bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chromosome-scale genome assembly for theFusarium oxysporumstrain Fo5176 to establish a modelArabidopsis-fungal pathosystem
Authors: Fokkens Like , Guo Li , Dora Susanne , Wang Bo , Ye Kai , Sánchez-Rodríguez Clara , Croll Daniel 
Published: May 2020

AbstractPlant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of theFusarium oxysporum(Fo) strain Fo5176.Focomprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infectsArabidopsis thalianaand, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read and Hi-C sequencing data to assemble the genome into 19 chromosomes and a total genome size of 67.98 Mb. The genome has a N50 of 4 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in theFof sp.conglutinansclade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified ∼18,000 genes including ten effector genes known from otherFoclades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of theBrassica oleracea, expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additionalFogenomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available forA. thaliana, the Fo5176 genome and annotation provides a crucial step towards the establishment of a highly promising pathosystem.
The coding capacity of SARS-CoV-2
Authors: Finkel Yaara , Mizrahi Orel , Nachshon Aharon , Weingarten-Gabbay Shira , Morgenstern David , Yahalom-Ronen Yfat , Tamir Hadas , Achdout Hagit , Stein Dana , Israeli Ofir , Beth-Din Adi , Melamed Sharon , Weiss Shay , Israely Tomer , Paran Nir , Schwartz Michal , Stern-Ginossar Noam 
Published: May 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing Coronavirus disease 19 (COVID-19) pandemic1,2. In order to understand SARS-CoV-2 pathogenicity and antigenic potential, and to develop diagnostic and therapeutic tools, it is essential to portray the full repertoire of its expressed proteins. The SARS-CoV-2 coding capacity map is currently based on computational predictions and relies on homology to other coronaviruses. Since coronaviruses differ in their protein array, especially in the variety of accessory proteins, it is crucial to characterize the specific collection of SARS-CoV-2 proteins in an unbiased and open-ended manner. Utilizing a suite of ribosome profiling techniques3–8, we present a high-resolution map of the SARS-CoV-2 coding regions, allowing us to accurately quantify the expression of canonical viral open reading frames (ORF)s and to identify 23 novel unannotated viral translated ORFs. These ORFs include upstream ORFs (uORFs) that are likely playing a regulatory role, several in-frame internal ORFs lying within existing ORFs, resulting in N-terminally truncated products, as well as internal out-of-frame ORFs, which generate novel polypeptides. We further show that viral mRNAs are not translated more efficiently than host mRNAs; rather, virus translation dominates host translation due to high levels of viral transcripts. Overall, our work reveals the full coding capacity of SARS-CoV-2 genome, providing a rich resource, which will form the basis of future functional studies and diagnostic efforts.
Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor
Authors: Hati Sanchita , Bhattacharyya Sudeep 
Published: May 2020

AbstractThe novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an ongoing pandemic of coronavirus disease (COVID-19), which started in 2019. This is a member of Coronaviridae family in the genus Betacoronavirus, which also includes SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). The angiotensin-converting enzyme 2 (ACE2) is the functional receptor for SARS-CoV and SARS-CoV-2 to enter the host cells. In particular, the interaction of viral spike proteins with ACE2 is a critical step in the viral replication cycle. The receptor binding domain of the viral spike proteins and ACE2 have several cysteine residues. In this study, the role of thiol-disulfide balance on the interactions between SARS-CoV/CoV-2 spike proteins and ACE2 was investigated using molecular dynamic simulations. The study revealed that the binding affinity was significantly impaired when all the disulfide bonds of both ACE2 and SARS-CoV/CoV-2 spike proteins were reduced to thiol groups. The impact on the binding affinity was less severe when the disulfide bridges of only one of the binding partners were reduced to thiols. This computational finding provides a molecular basis for the severity of COVID-19 infection due to the oxidative stress.
Evolution and genetic basis of the plant-penetrating ovipositor, a key adaptation in herbivorous Drosophilidae
Authors: Peláez Julianne N. , Gloss Andrew D. , Ray Julianne F. , Charboneau Joseph L.M. , Verster Kirsten I. , Whiteman Noah K. 
Published: May 2020

