bluuebunny/crossref_metadata_2025_split huggingface dataset:
Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples
Authors: Kubik Slawomir , Marques Ana Claudia , Xing Xiaobin , Silvery Janine , Bertelli Claire , De Maio Flavio , Pournaras Spyros , Burr Tom , Duffourd Yannis , Siemens Helena , Alloui Chakib , Song Lin , Wenger Yvan , Saitta Alexandra , Macheret Morgane , Smith Ewan W. , Menu Philippe , Brayer Marion , Steinmetz Lars M. , Si-Mohammed Ali , Chuisseu Josiane , Stevens Richard , Constantoulakis Pantelis , Sali Michela , Greub Gilbert , Tiemann Carsten , Pelechano Vicent , Willig Adrian , Xu Zhenyu 
Published: December 2020

AbstractBackgroundSARS-CoV-2 genotyping has been instrumental to monitor virus evolution and transmission during the pandemic. The reliability of the information extracted from the genotyping efforts depends on a number of aspects, including the quality of the input material, applied technology and potential laboratory-specific biases. These variables must be monitored to ensure genotype reliability. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in studies of viral spread and evolution.ResultsWe used clinical samples and synthetic viral genomes to evaluate the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination using an amplicon-based approach. We found that at least 1000 viral genomes are necessary to confidently detect variants in the genome at frequencies of 10% or higher. The broad applicability of our recommendations was validated in >200 clinical samples from six independent laboratories. The genotypes of clinical isolates with viral load above the recommended threshold cluster by sampling location and period. Our analysis also supports the rise in frequency of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was favoured by travelling during the summer 2020.ConclusionsWe present much-needed recommendations for reliable determination of SARS-CoV-2 genome sequence and demonstrate their broad applicability in a large cohort of clinical samples.
A comprehensive catalogue of regulatory variants in the cattle transcriptome
Authors: Liu Shuli , Gao Yahui , Canela-Xandri Oriol , Wang Sheng , Yu Ying , Cai Wentao , Li Bingjie , Xiang Ruidong , Chamberlain Amanda J. , Pairo-Castineira Erola , D’Mellow Kenton , Rawlik Konrad , Xia Charley , Yao Yuelin , Navarro Pau , Rocha Dominique , Li Xiujin , Yan Ze , Li Congjun , Rosen Benjamin D. , Van Tassell Curtis P. , Vanraden Paul M. , Zhang Shengli , Ma Li , Cole John B. , Liu George E. , Tenesa Albert , Fang Lingzhao 
Published: December 2020

AbstractCharacterization of genetic regulatory variants acting on the transcriptome of livestock is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here, we build a cattle Genotype-Tissue Expression atlas (cattle GTEx,http://cgtex.roslin.ed.ac.uk/) as part of the pilot phase of Farm animal GTEx (FarmGTEx) project for the research community based on publicly available 11,642 RNA-Seq datasets. We describe the landscape of the transcriptome across over 100 tissues and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 24 major tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multi-omics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association study (TWAS) and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.
Neutrophil and monocyte dysfunctional effector response towards bacterial challenge in critically-ill COVID-19 patients
Authors: Shambat Srikanth Mairpady , Gómez-Mejia Alejandro , Schweizer Tiziano A. , Huemer Markus , Chang Chun-Chi , Acevedo Claudio , Pijuan Judith Bergada , Vulin Clement , Miroshnikova Nataliya , Hofmänner Daniel A. , Wendel Garcia Pedro D. , Hilty Matthias P , Karl Philipp Bühler , Schüpbach Reto A. , Brugger Silvio D. , Zinkernagel Annelies S. 
Published: December 2020

