bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Staphylococcus aureusSigS induces expression of a regulatory protein pair that modulate its mRNA stability”
Authors: Ali Amer Al , Alsulami Jamilah , Aubee Joseph I , Idowu Ayotimofe , Tomlinson Brooke R. , Felton Emily A. , Jackson Jessica K. , Shaw Lindsey , Thompson Karl M 
Published: October 2022

ABSTRACTSigS is the sole extracytoplasmic function sigma inS. aureusand is necessary for virulence, immune evasion, as well as surviving exposure to toxic chemicals and environmental stressors. Despite the contribution of SigS to a myriad of critical phenotypes, the downstream effectors of the SigS-dependentS. aureuspathogenesis, immune evasion, and stress response remain elusive. To address this knowledge gap, we analyzed theS. aureustranscriptome following transient over-expression of SigS. We identified a bi-cistronic transcript, up-regulated by 1000-fold, containing two mid-sized genes each containing single domains of unknown function (DUF). We renamed these genessroA(SigSregulatedorfA) andsroB(SigSregulatedorfB). We demonstrated that the SigS regulation of thesroABoperon is direct using in vitro transcription analysis. Using northern blot analysis, we also demonstrated that SroA and SroB have opposing auto- regulatory functions on the transcriptional architecture of thesigSlocus; with SroA stimulated SigS mRNA levels and SroB stimulating s750 (SigS antisense) levels. We hypothesized that these this opposing regulatory effects were due to a direct interaction. We demonstrated an interaction between SroA and SroB using an in-vivo surrogate genetics approach via Bacterial Two Hybrid. We demonstrated that the SroA effect on SigS is at the post-transcriptional level of mRNA stability, highlighting a mechanism likely used byS. aureusto tightly control SigS levels. Finally, we demonstrate that thesroABlocus promotes virulence in a female murine pneumonia model of infection.
Pseudomonas aeruginosaincreases the susceptibility ofCandida albicansto amphotericin B in dual species biofilms
Authors: Alam Farhana , Blackburn Sarah , Correia Joao , Blair Jessica , Hall Rebecca A 
Published: October 2022

AbstractBiofilms are the leading cause of nosocomial infections, and are hard to eradicate due to their inherent antimicrobial resistance.Candida albicansis the leading cause of nosocomial fungal infections, and is frequently co-isolated with the bacteriumPseudomonas aeruginosafrom biofilms in the Cystic Fibrosis lung and severe burn wounds. The presence ofC. albicansin multi-species biofilms is associated with enhanced antibacterial resistance, which is largely mediated through fungal extracellular carbohydrates sequestering the antibiotics. However, significantly less is known regarding the impact of polymicrobial biofilms on antifungal resistance. Here we show that, in dual species biofilms,P. aeruginosaenhances the sensitivity ofC. albicansto amphotericin B, an effect that was biofilm specific. Transcriptional analysis combined with gene ontology enrichment analysis identified severalC. albicansprocesses associated with oxidative stress to be differentially regulated in dual species biofilms, suggesting thatP. aeruginosaexerts oxidative stress onC. albicans, likely through the actions of secreted phenazines. However, the mitochondrial superoxide dismutaseSOD2was significantly downregulated in the presence ofP. aeruginosa.Monospecies biofilms of thesod2Δ mutant were more susceptible to amphotericin B, and the susceptibility of these biofilms was further enhanced by the addition of exogenous phenazines. Therefore, we propose that in dual species biofilms,P. aeruginosasimultaneously induces mitochondrial oxidative stress, whilst downregulating key detoxification enzymes, which preventC. albicansmounting an appropriate oxidative stress response to amphotericin B, leading to fungal cell death. This work highlights the importance of understanding the impact of polymicrobial interactions on antimicrobial susceptibility.ImportanceBiofilms are aggregates of cells encased in an extracellular matrix, and are responsible for the majority of infections in hospitals. The Gram-negative bacteriumPseudomonas aeruginosa, and the fungal pathogenCandida albicansare frequently co-isolated from biofilms in the Cystic Fibrosis lung, and in burn wounds. Here we show that in these biofilms,P. aeruginosasecreted phenazines induce mitochondrial reactive oxygen species stress, which enhances the sensitivity ofC. albicansto the antifungal amphotericin B. This work highlights the importance of understanding the impact of polymicrobial interactions on antimicrobial susceptibility.
High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality
Authors: Ghomi Fatemeh A. , Langridge Gemma C. , Cain Amy K. , Boinett Christine , Abd El Ghany Moataz , Pickard Derek J. , Kingsley Robert A. , Thomson Nicholas R. , Parkhill Julian , Gardner Paul P. , Barquist Lars 
Published: October 2022

