bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual RNA-seq identifies proteins and pathways modulated duringClostridioides difficilecolonisation
Authors: Frost Lucy R. , Stark Richard , Anonye Blessing , Ferreira Ludmila R. P. , Unnikrishnan Meera 
Published: January 2023

AbstractThe gastrointestinal pathogen,Clostridioides difficile, is the most common cause of hospital-acquired diarrhoea. Bacterial interactions with the gut mucosa are crucial for colonisation and establishment ofC. difficileinfection, however, key infection events like bacterial attachment and gut penetration are still poorly defined. To better understand the initial events that occur when this anaerobic pathogen interacts with human gut epithelial cells, we employed a dual RNA-sequencing approach to study the bacterial and host transcriptomic profiles duringC. difficileinfection in a dual-environmentin vitrohuman gut model. Temporal changes in gene expression during infection were studied in the bacterium and the host cells over the course of 3-24 hours. While there were several common differentially expressed bacterial genes across the different times after infection, mammalian transcriptional profiles were quite distinct with little overlap. Interestingly, an induction of colonic receptors forC. difficiletoxins was observed, along with the expression downregulation of genes encoding immune response markers. Several cell wall associated proteins were downregulated inC. difficilewhen in association with host cells, includingslpA, which encodes the main S-layer protein. Gene function and pathway enrichment analyses revealed a potential modulation of the purine/pyrimidine synthesis pathways both in the mammalian and the bacterial cells. We observed that proline-proline endopeptidase, a secreted metalloprotease responsible for cell surface protein cleavage, is downregulated during infection, and a mutant lacking this enzyme demonstrated enhanced adhesion to epithelial cells during infection. This study provides new insight into the host and bacterial pathways based on gene expression modulation during the initial contact ofC. difficilewith gut cells.ImportanceThe initial interactions between the colonic epithelium and the bacterium are likely critical in the establishment ofClostridioides difficileinfection, one of the major causes of hospital acquired diarrhoea worldwide. Molecular interactions betweenC. difficileand human gut cells have not been well defined mainly due to the technical challenges of studying cellular host-pathogen interactions with this anaerobe. Here we have examined transcriptional changes occurring in the pathogen and host cells during the initial 24 hours of infection. Our data indicate several changes in metabolic pathways and virulence-associated factors during the initial bacterium-host cell contact and early stages of infection. We describe canonical pathways enriched based on the expression profiles of a dual RNAseq in the host and the bacterium, and functions of bacterial factors modulated during infection. This study provides insight into the early infection process at a molecular level.
Identification of functionalNpuDnaE and gp41-1 inteins split in three fragments
Authors: Weis Daniel , Palanisamy Navaneethan , Ballestin Jara Ballestin , Öztürk Mehmet Ali , Di Ventura Barbara 
Published: January 2023

AbstractInteins are special proteins that auto-catalytically carry out a protein splicing reaction. Due to their ability to post-translationally modify target proteinsin vitroandin vivo, they are used in different applications, ranging from protein purification to the construction of Boolean logic gates. So far inteins have been found to be either encoded by a single gene (contiguous inteins) or by two separate ones (split inteins). Previously, it has been shown that the contiguousSspandRmaDnaB inteins and the splitNpuDnaE intein could be artificially split in three fragments and retain functionality. Here we report the identification of novel split sites within the N-terminal fragments of theNpuDnaE and gp41-1 split inteins that lead to synthetic functional three-piece versions of these inteins. These variants contribute to the toolkit of three-piece inteins that could be used in biotechnological applications based on highly-fragmented inteins.
Adaptive and maladaptive consequences of deregulation in a bacterial gene regulatory network
Authors: Vinchhi Rhea , Yelpure Chetna , Balachandran Manasvi , Matange Nishad 
Published: January 2023

AbstractThe archetypal PhoQP two-component system from Enterobacteria regulates crucial pathways like magnesium homeostasis inEscherichia coliand virulence factor expression inSalmonella enterica. Previously we had reported that a laboratory strain ofE. colirapidly accumulated loss-of-function mutations in themgrBgene, a negative feedback regulator of PhoQP, when evolved in the presence of the antibiotic trimethoprim. Hyperactive PhoQP enhanced the expression of dihydrofolate reductase (folA), target of trimethoprim, resulting in antibiotic tolerance. Here we ask, firstly, how important are mutations inmgrBfor trimethoprim resistance? Using laboratory evolution, we show that trimethoprim resistance evolves by different mutational trajectories under condition of high and low PhoQP activity. Mutations inmgrBare only fixed when PhoQP is active. Importantly, loss of functional MgrB, though itself only mildly beneficial, enhances the fixation probability of trimethoprim-resistant bacteria under selection and this can be explained by epistasis betweenmgrBandfolAloci. As a result, the activation status of PhoQP directly impacts how fast resistance is acquired by evolving populations ofE. coli. Secondly, we investigate why negative feedback may be needed in the PhoQP system. We show that under drug-free conditions MgrB is required to mitigate the fitness costs of pervasive gene dysregulation by hyperactive PhoQP. Using RNA-seq transcriptomics and genetic analyses, we demonstrate that PhoQP-hyperactivation perturbs the balance of RpoS and RpoD-regulated transcriptional programs, and spontaneous mutations inrpoSrectify this imbalance. We propose that deregulation can be adaptive or maladaptive depending on the environmental context and this explain the evolution of negative feedback in bacterial gene regulatory networks.
Structure of a Membrane Tethering Complex Incorporating Multiple SNAREs
Authors: DAmico Kevin A. , Stanton Abigail E. , Shirkey Jaden D. , Travis Sophie M. , Jeffrey Philip D. , Hughson Frederick M. 
Published: January 2023

