bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fruits and vegetables consumption and the risk of gallstone diasease
Authors: Zhang Jun-Wei , Xiong Jian-Ping , Xu Wei-Yu , Sang Xin-Ting , Huang Han-Chun , Bian Jin , Xu Yi-Yao , Lu Xin , Zhao Hai-tao 
Published: July 2019

Abstract

Background:
The role of fruit and vegetables (FVs) consumption in decreasing gallstone disease risk remains contradictory. We performed a meta-analysis to analyze this potential correlation, followed by investigation of dose-response relationship of FVs consumption with gallstone disease.

Materials and methods:
PubMed, Embase, as well as Web of Science were searched to determine all published researches about the connection of FVs consumption with gallstone disease before March 2018. Relative risks (RRs) or odds ratios (ORs) along with corresponding 95% confidence intervals (CIs) was pooled utilizing random effect models, aiming at examining the correlation of FVs consumption with gallstone disease risk.

Results:
One cross-sectional study, our case-control studies as well as nine cohort studies were enrolled, covering approximately 33,983 patients with gallstone disease and 1,53,3752 participants. In a pooled analysis, vegetables consumption was significantly related to a decreased gallstone disease risk, (RR = 0.83, 95% CI, 0.74–0.94, I
2 = 91.1%), and for fruits consumption, RR was similar (RR = 0.88, 95%CI, 0.83–0.92, I
2 = 0.01%). This inverse correlation of FVs consumption with gallstone disease risk was solid in most subgroup analysis. The nonlinear dose-response correlation indicated that gallstone risk was reduced by 4% (RR = 0.96, 95%CI, 0.93–0.98) and 3% (RR = 0.97, 95%CI, 0.96–0.98) for every 200 g per day increment in vegetables consumption (P = .001) and fruits consumption (P = .001), respectively.

Conclusion:
This study suggests vegetables and fruits consumption is correlated with a significantly reduced risk of gallstone disease.
Significant association of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) rs3846662 and sirtuin 1 (SIRT1) rs7895833 and apolipoprotein E (APOE) hypermethylation with mild cognitive impairment (MCI)
Authors: Zou Ting , Duan Yali , Zhou Xiaohui , Chen Wei , Ying Xiuru , Liu Guili , Zhao Yongjie , Zhu Meisheng , Pari Abuliz , Alimu Kader , Miao Haijun , Kabinur Keyim , Zhang Lei , Wang Qinwen , Duan Shiwei 
Published: July 2019

Abstract
Our study investigated the association of five genes with MCI in the Xinjiang Uygur population in China. In addition, we also analyzed the association between APOE methylation and MCI.
Forty-three MCI and 125 controls were included in the present study. Genotyping was done by Sanger sequencing. DNA methylation assay was done using quantitative methylation-specific polymerase chain reaction (qMSP).
The distribution of HMGCR rs3846662 allele frequencies was significantly different between the MCI group and the control group (P = .04), especially in women (P = .032). Subgroup analysis showed that there was a statistically significant association of HMGCR rs3846662 with MCI in the non-APOE ε4 group (P = .024), especially in the females with non-APOE ε4. Similarly, HMGCR rs3846662 genotype and allele frequency in the ApoE E2 protein group were significantly different in the MCI group and the control group (genotype P = .021; allele P = .007). In addition, SIRT1 rs7895833 genotype frequency in the APOE ε4 group was found to be significantly different between the MCI and the control group (P = .005). We also observed a significant association of SIRT1 rs7895833 with MCI in the ApoE E4 protein subgroup (P = .005). In addition, APOE methylation levels were significantly different between the MCI group and the control group (P = .021), especially in men (P = .006). Subgroup analysis showed that APOE methylation levels were significantly associated with MCI in the non-APOE ε4 group (P = .009), especially in men (P = .015).
This study found a significant association of HMGCR rs3846662 with MCI in females independent of APOE ε4. In contrast, we revealed that the association of SIRT1 rs7895833 with MCI was dependent on with APOE ε4. We also showed that hypermethylation of APOE in MCI was independent of APOE ε4.
Tobacco smoke exposure and the risk of childhood acute lymphoblastic leukemia and acute myeloid leukemia
Authors: Chunxia Dong , Meifang Wang , Jianhua Zhang , Ruijuan Zhang , Xiue Liu , Zhuanzhen Zheng , Linhua Yang 
Published: July 2019

Abstract

Objective:
Tobacco smoke contains carcinogens known to damage somatic and germ cells. In this study, we investigated the effect of tobacco smoking on the risk of childhood acute lymphoblastic leukemia (ALL) and myeloid leukemia (AML).