AbstractThe Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the gut commensal and model organismEscherichia coli, as well as several major human pathogens including multiple serovars ofSalmonella entericaandKlebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, with theE. coliKeio single-gene deletion library often regarded as a gold standard for gene essentiality studies. However, it remains unclear how gene essentiality varies between related strains and species. To investigate this, we have assembled a collection of thirteen sequenced high-density transposon mutant libraries from five genera within the Enterobacteriaceae. We first benchmark a number of gene essentiality prediction approaches, investigate the effects of transposon density on essentiality prediction, and identify biases in transposon insertion sequencing data. Based on these investigations we develop a new classifier for gene essentiality. Using this new classifier, we define a core essential genome in the Enterobacteriaceae of 201 universally essential genes, and reconstruct an ancestral essential gene set of 296 genes. Despite the presence of a large cohort of variably essential genes, surprisingly we find an absence of evidence for genus-specific essential genes. A clear example of this sporadic essentiality is given by the set of genes regulating the σEextracytoplasmic stress response, which appears to have independently become essential multiple times in the Enterobacteriaceae. Finally, we compare our essential gene sets to the natural experiment of gene loss in obligate insect endosymbionts that have emerged from within the Enterobacteriaceae. This isolates a remarkably small set of genes absolutely required for survival, and uncovers several instances of essential stress responses masked by redundancy in free-living bacteria.
Modifications in the piperazine ring of nucleozin affects anti-influenza activity
Authors: Correa-Padilla Erick , Hernández-Cano Alejandro , Cuevas Gabriel , Acevedo-Betancur Yunuen , Esquivel-Guadarrama Fernando , Madariaga-Mazon Abraham , Martinez-Mayorga Karina 
Published: October 2022

ABSTRACTThe infection caused by influenza virus is a latent tret, to contribute on the advancement of the discovery and design of nucleozin analogs, a molecule with antiinfluenza activity, we analyzed nucleozin analogs with modifications in the piperazine system, which leads to molecules with larger conformational freedom. Following a new nucleozin synthetic strategy, we obtained three new nucleozin analogs, and two of them were biologically evaluatedin vitroand were less active than nucleozin. The loss of activity in the more flexible molecules highlights the need for the piperazine ring to maintain the activity of nucleozin analogues. Interestingly, this coincides with a QSAR model developed here for the prediction of the anti-influenza activity. The proposed model, along with the synthetic route, will be useful for further development of nucleozin analogues with antiviral activity.
De novodesign of anti-variant COVID-19 Vaccine
Authors: Goswami Arpita , Kumar S. Madan , Ullah Samee , Gore Milind M. 
Published: October 2022

