bluuebunny/crossref_metadata_2025_split huggingface dataset:
Redefining theClostridioides difficileσBregulon: σBactivates genes involved in detoxifying radicals that can result from the exposure to antimicrobials and hydrogen peroxide
Authors: Boekhoud Ilse M. , Michel Annika-Marisa , Corver Jeroen , Jahn Dieter , Smits Wiep Klaas 
Published: July 2020

AbstractIn many gram-positive bacteria the general stress response is regulated at the transcriptional level by the alternative sigma factor sigma B (σB). InC. difficileσBhas been implicated in protection against stressors such as reactive oxygen species and antimicrobial compounds. Here, we used an anti-σBantibody to demonstrate time-limited overproduction of σBinC. difficiledespite its toxicity at higher cellular concentrations. This toxicity eventually led to the loss of the plasmid used for anhydrotetracycline-induced σBgene expression. Inducible σBoverproduction uncouples σBexpression from its native regulatory network and allowed for the refinement of the previously proposed σBregulon. At least 32% the regulon was found to consist of genes involved in the response to reactive radicals. Direct gene activation byC. difficileσBwas demonstrated throughin vitrorun-off transcription of specific target genes (cd0350, cd3614, cd3605, cd2963). Finally, we demonstrated that different antimicrobials and hydrogen peroxide induce these genes in a manner dependent on this sigma factor, using a plate-based luciferase reporter assay. Together, our work suggests that lethal exposure to antimicrobials may result in the formation of toxic radicals that lead to σB-dependent gene activation.ImportanceSigma B is the alternative sigma factor governing stress response in many gram-positive bacteria. InC. difficile, asigBmutant shows pleiotropic transcriptional effects. Here, we determine genes that are likely direct targets of σBby evaluating the transcriptional effects of σBoverproduction, provide biochemical evidence of direct transcriptional activation by σB, and show that σB-dependent genes can be activated by antimicrobials. Together our data suggest that σBis a key player in dealing with toxic radicals.
Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes
Authors: Youngblut Nicholas D. , de la Cuesta-Zuluaga Jacobo , Ley Ruth E. 
Published: July 2020

AbstractTree-based diversity measures incorporate phylogenetic or functional relatedness into comparisons of microbial communities. This can improve the identification of explanatory factors compared to tree-agnostic diversity measures. However, applying tree-based diversity measures to metagenome data is more challenging than for single-locus sequencing (e.g., 16S rRNA gene). The Genome Taxonomy Database (GTDB) provides a genome-based reference database that can be used for species-level metagenome profiling, and a multi-locus phylogeny of all genomes that can be employed for diversity calculations. This approach also allows for functional diversity measures based on genomic content or traits inferred from it. Still, it is unclear how metagenome-based assessments of microbiome diversity benefit from incorporating phylogeny or function into measures of diversity. We assessed this by measuring phylogeny-based, function-based, and tree-agnostic diversity measures from a large, global collection of human gut metagenomes composed of 33 studies and 3348 samples. We found tree-based measures to explain phenotypic variation (e.g., westernization, disease status, and gender) better or on par with tree-agnostic measures. Ecophylogenetic and functional diversity measures provided unique insight into how microbiome diversity was partitioned by phenotype. Tree-based measures greatly improved machine learning model performance for predicting westernization, disease status, and gender, relative to models trained solely on tree-agnostic measures. Notably, ecophylogenetic and functional diversity measures were generally the most important features for predictive performance. Our findings illustrate the usefulness of tree- and function-based measures for metagenomic assessments of microbial diversity – a fundamental component of microbiome science.ImportanceEstimations of microbiome diversity are fundamental to understanding spatiotemporal changes of microbial communities and identifying which factors mediate such changes. Tree-based measures of diversity, which consider species relatedness, are widespread for amplicon-based microbiome studies due to their utility relative to tree-agnostic measures. However, tree-based measures are seldomly applied to shotgun metagenomics data. We evaluated the utility of phylogeny, functional relatedness, and tree-agnostic diversity measures on a large scale human gut metagenome dataset to help guide researchers with the complex task of evaluating microbiome diversity via metagenomics.
VNTR prediction on sequence characteristics using long-read annotation and validation by short-read pileup
Authors: van Batenburg Diederik Cames , Linthorst Jasper , Holstege Henne , Reinders Marcel 
Published: July 2020