AbstractHerbivorous insects are extraordinarily diverse, yet are found in only one-third of insect orders. This skew may result from barriers to plant colonization, coupled with phylogenetic constraint on plant-colonizing adaptations. Physical barriers have been surmounted through the evolution of key morphological innovations, such as the plant-penetrating ovipositor. Despite their significance, the evolution and genetic basis of such innovations have not been well studied. Ovipositors densely lined with hard bristles have evolved repeatedly in herbivorous lineages within the Drosophilidae. Here, we focus on the evolution of this trait in Scaptomyza, an herbivorous radiation nested in a microbe-feeding clade, sister to Hawaiian Drosophila. Our phylogenetic approach revealed that ovipositor bristle number increased as herbivory evolved. We then dissected the genomic architecture of variation in ovipositor bristle number within S. flava through a genome wide association study. Top associated variants were enriched for transcriptional repressors, and the strongest associations included genes contributing to peripheral nervous system development. Genotyping individual flies replicated the association at a variant upstream of Gαi, a neural development gene, contributing to a gain of 0.58 bristles/major allele. These results suggest that regulatory variation involving conserved developmental genes contributes to a key morphological adaptation required for plant colonization.
Disentangling selection on genetically correlated polygenic traits using whole-genome genealogies
Authors: Stern Aaron J. , Speidel Leo , Zaitlen Noah A. , Nielsen Rasmus 
Published: May 2020

AbstractWe present a full-likelihood method to estimate and quantify polygenic adaptation from contemporary DNA sequence data. The method combines population genetic DNA sequence data and GWAS summary statistics from up to thousands of nucleotide sites in a joint likelihood function to estimate the strength of transient directional selection acting on a polygenic trait. Through population genetic simulations of polygenic trait architectures and GWAS, we show that the method substantially improves power over current methods. We examine the robustness of the method under uncorrected GWAS stratification, uncertainty and ascertainment bias in the GWAS estimates of SNP effects, uncertainty in the identification of causal SNPs, allelic heterogeneity, negative selection, and low GWAS sample size. The method can quantify selection acting on correlated traits, fully controlling for pleiotropy even among traits with strong genetic correlation (|rg| = 80%; c.f. schizophrenia and bipolar disorder) while retaining high power to attribute selection to the causal trait. We apply the method to study 56 human polygenic traits for signs of recent adaptation. We find signals of directional selection on pigmentation (tanning, sunburn, hair,P=5.5e-15, 1.1e-11, 2.2e-6, respectively), life history traits (age at first birth, EduYears,P=2.5e-4, 2.6e-4, respectively), glycated hemoglobin (HbA1c,P=1.2e-3), bone mineral density (P=1.1e-3), and neuroticism (P=5.5e-3). We also conduct joint testing of 137 pairs of genetically correlated traits. We find evidence of widespread correlated response acting on these traits (2.6-fold enrichment over the null expectation,P=1.5e-7). We find that for several traits previously reported as adaptive, such as educational attainment and hair color, a significant proportion of the signal of selection on these traits can be attributed to correlated response,vsdirect selection (P=2.9e-6, 1.7e-4, respectively). Lastly, our joint test uncovers antagonistic selection that has acted to increase type 2 diabetes (T2D) risk and decrease HbA1c (P=1.5e-5).
Using social design to visualize outcomes of sustainable tourism planning: a multiphase, transdisciplinary approach
Authors: Arbogast Doug , Butler Peter , Faulkes Eve , Eades Daniel , Deng Jinyang , Maumbe Kudzayi , Smaldone David 
Published: May 2020

Purpose
This paper aims to describe the transdisciplinary, multiphase, mixed methods, generative design research, participatory planning and social design activities developed and implemented by the West Virginia University Rural Tourism Design Team and associated outcomes.

