bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coronary Artery Spasm as Related to Anxiety and Depression: A Nationwide Population-Based Study
Authors: Hung Ming-Yow , Mao Chun-Tai , Hung Ming-Jui , Wang Jiunn-Kae , Lee Hsin-Chien , Yeh Chi-Tai , Hu Patrick , Chen Tien-Hsing , Chang Nen-Chung 
Published: January 2019

ABSTRACTObjectiveAnxiety and depression are risk factors for obstructive coronary artery disease (CAD), but their effects on coronary artery spasm (CAS) remain unestablished.MethodsPatient records in this population-based study were retrospectively collected from the Taiwan National Health Insurance Research Database. Using propensity score matching, we used 1:1:1 ratio stratification into a control group of 10,325 individuals without CAS or CAD, a CAS group comprising 10,473 patients, and a CAD group comprising 10,473 patients during 2000–2012.ResultsThe prevalence of CAS and CAD was 0.067% and 8.7%, respectively, in the general population. The prevalence of anxiety and depression diagnoses was significantly higher in patients with new-onset CAS than in those with new-onset CAD and controls without CAS/CAD, even after propensity score matching. Compared with CAD, anxiety and depression diagnoses conferred a higher risk of developing CAS (odds ratio [OR] = 2.29, 95% confidence interval [CI], 2.14–2.45,p< .001, and OR = 1.34, 95% CI, 1.08–1.66,p= .007, respectively). The association was even stronger when comparing CAS with the control group without CAD or CAS (OR = 5.20, 95% CI, 4.72–5.74,p< .001, and OR = 1.98, 95% CI, 1.50–2.62,p< .001, respectively). The increased risk of new-onset CAS as related to previous anxiety and depression diagnoses was comparable between males and females.ConclusionsCompared with CAD or the general population, anxiety and depression diagnoses confer a higher risk of developing CAS. No sex differences are found for the association of anxiety and depression with CAS.
Analyzing Our International Facial Reconstructive Mission Work: A Review of Patients Treated by American Academy of Facial Plastic and Reconstructive Surgery Sanctioned Trips
Authors: Rousso Joseph J. , Abraham Manoj T. , Rozanski Collin 
Published: January 2019

Importance:
To identify ways to improve care to underserved international populations.

Objective:
To analyze the authors’ data in hopes of meeting further needs.

Design:
This is a retrospective review of medical missions using data from the American Academy of Facial Plastic and Reconstructive Surgery (AAFPRS) Face to Face) Database.

Setting:
International sites of AAFPRS approved surgical mission trips.

Participants:
One thousand six hundred forty-six patients who were seen by an AAFPRS mission trip between January 12, 2010 and April 27, 2017.

Outcomes/Measures:
Patient and mission data, procedure data, characteristics of cleft patients, patient follow-up data, repeat patient data, and factors affecting whether a patient was provided service were all evaluated.

Results:
Patients were seen over the course of 26 trips to 6 different countries. Patients (n, mean, median age) who underwent a primary cleft lip repair only (175, 2.5 years, 0.6 years) and those who underwent a primary cleft palate repair only (268, 6.4 years, 3.6 years) were significantly older than what is identified as the upper range of normal in surgical literature
13,14
(Wilcoxon Signed-Rank test Z = −4.3, P < 0.001 for lip and Z = −10.1, P < 0.001 for palate). Patients (n, median, mean rank) receiving a primary cleft palate repair were significantly younger in Peru (160, 3.0 years, 126) compared with patients in other countries (108, 5.0 years, 147) (Z = −2.1, P < 0.05). The odds of a patient returning unplanned were 2.8 (OR, 95% CI 1.52–4.98; P < 0.01) times higher if they were diagnosed with a cleft palate only and 0.91 (OR, 95% CI 0.90–0.93; P < 0.05) times lower if they were diagnosed with combined cleft lip with cleft palate at their first visit. Patients (median age, mean rank) who were provided a service (6.0 years, 724.70) were younger than patients who were not provided a service (8.0 years, 637.23) at their first visit (Mann–Whitney, U = 164,275; P < 0.001).

