bluuebunny/crossref_metadata_2025_split huggingface dataset:
chimeraviz: a tool for visualizing chimeric RNA
Authors: Lågstad Stian , Zhao Sen , Hoff Andreas M , Johannessen Bjarne , Lingjærde Ole Christian , Skotheim Rolf I 
Published: May 2017

Abstract

Summary
Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and this can be helped by a visualization framework that automatically integrates RNA data with known genomic features. Here we present chimeraviz, a Bioconductor package that automates the creation of chimeric RNA visualizations. The package supports input from nine different fusion-finder tools: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPfuse and STAR-FUSION.

Availability and implementation
chimeraviz is an R package available via Bioconductor (https://bioconductor.org/packages/release/bioc/html/chimeraviz.html) under Artistic-2.0. Source code and support is available at GitHub (https://github.com/stianlagstad/chimeraviz).

Supplementary information
Supplementary data are available at Bioinformatics online.
Predicting ultraluminous X-ray source demographics from geometrical beaming
Authors: Middleton Matthew J. , King Andrew 
Published: May 2017

Abstract
The ultraluminous X-ray source (ULX) population is known to contain neutron stars (NS), but the relative number of these compared to black hole (BH) primaries is unknown. Assuming classical supercritical accretion and resultant geometrical beaming, we show that the observed population ratio can be predicted from the mean masses of each family of compact objects and the relative spatial density of NSs to BHs. Conversely – and perhaps more importantly – given even a crude estimate for the spatial densities, an estimate of the fraction of the population containing NSs will begin to constrain the mean mass of BHs in ultraluminous X-ray sources.
Can the helium-enriched main-sequence donor scenario hide enough hydrogen to explain Type Ia supernovae?
Authors: Liu Zheng-Wei , Stancliffe Richard J. 
Published: May 2017

Abstract
Hydrodynamical simulations predict that a large amount of hydrogen (≳0.1 M⊙) is removed from a hydrogen-rich companion star by the SN explosion in the single-degenerate scenario of Type Ia supernovae (SNe Ia). However, non-detection of hydrogen-rich material in the late-time spectra of SNe Ia suggests that the hydrogen mass stripped from the progenitor system is ≲0.001–0.058 M⊙. In this Letter, we include thermohaline mixing into self-consistent binary evolution calculations for the helium-enriched main-sequence (HEMS) donor channel of SNe Ia for the first time. We find that the swept-up hydrogen masses expected in this channel are around 0.10–0.17 M⊙, which is higher than the observational limits, although the companion star is strongly helium-enriched when the SN explodes. This presents a serious challenge to the HEMS donor channel.
Sertraline for Major Depression During the Year Following Traumatic Brain Injury: A Randomized Controlled Trial
Authors: Fann Jesse R. , Bombardier Charles H. , Temkin Nancy , Esselman Peter , Warms Catherine , Barber Jason , Dikmen Sureyya 
Published: May 2017

Objective:
Major depressive disorder (MDD) is common and associated with impaired functioning after traumatic brain injury (TBI). Few placebo-controlled antidepressant trials exist in this population. We evaluated the efficacy and tolerability of sertraline for MDD within 1 year of sustaining a TBI.

Setting:
Level I trauma center.

Participants:
Adults with MDD within 1 year of hospitalization for complicated mild to severe TBI.

Design:
Randomized, double-blind, placebo-controlled trial.

Main Measures:
Twelve-week treatment response on the 17-item Hamilton Depression Rating Scale. We also assessed symptom improvement and remission.

Results:
We randomized 62 participants: 32% sustained a severe TBI, 68% had significant anxiety, 63% had a history of prior MDD, and 69% had a history of alcohol or drug dependence. Depression significantly improved from baseline to 12 weeks in both treatment groups (P < .001). There were no significant differences between the sertraline and placebo groups over 12 weeks on depression severity, response, or remission. The sertraline group had significant improvement on speed of information processing compared with the placebo group (P < .006).