Design/methodology/approach
The multiphase methodology included quantitative and qualitative research in initial stages of the study (key informant interviews, resident attitudes toward tourism survey, visitor preferences survey, economic impact analysis) which informed social design activities at latter stages (asset mapping, landscape design/visualization of opportunities and sites targeted for development and cultural identity design) using generative design tools facilitating co-design with the communities and helping the destination take sequential steps toward achieving their goals and objectives.

Findings
Opportunities and challenges identified through multiple methods were triangulated and pointed to the same conclusions including the need for long term planning and managed growth; protecting community values; underutilized natural, cultural and historic assets; the opportunity to develop nature-based, cultural and historical attractions; and the need for a common vision and collective identity.

Research limitations/implications
This study makes a unique contribution to literature on sustainable tourism planning by incorporating social design activities to visualize findings of more traditional planning methods and provide tangible, visible outcomes of planning activities which can guide local stakeholders in rural destinations more directly to funding for planning recommendations and project implementation.

Practical implications
The transdisciplinary and social/generative/participatory approach provided a scaffolding of outputs to the community with citizen control and active involvement throughout the planning and design process. The incorporation of social design provided tangible outcomes including site designs and a cultural identity. Generative design research gives people a language with which they can imagine and express their ideas and dreams for future experiences.

Originality/value
This paper investigates the role of social design in a transdisciplinary, multiphase project to support sustainable tourism planning.
Exploring the relationship between entrepreneurial failure and conflict between work and family from the conservation of resources perspective
Authors: Yu Xiaoyu , Meng Xiaotong , Cao Gang , Jia Yingya 
Published: May 2020

PurposeConflict between work and family is a significant issue for entrepreneurs. The purpose of this study is to explore the effect of entrepreneurial failure on both family–work conflict (FWC) and work–family conflict (WFC) and the moderating role of perceived control of time and organizational slack based on conservation of resources (COR) theory.Design/methodology/approachThis study used a questionnaire to explore the relationship between entrepreneurial failure, FWC/WFC, perceived control of time and organizational slack. Data were collected from the Chinese context in 2018 and as a result received 318 valid questionnaires, obtaining a response rate of 63.6 per cent.FindingsThe study finds that entrepreneurial failure has a significant relationship with FWC but a nonsignificant relationship with WFC and that perceived control of time and organizational slack moderate the relationship between entrepreneurial failure and FWC/WFC.Originality/valueThis study aligns the field of family–work (work–family) conflict and entrepreneurial failure. It addresses a research gap in the conflict literature by introducing one form of resource loss: entrepreneurial failure as a source of conflict between work and family based on COR theory and the work–home resources model. The study also enriches the literature on the social cost of entrepreneurial failure by exploring the crossover effect of entrepreneurial failure on conflicts in the family domain. Furthermore, the study advances the understanding of managing conflict between work and family after entrepreneurial failure.
Cost of illness study for adult atopic dermatitis in Japan: A cross‐sectional Web‐based survey
Authors: Murota Hiroyuki , Inoue Sachie , Yoshida Kazufumi , Ishimoto Atsushi 
Published: May 2020

