. The follow-up surveys are ongoing. A total of 11,410 individuals aged 65 years or older participated in the study. The mean age was 74.4 years, and 41.9% were male. The prevalence of dementia at baseline was 8.5% in overall participants. However, it was 16.4% among three sites where additional home visit and/or nursing home visit surveys were performed. Approximately two-thirds of dementia cases at baseline were Alzheimer’s disease.

Conclusions
The prospective cohort data from the JPSC-AD will provide valuable insights regarding the risk factors and etiology of dementia as well as for the development of predictive models and diagnostic markers for the future onset of dementia. The findings of this study will improve our understanding of dementia and provide helpful information to establish effective preventive strategies for dementia in Japan.
Economic impact of autonomous vehicles in Spain
Authors: Alonso Efrén , Arpón Cristina , González María , Fernández Ramón Ángel , Nieto Mariano 
Published: October 2020

AbstractBackgroundPollution, traffic accidents, and congestion are huge problems in most urban areas. Autonomous and electric vehicles are leading our society to a new mobility model, also known as the New Era of Transportation (NERTRA). Mobility is a strategic issue for any country, and this change of model will mean, in addition to a great technological revolution, an economic revolution.MethodologyThe purpose of this work is to carry out a study of the main economic sectors affected in Spain and evaluate the economic impact that autonomous vehicles will have on each one. Data from this sector have been collected, analyzing the economic and technological factors that will affect to a greater or lesser extent and made evolution forecasts.ResultsThe study presents three different scenarios depending on how the transition progresses. The results are presented by each sector in each of these scenarios. These results have great value for the industry itself and the professionals affected, as well as for the authorities of the country to take the appropriate measures from the beginning of the transition. The sectors directly affected by this change represent more than 38% of the gross domestic product of Spain. Key factors, such as technological innovation in vehicles, and the emergence of new business and mobility models determine drastic changes in some important sectors. It is important to make quick decisions both from administrations and from the industry itself to adapt to new mobility.
ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom
Authors: Moore Marten , Wesemann Corinna , Gossmann Nikolaj , Sahm Arne , Krüger Jan , Sczyrba Alexander , Dietz Karl-Josef 
Published: October 2020

Abstract

Background
Post-translational modifications (PTM) of amino acid (AA) side chains in peptides control protein structure and functionality. PTMs depend on the specific AA characteristics. The reactivity of cysteine thiol-based PTMs are unique among all proteinaceous AA. This pipeline aims to ease the identification of conserved AA of polypeptides or protein families based on the phylogenetic occurrence in the plant kingdom. The tool is customizable to include any species.
The degree of AA conservation is taken as indicator for structural and functional significance, especially for PTM-based regulation. Further, this pipeline tool gives insight into the evolution of these potentially regulatory important peptides.

Results
The web-based or stand-alone pipeline tool Conserved Cysteine Finder (ConCysFind) was developed to identify conserved AA such as cysteine, tryptophan, serine, threonine, tyrosin and methionine. ConCysFind evaluates multiple alignments considering the proteome of 21 plant species. This exemplar study focused on Cys as evolutionarily conserved target for multiple redox PTM. Phylogenetic trees and tables with the compressed results of the scoring algorithm are generated for each Cys in the query polypeptide. Analysis of 33 translation elongation and release factors alongside of known redox proteins from Arabidopsis thaliana for conserved Cys residues confirmed the suitability of the tool for identifying conserved and functional PTM sites. Exemplarily, the redox sensitivity of cysteines in the eukaryotic release factor 1-1 (eRF1-1) was experimentally validated.

Conclusion
ConCysFind is a valuable tool for prediction of new potential protein PTM targets in a broad spectrum of species, based on conserved AA throughout the plant kingdom. The identified targets were successfully verified through protein biochemical assays. The pipeline is universally applicable to other phylogenetic branches by customization of the database.
simplePHENOTYPES: SIMulation of pleiotropic, linked and epistatic phenotypes
Authors: Fernandes Samuel B. , Lipka Alexander E. 
Published: October 2020

Abstract

Background
Advances in genotyping and phenotyping techniques have enabled the acquisition of a great amount of data. Consequently, there is an interest in multivariate statistical analyses that identify genomic regions likely to contain causal mutations affecting multiple traits (i.e., pleiotropy). As the demand for multivariate analyses increases, it is imperative that optimal tools are available to assess their performance. To facilitate the testing and validation of these multivariate approaches, we developed simplePHENOTYPES, an R/CRAN package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in a wide range of genetic architectures, including additive, dominance and epistatic models.

