bluuebunny/crossref_metadata_2025_split huggingface dataset:
ST-Steiner: a spatio-temporal gene discovery algorithm
Authors: Norman Utku , Cicek A Ercument 
Published: February 2019

Abstract

Motivation
Whole exome sequencing (WES) studies for autism spectrum disorder (ASD) could identify only around six dozen risk genes to date because the genetic architecture of the disorder is highly complex. To speed the gene discovery process up, a few network-based ASD gene discovery algorithms were proposed. Although these methods use static gene interaction networks, functional clustering of genes is bound to evolve during neurodevelopment and disruptions are likely to have a cascading effect on the future associations. Thus, approaches that disregard the dynamic nature of neurodevelopment are limited.

Results
Here, we present a spatio-temporal gene discovery algorithm, which leverages information from evolving gene co-expression networks of neurodevelopment. The algorithm solves a prize-collecting Steiner forest-based problem on co-expression networks, adapted to model neurodevelopment and transfer information from precursor neurodevelopmental windows. The decisions made by the algorithm can be traced back, adding interpretability to the results. We apply the algorithm on ASD WES data of 3871 samples and identify risk clusters using BrainSpan co-expression networks of early- and mid-fetal periods. On an independent dataset, we show that incorporation of the temporal dimension increases the predictive power: predicted clusters are hit more and show higher enrichment in ASD-related functions compared with the state-of-the-art.

Availability and implementation
The code is available at http://ciceklab.cs.bilkent.edu.tr/st-steiner.

Supplementary information
Supplementary data are available at Bioinformatics online.
Finding enzyme cofactors in Protein Data Bank
Authors: Mukhopadhyay Abhik , Borkakoti Neera , Pravda Lukáš , Tyzack Jonathan D , Thornton Janet M , Velankar Sameer 
Published: February 2019

Abstract

Motivation
Cofactors are essential for many enzyme reactions. The Protein Data Bank (PDB) contains &gt;67 000 entries containing enzyme structures, many with bound cofactor or cofactor-like molecules. This work aims to identify and categorize these small molecules in the PDB and make it easier to find them.

Results
The Protein Data Bank in Europe (PDBe; pdbe.org) has implemented a pipeline to identify enzyme cofactor and cofactor-like molecules, which are now part of the PDBe weekly release process.

Availability and implementation
Information is made available on the individual PDBe entry pages at pdbe.org and programmatically through the PDBe REST API (pdbe.org/api).

Supplementary information
Supplementary data are available at Bioinformatics online.
The DECam minute cadence survey – II. 49 variables but no planetary transits of a white dwarf
Authors: Dame Kyra , Belardi Claudia , Kilic Mukremin , Rest Armin , Gianninas A , Barber Sara , Brown Warren R 
Published: February 2019

Abstract
We present minute cadence photometry of 31 732 point sources observed in one 3 $\rm deg^{2}$ DECam pointing centred at RA = 09:03:02 and Dec. = −04:35:00 over eight consecutive half-nights. We use these data to search for eclipse-like events consistent with a planetary transit of a white dwarf and other sources of stellar variability within the field. We do not find any significant evidence for minute-long transits around our targets, hence we rule out planetary transits around ∼370 white dwarfs that should be present in this field. Additionally, we identify 49 variables, including 40 new systems. These include 23 detached or contact stellar binaries, one eclipsing white dwarf + M dwarf binary, 16 δ Scuti, three RR Lyrae, and two ZZ Ceti pulsators. Results from the remaining two fields in our survey will allow us to place more stringent constraints on the frequency of planets orbiting white dwarfs in the habitable zone.
Prevalence of Smoking and Knowledge About the Hazards of Smoking Among 170 000 Chinese Adults, 2013–2014
Authors: Zhang Mei , Liu Shiwei , Yang Ling , Jiang Yong , Huang Zhengjing , Zhao Zhenping , Deng Qian , Li Yichong , Zhou Maigeng , Wang Linhong , Chen Zhengming , Wang Limin 
Published: February 2019

Abstract

Introduction
Periodic population surveys of smoking behavior can inform development of effective tobacco control strategies. We investigated smoking patterns, cessation, and knowledge about smoking hazards in China.