Methods:
Information about tobacco smoking exposures of the mother before, during, and after pregnancy was collected via PubMed, Embase, and Web of Science databases through November 5, 2018. We performed to evaluate the association between smoking exposure and the risk of childhood ALL and AML. Study selection, data abstraction, and quality assessment were performed by 2 independent reviewers. Random effects models were used to obtain summary odds ratios (ORs) and 95% confidence intervals (CIs).

Results:
Nineteen case–control studies of childhood leukemia (age < 15 years) conducted in 9 countries from 1974 to 2018. Maternal smoking exposures did not a significant association with childhood ALL (OR = 1.004, 95% CI 0.953–1.058, P = .881) and AML (OR = 0.92, 95% CI 0.815–1.038, P = .177) during exposure time windows. However, there was an association with paternal smoking and ALL (OR = 1.15, 95% CI 1.038–1.275, P = .007). Paternal smoking in AML showed there was no association with smoking exposures and childhood AML (OR = 1.133, 95% CI 0.943–1.362, P = .181). Next, maternal daily cigarettes consumption showed no associations with ALL (OR = 1.08, 95% CI 1.000–1.168, P = .051) during pregnancy. No association with maternal daily smoking and AML (OR = 0.909, 95% CI 0.682–1.211, P = .514). Paternal daily cigarettes consumption was associated with increased risks of childhood ALL (OR = 1.200, 95% CI 1.112–1.302, P = .000). The higher consumption of paternal smoking (more than 10 per day) was significantly related to childhood ALL. Paternal daily smoking consumption also was related to AML (OR = 1.242, 95% CI 1.031–1.496, P = .022).

Conclusion:
Maternal smoking before, during, or after pregnancy was not associated with childhood ALL or AML. However, paternal smoking was related to a significantly elevated risk of childhood ALL during pregnancy, but not for AML. Maternal daily smoking consumption was not associated with ALL or AML during pregnancy. The higher consumption of paternal smoking were, the higher the risk of childhood ALL or AML.
Colon Perforation by Compressed Air
Authors: Das Siddhartha , Hanuman Srinivas Bheemanathi , Toi Pampa Ch , Subramania Deepak Barathi , Yanamadala Siva Pradeep 
Published: July 2019

Abstract
Barotrauma-associated perforation of the colon is not common and usually occurs due to the passage of compressed air through the anus. Most of the cases are accidental and done for fun often at the victim's workplace. Therefore, it is necessary that the workers should be made aware of the dangers of the equipment they regularly use at their workplace. Here, we describe one such case where a rice mill worker died when compressed air through an air pump pipe entered his rectum. His chief complaint was abdominal pain and breathing difficulty. Computed tomography scan of the abdomen and thorax showed pneumoperitoneum, pneumomediastinum, and soft tissue emphysema. There was a complete tear in the rectosigmoid junction of the colon. The mucosa was deeply hemorrhagic and congested. Histopathology of this segment showed hemorrhagic necrosis of the mucosa.
Current and new rotavirus vaccines
Authors: Burke Rachel M. , Tate Jacqueline E. , Kirkwood Carl D. , Steele A. Duncan , Parashar Umesh D. 
Published: July 2019

Purpose of review
As of 2019, four rotavirus vaccines have been prequalified by the WHO for use worldwide. This review highlights current knowledge regarding rotavirus vaccines available, and provides a brief summary of the rotavirus vaccine pipeline.

