bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATAC-pipe: general analysis of genome-wide chromatin accessibility
Authors: Zuo Zuqi , Jin Yonghao , Zhang Wen , Lu Yichen , Li Bin , Qu Kun 
Published: June 2018

AbstractAssay of Transposase-Accessible Chromatin by deep sequencing (ATAC-seq) has been widely used to profile the chromatin accessibility genome-wide. For the absence of an integrated scheme for deep data mining of specific biological issues, here we present ATAC-pipe, an efficient pipeline for general analysis of chromatin accessibility data obtained from ATAC-seq experiments. ATAC-pipe captures information includes not only the quality of original data and genome-wide chromatin accessibility but also signatures of significant differential peaks, transcription factor (TF) occupancy and nucleosome positions around regulatory sites. In addition, ATAC-pipe automatically converts statistic results into intuitive plots at publication quality, such as the read length distribution, heatmaps of sample clustering and cell-type-specific regulatory elements, enriched TF occupancy with motifs footprints and TF-driven regulatory networks. ATAC-pipe provides convenient workflow for researchers to study chromatin accessibility and gene regulation.Availability https://github.com/QuKunLab/ATAC-pipe
Detection of multi-dimensional co-exclusion patterns in microbial communities
Authors: Albayrak Levent , Khanipov Kamil , Golovko George , Fofanov Yuriy 
Published: June 2018

Abstract

Motivation
Identification of complex relationships among members of microbial communities is key to understand and control the microbiota. Co-exclusion is arguably one of the most important patterns reflecting micro-organisms’ intolerance to each other’s presence. Knowing these relations opens an opportunity to manipulate microbiotas, personalize anti-microbial and probiotic treatments as well as guide microbiota transplantation. The co-exclusion pattern however, cannot be appropriately described by a linear function nor its strength be estimated using covariance or (negative) Pearson and Spearman correlation coefficients. This manuscript proposes a way to quantify the strength and evaluate the statistical significance of co-exclusion patterns between two, three or more variables describing a microbiota and allows one to extend analysis beyond micro-organism abundance by including other microbiome associated measurements such as, pH, temperature etc., as well as estimate the expected numbers of false positive co-exclusion patterns in a co-exclusion network.

Results
The implemented computational pipeline (CoEx) tested against 2380 microbial profiles (samples) from The Human Microbiome Project resulted in body-site specific pairwise co-exclusion patterns.

Availability and implementation
C++ source code for calculation of the score and P-value for two, three and four dimensional co-exclusion patterns as well as source code and executable files for the CoEx pipeline are available at https://scsb.utmb.edu/labgroups/fofanov/co-exclusion_in_microbial_communities.asp.

Supplementary information
Supplementary data are available at Bioinformatics online.
Disentangling the Stress Process: Race/Ethnic Differences in the Exposure and Appraisal of Chronic Stressors Among Older Adults
Authors: Brown Lauren L , Mitchell Uchechi A , Ailshire Jennifer A 
Published: June 2018

AbstractObjectivesExposure to stressors is differentially distributed by race/ethnicity with minority groups reporting a higher stress burden than their white counterparts. However, to really understand the extent to which some groups bear a disproportionate stress burden, we need to consider race/ethnic differences in stress appraisal, specifically how upsetting stressors may be, in addition to stress exposure. We examine racial/ethnic differences in both the number of reported chronic stressors across five domains (health, financial, residential, relationship, and caregiving) and their appraised stressfulness among a diverse sample of older adults.MethodData come from 6,567 adults ages 52+ from the 2006 Health and Retirement Study.ResultsResults show older blacks, U.S. and foreign-born Hispanics report more chronic stress exposure than whites and are two to three times as likely to experience financial strain and housing-related stress. Socioeconomic factors fully explain the Hispanic–white difference in stress exposure, but black–white differences remain. Despite experiencing a greater number of stressors, blacks and U.S.-born Hispanics are less likely to be upset by exposure to stressors than whites. U.S.-born Hispanics are less upset by relationship-based stressors specifically, while blacks are less upset across all stress domains in fully-adjusted models. Foreign-born Hispanics are only less upset by caregiving strain.DiscussionThe distinction between exposure and appraisal-based measures of stress may shed light on important pathways that differentially contribute to race/ethnic physical and mental health disparities.
Ensemble-based estimates of eigenvector error for empirical covariance matrices
Authors: Taylor Dane , Restrepo Juan G , Meyer François G 
Published: June 2018

