bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability
Authors: Reitz Diedre , Djeghmoum Yasmina , Watson Ruth A. , Rajput Pallavi , Argueso Juan Lucas , Heyer Wolf-Dietrich , Piazza Aurèle 
Published: March 2023

AbstractPunctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide sequencing approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis, and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR sub-pathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology, and results in sequence insertion without additional break or SV. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.
HuR enhances SARS-CoV-2 non-structural protein translation through the genomic 5’-UTR, by promoting polypyrimidine tract-binding protein binding
Authors: Raheja Harsha , Sahu Risabh , Ghosh Trinath , Rani Priya , George Biju , Khatun Oyahida , Tripathi Shashank , Das Saumitra 
Published: March 2023

AbstractSevere acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) viral RNA associates with different RNA-binding host proteins at each stage of its life cycle. We found sequence dependent binding of one such important protein, human antigen R (HuR) to SARS-CoV-2 5′UTR and studied its potential role in virus life cycle. The knockdown and knockout studies revealed importance of such binding in viral translation. We identified 5′-UTR mutations in SARS-CoV-2 variants of concern that altered the HuR-binding affinity. Interestingly, HuR enhanced non-structural protein translation through the genomic 5′-UTR, by promoting polypyrimidine tract-binding protein binding to the 5′-UTR. However, HuR suppressed the structural protein translation from sub genomic 5’UTR. HuR knockout increased the sensitivity to remdesivir treatment by decreasing its half-maximal inhibitory concentration. An antisense oligonucleotide (whose binding site overlapped the HuR-binding site) reduced viral RNA levels in wild-type cells but not HuR-knockout cells. Our results indicate that HuR regulates the balance between SARS-CoV-2 structural and non-structural proteins and guides the infection of viral variants, implying that HuR can potentially be targeted for therapeutic interventions.Author SummaryViruses interacts with various host proteins throughout their life cycle. One significant protein is HuR, an RNA-binding protein that regulates RNA stability and translation. HuR binds to viral RNAs at the 5’UTR or 3’UTR, impacting their translation and replication. We identified conserved HuR binding sites in the SARS-CoV-2 5’UTR across different beta coronaviruses. This binding enhanced the initiation of translation from the genomic 5’ UTR, increasing the production of non-structural proteins essential for viral replication. Additionally, we discovered that another host protein, PTB, promotes HuR binding to the viral 5’ UTR, facilitating its loading onto ribosomes. Conversely, HuR plays an antagonistic role concerning subgenomic RNAs (sgRNAs), which code for structural proteins, by regulating and limiting their levels. This dual regulation indicates that the virus exploits HuR for its benefit while the host employs it to control viral spread. Targeting HuR may help manipulate the SARS-CoV-2 life cycle. We found that HuR knockout increased sensitivity to the antiviral drug Remdesivir. Using an antisense oligonucleotide to block HuR binding effectively reduced viral RNA levels. Our findings highlight the critical role of HuR in regulating viral protein production and its potential as a therapeutic target.
A protein hydroxylase couples epithelial membrane biology to nucleolar ribosome biogenesis
Authors: Hendrix Eline , Andrijes Regina , Boora Uncaar , Kaur Arashpreet , Bundred James R , Officer-Jones Leah , Pennie Rachel , Powley Ian R , Zayer Adam , Heilig Raphael , Westrip Christian A E , Fletcher Sally C , Eaton Charlotte D , Kennedy Tristan J , Piasecka Sonia , Fischer Roman , Smerdon Stephen J , Le Quesne John , Coleman Mathew L 
Published: March 2023

AbstractJumonji-C (JmjC) ribosomal protein hydroxylases are an ancient class of oxygen- and Fe(II)-dependent oxygenases that spawned the wider JmjC family and Histone Lysine Demethylases (KDMs) in eukaryotes. Myc-induced Antigen (MINA) has been implicated in ribosome biogenesis and was assigned as a nucleolar-localized JmjC histidyl hydroxylase of the large ribosomal subunit protein RPL27A, consistent with reports that it supports cell growth and viability in a variety of tumor cell types. Reported roles in diverse aspects of disease biology may be consistent with additional MINA functions, although the molecular mechanisms involved remain unclear. Here, we describe an extra-nucleolar interaction of MINA with the Hinge domain of the membrane-associated guanylate kinase, MPP6. We show that MINA promotes the expression and membrane localization of MPP6 and that the MINA-MPP6 pathway is required for epithelial tight junction integrity and barrier function. The function of MINA in this novel pathway is suppressed by ribosomal RNA transcription and the nucleolar MINA interactome. In this way, MINA couples epithelial membrane biology to nucleolar ribosome biogenesis. Our work sheds light on how quiescent cells lose adhesion as they switch to proliferative states associated with increased ribosome biogenesis.
An alphacoronavirus polymerase structure reveals conserved co-factor functions
Authors: Anderson Thomas K. , Hoferle Peter J. , Lee Kenneth W. , Coon Joshua J. , Kirchdoerfer Robert N. 
Published: March 2023

AbstractCoronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from the betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent of COVID-19. In contrast, members of the alphacoronavirus genus are relatively understudied despite their importance in human and animal health. Here we have used cryoelectron microscopy to determine the structure of the alphacoronavirus porcine epidemic diarrhea virus (PEDV) core polymerase complex bound to RNA. Our structure shows an unexpected nsp8 stoichiometry in comparison to other published coronavirus polymerase structures. Biochemical analysis shows that the N-terminal extension of one nsp8 is not required forin vitroRNA synthesis for alpha and betacoronaviruses as previously hypothesized. Our work shows the importance of studying diverse coronaviruses to reveal aspects of coronavirus replication while also identifying areas of conservation to be targeted by antiviral drugs.Significance StatementCoronaviruses are important human and animal pathogens with a history of crossing over from animal reservoirs into humans leading to epidemics or pandemics. Betacoronaviruses, such as SARS-CoV and SARS-CoV-2, have been the focus of research efforts in the field of coronaviruses, leaving other genera (alpha, gamma, and delta) understudied. To broaden our understanding, we studied an alphacoronavirus polymerase complex. We solved the first structure of a non-betacoronavirus replication complex, and in doing so identified previously unknown, and conserved, aspects of polymerase cofactor interactions. Our work displays the importance of studying coronaviruses from all genera and provides important insight into coronavirus replication that can be used for antiviral drug development.
The highly conserved stem-loop II motif is dispensable for SARS-CoV-2
Authors: Jiang Hongbing , Joshi Astha , Gan Tianyu , Janowski Andrew B , Fujii Chika , Bricker Traci L , Darling Tamarand L , Harastani Houda H. , Seehra Kuljeet , Chen Hongwei , Tahan Stephen , Jung Ana , Febles Binita , Blatter Joshua A , Handley Scott A , Parikh Bijal A , Wang David , Boon Adrianus CM 
Published: March 2023

ABSTRACTThe stem-loop II motif (s2m) is a RNA structural element that is found in the 3’ untranslated region (UTR) of many RNA viruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Though the motif was discovered over twenty-five years ago, its functional significance is unknown. In order to understand the importance of s2m, we created viruses with deletions or mutations of the s2m by reverse genetics and also evaluated a clinical isolate harboring a unique s2m deletion. Deletion or mutation of the s2m had no effect on growthin vitro, or growth and viral fitness in Syrian hamstersin vivo. We also compared the secondary structure of the 3’ UTR of wild type and s2m deletion viruses using SHAPE-MaP and DMS-MaPseq. These experiments demonstrate that the s2m forms an independent structure and that its deletion does not alter the overall remaining 3’UTR RNA structure. Together, these findings suggest that s2m is dispensable for SARS-CoV-2.IMPORTANCERNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contain functional structures to support virus replication, translation and evasion of the host antiviral immune response. The 3’ untranslated region of early isolates of SARS-CoV-2 contained a stem-loop II motif (s2m), which is a RNA structural element that is found in many RNA viruses. This motif was discovered over twenty-five years ago, but its functional significance is unknown. We created SARS-CoV-2 with deletions or mutations of the s2m and determined the effect of these changes on viral growth in tissue culture and in rodent models of infection. Deletion or mutation of the s2m element had no effect on growthin vitro, or growth and viral fitness in Syrian hamstersin vivo. We also observed no impact of the deletion on other known RNA structures in the same region of the genome. These experiments demonstrate that the s2m is dispensable for SARS-CoV-2.
Promoting a resilient food supply chain model facing disruptions associated with black sky hazards
Authors: Orengo Serra Karen Lizzette , Sánchez-Jauregui María 
Published: March 2023