AbstractRecent studies have shown the efficacy of hybrid SARS-COV-2 vaccines using wild-type nucleocapsid (N) and Spike (S) protein. We upgraded this strategy one step further using clinically proven spike protein by considering the delta and post-delta omicron variant of concern (VOC) mutations and nucleocapsid peptides conferring T-cell immunity. Nucleocapsid peptides are considered much better immunological replacement of nucleocapsid proteins. Hence, peptide linking strategy is applied which is more economic for cellular biosynthesis than whole proteins. An envelope peptide with potent T-cell immune response is also selected. All these peptides are clustered in this hybrid spike’s designed cytoplasmic region separated by non-immunogenic helical linkers. The resulting domain is more folded in the construct devoid of transmembrane domain after AlphaFold analysis. Alongside, we also propose the idea of introduction of any T-cell peptide like other Human Corona Viruses (HuCoV) in these linker regions whenever required. In addition to SARS-COV-2, the same approach can be applied for any emergency or even long-term unsolved outbreaks of Influenza, Dengue and West Nile Virus etc. In this era of novelty as presented by subunit and nucleic acid vaccines, multiepitope strategies like this can help to combat multiple diseases successfully in real time to give hope for better future.
Identifying Genetic Regulatory Variants that Affect Transcription Factor Activity
Authors: Li Xiaoting , Lappalainen Tuuli , Bussemaker Harmen J. 
Published: October 2022

SUMMARYAssessing the functional impact of genetic variants across the human genome is essential for understanding the molecular mechanisms underlying complex traits and disease risk. Genetic variation that causes changes in gene expression can analyzed through parallel genotyping and functional genomics assays across sets of individuals. Trans-acting variants are of particular interest, but more challenging to identify than cis-acting variants. Here, to map variants that impact the expression of many genes simultaneously through a shared transcription factor (TF), we use an approach in which the protein-level regulatory activity of the TF is inferred from genome-wide expression data and then genetically mapped as a quantitative trait. To analyze RNA-seq profiles from the Genotype Tissue Expression (GTEx) project, we developed a generalized linear model (GLM) to estimate TF activity levels in an individual-specific manner. A key feature is that we fit a beta-binomial GLM at the level of pairs of neighboring genes in order to control for variation in local chromatin structure along the genome and other confounding effects. As a predictor in our model we use differential gene expression signatures from TF perturbation experiments. We estimated genotype-specific activities for 55 TFs across 49 tissues and performed genome-wide association analysis on the virtual TF activity trait. This revealed hundreds of TF activity quantitative trait loci, or aQTLs. Altogether, the set of tools we introduce here highlights the potential of genetic association studies for cellular endophenotypes based on a network-based multi-omic approach.
The comparative advantages in the wooden furniture industry: does the export price matter?
Authors: Topcu Yunus Emre 
Published: October 2022

Purpose
The purpose of this paper is to evaluate the global competitiveness of the top ten wooden furniture exporting countries with several approaches and to test the effect of export prices (EXPRs) on the global competition.

Design/methodology/approach
Countries' competitiveness levels were measured with revealed comparative advantage (RCA), normalised RCA (NRCA), revealed symmetric comparative advantage (RSCA) and trade balance index. Furthermore, panel regression analysis techniques were used to test the effects of EXPR on RCA, NRCA and RSCA in the wooden furniture industry (WFI).

Findings
Although the comparative advantage approaches give different results, the global competitiveness of Poland and Vietnam is at a high level in all approaches. Canada has been the country with the weakest global competitiveness in all approaches. According to the results of the analysis, EXPRs positively affect all the competitive advantage indexes. As a result, the competitiveness of the WFI is affected by the non-price factors instead of the EXPR.

Research limitations/implications
The framework allows us to measure and illustrate the export competitiveness of the WFI and permits a global comparison. Similar analyses can be made for different labour-intensive sectors. In addition, analysis can be made to identify non-price factors for the WFI sector. Thus, more specific inferences can be made.

Practical implications
This study is useful for policymakers, government officials, the industry associations and the company executives to assess their export competitiveness in the WFI. Thus, they can determine whether to shift scarce resources to this industry or other industries. In addition, this study may affect the price competition policy of the sector representatives in the global market.