AbstractTandem repeats (TRs) are contiguously repetitive sequences with a high mutation rate. Several human diseases have been associated with an expansion of TR, a mutation which constitutes a change in their number of repetitions. Nevertheless, these Variable Number Tandem Repeats (VNTRs) have not been included in many genome-wide studies. The reason is that VNTR genotyping is inaccurate using short-read sequencing while new technology like long-read sequencing is expensive and lacks throughput.Here, we propose a sequence based random forest classifier that is able to predict variable expansion of TR regions, given by incomplete VNTR annotation from long-read sequencing of 5 haplotypes. The classifier mainly predicted VNTRs using the features TR length. The second most used feature is a novel finding: the Mfold predicted likelihood of self-folding for which more stable foldings are correlated with VNTRs. We validated VNTR candidates predicted by this classifier by clustering short-read pileup patterns compared across 17 genomes. TRs labeled VNTR by the classifier showed similar local variance in their pileup profiles.Contactdiederik.cvb@gmail.comSupplementary informationSupplementary data are available at bioRxiv
Impact of climatic, demographic and disease control factors on the transmission dynamics of COVID-19 in large cities worldwide
Authors: Metelmann Soeren , Pattni Karan , Brierley Liam , Cavalerie Lisa , Caminade Cyril , Blagrove Marcus S C , Turner Joanne , Sharkey Kieran J , Baylis Matthew 
Published: July 2020

AbstractWe are now over seven months into a pandemic of COVID-19 caused by the SARS-CoV-2 virus and global incidence continues to rise. In some regions such as the temperate northern hemisphere there are fears of “second waves” of infections over the coming months, while in other, vulnerable regions such as Africa and South America, concerns remain that cases may still rise, further impacting local economies and livelihoods. Despite substantial research efforts to date, it remains unresolved as to whether COVID-19 transmission has the same sensitivity to climate and seasonality observed for other common respiratory viruses such as seasonal influenza. Here we investigate any empirical evidence of seasonality using a robust estimation framework. For 304 large cities across the world, we estimated the basic reproduction number (R0) using logistic growth curves fitted to cumulative case data. We then assessed evidence for association with climatic variables through mixed-effects and ordinary least squares (OLS) regression while adjusting for city-level variation in demographic and disease control factors. We find evidence of association between temperature and R0 during the early phase of the epidemic in China only. During subsequent pandemic spread outside China, we instead find evidence of seasonal change in R0, with greater R0 within cities experiencing shorter daylight hours (direct effect coefficient = −0.247, p = 0.006), after separating out effects of calendar day. The effect of daylight hours may be driven by levels of UV radiation, which is known to have detrimental effects on coronaviruses, including SARS-CoV-2. In the global analysis excluding China, climatic variables had weaker explanatory power compared to demographic or disease control factors. Overall, we find a weak but detectable signal of climate variables on the transmission of COVID-19. As seasonal changes occur later in 2020, it is feasible that the transmission dynamics of COVID-19 may shift in a detectable manner. However, rates of transmission and health burden of the pandemic in the coming months will be ultimately determined by population factors and disease control policies.
Leave no stone unturned: The hidden potential of carbon and nitrogen cycling by novel, highly adapted Thaumarchaeota in the Atacama Desert hyperarid core
Authors: Hwang Yunha , Schulze-Makuch Dirk , Arens Felix L. , Saenz Johan S. , Adam Panagiotis S. , Bornemann Till L. V. , Airo Alessandro , Schloter Michael , Probst Alexander J. 
Published: July 2020

AbstractThe hyperarid core of the Atacama Desert is an extremely harsh environment previously thought to be colonized by only a few heterotrophic bacterial species. In addition, carbon and nitrogen cycling in these highly oligotrophic ecosystems are poorly understood. Here we genomically resolved a novel genus of Thaumarchaeota, Ca. Nitrosodesertus, found below boulders of the Atacama hyperarid core, and used comparative genomics to analyze their pangenome and site-specific adaptations. Their genomes contain genes for ammonia oxidation and the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, indicating a chemolithoautotrophic lifestyle. Ca. Nitrosodesertus possesses the capacity for tolerating extensive environmental stress highlighted by the presence of genes against oxidative stress, DNA damage and genes for the formation of biofilms. These features are likely responsible for their dominance in samples with extremely low water content across three different boulder fields and eight different boulders. Genome-specific adaptations of the genomes included the presence of additional genes for UV resistance, heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. Our results suggest that Thaumarchaeota mediate important carbon and nitrogen cycling in the hyperarid core of the Atacama and are part of its continuous and indigenous microbiome.
Young consumers' views on humorous BELFcommunication
Authors: Vuorela Taina , Alatalo Sari , Oikarinen Eeva-Liisa , Poutiainen Anne 
Published: July 2020

