bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional profiling of immune and inflammatory responses in the context of SARS-CoV-2 fungal superinfection in a human airway epithelial model
Authors: de Lamballerie Claire Nicolas , Pizzorno Andrés , Fouret Julien , Szpiro Lea , Padey Blandine , Dubois Julia , Julien Thomas , Traversier Aurélien , Dulière Victoria , Brun Pauline , Lina Bruno , Rosa-Calatrava Manuel , Terrier Olivier 
Published: May 2020

AbstractSuperinfections of bacterial/fungal origin are known to affect the course and severity of respiratory viral infections. An increasing number of evidence indicate a relatively high prevalence of superinfections associated with COVID-19, including invasive aspergillosis, but the underlying mechanisms remain to be characterized. In the present study, to better understand the biological impact of superinfection we sought to determine and compare the host transcriptional response to SARS-CoV-2 versusAspergillussuperinfection, using a model of reconstituted humain airway epithelium. Our analyses reveal that both simple infection and superinfection induce a strong deregulation of core components of innate immune and inflammatory responses, with a stronger response to superinfection in the bronchial epithelial model compared to its nasal counterpart. Our results also highlight unique transcriptional footprints of SARS-CoV-2Aspergillussuperinfection, such as an imbalanced type I/type III IFN, and an induction of several monocyte- and neutrophil associated chemokines, that could be useful for the understanding ofAspergillus-associated COVID-19 and but also management of severe forms of aspergillosis in this specific context.
AnAms1.0: A high-quality chromosome-scale assembly of a domestic catFelis catusof American Shorthair breed
Authors: Isobe Sachiko , Matsumoto Yuki , Chung Claire , Sakamoto Mika , Chan Ting-Fung , Hirakawa Hideki , Ishihara Genki , Lam Hon-Ming , Nakayama Shinobu , Sasamoto Shigemi , Tanizawa Yasuhiro , Watanabe Akiko , Watanabe Kei , Yagura Masaru , Nakamura Yasukazu 
Published: May 2020

AbstractThe domestic cat (Felis catus) is one of the most popular companion animals in the world. Comprehensive genomic resources will aid the development and application of veterinary medicine including to improve feline health, in particular, to enable precision medicine which is promising in human application. However, currently available cat genome assemblies were mostly built based on the Abyssinian cat breed which is highly inbred and has limited power in representing the vast diversity of the cat population. Moreover, the current reference assembly remains fragmented with sequences contained in thousands of scaffolds. We constructed a reference-grade chromosome-scale genome assembly of a domestic cat,Felis catusgenome of American Shorthair breed, Anicom American shorthair 1.0 (AnAms1.0) with high contiguity (scaffold N50 > 120 Mb), by combining multiple advanced genomic technologies, including PacBio long-read sequencing as well as sequence scaffolding by long-range genomic information obtained from Hi-C and optical mapping data. Homology-based andab initiogene annotation was performed with the Iso-Seq data. Analyzed data is be publicly accessible on Cats genome informatics (Cats-I,https://cat.annotation.jp/), a cat genome database established as a platform to facilitate the accumulation and sharing of genomic resources to improve veterinary care.
Emerging phylogenetic structure of the SARS-CoV-2 pandemic
Authors: Fountain-Jones Nicholas M. , Appaw Raima Carol , Carver Scott , Didelot Xavier , Volz Erik , Charleston Michael 
Published: May 2020

AbstractSince spilling over into humans, SARS-CoV-2 has rapidly spread across the globe, accumulating significant genetic diversity. The structure of this genetic diversity, and whether it reveals epidemiological insights, are fundamental questions for understanding the evolutionary trajectory of this virus. Here we use a recently developed phylodynamic approach to uncover phylogenetic structures underlying the SARS-CoV-2 pandemic. We find support for three SARS-CoV-2 lineages co-circulating, each with significantly different demographic dynamics concordant with known epidemiological factors. For example, Lineage C emerged in Europe with a high growth rate in late February, just prior to the exponential increase in cases in several European countries. Mutations that characterize Lineage C in particular are non-synonymous and occur in functionally important gene regions responsible for viral replication and cell entry. Even though Lineages A and B had distinct demographic patterns, they were much more difficult to distinguish. Continuous application of phylogenetic approaches to track the evolutionary epidemiology of SARS-CoV-2 lineages will be increasingly important to validate the efficacy of control efforts and monitor significant evolutionary events in the future.
A ChIC solution for ChIP-seq quality assessment
Authors: Livi Carmen Maria , Tagliaferri Ilario , Pal Koustav , Sebestyén Endre , Lucini Federica , Bianchi Andrea , Valsoni Sara , Lanzuolo Chiara , Ferrari Francesco 
Published: May 2020

