bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Distance Precision Matrix: computing networks from non-linear relationships
Authors: Ghanbari Mahsa , Lasserre Julia , Vingron Martin 
Published: August 2018

AbstractMotivationFull-order partial correlation, a fundamental approach for network reconstruction, e.g. in the context of gene regulation, relies on the precision matrix (the inverse of the covariance matrix) as an indicator of which variables are directly associated. The precision matrix assumes Gaussian linear data and its entries are zero for pairs of variables that are independent given all other variables. However, there is still very little theory on network reconstruction under the assumption of non-linear interactions among variables.ResultsWe propose Distance Precision Matrix, a network reconstruction method aimed at both linear and non-linear data. Like partial distance correlation, it builds on distance covariance, a measure of possibly non-linear association, and on the idea of full-order partial correlation, which allows to discard indirect associations. We provide evidence that the Distance Precision Matrix method can successfully compute networks from linear and non-linear data, and consistently so across different datasets, even if sample size is low. The method is fast enough to compute networks on hundreds of nodes.Availability and implementationAn R package DPM is available at https://github.molgen.mpg.de/ghanbari/DPM.Supplementary informationSupplementary data are available at Bioinformatics online.
PolyQTL: Bayesian multiple eQTL detection with control for population structure and sample relatedness
Authors: Zeng Biao , Gibson Greg 
Published: August 2018

Abstract

Motivation
Expression quantitative loci (eQTL) are being used widely to annotate and interpret GWAS hits. Recent studies have demonstrated that individual gene expression is often regulated by multiple independent cis-acting eQTL. Diverse methods, frequentist and Bayesian, have already been developed to simultaneously detect and fine-map such multiple eQTL, but most of these ignore sample relatedness and potential population structure. This can result in false positives and disrupt the accuracy of fine-mapping. Here we introduce PolyQTL software for identifying and estimating eQTL effects. The package incorporates a genetic relatedness matrix to remove the influence of population structure and sample relatedness, while utilizing a Bayesian multiple eQTL detection pipeline to identify the most plausible candidate causal variants at one or more independent loci influencing abundance of a transcript.

Results
Simulations demonstrate that our approach improves the rate of discovery of causal variants relative to methods that do not account for relatedness.

Availability and implementation
The software is written in C++, and freely available for download at https://github.com/jxzb1988/PolyQTL.
AncestryView: data-driven visualization of whole-genome local-ancestry
Authors: Zhao Yan , Ma Li , Jiang Sukun , Song George D , He Shaohua , Li Hong , Song Qing 
Published: August 2018

Abstract

Summary
Data visualization is a crucial tool for data exploration, analysis and interpretation. To visualize the ancestry data, we developed a new software tool, called AncestryView. We demonstrate its functionality with the data from admixed individuals.

Availability and implementation
Freely available to non-commercial users on the web at https://f001.backblazeb2.com/file/=4DGenome/AncestryView.zip.

Supplementary information
Supplementary data are available at Bioinformatics online.
Large-scale comparative analysis of microbial pan-genomes using PanOCT
Authors: Inman Jason M , Sutton Granger G , Beck Erin , Brinkac Lauren M , Clarke Thomas H , Fouts Derrick E 
Published: August 2018

Abstract

Summary
The JCVI pan-genome pipeline is a collection of programs to run PanOCT and tools that support and extend the capabilities of PanOCT. PanOCT (pan-genome ortholog clustering tool) is a tool for pan-genome analysis of closely related prokaryotic species or strains. The JCVI Pan-Genome Pipeline wrapper invokes command-line utilities that prepare input genomes, invoke third-party tools such as NCBI Blast+, run PanOCT, generate a consensus pan-genome, annotate features of the pan-genome, detect sets of genes of interest such as antimicrobial resistance (AMR) genes and generate figures, tables and html pages to visualize the results. The pipeline can run in a hierarchical mode, lowering the RAM and compute resources used.