Results
We illustrate simplePHENOTYPES’ ability to simulate thousands of phenotypes in less than one minute. We then provide two vignettes illustrating how to simulate sets of correlated traits in simplePHENOTYPES. Finally, we demonstrate the use of results from simplePHENOTYPES in a standard GWAS software, as well as the equivalence of simulated phenotypes from simplePHENOTYPES and other packages with similar capabilities.

Conclusions
simplePHENOTYPES is a R/CRAN package that makes it possible to simulate multiple traits controlled by loci with varying degrees of pleiotropy. Its ability to interface with both commonly-used marker data formats and downstream quantitative genetics software and packages should facilitate a rigorous assessment of both existing and emerging statistical GWAS and GS approaches. simplePHENOTYPES is also available at https://github.com/samuelbfernandes/simplePHENOTYPES.
Improved cytokine–receptor interaction prediction by exploiting the negative sample space
Authors: Nath Abhigyan , Leier André 
Published: October 2020

Abstract

Background
Cytokines act by binding to specific receptors in the plasma membrane of target cells. Knowledge of cytokine–receptor interaction (CRI) is very important for understanding the pathogenesis of various human diseases—notably autoimmune, inflammatory and infectious diseases—and identifying potential therapeutic targets. Recently, machine learning algorithms have been used to predict CRIs. “Gold Standard” negative datasets are still lacking and strong biases in negative datasets can significantly affect the training of learning algorithms and their evaluation. To mitigate the unrepresentativeness and bias inherent in the negative sample selection (non-interacting proteins), we propose a clustering-based approach for representative negative sample selection.

Results
We used deep autoencoders to investigate the effect of different sampling approaches for non-interacting pairs on the training and the performance of machine learning classifiers. By using the anomaly detection capabilities of deep autoencoders we deduced the effects of different categories of negative samples on the training of learning algorithms. Random sampling for selecting non-interacting pairs results in either over- or under-representation of hard or easy to classify instances. When K-means based sampling of negative datasets is applied to mitigate the inadequacies of random sampling, random forest (RF) together with the combined feature set of atomic composition, physicochemical-2grams and two different representations of evolutionary information performs best. Average model performances based on leave-one-out cross validation (loocv) over ten different negative sample sets that each model was trained with, show that RF models significantly outperform the previous best CRI predictor in terms of accuracy (+ 5.1%), specificity (+ 13%), mcc (+ 0.1) and g-means value (+ 5.1). Evaluations using tenfold cv and training/testing splits confirm the competitive performance.

Conclusions
A comparative analysis was performed to assess the effect of three different sampling methods (random, K-means and uniform sampling) on the training of learning algorithms using different evaluation methods. Models trained on K-means sampled datasets generally show a significantly improved performance compared to those trained on random selections—with RF seemingly benefiting most in our particular setting. Our findings on the sampling are highly relevant and apply to many applications of supervised learning approaches in bioinformatics.
Neurologic effects of short-term treatment with a soluble epoxide hydrolase inhibitor after cardiac arrest in pediatric swine
Authors: O’Brien Caitlin E. , Santos Polan T. , Kulikowicz Ewa , Lee Jennifer K. , Koehler Raymond C. , Martin Lee J. 
Published: October 2020

Abstract

Background
Cardiac arrest (CA) is the most common cause of acute neurologic insult in children. Many survivors have significant neurocognitive deficits at 1 year of recovery. Epoxyeicosatrienoic acids (EETs) are multifunctional endogenous lipid signaling molecules that are involved in brain pathobiology and may be therapeutically relevant. However, EETs are rapidly metabolized to less active dihydroxyeicosatrienoic acids by soluble epoxide hydrolase (sEH), limiting their bioavailability. We hypothesized that sEH inhibition would improve outcomes after CA in an infant swine model. Male piglets (3–4 kg, 2 weeks old) underwent hypoxic-asphyxic CA. After resuscitation, they were randomized to intravenous treatment with an sEH inhibitor (TPPU, 1 mg/kg; n = 8) or vehicle (10% poly(ethylene glycol); n = 9) administered at 30 min and 24 h after return of spontaneous circulation. Two sham-operated groups received either TPPU (n = 9) or vehicle (n = 8). Neurons were counted in hematoxylin- and eosin-stained sections from putamen and motor cortex in 4-day survivors.

Results
Piglets in the CA + vehicle groups had fewer neurons than sham animals in both putamen and motor cortex. However, the number of neurons after CA did not differ between vehicle- and TPPU-treated groups in either anatomic area. Further, 20% of putamen neurons in the Sham + TPPU group had abnormal morphology, with cell body attrition and nuclear condensation. TPPU treatment also did not reduce neurologic deficits.