ABSTRACTDespite the widespread adoption of the ChIP-seq technique, there is still no consensus on quality assessment procedures. Quantitative metrics previously proposed in literature are not always effective in discriminating the success or failure of an experiment, thus hampering objectivity and reproducibility of quality control. Here we introduce ChIC, a new framework for ChIP-seq data quality assessment that overcomes the limitations of previous solutions. ChIC is the first method for ChIP-seq quality control directly considering the enrichment profile shape, thus achieving good performances on ChIP targets yielding sharp and broad peaks alike. We integrate a comprehensive set of quality control metrics into one single score reliably summarizing the sample quality. The ChIC score is based on a machine learning classifier trained on a compendium with thousands of ChIP-seq profiles, which can also be used as a reference for easier evaluation of new datasets. ChIC is implemented as a user-friendly R/Bioconductor package.
Genetic Analysis of The Endangered Cleveland Bay Horse: A Century of Breeding Characterised by Pedigree and Microsatellite Data
Authors: Dell Andrew , Curry Mark , Yarnell Kelly , Starbuck Gareth , Wilson Philippe B. 
Published: May 2020

AbstractThe Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. The breed is one of five equine breeds listed as “critical” (<300 registered adult breeding females) by the UK Rare Breeds Survival Trust in their annual Watchlist. Due to their critically endangered status, the current breadth of their genetic diversity is of concern, and assessment of this can lead to improved breed management strategies. Herein, both genealogical and molecular methods are combined in order to assess founder representation, lineage, and allelic diversity. Data from 16 microsatellite loci from a reference population of 402 individuals determined a loss of 91% and 48% of stallion and dam lines, respectively in the reference population. Only 3 ancestors determine 50% of the genome in the living population, with 70% of maternal lineage being derived from 3 founder females, and all paternal lineages traced back to a single founder stallion. Methods and theory are described in detail in order to demonstrate the scope of this analysis for wider conservation strategies. We quantitatively demonstrate the critical nature of the genetic resources within the breed, and offer a perspective on implementing this data in considered breed management strategies.
Actin-binding compounds, discovered by FRET-based high-throughput screening, differentially affect skeletal and cardiac muscle
Authors: Guhathakurta Piyali , Phung Lien A. , Prochniewicz Ewa , Lichtenberger Sarah , Wilson Anna , Thomas David D. 
Published: May 2020

AbstractWe have used spectroscopic and functional assays to evaluate the effects of a group of actin-binding compounds on striated muscle protein structure and function. Actin is present in every human cell, and its interaction with multiple myosin isoforms and multiple actin-binding proteins is essential for cellular viability. A previous high-throughput time-resolved fluorescence resonance energy transfer (TR-FRET) assay from our group identified a class of compounds that bind to actin and affect actomyosin structure and function. In the current study, we tested their effects on the two isoforms of striated muscle α-actins, skeletal and cardiac. We found that a majority of these compounds affected the transition of monomeric G-actin to filamentous F-actin, and that these effects were different for the two actin isoforms, suggesting a different mode of action. To determine the effects of these compounds on sarcomeric function, we further tested their activity on skeletal and cardiac myofibrils. We found that several compounds affected ATPase activity of skeletal and cardiac myofibrils differently, suggesting different mechanisms of action of these compounds for the two muscle types. We conclude that these structural and biochemical assays can be used to identify actin-binding compounds that differentially affect skeletal and cardiac muscles. The results of this study set the stage for screening of large chemical libraries for discovery of novel compounds that act therapeutically and specifically on cardiac or skeletal muscle.
A role for neutral variation in the evolution of C4photosynthesis
Authors: Karki Shanta , Lin HsiangChun , Danila Florence R , Abu-Jamous Basel , Giuliani Rita , Emms David M , Coe Robert A , Covshoff Sarah , Woodfield Helen , Bagunu Efren , Thakur Vivek , Wanchana Samart , Slamet-Loedin Inez , Cousins Asaph B. , Hibberd Julian M , Kelly Steven , Quick W Paul 
Published: May 2020

