bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary rescue in one dimensional stepping stone models
Authors: Tomasini Matteo , Peischl Stephan 
Published: October 2020

AbstractGenetic variation and population sizes are critical factors for successful adaptation to novel environmental conditions. Gene flow between sub-populations is a potent mechanism to provide such variation and can hence facilitate adaptation, for instance by increasing genetic variation or via the introduction of beneficial variants. On the other hand, if gene flow between different habitats is too strong, locally beneficial alleles may not be able to establish permanently. In the context of evolutionary rescue, intermediate levels of gene flow are therefore often optimal for maximizing a species chance for survival in metapopulations without spatial structure. To which extent and under which conditions gene flow facilitates or hinders evolutionary rescue in spatially structured populations remains unresolved. We address this question by studying the differences between evolutionary rescue in the island model and in the stepping stone model in a gradually deteriorating habitat. We show that evolutionary rescue is modulated by the rate of gene flow between different habitats, which in turn depends strongly on the spatial structure and the pattern of environmental deterioration. We use these insights to show that in many cases spatially structured models can be translated into a simpler island model using an appropriately scaled effective migration rate.
Structure-based functional study of a peptide of an ecdysozoan superfamily: reveling a common molecular architecture and receptor-interacting residues
Authors: Chen Yun-Ru , Hsiao Nai-Wan , Huang Shiau-Shan , Chang Chih-Chun , Lee Yi-Zong , Tsai Jyuan-Ru , Lin Hui-Chen , Toullec Jean-Yves , Lee Chi-Ying , Lyu Ping-Chiang 
Published: October 2020

ABSTRACTA neuropeptide (Sco-CHH-L), belonging to the crustacean hyperglycemic hormone (CHH) superfamily and preferentially expressed in the pericardial organs (POs) of the mud crabScylla olivacea, was functionally and structurally studied. Its expression levels were significantly higher than the alternative splice form (Sco-CHH) in the POs and increased significantly after animals were subjected to a hypo-osmotic stress. Sco-CHH-L, but not Sco-CHH, significantly stimulatedin vitrothe Na+, K+-ATPase activity in the posterior (6th) gills. Furthermore, solution structure of Sco-CHH-L was resolved using nuclear magnetic resonance spectroscopy revealing that it has an N-terminal tail, three α-helices (α2, Gly9−Asn28; α3, His34−Gly38; α5, Glu62−Arg72), and a π-helix (π4, Cys43−Tyr53) and is structurally constrained by a pattern of disulfide bonds (Cys7-Cys43, Cys23-Cys39, Cys26-Cys52), which is characteristic of the CHH superfamily-peptides. Sco-CHH-L is topologically most similar to the molt-inhibiting hormone from the Kuruma prawnMarsupenaeus japonicuswith a backbone root-mean-square-deviation of 3.12 Å. Ten residues of Sco-CHH-L were chosen for alanine-substituted and the resulting mutants were functionally tested using the gill Na+, K+-ATPase activity assay, showing that the functionally important residues (I2, F3, E45, D69, I71, G73) are located at either end of the sequence, which are sterically close to each other and presumably constitutes the receptor binding sites. Sco-CHH-L was compared with other members of the superfamily revealing a molecular architecture, which is suggested to be common for the crustacean members of the superfamily, with the properties of the residues constituting the presumed receptor binding sites being the major factors dictating the ligand-receptor binding specificity.
A Library of Induced Pluripotent Stem Cells from Clinically Well-Characterized, Diverse Healthy Human Individuals
Authors: Schaniel Christoph , Dhanan Priyanka , Hu Bin , Xiong Yuguang , Raghunandan Teeya , Gonzalez David M. , Dariolli Rafael , D’Souza Sunita L. , Yadaw Arjun S. , Hansen Jens , Jayaraman Gomathi , Mathew Bino , Machado Moara , Berger Seth I. , Tripodi Joseph , Najfeld Vesna , Garg Jalaj , Miller Marc , Lynch Colleen S. , Michelis Katherine C. , Tangirala Neelima C. , Weerahandi Himali , Thomas David C. , Beaumont Kristin G. , Sebra Robert , Mahajan Milind , Schadt Eric , Vidovic Dusica , Schürer Stephan C. , Goldfarb Joseph , Azeloglu Evren U. , Birtwistle Marc R. , Sobie Eric A. , Kovacic Jason C. , Dubois Nicole C. , Iyengar Ravi 
Published: October 2020