Abstract
Covariance matrices are fundamental to the analysis and forecast of economic, physical and biological systems. Although the eigenvalues $\{\lambda _i\}$ and eigenvectors $\{\boldsymbol{u}_i\}$ of a covariance matrix are central to such endeavours, in practice one must inevitably approximate the covariance matrix based on data with finite sample size $n$ to obtain empirical eigenvalues $\{\tilde{\lambda }_i\}$ and eigenvectors $\{\tilde{\boldsymbol{u}}_i\}$, and therefore understanding the error so introduced is of central importance. We analyse eigenvector error $\|\boldsymbol{u}_i - \tilde{\boldsymbol{u}}_i \|^2$ while leveraging the assumption that the true covariance matrix having size $p$ is drawn from a matrix ensemble with known spectral properties—particularly, we assume the distribution of population eigenvalues weakly converges as $p\to \infty $ to a spectral density $\rho (\lambda )$ and that the spacing between population eigenvalues is similar to that for the Gaussian orthogonal ensemble. Our approach complements previous analyses of eigenvector error that require the full set of eigenvalues to be known, which can be computationally infeasible when $p$ is large. To provide a scalable approach for uncertainty quantification of eigenvector error, we consider a fixed eigenvalue $\lambda $ and approximate the distribution of the expected square error $r= \mathbb{E}\left [\| \boldsymbol{u}_i - \tilde{\boldsymbol{u}}_i \|^2\right ]$ across the matrix ensemble for all $\boldsymbol{u}_i$ associated with $\lambda _i=\lambda $. We find, for example, that for sufficiently large matrix size $p$ and sample size $n&gt; p$, the probability density of $r$ scales as $1/nr^2$. This power-law scaling implies that the eigenvector error is extremely heterogeneous—even if $r$ is very small for most eigenvectors, it can be large for others with non-negligible probability. We support this and further results with numerical experiments.
Clinical decision support directed to primary care patients and providers reduces cardiovascular risk: a randomized trial
Authors: Sperl-Hillen JoAnn M , Crain A Lauren , Margolis Karen L , Ekstrom Heidi L , Appana Deepika , Amundson Gerald , Sharma Rashmi , Desai Jay R , O’Connor Patrick J 
Published: June 2018

Abstract

Objective
To test the hypothesis that use of a clinical decision support (CDS) system in a primary care setting can reduce cardiovascular (CV) risk in patients.

Materials and Methods
Twenty primary care clinics were randomly assigned to usual care (UC) or CDS. For CDS clinic patients identified algorithmically with high CV risk, rooming staff were prompted by the electronic health record (EHR) to print CDS that identified evidence-based treatment options for lipid, blood pressure, weight, tobacco, or aspirin management and prioritized them based on potential benefit to the patient. The intention-to-treat analysis included 7914 adults who met high CV risk criteria at an index clinic visit and had at least one post-index visit, accounted for clustering, and assessed impact on predicted annual rate of change in 10-year CV risk over a 14-month period.

Results
The CDS was printed at 75% of targeted visits, and providers reported 85% to 98% satisfaction with various aspects of the intervention. Predicted annual rate of change in absolute 10-year CV risk was significantly better in CDS clinics than in UC clinics (-0.59% vs. +1.66%, −2.24%; P &lt; .001), with difference in 10-year CV risk at 12 months post-index favoring the CDS group (UC 24.4%, CDS 22.5%, P &lt; .03).

Discussion
Deploying to both patients and providers within primary care visit workflow and limiting CDS display and print burden to two mouse clicks by rooming staff contributed to high CDS use rates and high provider satisfaction.

