bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reverse-transcription recombinase-aided amplification assay for H5 subtype avian influenza virus
Authors: Wang Suchun , Li Yang , Jiang Nan , Zhang Fuyou , Zhuang Qingye , Hou Guangyu , Jiang Lijian , Yu Jianmin , Yu Xiaohui , Liu Hualei , Zhao Chenglong , Yuan Liping , Huang Baoxu , Wang Kaicheng 
Published: October 2020

AbstractThe H5 subtype Avian Influenza Virus has caused huge economic losses to the poultry industry and is a threat to human health. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks. In this study, we developed a reverse-transcription recombinase-aided amplification assay for the detection of H5 subtype avian influenza virus. Assays were performed at a single temperature (39°C), and the results were obtained within 20 min. The assay showed no cross-detection with Newcastle disease virus or infectious bronchitis virus. The analytical sensitivity was 103RNA copies per reaction at a 95% confidence interval according to probit regression analysis, with 100% specificity. Compared with published reverse-transcription quantitative real-time polymerase chain reaction assays, the κ value of the reverse transcription recombinase-aided amplification assay in 365 avian clinical samples was 0.970 (p < 0.001). The sensitivity for avian clinical sample detection was 94.44% (95%CI, 70.63% - 99.71%), and the specificity was 100% (95%CI, 98.64% - 100%). These results indicated that our reverse-transcription recombinase-aided amplification assay may be a valuable tool for detecting H5 subtype avian influenza virus.
Smelling in the dark: phylogenomic insights on the chemosensory system of a subterranean beetle
Authors: Balart-García Pau , Cieslak Alexandra , Escuer Paula , Rozas Julio , Ribera Ignacio , Fernández Rosa 
Published: October 2020

ABSTRACTThe chemosensory system has experienced relevant changes in subterranean animals, facilitating the orientation into darkness via the perception of specific chemical signals critical to survive in this particular environment. However, the genomic basis of chemoreception in cave-dwelling fauna is largely unexplored. We generated de novo transcriptomes for antennae and body samples of the troglobitic beetle Speonomus longicornis (whose characters suggest an extreme adaptation to the deep subterranean) in order to interrogate the evolutionary origin and diversification of the chemosensory gene repertoire across coleopterans through a phylogenomic approach. Our results suggested a diminished diversity of odorant and gustatory gene repertoires compared to polyphagous epigean beetles. Moreover, S. longicornis showed a large diversity of odorant-binding proteins, suggesting an important role of these proteins in capturing airborne chemical cues. We identified a gene duplication in the ionotropic co-receptor I R25a, a highly conserved single-copy gene in protostomes involved in thermal and humidity sensing. In addition, no homologous genes to sugar receptors or the ionotropic receptor IR41a were detected. Our findings suggest that the chemosensory gene repertoire of this cave beetle may have been reshaped by the low complexity of chemical signals of this particular environment, and that gene duplication and loss may have played an important role in the evolution of genes involved in chemoreception. Altogether, our results shed light on the genomic basis of chemoreception in a cave-dwelling invertebrate and pave the road towards understanding the genomic underpinnings of adaptation to the subterranean lifestyle at a deeper level.
Multivariate genome-wide association study identifies 780 unique genetic loci associated with cortical morphology
Authors: Shadrin Alexey A. , Kaufmann Tobias , van der Meer Dennis , Palmer Clare E. , Makowski Carolina , Loughnan Robert , Jernigan Terry L. , Seibert Tyler M. , Hagler Donald J , Smeland Olav B. , Chu Yunhan , Lin Aihua , Cheng Weiqiu , Hindley Guy , Thompson Wesley K. , Fan Chun C. , Holland Dominic , Westlye Lars T. , Frei Oleksandr , Andreassen Ole A. , Dale Anders M. 
Published: October 2020

AbstractBrain morphology has been shown to be highly heritable, yet only a small portion of the heritability is explained by the genetic variants discovered so far. Here we exploit the distributed nature of genetic effects across the brain and apply the Multivariate Omnibus Statistical Test (MOSTest) to genome-wide association studies (GWAS) of vertex-wise structural magnetic resonance imaging (MRI) cortical measures from N=35,657 participants in the UK Biobank. We identified 695 loci for cortical surface area and 539 for cortical thickness, in total 780 unique genetic loci associated with cortical morphology. This reflects an approximate 10-fold increase compared to the commonly applied univariate GWAS methods. Power analysis indicates that applying MOSTest to vertex-wise structural MRI data triples the effective sample size compared to conventional univariate GWAS approaches. Functional follow up including gene-based analyses implicate 10% of all protein-coding genes and point towards pathways involved in neurogenesis and cell differentiation.
Contributions of Implicit and Explicit Memories to Sensorimotor Adaptation of Movement Extent During Goal-Directed Reaching
Authors: Lantagne Devon D , Mrotek Leigh Ann , Slick Rebecca A , Beardsley Scott A , Thomas Danny G , Scheidt Robert A 
Published: October 2020