Availability and implementation
Source code, demo data, and detailed documentation are freely available at https://github.com/JCVenterInstitute/PanGenomePipeline.
RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation
Authors: Wong Wai Yee , Simakov Oleg 
Published: August 2018

Abstract

Summary
Repetitive elements comprise large proportion of many genomes. They have impact on both genome evolution and regulation. Their classification and the study of evolutionary history is a major emerging field. Various software exist to-date to classify and map repeats across genomes. The major unresolved drawback, however, is the fragmented nature of many identified repeat loci. This ultimately makes the classification of novel repeats and their evolutionary analyses difficult. To improve on this, we developed a pipeline (RepeatCraft) that integrates results from several repeat element classification tools based on both sequence similarity and structural features. The pipeline de-fragments closely spaced repeat loci in the genomes, reconstructing longer copies, thus allowing for a better annotation and sequence comparisons. The pipeline also includes a user interface that can run in a web browser allowing for an easy access and exploration of the repeat data.

Availability and implementation
RepeatCraft is implemented in Python and the web application is implemented in R. Download and documentation is freely available at https://github.com/niccw/repeatCraftp.

Supplementary information
Supplementary data are available at Bioinformatics online.
Structural analysis of estrogen receptors: interaction between estrogen receptors and cav-1 within the caveolae†
Authors: Pastore Mayra B , Landeros Rosalina Villalon , Chen Dong-bao , Magness Ronald R 
Published: August 2018

AbstractPregnancy is a physiologic state of substantially elevated estrogen biosynthesis that maintains vasodilator production by uterine artery endothelial cells (P-UAECs) and thus uterine perfusion. Estrogen receptors (ER-α and ER-β; ESR1 and ESR2) stimulate nongenomic rapid vasodilatory responses partly through activation of endothelial nitric oxide synthase (eNOS). Rapid estrogenic responses are initiated by the ∼4% ESRs localized to the plasmalemma of endothelial cells. Caveolin-1 (Cav-1) interactions within the caveolae are theorized to influence estrogenic effects mediated by both ESRs. Hypothesis: Both ESR1 and ESR2 display similar spatial partitioning between the plasmalemma and nucleus of UAECs and have similar interactions with Cav-1 at the plasmalemma. Using transmission electron microscopy, we observed numerous caveolae structures in UAECs, while immunogold labeling and subcellular fractionations identified ESR1 and ESR2 in three subcellular locations: membrane, cytosol, and nucleus. Bioinformatics approaches to analyze ESR1 and ESR2 transmembrane domains identified no regions that facilitate ESR interaction with plasmalemma. However, sucrose density centrifugation and Cav-1 immunoisolation columns uniquely demonstrated very high protein–protein association only between ESR1, but not ESR2, with Cav-1. These data demonstrate (1) both ESRs localize to the plasmalemma, cytosol and nucleus; (2) neither ESR1 nor ESR2 contain a classic region that crosses the plasmalemma to facilitate attachment; and (3) ESR1, but not ESR2, can be detected in the caveolar subcellular domain demonstrating ESR1 is the only ESR bound in close proximity to Cav-1 and eNOS within this microdomain. Lack of protein–protein interaction between Cav-1 and ESR2 demonstrates a novel independent association of these proteins at the plasmalemma.
The upstrap
Authors: Crainiceanu Ciprian M , Crainiceanu Adina 
Published: August 2018

SUMMARY
The bootstrap, introduced in Efron (1979. Bootstrap methods: another look at the jackknife. The Annals of Statistics7, 1–26), is a landmark method for quantifying variability. It uses sampling with replacement with a sample size equal to that of the original data. We propose the upstrap, which samples with replacement either more or fewer samples than the original sample size. We illustrate the upstrap by solving a hard, but common, sample size calculation problem. The data and code used for the analysis in this article are available on GitHub (2018. https://github.com/ccrainic/upstrap).
Neural Correlates of Group Bias During Natural Viewing
Authors: Andrews Timothy J , Smith Ryan K , Hoggart Richard L , Ulrich Philip I N , Gouws Andre D 
Published: August 2018