Conclusion:
Sertraline monotherapy was not superior to placebo for MDD in people with post–acute complicated mild to severe TBI. Research is needed on the effectiveness of interventions that also address the significant psychosocial needs of this population.
Relationship Stability After Traumatic Brain Injury Among Veterans and Service Members: A VA TBI Model Systems Study
Authors: Stevens Lillian Flores , Lapis Yanna , Tang Xinyu , Sander Angelle M. , Dreer Laura E. , Hammond Flora M. , Kreutzer Jeffrey S. , O'Neil-Pirozzi Therese M. , Nakase-Richardson Risa 
Published: May 2017

Objective:
To explore stability of relationships and predictors of change in relationship status 2 years following TBI/polytrauma.

Setting:
Five Department of Veterans Affairs Polytrauma Rehabilitation Centers (VA PRCs).

Participants:
A total of 357 active duty service members and Veterans enrolled in the Veterans Affairs Polytrauma Rehabilitation Centers Traumatic Brain Injury Model Systems database with complete marital status information at 2 years postinjury.

Design:
Prospective, longitudinal, multisite.

Main Measures:
Relationship status change was defined as change in marital status (single/never married; married; divorced/separated) at 2-year follow-up, compared with status at enrollment.

Results:
At the time of enrollment, 134 participants (38%) were single/never married; 151 (42%) were married, and 72 (20%) were divorced/separated. Of those married at enrollment, 78% remained married at year 2 while 22% underwent negative change. Multivariable analyses revealed that age and education at the time of injury and mental health utilization prior to injury were significant predictors of relationship change. Among those who were single/divorced/separated at the time of enrollment, 87% remained so at year 2 while 13% underwent positive change. Injury during deployment significantly predicted positive relationship change.

Conclusions:
The unmalleable, preinjury characteristics identified may be used as potential triggers for education, prevention, surveillance, and couples therapy, if needed.
Brief Report: Late Efavirenz-Induced Ataxia and Encephalopathy: A Case Series
Authors: Variava Ebrahim , Sigauke Farai R. , Norman Jennifer , Rakgokong Modiehi , Muchichwa Petudzai , Mochan Andre , Maartens Gary , Martinson Neil A. 
Published: May 2017

Background:
WHO treatment guidelines recommend efavirenz in first-line antiretroviral therapy (ART). Efavirenz commonly causes early transient neuropsychiatric adverse events. We present 20 cases with severe encephalopathy accompanied by ataxia due to efavirenz toxicity.

Methods:
Consecutive HIV-infected adults taking efavirenz-containing ART admitted to Tshepong hospital, Klerksdorp, South Africa with ataxia and encephalopathy were included in this case series.

Results:
We identified 20 women admitted to hospital with severe ataxia. All received efavirenz-based ART for a median of 2 years. All had severe ataxia and none had nystagmus. Eleven had features of encephalopathy. Median weight was 34 kg [interquartile range (IQR): 29.7–35.3]; median CD4 count 299 cells/mm3 (IQR: 258–300) and most (18 of 19) were virally suppressed. Eight patients had a record of prior weights and 7 of 8 showed significant weight loss with a median weight loss of 10.8 kg (IQR: 8–11.6). All cases had plasma efavirenz assays, 19 were supratherapeutic (more than twice the upper level of therapeutic range), and 15 had concentrations above the upper limit of assay detection. Ataxia resolved after withdrawal of efavirenz at a median time of 2 months (IQR: 1.25–4) and recurred in 2 of 3 patients when rechallenged. Admissions before diagnosis were frequent with 10 cases admitted previously. Three women died.

Conclusions:
Efavirenz toxicity may present with severe reversible ataxia often with encephalopathy years after its initiation, likely in genetic slow metabolizers. We recommend that patients whose weight is <40 kg receive lower doses of efavirenz and that therapeutic drug monitoring be considered, and efavirenz stopped in patients presenting with ataxia. Eight patients had a record of prior subsequent weights and 7 of 8 showed significant weight loss gain; median gain of 10.8 kg (IQR: 8–11.6).
An Ovine Model of Hyperdynamic Endotoxemia and Vital Organ Metabolism
Authors: Byrne Liam , Obonyo Nchafatso G. , Diab Sara , Dunster Kimble , Passmore Margaret , Boon Ai Ching , Hoe Louise See , Hay Karen , Van Haren Frank , Tung John-Paul , Cullen Louise , Shekar Kiran , Maitland Kathryn , Fraser John F. 
Published: May 2017

ABSTRACT

Background:
Animal models of endotoxemia are frequently used to understand the pathophysiology of sepsis and test new therapies. However, important differences exist between commonly used experimental models of endotoxemia and clinical sepsis. Animal models of endotoxemia frequently produce hypodynamic shock in contrast to clinical hyperdynamic shock. This difference may exaggerate the importance of hypoperfusion as a causative factor in organ dysfunction. This study sought to develop an ovine model of hyperdynamic endotoxemia and assess if there is evidence of impaired oxidative metabolism in the vital organs.

