bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterologous protection against Asian Zika virus challenge in rhesus macaques
Authors: Aliota Matthew T. , Dudley Dawn M. , Newman Christina M. , Mohr Emma L. , Gellerup Dane D. , Breitbach Meghan E. , Buechler Connor R. , Rasheed Mustafa N. , Mohns Mariel S. , Weiler Andrea M. , Barry Gabrielle L. , Weisgrau Kim L. , Eudailey Josh A. , Rakasz Eva G. , Vosler Logan J. , Post Jennifer , Capuano Saverio , Golos Thaddeus G. , Anthony Moody M. , Permar Sallie R. , Osorio Jorge E. , Friedrich Thomas C. , O’Connor Shelby L. , O’Connor David H. 
Published: June 2016

SummaryZika virus (ZIKV) isolates are genetically diverse, but belong to two recognized lineages, termed “African” and “Asian.” Asian ZIKV infection during pregnancy causes fetal abnormalities including microcephaly. Developing an effective preventative Zika virus vaccine that protects pregnant women is essential for minimizing fetal abnormalities; at least 18 groups are developing ZIKV vaccines (Hayden, 2016). The genetic and antigenic variability of many RNA viruses limits the effectiveness of vaccines, and the degree to which immunity against one ZIKV strain could provide protection against another is unknown. Here we show that rhesus macaques infected with East African ZIKV strain MR766 are completely protected from subsequent infection with heterologous Asian ZIKV. MR766 is more genetically divergent from all known Asian ZIKV strains than Asian ZIKV strains are from one another. Therefore, ZIKV strain selection is unlikely to compromise vaccine effectiveness.HighlightsAfrican Zika virus (ZIKV) strain MR766 productively infects macaques (68 characters)Immunity elicited by MR766 protects macaques against heterologous Asian ZIKV (77 characters)In vivo restoration of a putative N-linked glycosylation site in MR766 (70 characters)Immunogen selection is unlikely to adversely affect the breadth of vaccine protection (85 characters)eTOCAn effective Zika virus vaccine is needed to prevent infection-associated fetal abnormalities. Macaques whose immune responses are primed by infection with East African ZIKV are completely protected from reinfection with heterologous Asian ZIKV. Any Asian ZIKV immunogen that protects against homologous challenge will likely confer protection against all other Asian ZIKV strains.
Biodiversity as insurance for sapling survival in experimental tree plantations
Authors: Van de Peer Thomas , Verheyen Kris , Baeten Lander , Ponette Quentin , Muys Bart 
Published: June 2016

Summary

Biodiversity can insure ecosystems against declines in their functioning by increasing the mean level of ecosystem processes and decreasing the spatial or temporal variance of these processes. On this basis, mixing tree species is expected to be an effective management strategy to reduce the risk of planting failure in young plantations.

We examined the effects of biodiversity insurance on sapling survival in three tree diversity experiments across Belgium. Based on the survival scoring of 89 254 saplings, planted in 126 plots with up to four‐species mixtures, we tested two hypotheses: (i) variability in plot‐level survival is lower for mixtures compared to monocultures due to compensation among the species (i.e. buffering effect) and (ii) mean survival is higher due to facilitation (i.e. performance‐enhancing effect).

Variation in plot‐level survival decreased strongly with diversity, indicating a buffering effect. The risk of severe planting failure was reduced in mixtures because species exhibit different survival rates; therefore, mixing ensures that not all trees in the plantation are equally susceptible to environmental stressors. In contrast, the mean plot‐level survival did not increase with diversity, and thus, an overall performance‐enhancing effect was lacking. However, species‐level analyses did show performance‐enhancing effects, where some species profited from mixing while others did not.

Synthesis and applications. We conclude that biodiversity through mixing tree species insures young experimental plantations against planting failure and is therefore highly recommended as a planting management strategy. The risk of large mortality gaps is reduced if tree plantation saplings are mixed at the scale of individual trees or small cells of trees.
Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail
Authors: Fournier Auriel M. V. , Sullivan Alexis R. , Bump Joseph K. , Perkins Marie , Shieldcastle Mark C. , King Sammy L. 
Published: June 2016

Summary

Stable hydrogen isotope (δD) methods for tracking animal movement are widely used yet often produce low resolution assignments. Incorporating prior knowledge of abundance, distribution or movement patterns can ameliorate this limitation, but data are lacking for most species. We demonstrate how observations reported by citizen scientists can be used to develop robust estimates of species distributions and to constrain δD assignments.

