bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial and temporal control of norovirus protease activity is determined by polyprotein processing and intermolecular interactions within the viral replication complex
Authors: Emmott Edward , de Rougemont Alexis , Haas Jürgen , Goodfellow Ian 
Published: August 2017

AbstractNorovirus infections are a major cause of acute viral gastroenteritis and a significant burden to human health globally. A vital process for norovirus replication is the processing of the nonstructural polyprotein, by an internal protease, into the necessary viral components required to form the viral replication complex. This cleavage occurs at different rates resulting in the accumulation of stable precursor forms. In this report, we characterized how precursor forms of the norovirus protease accumulate during infection. Using stable forms of the protease precursors we demonstrated that these are all proteolytically activein vitro, but that when expressed in cells, activity is determined by both substrate and protease localization. Whilst all precursors could cleave a replication complex-associated substrate, only a subset of precursors lacking NS4 were capable of efficiently cleaving a cytoplasmic substrate. For the first time, the full range of protein-protein interactions between murine and human norovirus proteins were mapped by LUMIER assay, with conserved interactions between replication complex members, modifying the localization of a subset of precursors. Finally, we demonstrate that re-targeting of a poorly cleaved artificial cytoplasmic substrate to the replication complex is sufficient to permit efficient cleavage in the context of norovirus infection. This offers a model for how norovirus can regulate the timing of substrate cleavage throughout the replication cycle. The norovirus protease represents a key target in the search for effective antiviral treatments for norovirus infection. An improved understanding of protease function and regulation, as well as identification of interactions between the other non-structural proteins, offers new avenues for antiviral drug design.
Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat
Authors: Brinton Jemima , Simmonds James , Uauy Cristobal 
Published: August 2017

AbstractBackgroundThere is an urgent need to increase global crop production. Identifying and combining genes controlling indidviual yield components, such as grain weight, holds the potential to enhance crop yields. Transcriptomics is a powerful tool to gain insights into the complex gene regulatory networks that underlie such traits, but relies on the availability of a high-quality reference sequence and accurate gene models. Previously, we identified a grain weight QTL on wheat chromosome 5A (5A QTL) which acts during early grain development to increase grain length through cell expansion in the pericarp. In this study, we performed RNA-sequencing on near isogenic lines (NILs) segregating for the 5A QTL and used the latest gene models to identify differentially expressed (DE) genes and pathways that potentially influence pericarp cell size and grain weight in wheat.ResultsWe sampled grains at four and eight days post anthesis and found genes associated with metabolism, biosynthesis, proteoloysis and defence response to be upregulated during this stage of grain development in both NILs. We identified a specific set of 112 transcripts DE between 5A NILs at either time point, including seven potential candidates for the causal gene underlying the 5A QTL. The 112 DE transcripts had functional annotations including non-coding RNA, transpon-associated, cell-cycle control, and ubiquitin-related processes. Many of the wheat genes identified belong to families that have been previously associated with seed/grain development in other species. However, few of these wheat genes are the direct orthologs and none have been previously characterised in wheat. Notably, we identified DE transcripts at almost all steps of the pathway associated with ubiquitin-mediated protein degradation. In the promoters of a subset of DE transcripts we identified enrichment of binding sites associated with C2H2, MYB/SANT, YABBY, AT HOOK and Trihelix transcription factor families.ConclusionsIn this study, we identified DE transcripts with a diverse range of predicted biological functions, reflecting the complex nature of the pathways that control early grain development. Further functional characterisation of these candidates and how they interact could provide new insights into the control of grain size in cereals, ultimately improving crop yield.
Family-based association analysis identifies variance-controlling loci without confounding by genotype-environment correlations
Authors: Conley Dalton , Johnson Rebecca , Domingue Ben , Dawes Christopher , Boardman Jason , Siegal Mark 
Published: August 2017

AbstractThe propensity of a trait to vary within a population may have evolutionary, ecological, or clinical significance. In the present study we deploy sibling models to offer a novel and unbiased way to ascertain loci associated with the extent to which phenotypes vary (variance-controlling quantitative trait loci, or vQTLs). Previous methods for vQTL-mapping either exclude genetically related individuals or treat genetic relatedness among individuals as a complicating factor addressed by adjusting estimates for non-independence in phenotypes. The present method uses genetic relatedness as a tool to obtain unbiased estimates of variance effects rather than as a nuisance. The family-based approach, which utilizes random variation between siblings in minor allele counts at a locus, also allows controls for parental genotype, mean effects, and non-linear (dominance) effects that may spuriously appear to generate variation.Simulations show that the approach performs equally well as two existing methods (squared Z-score and DGLM) in controlling type I error rates when there is no unobserved confounding, and performs significantly better than these methods in the presence of confounding. Using height and BMI as empirical applications, we investigate SNPs that alter within-family variation in height and BMI, as well as pathways that appear to be enriched. One significant SNP for BMI variability, in the MAST4 gene, replicated. Pathway analysis revealed one gene set, encoding members of several signaling pathways related to gap junction function, which appears significantly enriched for associations with within-family height variation in both datasets (while not enriched in analysis of mean levels). We recommend approximating laboratory random assignment of genotype using family data and more careful attention to the possible conflation of mean and variance effects.
Persisting in defaunated landscapes: Reduced plant population connectivity after seed dispersal collapse
Authors: Pérez‐Méndez Néstor , Jordano Pedro , Valido Alfredo 
Published: August 2017

