bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complications in tube thoracostomy: Systematic review and meta-analysis
Authors: Hernandez Matthew C. , El Khatib Moustafah , Prokop Larry , Zielinski Martin D. , Aho Johnathon M. 
Published: February 2018

BACKGROUND
Tube thoracostomy (TT) complications and their reported rates are highly variable (1–40%) and inconsistently classified. Consistent TT complication classification must be applied to compare reported literature to standardize TT placement. We aim to determine the overall TT-related complication rates in patients receiving TT for traumatic indications using uniform definitions.

METHODS
Systematic review and meta-analysis was performed assessing TT-related complications. Comprehensive search of several databases (1975–2015) was conducted. We included studies that reported on bedside TT insertion (≥22 Fr) in trauma patients. Data were abstracted from eligible articles by independent reviewers with discrepancies reconciled by a third. Analyses were based on complication category subtypes: insertional, positional, removal, infection/immunologic/education, and malfunction.

RESULTS
Database search resulted in 478 studies; after applying criteria 29 studies were analyzed representing 4,981 TTs. Injury mechanisms included blunt 60% (49–71), stab 27% (17–34), and gunshot 13% (7.8–10). Overall, median complication rate was 19% (95% confidence interval, 14–24.3). Complication subtypes included insertional (15.3%), positional (53.1%), removal (16.2%), infection/immunologic (14.8%), and malfunction (0.6%). Complication rates did not change significantly over time for insertional, immunologic, or removal p = 0.8. Over time, there was a decrease in infectious TT-related complications as well as an increase in positional TT complications.

CONCLUSION
Generation of evidence-based approaches to improve TT insertion outcomes is difficult because a variety of complication classifications has been used. This meta-analysis of complications after TT insertion in trauma patients suggests that complications have not changed over time remaining stable at 19% over the past three decades.

LEVEL OF EVIDENCE
Systematic review and meta-analysis, level III.
Universal screening for intimate partner and sexual violence in trauma patients—What about the men? An Eastern Association for the Surgery of Trauma Multicenter Trial
Authors: Zakrison Tanya L. , Rattan Rishi , Milian Valdés Davel , Ruiz Xiomara , Gelbard Rondi , Cline John , Turay David , Luo-Owen Xian , Namias Nicholas , George Jessica , Yeh Dante , Pust Daniel , Williams Brian H. 
Published: February 2018

BACKGROUND
A recent Eastern Association for the Surgery of Trauma–supported multicenter trial demonstrated a similar rate of intimate partner and sexual violence (IPSV) between male and female trauma patients, regardless of mechanism. Our objective was to perform a subgroup analysis of our affected male cohort because this remains an understudied group in the trauma literature.

METHODS
We conducted a recent Eastern Association for the Surgery of Trauma-supported, cross-sectional, multicenter trial over one year (March 2015 to April 2016) involving four Level I trauma centers throughout the United States. We performed universal screening of adult trauma patients using the validated Hurt, Insult, Threaten, Scream and sexual violence screening surveys. Risk factors for male patients were identified. χ2 Test compared categorical variables with significance at p values less than 0.05. Parametric data are presented as mean ± standard deviation.

RESULTS
A total of 2,034 trauma patients were screened, of which 1,281 (63%) were men. Of this cohort, 119 (9.3%) men screened positive for intimate partner violence, 14.1% for IPSV, and 6.5% for sexual violence. On categorical analysis of the Hurt, Insult, Threaten, Scream screen, the proportion of men that were physically hurt was 4.8% compared to 4.3% for women (p = 0.896). A total of 4.8% of men screened positive for both IPSV. The total proportion of men who presented with any history of intimate partner violence, sexual violence, or both (IPSV) was 15.8%. More men affected by penetrating trauma screened positive for IPSV (p < 0.00001). The IPSV positivity in men was associated with mental illness, substance abuse, and trauma recidivism.