ABSTRACTMost membrane fusion reactions in eukaryotic cells are mediated by membrane tethering complexes (MTCs) and SNARE proteins. MTCs are much larger than SNAREs and are thought to mediate the initial attachment of two membranes. Complementary SNAREs then form membrane-bridging complexes whose assembly draws the membranes together for fusion. Here, we present a cryo-EM structure of the simplest known MTC, the 255-kDa Dsl1 complex, bound to the two SNAREs that anchor it to the endoplasmic reticulum. N-terminal domains of the SNAREs form an integral part of the structure, stabilizing a Dsl1 complex configuration with remarkable and unexpected similarities to the 850-kDa exocyst MTC. The structure of the SNARE-anchored Dsl1 complex and its comparison with exocyst reveal what are likely to be common principles underlying MTC function. Our structure also implies that tethers and SNAREs can work together as a single integrated machine.
Human Amylin in the Presence of SARS-COV-2 Protein Fragments
Authors: Chesney Andrew D. , Maiti Buddhadev , Hansmann Ulrich H. E. 
Published: January 2023

ABSTRACTCovid-19 can lead to the onset of type-II diabetes which is associated with aggregation of islet amyloid polypeptides, also called amylin. Using molecular dynamics simulations, we investigate how the equilibrium, between amylin monomers in its functional form and fibrils associated with diabetes, is altered in presence of SARS-COV-2 protein fragments. For this purpose, we study the interaction between the fragment SFYVYSRVK of the Envelope protein or the fragment FKNIDGYFKI of the Spike protein with the monomer and two amylin fibril models. Our results are compared with earlier work studying such interactions for two different proteins.
Fitness effects of mutations to SARS-CoV-2 proteins
Authors: Bloom Jesse D. , Neher Richard A. 
Published: January 2023

ABSTRACTKnowledge of the fitness effects of mutations to SARS-CoV-2 can inform assessment of new variants, design of therapeutics resistant to escape, and understanding of the functions of viral proteins. However, experimentally measuring effects of mutations is challenging: we lack tractable lab assays for many SARS-CoV-2 proteins, and comprehensive deep mutational scanning has been applied to only two SARS-CoV-2 proteins. Here we develop an approach that leverages millions of publicly available SARS-CoV-2 sequences to estimate effects of mutations. We first calculate how many independent occurrences of each mutation are expected to be observed along the SARS-CoV-2 phylogeny in the absence of selection. We then compare these expected observations to the actual observations to estimate the effect of each mutation. These estimates correlate well with deep mutational scanning measurements. For most genes, synonymous mutations are nearly neutral, stop-codon mutations are deleterious, and amino-acid mutations have a range of effects. However, some viral accessory proteins are under little to no selection. We provide interactive visualizations of effects of mutations to all SARS-CoV-2 proteins (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework we describe is applicable to any virus for which the number of available sequences is sufficiently large that many independent occurrences of each neutral mutation are observed.
Evaluating workforce needs for higher specialist training for psychiatry of intellectual disability in Kent, Surrey and Sussex: a workforce scoping service evaluation
Authors: Mukherjee Raja A.S. , Ondrusz Mary 
Published: January 2023

Purpose
Whilst recruitment and retention of high-quality staff is vital to providing a good service, at the time of the evaluations, Kent, Surrey and Sussex (KSS) was the only area of the UK without a Higher Specialist Training (HST) scheme in intellectual disability (ID). The purpose of this project was to identify barriers to recruitment and support the need for change.

Design/methodology/approach
This evaluation included conducting interviews with 16 practitioners in the region with links to ID to consider the gaps in training and find solutions.

Findings
Four themes were identified, namely, good experiences are important to recruiting people into the ID field; bad experiences or lack of exposure to people with ID are likely to prevent engagement with this field; there is an ongoing need for specialist psychiatrists in ID services; and there is a developing need for specialists in neurodevelopmental disorders. Finally, the challenge means we need to think differently about developing a workforce. Seven recommendations to support workforce delivery in KSS were developed.