Recent findings
Data generated from use of currently available products supports their effectiveness and impact in diverse settings. Rotavirus vaccines have a favorable risk–benefit profile, but previous associations of rotavirus vaccination with intussusception necessitate continued monitoring for this rare but serious adverse event. Implementation of rotavirus vaccines was jeopardized in late 2018 and 2019 by a shortage of vaccine supply. Fortunately, with the prequalification of two additional vaccines in 2018, countries have increased choice in products with different characteristics, pricing, and implementation strategies. Other vaccines currently in development may open up further immunization strategies, such as neonatal vaccination schedules or parenteral administration.

Summary
Rotavirus vaccines have demonstrated impact in reducing diarrheal morbidity and mortality worldwide. As countries begin to introduce the newly prequalified vaccines, additional data will become available on the safety and effectiveness of those products. Products in the pipeline have distinct profiles and could be an essential part of the expansion of rotavirus vaccine use worldwide.
Association of TDP-43 Pathology With Domain-specific Literacy in Older Persons
Authors: Kapasi Alifiya , Yu Lei , Stewart Christopher C. , Schneider Julie A. , Bennett David A. , Boyle Patricia A. 
Published: July 2019

Background:
Low health and financial literacy may be an early behavioral manifestation of cognitive impairment, dementia, and accumulating Alzheimer pathology. However, there are limited studies investigating the behavioral features associated with hyperphosphorylated transactive response DNA-binding protein-43 (TDP-43), a common age-related pathology, and even fewer studies investigating the neurobiological basis underlying low literacy in aging.

Objective:
To test the hypothesis that TDP-43 pathology is associated with lower literacy.

Materials and Methods:
Data came from 293 community-based older persons who were enrolled in 2 ongoing studies of aging. Participants completed literacy and cognitive assessments, consented to brain donation, and underwent detailed neuropathologic evaluation for Alzheimer disease (AD) and TDP-43. Linear regression models assessed the association of TDP-43 with literacy after adjusting for demographics, and AD pathology. Posthoc pairwise comparisons examined whether the level of literacy differed by TDP-43 stage.

Results:
TDP-43 pathology was associated with lower literacy (estimate=−3.16; SE=0.86; P<0.001), above and beyond demographics and AD pathology, and this association persisted even after additionally adjusting for global cognition (estimate=−1.53; SE=0.74; P=0.038). Further, literacy was lower among persons with neocortical TDP-43 pathology compared with those without TDP-43 pathology.

Conclusions:
TDP-43 pathology is associated with lower health and financial literacy in old age, above and beyond AD pathology.
Practice and Training Needs of Staff Nurses Caring for Patients With Intestinal Ostomies in Primary and Secondary Hospitals in China
Authors: Li Fei , Deng Bo , Xu Linxia , Song Meixuan , Li Xianrong 
Published: July 2019

PURPOSE:
The purpose of this study was to describe staff nurses' intestinal ostomy care practice in primary and secondary hospitals in China and their ostomy-related training needs.

SUBJECTS AND SETTING:
The target population for this study was first-line staff nurses working in general surgical departments in primary and secondary care hospitals in Luzhou, located in Sichuan Province, Southwest China. Hospitals in China are divided into 3 tiers; first tier facilities are usually located in townships and have fewer than 100 inpatients beds; secondary hospitals are usually found in medium-sized cities or districts and have between 100 and 500 inpatient beds.

DESIGN:
Descriptive, cross-sectional.

METHODS:
Participants were recruited through a stratified cluster sampling method based on hospital tier and the presence of general surgical department. Data were collected via a questionnaire that comprised 3 sections; the first section queried demographic and professional practice data, the second queried practice related to patients with intestinal ostomies, and the third queried nurses' stoma-related training needs. Links to the electronic survey were distributed through e-mail.

RESULTS:
Three hundred and eighteen nurses were invited to participate in the survey, and 280 questionnaires were returned, yielding a response rate of 88.05%. Review of data found that 214 questionnaires were sufficiently complete to be used in our data analysis. The mean intestinal ostomy practice score was 26.61 ± 7.98, indicating less than optimal engagement in ostomy care. Lack of manpower in the workplace and heavy workload of daily nursing were identified as leading barriers to continuing education in this area of practice.