Abstract

Defaunation of large‐bodied frugivores could be causing severe losses of crucial ecosystem functions such as seed dispersal. The immediate ecological consequences may include alteration or even collapse of seed‐mediated gene flow affecting plant population connectivity, with impacts on the regional scale distribution of genetic variation. Yet, these far‐reaching consequences of defaunation remain understudied.

Here, we tested whether human‐induced defaunation of the Canarian frugivorous lizards (Gallotia, Lacertidae) altered within‐island population connectivity and the amount and large‐scale distribution of genetic variation of Neochamaelea pulverulenta (Rutaceae), which relies exclusively on these lizards for seed dispersal. Our study system defines a lizard downsizing gradient with three contrasted ecological scenarios (islands) with relatively optimal (Gran Canaria; large‐sized lizards), suboptimal (Tenerife; medium) and collapsed seed dispersal processes (La Gomera; small). We extensively sampled individual plant genotypes from 80 populations spanning the full geographical range of the plant to examine their genetic diversity, population‐genetic network topologies, and the patterns of isolation both by distance (IBD) and resistance (IBR) across these three ecological scenarios.

Plant genetic diversity appeared unaffected by defaunation‐mediated downsizing of frugivorous lizards. However, we found a reduced overall plant population connectivity together with an increased isolation by distance within the most defaunated islands (La Gomera and, to a lesser extent, Tenerife) when compared with the scenario preserving the functionality of lizard‐mediated seed dispersal (Gran Canaria). The results, with a significant effect of lizard downsizing, were robust when controlling for biotic/abiotic differences among the three islands by means of isolation by resistance models (IBR).

Synthesis. Our results provide valuable insights into the far‐reaching consequences of the deterioration of mutualisms on plant population dynamics over very large spatial scales. Conservation of large‐bodied frugivores is, thus, essential because their irreplaceable mutualistic dispersal services maintain an extensive movement of seeds across the landscape, crucial for maintaining the genetic cohesiveness of metapopulations and the adaptive potential of plant species across their entire geographical range.
Environmental Hazards and Mortgage Credit Risk: Evidence from Texas Pipeline Incidents
Authors: Xu Minhong , Xu Yilan 
Published: August 2017

AbstractThis study examines the effects of pipeline hazards on credit risk using evidence from the 2005–2011 home mortgage loans in Texas. Difference‐in‐difference analyses show a permanently lower origination rate by 1.9% in the pipeline‐present areas compared to the pipeline‐free areas, which was further enlarged by 1.8% whenever pipeline incidents happened. Evidence suggests that the permanent difference in credit access reflects lenders’ concerns about collateral value and borrowers’ repayment ability. The elevated post‐incident risk perceptions indicate lenders’ aversion to environmental liabilities. Lenders’ risk management strategies differed by borrowers’ income and evolved with the tightening of the securitization market.
Imperfect pathogen detection from non‐invasive skin swabs biases disease inference
Authors: DiRenzo Graziella V. , Campbell Grant Evan H. , Longo Ana V. , Che‐Castaldo Christian , Zamudio Kelly R. , Lips Karen R. 
Published: August 2017

Abstract

Conservation managers rely on accurate estimates of disease parameters, such as pathogen prevalence and infection intensity, to assess disease status of a host population. However, these disease metrics may be biased if low‐level infection intensities are missed by sampling methods or laboratory diagnostic tests. These false negatives underestimate pathogen prevalence and overestimate mean infection intensity of infected individuals.

Our objectives were two‐fold. First, we quantified false negative error rates of Batrachochytrium dendrobatidis (Bd) on non‐invasive skin swabs collected from an amphibian community in El Copé, Panama. We swabbed amphibians twice in sequence, and we used a recently developed hierarchical Bayesian estimator to assess disease status of the population. Second, we developed a novel hierarchical Bayesian model to simultaneously account for imperfect pathogen detection from field sampling and laboratory diagnostic testing. We evaluated the performance of the model, using simulations and varying sampling design to quantify the magnitude of bias in estimates of pathogen prevalence and infection intensity.