Originality/value
This paper highlights an important rationale for ongoing need for HST in ID work and also reasons to engage people in this field. This has not been undertaken in the ID field in this way previously.
“My contract is breached, and I want to leave, but I am embedded!” how do reluctant stayers respond?
Authors: Singh Riann 
Published: January 2023

PurposeThis study takes a unique perspective on the role of psychological contract breach, turnover intentions and off-the-job embeddedness in influencing the behavior of reluctant stayers. More specifically, reluctant stayers are defined as employees who are high on turnover intentions and off-the-job embeddedness. It proposes that employees who perceive psychological contract breaches are more likely to develop turnover intentions. Such breaches are expected to indirectly spur organizational deviance, with turnover intentions as the mediator. Finally, a moderated-mediation model is proposed where off-the-job embeddedness is expected to moderate the relationship between turnover intentions and organizational deviance.Design/methodology/approachData were collected from 231 employees across the energy sector within the Caribbean nation of Trinidad, using a two-wave research design and a path-analytic approach.FindingsThe findings provide support for the propositions that perceived psychological contract breach predicts turnover intentions and that turnover intentions mediate the contract breach–organizational deviance relationship. Further, the proposition that off-the-job embeddedness moderates the relationship between turnover intentions and organizational deviance was supported by the sample data. Consequently, reluctant stayers (employees with high turnover intentions and high off-the-job embeddedness) responded to perceived psychological contract breach with higher levels of organizational deviance when they were more deeply embedded.Originality/valueLimited studies have explored the behaviors of reluctant stayers, and hence this study adds to research on this emerging classification of employees. Furthermore, no study has yet explored the role of high turnover intentions and off-the-job embeddedness in creating reluctant stayers.
Critical project management success factors analysis for the construction industry of Bangladesh
Authors: Datta Shuvo Dip , Sobuz Md. Habibur Rahman , Nafe Assafi Mohammad , Sutan Norsuzailina Mohamed , Islam Md. Nazrul , Mannan Maria Binte , Akid Abu Sayed Mohammad , Hasan Noor Md. Sadiqul 
Published: January 2023

PurposeThis paper aims to identify the critical project management success factors and analyze those factors to achieve a sustainable construction industry in Bangladesh.Design/methodology/approachThis study identified 41 major problematic factors from the related literature. In this research, a detailed questionnaire survey was conducted among the experts and stakeholders of the construction industry of Bangladesh. The survey was carried out on a Likert scale and ranked the critical factors using the relative importance index (RII). The 41 problematic factors were divided into five group factors and ranked by the RII index to prioritize the factors. Finally, stakeholders' opinions were analyzed with the critical assessed factors, which was a very effective technique to eliminate the risks and uncertain occurrences in the construction industry of Bangladesh.FindingsThe factors analysis revealed that cost overrun, traffic jam, low wedges, slow payment for completed works and financial issues of the owner were leading critical factors in construction projects. Moreover, the critical factors are divided into five-factor groups, namely, financial management, monitoring and feedback, competency management, communication and coordination management, and risk management, which exhibit 0.767, 0.720, 0.711, 0.710 and 0.658 RII values. After all, the stakeholders' opinion suggested that implementing modern tools and techniques can help to avoid the critical situation in the construction industry of Bangladesh.Practical implicationsThe construction industry of Bangladesh is moving away from stable construction work day by day. Previously, the potential CSFs were discussed unstructured way. Hence, detecting early warning signals in a structured way has become necessary for the building firm's survival.Originality/valueThough some scattered critical issues are discussed in different literature, the critical issues of the Bangladeshi construction industry were not investigated extensively. Therefore, this study finds out the potential critical issues of the construction industry of Bangladesh to accumulate such harmful construction issues in a single platform so that the construction industry can have an overview of them with the help of innovative technologies.
Breaking out of the expatriate bubble in Denmark: insights from the challenge of making connections with local Danes
Authors: van Bakel Marian , Vance Charles M. 
Published: January 2023