We developed a Bayesian framework to refine isotopic estimates of migrant animal origins conditional on species distribution models constructed from citizen scientist observations. To illustrate this approach, we analysed the migratory connectivity of the Virginia rail Rallus limicola, a secretive and declining migratory game bird in North America.

Citizen science observations enabled both estimation of sampling bias and construction of bias‐corrected species distribution models. Conditioning δD assignments on these species distribution models yielded comparably high‐resolution assignments.

Most Virginia rails wintering across five Gulf Coast sites spent the previous summer near the Great Lakes, although a considerable minority originated from the Chesapeake Bay watershed or Prairie Pothole region of North Dakota. Conversely, the majority of migrating Virginia rails from a site in the Great Lakes most likely spent the previous winter on the Gulf Coast between Texas and Louisiana.

Synthesis and applications. In this analysis, Virginia rail migratory connectivity does not fully correspond to the administrative flyways used to manage migratory birds. This example demonstrates that with the increasing availability of citizen science data to create species distribution models, our framework can produce high‐resolution estimates of migratory connectivity for many animals, including cryptic species. Empirical evidence of links between seasonal habitats will help enable effective habitat management, hunting quotas and population monitoring and also highlight critical knowledge gaps.
Genome‐centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion
Authors: Vanwonterghem Inka , Jensen Paul D. , Rabaey Korneel , Tyson Gene W. 
Published: June 2016

SummaryOur understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome‐centric metagenomic analysis was performed of lab‐scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near‐complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome‐centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities.
Feeding on compatible solutes: A substrate‐induced pathway for uptake and catabolism of ectoines and its genetic control by EnuR
Authors: Schulz Annina , Stöveken Nadine , Binzen Ina M. , Hoffmann Tamara , Heider Johann , Bremer Erhard 
Published: June 2016

SummaryEctoine and 5‐hydroxyectoine are widely synthesized microbial osmostress protectants. They are also versatile nutrients but their catabolism and the genetic regulation of the corresponding genes are incompletely understood. Using the marine bacterium Ruegeria pomeroyi DSS‐3, we investigated the utilization of ectoines and propose a seven steps comprising catabolic route that entails an initial conversion of 5‐hydroxyectoine to ectoine, the opening of the ectoine ring, and the subsequent degradation of this intermediate to l‐aspartate. The catabolic genes are co‐transcribed with three genes encoding a 5‐hydroxyectoine/ectoine‐specific TRAP transporter. A chromosomal deletion of this entire gene cluster abolishes the utilization of ectoines as carbon and nitrogen sources. The presence of ectoines in the growth medium triggers enhanced expression of the importer and catabolic operon, a process dependent on a substrate‐inducible promoter that precedes this gene cluster. EnuR, a member of the MocR/GabR‐type transcriptional regulators, controls the activity of this promoter and functions as a repressor. EnuR contains a covalently bound pyridoxal‐5’‐phosphate, and we suggest that this co‐factor is critical for the substrate‐mediated induction of the 5‐hydroxyectoine/ectoine import and catabolic genes. Bioinformatics showed that ectoine consumers are restricted to the Proteobacteria and that EnuR is likely a central regulator for most ectoine/5‐hydroxyectoine catabolic genes.
Fetal sex and maternal risk of pre‐eclampsia/eclampsia: a systematic review and meta‐analysis
Authors: Jaskolka D , Retnakaran R , Zinman B , Kramer CK 
Published: June 2016

BackgroundA preponderance of male fetuses in pregnancies complicated by pre‐eclampsia was described over 40 years ago. Since then, however, there has been conflicting evidence in the literature, with some studies supporting a male preponderance, some demonstrating no relationship with fetal sex, and others reporting increased risk in pregnancies bearing females.ObjectivesIn this context, we sought to conduct a systematic review and meta‐analysis to objectively evaluate the relationship between fetal sex and maternal risk of pre‐eclampsia/eclampsia.Search strategyStudies from January 1950 to April 2015 were identified from PUBMED and EMBASE.Selection criteriaThis systematic review and meta‐analysis evaluated 22 articles reporting data on fetal sex and prevalence of pre‐eclampsia/eclampsia.Data collection and analysisData were extracted by two independent reviewers. Pooled estimates of the relative risk (RR) were calculated by random‐effects model.Main resultsMale fetus was considered the exposure and prevalence of maternal pre‐eclampsia/eclampsia was the outcome of interest. We identified 534 studies through electronic searches and three studies through manual searches. Twenty‐two studies fulfilled the inclusion criteria, yielding data on 3 163 735 women. Pooled analyses of these studies showed no association between male fetal sex and maternal risk of pre‐eclampsia/eclampsia (RR 1.01; 95% confidence interval, 95% CI 0.97–1.05); however, a subgroup analysis including only studies that evaluated the non‐Asian population (n = 2 931 771 women) demonstrated that male fetal sex was associated with increased maternal risk of pre‐eclampsia/eclampsia (RR 1.05; 95% CI 1.03–1.06; I2 = 10%; P = 0.33).ConclusionMale fetal sex is associated with maternal risk of pre‐eclampsia/eclampsia in the non‐Asian population.Tweetable abstractFetal sex is associated with maternal risk of pre‐eclampsia/eclampsia in the non‐Asian population.
Relationship between biodiversity and landscape structure in the Gyungan stream basin, central Korea
Authors: Lim Chi Hong , Kim Gyung Soon , An Ji Hong , You Byung Ho , Bae Yang Seop , Byun Hwa Geun , Lee Chang Seok 
Published: June 2016