AbstractConvergent trait evolution is a recurrent phenomenon in all domains of the tree of life. While some convergent traits are caused by simple sequence changes, many are associated with extensive changes to the sequence and regulation of large cohorts of genes. It is unknown how organisms traverse this expansive genotype space to assemble such complex convergent phenotypes. C4photosynthesis is a paradigm of large-scale phenotypic convergence. Conceptual and mathematical models propose that C4photosynthesis evolved from ancestral C3photosynthesis through sequential adaptive changes. These adaptive changes could have been rapidly assembled if modifications to the activity and abundance of enzymes of the C4cycle was neutral in C3plants. This neutrality would enable populations of C3plants to maintain genotypes with expression levels of C4enzymes analogous to those in C4species and thus enable rapid assembly of a functional C4cycle from naturally occurring genotypes given shared environmental selection. Here we show that there is substantial natural variation in expression of genes encoding C4cycle enzymes between natural accessions of the C3plantArabidopsis thaliana. We further show through targeted transgenic experiments in the C3cropOryza sativa, that high expression of the majority of C4cycle enzymes in rice is neutral with respect to growth, development, biomass and photosynthesis. Thus, substantial variation in the abundance and activity of C4cycle enzymes is permissible within the limits of operation of C3photosynthesis and the emergence of component parts of this complex convergent trait can be facilitated by neutral variation.
Are flowers tuned to buzzing pollinators? Variation in the natural frequency of stamens with different morphologies and its relationship to bee vibrations
Authors: Nunes Carlos Eduardo Pereira , Nevard Lucy , Montealegre-Zapata Fernando , Vallejo-Marin Mario 
Published: May 2020

AbstractDuring buzz pollination, bees use vibrations to remove pollen from flowers. Vibrations at the natural frequency of pollen-carrying stamens are amplified through resonance, resulting in higher-amplitude vibrations. Because pollen release depends on vibration amplitude, bees could increase pollen removal by vibrating at the natural frequency of stamens. Yet, few studies have characterized the natural frequencies of stamens and compared them to frequencies of buzz-pollinating bees. Here we use laser Doppler vibrometry to characterise natural frequencies of stamens of six buzz-pollinatedSolanumtaxa of contrasting stamen morphology. We also compare the fundamental frequency of bumblebee buzzes produced on twoSolanumspecies with different natural frequencies. We found that stamen morphology and plant identity explain variation in natural frequency of stamens. Our results show that medium-sized pollinators, such as bumblebees, produce buzzes of frequencies higher than the natural frequency of most (5/6) of theSolanumspecies we studied. However, the observed natural frequency ofSolanumstamens is at the low end of the range of frequencies produced by other buzz-pollinating bees. Thus, our findings suggest that in some buzz pollination interactions, but not others, stamen resonance may play a role in mediating pollen release.
Interplay between bacterial deubiquitinase and ubiquitin E3 ligase regulates ubiquitin dynamics onLegionellaphagosomes
Authors: Liu Shuxin , Luo Jiwei , Zhen Xiangkai , Qiu Jiazhang , Ouyang Songying , Luo Zhao-Qing 
Published: May 2020