We show that Bd detection probability from skin swabs was related to host infection intensity, where Bd infections <10 zoospores have <95% probability of being detected. If imperfect Bd detection was not considered, then Bd prevalence was underestimated by as much as 71%. In the Bd‐amphibian system, this indicates a need to correct for imperfect pathogen detection in enzootic host populations persisting with low‐level infections. More generally, our results have implications for study designs in other disease systems, particularly those with similar objectives, biology, and sampling decisions.

Uncertainty in pathogen detection is an inherent property of most sampling protocols and diagnostic tests, where the magnitude of bias depends on the study system, type of infection, and false negative error rates. Given that it may be difficult to know this information in advance, we advocate that the most cautious approach is to assume all errors are possible and to accommodate them by adjusting sampling designs. The modelling framework presented here improves the accuracy in estimating pathogen prevalence and infection intensity.
Environmental factors affecting the distribution of African elephants in the Kasigau wildlife corridor, SE Kenya
Authors: Williams Harry F. , Bartholomew David C. , Amakobe Bernard , Githiru Mwangi 
Published: August 2017

AbstractThe African elephant, Loxodonta africana, is under threat from habitat loss, poaching and human–elephant conflict. To mitigate for impact of habitat loss and reduce conflict, connectivity between elephant habitats can be improved through the protection of corridor areas. This study looks at elephant distribution and movement patterns within the Kasigau Wildlife Corridor (KWC) within the Tsavo Conservation Area in South‐east Kenya. Elephant presence data were obtained from observations by rangers during routine patrols across KWC, and were analysed in MaxEnt. The environmental factors predicting elephant distribution and density were tested, as well as the relationship between elephant maximum entropy and the presence and abundance of other wildlife. Seasonal variations in temperature and precipitation, plus presence of waterholes were found to play significant roles in elephant distribution across KWC. Higher elephant densities were not found to correlate with lower densities of other wildlife species; indeed, during the dry seasons, elephant presence was associated with greater wild herbivore densities. Besides illustrating the importance of the KWC for elephant conservation in the Tsavo ecosystem, both as a key corridor and habitat, this study also hopes to highlight the untapped utility of routine ranger patrol data, and encourage the use of such presence‐only data for deducing important knowledge for conservation of biodiversity.
Mindfulness of voices, self‐compassion, and secure attachment in relation to the experience of hearing voices
Authors: Dudley James , Eames Catrin , Mulligan John , Fisher Naomi 
Published: August 2017

ObjectivesDeveloping compassion towards oneself has been linked to improvement in many areas of psychological well‐being, including psychosis. Furthermore, developing a non‐judgemental, accepting way of relating to voices is associated with lower levels of distress for people who hear voices. These factors have also been associated with secure attachment. This study explores associations between the constructs of mindfulness of voices, self‐compassion, and distress from hearing voices and how secure attachment style related to each of these variables.DesignCross‐sectional online.MethodOne hundred and twenty‐eight people (73% female; Mage = 37.5; 87.5% Caucasian) who currently hear voices completed the Self‐Compassion Scale, Southampton Mindfulness of Voices Questionnaire, Relationships Questionnaire, and Hamilton Programme for Schizophrenia Voices Questionnaire.ResultsResults showed that mindfulness of voices mediated the relationship between self‐compassion and severity of voices, and self‐compassion mediated the relationship between mindfulness of voices and severity of voices. Self‐compassion and mindfulness of voices were significantly positively correlated with each other and negatively correlated with distress and severity of voices.ConclusionMindful relation to voices and self‐compassion are associated with reduced distress and severity of voices, which supports the proposed potential benefits of mindful relating to voices and self‐compassion as therapeutic skills for people experiencing distress by voice hearing.Practitioner points

Greater self‐compassion and mindfulness of voices were significantly associated with less distress from voices. These findings support theory underlining compassionate mind training.

Mindfulness of voices mediated the relationship between self‐compassion and distress from voices, indicating a synergistic relationship between the constructs.

Although the current findings do not give a direction of causation, consideration is given to the potential impact of mindful and compassionate approaches to voices.
The relationship between learning mathematics and general cognitive ability in primary school
Authors: Cowan Richard , Hurry Jane , Midouhas Emily 
Published: August 2017

Three relationships between learning mathematics and general cognitive ability have been hypothesized: The educational hypothesis that learning mathematics develops general cognitive skills, the psychometric hypothesis that differences in general cognitive ability cause differences in mathematical attainment, and the reciprocal influence hypothesis that developments in mathematical ability and general cognitive ability influence each other. These hypotheses are assessed with a sample of 948 children from the Twins Early Development Study who were assessed at 7, 9, and 10 years on mathematics, English, and general cognitive ability. A cross‐lagged path analysis with mathematics and general cognitive ability measures supports the reciprocal influence hypothesis between 7 and 9 and between 9 and 10. A second analysis including English assessments only provides evidence of a reciprocal relationship between 7 and 9.
Statement of Contribution

What is already known on this subject?