AbstractAtopic dermatitis is a pruritic, eczematous dermatitis, the symptoms of which chronically fluctuate with remissions and relapses. Although a high psychosomatic and economic burden caused by atopic dermatitis is expected, few studies have been conducted estimating the cost of illness, including the self‐medication costs and productivity loss due to atopic dermatitis. The aim of this study was to conduct a cross‐sectional, Web‐based survey of the direct medical costs, self‐medication costs and productivity loss for adult atopic dermatitis patients, and estimate the burden of Japanese adult atopic dermatitis patients by disease severity. In a physician survey, the medical resource consumption related to medical treatments was surveyed by disease severity. The direct medical costs were calculated by multiplying the medical resource consumption and medical fee corresponding to each treatment. Based on the results of a patient survey, the self‐medication costs and productivity loss were estimated by sex and disease severity. Atopic dermatitis‐related productivity loss was calculated based on absenteeism, presenteeism, overall work impairment for employed workers and activity impairment for housewives. The nationwide estimations were calculated based on the estimated number of atopic dermatitis patients, employed workers with atopic dermatitis, and housewives with atopic dermatitis in their 20s–50s in Japan. Based on the surveys, all costs per patient and the scores increased with disease severity. The cost of illness for adult atopic dermatitis patients in Japan was estimated to be approximately JPY 3 trillion/year. Considering the physical and mental burdens, the burden of illness for adult atopic dermatitis was demonstrated to be vast.
Rapid decrease of serum surfactant protein‐D levels predicts the reactivity of rituximab therapy in systemic sclerosis‐associated interstitial lung disease
Authors: Ebata Satoshi , Yoshizaki Ayumi , Fukasawa Takemichi , Asano Yoshihide , Oba Koji , Sato Shinichi 
Published: May 2020

AbstractSystemic sclerosis (SSc) is an autoimmune disorder characterized by vascular damage and excessive fibrosis. SSc‐associated interstitial lung disease (ILD) is a leading cause of death in SSc. Several studies have shown the efficacy of rituximab (RTX) in SSc‐ILD, but no study has examined the relation between RTX reactivity and change of serum marker levels. In this study we examined the relation between change of serum surfactant protein‐D (SP‐D) levels and change of percentage forced vital capacity (FVC) in 11 SSc‐ILD patients with anti‐topoisomerase I antibody treated by RTX. Serum SP‐D levels were significantly decreased compared with baseline at 2 weeks after first RTX infusion in good responders (P = 0.04), while not in poor responders (P = 0.77). Moreover, ΔSP‐D at 2 weeks negatively correlated with Δ%FVC at 24 weeks (P = 0.001). In conclusion, we suggested that the rapid decrease of SP‐D levels may be a predictive marker of RTX effect against SSc‐ILD.
Survival varies seasonally in a migratory bird: Linkages between breeding and non‐breeding periods
Authors: Robinson Robert A. , Meier Christoph M. , Witvliet Willem , Kéry Marc , Schaub Michael 
Published: May 2020

Abstract

Migratory species form an important component of biodiversity; they link ecosystems across the globe, but are increasingly threatened by global environmental change. Understanding and mitigating threats requires knowledge of how demographic processes operate throughout the annual cycle, but this can be difficult to achieve when breeding and non‐breeding grounds are widely separated.

Our goal is to quantify the importance of variability in survival during the breeding and non‐breeding seasons in determining variation in annual survival using a single population and, more broadly, the extent to which annual survival across species reflects variation in probability of surviving the migratory period.

We use a 25‐year dataset in which individuals of a long‐distance migratory bird, the alpine swift Tachymarptis melba, were captured towards the beginning and end of each breeding season to estimate age‐ and season‐specific survival probabilities and incorporate explicit estimation of the correlations in survival between age‐classes and seasons.

Monthly survival was higher during the breeding period than during the rest of the year and strongly affected by conditions in the breeding season; effects that remained apparent in the following non‐breeding season, but not subsequently. Recruitment of juveniles was dependent on the timing of breeding, being higher if egg‐laying commenced before the median date, and substantially lower if not.

