bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intensification with pegylated interferon during treatment with tenofovir in HIV–hepatitis B virus co‐infected patients
Authors: Boyd A. , Piroth L. , Maylin S. , Maynard‐Muet M. , Lebossé F. , Bouix C. , Lascoux‐Combe C. , Mahjoub N. , Girard P.‐M. , Delaugerre C. , Carrat F. , Lacombe K. , Miailhes P. 
Published: August 2016

SummaryIn hepatitis B “e” antigen (HBeAg) positive patients with hepatitis B virus (HBV) mono‐infection, intensification of nucleos(t)ide analogue treatment with pegylated interferon (PegIFN) could help induce higher HBeAg seroclearance rates. Our aim was to determine the long‐term effect of adding PegIFN to tenofovir (TDF)‐containing antiretroviral therapy on seroclearance in HBeAg‐positive patients co‐infected with the human immunodeficiency virus (HIV) and HBV. In this prospective matched cohort study, 46 patients with 1‐year PegIFN intensification during TDF‐containing antiretroviral therapy (TDF+PegIFN) were matched 1:1 to controls undergoing TDF without PegIFN (TDF) using a time‐dependent propensity score based on age, CD4+ count and liver cirrhosis status. Kinetics of HBeAg quantification (qHBeAg) and hepatitis B surface antigen quantification (qHBsAg) were estimated using mixed‐effect linear regression and time to HBeAg seroclearance or HBsAg seroclearance was modelled using proportional hazards regression. At baseline, previous TDF exposure was a median 39.8 months (IQR=21.4–59.4) and median qHBeAg and qHBsAg levels were 6.9 PEIU/mL and 3.72 log10IU/mL, respectively (P>.5 between groups). Median follow‐up was 33.4 months (IQR=19.0–36.3). During intensification, faster average declines of qHBeAg (−0.066 vs −0.027 PEIU/mL/month, P=.001) and qHBsAg (−0.049 vs −0.026 log10IU/mL/month, P=.09) were observed in patients undergoing TDF+PegIFN vs TDF, respectively. After intensification, qHBeAg and qHBsAg decline was no different between groups (P=.7 and P=.9, respectively). Overall, no differences were observed in HBeAg seroclearance (TDF+PegIFN=13.2 vs TDF=12.6/100 person·years, P=.5) or HBsAg seroclearance rates (TDF+PegIFN=1.8 vs TDF=1.3/100 person·years, P=.7). In conclusion, PegIFN intensification in HBeAg‐positive co‐infected patients did not lead to increased rates of HBeAg or HBsAg clearance, despite faster declines of antigen levels while on PegIFN.
Intermittent At‐Home Suctioning of Esophageal Content for Prevention of Recurrent Aspiration Pneumonia in 4 Dogs with Megaesophagus
Authors: Manning K. , Birkenheuer A.J. , Briley J. , Montgomery S.A. , Harris J. , Vanone S.L. , Gookin J.L. 
Published: August 2016

BackgroundMegaesophagus carries a poor to guarded prognosis due to death from aspiration pneumonia. Options for medical management of regurgitation are limited to strategic oral or gastrostomy tube feeding.ObjectivesTo describe the use and efficacy of intermittent esophageal suctioning to prevent regurgitation and associated episodes of aspiration pneumonia in dogs with megaesophagus.AnimalsFour dogs with acquired idiopathic megaesophagus and recurrent aspiration pneumonia.MethodsRetrospective review of medical records of dogs with megaesophagus in which intermittent suctioning of esophageal content was employed for management of recurrent aspiration pneumonia.ResultsIntermittent suctioning of the esophagus was initiated in 4 dogs after failure of strict gastrostomy tube feeding failed to prevent regurgitation and repeated episodes of aspiration pneumonia. Suctioning was accomplished by esophagostomy tube in 3 dogs and per os in 1 dog. After initiation of esophageal suctioning, dogs survived for a median of 13.5 additional months (range, 10–30 months) during which time 2 dogs had no additional episodes of aspiration pneumonia and 2 dogs had infrequent episodes of pneumonia, but aspiration was suspected to be a contributing factor in their death. Complications included clogging of the esophagostomy tube, esophagostomy site infections, and esophagitis.Conclusions and Clinical ImportanceUse of intermittent esophageal suctioning in dogs with megaesophagus that continue to regurgitate despite gastrostomy tube feedings can reduce or abolish clinical episodes of aspiration pneumonia.
Impacts into quartz sand: Crater formation, shock metamorphism, and ejecta distribution in laboratory experiments and numerical models
Authors: Wünnemann Kai , Zhu Meng‐Hua , Stöffler Dieter 
Published: August 2016