SummaryA library of well-characterized human induced pluripotent stem cell (hiPSC) lines from clinically healthy human subjects could serve as a useful resource of normal controls forin vitrohuman development, disease modeling, genotype-phenotype association studies, and drug response evaluation. We report generation and extensive characterization of a gender-balanced, racially/ethnically diverse library of hiPSC lines from 40 clinically healthy human individuals who range in age from 22-61. The hiPSCs match the karyotype and short tandem repeat identity of their parental fibroblasts, and have a transcription profile characteristic of pluripotent stem cells. We provide whole genome sequencing data for one hiPSC clone from each individual, genomic ancestry determination, and analysis of Mendelian disease genes and risks. We document similar transcriptomic profiles, single-cell RNA-seq derived cell clusters and physiology of cardiomyocytes differentiated from multiple independent hiPSC lines. This extensive characterization makes this hiPSC library a valuable resource for many studies on human biology.
Global diversity and biogeography of theZostera marinamycobiome
Authors: Ettinger Cassandra L. , Vann Laura E. , Eisen Jonathan A. 
Published: October 2020

AbstractSeagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens or endophytes in global ecosystems. Here we characterize the distribution of fungi associated with the seagrass,Zostera marina,using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S ribosomal RNA gene, we first measured fungal community composition and diversity, then we tested hypotheses of neutral community assembly theory and the degree to which deviations suggested amplicon sequence variants (ASVs) were plant-selected or dispersal-limited, and finally we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. Our results show that the fungal community is significantly different between sites and follows a weak, but significant pattern of distance decay. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome. TheZ. marinacore leaf and root mycobiomes are dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp. andSaccharomycessp. A few ASVs (e.g.Lobulomycessp.) appear restricted to one or a handful of locations (e.g. possibly due to local adaptation, deterministic dispersal limitation or seasonal bloom events), while others (e.g.Saccharomycessp.) are more ubiquitous across all locations suggesting a true global distribution and possible plant-selection. Fungal guilds associated withZ. marinawere only weakly identified (10.12% of ITS region and 3.4% 18S rRNA gene ASV guild assignments were considered highly probable) including wood saprotrophs, ectomycorrhizal fungi, endophytic fungi and plant pathogens. Our results are similar to those found for other seagrass species. It is clear from the many unclassified fungal ASVs and fungal functional guilds, that our knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses.
Two decades of creating drought tolerant maize and underpinning prediction technologies in the US corn-belt: Review and perspectives on the future of crop design
Authors: Messina Carlos D. , Cooper Mark , Hammer Graeme L. , Berning Dan , Ciampitti Ignacio , Clark Randy , Diepenbrock Christine , Gho Carla , Jines Mike , Lee Travis , McCormick Ryan , Mihura Eduardo , Podlich Dean , Rotundo Jose , Smalley Matt , Tang Tom , Truong Sandra , van Eeuwijk Fred 
Published: October 2020

AbstractOver the last decade, society witnessed the largest expansion of agricultural land planted with drought tolerant (DT) maize (Zea maysL.) Dedicated efforts to drought breeding led to development of DT maize. Here we show that after two decades of sustained breeding efforts the rate of crop improvement under drought is in the range 1.0-1.6% yr−1, which is higher than rates (0.7% yr−1) reported prior to drought breeding. Prediction technologies that leverage biological understanding and statistical learning to improve upon the quantitative genetics framework will further accelerate genetic gain. A review of published and unpublished analyses conducted on data including 138 breeding populations and 93 environments between 2009 and 2019 demonstrated an average prediction skill (r) improvement around 0.2. These methods applied to pre-commercial stages showed accuracies higher that current statistical approaches (0.85 vs. 0.70). Improvement in hybrid and management choice can increase water productivity. Digital gap analyses are applicable at field scale suggesting the possibility of transition from evaluating hybrids to designing genotype x management (GxM) technologies for target cropping systems in drought prone areas. Due to the biocomplexity of drought, research and development efforts should be sustained to advance knowledge and iteratively improve models.HighlightCrop improvement rate in maize increased after implementation of drought breeding efforts. Harnessing crop, quantitative genetics and gap models will enable the transition from genetic evaluation to crop design.
Structure of the enterococcal T4SS protein PrgL reveals unique dimerization interface in the VirB8 protein family
Authors: Jäger Franziska , Lamy Anaïs , Guerini Nina , Sun Wei-Sheng , Berntsson Ronnie P-A 
Published: October 2020

