bluuebunny/crossref_metadata_2025_split huggingface dataset:
Holographic subregion complexity of a (1+1)-dimensional $p$-wave superconductor
Authors: Fujita Mitsutoshi 
Published: May 2019

Abstract
We analyze the holographic subregion complexity in a three-dimensional black hole with vector hair. This three-dimensional black hole is dual to a (1+1)-dimensional $p$-wave superconductor. We probe the black hole by changing the size of the interval and by fixing $q$ or $T$. We show that the universal part is finite across the superconductor phase transition and has competitive behaviors different from the finite part of the entanglement entropy. The behavior of the subregion complexity depends on the gravitational coupling constant divided by the gauge coupling constant. When this ratio is less than the critical value, the subregion complexity increases as temperature becomes low. This behavior is similar to that of the holographic (1+1)-dimensional $s$-wave superconductor [M. K. Zangeneh, Y. C. Ong, and B. Wang, Phys. Lett. B 771, 130 (2014)]. When the ratio is larger than the critical value, the subregion complexity has a non-monotonic behavior as a function of $q$ or $T$. We also find a discontinuous jump of the subregion complexity as a function of the size of the interval. The subregion complexity has a maximum when it wraps almost the entire spatial circle. Due to competitive behaviors between the normal and condensed phases, the universal term in the condensed phase becomes even smaller than that of the normal phase by probing the black hole horizon at a large interval. This implies that the condensate formed decreases the subregion complexity as in the case of the entanglement entropy.
Wassermann Before Wedding Bells: Premarital Examination Laws in the United States, 1937–1950
Authors: Doroshow Deborah B 
Published: May 2019

Summary
In the late 1930s, states began to pass laws requiring men and women applying for marriage licences to demonstrate proof of a blood test showing that they did not harbour communicable syphilis. Advocates of the laws positioned marriage as a public health checkpoint to identify new cases of syphilis as part of a broader effort to approach the disease as a public health problem, rather than a moral one. Although the laws appeared to have broad popular support, in reality they were a failed public health intervention. Couples rushed to the altar before laws went into effect and border-hopped to marry in states without blood test laws. The blood tests used to detect syphilis were difficult to interpret and physicians could not agree on a standard definition of communicable disease. But for over 30 years, premarital examination laws represented a tangible government presence in the private lives of most Americans.
Adverse childhood experiences affect sleep duration for up to 50 years later
Authors: Sullivan Kelly , Rochani Haresh , Huang Li-Ting , Donley Diane K , Zhang Jian 
Published: May 2019

Abstract

Study Objectives
The main objective for this study was to assess the association of adverse childhood experiences (ACEs) and subsequent short sleep duration among adults.

Methods
This cross-sectional examination used data from the 2011 Behavioral Risk Factor Surveillance System, a nationwide telephone-administered survey. Participants completed a standardized questionnaire to report childhood experiences of abuse, neglect, household challenges, and sleep time. Multinominal logistic regression analyses included survey weighting procedures and adjusted for age, race, education, income, sex, and body mass index; associations were also examined by age strata, using age as a proxy for time since ACEs occurred.

Results
Complete data were available for 22 403 adults (mean age = 46.66 years) including 14 587 (65%) with optimum sleep duration (7–9 h/night) and 2069 (9%) with short sleep duration (<6 h/night). Compared with adults with optimum sleep duration, the number of ACEs was associated with the odds of short sleep duration (odds ratio [OR] = 1.22, 95% CI = 1.16 to 1.28), and the odds increased as the number of ACEs increased. The association held for each decade of age until the 60s, although the magnitude attenuated. Mental health challenges or poor physical health did not account for the association.

Conclusion
ACEs increased the odds of chronic short sleep duration during adulthood and showed both a time-dependent and dose–response nature. These associations were independent of self-reported mental health challenges or poor physical health. The association of ACEs with short sleep duration throughout the adult lifespan emphasizes the importance of child health and identifying underlying psychological challenges in adults with sleep difficulties.
Olfactory ensheathing cells from the nasal mucosa and olfactory bulb have distinct membrane properties
Authors: Smith Katie E. , Whitcroft Katherine , Law Stuart , Andrews Peter , Choi David , Jagger Daniel J. 
Published: May 2019