Methods
A nationally representative cross-sectional survey recruited 176 318 people aged ≥18 years across 31 provinces of China in 2013–2014, using multi-stage stratified cluster sampling methods. The smoking patterns, cessation, and knowledge about smoking hazards were analyzed, overall and in population subgroups, adjusting for sample selection weight and post-stratification factors.

Results
Among men, 60.7% were ever-smokers, with proportions of regular, occasional and former smokers being 46.3%, 5.5%, and 8.8% respectively. Among women, only 2.8% had ever smoked. The prevalence of ever smoking in men was higher in rural than urban areas (63.2% vs. 57.6%) and varied from 39.5% to 67.4% across 31 provinces. Among male regular smokers, the mean daily number of cigarettes smoked was 17.8, with mean age at first starting to smoke daily being 20.1 years. Among current smokers, one-third (32.6% men, 32.1% women) had tried to quit before and 36.8% (36.8% men, 35.5% women) intended to quit in the future. Of the Chinese adults, 75.9% recognized that smoking was hazardous, with the proportions believing that smoking could cause lung cancer, heart attack or stroke being 67.0%, 33.2%, and 29.5%, respectively and with 26.0% reporting that smoking could cause all these conditions.

Conclusion
Among Chinese adults, the smoking prevalence remained high in men but was low in women. In both men and women, knowledge about smoking hazards was poor.

Implications
This study showed that tobacco smoking remained highly prevalent among adult men in China in 2013–2014. Moreover, men born in recent decades were more likely to start smoking at younger ages and to smoke more cigarettes than those born in previous generations. There was a large regional variation in male smoking prevalence, with the least economically developed regions having higher prevalence. In contrast, few women in China smoked, especially among those born in recent decades. The contrasting smoking patterns in men and women is likely to result in an increasingly large gender disparity in life expectancy in the coming decades.
Characterization of Volatile Organic Compound Metabolites in Cigarette Smokers, Electronic Nicotine Device Users, Dual Users, and Nonusers of Tobacco
Authors: Keith Rachel J , Fetterman Jessica L , Orimoloye Olusola A , Dardari Zeina , Lorkiewicz Pawel K , Hamburg Naomi M , DeFilippis Andrew P , Blaha Michael J , Bhatnagar Aruni 
Published: February 2019

Abstract

Introduction
Limited research exists about the possible cardiovascular effects of electronic nicotine delivery systems (ENDS). We therefore sought to compare exposure to known or potentially cardiotoxic volatile organic compounds (VOCs) in ENDS users, smokers, and dual users.

Methods
A total of 371 individuals from the Cardiovascular Injury due to Tobacco Use study, a cross-sectional study of healthy participants aged 21–45 years, were categorized as nonusers of tobacco (n = 87), sole ENDS users (n = 17), cigarette smokers (n = 237), and dual users (n = 30) based on 30-day self-reported tobacco product use patterns. Participants provided urine samples for VOC and nicotine metabolite measurement. We assessed associations between tobacco product use and VOC metabolite measures using multivariable-adjusted linear regression models.

Results
Mean (SD) age of the population was 32 (±6.8) years, 55% men. Mean urinary cotinine level in nonusers of tobacco was 2.6 ng/mg creatinine, whereas cotinine levels were similar across all tobacco product use categories (851.6–910.9 ng/mg creatinine). In multivariable-adjusted models, sole ENDS users had higher levels of metabolites of acrolein, acrylamide, acrylonitrile, and xylene compared with nonusers of tobacco, but lower levels of most VOC metabolites compared with cigarette smokers or dual users. In direct comparison of cigarettes smokers and dual users, we found lower levels of metabolites of styrene and xylene in dual users.

Conclusion
Although sole ENDS use may be associated with lower VOC exposure compared to cigarette smoking, further study is required to determine the potential health effects of the higher levels of certain reactive aldehydes, including acrolein, in ENDS users compared with nonusers of tobacco.