AbstractMultidrug resistant bacteria are one of the most important current threats to public health and a serious problem in hospital acquired infections (HAIs). Most antibiotic resistance genes are acquired via conjugative gene transfer, in a process that is mediated by a protein machinery called the Type 4 Secretion System (T4SS). The core of the T4SS is a multiprotein complex that spans both the cell wall and cellular membrane(s), serving as a channel for macromolecular secretion. Although the majority of multidrug resistant bacteria responsible for HAIs are of Gram-positive origin, with Enterococci being major contributors, mostly Gram-negative T4SSs have been characterized. Here we describe the structure and organisation of PrgL, one of the seven membrane proteins forming the translocation channel of the T4SS encoded by the pCF10 plasmid fromEnterococcus faecalis. We present the structure of the C-terminal domain of PrgL, which displays similarity to VirB8 proteins of Gram-negative secretion systems. PrgL forms dimers and higher order oligomers but does not interact strongly with the other T4SS components.In vitroexperiments show that the soluble domain alone is enough to drive both dimerization and dodecamerisation, with a dimerization interface that differs from all other known VirB8-like proteins. Our findings provide insight into the molecular building blocks of Gram-positive T4SS, highlighting similarities but also unique features in PrgL compared to other VirB8-like proteins.
Minding The Gap: Range Size And Economic Use Drive Functional Trait Data Shortfall In The Atlantic Forest
Authors: Petisco-Souza Ana Carolina , Brum Fernanda Thiesen , Marcilio-Silva Vinícius , Zwiener Victor P. , Zanella Andressa , Dias Arildo S. , González-Melo Andrés , Jansen Steven , Mazzochini Guilherme G. , Niinemets Ülo , Pillar Valério D. , Sosinski Enio , Marques Márcia C. M. , Carlucci Marcos B. 
Published: October 2020

ABSTRACTBiodiversity shortfalls are knowledge gaps that may result from uneven sampling through time and space and human interest biases. Gaps in data of functional traits of species may add uncertainty in functional diversity and structure measures and hinder inference on ecosystem functioning and ecosystem services, with negative implications for conservation and restoration practices, such as in Atlantic Forest hotspot. Here we investigate which are the potential drivers of trait data gaps and where geographically they are in the Atlantic Forest. We quantified trait gaps for four key plant functional traits of 2335 trees species, and evaluated which factors drive trait gap at the species and at the geographical level. At the species level, we found larger trait gaps for small-ranged and with no economic use. At the geographical level, we found larger gaps at the Atlantic Forest east coast. Trait gaps were higher away from urban areas, and among species with smaller mean range size and smaller mean economic use of wood, and smaller near protected areas. Efforts on reducing trait gaps of small-ranged and of species with economic use of wood can further advance theory-driven studies and improve knowledge coverage
Haploid mouse germ cell precursors from embryonic stem cells revealXistactivation from a single X chromosome
Authors: Aizawa Eishi , Kaufmann Corinne , Sting Sarah , Freimann Remo , Wutz Anton 
Published: October 2020