AbstractCOVID-19 displays diverse disease severities and symptoms. Elevated inflammation mediated by hypercytokinemia induces a detrimental dysregulation of immune cells. However, there is limited understanding of how SARS-CoV-2 pathogenesis impedes innate immune signaling and function against secondary bacterial infections. We assessed the influence of COVID-19 hypercytokinemia on the functional responses of neutrophils and monocytes upon bacterial challenges from acute and corresponding recovery COVID-19 ICU patients. We show that severe hypercytokinemia in COVID-19 patients correlated with bacterial superinfections. Neutrophils and monocytes from acute COVID-19 patients showed severely impaired microbicidal capacity, reflected by abrogated ROS and MPO production as well as reduced NETs upon bacterial challenges. We observed a distinct pattern of cell surface receptor expression on both neutrophils and monocytes leading to a suppressive autocrine and paracrine signaling during bacterial challenges. Our data provide insights into the innate immune status of COVID-19 patients mediated by their hypercytokinemia and its transient effect on immune dysregulation upon subsequent bacterial infections
Clostridium perfringenosumsp. nov., a closely related species toClostridium perfringensand its virulence factors, isolated from a human soft tissue infection
Authors: Rodríguez César , Kiu Raymond , Quesada-Gómez Carlos , Sandí Cindy , Hall Lindsay J 
Published: December 2020

AbstractTwo Gram-positive, anaerobic bacteria, designated 27733 and 27737, were isolated from a soft tissue infection from a human patient. They were preliminarily identified asClostridium perfringensthrough a series of phenotypic tests, including Gram-staining, determination of lipase and hemolytic activities, MALDI-ToF profiling, and a commercial biochemical identification system. In line with these results, genomes obtained for both isolates were ~3.56 Mbp in size, showed a DNA G+C content of ~28.4%, and containedC. perfringensribosomal markers (i.e. 16S rRNA gene identity >99.0% toC. perfringensATCC13124T). A closer examination of these sequences; however, revealed low average Nucleotide Identity (~87%) and digital DNA-DNA Hybridization (~35%) values between isolates 27733/27737 andC. perfringensATCC13124T, as well as substantial differences in gene content to multipleC. perfringensstrains, indicating that they represent a novel species within the genusClostridium.Congruently, Bayesian dating analyses placed the divergence of this new species andC. perfringensfrom its common ancestor hundreds of thousands of years ago. Isolates 27733/27737 are not genomically identical (34-197 SNPs apart) and carry genes forC. perfringens-liketoxins (<94% nucleotide sequence identity), includingplc(alpha toxin),pfoA(perfringolysin O, theta-toxin),nagHIJKL(hyalorudinase, mu-toxin),nanHIJ(exo-alpha sialidase), andcloSI(alpha-clostripain). They do not have known antibiotic resistance genes but were catalogued as resistant to clindamycin through phenotypic tests. On the basis of the presented evidence, and due to its resemblance and potential confusion withC. perfringens,we herein propose the speciesC. perfringenosumsp. nov. and strain 27733 as its type strain.
Multimodal Single-Cell Omics Analysis of COVID-19 Sex Differences in Human Immune Systems
Authors: Hou Yuan , Zhou Yadi , Gack Michaela U. , Lathia Justin D. , Kallianpur Asha , Mehra Reena , Chan Timothy , Jung Jae U. , Jehi Lara , Eng Charis , Cheng Feixiong 
Published: December 2020