Implications
ENDS use in conjunction with other tobacco products may not significantly reduce exposure to VOC, but sole use does generally reduce some VOC exposure and warrants more in-depth studies.
Smoking Among Immigrant Groups in the United States: Prevalence, Education Gradients, and Male-to-Female Ratios
Authors: Pampel Fred , Khlat Myriam , Bricard Damien , Legleye Stéphane 
Published: February 2019

Abstract

Introduction
Immigrants in the United States are less likely to smoke than those born in the United States, but studies have not fully described the diversity of their smoking patterns. We investigate smoking by world region of birth and duration of residence in the United States, with a comprehensive approach covering current prevalence levels, education gradients, and male-to-female ratios.

Methods
The data originate from the National Health Interview Surveys, 2000–2015, and the sample of 365 404 includes both US-born and foreign-born respondents aged 25–70 years. World region of birth and duration of residence in the United States measure immigrant characteristics. Current cigarette smoking was analyzed using logistic regression.

Results
Immigrant groups were protected from smoking and had weaker education gradients in smoking and larger male-to-female smoking ratios than the US-born population. However, large differences emerged among the immigrant groups for region of birth but less so for duration of residence in the United States. For example, immigrants from sub-Saharan Africa and the Indian subcontinent have low prevalence, weak education gradients, and high male-to-female ratios. Immigrants from Europe have the opposite pattern, and immigrants from Latin America fall between those two extremes.

Conclusion
The stage of the cigarette epidemic in the region of birth helps explain the diverse group profiles. Duration of residence in the United States does less to account for the differences in smoking than region of birth. The findings illustrate the heterogeneity of immigrant populations originating from diverse regions across the world and limited convergence with the host population after immigration.

Implications
The study identifies immigrant groups that, because of high smoking prevalence related to levels in the host country, should be targeted for cessation efforts. It also identifies immigrant groups with low prevalence for which anti-smoking programs should encourage maintenance of healthy habits. Many immigrant groups show strong education disparities in smoking, further suggesting that smokers with lower levels of education be targeted by public health programs.
Influence of Tattoo Ink on Hepatitis C Virus Infectiousness
Authors: Behrendt Patrick , Brüning Janina , Todt Daniel , Steinmann Eike 
Published: February 2019

Abstract
Hepatitis C virus (HCV) is a blood-borne virus and is most frequently transmitted through large or repeated direct percutaneous exposures to infected blood. The 2 most common exposures associated with transmission of HCV are blood transfusion and intravenous drug abuse. The association between HCV transmission and other suspected risk factors such as tattooing is more controversial. Although HCV can survive for days to weeks in suspension or on inanimate surfaces, its stability in tattooing supplies remains elusive. Here, we analyzed the influence of tattoo ink on HCV infectiousness.
Strain-level differences in gut microbiome composition determine fecal IgA levels and are modifiable by gut microbiota manipulation
Authors: Yang Chao , Mogno Ilaria , Contijoch Eduardo J. , Borgerding Joshua N. , Aggarwala Varun , Li Zhihua , Grasset Emilie K. , Helmus Drew S. , Dubinsky Marla C. , Mehandru Saurabh , Cerutti Andrea , Faith Jeremiah J. 
Published: February 2019

AbstractFecal IgA production depends on colonization by a gut microbiota. However, the bacterial strains that drive gut IgA production remain largely unknown. By accessing the IgA-inducing capacity of a diverse set of human gut microbial strains, we identified Bacteroides ovatus as the species that best induced gut IgA production. However, this induction varied biomodally across different B. ovatus strains. The high IgA-inducing B. ovatus strains preferentially elicited more IgA production in the large intestine through both T-cell-dependent and T-cell-independent B cell-activation pathways. Remarkably, a low-IgA phenotype in mice could be robustly and consistently converted into a high-IgA phenotype by transplanting a multiplex cocktail of high IgA-inducing B. ovatus strains but not individual ones. Thus, microbial strain specificity is essential for the optimal induction of high-IgA responses in the gut. Our results highlight the critical importance of microbial strains in driving phenotype variation in the mucosal immune system and provide a strategy to robustly modify a gut immune phenotype, including IgA production.
Theta and Gamma Bands Encode Acoustic Dynamics over Wide-ranging Timescales
Authors: Teng Xiangbin , Poeppel David 
Published: February 2019