PurposeThe purpose of this paper is to gain understanding of how young consumers with varying cultural and linguistic backgrounds experience and perceive humorous Business English lingua franca (BELF) mediated communication used in transit contexts.Design/methodology/approachFor the collection of qualitative data, the present study relies on focus group discussions in three European countries. The data were analyzed by the authors by applying the phenomenographic approach as a method.FindingsYoung European consumers expressed a preference for humor and playfulness in BELF-mediated communication, yet they can be a challenging group to be informed and entertained with humorous BELF communication, as they differ in their taste of humor due to varying language- and culture-based identities. However, BELF as a communication tool was seen as functional and unproblematic by the informants. These informants perceive the role of resonant – wit type of humor in BELF – messages with noncultural references as fulfilling some of the aims of the messages. Yet, the role of comic – wit humor in BELF – messages with cultural references is more challenging to interpret.Originality/valueThe present results bring original viewpoints on the use of humor in cross-cultural corporate communication via a unique perspective of how young consumers' perceive and value humor in BELF-mediated communication.
The propaganda of universal fascism: peace, empire and international co-operation in British Union of Fascists' publicity from 1932 to 1939
Authors: Thompson Gareth 
Published: July 2020

PurposeThis article presents a historical investigation into the foreign policy messages of the British Union of Fascists' (BUF) publicity and propaganda from its foundation in 1932 until the outbreak of World War II in 1939, along with a discussion of the methods and institutional arrangements used to propagate its ideas of peace, empire and transnational co-operation.Design/methodology/approachThe historical investigation is based upon scrutiny of original BUF documents relating to the period 1932–1939 from various archives. After cataloguing of the relevant publicity and propaganda materials in time sequence and thematically, analysis was organised using a historical institutionalism approach.FindingsThe article explains the different phases of the BUF's message development and how publications, meetings and media were used to project its ideas. It also discussed the impact of support from Viscount Rothermere's newspapers and financial support from Benito Mussolini. Consideration of publicity materials alongside files from BUF headquarters enabled identification and investigation into the communicative actors who did the publicity work, including Director of Publicity, John Beckett.Social implicationsThe article reflects upon how the British Union of Fascists' publicity and propaganda relates to modern manifestations of the communication of authoritarian and nationalistic political propositions and the historical continuities that endure therein.Originality/valueThe project makes an original contribution to the history of British political propaganda and public relations through an inquiry based upon scrutiny of historical documents in UK archives relating to BUF publicity related to foreign policy.
Multi-scale, multi-physics challenges for future aircraft and hierarchical zonal modelling
Authors: Tucker Paul G. 
Published: July 2020

Purpose
The purpose of this paper is to outline the extensive multi-scale and multi-physics challenges when simulating future aircraft and offer strategies to help deal with some of these challenges.

Design/methodology/approach
To help with the multi-scale challenges, in a hierarchical, zonal fashion both the handling of turbulence and geometry is considered.

Findings
Such modelling of geometry is necessary to help deal with the increasingly coupled nature of many aerodynamic problems more economically and the drive towards considering ever increasing levels of geometrical complexity/scale.

Originality/value
The proposed unified framework could be exploited all the way, through initial fast preliminary design to final numerical test involving various bespoke combinations of hierarchical components.
VBK Fibreo Tech Pvt. Ltd: product mix dilemma
Authors: Dhaigude Amol Subhash , Vandavasi Manikandan , Kasera Apurva Rakesh 
Published: July 2020

Subject area
Operations Research and Operation Management.

Study level/applicability
Undergraduate/MBA/Postgraduate.

Learning outcomes
The case depicts an opportunity for students to be exposed to optimization techniques using linear programming (LP). This case intends to: generate the LP model (identification of objective function and constraints); apply MS-Excel solver to arrive at an optimal solution; analyse manufacturing scenarios; and plan decision dependencies.

Case overview/synopsis
VBK Fibreo Tech Industries was a manufacturer of fibre reinforced plastic (FRP) products for industrial and domestic applications. Despite being a new entrant, it managed to exhibit great performance and attract a loyal base of customers. This case brings to light the problem that the company was facing that is demand exceeding capacity. The protagonist of the case Madhav, the Production Manager, was tasked to solve the problem of “product mix”. He was in a dilemma on how to fulfill customer orders while minimizing losses for his company. He knew that while losses were inevitable in the current scenario, they could be minimized with appropriate planning. Students are expected to use data and facts from the case and exhibit to formulate LP, by identifying the objective function and the constraints. They are also encouraged to use MS-Excel solver to find the optimal product mix and understand the decision dependencies.