AbstractSex differences in the risk of SARS-CoV-2 infection have been controversial and the underlying mechanisms of COVID-19 sexual dimorphism remain understudied. Here we inspected sex differences in SARS-CoV-2 positivity, hospitalization, admission to the intensive care unit (ICU), sera immune profiling, and two single-cell RNA-sequencing (snRNA-seq) profiles from nasal tissues and peripheral blood mononuclear cells (PBMCs) of COVID-19 patients with varying degrees of disease severity. Our propensity score-matching observations revealed that male individuals have a 29% increased likelihood of SARS-CoV-2 positivity, with a hazard ration (HR) 1.32 (95% confidence interval [CI] 1.18-1.48) for hospitalization and HR 1.51 (95% CI 1.24-1.84) for admission to ICU. Sera from male patients at hospital admission had decreased lymphocyte count and elevated inflammatory markers (C-reactive protein, procalcitonin, and neutrophils). We found that SARS-CoV-2 entry factors, including ACE2, TMPRSS2, FURIN and NRP1, have elevated expression in nasal squamous cells from males with moderate and severe COVID-19. Cell-cell network proximity analysis suggests possible epithelium-immune cell interactions and immune vulnerability underlying a higher mortality in males with COVID-19. Monocyte-elevated expression of Toll like receptor 7 (TLR7) and Bruton tyrosine kinase (BTK) is associated with severe outcomes in males with COVID-19. These findings provide basis for understanding immune responses underlying sex differences, and designing sex-specific targeted treatments and patient care for COVID-19.
Evaluation of the potential of commercial use of microalgae in the world and in Ukraine
Authors: Pavliukh Lesia , Shamanskyi Sergii , Boichenko Sergii , Jaworski Artur 
Published: December 2020

Purpose This paper aims to evaluate of the microalgae potential for commercial application, in particular to conduct experimental study of biogenic compounds removal from sewage waters by microalgae, and to calculate economical benefits from biofertizers and biofuel production.

Design/methodology/approach
Experimental study in the concentration change of nitrogen and phosphorus compounds in the cultivation of Chlorella Vulgaris microalgae in various types of sewage water was carried out.

Findings
The efficiency wastewater treatment by microalgae was confirmed. The economic benefit from the biomass utilization as biofuel production was calculated.

Practical implications
Implementation of wastewater treatment technology with biomass recycling for biofuel and biofertilizers production will minimize the impact on the environment.

Originality/value
As a results of experimental studies, the ability of microalgae to reduce biogenic elements in wastewater was confirmed. Microalgae can be used both for wastewater treatment to biogenic elements removal, such as phosphorous and nitrogen compounds, and biofuel, biofertilizers production. Prospects of the commercial use of microalgae are obvious. They are specially adapted to an environment dominated by viscous forces.
Perceptions of information literacy competencies among future psychology professionals: a comparative study in Spain and Portugal
Authors: Pinto María , Fernández-Pascual Rosaura , Lopes Carlos , Antunes Maria Luz , Sanches Tatiana 
Published: December 2020

PurposeThe aim of the study is to analyze the perceptions of belief-in-importance (BI), self-efficacy (SE) and preferred source of learning (SL) of information literacy (IL) competencies among psychology students in Spain and Portugal.Design/methodology/approachUnified protocol was based on the questionnaire IL-HUMASS (26 items). Quantitative diagnostic-comparative study was carried out, including factor and variance analysis. Hypothesis compliance was checked.FindingsBy country, there are no significant differences in students' perceptions, although the scores in BI are higher than in SE. By category, there are some significant differences, and the least valued is that of processing. By individual competency, seven of them show differences between countries. Learning preferences are for a mix of classroom and autonomous learning. Students barely realize the value of libraries. Within factor structures, which share the same components in each dimension, some emerging factors do appear.Practical implicationsMotivation (BI and SE) with respect to IL competencies is a key asset for future psychologists. Interest should focus on some emerging motivational factors. Students' appreciation of the library should enhance through the corresponding initiatives for improvement. This method could be complemented by qualitative studies.Originality/valueThis is probably the first diagnostic-comparative study on perceptions of IL competencies among future psychology professionals.
COVID-19 responsive teaching of undergraduate architecture programs in India: learnings for post-pandemic education
Authors: Varma Anurag , Jafri Mohammad Shoeb 
Published: December 2020