AbstractNatural sounds have broadband modulation spectra and contain acoustic dynamics ranging from tens to hundreds of milliseconds. How does the human auditory system encode acoustic information over wide-ranging timescales to achieve sound recognition? Previous work (Teng et al., 2017) demonstrated a temporal coding preference in the auditory system for the theta (4 – 7 Hz) and gamma (30 – 45 Hz) ranges, but it remains unclear how acoustic dynamics between these two ranges is encoded. Here we generated artificial sounds with temporal structures over timescales from ~200 ms to ~30 ms and investigated temporal coding on different timescales in the human auditory cortex. Participants discriminated sounds with temporal structures at different timescales while undergoing magnetoencephalography (MEG) recording. The data show robust neural entrainment in the theta and the gamma bands, but not in the alpha and beta bands. Classification analyses as well as stimulus reconstruction reveal that the acoustic information of all timescales can be differentiated through the theta and gamma bands, but the acoustic dynamics in the theta and gamma ranges are preferentially encoded. We replicate earlier findings of multi-time scale processing and further demonstrate that the theta and gamma bands show generality of temporal coding across all timescales with comparable capacity. The results support the hypothesis that the human auditory cortex primarily encodes auditory information employing neural processes within two discrete temporal regimes.SignificanceNatural sounds contain rich acoustic dynamics over wide-ranging timescales, but perceptually relevant regularities often occupy specific temporal ranges. For instance, speech carries phonemic information on a shorter timescale than syllabic information at ~ 200 ms. How does the brain efficiently ‘sample’ continuous acoustic input to perceive temporally structured sounds? We presented sounds with temporal structures at different timescales and measured cortical entrainment using magnetoencephalography. We found, unexpectedly, that the human auditory system preserves high temporal coding precision on two non-overlapping timescales, the slower (theta) and faster (gamma) bands, to track acoustic dynamics over all timescales. The results suggest that the acoustic environment which we experience as seamless and continuous is segregated by discontinuous neural processing, or ‘sampled.’
Aversive learning strengthens episodic memory in both adolescents and adults
Authors: Cohen Alexandra O. , Matese Nicholas G. , Filimontseva Anastasia , Shen Xinxu , Shi Tracey C. , Livne Ethan , Hartley Catherine A. 
Published: February 2019

AbstractAdolescence is often filled with positive and negative emotional experiences that may change how individuals remember and respond to stimuli in their environment. In adults, aversive events can both enhance memory for associated stimuli as well as generalize to enhance memory for unreinforced but conceptually related stimuli. The present study tested whether learned aversive associations similarly lead to better memory and generalization across a category of stimuli in adolescents. Participants completed an olfactory Pavlovian category conditioning task in which trial-unique exemplars from one of two categories were partially reinforced with an aversive odor. Participants then returned 24-hours later to complete a surprise recognition memory test. We found better corrected recognition memory for the reinforced versus the unreinforced category of stimuli in both adults and adolescents. Further analysis revealed that enhanced recognition memory was driven specifically by better memory for the reinforced exemplars. Autonomic arousal during learning was also related to subsequent memory. These findings build on previous work in adolescent and adult humans and rodents showing comparable acquisition of aversive Pavlovian conditioned responses across age groups and demonstrate that memory for stimuli with an acquired aversive association is enhanced in both adults and adolescents.
Earth-Gravity Congruent Motion Benefits Visual Gain For Parabolic Trajectories
Authors: Jörges Björn , López-Moliner Joan 
Published: February 2019