AbstractWe investigated the ejection mechanics by a complementary approach of cratering experiments, including the microscopic analysis of material sampled from these experiments, and 2‐D numerical modeling of vertical impacts. The study is based on cratering experiments in quartz sand targets performed at the NASA Ames Vertical Gun Range. In these experiments, the preimpact location in the target and the final position of ejecta was determined by using color‐coded sand and a catcher system for the ejecta. The results were compared with numerical simulations of the cratering and ejection process to validate the iSALE shock physics code. In turn the models provide further details on the ejection velocities and angles. We quantify the general assumption that ejecta thickness decreases with distance according to a power‐law and that the relative proportion of shocked material in the ejecta increase with distance. We distinguish three types of shock metamorphic particles (1) melt particles, (2) shock lithified aggregates, and (3) shock‐comminuted grains. The agreement between experiment and model was excellent, which provides confidence that the models can predict ejection angles, velocities, and the degree of shock loading of material expelled from a crater accurately if impact parameters such as impact velocity, impactor size, and gravity are varied beyond the experimental limitations. This study is relevant for a quantitative assessment of impact gardening on planetary surfaces and the evolution of regolith layers on atmosphereless bodies.
Possible Link Between Medical Students' Motivation for Academic Work and Time Engaged in Physical Exercise
Authors: Aung Myo Nyein , Somboonwong Juraiporn , Jaroonvanichkul Vorapol , Wannakrairot Pongsak 
Published: August 2016

ABSTRACTPhysical exercise results in an active well‐being. It is likely that students' engagement in physical exercise keeps them motivated to perform academic endeavors. This study aimed to assess the relation of time engaged in physical exercise with medical students' motivation for academic work. Prospectively, 296 second‐year medical students self‐administered Vallerand's Academic Motivation Scale. The frequency of exercise per week and the duration per time were multiplied to compute a weekly physical exercise engagement time. Multivariable regression model treated the intrinsic motivation construct as the dependent variable, adjusting relevant covariates such as sleeping time, sitting time, screen time, and vegetable intake. The level of intrinsic motivation was positively related to the student's physical exercise time per week (β 0.85, 95% confidence interval 0.42–1.26, p‐value < 0.001). Thus, generating conditions in which students can engage in physical exercise may contribute to fostering their intrinsic motivation for academic work.
The Neurocognitive Development of Episodic Prospection and Its Implications for Academic Achievement
Authors: Prabhakar Janani , Coughlin Christine , Ghetti Simona 
Published: August 2016

ABSTRACTEpisodic prospection is the ability to mentally simulate personal future events that are rich in contextual detail and plausible for the individual. It therefore incorporates episodic information (who, what, where, and when of a particular event), as well as details about one's self (e.g., knowledge, goals, motivations and desires). The ability to mentally simulate personal future events is thought to serve an adaptive purpose as it allows the individual to plan actions that align with his or her future goals and challenges. This review seeks to integrate research exploring how changes in episodic memory and self‐concept, and their associated neural mechanisms, contribute to the development of episodic prospection between childhood and adolescence. Elucidating the mechanisms contributing to this development is critical for understanding its potential influence on learning, goal achievement, and pedagogy between childhood and adolescence.
New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance
Authors: Decroocq Stéphane , Cornille Amandine , Tricon David , Babayeva Sevda , Chague Aurélie , Eyquard Jean‐Philippe , Karychev Raul , Dolgikh Svetlana , Kostritsyna Tatiana , Liu Shuo , Liu Weisheng , Geng Wenjuan , Liao Kang , Asma Bayram M. , Akparov Zeynal , Giraud Tatiana , Decroocq Véronique 
Published: August 2016

AbstractStudying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.
Differential influences of local subpopulations on regional diversity and differentiation for greater sage‐grouse (Centrocercus urophasianus)
Authors: Row Jeffrey R. , Oyler‐McCance Sara J. , Fedy Bradley C. 
Published: August 2016