CONCLUSIONS:
The ostomy-related practice of first-line staff nurses in Chinese primary and secondary hospitals showed less than optimal engagement in ostomy practice. We recommend creating additional ostomy-related continuing education targeted for nurses practicing in primary and secondary tier hospitals and removal of barriers to this education in order to improve ostomy care in primary and secondary tier hospitals in China.
Stem Cell Transplantation Patients and Situational Meaning: A Prospective and Longitudinal View
Authors: Blosser Jennifer , Sabo Roy , Candler Kathryn , Mullin Karen , Toor Amir , Chaber Denna 
Published: July 2019

ABSTRACTBackgroundThough there is thorough examination of psychosocial issues in SCT, there are few longitudinal studies examining the meaning SCT patients attribute to their treatment.ObjectiveThe object of this study was to examine change in situational appraisal over time, and to explore potential modifiers of that change.MethodsA prospective, longitudinal study of 146 autologous and allogeneic stem cell transplant (SCT) patients at Virginia Commonwealth University (VCU) was conducted to measure situational appraisal over time as per the meaning making model of Park and Folkman (1997) utilizing the Illness Perception Questionnaire-Revised (IPQ-R; Moss-Morris et al., 2002). Participants were administered the instrument prior to transplant, at one, three and six months, and at one-year post-transplant.ResultsChange over time was seen in different diagnoses, donor types, reduced intensity and standard pre-transplant preparative regimens, and between the two major ethnic groups (Caucasian and African American) studied. Many of the patient subgroups had statistically significant findings in measures of illness attribution.ConclusionThe appraisals SCT patients made of their situation in treatment revealed a complex process of appraisal affected by illness, treatment and patient characteristics including disease type, donor type, race, and pre-transplant regimen.
Analysis of mutations in West Australian populations ofBlumeria graminisf. sp.hordei CYP51conferring resistance to DMI fungicides
Authors: Tucker M. A. , Lopez-Ruiz F. , Cools H. J. , Mullins J. G. L. , Jayasena K. , Oliver R. P. 
Published: July 2019

SummaryPowdery mildew caused byBlumeria graminisf. sp.hordei(Bgh) is a constant threat to barley production but is generally well controlled through combinations of host genetics and fungicides. An epidemic of barley powdery mildew was observed from 2007 to 2013 in the West Australian wheatbelt (WA). We collected isolates, examined their sensitivity to demethylation inhibitor (DMI) fungicides and sequenced the Cyp51B target gene. Five amino acid substitutions were found of which four were novel. A clear association was established between combinations of mutations and altered levels of resistance to DMIs. The most resistant genotypes increased in prevalence from 0 in 2009 to 16% in 2010 and 90% in 2011. Yeast strains expressing theBghCyp51 genotypes replicated the altered sensitivity to various DMIs and these results were confirmed byin silicoprotein docking studies.
Effects of prefrontal tDCS on dopamine-mediated behavior and psychophysiology
Authors: Imburgio Michael J. , Ballard Hannah K. , Cornwall Astin C. , Worthy Darrell A. , Bernard Jessica A. , Orr Joseph M. 
Published: July 2019

AbstractThe ability to manipulate dopaminein vivothrough non-invasive, reversible mechanisms has the potential to impact clinical, translational, and basic research. Recent PET studies have demonstrated increased dopamine release in the striatum after prefrontal transcranial direct current stimulation (tDCS). We sought to extend this work by examining whether prefrontal tDCS could demonstrate an effect on behavioral and physiological correlates of subcortical dopamine activity. We conducted a between-subjects study (n = 30) with active and sham tDCS and used spontaneous eye blink rate (EBR), facial attractiveness ratings, and greyscales orienting bias as indirect proxies for dopamine functioning. The initial design and analyses were pre-registered (https://osf.io/gmnpc). Stimulation did not significantly affect any of the three measures, though effect sizes were often moderately large and were all in the predicted directions. Additional exploratory analyses suggested that stimulation’s effect on EBR might depend on pre-stimulation dopamine levels. Our results shed light on the sensitivity of indirect measures of dopamine in humans and add to a growing body of work demonstrating the importance of examining individual differences in tDCS response.
Regularized Bagged Canonical Component Analysis for Multiclass Learning in Brain Imaging
Authors: Sevilla-Salcedo Carlos , Gómez-Verdejo Vanessa , Tohka Jussi ,   Alzheimer’s Disease Neuroimaging Initiative
Published: July 2019