Methods:
Eight sheep had microdialysis catheters implanted into the brain, heart, liver, kidney, and arterial circulation. Shock was induced with a 4 h escalating dose infusion of endotoxin. After 3 h vasopressor support was initiated with noradrenaline and vasopressin. Animals were monitored for 12 h after endotoxemia. Blood samples were recovered for hemoglobin, white blood cell count, creatinine, and proinflammatory cytokines (IL-1Beta, IL-6, and IL-8).

Results:
The endotoxin infusion was successful in producing distributive shock with the mean arterial pressure decreasing from 84.5 ± 12.8 mm Hg to 49 ± 8.03 mm Hg (P < 0.001). Cardiac index remained within the normal range decreasing from 3.33 ± 0.56 L/min/m2 to 2.89l ± 0.36 L/min/m2 (P = 0.0845). Lactate/pyruvate ratios were not significantly abnormal in the heart, brain, kidney, or arterial circulation. Liver microdialysis samples demonstrated persistently high lactate/pyruvate ratios (mean 37.9 ± 3.3).

Conclusions:
An escalating dose endotoxin infusion was successful in producing hyperdynamic shock. There was evidence of impaired oxidative metabolism in the liver suggesting impaired splanchnic perfusion. This may be a modifiable factor in the progression to multiple organ dysfunction and death.
Calreticulin Ameliorates Hypoxia/Reoxygenation-Induced Human Microvascular Endothelial Cell Injury By Inhibiting Autophagy
Authors: Wang You , Tao Tian-Qi , Song Dan-Dan , Liu Xiu-Hua 
Published: May 2017

ABSTRACT

Background:
Autophagy has been found to be involved in myocardial ischemia/reperfusion injury. However, the underlying mechanism and significance of autophagy in reperfusion injury remain unclear. Herein, we evaluated the effects of exogenous calreticulin (CRT) on autophagy in hypoxia/reoxygenation (H/R)-treated human microvascular endothelial cells (MECs).

Methods:
Human MECs were pretreated with CRT (25 pg/mL) for 30 min, followed by exposure in an incubator filled with a gas mixture of 90% N2, 5% O2, and 5% CO2 for 8-h hypoxia. The cells were then placed back in the normoxic CO2 incubator for 16-h reoxygenation. Cell injury was assessed by the cell counting kit-8 assay. Autophagosomes were detected by transmission electron microscopy and immunofluorescence staining. Western blot analysis was performed to detect phosphorylated mammalian target of rapamycin (p-mTOR), Beclin 1, and microtubule-associated protein 1 light chain 3 (LC3).

Results:
H/R induced marked autophagy through the mTOR pathway. CRT suppressed rapamycin- and H/R-induced autophagosome formation, the LC3-II/LC3-I ratio, and Beclin 1 expression in human MECs by upregulating mTOR phosphorylation, consequently attenuating H/R-induced human MEC injury.

Conclusions:
Exogenous CRT attenuated H/R-induced human MEC injury by inhibiting autophagy.
Domino-like propagation of collective U-turns in fish schools
Authors: Lecheval Valentin , Jiang Li , Tichit Pierre , Sire Clément , Hemelrijk Charlotte K. , Theraulaz Guy 
Published: May 2017