AbstractIndividuals from different social groups interpret the world in different ways. This study explores the neural basis of these group differences using a paradigm that simulates natural viewing conditions. Our aim was to determine if group differences could be found in sensory regions involved in the perception of the world or were evident in higher-level regions that are important for the interpretation of sensory information. We measured brain responses from 2 groups of football supporters, while they watched a video of matches between their teams. The time-course of response was then compared between individuals supporting the same (within-group) or the different (between-group) team. We found high intersubject correlations in low-level and high-level regions of the visual brain. However, these regions of the brain did not show any group differences. Regions that showed higher correlations for individuals from the same group were found in a network of frontal and subcortical brain regions. The interplay between these regions suggests a range of cognitive processes from motor control to social cognition and reward are important in the establishment of social groups. These results suggest that group differences are primarily reflected in regions involved in the evaluation and interpretation of the sensory input.
On the Supersingular Reduction of K3 Surfaces with Complex Multiplication
Authors: Ito Kazuhiro 
Published: August 2018

Abstract
We study the good reduction modulo $p$ of $K3$ surfaces with complex multiplication. If a $K3$ surface with complex multiplication has good reduction, we calculate the Picard number and the height of the formal Brauer group of the reduction. Moreover, if the reduction is supersingular, we calculate its Artin invariant under some assumptions. Our results generalize some results of Shimada for $K3$ surfaces with Picard number $20$. Our methods rely on the main theorem of complex multiplication for $K3$ surfaces by Rizov, an explicit description of the Breuil–Kisin modules associated with Lubin–Tate characters due to Andreatta, Goren, Howard, and Madapusi Pera, and the integral comparison theorem recently established by Bhatt, Morrow, and Scholze.
Dopamine regulates cytokine secretion during innate and adaptive immune responses
Authors: Kawano Masaaki , Takagi Rie , Saika Kikue , Matsui Masanori , Matsushita Sho 
Published: August 2018

Abstract
Dopamine (DA) is synthesized by various immune cells. DA receptors (DARs), which comprise five isoforms, are expressed on the surface of these cells. Therefore, it is likely that DA plays a role in regulating innate and adaptive responses. However, the underlying molecular mechanism(s) is largely unknown. Here, we found that, during innate immune responses, DA suppressed secretion of IFN-γ, TNF-α and IL-1β, but promoted secretion of IL-10 and CXCL1 by lipopolysaccharide (LPS)-stimulated mouse splenocytes, suggesting that DA regulates cytokine secretion. Immune subset studies indicated that DA suppressed secretion of IFN-γ, TNF-α and IL-1β by NK cells, as well as secretion of TNF-α by neutrophils and monocytes; however, DA up-regulated IL-10 secretion by neutrophils, monocytes, B cells, macrophages (Mφs) and dendritic cells within the splenocyte population. In addition, DA up-regulated secretion of CXCL1 by LPS-stimulated NK cells and Mφs. Meanwhile, treatment with DAR agonists or antagonists suppressed secretion of inflammatory cytokines from LPS-stimulated splenocytes. Pre-treatment of LPS-stimulated splenocytes with the PI3K inhibitor wortmannin reversed DA-mediated suppression of IFN-γ secretion, indicating that DA regulates IFN-γ secretion via the inositol 1,4,5-trisphosphate signaling pathway in these cells. Administration of DA and LPS to mice immunized with chicken ovalbumin (OVA) increased secretion of IL-5 by mouse lung lymphocytes, suggesting that DA promotes OVA-specific Th2-mediated immune responses by these cells. Taken together, these findings indicate that DA regulates cytokine secretion during innate and adaptive immune responses.
Process in the Community, Detain Offshore or ‘Turn Back the Boats’? Predicting Australian Asylum-seeker Policy Support from False Beliefs, Prejudice and Political Ideology
Authors: Hartley Lisa K , Anderson Joel R , Pedersen Anne 
Published: August 2018