PurposeThis study explores how small- and medium-sized enterprises (SMEs) in the food industry in Puerto Rico can enhance resilience to cope with critical infrastructure (CI) collapse due to natural disasters. This study aims to validate the food supply chain (FSC) resilience model for SMEs in rural areas.Design/methodology/approachThis study used qualitative in-depth interviews to gather data and a coding process for the analysis. The participants were members of the FSC located in the municipality of Adjuntas and nearby towns in Puerto Rico. For this study, the sample participants selected to conduct the interviews were the farmers, producers and retailers.FindingsThe results show the importance of local CI backup, networks and flexibility among FSC members in alternating supply chain logistics and distribution. Other transportation modes include drone pilots, aerial and land, facilities to transport and deliver merchandise and positioning farmers and producers as important players in the FSC.Originality/valueA modified FSC resilience model from previous research is presented to include SMEs located in highly vulnerable remote zones, where access to resources is limited after a disruptive event, and a typology of enterprises with local CI backup according to their level of adoption of resilient practices. This study contributes to enhancing resilience and mitigating the vulnerabilities of SMEs after the CI collapses.
Music sentiment classification based on an optimized CNN-RF-QPSO model
Authors: Tian Rui , Yin Ruheng , Gan Feng 
Published: March 2023

PurposeMusic sentiment analysis helps to promote the diversification of music information retrieval methods. Traditional music emotion classification tasks suffer from high manual workload and low classification accuracy caused by difficulty in feature extraction and inaccurate manual determination of hyperparameter. In this paper, the authors propose an optimized convolution neural network-random forest (CNN-RF) model for music sentiment classification which is capable of optimizing the manually selected hyperparameters to improve the accuracy of music sentiment classification and reduce labor costs and human classification errors.Design/methodology/approachA CNN-RF music sentiment classification model is designed based on quantum particle swarm optimization (QPSO). First, the audio data are transformed into a Mel spectrogram, and feature extraction is conducted by a CNN. Second, the music features extracted are processed by RF algorithm to complete a preliminary emotion classification. Finally, to select the suitable hyperparameters for a CNN, the QPSO algorithm is adopted to extract the best hyperparameters and obtain the final classification results.FindingsThe model has gone through experimental validations and achieved a classification accuracy of 97 per cent for different sentiment categories with shortened training time. The proposed method with QPSO achieved 1.2 and 1.6 per cent higher accuracy than that with particle swarm optimization and genetic algorithm, respectively. The proposed model had great potential for music sentiment classification.Originality/valueThe dual contribution of this work comprises the proposed model which integrated two deep learning models and the introduction of a QPSO into model optimization. With these two innovations, the efficiency and accuracy of music emotion recognition and classification have been significantly improved.
How high-involvement HRM practices motivate knowledge sharing and innovation: the role of market turbulence
Authors: Le Hung Manh , Le Phong Ba 
Published: March 2023

PurposeThe purpose of this paper is to examine the impact of high-involvement human resource management (HRM) practices on innovation capabilities via the mediating role of knowledge sharing (KS) behaviors. This paper also investigates the potential moderating role of market turbulence in fostering the influence of KS behaviors on two forms of innovation capability, namely exploitative and exploratory innovation.Design/methodology/approachAnalysis of moment structures and structural equation modeling are applied to examine the correlation among the latent constructs based on the survey data collected from 125 manufacturing and service firms.FindingsThe findings of this study support the mediating role of KS behaviors in the relationship between high-involvement HRM practices and aspects of innovation capability. It highlights the important role of market turbulence in strengthening the influence of KS on exploitative and exploratory innovation.Research limitations/implicationsFuture research should investigate the impact of high-involvement HRM practices on innovation capability under the moderating effects of organizational variables, such as perceived organizational support, to bring better understanding on a new mechanism to pursuit innovation.Originality/valueThe paper significantly contributes to increasing knowledge and insights into the correlation between high-involvement HRM practices and specific forms of innovation. The understanding on the mediating role of KS behaviors and the moderating role of market turbulence contribute to advancing the body of knowledge of HRM and innovation theory.
Learning in the workplace: evidence on the role of behavioural job crafting on fostering self-perceived employability
Authors: Sartori Riccardo , Tommasi Francesco , Ceschi Andrea , Noventa Stefano , Zene Mattia 
Published: March 2023

Purpose
Given the instability and volatility of the labour market and the global talent scarcity, placing more attention on job employability is fundamental. In this context, the literature has already extensively examined employability as a crucial individual aspect, identifying some significant antecedents, including the applicability of training on the job. The present study aims to examine the impact that teaching employees to craft their job may have on the levels of applicability of training and if, in turn, this improves self-perceived employability.