Complexity academic level
This case can be used to teach LP in an undergraduate/postgraduate-level course on operations research. Students are exposed to the creation of a mathematical model for optimization and along with devising the implementation plan.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 9: Operations and logistics.
Top management teams characteristics and firms performance: literature review and avenues for future research
Authors: Aboramadan Mohammed 
Published: July 2020

PurposeThe purpose of this paper is to review the empirical literature on the relationship between the characteristics of the top management teams (TMTs) and the performance of entrepreneurial firms.Design/methodology/approachA literature review was carried out on 33 empirical studies related to TMTs and performance through analyzing and summarizing the quantitative studies conducted in this area.FindingsThe results of the literature review show that the relationship between TMTs (demographics and heterogeneity) and the performance of entrepreneurial firms is not straightforward and further investigation is still needed in this area.Practical implicationsThe author maps the theoretical and empirical research of TMT demographics and heterogeneity in relation to firms’ performance and possible moderators and mediators, which govern the relationship between TMT composition and firms’ performance.Originality/valueThe author presents a detailed future research agenda for the purpose of advancing the theoretical and empirical knowledge on TMT-performance links. The review provides a comprehensive picture of TMT-firms’ performance literature and what should be done to enrich the literature.
Servant leadership and affective commitment: the role of psychological ownership and person–organization fit
Authors: Dahleez Khalid Abed , Aboramadan Mohammed , Bansal Anjali 
Published: July 2020

PurposeBuilding on social exchange theory, this study aims to propose a research model to examine the relationship between servant leadership (SL) and employee affective commitment (AC) where psychological ownership (PO) and person–organization fit are theorized to play a mediating role.Design/methodology/approachThe study used quantitative research methods with a deductive approach to examine the proposed relationships and the underlying mechanisms. Data were collected from 346 employees working at higher education sector in Palestine. Data were analyzed using structural equation modeling.FindingsThe results reveal a significant mediating role of PO and person – organization (P-O) fit in explaining the relationship between SL and employee AC. Results indicate that the service orientation and humble attitude of servant leaders toward employees help employees develop a sense of ownership, leading to a better fit with organizational values and thus to a more committed workforce.Practical implicationsThe results of this study may be useful for managers working in higher education in a non-Western context who are considering using SL behaviors to improve outcomes.Originality/valueThe study advances SL research currently in its early stages (Zhanget al., 2019). Moreover, it increases understanding of the mediating roles played by PO and P-O fit.
Branding dilemma: the case of branding Hyderabad city
Authors: Nukhu Rhulia , Singh Sapna 
Published: July 2020

Purpose
Hyderabad City today is a blend of metro and heritage causing much dilemma to what it offers the visitors. A mixture of the “Nawabi – the good old days city” and “information technology hub – a new metropolitan city,” has changed the perception of the city. This has blurred the vision of positioning the city. The purpose of this paper is to analyze the existing city image and the execution of a clear brand message in the face of ambiguous essence of the place.

Design/methodology/approach
The exploratory case study was divided into two parts. In the first stage of the study, an in-depth interview was conducted on tour operators, hotels and hospitality managers, tourists and residents. In the second stage of the study, the review text was scrapped from TripAdvisor. Further text collocate, linked analysis and word trees were done on reviews of Hyderabad city using Voyant tools to find the core attributes of the city image.

Findings
The finding indicates that the city branding is diluted with a blended essence of heritage and metropolis, making the positioning of the city ambiguous. Moreover, the findings reveal that the blend of the two dichotomous characteristics of the city can study out through the implementation of the dual branding and story narration of the city.

Research limitations/implications
The study is no short of limitations, as it is a case-based, subjectivity is inevitable, the selection of the respondents for the interviews was on convenience-based. The number of interviewees for the study is limited thus cannot be generalized. In addition, another limitation of the study is that only few reviews on Hyderabad city were found on TripAdvisor not enough to sustain more elaborated results and, as the reviews were basically from tourists, further there may be some elimination of other important aspects of the city. Text analysis has its own limitation such as it cannot track sarcasm or identify the spelling errors or synonymous. Despite the limitations, the study attempts to shed some light on the city’s needs to rebranding.

Practical implications
One of the important contributions of the study is its implications, for tour operators and policymakers. For the former, the need to communicate and position the brand and develop a strategy that bridges the gap between heritage image and metropolis. In addition, for the later, for setting the national urban policies that conserve the heritage sites and improvise the management.

Social implications
To conserve the culture, tradition and heritage sites in the impetus of the city’s phenomenal urbanization and development.

Originality/value
City as a brand is complex, the present research brings out the complexity based on the essence of the city bridging the gap through an insightful approach. Expanding the body of knowledge, at the same time providing insightful implications for destination stakeholders such as managers, policymakers and destination management organizations.