AbstractOver the past few decades, there has been a progressive implementation of policies designed to deter the arrival of people seeking protection. In Australia, this has included offshore processing and towing boats of asylum seekers away from Australian waters. In a community survey of 164 Australians, this study examined the predictive role of false beliefs about asylum seekers, prejudice and political ideology in support of three policies. Multiple hierarchical regression models indicated that, although political ideology and prejudice were significant predictors of policy support, false beliefs was the strongest predictor. For the policy of processing asylum seekers in the community, less endorsement of false beliefs was a significant predictor, while, for the policy of offshore processing, more endorsement of false beliefs was a significant predictor. For the boat turn-back policy, an increase in false-belief endorsement was the strongest predictor; although increases in prejudice and a prejudice–political ideology interaction (i.e. the predictive value of prejudice was stronger for participants who identified as politically conservative) also independently predicted support. Practical implications and future research avenues are discussed.
Powerful mechanical-driven outflows in the central parsecs of the low-luminosity active galactic nucleus ESO 428-G14
Authors: May D , Rodríguez-Ardila A , Prieto M A , Fernández-Ontiveros J A , Diaz Y , Mazzalay X 
Published: August 2018

ABSTRACT
Low-luminosity Active Galactic Nuclei (LLAGNs) are characterized for low-radiative efficiency, much less than one percent of their Eddington limit. Nevertheless, their main energy release may be mechanical, opposite to powerful AGN classes like Seyfert and Quasars. This work reports on the jet-driven mechanical energy and the corresponding mass outflow deposited by the jet in the central 170 parsecs of the nearby LLAGN ESO 428-G14. The jet kinetic output is traced through the coronal line [Si vi] λ19641 Å. It is shown that its radial extension, up to hundreds of parsecs, requires a combination of photoionization by the central source and shock excitation as its origin. From the energetics of the ionized gas it is found that the mass outflow rate of the coronal gas is in the range from 3–8 M⊙ yr−1, comparable to those estimated from H i gas at kiloparsec scales in powerful radio galaxies.
Microbial growth, biomass production, and controls
Authors: Kirchman David L. 
Published: August 2018

Abstract
Soon after the discovery that bacteria are abundant in natural environments, the question arose as to whether or not they were active. Although the plate count method suggested that they were dormant if not dead, other methods indicated that a large fraction of bacteria and fungi are active, as discussed in this chapter. It goes on to discuss fundamental equations for exponential growth and logistic growth, and it describes phases of growth in batch cultures, continuous cultures, and chemostats. In contrast with measuring growth in laboratory cultures, it is difficult to measure in natural environments for complex communities with co-occurring mortality. Among many methods that have been suggested over the years, the most common one for bacteria is the leucine approach, while for fungi it is the acetate-in ergosterol method. These methods indicate that the growth rate of the bulk community is on the order of days for bacteria in their natural environment. It is faster in aquatic habitats than in soils, and bacteria grow faster than fungi in soils. But bulk rates for bacteria appear to be slower than those for phytoplankton. All of these rates for natural communities are much slower than rates measured for most microbes in the laboratory. Rates in subsurface environments hundreds of meters from light-driven primary production and high organic carbon conditions are even lower. Rates vary greatly among microbial taxa, according to data on 16S rRNA. Copiotrophic bacteria grow much faster than oligotrophic bacteria, but may have low growth rates when conditions turn unfavorable. Some of the factors limiting heterotrophic bacteria and fungi include temperature and inorganic nutrients, but the supply of organic compounds is perhaps most important in most environments.
Density in Plutarch
Authors: Hutchinson G. O. 
Published: August 2018

AbstractThe next move is to show that when rhythmic phrases are more densely packed together than usual, the passage calls for heightened attention. This illustrated from the climax of Plutarch’s Adversus Colotem. Then, to avert the possibility of chance, the book looks at passages in the Lives where at least twenty rhythmic closes come closely together, with few interruptions from unrhythmic closes or longer phrases. When they are looked at as a group, they are clearly not random. They come much more frequently in the second of pairs of Lives: a point with big implications for the conception of the work. They often come at key moments in the narrative (death, disaster, responses to these, triumphant summations of achievement); they also show significant connections with philosophy, substantial speeches, and comparison—the last an aspect of the Lives which they highlight far beyond the official pairings.
The association between driving time and unhealthy lifestyles: a cross-sectional, general population study of 386 493 UK Biobank participants
Authors: Mackay A , Mackay D F , Celis-Morales C A , Lyall D M , Gray S R , Sattar N , Gill J M R , Pell J P , Anderson J J 
Published: August 2018

ABSTRACT

Background
Driving is a common type of sedentary behaviour; an independent risk factor for poor health. The study explores whether driving is also associated with other unhealthy lifestyle factors.