CONCLUSION
One of every 20 men that present to trauma centers is a survivor of both IPSV, with one of every six men experiencing some form of violence. Men are at similar risk for physical abuse as women when this intimate partner violence occurs. The IPSV is associated with penetrating trauma in men. Support programs for this population may potentially impact associated mental illness, substance abuse, trauma recidivism, and even societal-level violence.

LEVEL OF EVIDENCE
Epidemiological study, level II.
Past and present role of extracorporeal membrane oxygenation in combat casualty care: How far will we go?
Authors: Cannon Jeremy W. , Mason Phillip E. , Batchinsky Andriy I. 
Published: February 2018

ABSTRACT
Advanced extracorporeal therapies have been successfully applied in the austere environment of combat casualty care over the previous decade. In this review, we describe the historic underpinnings of extracorporeal membrane oxygenation, review the recent experience with both partial and full lung support during combat operations, and critically assess both the current status of the Department of Defense extracorporeal membrane oxygenation program and the way forward to establish long-range lung rescue therapy as a routine capability for combat casualty care.
Stress matters: a double-blind, randomized controlled trial on the effects of a multispecies probiotic on neurocognition
Authors: S. Papalini , F. Michels , N. Kohn , J. Wegman , S. van Hemert , K. Roelofs , A. Arias-Vasquez , E. Aarts 
Published: February 2018

AbstractProbiotics are microorganisms that can provide health benefits when consumed. Recent animal studies have demonstrated that probiotics can reverse gut microbiome-related alterations in anxiety and depression-like symptoms, in hormonal responses to stress, and in cognition. However, in humans, the effects of probiotics on neurocognition remain poorly understood and a causal understanding of the gut-brain link in emotion and cognition is lacking. We aimed to fill this gap by studying the effects of a probiotics intervention versus placebo on neurocognition in healthy human volunteers.We set out to investigate the effects of a multispecies probiotic (Ecologic®Barrier) on specific neurocognitive measures of emotion reactivity, emotion regulation, and cognitive control using fMRI. Critically, we also tested whether the use of probiotics can buffer against the detrimental effects of acute stress on working memory. In a double blind, randomized, placebo-controlled, between-subjects intervention study, 58 healthy participants were tested twice, once before and once after 28 days of intervention with probiotics or placebo.Probiotics versus placebo did not affect emotion reactivity, emotion regulation, and cognitive control processes at brain or behavioral level, neither related self-report measures. However, relative to the placebo group, the probiotics group did show a significant stress-related increase in working memory performance after versus before supplementation (digit span backward, p=0.039, ηp2=.07). Interestingly, this change was associated with intervention-related neural changes in frontal cortex during cognitive control in the probiotics group, but not in the placebo group. Overall, our results show that neurocognitive effects of supplementation with a multispecies probiotic in healthy women become visible under challenging (stress) situations. Probiotics buffered against the detrimental effects of stress in terms of cognition, especially in those individuals with probiotics-induced changes in frontal brain regions during cognitive control.HighlightsWe ran a randomized placebo-controlled fMRI study with a multispecies probioticProbiotics did not affect neurocognitive measures of emotion and cognitive controlProbiotics did affect stress-related working memory and neural correlatesProbiotics in healthy individuals can support cognition under stress
Genotyping-by-sequencing supports a genetic basis for alpine wing-reduction in a New Zealand stonefly
Authors: Veale Andrew J. , Foster Brodie J. , Dearden Peter K. , Waters Jonathan M. 
Published: February 2018