Conclusion
This EHR-integrated, web-based outpatient CDS system significantly improved 10-year CV risk trajectory in targeted adults.
Extreme Conditional Tail Moment Estimation under Serial Dependence
Authors: Hoga Yannick 
Published: June 2018

Abstract
A wide range of risk measures can be written as functions of conditional tail moments (CTMs) and value-at-risk (VaR), for instance the expected shortfall (ES). In this paper, we derive joint central limit theory for semi-parametric estimates of CTMs, including in particular ES, at arbitrarily small risk levels. We also derive confidence corridors for VaR at different levels far out in the tail, which allows for simultaneous inference. We work under a semi-parametric Pareto-type assumption on the distributional tail of the observations and only require an extremal-near epoch dependence assumption on the serial dependence. In simulations, our semi-parametric ES estimate is often shown to be more accurate in terms of mean absolute deviation than extant non- and semi-parametric estimates. An empirical application to the extreme swings in Volkswagen log-returns during the failed takeover attempt by Porsche illustrates the proposed methods.
Evaluation of text representation schemes and distance measures for authorship linking
Authors: Kocher Mirco , Savoy Jacques 
Published: June 2018

Abstract
Based on n text excerpts, the authorship linking task is to determine a way to link pairs of documents written by the same person together. This problem is closely related to authorship attribution questions, and its solution can be used in the author clustering task. However, no training information is provided and the solution must be unsupervised. To achieve this, various text representation strategies can be applied, such as characters, punctuation symbols, or letter n-grams as well as words, lemmas, Part-Of-Speech (POS) tags, and sequences of them. To estimate the stylistic distance (or similarity) between two text excerpts, different measures have been suggested based on the L1 norm (e.g. Manhattan, Tanimoto), the L2 norm (e.g. Matusita), the inner product (e.g. Cosine), or the entropy paradigm (e.g. Jeffrey divergence). From those possible implementations, it is not clear which text representation and distance functions produce the best performance, and this study provides an answer to this question. Three corpora, extracted from French and English literature, have been evaluated using standard methodology. Moreover, we suggest an additional performance measure called high precision (HPrec) capable of judging the quality of a ranked list of links to provide only correct answers. No systematic difference can be found between token- or lemma-based text representations. Simple POS tags do not provide an effective solution but short sequences of them form a good text representation. Letter n-grams (with n = 4–6) give high HPrec rates. As distance measures, this study found that the Tanimoto, Matusita, and Clark distance measures perform better than the often-used Cosine function. Finally, applying a pruning procedure (e.g. culling terms appearing once or twice or limiting the vocabulary to the 500 most frequent words) reduces the representation complexity and might even improve the effectiveness of the attribution scheme.
Nuclear starburst activity induced by elongated bulges in spiral galaxies
Authors: Kim Eunbin , Kim Sungsoo S , Choi Yun-Young , Lee Gwang-Ho , de Grijs Richard , Lee Myung Gyoon , Hwang Ho Seong 
Published: June 2018

ABSTRACT
We study the effects of bulge elongation on the star formation activity in the centres of spiral galaxies using the data from the Sloan Digital Sky Survey Data Release 7. We construct a volume-limited sample of face-on spiral galaxies with Mr &lt; −19.5 mag at 0.02 ≤ $z$ &lt; 0.055 by excluding barred galaxies, where the aperture of the SDSS spectroscopic fibre covers the bulges of the galaxies. We adopt the ellipticity of bulges measured by Simard et al., who performed two-dimensional bulge + disc decompositions using the SDSS images of galaxies, and identify nuclear starbursts using the fibre specific star formation rates derived from the SDSS spectra. We find a statistically significant correlation between bulge elongation and nuclear starbursts in the sense that the fraction of nuclear starbursts increases with bulge elongation. This correlation is more prominent for fainter and redder galaxies, which exhibit higher ratios of elongated bulges. We find no significant environmental dependence of the correlation between bulge elongation and nuclear starbursts. These results suggest that non-axisymmetric bulges can efficiently feed the gas into the centre of galaxies to trigger nuclear starburst activity.
GAMA/H-ATLAS: the local dust mass function and cosmic density as a function of galaxy type – a benchmark for models of galaxy evolution
Authors: Beeston R A , Wright A H , Maddox S , Gomez H L , Dunne L , Driver S P , Robotham A , Clark C J R , Vinsen K , Takeuchi T T , Popping G , Bourne N , Bremer M N , Phillipps S , Moffett A J , Baes M , Bland-Hawthorn J , Brough S , De Vis P , Eales S A , Holwerda B W , Loveday J , Liske J , Smith M W L , Smith D J B , Valiante E , Vlahakis C , Wang L 
Published: June 2018