SummaryMammalian haploid cells have applications for genetic screening and substituting gametic genomes. Here we characterize a culture system for obtaining haploid primordial germ cell-like cells (PCGLCs) from haploid mouse embryonic stem cells (ESCs). We find that a haploid genome is maintained in PGCLCs with a high frequency indicating a substantially lower rate of diploidization than somatic cells. Characterization of the differentiating haploid ESCs reveals thatXistis activated from the single X chromosome. This observation suggests that X chromosome inactivation is initiated in haploid cells consistent with a model where autosomal blocking factors set a threshold for X-linked activators. The germline segregates from the epiblast and differs from somatic lineages in gene expression and epigenetic mechanisms. The ability of primordial germ cells for repressingXistmight contribute to the maintenance of a haploid genome.
The effects ofCSTBduplication on APP/amyloid-β pathology and cathepsin activity in a mouse model
Authors: Wu Yixing , Whittaker Heather T. , Noy Suzanna , Cleverley Karen , Brault Veronique , Herault Yann , Fisher Elizabeth M. C. , Wiseman Frances K. 
Published: October 2020

AbstractPeople with Down syndrome (DS), caused by trisomy of chromosome 21 have a greatly increased risk of developing Alzheimer’s disease (AD). This is in part because of triplication of a chromosome 21 gene,APP. This gene encodes amyloid precursor protein, which is cleaved to form amyloid-β that accumulates in the brains of people who have AD. Recent experimental results demonstrate that a gene or genes on chromosome 21, other thanAPP,when triplicated significantly accelerate amyloid pathology in a transgenic mouse model of amyloid-β deposition. Multiple lines of evidence indicate that cysteine cathepsin activity influences APP cleavage and amyloid-β accumulation. Located on human chromosome 21 (Hsa21) is an endogenous inhibitor of cathepsin proteases,CYSTATIN B(CSTB)which is proposed to regulate cysteine cathepsin activityin vivo. Here we determined if three copies of the mouse geneCstbis sufficient to modulate beta amyloid (Aβ) accumulation and cathepsin activity in a transgenicAPPmouse model. Duplication ofCstbresulted in an increase in transcriptional and translational levels ofCstbin the mouse cortex but had no effect on the deposition of insoluble Aβ plaques or the levels of soluble or insoluble Aβ42, Aβ40, or Aβ38in 6-month old mice. In addition, the increased CSTB did not alter the activity of cathepsin B enzyme in the cortex of 3-month old mice. These results indicate that the single-gene duplication ofCstbis insufficient to elicit a disease-modifying phenotype in the dupCstb x tgAPP mice, underscoring the complexity of the genetic basis of AD-DS and the importance of multiple gene interactions in disease.
Have changes in audit standards altered client perceptions of auditors?
Authors: Doxey Marcus , Ewing Robert 
Published: October 2020

PurposeChanges in external auditing over four decades motivates a historical investigation of how client employees' perceptions of auditors have changed across this period.Design/methodology/approachThis paper uses a longitudinal quasi-experiment to compare current client employees' perceptions of the auditor with results from 1972.FindingsChanges in client employees' perceptions of the audit, its usefulness and of auditor-client conflict suggest increases in auditor independence. However, this paper also finds that despite decades of efforts to strengthen auditor independence and skepticism, the primary analogy client employees apply to the external auditor remains “consultant”.Practical implicationsThe findings contribute to the discussion of whether regulatory and standard changes in the audit environment have changed aspects of client employees' perceptions of auditors.Originality/valueThe paper contributes by presenting a unique approach to partially replicating a historic study using a quasi-experimental research design.
Entrepreneurial orientation, new product development and firm performance: the moderating role of legitimacy in Chinese high-tech SMEs
Authors: Liu Yunqing , Wang Min 
Published: October 2020