Design/methodology/approach
The authors involved three private organizations that followed three workshops on job crafting behaviour. To empirically assess the intervention, the authors asked participants of the workshop to complete four quantitative diaries on a weekly basis, i.e. one per week, one before the intervention and three after the intervention. The diaries comprised measures of job crafting behaviours, applicability of training and self-perceived employability.

Findings
Multi-level analysis of data collected provided support to the positive associations between job crafting behaviour and self-perceived employability with the mediating effect of applicability of training. Notably, the applicability of training improves when individuals search for challenges, which indirectly affects perceived employability in terms of organizational sense.

Research limitations/implications
In the present study, no control group was used with which the results of our intervention could be compared. However, this does not affect the overall results, given the amount of intraindividual variability.

Originality/value
The paper proposes initial avenues for promoting employability at work via the use of behavioural job crafting intervention.
Diffusion of intellectual property knowledge in Zimbabwean universities: tools, programmes and strategies
Authors: Ngwenya Sibongile , Onyancha Omwoyo Bosire 
Published: March 2023

Purpose
This paper aims to explore the diffusion of Intellectual Property (IP) knowledge in universities in Zimbabwe. Specifically, the study examines the tools, policies, programmes and unique strategies used by the universities.

Design/methodology/approach
The paper reports the findings of a survey that was conducted on a population of lecturers (1,546), research officers (RO) (11), IP officer (1), faculty librarians (FLs) (27) and final year undergraduate students (9,224) at universities in Zimbabwe. Questionnaires were administered to the lecturers and students while interviews were administered to the IP officer, ROs and FLs. Data analysis comprised the use of Google forms and Microsoft Excel software.

Findings
The findings reveal diffusing IP knowledge in Zimbabwean universities involves mainly the use of policies and regulations, library web pages, workshops, although not specifically on IP, presentations on IP in the university, advice and guidance services and IP lectures/teaching.

Research limitations/implications
This study presents the IP situation in Zimbabwe and its findings may be applied to Africa and other developing countries.

Practical implications
This study endorses IP as a national issue and suggests a benchmark for diffusing knowledge on IP in Zimbabwean universities.

Originality/value
This study acknowledges the multi-disciplinary nature of IP and should lead to all university students graduating with adequate knowledge on IP.
Towards a better measure of productivity in India: a case of chemical and chemical products industry
Authors: Valiyattoor Vipin , Bhandari Anup Kumar 
Published: March 2023

Purpose
A brief review of earlier studies on the productivity scenario of Indian industry shows that most of the studies analysed are confined to either parametric approach or growth accounting approach of measuring productivity. At the same time, the few studies based on the non-parametric [namely, Malmquist productivity index (MPI)] overlook the returns to scale conditions as well as the bias involved in the estimation of distance functions. Given this backdrop, this study aims to provide a robust measure of productivity, which considers the returns to scale assumptions and correct for the bias involved in the estimation of productivity.

Design/methodology/approach
This study empirically tests for the returns to scale that exists in the chemical and chemical products industry in India. The test result suggests that Ray and Desli (1997) approach of MPI is the appropriate one for the present context. Initially, the conventional Ray and Desli (1997) estimation and decomposition of MPI for the period 2001 to 2017 is being used. Subsequently, to correct for the bias in the estimation of efficiency scores used for the estimation of MPI, the bootstrapping algorithm of Simar and Wilson (2007) has been extended into the context of MPI estimation.

Findings
The results from the conventional Malmquist productivity estimates testifies to an improvement of total factor productivity (TFP) in seven out of 16 years under consideration. On the contrary, TFP growth is recorded only in the four years throughout the period after the bias correction. A greater discrepancy between the two measures has been found in the case of scale change factor component of MPI.

Practical implications
The technical change (TC) component positively influences TFP, whereas scale change factor (SCF) deteriorates the TFP condition of this industry. It will be appropriate for these firms to identify and operate under an optimal scale of operation, along with reaping the benefits of technological change. From a methodological perspective, researchers should consider the potential bias that arise in estimation of TFP and use a larger sample whenever possible.

Originality/value
This paper brings in a new perspective to the existing literature on industrial productivity. As against earlier studies, this study empirically tests the returns to scale of the sector under consideration and uses the most appropriate approach to measure productivity. The effect of sampling bias on TFP and its components is analysed.