Originality/value
This study deals with the competitiveness of the WFI with different approaches. And this study determines the importance of price for global competition in this sector.
Family incivility and workplace bullying: mediating and moderating model of psychological safety, optimism and organization-based self-esteem
Authors: Paul Vincent Maria Tresita , P.M. Nimmi , Jose Geetha , John Anjali , Kuriakose Vijay 
Published: October 2022

Purpose
This study aims to explore how family incivility is linked to workplace bullying among employees. This study examines the role of psychological safety as an explanatory mechanism linking both. This paper also looks into the moderating roles of optimism between family incivility and psychological safety and organization-based self-esteem (OBSE) between psychological safety and workplace bullying.

Design/methodology/approach
Drawing from the conservation of resources theory and work home resources model, this study developed various hypotheses. The proposed relationships were tested using responses gathered from 260 teaching faculty across the universities in India. This study used Warp-PLS for data analysis.

Findings
The findings suggest that psychological safety mediated the relationship between experienced family incivility and workplace bullying. This study also found support for the mediating role of psychological safety. Further, this study has proved that trait optimism and OBSE are boundary conditions influencing the outcomes of family incivility.

Practical implications
The findings have practical implications for teachers, educational institution leaders and policymakers. This study augments the importance of cultivating optimism and OBSE to combat conflicting situations. Employees who practice optimism on a daily basis are high in psychological safety and when supported with OBSE by the institution, the impact of family incivility and its adverse effects in the workplace is reduced, curbing the instances of workplace bullying.

Originality/value
To the best of the authors’ knowledge, this is one of the first studies to establish the role of “organizational resource,” OBSE, as a coping mechanism in tackling the adverse effects of family incivility. From a resource perspective, this study is one of the first to look into the enablers and inhibitors of resource creation in an individual while experiencing family incivility.
Determination of health workers' perceptions of the disaster management process and gender inequality: the case of a state hospital in Turkey
Authors: Çoban Büşra Nur , İnal Önal Ebru 
Published: October 2022

PurposeThis study aims to identify levels of gender perception specific to disaster management process and gender-related factors among the health workers employed at Çan State Hospital, Turkey.Design/methodology/approachThe study was carried out with a survey form consisting of 41 questions created by researchers with 207 health workers working at Çan State Hospital and by means of face-to-face interview technique. SPSS ver. 19.0 statistics software package was used in the research for analysis of data.FindingsOf the participants, 70.24% had experienced a disaster before; 88.03% reported that women and men were equally affected by disasters and 72.94% reported that women and men were equally affected by the COVID-19 pandemic. The majority of the participants (70.29%) reported that the COVID-19 pandemic affected health workers of both genders equally. The health workers who consider that the disaster legislation is gender-sensitive, who have attended any disaster response training and who consider that women are included in the fragile/vulnerable group in disaster response activities have been found out to have significantly higher gender perception scores specific to disaster management process (p < 0.05). Most of the participants stated that both genders were affected equally by the disasters they experienced, which manifests that they adopted an egalitarian approach.Practical implicationsThis study revealed the importance of providing disaster training for health workers to improve the gender perceptions. It is of high significance to integrate gender into the disaster trainings.Originality/valueThis study identifies and evaluates health workers' disaster-specific perceptions of gender, and necessary response activities can be performed accordingly.
SARS-CoV-2 seroprevalence study after the first wave among persons living and working in an overcrowded Swiss prison
Authors: Gétaz Laurent , Wolff Hans , Gonçalves Leonel , Togni Giuseppe , Stringhini Silvia , Chacowry Pala Komal , Iten Anne , Guessous Idris , Kaiser Laurent , Chappuis Francois , Baggio Stéphanie 
Published: October 2022

Purpose
Prisons can be epicentres of infectious diseases. However, empirical evidence on the impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in prison is still scarce. This study aims to estimate the seroprevalence rates of anti-SARS-CoV-2 in the largest and most crowded Swiss prison and compare them with the seroprevalence rate in the general population.

Design/methodology/approach
A cross-sectional study was conducted in June 2020, one month after the first wave of SARS-CoV-2 in Switzerland. Groups included: people living in detention (PLDs) detained before the beginning of the pandemic (n = 116), PLDs incarcerated after the beginning of the pandemic (n = 61), prison staff and prison healthcare workers (n = 227) and a sample from the general population in the same time period (n = 3,404). The authors assessed anti-SARS-CoV-2 IgG antibodies.