AbstractTThere is evidence that humans rely on an earth gravity (9.81 m/s2) prior for a series of tasks involving perception and action, the reason being that gravity helps predict future positions of moving objects. Eye-movements in turn are partially guided by predictions about observed motion. Thus, the question arises whether knowledge about gravity is also used to guide eye-movements: If humans rely on a representation of earth gravity for the control of eye movements, earth-gravity-congruent motion should lead to improved visual pursuit. In a pre-registered experiment, we presented participants (n=10) with parabolic motion governed by six different gravities (−1/0.7/0.85/1/1.15/1.3g), two initial vertical velocities and two initial horizontal velocities in a 3D environment. Participants were instructed to follow the target with their eyes. We tracked their gaze and computed the visual gain (velocity of the eyes divided by velocity of the target) as proxy for the quality of pursuit. An LMM analysis with gravity condition as fixed effect and intercepts varying per subject showed that the gain was lower for −1g than for 1g (by −0.13, SE = 0.005). This model was significantly better than a null model without gravity as fixed effect (p<0.001), supporting our hypothesis. A comparison of 1g and the remaining gravity conditions revealed that 1.15g (by 0.043, SE=0.005) and 1.3g (by 0.065, SE=0.005) were associated with lower gains, while 0.7g (by 0.054, SE=0.005) and 0.85g (by 0.029, SE=0.005) were associated with higher gains. This model was again significantly better than a null model (p<0.001), contradicting our hypothesis. Post-hoc analyses reveal that confounds in the 0.7/0.85/1/1.15/1.3g condition may be responsible for these contradicting results. Despite these discrepancies, our data thus provide some support for the hypothesis that internalized knowledge about earth gravity guides eye movements.
lncRNADIGITand BRD3 protein form phase-separated condensates to regulate endoderm differentiation
Authors: Daneshvar Kaveh , Ardehali M. Behfar , Klein Isaac A. , Kratkiewicz Arcadia J. , Zhou Chan , Mahpour Amin , Cook Brett M. , Li Wenyang , Pondick Joshua V. , Moran Sean P. , Young Richard A. , Kingston Robert E. , Mullen Alan C. 
Published: February 2019

AbstractGene programs that control differentiation are regulated through the interplay between DNA, RNA, and protein. Cooperation among these fundamental cellular components can occur through highly structured interactions connecting domains formed by specific sequences of nucleotides, ribonucleotides, and/or amino acids and also through the assembly of biomolecular condensates. Here, we show that endoderm differentiation is regulated through the interaction of the long noncoding (lnc) RNADIGITand the bromodomain and extra-terminal (BET) domain family protein BRD3. BRD3 forms phase-separated condensates that containDIGIT, occupies enhancers of endoderm transcription factors, and is required for endoderm differentiation. Purified BRD3 binds to acetylated histone H3 lysine 18 (H3K18ac)in vitroand occupies regions of the genome enriched in H3K18ac during endoderm differentiation, including the key transcription factors that regulate endoderm differentiation.DIGITis also enriched in regions of H3K18ac, and depletion ofDIGITresults in decreased recruitment of BRD3 to these regions. Our findings support a model where cooperation betweenDIGITand BRD3 at regions of H3K18ac regulates the transcription factors that drive endoderm differentiation and suggest a broader role for protein-lncRNA phase-separated condensates as regulators of transcription in development.
Heterozygous missense RAD21 variant in a peripheral sclerocornea pedigree
Authors: Zhang Bi Ning , Yan Chan Tommy Chung , Sin Tam Pancy Oi , Liu Yu , Pang Chi Pui , Jhanji Vishal , Chen Li Jia , Chu Wai Kit 
Published: February 2019

AbstractBackgroundSclerocomea is a rare congenital disorder characterized with cornea opacification. We identified a heterozygous missense RAD21 variant in a non-cons anguineous Chinese family with multiple peripheral sclerocomea patients spanning across three generations inherited in an autosomal dominant manner.MethodsComprehensive ophthalmic examinations were conducted on all 14 members. Whole exome sequencing was used to identify the genetic alterations in the affected pedigree members. Lymphoblastoid cell lines (LCLs) were established using blood samples from all members. Cleavage of RAD21 protein was quantified in these cell lines.ResultsAll affected individuals showed features of scleralization over the peripheral cornea of both eyes. Mean horizontal and vertical corneal diameter were significantly decreased in the affected members. Significant differences were also observed on mean apex pachymetry between affected and unaffected subjects. A RAD21C1348T variant was co-segregated with affected members. Both the wild-type allele and the missense variant were expressed at the mRNA level. This variant caused RAD21 R450C substitution at the separase cleavage site, which led to reduced RAD21 cleavage.ConclusionWe believe this is the first report of genetic variant in sclerocornea without other syndromes. Further work is needed to confirm the RAD21R450C variant with sclerocomea.