AbstractMoving animal groups such as schools of fish or flocks of birds often undergo sudden collective changes of their travelling direction as a consequence of stochastic fluctuations in heading of the individuals. However, the mechanisms by which these behavioural fluctuations arise at the individual level and propagate within a group are still unclear. In the present study, we combine an experimental and theoretical approach to investigate spontaneous collective U-turns in groups of rummy-nose tetra (Hemigrammus rhodostomus) swimming in a ring-shaped tank. U-turns imply that fish switch their heading between the clockwise and anticlockwise direction. We reconstruct trajectories of individuals moving alone and in groups of different sizes. We show that the group decreases its swimming speed before a collective U-turn. This is in agreement with previous theoretical predictions showing that speed decrease facilitates an amplification of fluctuations in heading in the group, which can trigger U-turns. These collective U-turns are mostly initiated by individuals at the front of the group. Once an individual has initiated a U-turn, the new direction propagates through the group from front to back without amplification or dampening, resembling the dynamics of falling dominoes. The mean time between collective U-turns sharply increases as the size of the group increases. We develop an Ising spin model integrating anisotropic and asymmetrical interactions between fish and their tendency to follow the majority of their neighbours nonlinearly (social conformity). The model quantitatively reproduces key features of the dynamics and the frequency of collective U-turns observed in experiments.
A Comparison of Machine Learning and Bayesian Modelling for Molecular Serotyping
Authors: Newton Richard , Wernisch Lorenz 
Published: May 2017

AbstractBackgroundStreptococcus pneumoniaeis a human pathogen that is a major cause of infant mortality. Identifying the pneumococcal serotype is an important step in monitoring the impact of vaccines used to protect against disease. Genomic microarrays provide an effective method for molecular serotyping. Previously we developed an empirical Bayesian model for the classification of serotypes from a molecular serotyping array. With only few samples available, a model driven approach was the only option. In the meanwhile, several thousand samples have been made available to us, providing an opportunity to investigate serotype classification by machine learning methods, which could complement the Bayesian model.ResultsWe compare the performance of the original Bayesian model with two machine learning algorithms: Gradient Boosting Machines and Random Forests. We present our results as an example of a generic strategy whereby a preliminary probabilistic model is complemented or replaced by a machine learning classifier once enough data are available. Despite the availability of thousands of serotyping arrays, a problem encountered when applying machine learning methods is the lack of training data containing mixtures of serotypes; due to the large number of possible combinations. Most of the available training data comprises samples with only a single serotype. To overcome the lack of training data we implemented an iterative analysis, creating artificial training data of serotype mixtures by combining raw data from single serotype arrays.ConclusionsWith the enhanced training set the machine learning algorithms out perform the original Bayesian model. However, for serotypes currently lacking sufficient training data the best performing implementation was a combination of the results of the Bayesian Model and the Gradient Boosting Machine. As well as being an effective method for classifying biological data, machine learning can also be used as an efficient method for revealing subtle biological insights, which we illustrate with an example.
Exploiting general independence criteria for network inference
Authors: Verbyla Petras , Desgranges Nina , Richardson Sylvia , Wernisch Lorenz 
Published: May 2017

ABSTRACTInference of networks representing dependency relationships is a key tool for understanding data derived from biological systems. It has been shown that nonlinear relationships and non-Gaussian noise aid detection of directions of functional dependencies. In this study we explore how far generalised independence criteria for statistical independence proposed in the literature are better suited to the inference of networks compared to standard independence criteria based on linear relationships and Gaussian noise. We compare such criteria within the framework of the PC algorithm, a popular network inference algorithm for directed acyclic dependency graphs. We also propose and evaluate a method to apply unconditional independence criteria to assess conditional independence and a method to simulate data with desired properties from experimental data. Our main finding is that a recently proposed criterion based on distance covariance performs well compared to other independence criteria in terms of error rates, speed of computation, and need of fine-tuning parameters when applied to experimental biological datasets.
A comment on priors for Bayesian occupancy models
Authors: Northrup Joseph M. , Gerber Brian D. 
Published: May 2017