AbstractThe relationship between landscape structure and biodiversity was investigated in the Gyungan stream basin, central Korea, in order to prepare a biodiversity conservation plan. The study area was divided into upstream, midstream, downstream and Gonjiam stream sub‐watersheds based on the land use pattern of each sub‐watershed. The quality of the terrestrial landscape was assessed by connectivity and percentages of deciduous broad‐leaved forest and urbanized area. The quality of the terrestrial landscape was the highest in the downstream sub‐watershed followed by Gonjiam stream, midstream and upstream sub‐watersheds. The quality of the riparian landscape assessed by percentages of the number and the area that the wetland vegetation elements occupy in the whole area showed a similar trend to that of terrestrial landscape. The diversity of all taxa including fish, reptiles and amphibians, birds, mammals and wetland vegetation except benthic macroinvertebrates was the highest downstream. The diversity of benthic macroinvertebrates was the highest in the Gonjiam stream sub‐watershed. Thus, biodiversity was shown to be the highest in the downstream sub‐watershed, followed, in order, by Gonjiam stream, midstream and upstream sub‐watersheds in proportion to landscape quality. On the other hand, the quality of the aquatic environment based on the ecological score of benthic macroinvertebrate (ESB) index was the highest downstream, followed, in order, by upstream, Gonjiam stream and midstream areas. This trend is different from that of biodiversity. In order to improve landscape quality degraded by excessive land use and to increase biodiversity, we recommended a restoration plan that addresses both ecosystem and landscape.
The Effect of Joint Auditor Pair Composition on Audit Quality: Evidence from Impairment Tests
Authors: Lobo Gerald J. , Paugam Luc , Zhang Dana , Casta Jean François 
Published: June 2016

AbstractUsing a sample of firms from France, where the law requires the use of two auditors, we study the effect of auditor pair composition on audit quality by examining a specific account, goodwill impairment. We document that firms audited by a Big 4–non‐Big 4 auditor pair (BS) are more likely to book an impairment and book a larger impairment than firms audited by a Big 4–Big 4 auditor pair (BB) when low‐performance indicators suggest a greater likelihood of impairment. Moreover, firms audited by a BB pair reduce impairment disclosures when they book impairments, while firms audited by a BS pair do not, suggesting lower transparency for firms audited by a BB pair. Our results inform investors and firms in mandatory joint audit regimes, as well as regulators who are considering requiring joint audits.
Detecting evolutionarily significant units above the species level using the generalised mixed Yule coalescent method
Authors: Humphreys Aelys M. , Rydin Catarina , Jønsson Knud A. , Alsop David , Callender‐Crowe Leah M. , Barraclough Timothy G. 
Published: June 2016

Summary

There is renewed interest in inferring evolutionary history by modelling diversification rates using phylogenies. Understanding the performance of the methods used under different scenarios is essential for assessing empirical results. Recently, we introduced a new approach for analysing broadscale diversity patterns, using the generalised mixed Yule coalescent (GMYC) method to test for the existence of evolutionarily significant units above the species (higher ESUs). This approach focuses on identifying clades as well as estimating rates, and we refer to it as clade‐dependent. However, the ability of the GMYC to detect the phylogenetic signature of higher ESUs has not been fully explored, nor has it been placed in the context of other, clade‐independent approaches.

We simulated >32 000 trees under two clade‐independent models: constant‐rate birth‐death (CRBD) and variable‐rate birth‐death (VRBD), using parameter estimates from nine empirical trees and more general parameter values. The simulated trees were used to evaluate scenarios under which GMYC might incorrectly detect the presence of higher ESUs.