AbstractLegionella pneumophilaextensively modulates the host ubiquitin network to create theLegionella-containing vacuole (LCV) for its replication. Many of its virulence factors function as ubiquitin ligases or deubiquitinases (DUBs). Here we identified Lem27 as a DUB that displays a preference for diubiquitin formed by K6, K11 or K48. Lem27 is associated with the LCV where it regulates Rab10 ubiquitination in concert with SidC and SdcA, two bacterial E3 ubiquitin ligases. Structural analysis of the complex formed by an active fragment of Lem27 and the substrate-based suicide inhibitor ubiquitin-propargylamide (PA) reveals that it harbors a fold resembling those in the OTU1 DUB subfamily with a Cys-His catalytic dyad and that it recognizes ubiquitin via extensive hydrogen bonding at six contact sites. Our results establish Lem27 as a deubiquitinase that functions to regulate protein ubiquitination on L. pneumophila phagosomes by counteracting the activity of bacterial ubiquitin E3 ligases.
Fungi are more dispersal limited than bacteria among flowers
Authors: Vannette Rachel L. , McMunn Marshall S. , Hall Griffin W. , Mueller Tobias G. , Munkres Ivan , Perry Douglas 
Published: May 2020

AbstractVariation in dispersal ability among taxa affects community assembly and biodiversity maintenance within metacommunities. Although fungi and bacteria frequently coexist, their relative dispersal abilities are poorly understood. Nectar-inhabiting microbial communities affect plant reproduction and pollinator behavior, and are excellent models for studying dispersal of bacteria and fungi in a metacommunity framework. Here, we assay dispersal ability of common nectar bacteria and fungi in an insect-based dispersal experiment. We then compare these results to the incidence and abundance of culturable flower-inhabiting bacteria and fungi within naturally occurring flowers across two coflowering communities in California across two flowering seasons. Our microbial dispersal experiment demonstrates that bacteria disperse among habitat patches more readily than fungi via thrips. Across all flowers, bacterial and fungal incidence and abundance were positively correlated but bacteria were much more widespread, suggesting shared dispersal routes or habitat requirements but differences in dispersal and colonization frequency. The finding that bacteria are more common among flowers sampled here, in part due to superior insect-mediated dispersal, may have broad relevance for microbial life-history, community assembly of microbes and plant-pollinator interactions.
Glycans function as a Golgi export signal to promote the constitutive exocytic trafficking
Authors: Sun Xiuping , Tie Hieng Chiong , Chen Bing , Lu Lei 
Published: May 2020

AbstractMost proteins in the secretory pathway are glycosylated. However, the role of glycans in the membrane trafficking is still unclear. Here, we discovered that transmembrane secretory cargos, such as interleukin 2 receptor α subunit or Tac, transferrin receptor and cluster of differentiation 8a, unexpectedly displayed substantial Golgi localization when their O-glycosylation was compromised. By quantitatively measuring their Golgi residence times, we found that the apparent Golgi localization of these O-glycan deficient cargos is due to their slow Golgi export. The super-resolution microscopy method that we previously developed revealed that O-glycan deficient Tac chimeras localize at the interior of thetrans-Golgi cisternae. The O-glycan was observed to be both necessary and sufficient for the efficient Golgi export of Tac chimeras. By sequentially introducing O-glycosylation sites to β-galactoside α-2,6-sialyltransferase1, we demonstrated that the O-glycan’s effect on the Golgi export is probably additive. Finally, the finding that N-glycosylated GFP substantially reduces the Golgi residence time of Tac chimera suggests that the N-glycan might have a similar effect. Therefore, both O- and N-glycan might function as a generic Golgi export signal at thetrans-Golgi to promote the constitutive exocytic trafficking.
Influence of heat treatment on corrosion behavior of laser welded Mg-Gd-Y fusion zones
Authors: Wang Lyuyuan , Huang Jian , Peng Yong , Jia Yang , Ni Rong 
Published: May 2020

Purpose
This paper aims to evaluate the corrosion resistance of fusion zones in different heat treated condition from laser welded Mg-Gd-Y alloys and analyze their intrinsic corrosion mechanism.

Design/methodology/approach
The corrosion behavior of fusion zone from laser-welded Mg-Gd-Y alloy joints in the as-welded, ageing and solution + ageing conditions was investigated in the 3.5 wt.% NaCl solution by immersion tests.