AbstractUnderstanding patterns of species occurrence and the processes underlying these patterns is fundamental to the study of ecology. One of the more commonly used approaches to investigate species occurrence patterns is occupancy modeling, which can account for imperfect detection of a species during surveys. In recent years, there has been a proliferation of Bayesian modeling in ecology, which includes fitting Bayesian occupancy models. The Bayesian framework is appealing to ecologists for many reasons, including the ability to incorporate prior information through the specification of prior distributions on parameters. While ecologists often intend to choose priors so that they are “uninformative”; or “;vague”;, such priors can easily be unintentionally highly informative. Here we report on how the specification of a “vague” normally distributed (i.e., Gaussian) prior on coefficients in Bayesian occupancy models can unintentionally influence parameter estimation. Using both simulation and empirical examples, we illustrate how this issue likely compromises inference about species-habitat relationships. While the occurrence of this issue likely depends on the data set, researchers fitting Bayesian occupancy models should conduct sensitivity analyses to ensure intended inference, or use priors other than those most commonly used in the literature. We provide further suggestions for addressing this issue in occupancy studies, and an online tool for exploring this issue under different contexts.
On growth and form of the distal air exchange surfaces within the lung
Authors: Warburton David , Wigfall Clarence , Pollack Harvey , Koos David , AlAlam Denise , Shi Wei , Fraser Scott , Moats Rex 
Published: May 2017

Summary statementEmploying novel imaging and computational approaches we here deduce some new concepts as to how the distal shaping of airway lineage stem and progenitor cells may contribute to the growth and form of the air exchange surface (AES) of the lung, distal to the bronchoalveolar duct junction (BADJ). We then propose that the AES extrudes from the sides and tips of distinct families of small ducts, apparently by buckling of the thinning luminal epithelium into the surrounding mesenchyme, stabilized firstly by rings of elastin and later by rings of collagen and elastin fibers, that surround the mouth of each distal unit of the AES. We propose this mechanism as a parsimonious solution to achieving the optimum form, packing density and functional efficiency of the AES, while allowing sufficient space between for the plumbing of conducting airways, pulsatile capillary blood vessels, lymphatics, nerves and other key matrix and cellular components within the interstitial mesenchyme.AbstractHerein we show, using several novel imaging and computational approaches, how the air exchange units (AEUs) of the lung develop from the tips and sides of distinct families of tortuous ducts, that themselves ramify as distinct families distal to the bronchoalveolar duct junctions (BADJs), prenatally in humans but postnatally in mice. The mature AEUs thus consist of indented spheroids tightly packed between quite regularly spaced distal ducts. Since the diameter of the BADJs and the distal ducts increases rather than decreasing during the formation of AEUs, we further deduce that the AEUs must form by circular epithelial precursor buckling at their mouths with reulsting extrusion of their lumen into the surrounding mesenchyme, stabilized firstly by interlocking rings of elastin and later by rings of elastin and collagen fibers surrounding the mouth of each of the prospective AEUs. Furthermore, we show that the surface of each of the AEUs is highly rugose, being indented by the capillary network that lies close beneath the AES membranes. We propose that, the kissing theorem proposed of Newton tha expresses the number of times billiard balls may touch within their frame is a parsimonious solution to achieving optimum packing of the distal AES unit spaces, while allowing sufficient space between them to allow for conducting airways, closely applied pulsatile capillary blood vessels, lymphatics, nerves and other key components of the interstitial mesenchyme.
Environmental influences on the mating system of the common morning glory
Authors: Alvarado-Serrano D. F. , Chang S-M. , Baucom R. S 
Published: May 2017

ABSTRACTThe balance between selfing and outcrossing is a life history trait of major concern with deep evolutionary consequences in mixed mating species. Yet, our current understanding of the proximate and ultimate determinants of species’ mating system is still unsatisfactory and largely theoretical. Indeed, evolutionary biologists are still puzzled by the often dramatic variation of mating strategies within single species. Of particular concern is the extent to which environmental conditions shape patterns of variation and covariation of mating system components within species. Here, we address this concern in the common morning glory (Ipomoea purpurea) by taking advantage of an extensive dataset of floral traits, genetic estimates of selfing and inbreeding, and relevant environmental factors compiled for 22 populations of this species distributed along a disparate set of environments along Southeast and Midwest USA. Combining a powerful array of parametric and model-free statistical approaches, we robustly identify a set of natural and anthropogenic environmental factors underlying population-level variation in selfing, inbreeding, and flower morphology. Remarkably, individual mating system components are found to be associated with different environmental factors and only loosely associated with each other, and thus potentially under multiple different selective pressures. These results not only corroborate theoretical expectations of the significant role the environment plays in the local determination of mating systems, but also provide compelling evidence of complex underlying interactions between multiple evolutionary processes.