bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antisocial rewarding in structured populations
Authors: Santos Miguel dos , Peña Jorge 
Published: December 2016

ABSTRACTCooperation in collective action dilemmas usually breaks down in the absence of additional incentive mechanisms. This tragedy can be escaped if cooperators have the possibility to invest in reward funds that are shared exclusively among cooperators(prosocial rewarding). Yet, the presence of defectors who do not contribute to the public good but do reward themselves(antisocial rewarding) deters cooperation in the absence of additional countermeasures. A recent simulation study suggests that spatial structure is sufficient to prevent antisocial rewarding from deterring cooperation. Here we reinvestigate this issue assuming mixed strategies and weak selection on a game-theoretic model of social interactions, which we also validate using individual-based simulations. We show that increasing reward funds facilitates the maintenance of prosocial rewarding but prevents its evolution from rare, and that spatial structure can sometimes select against the evolution of prosocial rewarding. Our results suggest that, even in spatially structured populations, additional mechanisms are required to prevent antisocial rewarding from deterring cooperation in public goods dilemmas.
SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology
Authors: Petkau Aaron , Mabon Philip , Sieffert Cameron , Knox Natalie , Cabral Jennifer , Iskander Mariam , Iskander Mark , Weedmark Kelly , Zaheer Rahat , Katz Lee S. , Nadon Celine , Reimer Aleisha , Taboada Eduardo , Beiko Robert G. , Hsiao William , Brinkman Fiona , Graham Morag ,   the IRIDA Consortium, Van Domselaar Gary 
Published: December 2016

AbstractMotivationThe recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Transitioning the use of WGS data out of the research lab and into the front lines of surveillance and outbreak response requires user-friendly, reproducible, and scalable pipelines that have been well validated.ResultsSNVPhyl (Single Nucleotide Variant Phylogenomics) is a bioinformatics pipeline for identifying high-quality SNVs and constructing a whole genome phylogeny from a collection of WGS reads and a reference genome. Individual pipeline components are integrated into the Galaxy bioinformatics framework, enabling data analysis in a user-friendly, reproducible, and scalable environment. We show that SNVPhyl can detect SNVs with high sensitivity and specificity and identify and remove regions of high SNV density (indicative of recombination). SNVPhyl is able to correctly distinguish outbreak from non-outbreak isolates across a range of variant-calling settings, sequencing-coverage thresholds, or in the presence of contamination.AvailabilitySNVPhyl is available as a Galaxy workflow, Docker and virtual machine images, and a Unix-based command-line application. SNVPhyl is released under the Apache 2.0 license and available athttp://snvphyl.readthedocs.io/or athttps://github.com/phac-nml/snvphyl-galaxy.
Early survival and delayed death of developmentally-born dentate gyrus neurons
Authors: Cahill Shaina P. , Yu Ru Qi , Green Dylan , Todorova Evgenia V. , Snyder Jason S. 
Published: December 2016

ABSTRACTThe storage and persistence of memories depends on plasticity in the hippocampus. Adult neurogenesis produces new neurons that mature through critical periods for plasticity and cellular survival, which determine their contributions to learning and memory. However, most granule neurons are generated prior to adulthood; the maturational timecourse of these neurons is poorly understood compared to adult-born neurons, but is essential to identify how the dentate gyrus, as a whole, contributes to behavior. To characterize neurons born in the early postnatal period, we labeled dentate gyrus neurons born on postnatal day 6 (P6) with BrdU and quantified maturation and survival across early (1 hour to 8 weeks old) and late (2-6 months old) cell ages. We find that the dynamics of developmentally-born neuron survival is essentially the opposite of neurons born in adulthood: P6-born neurons did not go through a period of cell death during their immature stages (from 1-8 weeks). In contrast, 17% of P6-born neurons died after reaching maturity, between 2-6 months of age. Delayed death was evident from the loss of BrdU+cells as well as pyknotic BrdU+caspase3+neurons within the superficial granule cell layer. Patterns of DCX, NeuN and activity-dependent Fos expression indicate that developmentally-born neurons mature over several weeks and a sharp peak in zif268 expression at 2 weeks suggests that developmentally-born neurons mature faster than adult-born neurons (which peak at 3 weeks). Collectively, our findings are relevant for understanding how developmentally-born dentate gyrus neurons contribute to memory and disorders throughout the lifespan. High levels of early survival and zif268 expression may promote learning, while also rendering neurons sensitive to insults at defined stages. Late neuronal death in young adulthood may result in the loss of hundreds of thousands of dentate gyrus neurons, which could impact memory persistence and contribute to hippocampal/dentate gyrus atrophy in disorders such as depression.
Variability and stability of large-scale cortical oscillation patterns
Authors: Cox Roy , Schapiro Anna C , Stickgold Robert 
Published: December 2016