ABSTRACT
We present the dust mass function (DMF) of 15 750 galaxies with redshift $z$ &lt; 0.1, drawn from the overlapping area of the GAMA and H-ATLAS surveys. The DMF is derived using the density corrected Vmax method, where we estimate Vmax using: (i) the normal photometric selection limit (pVmax) and (ii) a bivariate brightness distribution (BBD) technique, which accounts for two selection effects. We fit the data with a Schechter function, and find $M^{*}=(4.65 \pm 0.18)\times 10^{7}\,h^2_{70}\, \mathrm{ M}_{\odot }$, α = (−1.22 ± 0.01), $\phi ^{*}=(6.26 \pm 0.28)\times 10^{-3}\,h^3_{70}\,\rm Mpc^{-3}\,dex^{-1}$. The resulting dust mass density parameter integrated down to 104 M⊙ is Ωd = (1.11 ± 0.02) × 10−6 which implies the mass fraction of baryons in dust is $f_{m_\mathrm{ b}}=(2.40\pm 0.04)\times 10^{-5}$; cosmic variance adds an extra  7–17 per cent uncertainty to the quoted statistical errors. Our measurements have fewer galaxies with high dust mass than predicted by semi-analytic models. This is because the models include too much dust in high stellar mass galaxies. Conversely, our measurements find more galaxies with high dust mass than predicted by hydrodynamical cosmological simulations. This is likely to be from the long time-scales for grain growth assumed in the models. We calculate DMFs split by galaxy type and find dust mass densities of Ωd = (0.88 ± 0.03) × 10−6 and Ωd = (0.060 ± 0.005) × 10−6 for late types and early types, respectively. Comparing to the equivalent galaxy stellar mass functions (GSMF) we find that the DMF for late types is well matched by the GSMF scaled by (8.07 ± 0.35) × 10−4.
Exposure to the Tobacco Power Wall Increases Adolescents’ Willingness to Use E-cigarettes in the Future
Authors: Dunbar Michael S , Martino Steven C , Setodji Claude M , Shadel William G 
Published: June 2018

Abstract

Introduction
Adolescents’ e-cigarette use is now more prevalent than their combustible cigarette use. Youth are exposed to e-cigarette advertising at retail point-of-sale (POS) locations via the tobacco power wall (TPW), but no studies have assessed whether exposure to the TPW influences susceptibility to future e-cigarette use.

Methods
The study was conducted in the RAND Store Lab (RSL), a life-sized replica of a convenience store developed to experimentally evaluate how POS advertising influences tobacco use risk under simulated shopping conditions. In a between-subjects experiment, 160 adolescents (M age = 13.82; 53% female, 56% white) were randomized to shop in the RSL under one of two conditions: (1) TPW located behind the cashier (n = 80); or (2) TPW hidden behind an opaque wall (n = 80). Youths rated willingness to use e-cigarettes (“If one of your best friends were to offer you an e-cigarette, would you try it?”; 1 = definitely not, 10 = definitely yes) before and after exposure. Linear regression assessed differences in pre-post changes in willingness to use across conditions.

Results
Ever-use of e-cigarettes was 5%; use of cigarettes was 8%; use of both e-cigarettes and cigarettes was 4%. There were no differences between TPW conditions on these or other baseline variables (eg, age, gender). Compared to the hidden condition, TPW exposure was associated with greater increases in willingness to use e-cigarettes in the future (B = 1.15, standard error [SE] = 0.50, p = .02).

Conclusions
Efforts to regulate visibility of the TPW at POS may help to reduce youths’ susceptibility to initiating e-cigarettes as well as conventional tobacco products like cigarettes.

Implications
Past work suggests that exposure to the TPW in common retail settings, like convenience stores, may increase adolescents’ susceptibility to smoking cigarettes. This experimental study builds upon prior research to show that exposure to the TPW at retail POS similarly increases adolescents’ willingness to use e-cigarettes in the future. Efforts to regulate the visibility of the TPW in retail settings may help to reduce youths’ susceptibility to initiating nicotine and tobacco products, including e-cigarettes.
β-Carotene Supplementation and Lung Cancer Incidence in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study: The Role of Tar and Nicotine
Authors: Middha Pooja , Weinstein Stephanie J , Männistö Satu , Albanes Demetrius , Mondul Alison M 
Published: June 2018

Abstract

Introduction
The Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study demonstrated that β-carotene supplementation increases lung cancer incidence in smokers. Further, cigarettes with higher tar and nicotine content are associated with a higher risk of lung cancer. However, no studies have examined whether the increased risk associated with β-carotene supplementation in smokers varies by the tar or nicotine content of cigarettes.