PurposeThe purpose of this paper is to have an overview of how Indian institutions offering undergraduate architecture programs have responded to the pandemic situation. It seeks to appraise the alternative approaches adopted for teaching-learning, communication, assignment and evaluation and assess their effectiveness for progressive improvisations or integration with pedagogy. The paper articulates a view on the suitability of online teaching for architecture education in India, on basis of educators' experiences of teaching during the pandemic.Design/methodology/approachAn online survey was conducted for obtaining primary data from the educators given the paucity of information. The questions elicited structured information on aspects of the transition process, IT/online platform and tools, the efficacy of online teaching-learning and trajectory of blended learning.FindingsAll institutions managed the transition to online teaching without much difficulty. However, the paper raises the need for professional training and feedback from students. One-third of the respondents express satisfaction with online teaching, despite low satisfaction about the effectiveness of online teaching of a design studio. The results convey the need for more engagement with digital tools and representational software on integrated platforms. The study finds consensus on the future potential of blended learning and advocates developing an integrated framework and curriculum for architecture education in India.Originality/valueThe paper synthesizes viewpoints on online teaching-learning of architecture program in wake of the pandemic from an educators' perspective. The emergent perspectives are viewed dialogically in context of global voices to articulate a future trajectory of blended learning in the domain of architecture education.
Adoption, use and management of process mining in practice
Authors: Grisold Thomas , Mendling Jan , Otto Markus , vom Brocke Jan 
Published: December 2020

PurposeThis study explores how process managers perceive the adoption, use and management of process mining in practice. While research in process mining predominantly focuses on the technical aspects, our work highlights organizational and managerial implications.Design/methodology/approachWe report on a focus group study conducted with process managers from various industries in Central Europe. This setting allowed us to gain diverse and in-depth insights about the needs and expectations of practitioners in relation to the adoption, use and management of process mining.FindingsWe find that process managers face four central challenges. These challenges are largely related to four stages; (1) planning and business case calculation, (2) process selection, (3) implementation, and (4) process mining use.Research limitations/implicationsWe point to research opportunities in relation to the adoption, use and management of process mining. We suggest that future research should apply interdisciplinary study designs to better understand the managerial and organizational implications of process mining.Practical implicationsThe reported challenges have various practical implications at the organizational and managerial level. We explore how existing BPM frameworks can be extended to meet these challenges.Originality/valueThis study is among the first attempts to explore process mining from the perspective of process managers. It clarifies important challenges and points to avenues for future research.
Abusive supervision and workplace deviance: the role of negative reciprocity
Authors: Faldetta Guglielmo 
Published: December 2020

Purpose
This study aims to explore the process that, from abusive supervision, leads to the different kinds of workplace deviant behaviors, using the norm of negative reciprocity as the main mechanism that can trigger this process.

Design/methodology/approach
This study is based on a literature review from organizational behavior and reciprocity fields and builds a theoretical model on the relationship between abusive supervision and workplace deviance within organizations.

Findings
This study develops a theoretical model where abusive supervision causes a feeling of injustice, which can motivate employees to seek revenge in the form of workplace deviant behaviors. Moreover, negative direct balanced reciprocity will moderate the relationship between the desire for revenge and minor interpersonal workplace deviance; negative direct non-balanced reciprocity will moderate the relationship between the desire for revenge and severe interpersonal workplace deviance; negative generalized balanced reciprocity will moderate the relationship between the desire for revenge and minor organizational workplace deviance; negative generalized non-balanced reciprocity will moderate the relationship between the desire for revenge and severe organizational workplace deviance.

Originality/value
Previous studies have used negative reciprocity as a moderator, but for the first time, it is split in direct and generalized and in balanced and non-balanced. In particular, when direct negative reciprocity is present, the revenge will take the form of interpersonal workplace deviance; when generalized negative reciprocity is present, the revenge will take the form of organizational workplace deviance. On the other side, when balanced reciprocity is present, revenge will take the form of minor workplace deviance, while when non-balanced reciprocity is present, revenge will take the form of severe workplace deviance.
Centering community in COVID-19 responses: refugee women's livelihoods in a global pandemic
Authors: Golesorkhi Lara-Zuzan , Fortson Grace , Harder Katherine , Riedmann Trevor 
Published: December 2020