AbstractIndividual differences in brain organization exist at many spatial and temporal scales, contributing to the substantial heterogeneity underlying human thought and behavior. Oscillatory neural activity is crucial for these behaviors, but how such rhythms are expressed across the cortex within and across individuals has not been thoroughly characterized. Combining electroencephalography (EEG) with representational similarity and multivariate classification techniques, we provide a systematic characterization of brain-wide activity across frequency bands and oscillatory features during rest and task performance. Results indicate that oscillatory profiles exhibit sizable group-level correspondences, indicating the presence of common templates of oscillatory organization. At the same time, we observed well-defined subject-specific network profiles that were discernible above and beyond the structure shared across individuals. These individualized patterns were sufficiently stable over time to allow successful classification of individuals several months later. Finally, our findings indicate that the network structure of rhythmic activity varies considerably across distinct oscillatory frequencies and features, suggesting the existence of multiple, parallel information processing streams embedded in distributed electrophysiological activity. Together, these findings affirm the richness of spatiotemporal EEG signals and emphasize the utility of multivariate network analyses for understanding the role of brain oscillations in physiology and behavior.
Efficacy, safety and drug survival of conventional agents in pediatric psoriasis: A multicenter, cohort study
Authors: Ergun Tulin , Seckin Gencosmanoglu Dilek , Alpsoy Erkan , Bulbul‐Baskan Emel , Saricam Merve Hatun , Salman Andac , Onsun Nahide , Sarioz Abdullah 
Published: December 2016

AbstractThe data on long‐term efficacy, safety and drug survival rates of conventional systemic therapeutics in pediatric psoriasis is lacking. The primary aim of this study is to investigate acitretin, methotrexate, cyclosporin efficacy, safety and drug survival rates in pediatric patients as well as predictors of drug survival. This is a multicenter study including 289 pediatric cases being treated with acitretin, methotrexate and cyclosporin in four academic referral centers. Efficacy, adverse events, reasons for discontinuation, 1, 2‐ and 3‐year drug survival rates, and determinants of drug survival were analyzed. A 75% reduction of Psoriasis Area and Severity Index score or better response rate was obtained in 47.5%, 34.1% and 40% of the patients who were treated with acitretin, methotrexate and cyclosporin, respectively. One‐year drug survival rates for acitretin, methotrexate and cyclosporin were 36.3%, 21.1% and 15.1%, respectively. The most significant determinant of drug survival, which diminished over time, was treatment response whereas arthritis, body mass index and sex had no influence. Although all three medications are effective and relatively safe in children, drug survival rates are low due to safety concerns at this age group. Effective disease control through their rational use can be expected to improve survival rates.
Density‐dependent vulnerability of forest ecosystems to drought
Authors: Bottero Alessandra , D'Amato Anthony W. , Palik Brian J. , Bradford John B. , Fraver Shawn , Battaglia Mike A. , Asherin Lance A. 
Published: December 2016

Summary

Climate models predict increasing drought intensity and frequency for many regions, which may have negative consequences for tree recruitment, growth and mortality, as well as forest ecosystem services. Furthermore, practical strategies for minimizing vulnerability to drought are limited. Tree population density, a metric of tree abundance in a given area, is a primary driver of competitive intensity among trees, which influences tree growth and mortality. Manipulating tree population density may be a mechanism for moderating drought‐induced stress and growth reductions, although the relationship between tree population density and tree drought vulnerability remains poorly quantified, especially across climatic gradients.

In this study, we examined three long‐term forest ecosystem experiments in two widely distributed North American pine species, ponderosa pine Pinus ponderosa (Lawson & C. Lawson) and red pine Pinus resinosa (Aiton), to better elucidate the relationship between tree population density, growth and drought. These experiments span a broad latitude and aridity range and include tree population density treatments that have been purposefully maintained for several decades. We investigated how tree population density influenced resistance (growth during drought) and resilience (growth after drought compared to pre‐drought growth) of stand‐level growth during and after documented drought events.

Our results show that relative tree population density was negatively related to drought resistance and resilience, indicating that trees growing at lower densities were less vulnerable to drought. This result was apparent in all three forest ecosystems, and was consistent across species, stand age and drought intensity.