AbstractTransplantation of Olfactory Ensheathing Cells (OECs) is a potential therapy for the regeneration of damaged neurons. While they maintain tissue homeostasis in the olfactory mucosa (OM) and olfactory bulb (OB), their regenerative properties also support the normal sense of smell by enabling continual turnover and axonal regrowth of olfactory sensory neurons (OSNs). However, the molecular physiology of OECs is not fully understood, especially that of OECs from the mucosa. Here, we carried out whole-cell patch clamp recordings from individual OECs cultured from the OM and OB of the adult rat, and from the human OM. A subset of OECs from the rat OM cultured 1-3 days in vitro (DIV) had large weakly rectifying K+ currents, which were sensitive to Ba2+ and desipramine, blockers of Kir4-family channels. Kir4.1 immunofluorescence was detectable in OM cells co-labelled for the OEC marker S100, and found adjacent to axons of OSNs. OECs cultured from rat OB had distinct properties though, displaying strongly rectifying inward currents at hyperpolarized membrane potentials and strongly rectifying outward currents at depolarized potentials. Kir4.1 immunofluorescence was not evident in OECs adjacent to axons of OSNs in the OB. A subset of human OECs cultured from the OM of adults had membrane properties comparable to those of the rat OM, i.e. dominated by Ba2+-sensitive weak inwardly rectifying currents. The membrane properties of peripheral OECs are different to those in central OECs, suggesting they may play distinct roles during olfaction.Table of Contents ImageMain pointsPeripheral and central OECs are functionally distinctPeripheral OECs have large weak inward rectifier currentsCentral OECs have strong inward and outward rectifier currents
Guided proposals for efficient weighted stochastic simulation
Authors: Gillespie Colin S. , Golightly Andrew 
Published: May 2019

AbstractRare event probabilities play an important role in the understanding of the behaviour of biochemical systems. Due to the intractability of the most natural Markov jump process representation of a system of interest, rare event probabilities are typically estimated using importance sampling. While the resulting algorithm is reasonably well developed, the problem of choosing a suitable importance density is far from straightforward. We therefore leverage recent developments on simulation of conditioned jump processes to propose an importance density that is simple to implement and requires no tuning. Our results demonstrate superior performance over some existing approaches.
Site-specific effects of online rTMS during a working memory task in healthy older adults
Authors: Beynel Lysianne , Davis Simon W. , Crowell Courtney A. , Dannhauer Moritz , Lim Wesley , Palmer Hannah , Hilbig Susan A. , Brito Alexandra , Hile Connor , Luber Bruce , Lisanby Sarah H. , Peterchev Angel V. , Cabeza Roberto , Appelbaum Lawrence G. 
Published: May 2019

AbstractThe process of manipulating information within working memory (WM) is central to many cognitive functions, but also declines rapidly in old age. Given the importance of WM manipulation for maintaining healthy cognition, improving this process could markedly enhance health-span in older adults. The current pre-registered study tested the potential of online repetitive transcranial magnetic stimulation (rTMS) to enhance WM manipulation in healthy elderly adults. Online 5Hz rTMS was applied over the left lateral parietal cortex of 15 subjects to test the hypothesis that active rTMS would significantly improve performance compared to sham stimulation, and that these effects would be most pronounced in conditions with the highest cognitive demand. rTMS was applied while participants performed a delayed-response alphabetization task with two individually-titrated levels of difficulty. Sham stimulation was applied using an electrical sham coil that produced similar clicking sounds and somatosensory sensation as active stimulation but induced negligible effects on the brain. A stimulation site in left lateral parietal cortex was identified from fMRI activation maps and was targeted using individualized electric field modeling, stereotactic neuronavigation, and real-time robotic positioning, allowing optimal coil placement during the stimulation. Contrary to the a priori hypothesis, active rTMS significantly decreased accuracy relative to sham, and only in the hardest difficulty level. These results, therefore, demonstrate engagement of cortical WM processing, but not the anticipated facilitation, and provide a prescription for future studies that may attempt to enhance memory through application of different stimulation parameters.HighlightsThis study is one of the first attempts to enhance WM manipulation with online rTMSOnline 5Hz rTMS and sham were applied over the left parietal cortex of older adultsIndividualized fMRI and electric field modeling were used to optimize targetingContrary to expectations, rTMS disrupted working memory manipulation abilitiesThis demonstrates that parietal cortex is involved in WM and modifiable with rTMS
Microbial Food Safety in the Maryland Direct-to-Consumer Poultry Supply Chain
Authors: Baron Patrick A. , Love David C. , Ludwig Shanna , Dalton Kathryn , Larsen Jesper , Innes Gabriel K. , Davis Meghan F. , Heaney Christopher D. 
Published: May 2019