Conclusion
Treatment with an sEH inhibitor at 30 min and 24 h after resuscitation from asphyxic CA does not protect neurons or improve acute neurologic outcomes in piglets.
Atrial matrix remodeling in atrial fibrillation patients with aortic stenosis
Authors: Fragão-Marques Mariana , Miranda I. , Martins D. , Barroso I. , Mendes C. , Pereira-Neves A. , Falcão-Pires I. , Leite-Moreira A. 
Published: October 2020

Abstract

Background
This study aimed to evaluate atrium extracellular matrix remodeling in atrial fibrillation (AF) patients with severe aortic stenosis, through histological fibrosis quantification and extracellular matrix gene expression analysis, as well as serum quantification of selected protein targets.

Methods
A posthoc analysis of a prospective study was performed in a cohort of aortic stenosis patients. Between 2014 and 2019, 56 patients with severe aortic stenosis submitted to aortic valve replacement surgery in a tertiary hospital were selected.

Results
Fibrosis was significantly increased in the AF group when compared to sinus rhythm (SR) patients (p = 0.024). Moreover, cardiomyocyte area was significantly higher in AF patients versus SR patients (p = 0.008). Conversely, collagen III gene expression was increased in AF patients (p = 0.038). TIMP1 was less expressed in the atria of AF patients. MMP16/TIMP4 ratio was significantly decreased in AF patients (p = 0.006). TIMP1 (p = 0.004) and TIMP2 (p = 0.012) were significantly increased in the serum of AF patients. Aortic valve maximum (p = 0.0159) and mean (p = 0.031) gradients demonstrated a negative association with serum TIMP1.

Conclusions
Atrial fibrillation patients with severe aortic stenosis present increased atrial fibrosis and collagen type III synthesis, with extracellular matrix remodelling demonstrated by a decrease in the MMP16/TIMP4 ratio, along with an increased serum TIMP1 and TIMP2 proteins.
Home-based palliative care management: what are the useful resources for general practitioners? a qualitative study among GPs in France
Authors: Boudy Carol-Anne , Bouchez Tiphanie , Caprini Didier , Pourrat Isabelle , Munck Stéphane , Barbaroux Adriaan 
Published: October 2020

AbstractBackgroundMost French people (71%) would like to die at home, but only one out of four actually do. While the difficulties inherent in the practice of home-based palliative care are well described, few studies highlight the resources currently used by general practitioners (GPs) in real life. We have therefore sought to highlight the resources actually used by GPs providing home-based palliative care.MethodsTwenty-one GPs of different ages and practice patterns agreed to participate to this qualitative study based upon semi-structured interviews. They were recruited according to a purposive sampling. Transcripts analysis was based upon General Inductive Analysis.ResultsThe resources highlighted have been classified into two main categories according to whether they were internal or external to the GPs. The internal resources raised included the doctor’s practical experience and continuous medical education, personal history, work time organization and a tacit moral contract related to the referring GP’s position. External resources included resource personnel, regional assistance platforms and health facilities, legislation.ConclusionThis study provides a simple list that is easy to share and pragmatic solutions for GPs and policymakers. Home-based palliative care practice can simultaneously be burdensome and yet a fulfilling, meaningful activity, depending on self-efficacy and professional exhaustion (burnout), perhaps to a greater extent than on medical knowledge. Home-based palliative care promotion is a matter of social responsibility. The availability of multidisciplinary teams such as regional assistance platforms and Hospitalization at Home is particularly important for the management of palliative care. Policymakers should consolidate these specific resources out of hospitals, in community settings where the patients wish to end their life.
Impact of morbidity on care need increase and mortality in nursing homes: a retrospective longitudinal study using administrative claims data
Authors: Reber Katrin C. , Lindlbauer Ivonne , Schulz Claudia , Rapp Kilian , König Hans-Helmut 
Published: October 2020