Synthesis and applications. Our results highlighted that managing pine forest ecosystems at low tree population density represents a promising adaptive strategy for reducing the adverse impacts of drought on forest growth in coming decades. Nonetheless, the broader applicability of our findings to other types of forest ecosystems merits additional investigation.
Impact of hunting along the migration corridor of pink‐footed geeseAnser brachyrhynchus– implications for sustainable harvest management
Authors: Clausen Kevin Kuhlmann , Christensen Thomas Kjær , Gundersen Ove Martin , Madsen Jesper 
Published: December 2016

SummaryHunting can potentially affect population size, age composition, sex‐ratio, behaviour and distribution of natural populations, and understanding its impacts is a prerequisite to manage quarry species sustainably. Harvest management relies strongly on the existence of both strictly regulated hunting efforts and efficient monitoring of populations, their demography and harvest. These conditions are rarely met in practice.For the Svalbard‐breeding population of the pink‐footed gooseAnser brachyrhynchus, an internationally coordinated adaptive harvest management framework enables a flyway‐based assessment of harvest impact. Based on 25 years of population assessment and harvest data, we evaluate the differential impact of harvest along the migration corridor of the population.The analysis reveals that (i) total harvest and harvest rate (proportion of the population killed by hunting) have increased substantially in recent years, (ii) compared to adult geese, juveniles were overrepresented in the hunting bag by a factor of 3·7, (iii) the proportion of juveniles in the hunting bag differed between the two countries (Norway and Denmark) with an open season, and was more than twice as high in the former compared to the latter, and (iv) the increase in harvest rate seemed to be driven by increased hunting mortality of juvenile birds, with no clear impact on the growth rate of the population. However, this may partly relate to the transient dynamics and population inertia commonly seen in long‐lived species such as geese, and a 3‐year consecutive decline towards the end of our study period might be the first signs of an impending decline.Synthesis and applications. Our findings highlight that the impact of harvest varies along the migration corridor and between age classes of a single species and suggest that allocation of hunting effort in time and space is important to optimise harvest. Our example demonstrates the need for internationally coordinated, detailed population and harvest data which are essential for sustainable harvest management.
Cats, connectivity and conservation: incorporating data sets and integrating scales for wildlife management
Authors: Pitman Ross T. , Fattebert Julien , Williams Samual T. , Williams Kathryn S. , Hill Russell A. , Hunter Luke T. B. , Robinson Hugh , Power John , Swanepoel Lourens , Slotow Rob , Balme Guy A. 
Published: December 2016

Summary

Understanding resource selection and quantifying habitat connectivity are fundamental to conservation planning for both land‐use and species management plans. However, data sets available to management authorities for resource selection and connectivity analyses are often highly limited and fragmentary. As a result, measuring connectivity is challenging, and often poorly integrated within conservation planning and wildlife management. To exacerbate the challenge, scale‐dependent resource use makes inference across scales problematic, resource use is often modelled in areas where the species is not present, and connectivity is typically measured using a source‐to‐sink approach, erroneously assuming animals possess predefined destinations.

Here, we used a large carnivore, the leopard Panthera pardus, to characterise resource use and landscape connectivity across a vast, biodiverse region of southern Africa. Using a range of data sets to counter data deficiencies inherent in carnivore management, we overcame methodological limitations by employing occupancy modelling and resource selection functions across three orders of selection, and estimated landscape‐scale habitat connectivity – independent of a priori source and sink locations – using circuit theory. We evaluated whether occupancy modelling on its own was capable of accurately informing habitat connectivity, and identified conservation priorities necessary for applied management.

We detected markedly different scale‐dependent relationships across all selection orders. Our multi‐data, multi‐scale approach accurately predicted resource use across multiple scales and demonstrates how management authorities can more suitably utilise fragmentary data sets. We further developed an unbiased landscape‐scale depiction of habitat connectivity, and identified key linkages in need of targeted management. We did not find support for the use of occupancy modelling as a proxy for landscape‐scale habitat connectivity and further caution its use within a management context.

Synthesis and applications. Maintaining habitat connectivity remains a fundamental component of wildlife management and conservation, yet data to inform these biological and ecological processes are often scarce. We present a robust approach that incorporates multi‐scale fragmentary data sets (e.g. mortality data, permit data, sightings data), routinely collected by management authorities, to inform wildlife management and land‐use planning. We recommend that management authorities employ a multi‐data, multi‐scale connectivity approach – as we present here – to identify management units at risk of low connectivity.
Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity
Authors: Coyotzi Sara , Doxey Andrew C. , Clark Ian D. , Lapen David R. , Van Cappellen Philippe , Neufeld Josh D. 
Published: December 2016