AbstractDirect-to-consumer food marketing is a growing niche in the United States food supply chain. Food animal producers who use direct marketing may employ different production models and standard practices from producers selling animal products to the conventional food system. Direct-to-consumer food supply chains (generally and specifically regarding food animal products) are relatively unexplored in food safety and health research. We conducted a cross-sectional, market-basket analysis of the Maryland direct-to-consumer poultry supply chain to assess food safety. We analyzed 40 direct-to-consumer commercial poultry meat products (one product per farm) forEscherichia coli, Staphylococcus aureusandSalmonella spp.using culture-based methods. Isolates underwent antimicrobial susceptibility testing.E. coliandS. aureuswere recovered from 9/40 (23%) and 12/40 (30%) of poultry meat samples, respectively. Of interest for comparing direct-market and mainstream supply chains for food safety risks, noSalmonellaisolates were recovered from any direct-market sampled poultry products and no multidrug resistance was observed inE. coliandS. aureusisolates. Microbial outcomes were compared to a survey of poultry production and processing practices within the same study population.ImportanceThis study demonstrates substantially lower rates of antimicrobial-resistant (AMR) microbial pathogens in the market-basket products from Maryland direct-market broiler poultry supply chain compared to rates of AMR in the conventional supply chain for similar retail meat products from NARMS. We further describe the landscape of the statewide supply chain for direct-market poultry, focusing on characteristics related to risk management strategies applied to microbial food safety. These findings are of public health significance for both the research and policy communities; these data provide an initial evidence base for more targeted research evaluating potential risk factors for microbial food safety in the direct-to-consumer supply chain. These data will also assist the Maryland Department of Agriculture and other state-level agencies with oversight of food safety issues to guide policy efforts for direct-market poultry production and sales.
Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays
Authors: Krishnan Vandhana , Utiramerur Sowmi , Ng Zena , Datta Somalee , Snyder Michael P. , Ashley Euan A. 
Published: May 2019

AbstractBenchmarking the performance of complex analytical pipelines is an essential part of developing Laboratory Developed Assays (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) Consortium have enabled the evaluation of analytical methods. However, the performance of such methods is not uniform across the different regions of the genome/exome and different variant types and lengths. Here we present a scalable and reproducible, cloud-based benchmarking workflow that can be used by clinical laboratories to rapidly access and validate the performance of LDT assays, across their regions of interest and reportable range, using a broad set of benchmarking samples.
Genome-wide RNAi screen for context-dependent tumor suppressors identified using in vivo models for neoplasia in Drosophila
Authors: Groth Casper , Vaid Pooja , Khatpe Aditi , Prashali Nelchi , Ahiya Avantika , Andrejeva Diana , Chakladar Madhumita , Nagarkar Sanket , Paul Rachel , Eichenlaub Teresa , Herranz Hector , Sridhar TS , Cohen Stephen M. , Shashidhara LS 
Published: May 2019

AbstractGenetic approaches in Drosophila have successfully identified many genes involved in regulation of growth control as well as genetic interactions relevant to the initiation and progression of cancer in vivo. Here, we report on large-scale RNAi-based screens to identify potential tumor suppressor genes that interact with known cancer-drivers: The Epidermal Growth Factor Receptor and the Hippo pathway transcriptional cofactor Yorkie. These screens were designed to identify genes whose depletion drove tissue expressing EGFR or Yki from a state of benign overgrowth into neoplastic transformation in vivo. We also report on an independent screen aimed to identify genes whose depletion suppressed formation of neoplastic tumors in an existing EGFR-dependent neoplasia model. Many of the positives identified here are known to be functional in growth control pathways. We also find a number of novel connections to Yki and EGFR driven tissue growth, mostly unique to one of the two. Thus, resources provided here would be useful to all researchers who study negative regulators of growth in the context of activated EGFR and/or Yki and positive regulators of growth in the context of activated EGFR.
Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum
Authors: Fernández Rosa , Marcet-Houben Marina , Legeai Fabrice , Richard Gautier , Robin Stéphanie , Wucher Valentin , Pegueroles Cinta , Gabaldón Toni , Tagu Denis 
Published: May 2019

AbstractEcology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem-sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there is a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed to tackle the history of duplicated genes to pave the road towards understanding the role of gene duplication in ecological adaptation.
Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals
Authors: Rousselle M , Simion P , Tilak MK , Figuet E , Nabholz B , Galtier N 
Published: May 2019