AbstractThe distribution of spatial genetic variation across a region can shape evolutionary dynamics and impact population persistence. Local population dynamics and among‐population dispersal rates are strong drivers of this spatial genetic variation, yet for many species we lack a clear understanding of how these population processes interact in space to shape within‐species genetic variation. Here, we used extensive genetic and demographic data from 10 subpopulations of greater sage‐grouse to parameterize a simulated approximate Bayesian computation (ABC) model and (i) test for regional differences in population density and dispersal rates for greater sage‐grouse subpopulations in Wyoming, and (ii) quantify how these differences impact subpopulation regional influence on genetic variation. We found a close match between observed and simulated data under our parameterized model and strong variation in density and dispersal rates across Wyoming. Sensitivity analyses suggested that changes in dispersal (via landscape resistance) had a greater influence on regional differentiation, whereas changes in density had a greater influence on mean diversity across all subpopulations. Local subpopulations, however, varied in their regional influence on genetic variation. Decreases in the size and dispersal rates of central populations with low overall and net immigration (i.e. population sources) had the greatest negative impact on genetic variation. Overall, our results provide insight into the interactions among demography, dispersal and genetic variation and highlight the potential of ABC to disentangle the complexity of regional population dynamics and project the genetic impact of changing conditions.
Inbreeding effects on gene‐specific DNA methylation among tissues of Chinook salmon
Authors: Venney Clare J. , Johansson Mattias L. , Heath Daniel D. 
Published: August 2016

AbstractInbreeding depression is the loss of fitness resulting from the mating of genetically related individuals. Traditionally, the study of inbreeding depression focused on genetic effects, although recent research has identified DNA methylation as also having a role in inbreeding effects. Since inbreeding depression and DNA methylation change with age and environmental stress, DNA methylation is a likely candidate for the regulation of genes associated with inbreeding depression. Here, we use a targeted, multigene approach to assess methylation at 22 growth‐, metabolic‐, immune‐ and stress‐related genes. We developed PCR‐based DNA methylation assays to test the effects of intense inbreeding on intragenic gene‐specific methylation in inbred and outbred Chinook salmon. Inbred fish had altered methylation at three genes, CK‐1, GTIIBS and hsp70, suggesting that methylation changes associated with inbreeding depression are targeted to specific genes and are not whole‐genome effects. While we did not find a significant inbreeding by age interaction, we found that DNA methylation generally increases with age, although methylation decreased with age in five genes, CK‐1, IFN‐ɣ, HNRNPL, hsc71 and FSHb, potentially due to environmental context and sexual maturation. As expected, we found methylation patterns differed among tissue types, highlighting the need for careful selection of target tissue for methylation studies. This study provides insight into the role of epigenetic effects on ageing, environmental response and tissue function in Chinook salmon and shows that methylation is a targeted and regulated cellular process. We provide the first evidence of epigenetically based inbreeding depression in vertebrates.
Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution
Authors: Coelho Francisco J. R. C. , Cleary Daniel F. R. , Costa Rodrigo , Ferreira Marina , Polónia Ana R. M. , Silva Artur M. S. , Simões Mário M. Q. , Oliveira Vanessa , Gomes Newton C. M. 
Published: August 2016

AbstractThere is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)‐based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate‐reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH–oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH–oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH–oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH–oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k‐/r‐strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events.
Sex‐specific allelic transmission bias suggests sexual conflict at MC1R
Authors: Ducret Valérie , Gaigher Arnaud , Simon Céline , Goudet Jérôme , Roulin Alexandre 
Published: August 2016

AbstractSexual conflict arises when selection in one sex causes the displacement of the other sex from its phenotypic optimum, leading to an inevitable tension within the genome – called intralocus sexual conflict. Although the autosomal melanocortin‐1‐receptor gene (MC1R) can generate colour variation in sexually dichromatic species, most previous studies have not considered the possibility that MC1R may be subject to sexual conflict. In the barn owl (Tyto alba), the allele MC1RWHITE is associated with whitish plumage coloration, typical of males, and the allele MC1RRUFOUS is associated with dark rufous coloration, typical of females, although each sex can express any phenotype. Because each colour variant is adapted to specific environmental conditions, the allele MC1RWHITE may be more strongly selected in males and the allele MC1RRUFOUS in females. We therefore investigated whether MC1R genotypes are in excess or deficit in male and female fledglings compared with the expected Hardy–Weinberg proportions. Our results show an overall deficit of 7.5% in the proportion of heterozygotes in males and of 12.9% in females. In males, interannual variation in assortative pairing with respect to MC1R explained the year‐specific deviations from Hardy–Weinberg proportions, whereas in females, the deficit was better explained by the interannual variation in the probability of inheriting the MC1RWHITE or MC1RRUFOUS allele. Additionally, we observed that sons inherit the MC1RRUFOUS allele from their fathers on average slightly less often than expected under the first Mendelian law. Transmission ratio distortion may be adaptive in this sexually dichromatic species if males and females are, respectively, selected to display white and rufous plumages.
Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila
Authors: De Panis Diego N. , Padró Julián , Furió‐Tarí Pedro , Tarazona Sonia , Milla Carmona Pablo S. , Soto Ignacio M. , Dopazo Hernán , Conesa Ana , Hasson Esteban 
Published: August 2016