SummaryDenitrification transforms nitrogen applied as fertilizer and emits N2O, which is a potent greenhouse gas. Very little is known about the identities of abundant and active denitrifiers in agricultural soils. We coupled DNA stable‐isotope probing (DNA‐SIP) with flow‐through reactors (FTRs) to detect active agricultural soil denitrifiers. The FTRs were incubated with nitrate and 13C6‐glucose under anoxic conditions and sampled at multiple time points. Labelled DNA from active microorganisms was analyzed by 16S rRNA gene fingerprinting, amplicon and shotgun metagenomic sequencing. Taxonomic representation of heavy fractions was consistent across sites and time points, including Betaproteobacteria (71%; Janthinobacterium, Acidovorax, Azoarcus and Dechloromonas), Alphaproteobacteria (8%; Rhizobium), Gammaproteobacteria (4%; Pseudomonas) and Actinobacteria (4%; Streptomycetaceae). Most nitrite‐reductase reads from heavy DNA annotated to the copper‐containing form (nirK). Assigned taxonomies of active denitrifiers based on reads matching the nirK gene were comparable to those obtained through nitric oxide (norB) and RNA polymerase (rpoB) annotations but not the nitrous oxide reductase gene (nosZ). Analysis of recovered metagenomes from heavy DNA demonstrated extensive nirK sequence family diversity, including novel taxonomic groups that are not captured by existing primers.
The expression of Longus type 4 pilus of enterotoxigenic Escherichia coli is regulated by LngR and LngS and by H‐NS, CpxR and CRP global regulators
Authors: De la Cruz Miguel A. , Ruiz‐Tagle Alejandro , Ares Miguel A. , Pacheco Sabino , Yáñez Jorge A. , Cedillo Lilia , Torres Javier , Girón Jorge A. 
Published: December 2016

SummaryEnterotoxigenic Escherichia coli produces a long type 4 pilus called Longus. The regulatory elements and the environmental signals controlling the expression of Longus‐encoding genes are unknown. We identified two genes lngR and lngS in the Longus operon, whose predicted products share homology with transcriptional regulators. Isogenic lngR and lngS mutants were considerably affected in transcription of lngA pilin gene. The expression of lngA, lngR and lngS genes was optimally expressed at 37°C at pH 7.5. The presence of glucose and sodium chloride had a positive effect on Longus expression. The presence of divalent ions, particularly calcium, appears to be an important stimulus for Longus production. In addition, we studied H‐NS, CpxR and CRP global regulators, on Longus expression. The response regulator CpxR appears to function as a positive regulator of lng genes as the cpxR mutant showed reduced levels of lngRSA expression. In contrast, H‐NS and CRP function as negative regulators since expression of lngA was up‐regulated in isogenic hns and crp mutants. H‐NS and CRP were required for salt‐ and glucose‐mediated regulation of Longus. Our data suggest the existence of a complex regulatory network controlling Longus expression, involving both local and global regulators in response to different environmental signals.
The Political Limitations of Evidence: A Critique of the Electoral Reform Society's It's Good To Talk
Authors: Cunningham Michael 
Published: December 2016

AbstractThe Electoral Reform Society has called for more and better quality information to improve democratic debate in relation to referendums. This article argues that, particularly in relation to the European Union referendum, this would have had a marginal impact, because much of the debate was not reducible to facts and emotional and dispositional factors were of particular significance in the campaign.
Gallic acid improves endothelium‐dependent vasodilatory response to histamine in the mesenteric vascular bed of diabetic rats
Authors: Badavi Mohammad , Bazaz Amir , Dianat Mahin , Sarkaki Alireza 
Published: December 2016

AbstractBackgroundEndothelial dysfunction is one of the many complications caused by diabetes mellitus. The aim of the present study was to evaluate the effects of gallic acid (GA) on the mesenteric vascular bed (MVB) response to histamine in diabetic rats.MethodsForty male Wistar rats were randomly assigned to a control group, an untreated alloxan‐induced diabetic group and three diabetic groups treated with different doses of GA. Six weeks after induction of diabetes and GA treatment, total antioxidant capacity (TAC), malondialdehyde (MDA) concentrations, and the vasodilatory response to histamine of the MVB (measured as changes in perfusion pressure) were determined.ResultsThe vasodilatory response to histamine and TAC decreased, whereas MDA increased in the plasma from diabetic rats (P < 0.01). However, in the presence of 3 × 10−5 mol/L N

G
‐nitro‐l‐arginine methyl ester (a nitric oxide synthase inhibitor) and 1 × 10−5 mol/L indomethacin (an inhibitor of prostaglandin production), the vasodilatory response of the MVB to histamine was reduced in all groups (P < 0.001). Treatment of diabetic rats with 20 and 40 mg/kg per day GA, but not 10 mg/kg per day GA, increased TAC and decreased MDA concentrations (P < 0.01 and P < 0.001 vs untreated diabetic rats, respectively) and significantly improved the vasodilatory response to histamine (P < 0.05 and P < 0.001, respectively).ConclusionThe results show that, in diabetic rats, the endothelium‐dependent vasodilatory response of the MVB to histamine is significantly decreased and depends on both nitric oxide‐ and prostaglandin‐producing pathways and may be mediated by oxidative stress. Treatment with the antioxidant GA restored the vasodilatory response of the MVB to histamine.