ABSTRACTWhether adaptation is limited by the beneficial mutation supply is a long-standing question of evolutionary genetics, which is more generally related to the determination of the adaptive substitution rate and its relationship with the effective population size Ne. Empirical evidence reported so far is equivocal, with some but not all studies supporting a higher adaptive substitution rate in large-Nethan in small-Nespecies.We gathered coding sequence polymorphism data and estimated the adaptive amino-acid substitution rate ωa, in 50 species from ten distant groups of animals with markedly different population mutation rate θ. We reveal the existence of a complex, timescale dependent relationship between species adaptive substitution rate and genetic diversity. We find a positive relationship between ωaand θ among closely related species, indicating that adaptation is indeed limited by the mutation supply, but this was only true in relatively low-θ taxa. In contrast, we uncover a weak negative correlation between ωaand θ at a larger taxonomic scale. This result is consistent with Fisher’s geometrical model predictions and suggests that the proportion of beneficial mutations scales negatively with species’ long-term Ne.
Extracting T Cell Function and Differentiation Characteristics from the Biomedical Literature
Authors: Czech Eric , Hammerbacher Jeff 
Published: May 2019

AbstractThe role of many cytokines and transcription factors in the function and development of human T cells has been the subject of extensive research, however much of this work only demonstrates experimental findings for a relatively small portion of the molecular signaling network that enables the plasticity inherent to these cells. We apply recent advancements in methods for weak supervision and transfer learning for natural language models to aid in extracting these individual findings as 283k cell type, cytokine, and transcription factor relations from 64k relevant documents (53k full-text PMC articles and 11k PubMed abstracts). All data, results and source code available athttps://github.com/hammerlab/t-cell-relation-extraction.
A short review of machine learning methods for classifying the outcome of Gestational Diabetes
Authors: Banerji Shreeya 
Published: May 2019

AbstractDiabetes mellitus is a growing problem, especially in developing countries. People suffering from diabetes have an increased risk of developing a number of serious health problems. Consistently high blood glucose levels can lead to serious diseases affecting the heart and blood vessels, eyes, kidney, etc. In addition, people with diabetes also have a higher risk of developing infections.This paper aims to use suitable data mining and classification techniques which include the Logit model, the Probit model, the Classification tree technique, Artificial Neural Networks, Support Vector Machines, Ridge Regression technique and the Least Absolute Shrinkage and Selection Operator(LASSO) in order to determine the best method which can be used to classify the patients as suffering from gestational diabetes or not. The misclassification rate is calculated for different methods and the method having the least misclassification rate is said to be the most suitable to be applied to the given data, which is the PIMA Indians diabetes dataset.
The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair
Authors: Barnett JT , Kuper J , Koelmel W , Kisker C , Kad NM 
Published: May 2019

AbstractNucleotide excision repair (NER) protects the genome following exposure to diverse types of DNA damage, including UV light and chemotherapeutics. Mutations in mammalian NER genes lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, and Cockayne syndrome. In eukaryotes, the major transcription factor TFIIH is the central hub of NER. The core components of TFIIH include the helicases XPB, XPD, and five ‘structural’ subunits. Two of these structural TFIIH proteins, p44 and p62 remain relatively unstudied; p44 is known to regulate the helicase activity of XPD during NER whereas p62’s role is thought to be structural. However, a recent cryo-EM structure shows that p44, p62, and XPD make extensive contacts within TFIIH, with part of p62 occupying XPD’s DNA binding site. This observation implies a more extensive role in DNA repair beyond the structural integrity of TFIIH. Here, we show that p44 stimulates XPD’s ATPase but upon encountering DNA damage, further stimulation is only observed when p62 is part of the ternary complex; suggesting a role for the p44/p62 heterodimer in TFIIH’s mechanism of damage detection. Using single molecule imaging, we demonstrate that p44/p62 independently interacts with DNA; it is seen to diffuse, however, in the presence of UV-induced DNA lesions the complex stalls. Combined with the analysis of a recent cryo-EM structure we suggest that p44/p62 acts as a novel DNA-binding entity within TFIIH that is capable of recognizing DNA damage. This revises our understanding of TFIIH and prompts more extensive investigation into the core subunits for an active role during both DNA repair and transcription.
gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
Authors: Magno Ramiro , Maia Ana -Teresa 
Published: May 2019

AbstractMotivationThe NHGRI Catalog of Published Genome-Wide Association Studies (GWAS) Catalog has collected, curated, and made available data from over 3 900 studies. The recently developed GWAS Catalog REST API is the only method allowing programmatic access to this resource.ResultsHere, we describe gwasrapidd, an R package that provides a client interface to the GWAS Catalog REST API, representing an important software counterpart to the server-side component. gwasrapidd enables users to quickly retrieve, filter and integrate data with comprehensive bioinformatics analysis tools, which is particularly critical for those looking into functional characterisation of risk loci.Availabilitygwasrapidd is freely available under an MIT License, and can be accessed from https://github.com/ramiromagno/gwasrapidd.