PurposeThis paper examines the relationship of entrepreneurial orientation (EO), new product development (NPD), legitimacy (political and market) and firm performance (FP). The authors investigate how and when EO improves FP in high-tech small and medium-size enterprises (SMEs).Design/methodology/approachThe paper formulates 5 hypotheses from literature review and theoretical deduction. The hypotheses are tested using ordinary least squares (OLS) regression with data collected from 219 randomly selected SMEs operating in high-tech industries of China.FindingsThe findings show that the mechanism of EO improve FP in high-tech SMEs by considering NPD as a mediator and legitimacy as moderators: (1) NPD plays a mediating role in the relationship between EO and FP, (2) market legitimacy (ML) positively moderating the effect of EO on FP and (3) both political legitimacy (PL) and ML positively moderating the effect of NPD on FP.Research limitations/implicationsFor the limitations, the firms the authors’ surveyed are SMEs that are not listed companies, which cause some limitations. For the implications, the authors propose some recommendations based on the findings to help Chinese SMEs to enhance performance.Originality/valueThe existing research on EO–FP linkage remains elusive findings. The paper reconciled the inconsistency by providing a nuanced mechanism of how EO promotes FP in high-tech SMEs of Chinese transition economy. By explain the important role of NPD in high-tech SMEs, the findings shed light on the mediators between EO and FP and the moderators. By emphasize the different role of ML and PL in determining EO–FP and NPD–FP linkages, the findings illustrate the peculiarity of contingency factors in a transition economy.
Prevalence of COPD by age, sex, socioeconomic position and smoking status; a cross-sectional study
Authors: Levin Kate Ann , Anderson David , Crighton Emilia 
Published: October 2020

PurposeThe purpose of this study is to calculate gender and socioeconomic status (SES) inequalities in chronic obstructive pulmonary disease (COPD) in Greater Glasgow and Clyde and measure the proportion of inequalities explained by smoking.Design/methodology/approachMedical records until May 2016 were linked to mortality data to measure COPD prevalence. Population estimates for smoking status were calculated by merging three (2013–2015) Scottish Household Survey rounds. Poisson regression was carried out to analyse the relationship between SES and gender inequalities in COPD, and smoking.FindingsCrude COPD prevalence for ages 16+ years was 3.29% and for ages 45 years+ was 6.26%, and higher in females than males. Adjusting for age and sex, prevalence of COPD in the most deprived quintile was 4.5 times of that in the least deprived. Adjustment for smoking explains almost half of the relative difference between Scottish Indicator for Multiple Deprivation (SIMD) 1 (least affluent quintile of deprivation) and SIMD 5 (most affluent quintile) and a fifth of the absolute difference. There is a higher risk of COPD among male non-smokers than female, but among smokers the risk is greater for females than males.Research limitations/implicationsRisk factors specific to respiratory health beyond smoking and common risk factors of morbidity more generally should be considered in understanding inequalities in COPD.Originality/valuePrevalence of COPD is higher than previously thought. Smoking explains less than half of inequalities in COPD. Gender inequalities in COPD are dependent on smoking status and the smoking indicator used.
Public health leadership in the times of COVID-19: a comparative case study of three countries
Authors: Glenn Jeffrey , Chaumont Claire , Villalobos Dintrans Pablo 
Published: October 2020

PurposeThe purpose is to understand the role of public leadership during the COVID-19 pandemic and advocate for a more active role of public health professionals in helping manage the crisis.Design/methodology/approachThe authors use the framework developed by Boinet al.(2005) on crisis leadership. The authors focus on three of the core tasks – sense-making, decision-making and meaning-making – that are relevant to explain the role of public leaders during the ongoing crisis. The authors draw from the experience of three countries – Chile, France and the United States – to illustrate how these tasks were exercised with concrete examples.FindingsSeveral examples of the way in which public leaders reacted to the crisis are found in the selected countries. Countries show different responses to the way they assessed and reacted to the COVID-19 as a crisis, the decisions taken to prevent infections and mitigate consequences, and the way they communicate information to the population.Practical implicationsA better understanding public leadership as a key for better crisis management, particularly for designing policy responses to public health crises. Public health leaders need to assume a more active role in the crisis management process, which also implies the emergence of a new class of public health leaders and a more prominent role for public health in the public eye.Originality/valueThe use of examples from three different countries, as well as the focus on the core leadership tasks during an ongoing crisis help not only assessing the crisis management but also extracting lessons for the coming months, as well as future public health emergencies. The three authors have a first-hand experience on the evolution of the crisis in their countries and the environment, since they are currently living and working in public health in Chile, France and the United States.