PurposeThe purpose of this commentary is to share preliminary findings from our ethnographic research on refugee women's livelihoods during the COVID-19 pandemic in Portland, Oregon (USA), and to highlight the significance of community efforts in providing gender-responsive measures that address the specific needs and challenges of refugee women.Design/methodology/approachThis commentary draws on a mixed-method approach, including ethnographic research (interviews and observations) as well as an analysis of emerging research on the social implications of COVID-19 in the fields of migration and gender.FindingsRefugee women's livelihoods have been impacted by the COVID-19 pandemic in various specific ways: from losing jobs and healthcare to becoming essential workers and assuming additional caretaker roles, to finding oneself again in unprecedented situations of limited mobility and social isolation. These impacts have been informed by restricted access to resources and services, lack of information about resources and services, and paramount fear due to ever-changing policy. Based on interviews and observations the authors conducted, they find that in many ways, community efforts have addressed the specific needs and challenges of refugee women in the absence of gender-responsive COVID-19 measures across institutional levels and policy areas.Originality/valueIn this commentary, the authors present original data from their ethnographic research on a particularly marginalized, yet resilient population: refugee women. By centering refugee women's experiences, the authors highlight the lack of gender-responsiveness in COVID-19 measures and provide insights into social implications of COVID-19 that often remain overlooked and understudied in discourse and politics.
Value (co-)creation in B2B sales ecosystems
Authors: Rusthollkarhu Sami , Hautamaki Pia , Aarikka-Stenroos Leena 
Published: December 2020

Purpose
Digital ecosystemic business environments challenge dyadic approaches to value creation and particularly to business-to-business (B2B) sales. This paper aims to offer a novel conceptualization of the connection between value creation and B2B sales, which indicates practical implications and builds an agenda for future research.

Design/methodology/approach
This conceptual paper integrates theoretical insights on service-dominant logic, service ecosystems, interactional value co-creation and B2B sales. This paper uses anecdotal evidence from the field of B2B sales to illustrate theoretical concepts developed in the paper.

Findings
The paper develops the concept of value idea emergence (VIE), the process through which B2B entities become aware of a pursuable benefit. The paper further proposes that value (co-)creation in ecosystems happens through VIE’s intertwinement with the process of value proposition creation, a process, which includes all activities needed to bring a value proposition to a customer. The paper then discusses the role of B2B in these processes and proposes an agenda for future research.

Practical implications
The novel conceptualizations of value (co-)creation can help B2B sales managers to understand the ecosystemic nature of the interactions that affect sales and value creation in the current business environment.

Originality/value
The paper contributes to the literature on B2B sales and value creation by proposing a novel concept of VIE, introducing a conceptual model of interactive value (co-)creation in ecosystems and reformulating the role of B2B sales in value creation. These theory-developing insights can be used to guide both academic and managerial attention to interactions happening in the ecosystem outside of the buyer-seller dyad.
Tourism as a lever for a more inclusive society
Authors: Moreno de la Santa Javier González-Soria 
Published: December 2020

Purpose
Tourism is an industry with an enormous capacity for galvanizing local economies and for offering economic and social opportunities to broad sectors of the population. But it is not sufficient to just create and develop new destinations, products and services; new models for development that have inclusion at their core need to be adopted, taking up the opportunities offered by a prosperous and growing market.

Design/methodology/approach
This paper provides a viewpoint analysis of the link between inclusive tourism and tourism development.

Findings
This paper demonstrates that tourism is about reducing uncertainty around what to expect from a destination or service. It is also about creating an environment where all people feel welcome and included. It creates choice and instils confidence in all people, empowering them to sign up for new experiences.

Practical implications
In the light of growing inequality globally, this paper demonstrates that it is important to consider how to make tourism, one of the world’s largest industries, more inclusive.

Originality/value
This paper offers an experience-based analysis and reflection of the bridge between tourism and inclusiveness, particularly in remote and less developed areas.