AbstractWe examined how explicit memory of kinematic performance contributes to motor adaptation during goal-directed reaching. Twenty subjects grasped the handle of a horizontal planar robot that rendered spring-like resistance to movement. Subjects made rapid “out-and-back” reaches to capture a remembered visual target at the point of maximal reach extent. The robot’s resistance changed unpredictably between reaches, inducing target capture errors that subjects attempted to correct from one trial to the next. The subjects performed four sets of trials. Three were performed without concurrent visual cursor feedback of hand motion. Two of these required self-assessment of performance between trials, whereby subjects reported peak reach extent on the most recent trial. This was done by either moving a cursor on a horizontal display (visual self-assessment), or by moving the robot’s handle back to the recalled location (proprioceptive self-assessment). Two control conditions were performed either without or with concurrent visual cursor feedback of hand motion. We analyzed movement kinematics and used regression analyses to quantify the extent to which prior reach errors and explicit memories of prior performance contribute to subsequent reach performance. Consistent with prior reports, providing concurrent visual feedback of hand motion increased reach accuracy and reduced the impact of past performance errors on future performance, relative to the no-vision control condition. By contrast, we found no impact of interposed self-assessment on reach kinematics or on how prior target capture errors influence subsequent reach performance. Self-assessments were biased toward the remembered target location, differing markedly from actual reach performances. Including self-assessments as explicit memory of performance in the regression analyses did not improve model predictive accuracy. Therefore, we conclude that explicit memories of prior kinematic performance do not contribute to implicit sensorimotor adaptation of movement extent.
Altered food habits? Understanding the feeding preference of free-ranging Grey langur (Semnopithecus entellus) within an urban settlement
Authors: Dasgupta Dishari , Banerjee Arnab , Karar Rikita , Banerjee Debolina , Mitra Shohini , Sardar Purnendu , Karmakar Srijita , Bhattacharya Aparajita , Ghosh Swastika , Bhattacharjee Pritha , Paul Manabi 
Published: October 2020

ABSTRACTUrbanization affects concurrent human-animal movements as a result of altered resource availability and land use pattern, which leads to considerable ecological consequences. While some animals find themselves adrift, homeless with the uncertainty of resources resulting from the urban encroachment, few of them manage to survive by altering their natural behavioural patterns, and co-exist with humans. Folivorous colobines, such as grey langur, whose feeding repertoire largely consists of plant parts, tend to be more attuned to the urban high-calorie food sources to attain maximum fitness benefits within the concrete jungle having an insignificant green cover. However, such a mismatch between their generalized feeding behaviour and specialized gut physiology reminds us of the Liem’s paradox and demands considerable scientific attention which could tell us the story behind colobines’ successful co-existence within human settlements. Besides understanding their population dynamics, the effective management of these urbanized, free-ranging, non-human primate populations also depends on their altered feeding preferences, altogether which could lead us to the development of an ecologically sound urban ecosystem. Here, we have used a field-based experimental set up which allows langurs to choose between natural and urban food options, being independent of any inter-specific conflicts over resources due to food scarcity. The multinomial logit model reveals the choice-based decision making of these free-ranging grey langurs in an urban settlement of West Bengal, India, where they have not only learned to approach the human-provisioned urban food items but also shown a keen interest in it. While urbanization imposes tremendous survival challenges to these animals, it also opens up for various alternative options for human-animal co-existence which is reflected in this study, and could guide us for the establishment of a sustainable urban ecosystem in the future.HIGHLIGHTSThe feeding repertoire of free-ranging grey langurs at Dakshineswar largely consists of urban food items in contrast to the langurs of Nangi, and Nalpur who mostly depend on natural food sources.High human-langur interactions together with the scarcity of natural plant-based food sources could be considered as an intriguing driving force behind langurs’ altered feeding habits in Dakhineswar.The field-based experimental set up allows free-ranging langurs to choose between natural and urban food options in an urban settlement like Dakhineswar.Urban food items outperformed natural food items as the most chosen one, indicating langurs’ altered feeding preferences which facilitate their successful co-existence within an urban ecosystem.
Small-MoleculeIn VitroInhibitors of the Coronavirus Spike – ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2
Authors: Bojadzic Damir , Alcazar Oscar , Chen Jinshui , Buchwald Peter 
Published: October 2020