AbstractA fundamental problem of supervised learning algorithms for brain imaging applications is that the number of features far exceeds the number of subjects. In this paper, we propose a combined feature selection and extraction approach for multiclass problems. This method starts with a bagging procedure which calculates the sign consistency of the multivariate analysis (MVA) projection matrix feature-wise to determine the relevance of each feature. This relevance measure provides a parsimonious matrix, which is combined with a hypothesis test to automatically determine the number of selected features. Then, a novel MVA regularized with the sign and magnitude consistency of the features is used to generate a reduced set of summary components providing a compact data description.We evaluated the proposed method with two multiclass brain imaging problems: 1) the classification of the elderly subjects in four classes (cognitively normal, stable mild cognitive impairment (MCI), MCI converting to AD in 3 years, and Alzheimer’s disease) based on structural brain imaging data from the ADNI cohort; 2) the classification of children in 3 classes (typically developing, and 2 types of Attention Deficit/Hyperactivity Disorder (ADHD)) based on functional connectivity. Experimental results confirmed that each brain image (defined by 29.852 features in the ADNI database and 61.425 in the ADHD) could be represented with only 30 – 45% of the original features. Furthermore, this information could be redefined into two or three summary components, providing not only a gain of interpretability but also classification rate improvements when compared to state-of-art reference methods.
Updated phylogeny of Chikungunya virus suggests lineage-specific RNA architecture
Authors: de Bernardi Schneider Adriano , Ochsenreiter Roman , Hostager Reilly , Hofacker Ivo L. , Janies Daniel , Wolfinger Michael T. 
Published: July 2019

AbstractChikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3’UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3’UTR architecture among different CHIKV lineages.
Refgenie: a reference genome resource manager
Authors: Stolarczyk Michal , Reuter Vincent P. , Magee Neal E. , Sheffield Nathan C. 
Published: July 2019

Reference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on disk alongside related resources; for example, many sequence aligners require the assembly to be indexed. The resulting indexes are broadly applicable for downstream analysis, so it makes sense to share them. However, there is no simple tool to do this. To this end, we introduce refgenie, a reference genome assembly asset manager. Refgenie makes it easier to organize, retrieve, and share genome analysis resources. In addition to genome indexes, refgenie can manage any files related to reference genomes, including sequences and annotation files. Refgenie includes a command-line interface and a server application that provides a RESTful API, so it is useful for both tool development and analysis.Availabilityhttps://refgenie.databio.org
Gene expression profiles complement the analysis of genomic modifiers of the clinical onset of Huntington disease
Authors: Wright Galen E.B. , Caron Nicholas S. , Ng Bernard , Casal Lorenzo , Xu Xiaohong , Ooi Jolene , Pouladi Mahmoud A. , Mostafavi Sara , Ross Colin J.D. , Hayden Michael R. 
Published: July 2019

ABSTRACTHuntington disease (HD) is a neurodegenerative disorder that is caused by a CAG repeat expansion in the HTT gene. In an attempt to identify genomic modifiers that contribute towards the age of onset of HD, we performed a transcriptome wide association study assessing heritable differences in genetically determined expression in diverse tissues, employing genome wide data from over 4,000 patients. This identified genes that showed evidence for colocalization and replication, with downstream functional validation being performed in isogenic HD stem cells and patient brains. Enrichment analyses detected associations with various biologically-relevant gene sets and striatal coexpression modules that are mediated by CAG length. Further, cortical coexpression modules that are relevant for HD onset were also associated with cognitive decline and HD-related traits in a longitudinal cohort. In summary, the combination of population-scale gene expression information with HD patient genomic data identified novel modifier genes for the disorder.