Findings
PLDs who were incarcerated before the beginning of the pandemic had a significantly lower seroprevalence rate [0.9%, confidence interval (CI)95%: 0.1%–5.9%] compared to the general population (6.3%, CI 95%: 5.6–7.3%) (p = 0.041). The differences between PLDs who were incarcerated before and other groups were marginally significant (PLDs incarcerated after the beginning of the pandemic: 6.6%, CI 95%: 2.5%–16.6%, p = 0.063; prison staff CI 95%: 4.8%, 2.7%–8.6%, p = 0.093). The seroprevalence of prison staff was only slightly and non-significantly lower than that of the general population.

Originality/value
During the first wave, despite overcrowding and interaction with the community, the prison was not a hotspot of SARS-CoV-2 infection. Preventive measures probably helped avoiding clusters of infection. The authors suggest that preventive measures that impact social welfare could be relaxed when overall circulation in the community is low to prevent the negative impact of isolation.
SNS use reduction: a two-facet privacy concern perspective
Authors: Neves Joana , Turel Ofir , Oliveira Tiago 
Published: October 2022

PurposeWhile social networking sites (SNS) have many positive aspects, they can have several adverse outcomes, among which privacy violations are a vital concern. The authors first posit that concerns regarding privacy violations can drive attempts to reduce SNS use. Next, the authors note that these violations can have two sources: peers and the social media provider. Thus, there is a need to understand how this complex system of privacy concerns affects use reduction decisions. To do so, this paper aims to examine the separate and joint roles of institutional and peer privacy concerns in driving SNS use reduction.Design/methodology/approachBased on privacy calculus theory, the authors propose a theoretical model to explain SNS use reduction, with institutional and peer privacy concerns as independent variables. The authors empirically examine the research model using a sample of 258 SNS users.FindingsThis study reveals that institutional and peer privacy concerns independently increase one's intention to reduce SNS use and that institutional privacy concern strengthen the relation between peer privacy concern and the intention to reduce SNS use.Originality/valueResearch thus far has not examined how the two facets of privacy work in tandem to affect 'users' decisions to change their behaviors on SNS platforms. Considering the unique and joint effect of these facets can thus provide a more precise and realistic perspective. This paper informs theories and models of privacy and online user behavior change.
Searching for Swedish LGBTQI fiction: challenges and solutions
Authors: Golub Koraljka , Bergenmar Jenny , Humlesjö Siska 
Published: October 2022

PurposeThe purpose of this study is to investigate the needs of potential end-users of a database dedicated to Swedish lesbian, gay, bisexual, transgender, queer, and intersex (LGBTQI) literature (e.g. prose, poetry, drama, graphic novels/comics, and illustrated books), in order to inform the development of a database, search interface functionalities, and an LGBTQI thesaurus for fiction.Design/methodology/approachA web questionnaire was distributed in autumn 2021 to potential end-users. The questions covered people's reasons for reading LGBTQI fiction, ways of finding LGBTQI fiction, experience of searching for LGBTQI fiction, usual search elements applied, latest search for LGBTQI fiction, desired subjects to search for, and ideal search functionalities.FindingsThe 101 completed questionnaires showed that most respondents found relevant literature through social media or friends and that most obtained copies of literature from a library. Regarding desirable search functionalities, most respondents would like to see suggestions for related terms to support broader search results (i.e. higher recall). Many also wanted search support that would enable retrieving more specific results based on narrower terms when too many results are retrieved (i.e. higher precision). Over half would also appreciate the option to browse by hierarchically arranged subjects.Originality/valueThis study is the first to show how readers of LGBTQI fiction in Sweden search for and obtain relevant literature. The authors have identified end-user needs that can inform the development of a new database and a thesaurus dedicated to LGBTQI fiction.