The correlations between mathematical attainment, literacy, and measures of general cognitive skills are well established.

The role of literacy in developing general cognitive skills is emerging.

What the present study adds?

Mathematics contributes to the development of general cognitive skills.

General cognitive ability contributes to mathematical development between 7 and 10.

These findings support the hypothesis of reciprocal influence between mathematics and general cognitive ability, at least between 7 and 9.
Anesthetic management for intestinal transplantation: A decade of experience
Authors: Zerillo Jeron , Kim Sang , Hill Bryan , Shapiro David , Lin Hung‐Mo , Burnham Alyssa , Moon Jang , Iyer Kishore , DeMaria Samuel 
Published: August 2017

AbstractBackgroundIntestinal transplantation (ITx) is the definitive therapy for patients suffering from intestinal failure. Previously published reports suggest that these cases should be managed perioperatively with the same intensive monitors and techniques as in liver transplantation.MethodsWe retrospectively reviewed the anesthetic management of 67 isolated intestinal, intestinal‐pancreas, and intestinal‐kidney transplants over the previous decade (2005‐2015) in our tertiary care institution.ResultsPatients were typically managed with a single arterial line, a single central venous catheter, and rarely intensive modalities such as a pulmonary artery catheter, a transesophageal echocardiography, a second arterial catheter or central venous catheter, a rapid infusion system, a cell salvage device, or viscoelastic testing. Significant hemodynamic derangements were rare, and the rate of postreperfusion syndrome was 8.96%. Our fluid administration type and volume and transfusion type and volume were similar to previous reports in which more intensive anesthetic management was employed.ConclusionWe demonstrate that ITx can safely occur without utilizing the intensive resources requisite for a liver transplant.
Improving monitoring tools for spotted wing drosophila, Drosophila suzukii
Authors: Kirkpatrick D.M. , McGhee P.S. , Gut L.J. , Miller J.R. 
Published: August 2017

AbstractDrosophila suzukii (Matsumura) (Diptera: Drosophilidae) were trapped in the field using colored plastic sphere traps coated with insect Tangle‐trap. Red and black spheres captured significantly more D. suzukii than white spheres. Translucent deli‐cup traps deployed in cherry orchards and baited with yeast, the Alpha Scents lure, or the Scentry lure captured significantly more flies than the Trécé lure and Suzukii bait; all attractants had poor selectivity for D. suzukii. No‐choice evaluations of attractants conducted in field cages corroborated the cherry orchard field study, though translucent deli‐cup traps provisioned with the yeast bait captured significantly more flies than those baited with the Alpha Scents lure. Red sphere traps baited with the Scentry lure captured 3–6× more flies than the deli‐cup trap baited with the same lure, and 3–4× more flies than the deli‐cup trap baited with yeast bait, demonstrating that a trap integrating both visual and olfactory cues is a superior tool for monitoring D. suzukii. Moreover, this simple sticky, dry trap design requires far less labor and maintenance than does a liquid‐based deli‐cup trap.
Semiochemical attractants for the beech leaf‐mining weevil,Orchestes fagi
Authors: Silk P.J. , Mayo P.D. , LeClair G. , Brophy M. , Pawlowski S. , MacKay C. , Hillier N.K. , Hughes C. , Sweeney J.D. 
Published: August 2017

AbstractThe beech leaf‐mining weevil,Orchestes fagiL. (Curculionidae:Curculioninae:Rhamphini), a pest of European beech,Fagus sylvaticaL. (Fagaceae), was recently discovered infesting American beech,Fagus grandifoliaEhrh., in Nova Scotia, Canada. AdultO. fagifeed on both young and mature leaves of beech as well as on other species (e.g., raspberry,Rubusspp.), but oviposition and larval feeding are restricted to beech. Females oviposit in young developing beech leaves at the time of bud burst. We characterized volatiles emitted from buds, leaves, and sapwood of American beech and examined their potential as attractants alone or when combined with other weevil pheromones forO. fagi. We predicted that adults would be attracted to volatiles emitted from beech leaves, especially those emitted from bursting beech buds. Gas chromatography/mass spectrometry (GC/MS) analyses of volatiles collected from buds at pre‐ and post‐budburst identified two diterpene hydrocarbons, 9‐geranyl‐p‐cymene (1) and 9‐geranyl‐α‐terpinene (2a), that were emitted in large amounts at the time of bud burst. Compound1significantly increased mean catch of males and totalO. fagi(but not females) on sticky traps compared with unbaited controls. Y‐tube bioassays confirmed attraction of maleO. fagito bursting beech buds and compound1. Attraction of maleO. fagito1, emitted in large quantities from American beech, is likely adaptive because both oviposition and mating ofO. fagicoincide with budburst. Our data suggest that traps baited with1may be useful for monitoring the spread ofO. fagiin North America.