AbstractWing polymorphism is a prominent feature of numerous insect groups, but the genomic basis for this diversity remains poorly understood. Wing reduction is a commonly observed trait in many species of stoneflies, particularly in cold or alpine environments. The widespread New Zealand stoneflyZelandoperla fenestrataspecies group (Z. fenestrata, Z. tillyardi, Z. pennulata) contains populations ranging from long-winged (macropterous) to vestigial-winged (micropterous), with the latter phenotype typically associated with high altitudes. The presence of flightless forms on numerous mountain ranges, separated by lowland fully winged populations, suggests wing reduction has occurred multiple times. We use Genotyping by Sequencing (GBS) to test for genetic differentiation between fully winged (n=62) and vestigial-winged (n=34) individuals, sampled from a sympatric population of distinct wing morphotypes, to test for a genetic basis for wing morphology. We found no population genetic differentiation between these two morphotypes across 6,843 SNP loci, however we did detect several outlier loci that strongly differentiated morphotypes across independent tests. This indicates small regions of the genome are likely to be highly differentiated between morphotypes, indicating a genetic basis for morphotype differentiation. These results provide a clear basis for ongoing genomic analysis to elucidate critical regulatory pathways for wing development in Pterygota.
HLA-B*39:06 Efficiently Mediates Type 1 Diabetes in a Mouse Model Incorporating Reduced Thymic Insulin Expression1
Authors: Schloss Jennifer , Ali Riyasat , Racine Jeremy J. , Chapman Harold D. , Serreze David V. , DiLorenzo Teresa P. 
Published: February 2018

ABSTRACTType 1 diabetes (T1D) is characterized by T cell-mediated destruction of the insulin-producing βcells of the pancreatic islets. Among the loci associated with T1D risk, those most predisposing are found in the MHC region. HLA-B*39:06 is the most predisposing class I MHC allele and is associated with an early age of onset. To establish an NOD mouse model for the study of HLA-B*39:06, we expressed it in the absence of murine class I MHC. HLA-B*39:06 was able to mediate the development of CD8 T cells, support lymphocytic infiltration of the islets, and confer T1D susceptibility. Because reduced thymic insulin expression is associated with increased T1D risk in patients, we incorporated this in our model as well, finding that HLA-B*39:06-transgenic NOD mice with reduced thymic insulin expression have an earlier age of disease onset and a higher overall prevalence as compared to littermates with typical thymic insulin expression. This was despite virtually indistinguishable blood insulin levels, T cell subset percentages, and TCR Vβ family usage, indicating that reduced thymic insulin expression does not impact T cell development on a global scale. Rather, we propose that it allows the thymic escape of insulin-reactive HLA-B*39:06-restricted T cells which participate in β cell destruction. We also found that in mice expressing either HLA-B*39:06 or HLA-A*02:01 in the absence of murine class I MHC, HLA transgene identity alters TCR Vβ usage, which may contribute to varying diabetogenic CD8 T cell repertoires in the presence of different HLA class I alleles.
Reducing fluctuations in species composition facilitates artificial selection of microbial community function
Authors: Xie Li , Shou Wenying 
Published: February 2018

AbstractMulti-species microbial communities often display functions - biochemical activities unattainable by member species alone, such as fighting pathogens. To improve community function, we can artificially select communities by growing “Newborn” communities over “maturation time” into “Adult” communities, and selecting highest-functioning Adults to “reproduce” by diluting each into multiple Newborns of the next cycle. Community selection has been attempted a few times on complex communities, often generating mixed results that are difficult to interpret. Here, we ask how costly community function may be improved via mutations and community selection. We simulate selection of two-species communities where Helpers digest Waste and generate Byproduct essential to Manufacturers; Manufacturers divert a fraction of their growth to make Product. Community function, the total Product in an “Adult”, is sub-optimal even when both species have been pre-optimized as monocultures. If we dilute an Adult into Newborns by pipetting (a common experimental procedure), stochastic fluctuations in Newborn composition prevents community function from improving. Reducing fluctuations via cell sorting allows selection to work. Our conclusions hold regardless of whether H and M are commensal or mutualistic, or variations in model assumptions.
Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells
Authors: Hollerer Ina , Barker Juliet C. , Jorgensen Victoria , Tresenrider Amy , Dugast-Darzacq Claire , Chan Leon Y. , Darzacq Xavier , Tjian Robert , Ünal Elçin , Brar Gloria A. 
Published: February 2018