Conclusion/Relevance:
This data indicates that disparities exist among patients treated on mission trips compared with those in higher income countries. Furthermore, the authors’ data indicate that multiple mission trips to the same country within the same year decrease some of these disparities. Additionally, isolated cleft palate patients are most likely to return unplanned indicating need for standardized postoperative visits. The preferential care of younger patients with unrepaired clefts as compared with older patients and those with palatal fistulas indicates a need for additional resource allocation.
Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle
Authors: Fang Zih-Hua , Pausch Hubert 
Published: January 2019

AbstractBackgroundThe Brown Swiss dual-purpose cattle breed is renowned for high milk and protein yield and long productive lifetime under different production conditions. However, little is known about the genetic architecture of those traits because only few genome-wide association studies (GWAS) have been carried out in this breed. Moreover, most GWAS had been performed for single traits, thus preventing insights into potentially existing pleiotropic effects of trait-associated loci.ResultsTo compile a comprehensive catalogue of large-effect QTL segregating in Brown Swiss cattle, we carried out association tests between partially imputed genotypes at 598,016 SNPs and daughter-derived phenotypes for more than 50 economically important traits, including milk production, growth and carcass quality, body conformation, reproduction and calving traits in 4,578 artificial insemination bulls from two cohorts of Brown Swiss cattle (Austrian-German and Swiss populations). Across-cohort multi-trait meta-analyses of the results from the single-trait GWAS revealed 25 quantitative trait loci (QTL;P< 8.36 x 10−8) for economically relevant traits on 17Bos taurusautosomes (BTA). Evidence of pleiotropy was detected at five QTL located on BTA5, 6, 17, 21 and 25. Of these, two QTL at BTA6:90,486,780 and BTA25:1,455,150 affect a diverse range of economically important traits, including traits related to body conformation, calving, longevity and milking speed. Furthermore, the QTL at BTA6:90,486,780 seems to be a target of ongoing selection as evidenced by an integrated haplotype score of 2.49 and significant changes in allele frequency over the past 25 years, whereas either no or only weak evidence of selection was detected at all other QTL.ConclusionsOur findings provide a comprehensive overview of QTL segregating in Brown Swiss cattle. Detected QTL explain between 2 and 10% of the variation in the daughter-derived phenotypes and thus may be considered as the most important QTL segregating in the Brown Swiss cattle breed. Multi-trait association testing boosts the power to detect pleiotropic QTL and assesses the full spectrum of phenotypes that are affected by trait-associated variants.
Adapting genotyping-by-sequencing and variant calling for heterogeneous stock rats
Authors: Gileta Alexander F. , Gao Jianjun , Chitre Apurva S. , Bimschleger Hannah V. , St. Pierre Celine L. , Gopalakrishnan Shyam , Palmer Abraham A. 
Published: January 2019

ABSTRACTThe heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We also evaluate multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.
Human discrimination and categorization of emotions in voices: a functional Near-Infrared Spectroscopy (fNIRS) study
Authors: Gruber T. , Debracque C. , Ceravolo L. , Igloi K. , Marin Bosch B. , Frühholz S. , Grandjean D. 
Published: January 2019

AbstractVariations of the vocal tone of the voice during speech production, known as prosody, provide information about the emotional state of the speaker. In recent years, functional imaging has suggested a role of both right and left inferior frontal cortices in attentive decoding and cognitive evaluation of emotional cues in human vocalizations. Here, we investigated the suitability of functional Near-Infrared Spectroscopy (fNIRS) to study frontal lateralization of human emotion vocalization processing during explicit and implicit categorization and discrimination. Participants listened to speech-like but semantically meaningless words spoken in a neutral, angry or fearful tone and had to categorize or discriminate them based on their emotional or linguistic content. Behaviorally, participants were faster to discriminate than to categorize and they processed the linguistic content of stimuli faster than their emotional content, while an interaction between condition (emotion/word) and task (discrimination/categorization) influenced accuracy. At the brain level, we found a four-way interaction in the fNIRS signal between condition, task, emotion and channel, highlighting the involvement of the right hemisphere to process fear stimuli, and of both hemispheres to treat anger stimuli. Our results show that fNIRS is suitable to study vocal emotion evaluation in humans, fostering its application to study emotional appraisal.
Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture
Authors: Hou Kangcheng , Burch Kathryn S. , Majumdar Arunabha , Shi Huwenbo , Mancuso Nicholas , Wu Yue , Sankararaman Sriram , Pasaniuc Bogdan 
Published: January 2019

AbstractThe proportion of phenotypic variance attributable to the additive effects of a given set of genotyped SNPs (i.e. SNP-heritability) is a fundamental quantity in the study of complex traits. Recent works have shown that existing methods to estimate genome-wide SNP-heritability often yield biases when their assumptions are violated. While various approaches have been proposed to account for frequency- and LD-dependent genetic architectures, it remains unclear which estimates of SNP-heritability reported in the literature are reliable. Here we show that genome-wide SNP-heritability can be accurately estimated from biobank-scale data irrespective of the underlying genetic architecture of the trait, without specifying a heritability model or partitioning SNPs by minor allele frequency and/or LD. We use theoretical justifications coupled with extensive simulations starting from real genotypes from the UK Biobank (N=337K) to show that, unlike existing methods, our closed-form estimator for SNP-heritability is highly accurate across a wide range of architectures. We provide estimates of SNP-heritability for 22 complex traits and diseases in the UK Biobank and show that, consistent with our results in simulations, existing biobank-scale methods yield estimates up to 30% different from our theoretically-justified approach.
Mitigative effects of Alpha-lipoic acid for the toxicity of Dimethoate in male rats
Authors: Abdelsalam Hani M. 
Published: January 2019