Methods
In a cross-sectional study of UK Biobank participants, driving time was treated as an ordinal variable and other lifestyle factors dichotomized into low/high risk based on guidelines. The associations were explored using chi-square tests for trend and binary logistic regression.

Results
Of the 386 493 participants who drove, 153 717 (39.8%) drove &lt;1 h/day; 140 140 (36.3%) 1 h/day; 60 973 (15.8%) 2 h/day; and 31 663 (8.2%) ≥3 h/day. Following adjustment for potential confounders, driving ≥3 h/day was associated with being overweight/obese (OR = 1.74, 95% CI: 1.64–1.85), smoking (OR = 1.48, 95% CI: 1.37–1.63), insufficient sleep (1.70, 95% CI: 1.61–1.80), low fruit/vegetable intake (OR = 1.26, 95% CI: 1.18–1.35) and low physical activity (OR = 1.05, 95% CI: 1.00–1.11), with dose relationships for the first three, but was not associated with higher alcohol consumption (OR = 0.94, 95% CI: 0.87–1.02).

Conclusions
Sedentary behaviour, such as driving, is known to have an independent association with adverse health outcomes. It may have additional impact mediated through its effect on other aspects of lifestyle. People with long driving times are at higher risk and might benefit from targeted interventions.
Dual regulatory role of CCNA2 in modulating CDK6 and MET‐mediated cell‐cycle pathway and EMT progression is blocked by miR‐381‐3p in bladder cancer
Authors: Li Jiangfeng , Ying Yufan , Xie Haiyun , Jin Ke , Yan Huaqing , Wang Song , Xu Mingjie , Xu Xin , Wang Xiao , Yang Kai , Zheng Xiangyi , Xie Liping 
Published: August 2018

ABSTRACTEmerging evidence has elucidated that microRNAs (miRNAs) transcribed from miRNA cluster at DLK‐DIO3 imprinted domain are involved in various cancers. However, as one member of this cluster, the underlying mechanisms and functions of miR‐381‐3p in bladder cancer (BCa) still remains elusive. Here we demonstrate that the hypermethylated status of upstream maternally expressed gene 3 divergent methylation region reduces the expression of miR‐381‐3p in BCa by bisulfite‐sequencing PCR. In vitro and in vivo experiments indicate that overexpression of miR‐381‐3p significantly inhibits cell proliferation via inducing G1 phase arrest and migration via down‐regulating MET and CCNA2 induced EMT progression. CDK6/CCNA2/MET are all identified as the direct targets of miR‐381‐3p by bioinformatics analysis and dual‐luciferase reporter assay. Furthermore, inhibition of CCNA2 mediated by miR‐381‐3p as the crucial biregulator not only participates in the proliferation regulation with CDK6 in cell cycle but also modulates the EMT progression via ROCK/AKT/β‐catenin/SNAIL pathway, which establishes an EMT circuit combined with miR‐381‐3p/MET/AKT/GSK‐3β/SNAIL pathway, and SNAIL is the last confocal target to induce EMT progression. To conclude, we propose 2 novel regulatory circuits mediated by miR‐381‐3p in BCa, which may assist in the development of more effective therapies against BCa in the future.—Li, J., Ying, Y., Xie, H., Jin, K., Yan, H., Wang, S., Xu, M., Xu, X., Wang, X., Yang, K., Zheng, X., Xie, L. Dual regulatory role of CCNA2 in modulating CDK6 and MET‐mediated cell‐cycle pathway and EMT progression is blocked by miR‐381‐3p in bladder cancer. FASEB J. 33, 1374–1388 (2019). www.fasebj.org