Across migratory bird species, variation in annual survival largely reflects variation in the probability of surviving the migratory period. Using a double‐capture approach, even within a single season, provides valuable insights into the demography of migratory species, which will help understand the extent and impacts of the threats they face in a changing world.
Glacial microbiota are hydrologically connected and temporally variable
Authors: Cameron Karen A. , Müller Oliver , Stibal Marek , Edwards Arwyn , Jacobsen Carsten Suhr 
Published: May 2020

SummaryGlaciers are melting rapidly. The concurrent export of microbial assemblages alongside glacial meltwater is expected to impact the ecology of adjoining ecosystems. Currently, the source of exported assemblages is poorly understood, yet this information may be critical for understanding how current and future glacial melt seasons may influence downstream environments. We report on the connectivity and temporal variability of microbiota sampled from supraglacial, subglacial and periglacial habitats and water bodies within a glacial catchment. Sampled assemblages showed evidence of being biologically connected through hydrological flowpaths, leading to a meltwater system that accumulates prokaryotic biota as it travels downstream. Temporal changes in the connected assemblages were similarly observed. Snow assemblages changed markedly throughout the sample period, likely reflecting changes in the surrounding environment. Changes in supraglacial meltwater assemblages reflected the transition of the glacial surface from snow‐covered to bare‐ice. Marked snowmelt across the surrounding periglacial environment resulted in the flushing of soil assemblages into the riverine system. In contrast, surface ice within the ablation zone and subglacial meltwaters remained relatively stable throughout the sample period. Our results are indicative that changes in snow and ice melt across glacial environments will influence the abundance and diversity of microbial assemblages transported downstream.
Phage biocontrol to combat Pseudomonas syringae pathogens causing disease in cherry
Authors: Rabiey Mojgan , Roy Shyamali R. , Holtappels Dominique , Franceschetti Linda , Quilty Billy J. , Creeth Ryan , Sundin George W. , Wagemans Jeroen , Lavigne Rob , Jackson Robert W. 
Published: May 2020

SummaryBacterial canker is a major disease of Prunus species, such as cherry (Prunus avium). It is caused by Pseudomonas syringae pathovars, including P. syringae pv. syringae (Pss) and P. syringae pv. morsprunorum race 1 (Psm1) and race 2 (Psm2). Concerns over the environmental impact of, and the development of bacterial resistance to, traditional copper controls calls for new approaches to disease management. Bacteriophage‐based biocontrol could provide a sustainable and natural alternative approach to combat bacterial pathogens. Therefore, seventy phages were isolated from soil, leaf and bark of cherry trees in six locations in the south east of England. Subsequently, their host range was assessed against strains of Pss, Psm1 and Psm2. While these phages lysed different Pss, Psm and some other P. syringae pathovar isolates, they did not infect beneficial bacteria such as Pseudomonas fluorescens. A subset of thirteen phages were further characterized by genome sequencing, revealing five distinct clades in which the phages could be clustered. No known toxins or lysogeny‐associated genes could be identified. Using bioassays, selected phages could effectively reduce disease progression in vivo, both individually and in cocktails, reinforcing their potential as biocontrol agents in agriculture.
Species delimitation and geography
Authors: Hausdorf Bernhard , Hennig Christian 
Published: May 2020

Abstract
Despite the importance of the geographical arrangement of populations for the inference of species boundaries, only a few approaches that integrate spatial information into species delimitation have thus far been developed. Persistent differentiation of sympatric groups of individuals is the best criterion for species status. Species delimitation becomes more prone to error if allopatric metapopulations are considered because it is often difficult to assess whether observed differences between allopatric metapopulations would be sufficient to prevent the fusion of these metapopulations upon contact. We propose a novel approach for testing the hypothesis that the multilocus genetic distances between individuals or populations belonging to two different candidate species are not larger than expected based on their geographical distances and the relationship of genetic and geographical distances within the candidate species. A rejection of this null hypothesis is an argument for classifying the two studied candidate species as distinct species. Case studies show that the proposed tests are suitable to distinguish between intra‐ and interspecific differentiation. The regression approach proposed here is more appropriate for testing species hypotheses with regard to isolation by distance than (partial) Mantel tests. Our tests assume a linear relationship between genetic and (transformed) geographical distances. This assumption can be compromised by a high genetic variability within populations as found in a case study with microsatellite markers.