AbstractBackgroundOrganophosphates are widely used by human nowadays, but these compounds have tremendous negative effect on the man health. So this study aims to use of Alpha-lipoic acid (ALA) to alleviates the negative effects of Dimethoate (DM).MethodsThis study is designed as follows, Thirty adult male Wistar albino rats were utilized, further subdivided into control, DM and DM+ALA groups. Liver and renal cortex sections from all groups were processed for histopathological examination, biochemical estimation of liver function tests, serum Urea, Creatinine, BUN, testosterone and lipid profile were performed.ResultsThis study clarified the improvement effects of ALA against the negative effects of DM where ALA caused a significant recovery of the hepatic (ALT, AST, ALP and total protein) and renal functions by normalizing them in DM + ALA group and to some extent improvement of lipid profile and testosterone levels. Also, ALA restored normal hepatic and renal histomorphology.ConclusionIt is concluded that ALA therapy can ameliorate the negative effects of DM that affect the vital organs as the liver and kidney. Also ALA can reduce the occurrence of atherogensis by reducing the levels of bad cholesterol in the blood. ALA boosts the levels of testosterone so it augments the male sexual characters.
Phenotypic evolution is more constrained in simpler food webs
Authors: Barbour Matthew A. , Greyson-Gaito Christopher J. , Sootodeh Arezoo , Locke Brendan , Bascompte Jordi 
Published: January 2019

AbstractGlobal change is simplifying the structure of ecological networks; however, we are currently in a poor position to predict how these simplified communities will affect the evolutionary potential of remaining populations. Theory on adaptive landscapes provides a framework for predicting how selection constrains phenotypic evolution, but often treats the community context of evolving populations as a “black box”. Here, we integrate ecological networks and adaptive landscapes to examine how changes in food-web complexity shape evolutionary constraints. We conducted a field experiment that manipulated the diversity of insect parasitoids (food-web complexity) that were able to impose selection on an insect herbivore. We then measured herbivore survival as a function of three key phenotypic traits. We found that more traits were under selection in simpler vs. more complex food webs. The adaptive landscape was more neutral in complex food webs because different parasitoid species impose different selection pressures, minimizing relative fitness differences among phenotypes. Our results suggest that phenotypic evolution becomes more constrained in simplified food webs. This indicates that the simplification of ecological communities may constrain the adaptive potential of remaining populations to future environmental change. “What escapes the eye, however, is a much more insidious kind of extinction: the extinction of ecological interactions.” Janzen (1974)
Microbial regulation of enteric eosinophils and its impact on tissue remodeling and Th2 immunity
Authors: Jiménez-Saiz Rodrigo , Anipindi Varun C. , Galipeau Heather , Ellenbogen Yosef , Chaudhary Roopali , Koenig Joshua F. , Gordon Melissa E. , Walker Tina D. , Mandur Talveer S. , Abed Soumeya , Humbles Alison , Chu Derek K. , Ask Kjetil , Verdú Elena F. , Jordana Manel 
Published: January 2019

ABSTRACTEosinophils have emerged as multifaceted cells that contribute to tissue homeostasis. However, the factors that control their frequency and function at mucosal sites remain unclear. Here, we investigated the role of the microbiota in regulating enteric eosinophils. We found that small intestinal (SI) eosinophilia was significantly greater in germ-free (GF) mice compared to specific pathogen free (SPF) controls. This phenomenon was associated with enteric overexpression of signals that mediate attraction, retention and survival of eosinophils, and was reversed by colonization. Additionally, we generated a novel strain of eosinophil-deficient GF mice. These mice displayed intestinal fibrosis and were less prone to allergic sensitization as compared to GF controls. Overall, our study demonstrates that commensal microbes regulate intestinal eosinophil frequency and function, which impacts tissue repair and allergic sensitization to food antigens. These data support a critical interplay between the commensal microbiota and intestinal eosinophils in shaping homeostatic, innate and adaptive immune processes in health and disease.
The number of spaced-word matches between twoDNAsequences as a function of the underlying pattern weight
Authors: Röhling Sophie , Morgenstern Burkhard 
Published: January 2019