ABSTRACTInhibitors of the protein-protein interaction (PPI) between the SARS-CoV-2 spike protein and ACE2, which acts as a ligand-receptor pair that initiates the viral attachment and cellular entry of this coronavirus causing the ongoing COVID-19 pandemic, are of considerable interest as potential antiviral agents. While blockade of such PPIs with small molecules is more challenging than with antibodies, small-molecule inhibitors (SMIs) might offer alternatives that are less strain- and mutation-sensitive, suitable for oral or inhaled administration, and more controllable / less immunogenic. Here, we report the identification of SMIs of this PPI by screening our compound-library that is focused on the chemical space of organic dyes. Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel drug-like compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50s of 0.2-3.0 μM); whereas, control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. Protein thermal shift assays indicated that the SMIs identified here bind SARS-CoV-2-S and not ACE2. Selected promising compounds inhibited the entry of a SARS-CoV-2-S expressing pseudovirus into ACE2-expressing cells in concentration-dependent manner with low micromolar IC50s (6-30 μM). This provides proof-of-principle evidence for the feasibility of small-molecule inhibition of PPIs critical for coronavirus attachment/entry and serves as a first guide in the search for SMI-based alternative antiviral therapies for the prevention and treatment of diseases caused by coronaviruses in general and COVID-19 in particular.
Glycolysis Inhibition Regulates Endothelial Junctions by Perturbing Actin and Focal Adhesions
Authors: Schwarz G. , Gajwani P. , Rehman J. , Leckband D. 
Published: October 2020

AbstractOne of the central functions of the endothelium is to maintain a vascular barrier that prevents fluid leakiness and immune cell influx from the circulating blood into the tissue. The barrier integrity of the endothelium is largely controlled by adherens junctions (AJs) and the key AJ molecule VE-cadherin, which maintains cell cohesion via homotypic trans-interaction with VE-cadherin molecules on neighboring endothelial cells. Tension is required to maintain junction homeostasis, but little is known about the role of endothelial metabolism and bioenergetics in regulating junctional forces. Because glycolysis is the main source of ATP generation in endothelial cells, we examined the bioenergetic control of the mechanics of VE-cadherin junctions, by focusing on the glycolysis regulatory enzyme 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3). Results from traction force imbalance measurements and a VE-cadherin tension sensor revealed that inhibiting PFKFB3 significantly reduced the average junctional tension and the force on VE-cadherin complexes. The decrease in tension was largely due to mechanical changes distal from the cell-cell contacts. Specifically, inhibiting glycolysis perturbs focal adhesions and disrupts actin organization, directly impacting the net force on intercellular contacts. These findings identify a critical role of cellular metabolism for the mechanics and integrity of vascular endothelial junctions, by maintaining global cell mechanics.Statement of SignificanceThis study examines how forces at intercellular junctions are bioenergetically regulated. Results reveal altered mechanical force generation and transmission due to the breakdown of stress-transmitting fibers during lung injury. These junctions control the barrier function of the vascular endothelium, which requires tight inter cellular adhesions to prevent fluid and macromolecules from passing through the endothelial barrier. We determined how the availability of ATP affects the tension between human endothelial cells, by regulating forces produced remotely from the junctions. These global changes alter both the force at the junctions themselves, and the force transmitted across the entire cell through actin fibers.
Training-induced prefrontal neuronal changes transfer between tasks
Authors: Tang Hua , Riley Mitchell R. , Singh Balbir , Qi Xue-Lian , Blake David T. , Constantinidis Christos 
Published: October 2020

AbstractTraining to improve working memory is associated with changes in prefrontal activation and confers lasting benefits, some of which generalize to untrained tasks, though the issue remains contentious and the neural substrate underlying such transfer are unknown. To assess how neural activity changes induced by training transfer across tasks, we recorded single units, multi-unit activity (MUA) and local field potentials (LFP) with chronic electrode arrays implanted in the prefrontal cortex of two monkeys, as they were trained to perform cognitive tasks. Mastering different tasks was associated with distinct changes in neural activity, which included redistribution of power across frequency bands in the LFP, recruitment of larger numbers of MUA sites, and increase or decrease of mean neural activity across single units. In every training phase, changes induced by the actively learned task transferred to an untrained control task, which remained the same across the training period. The results explicate the neural basis through which training can transfer across cognitive tasks.
A Bacterial Signaling Network Controls Antibiotic Resistance by Regulating Anaplerosis of 2-oxoglutarate
Authors: Hurst M. N. , Beebout C. J. , Mersfelder R. , Hollingsworth A. , Guckes K. R. , Bermudez T. , Floyd K. A. , Reasoner S. A. , Williams D. , Hadjifrangiskou M. 
Published: October 2020