ABSTRACTWe recently described an unconventional mode of gene regulation in budding yeast by which transcriptional and translational interference were used in an integrated manner to down-regulate protein expression. Developmentally timed transcriptional interference inhibited production of a well translated mRNA isoform and resulted in the production of an mRNA isoform containing inhibitory upstream open reading frames (uORFs) that blocked translation of the ORF. Transcriptional interference and uORF-based translational repression are established mechanisms outside of yeast, but whether this type of integrated regulation was conserved was unknown. Here we find that, indeed, a similar type of regulation occurs at the locus for the human oncogene MDM2. We observe evidence of transcriptional interference between the two MDM2 promoters, which produce a poorly translated distal promoter-derived uORF-containing mRNA isoform and a well-translated proximal promoter-derived transcript. Down-regulation of distal promoter activity markedly up-regulates proximal promoter-driven expression and results in local reduction of histone H3K36 trimethylation. Moreover, we observe that this transcript toggling between the two MDM2 isoforms naturally occurs during human embryonic stem cell differentiation programs.
The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand
Authors: Zuber Philipp K. , Artsimovitch Irina , NandyMazumdar Monali , Liu Zhaokun , Nedialkov Yuri , Schweimer Kristian , Rösch Paul , Knauer Stefan H. 
Published: February 2018

AbstractRfaH, a transcription regulator of the universally conserved NusG/Spt5 family, utilizes a unique mode of recruitment to elongating RNA polymerase to activate virulence genes. RfaH function depends critically on an ops sequence, an exemplar of a consensus pause, in the non-template DNA strand of the transcription bubble. We used structural and functional analyses to elucidate the role of ops in RfaH recruitment. Our results demonstrate that ops induces pausing to facilitate RfaH binding and establishes direct contacts with RfaH. Strikingly, the non-template DNA forms a hairpin in the RfaH: ops complex structure, flipping out a conserved T residue that is specifically recognized by RfaH. Molecular modeling and genetic evidence support the notion that ops hairpin is required for RfaH recruitment. We argue that both the sequence and the structure of the non-template strand are read out by transcription factors, expanding the repertoire of transcriptional regulators in all domains of life.
Mef-2 and p300 interact to regulate expression of the homeostatic regulator Pumilio inDrosophila
Authors: Lin Wei-Hsiang , Baines Richard A. 
Published: February 2018

Abstract (174 words)Pumilio (Pum) is a key component of neuron firing-rate homeostasis that maintains stability of neural circuit activity. Whilst Pum is ubiquitously expressed, we understand little about how synaptic excitation regulates its expression. Here, we characterised theDrosophila dpumpromoter and identified multiple Myocyte enhancer factor-2 (Mef2)-binding elements. To understand the transactivation capability of dMef2, we cloned 12dmef2splice variants and used a luciferase-based assay to monitordpumpromoter activity. Whilst all 12 dMef2 splice variants enhancedpumpromoter activity, exon 10-containing variants induce greater transactivation. Previous work shows dPum expression increases with synaptic excitation. However, we observe no change indmef2transcript in CNS exposed to picrotoxin (PTX). The lack of activity-dependence is indicative of additional regulation. We identified p300 as a likely candidate. We show that by binding to dMef2, p300 repressesdpumtransactivation. Significantly,p300transcript is down-regulated by enhanced synaptic excitation (PTX) which, in turn, increases transcription ofdpumthrough derepression of dMef2. These results suggest the activity-dependent expression ofdpumis regulated by an interaction between p300 and dMef2.
The impact on authors and editors of introducing Data Availability Statements at Nature journals
Authors: Grant Rebecca , Hrynaszkiewicz Iain 
Published: February 2018

AbstractThis paper describes the adoption of a standard policy for the inclusion of data availability statements in all research articles published at the Nature family of journals, and the subsequent research which assessed the impacts that these policies had on authors, editors, and the availability of datasets. The key findings of this research project include the determination of average and median times required to add a data availability statement to an article; and a correlation between the way researchers make their data available, and the time required to add a data availability statement. This paper will be presented at the International Digital Curation Conference 2018, and has been submitted to the International Journal of Digital curation.
MethCP: Differentially Methylated Region Detection with Change Point Models
Authors: Gong Boying , Purdom Elizabeth 
Published: February 2018