PurposeThe social context of expatriation is crucial for expatriate success, including for building local host country national (HCN) social network support that can facilitate effective adjustment through information exchange. However, expatriates have particular difficulties in breaking out of the expatriate bubble and building social ties with HCNs in certain countries, especially in Scandinavia. This paper focuses on the case of Denmark and explains why many expatriates find it difficult to make social connections with Danes.Design/methodology/approachThis study involves a meta-ethnography of literature on Danish culture, as well as semistructured interviews with a total of 16 expatriates in Denmark.FindingsThree main cultural elements are identified as crucial for explaining the difficulty expatriates face in connecting with Danes, namely homogeneity, the value placed on equality and the public–private divide. The homogeneity and inward-looking mentality make it more difficult for outsiders to break into the social circle. Outsiders have to earn the trust that is difficult to obtain, reflecting Denmark's high score on GLOBE's institutional collectivism.Practical implicationsIn light of the challenges that many expatriates face in creating a new social network abroad, organizations can support them in several ways. The authors discuss context-specific strategies for making new social connections in Denmark, which may be usefully applied in other countries.Originality/valueThis study focuses on the context of expatriate social network formation and shows that cultural differences in socializing affect the ease with which expatriates can make connections with HCNs, who can have a positive impact on expatriate adjustment and performance success.
Risk analysis of the rice supply chain in Cambodia
Authors: Rath Bunhorng , Wonginta Thitima , Amchang Chompoonut 
Published: January 2023

PurposeThis paper aims to analyze the risks faced by the Cambodian rice supply chain (RSC), including risk identification, risk investigation and risk management.Design/methodology/approachThe first qualitative area of exploration from this exploratory sequential design is to identify the potential risks, in which the authors conduct in-depth interviews with ten different experts in Cambodia. Using the structural equation model (SEM) in AMOS and descriptive statistics analysis, this study investigates the risks that affect the RSC performance on an environmental, social and economic basis and subsequently proposes risk management strategies. The authors collect quantitative data from 200 Cambodian farmers through interviews and surveys.FindingsThe results illustrate that the farm households face 18 risk factors. The researchers consolidate 18 risk factors into four classifications: supply risks, production risks, demand risks and environmental risks. Nine experts out of the ten who were interviewed (90%) consider themselves “highly vulnerable” (with a rating of 4 or 5 on the Likert scale), while only one expert has a “neutral” stance (with a rating of 3 on the Likert scale); these results concerning risk identification are visualized in the likelihood effect matrix of the RSC. After investigating the risks, the authors found that RSC performance is significantly affected by the RSC risks. In particular, four groups are created, representing two different approaches to mitigate, avoid, transfer and cope with agricultural risks, i.e. ex ante and ex post risk management strategies.Originality/valueThis study fully answers research questions regarding risk identification, risk investigation and risk management.
His, hers and theirs: comparative narratives from young people who use violence
Authors: Rak Louise , Warton Timothy 
Published: January 2023

PurposeThis paper aims to explore narratives of violence in the lives of young men and young women in Australia. Through partnering with young people to understand and make meaning of their stories, the authors highlight similarities and differences in gendered experiences of violence, and the implications of these for cross-disciplinary practice.Design/methodology/approachThis article presents the synthesis of narrative data from two separate studies that worked with justice-involved young men and young women, who had both experienced and used violence. Study 1 used a thematic analysis of practitioner narratives and qualitative data from in-session narratives. Study 2 used a thematic analysis of interview data using grounded approach and peer review to promote trustworthiness and inter-rater reliability.FindingsInsights on the experiences of young people who use violence are notably absent in most forms of violence discourse, practice and research. Findings demonstrate that understandings of youth violence are linked to identity, but also situated within contexts of trauma, place, gender, relationality and community. This conceptualisation of violence is particularly important to understandings of young female violence.Originality/valueThrough collaborative approaches of co-design and co-production, the paper outlines that a stronger understanding of the experiences of young men and young women (often an over-looked cohort) in the justice system can help improve the trauma-informed and gender responsiveness of interventions across practice settings. The authors highlight that exploring gendered differences in narratives of youth violence is necessary and seeking lived experiences of youth justice young people is instructive to academia, policy and practice.
Psychometric attributes associated with attrition within a prison-based democratic therapeutic community
Authors: Pointon Victoria Jade , Roberts Rachel 
Published: January 2023

Purpose
The purpose of this paper is to examine the psychometric characteristics of male offenders who joined a democratic therapeutic community and their relationship to attrition.

Design/methodology/approach
Residents who left therapy prematurely during the assessment phase (N = 46) and residents who left therapy prematurely during core therapy (N = 202) were compared to residents who completed therapy (N = 52) on two psychometric measures: Raven’s Standard Progressive Matrices and The Blame Attribution Inventory.

Findings
A multinomial logistic regression analysis showed higher levels of external blame can predict attrition during therapy; those with higher levels of external attribution are significantly more likely to leave therapy prematurely, including both during the assessment phase and during core therapy. Raven's Standard Progressive Matrices score did not significantly predict whether an individual left therapy prematurely.

Originality/value
Support was found for existing research within the academic evidence base. The findings have both empirical and clinical utility, suggesting during the assessment phase of therapy, practitioners can identify residents that may require additional support to maintain engagement, minimising the potential for premature departure. The implications of the findings are discussed, with suggestions made for future research.