AbstractBackgroundA growing number of older people are care dependent and live in nursing homes, which accounts for the majority of long-term-care spending. Specific medical conditions and resident characteristics may serve as risk factors predicting negative health outcomes. We investigated the association between the risk of increasing care need and chronic medical conditions among nursing home residents, allowing for the competing risk of mortality.MethodsIn this retrospective longitudinal study based on health insurance claims data, we investigated 20,485 older adults (≥65 years) admitted to German nursing homes between April 2007 and March 2014 with care need level 1 or 2 (according to the three level classification of the German long-term care insurance). This classification is based on required daily time needed for assistance. The outcome was care level change. Medical conditions were determined according to 31 Charlson and Elixhauser conditions. Competing risks analyses were applied to identify chronic medical conditions associated with risk of care level change and mortality.ResultsThe probability for care level change and mortality acted in opposite directions. Dementia was associated with increased probability of care level change compared to other conditions. Patients who had cancer, myocardial infarction, congestive heart failure, cardiac arrhythmias, renal failure, chronic pulmonary disease, weight loss, or recent hospitalization were more likely to die, as well as residents with paralysis and obesity when admitted with care level 2.ConclusionThis paper identified risk groups of nursing home residents which are particularly prone to increasing care need or mortality. This enables focusing on these risk group to offer prevention or special treatment. Moreover, residents seemed to follow specific trajectories depending on their medical conditions. Some were more prone to increased care need while others had a high risk of mortality instead. Several conditions were neither related to increased care need nor mortality, e.g., valvular, cerebrovascular or liver disease, peripheral vascular disorder, blood loss anemia, depression, drug abuse and psychosis. Knowledge of functional status trajectories of residents over time after nursing home admission can help decision-makers when planning and preparing future care provision strategies (e.g., planning of staffing, physical equipment and financial resources).
Prevalence of and risk factors for HBV and HCV among incarcerated people who inject drugs in Iran: A cross sectional study
Authors: Moradi Ghobad , Mohamadi Parvin , Zareie Bushra , Rasouli Mohammad Aziz , Gouya Mohammad Mehdi , Jafari Saeede 
Published: October 2020

AbstractBackgroundThis study aimed at determining the prevalence of and risk factors for hepatitis B virus (HBV) and hepatitis C virus (HCV) among incarcerated people who inject drugs (PWID) in Iran in 2015–16.MethodsThe required data was collected from a database provided by Iranian national bio-behavioral surveillance surveys (BBSSs) on 11,988 prisoners selected from among 55 prisons in 19 provinces in 2015–16. The data on demographics and behavioral variables were collected through interviews and the status of exposure to HBV and HCV were determined using ELISA blood test. A total of 1387 individuals with a history of drug injection in their lifetime were enrolled into the study. Data were analyzed using the survey package in Stata/SE software, Version 14.0. Univariate and multivariate logistic regression tests were used to investigate the relationships between risk factors and outcomes.ResultsThe mean age of the incarcerated PWID was 36.83 ± 8.13 years. Of all the studied subjects, 98.46% were male and 50.97% were married. The prevalence of HCV and HBV among the subjects were 40.52 and 2.46%, respectively. The prevalence of HCV was associated with age ≥ 30 years, being single, illiteracy and low level of education, prison term> 5 years, history of piercing, and extramarital sex in lifetime (P < 0.05).ConclusionsThe prevalence of HCV is alarmingly high. In general, it is recommended to adopt measures to screen and treat patients with HCV and vaccinat incarcerated PWID without a history of vaccination against HBV.
A novel PIK3R1 mutation of SHORT syndrome in a Chinese female with diffuse thyroid disease: a case report and review of literature
Authors: Sun Liying , Zhang Qianwen , Li Qun , Tang Yijun , Wang Yirou , Li Xin , Li Niu , Wang Jian , Wang Xiumin 
Published: October 2020

Abstract

Background
SHORT syndrome is a rare genetic disease named with the acronyms of short stature, hyper-extensibility of joints, ocular depression, Rieger anomaly and teething delay. It is inherited in an autosomal dominant manner confirmed by the identification of heterozygous mutations in PIK3R1. This study hereby presents a 15-year-old female with intrauterine growth restriction, short stature, teething delay, characteristic facial gestalts who was identified a novel de novo nonsense mutation in PIK3R1.

Case presentation
The proband was admitted to our department due to irregular menstrual cycle and hirsutism with short stature, who had a history of intrauterine growth restriction and presented with short stature, teething delay, characteristic facial gestalts, hirsutism, and thyroid disease. Whole-exome sequencing and Sanger sequencing revealed c.1960C > T, a novel de novo nonsense mutation, leading to the termination of protein translation (p. Gln654*).

Conclusions
This is the first case report of SHORT syndrome complicated with thyroid disease in China, identifying a novel de novo heterozygous nonsense mutation in PIK3R1 gene (p. Gln654*). The phenotypes are mildly different from other cases previously described in the literature, in which our patient presents with lipoatrophy, facial feature, and first reported thyroid disease. Thyroid disease may be a new clinical symptom of patients with SHORT syndrome.