The GMYC null model was rejected at a high rate on CRBD‐simulated trees. This would lead to spurious inference of higher ESUs. However, the support for the GMYC model was significantly greater in most of the empirical clades than expected under a CRBD process. Simulations with empirically derived parameter values could therefore be used to exclude CRBD as an explanation for diversification patterns. In contrast, a VRBD process could not be ruled out as an alternative explanation for the apparent signature of hESUs in the empirical clades, based on the GMYC method alone. Other metrics of tree shape, however, differed notably between the empirical and VRBD‐simulated trees. These metrics could be used in future to distinguish clade‐dependent and clade‐independent models.

In conclusion, detection of higher ESUs using the GMYC is robust against some clade‐independent models, as long as simulations are used to evaluate these alternatives, but not against others. The differences between clade‐dependent and clade‐independent processes are biologically interesting, but most current models focus on the latter. We advocate more research into clade‐dependent models for broad diversity patterns.
Evaluation of statistical methods and sampling designs for the assessment of microhabitat selection based on point data
Authors: Gorosito Irene L. , Marziali Bermúdez Mariano , Douglass Richard J. , Busch María 
Published: June 2016

Summary

Information on resource selection by a species is essential for understanding the species’ ecology, distribution and requirements for survival. Research on habitat selection frequently relies on animal detection at point locations to determine which resource units are used. A variety of approaches and statistical tools can be employed for assessing selection based on habitat variables measured in those units. The aim of this work was to evaluate the reliability of common sampling designs and statistical methods in detecting habitat selection at fine scales based on point data

We reviewed literature on microhabitat selection to determine characteristics of typical studies and analysed simulated small‐mammal live‐trapping data as a case study. We considered various scenarios differing in the number of sampled units and sampling duration. For each scenario, a set of simulated surveys was analysed through two univariate tests (Welch's t‐ and Mann–Whitney U‐test), generalized linear models (GLMs), mixed‐effect models (GLMMs) and occupancy models (OMs).

Analysis of simulated data revealed that overall performance of all statistical methods improved with increased trapping effort. Univariate tests were especially sensitive to the number of sampling units, while modelling methods took also advantage of longer trapping sessions. Univariate tests and GLMs provided partially correct information in most cases, whereas GLMMs and OMs offered higher probabilities of fully describing simulated habitat preferences.

With typical sampling efforts, appropriate statistical analysis of point data is able to provide a moderately accurate description of habitat selection at small scales, in spite of the violation of closure and independence assumptions of applied models. Modelling approaches are proliferating; we encourage using models that can deal with multiple sources of variability, such as GLMMs and OMs, when data are hierarchically structured. There is no a priori best survey design; it should be chosen according to the scope and goals of the study, environment heterogeneity, species characteristics and practical constraints. Researchers should realize that sampling design and statistical methods likely affect conclusions regarding habitat selection.
Triplet MaxCut: a new toolkit for rooted supertree
Authors: Sevillya Gur , Frenkel Zeev , Snir Sagi 
Published: June 2016

Summary

The rapid increase of molecular, as well as other types, of available classification data has created the need to combine this data into a unified hypothesis.

Supertree methods are essential when amalgamating phylogenetic information from various, possibly conflicting, sources into a single tree. The goal of a supertree algorithm is to satisfy maximally each such source of information in the output tree.

Triplets, rooted trees over three leaves, are the minimal piece of such information when dealing with rooted trees. Due to its fundamental role in phylogenetics, extensive effort has been dedicated to several aspects regarding triplets’ research.

We have devised a new tool, Triplet MaxCut (TMC), performing various operations in rooted supertree, principally amalgamating rooted trees based on amalgamating rooted triplets. The utility and efficiency of the algorithm is demonstrated by both simulation study and four real data supertree inputs.
Selection biases in observational studies affect associations between ‘moderate’ alcohol consumption and mortality
Authors: Naimi Timothy S. , Stockwell Timothy , Zhao Jinhui , Xuan Ziming , Dangardt Frida , Saitz Rich , Liang Wenbin , Chikritzhs Tanya 
Published: June 2016

AbstractSelection biases may lead to systematic overestimate of protective effects from ‘moderate’ alcohol consumption. Overall, most sources of selection bias favor low‐volume drinkers in relation to non‐drinkers. Studies that attempt to address these types of bias generally find attenuated or non‐significant relationships between low‐volume alcohol consumption and cardiovascular disease, which is the major source of possible protective effects on mortality from low‐volume consumption. Furthermore, observed mortality effects among established low‐volume consumers are of limited relevance to health‐related decisions about whether to initiate consumption or to continue drinking purposefully into old age. Short of randomized trials with mortality end‐points, there are a number of approaches that can minimize selection bias involving low‐volume alcohol consumption.