Abstract.Whole-genome bisulfite sequencing (WGBS) provides a precise measure of methylation across the genome, yet presents a challenge in identifying regions that are differentially methylated (DMRs) between different conditions. A number of methods have been proposed which mainly focusing on the setting of two-group comparison. We develop a DMR detecting method MethCP for WGBS data, which is applicable for a wide range of experimental designs beyond the two-group comparisons, such as time-course data. MethCP identifies DMRs based on change point detection, which naturally segments the genome and provides region-level differential analysis. For simple two-group comparison, we show that our method outperforms developed methods in accurately detecting the complete DM region on a simulated dataset and an Arabidopsis dataset. Moreover, we show that MethCP is capable of detecting wide regions with small effect sizes, which can be common in some settings but existing techniques are poor in detecting such DMRs. We also demonstrate the use of MethCP for time-course data on another dataset following methylation throughout seed germination in Arabidopsis.
Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities
Authors: Bottos Eric M. , Kennedy David W. , Romero Elvira B. , Fansler Sarah J. , Brown Joseph M. , Bramer Lisa M. , Chu Rosalie K. , Tfaily Malak M. , Jansson Janet K. , Stegen James C. 
Published: February 2018

AbstractUnderstanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw, however studies describing ecological controls on these communities are lacking. We hypothesize that permafrost communities are uniquely shaped by constraints imposed by prolonged freezing, and decoupled from factors that influence non-permafrost soil communities. To test this hypothesis, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape. We used null modeling to estimate the relative importance of selective and neutral assembly processes on community composition, and identified environmental factors influencing ecological selection through regression and structural equation modeling (SEM). Proportionally, the strongest process influencing community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21), variable selection (0.16), and homogenizing dispersal (0.05). Fe(II) content was the most important factor explaining variable selection, and was significantly associated with total selection by univariate regression (R2=0.14, p=0.003). SEM supported a model in which Fe(II) content mediated influences of the Gibbs free energy of the organic matter pool and organic acid concentration on total selection. These findings reveal that the processes shaping microbial communities in permafrost are distinct from those in non-permafrost soils, as the stability of the permafrost environment imposes dispersal and thermodynamic constraints on permafrost communities. Models of permafrost community composition will need to account for these unique drivers in order to predict community characteristics across permafrost landscapes, and in efforts to understand how pre-thaw conditions will influence post-thaw ecological and biogeochemical processes.
Transcriptional Activation of Elephant Shark Mineralocorticoid Receptor by Corticosteroids, Progesterone and Spironolactone
Authors: Katsu Yoshinao , Kohno Satomi , Oka Kaori , Lin Xiaozhi , Otake Sumika , Pillai Nisha E. , Takagi Wataru , Hyodo Susumu , Venkatesh Byrappa , Baker Michael E. 
Published: February 2018

AbstractWe report the analysis of activation of full-length mineralocorticoid receptor (MR) from elephant shark, a cartilaginous fish belonging to the oldest group of jawed vertebrates by corticosteroids and progesterone. Based on their measured activities, aldosterone, cortisol, 11-deoxycorticosterone, corticosterone, 11-deoxcortisol, progesterone and 19-norprogesterone are potential physiological mineralocorticoids. However, aldosterone, the physiological mineralocorticoid in humans and other terrestrial vertebrates, is not found in cartilaginous or ray-finned fishes. Although progesterone activates ray-finned fish MRs, progesterone does not activate human, amphibian or alligator MRs, suggesting that during the transition to terrestrial vertebrates, progesterone lost the ability to activate the MR. Both elephant shark MR and human MR are expressed in the brain, heart, ovary, testis and other non-epithelial tissues, indicating that MR expression in diverse tissues evolved in the common ancestor of jawed vertebrates. Our data suggest that progesterone-activated MR may have unappreciated functions in elephant shark ovary and testis.