AbstractAntibiotic resistance has become a global threat. In addition to acquiring resistance via horizontal gene transfer, bacteria can evade killing by temporarily modifying their cell envelope to prevent antibiotic-bacterial interactions. A critical gap in knowledge is how bacteria balance the metabolic needs of altering the cell envelope with the constant need to generate energy. Cross-regulation between two signaling networks inEscherichia coliincreases resistance to positively charged antibiotics. We show that increased resistance is supported by metabolic re-wiring controlled by the QseB transcription factor. QseB controls the increase in 2-oxoglutarate required for lipid A modification, by upregulating three anaplerotic pathways that feed acetyl Co-A, succinate and fumarate into the TCA cycle. Exogenous addition of 2-oxoglutarate restores antibiotic resistance in theqseBdeletion mutant. Antibiotic resistant clinical isolates bear mutations within QseB-mediated anaplerotic pathways. These findings are significant, because they uncover a previously unknown mechanism of metabolic control of antibiotic resistance.
Tastes for blubber: diversity and locality of whale meat foodways in Japan
Authors: Akamine Jun 
Published: October 2020

PurposeThis paper aims to discuss how whale meat foodways in Japan is a local practice, contrary to the prevailing political belief that it is national, and to examine two local whale meat foodways in Japan by focusing on the usage of blubber. To understand complexity of whaling issue, one needs to be careful of species rather than general “whale.”Design/methodology/approachBy investigating two kinds of recipe books, one published in the early 19th century and the other the early 20th century on whale meat dish, the paper clarifies blubber has been widely consumed rather than lean meat, and blubber was more important than lean meat as whale meat.FindingsThe western part of Japan has rich whale meat foodways compared to other parts of Japan. It is because of their history of whaling since the 17th century. They have inherited rich whale meat foodways.Originality/valueAlthough whale sashimi and deep-fried lean meat are popular nationwide regardless of their communities' history, former whaling communities in the western part of Japan developed a preference for blubber, skin, tongue and offal over lean meat. Whale meat foodways in Japan, therefore, is a local heritage. This fact should be the starting point for analyzing Japanese whaling and whale meat foodways.
Communities of practice as a multidisciplinary response in times of crisis: adapting to successful online learning practices
Authors: Sadiq Kerrie 
Published: October 2020

Purpose
There are many success stories during Covid-19 of academics providing expertly delivered online learning experiences for tertiary students locally and around the world. This paper aims to consider how success was achieved by academics who are not specifically educated with the knowledge and skills to convert a traditional delivery model into an online format and who conventionally spend years working on single projects before they come to fruition.

Design/methodology/approach
This study provides, as a possible explanation for success, the willingness of academics to embrace a tertiary sector rather than discipline-specific collaborative learning approach to their own informal education in online learning practices through communities of practice. Using learning theory, both analytical and reflective methodologies are adopted through an examination of an example of a successful academic community of practice.

Findings
Engaging with a multidisciplinary community of practice can be highly beneficial for academics not specifically educated with the knowledge and skills to convert a traditional delivery model into an online format. Communities of practice provide more than online educational skills; they foster a sense of togetherness and a safe environment to share concerns and challenges on both a professional and personal level.

Originality/value
The benefits of communities of practice for academics during a period of profound operational disruption have yet to be documented in the literature. Specifically, this study highlights the supportive environment provided by a community of practice by examining the successful large-scale transition from face-to-face learning to an online environment during a pandemic.
Tracing the links between executive compensation structure and firm performance: evidence from the Brazilian market
Authors: Dias Alexandre , Vieira Victor , Figlioli Bruno 
Published: October 2020

PurposeThis study aims to investigate how different executive compensation structures were related to the performance of firms.Design/methodology/approachThis study was based on a sample of companies with the highest standards of corporate governance listed on the Brazilian Stock Exchange. We adopted the multiple correspondence analysis followed by the hierarchical cluster analysis to propose a typology defined by fixed and variable components of the executive compensation and multiple firm performance indicators.FindingsThe analysis produced three clusters, which were submitted to robustness tests, highlighting that companies used the compensatory incentives in striking distinct ways as governance mechanisms. The study found a positive relationship between the performance of companies and the variable incentives of executive compensation, especially the long-term incentive, as well as a negative relationship between the performance of firms and the fixed component of the compensation structure.Research limitations/implicationsThis research, whose sample was based on an emerging market, adds empirical evidence to the literature. However, future studies are invited to address the relationships between executive compensation structures and firm performance in other markets, as well as to examine these relationships in companies with distinct levels of governance.Practical implicationsThis study provides insights on how the incentive structure can be adopted as an efficient governance mechanism, especially for companies in emerging markets.Originality/valueThe main novelty of this paper is that the methodological strategy used here enabled the authors to discriminate distinct executive compensation structures and establish a relationship between these compensation structures and different types of performance indicators.