AbstractWe study the numberNkof (spaced) word matches between pairs of evolutionarily related DNA sequences depending on the word length or pattern weightk, respectively. We show that, under theJukes-Cantormodel, the number of substitutions per site that occurred since two sequences evolved from their last common ancestor, can be esti-mated from the slope of a certain function ofNk. Based on these considerations, we implemented a software program for alignment-free sequence comparison calledSlope-SpaM. Test runs on simulated sequence data show thatSlope-SpaMcan estimate phylogenetic dis-tances with high accuracy for up to around 0.5 substitutions per po-sitions. The statistical stability of our results is improved if spaced words are used instead of contiguousk-mers. Unlike previous methods that are based on the number of (spaced) word matches, our approach can deal with sequences that share only local homologies.
Partitioning stable and unstable expression level variation in cell populations: a theoretical framework with application to the T cell receptor
Authors: Guzella Thiago S. , Barreto Vasco M. , Carneiro Jorge 
Published: January 2019

AbstractPhenotypic variation in the copy number of gene products expressed by cells or tissues has been the focus of intense investigation. To what extent the observed differences in cellular expression levels are persistent or transient is an intriguing question. Here, we develop a quantitative framework that resolves the expression variation into stable and unstable components. The difference between the expression means in two cohorts isolated from any cell population is shown to converge to an asymptotic value, with a characteristic time,τT, that measures the timescale of the unstable dynamics. The asymptotic difference in the means, relative to the initial value, measures the stable proportion of the original population variance. Empowered by this insight, we analysed the T-cell receptor (TCR) expression variation in CD4 T cells. About 70% of TCR expression variance is stable in a diverse polyclonal population, while over 80% of the variance in an isogenic TCR transgenic population is volatile. In both populations the TCR levels fluctuate with a characteristic time of 32 hours. This systematic characterisation of the expression variation dynamics, relying on time series of cohorts’ means, can be combined with technologies that measure gene or protein expression in single cells or in bulk.
Mobile genetic element insertions drive antibiotic resistance across pathogens
Authors: Durrant Matthew G. , Li Michelle M. , Siranosian Ben , Bhatt Ami S. 
Published: January 2019

AbstractMobile genetic elements contribute to bacterial adaptation and evolution; however, detecting these elements in a high-throughput and unbiased manner remains challenging. Here, we demonstrate ade novoapproach to identify mobile elements from short-read sequencing data. The method identifies the precise site of mobile element insertion and infers the identity of the inserted sequence. This is an improvement over previous methods that either rely on curated databases of known mobile elements or rely on ‘split-read’ alignments that assume the inserted element exists within the reference genome. We apply our approach to 12,419 sequenced isolates of nine prevalent bacterial pathogens, and we identify hundreds of known and novel mobile genetic elements, including many candidate insertion sequences. We find that the mobile element repertoire and insertion rate vary considerably across species, and that many of the identified mobile elements are biased toward certain target sequences, several of them being highly specific. Mobile element insertion hotspots often cluster near genes involved in mechanisms of antibiotic resistance, and such insertions are associated with antibiotic resistance in laboratory experiments and clinical isolates. Finally, we demonstrate that mutagenesis caused by these mobile elements contributes to antibiotic resistance in a genome-wide association study of mobile element insertions in pathogenicEscherichia coli. In summary, by applying ade novoapproach to precisely identify mobile genetic elements and their insertion sites, we thoroughly characterize the mobile element repertoire and insertion spectrum of nine pathogenic bacterial species and find that mobile element insertions play a significant role in the evolution of clinically relevant phenotypes, such as antibiotic resistance.
Parallel control of mechanosensory hair cell orientation by the PCP and Wnt pathways
Authors: Acedo Joaquin Navajas , Voas Matthew G. , Alexander Richard , Woolley Thomas , Unruh Jay R. , Li Hua , Moens Cecilia , Piotrowski Tatjana 
Published: January 2019

ABSTRACTCell polarity plays a crucial role during development of vertebrates and invertebrates. Planar Cell Polarity (PCP) is defined as the coordinated polarity of cells within a tissue axis and is essential for processes such as gastrulation, neural tube closure or hearing. Wnt ligands can be instructive or permissive during PCP-dependent processes, and Wnt pathway mutants are often classified as PCP mutants due to the complexity and the similarities between their phenotypes. Our studies of the zebrafish sensory lateral line reveal that disruptions of the PCP and Wnt pathways have differential effects on hair cell orientations. While mutations in PCP genes cause random orientations of hair cells, mutations in Wnt pathway members induce hair cells to adopt a concentric pattern. We show that PCP signaling is normal in hair cells of Wnt pathway mutants and that the concentric hair cell phenotype is due to altered organization of the surrounding support cells. Thus, the PCP and Wnt pathways work in parallel, as separate pathways to establish proper hair cell orientation. Our data suggest that coordinated support cell organization is established during the formation of lateral line primordia, much earlier than the appearance of hair cells. Together, these finding reveal that hair cell orientation defects are not solely explained by defects in PCP signaling and that some hair cell phenotypes warrant reevaluation.