Methods
The ATBC Study was a randomized, double-blind intervention trial conducted in southwest Finland. A total of 29 133 male smokers, aged 50–69 years, were enrolled and randomly assigned to one of four groups (α-tocopherol, β-carotene, both, or placebo). Cox proportional hazards models were used to estimate the hazard ratio (HR) and 95% confidence intervals (CI) of lung cancer risk by β-carotene trial assignment stratified by a priori categories of cigarette tar and nicotine content.

Results
The β-carotene supplementation group had significantly higher risk of developing lung cancer in all categories of tar content (yes vs. no β-carotene supplementation—ultralight cigarettes [≤7 mg tar]: HR = 1.31, 95% CI = 0.91 to 1.89; nonfiltered cigarettes [≥21 mg tar]: HR = 1.22, 95% CI = 0.91 to 1.64; p for interaction = .91). Similarly, there was no interaction with nicotine content (yes vs. no β-carotene supplementation—ventilated cigarettes [≤0.8 µg nicotine]: HR = 1.23, 95% CI = 0.98 to 1.54; nonfiltered cigarettes [≥1.3 µg nicotine]: HR = 1.22, 95% CI = 0.91 to 1.64; p for interaction = .83).

Conclusion
These findings support the conclusion that supplementation with β-carotene increases the risk of lung cancer in smokers regardless of the tar or nicotine content of cigarettes smoked. Our data suggest that all smokers should continue to avoid β-carotene supplementation.

Implications
Previous studies demonstrated that β-carotene supplementation increases risk of lung cancer in smokers. This study moves the field forward by examining the potential for modification of risk of lung cancer with different levels of tar and nicotine in cigarettes smoked, as interaction with carcinogens in these components of cigarette smoke is hypothesized to be the mechanism by which β-carotene increases risk. Our study provides evidence that the increased risk of lung cancer in smokers who take β-carotene supplements is not dependent upon the tar or nicotine level of cigarettes smoked and suggests that all smokers should continue to avoid β-carotene supplementation.
Immunization Mandates, Vaccination Coverage, and Exemption Rates in the United States
Authors: Shaw Jana , Mader Emily M , Bennett Brittany E , Vernyi-Kellogg Olesya K , Yang Y Tony , Morley Christopher P 
Published: June 2018

Abstract

Background
Vaccination coverage among children entering kindergarten in the United States is high, but interstate variations exist. The relationship between state immunization laws and vaccination coverage has not been fully assessed. We evaluated associations of state laws on both measles, mumps, and rubella (MMR) and diphtheria, tetanus, and pertussis (DTaP) vaccination coverage and exemptions to school immunization requirements.

Methods
We conducted a retrospective, longitudinal analysis of the effect of state immunization laws on vaccination coverage and exemptions among US kindergarteners from SY 2008 to SY 2014. The primary outcome measures were state-level kindergarten entry vaccination coverage rates for 2-dose MMR and 4-dose DTaP vaccines. Secondary outcome measures included rates of state-level exemptions (ie, medical, religious, philosophical) to school immunization requirements.

Results
We found that state policies that refer to Advisory Committee on Immunization Practices recommendations were associated with 3.5% and 2.8% increases in MMR and DTaP vaccination rates. Health Department–led parental education was associated with 5.1% and 4.5% increases in vaccination rates. Permission of religious and philosophical exemptions was associated with 2.3% and 1.9% decreases in MMR and DTaP coverage, respectively, and a 1.5% increase in both total exemptions and nonmedical exemptions, respectively.

Conclusions
We found higher vaccination coverage and lower nonmedical exemption rates for MMR and DTaP vaccines in states adopting Advisory Committee on Immunization Practices guidelines for school entry. Adherence to these best practices was a successful strategy to increase vaccination coverage and reduce vaccination exemptions.