AbstractHigh‐throughput transcriptome studies are breaking new ground to investigate the responses that organisms deploy in alternative environments. Nevertheless, much remains to be understood about the genetic basis of host plant adaptation. Here, we investigate genome‐wide expression in the fly Drosophila buzzatii raised in different conditions. This species uses decaying tissues of cactus of the genus Opuntia as primary rearing substrate and secondarily, the necrotic tissues of the columnar cactus Trichocereus terscheckii. The latter constitutes a harmful host, rich in mescaline and other related phenylethylamine alkaloids. We assessed the transcriptomic responses of larvae reared in Opuntia sulphurea and T. terscheckii, with and without the addition of alkaloids extracted from the latter. Whole‐genome expression profiles were massively modulated by the rearing environment, mainly by the presence of T. terscheckii alkaloids. Differentially expressed genes were mainly related to detoxification, oxidation–reduction and stress response; however, we also found genes involved in development and neurobiological processes. In conclusion, our study contributes new data onto the role of transcriptional plasticity in response to alternative rearing environments.
Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species
Authors: Irwin Darren E. , Alcaide Miguel , Delmore Kira E. , Irwin Jessica H. , Owens Gregory L. 
Published: August 2016

AbstractRecent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 nucleotide sites along a new greenish warbler consensus genome assembly. Genomic regions of low within‐group variation are remarkably consistent between the three populations. These regions show high relative differentiation but low absolute differentiation between populations. Comparisons with outgroup species show the locations of these peaks of relative differentiation are not well explained by phylogenetically conserved variation in recombination rates or selection. These patterns are consistent with a model in which selection in an ancestral form has reduced variation at some parts of the genome, and those same regions experience recurrent selection that subsequently reduces variation within each subspecies. The degree of heterogeneity in nucleotide diversity is greater than explained by models of background selection, but is consistent with selective sweeps. Given the evidence that greenish warblers have had both population differentiation for a long period of time and periods of gene flow between those populations, we propose that some genomic regions underwent selective sweeps over a broad geographic area followed by within‐population selection‐induced reductions in variation. An important implication of this ‘sweep‐before‐differentiation’ model is that genomic regions of high relative differentiation may have moved among populations more recently than other genomic regions.
Population genomics reveals multiple drivers of population differentiation in a sex‐role‐reversed pipefish
Authors: Flanagan Sarah P. , Rose Emily , Jones Adam G. 
Published: August 2016

AbstractA major goal of molecular ecology is to identify the causes of genetic and phenotypic differentiation among populations. Population genomics is suitably poised to tackle these key questions by diagnosing the evolutionary mechanisms driving divergence in nature. Here, we set out to investigate the evolutionary processes underlying population differentiation in the Gulf pipefish, Syngnathus scovelli. We sampled approximately 50 fish from each of 12 populations distributed from the Gulf coast of Texas to the Atlantic coast of Florida and performed restriction‐site‐associated DNA sequencing to identify SNPs throughout the genome. After imposing quality and stringency filters, we selected a panel of 6348 SNPs present in all 12 populations, 1753 of which were not physically linked. We identified a genome‐wide pattern of isolation by distance, in addition to a more substantial genetic break separating populations in the Gulf of Mexico from those in the Atlantic. We also used several divergence outlier approaches and tests for genotype–environment correlations to identify 400 SNPs putatively involved in local adaptation. Patterns of phenotypic differentiation and variation diverged from the overall genomic pattern, suggesting that selection, phenotypic plasticity or demographic factors may be shaping phenotypes in distinct populations. Overall, our results suggest that population divergence is driven by a variety of factors in S. scovelli, including neutral processes and selection on multiple traits.