Findings
The corroded surface of as-welded fusion zone consists of dark and bright regions, and the bright regions were composed of high-density needle-like products, whereas some different extended direction of the cracks with lots of long ultrafine needle-shaped corrosion products appeared in the dark regions. The corrosion resistance of the fusion zone is slightly decreased after the ageing treatment.

Originality/value
The solution + ageing treated fusion zone exhibits the highest corrosion resistance than that of the as-welded and ageing treated state because of the full dissolution of the cathodic coarse eutectic compound, grains growth and relatively compact protective films. The inhomogeneous distribution of the β′ can somewhat improve the corrosion rate of solution + ageing treated fusion zone when compared with base metal.
Big data analytics of corporate internet disclosures
Authors: Basuony Mohamed A.K. , Mohamed Ehab K.A. , Elragal Ahmed , Hussainey Khaled 
Published: May 2020

Purpose
This study aims to investigate the extent and characteristics of corporate internet disclosure via companies’ websites as well via social media and networks sites in the four leading English-speaking stock markets, namely, Australia, Canada, the UK and the USA.

Design/methodology/approach
A disclosure index comprising a set of items that encompasses two facets of online disclosure, namely, company websites and social media sites, is used. This paper adopts a data science approach to investigate corporate internet disclosure practices among top listed firms in Australia, Canada, the UK and the USA.

Findings
The results reveal the underlying relations between the determining factors of corporate disclosure, i.e. profitability, leverage, liquidity and firm size. Profitability in its own has no great effect on the degree of corporate internet disclosure whether via company websites or social media sites. Liquidity has an impact on the degree of disclosure. Firm size and leverage appear to be the most important factors driving better disclosure via social media. American companies tend to be on the cutting edge of technology when it comes to corporate disclosure.

Practical implications
This paper provides new insights into corporate internet disclosure that will benefit all stakeholders with an interest in corporate reporting. Social media is an influential means of communication that can enable corporate office to get instant feedback enhancing their decision-making process.

Originality/value
To the best of the authors’ knowledge, this study is amongst few studies of corporate disclosure via social media platforms. This study has adopted disclosure index incorporating social media as well as applying data science approach in disclosure in an attempt to unfold how accounting could benefit from data science techniques.
Antecedents of company secretaries’ behaviour and their relationship and effect on intended whistleblowing
Authors: May-Amy Yeo Chu , Han-Rashwin Loke Yew , Carter Steve 
Published: May 2020

PurposeThis study aims to examine the antecedents of company secretaries’ behaviour and their relationship and effect on intended whistleblowing with the role of neutralisation as a moderating factor on an individual’s ethical decision-making in whistleblowing.Design/methodology/approachUsing a modified version of the theory of planned behaviour as a framework and a quantitative research approach, a Likert-type scaled, self-administered questionnaire was conducted on a non-probability sample, totalling 208 company secretaries, currently working for various consultancy, audit and secretarial firms in Malaysia. The data obtained were analysed through structural equation modelling.FindingsFindings indicated that attitude, subjective norm, perceived behavioural control, ethical obligation as well as self-identity were found to be predictors in a company secretary’s intended behaviour to whistle-blow. However, neutralisation was proved not to be a contributing factor in whistleblowing between intention and behaviour.Research limitations/implicationsThe quantitative measures of intention and behaviour are incompatible based on their levels of specificity or generality. Also, there may be an existence of social desirability bias among the respondents, indicating the need for a wider sample.Practical implicationsThe study offers valuable knowledge by providing organisations and regulators with several insights into improving the company secretaries’ whistleblowing behaviour, including the need to strengthen whistleblowers’ support and alleged malpractice investigation and analysis systems. It also enables company directors and regulators to implement whistleblowing policies as an internal control mechanism, thus realising an individual’s intention to highly engage in whistleblowing.Originality/valueTo the best of the authors’ knowledge, this study represents the first research that has empirically tested the relationship and effect of antecedents of company secretaries’ whistleblowing intention and behaviour using a modified version of the theory of planned behaviour, thus adding to the stock of literature on this topic and showing that “neutralisation” had an insignificant effect on the possibility of fraudulent reporting.