bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation of Protein Kinase R (PKR) Plays a Pro-Viral Role in Mammarenavirus Infected Cells
Authors: Witwit Haydar , Khafaji Roaa , Salaniwal Arul , Kim Arthur S. , Cubitt Beatrice , Jackson Nathaniel , Ye Chengjin , Weiss Susan R , Martinez-Sobrido Luis , de la Torre Juan Carlos 
Published: December 2023

ABSTRACTMany viruses, including mammarenaviruses, have evolved mechanisms to counteract different components of the host cell innate immunity, which is required to facilitate robust virus multiplication. The double strand (ds)RNA sensor protein kinase receptor (PKR) pathway plays a critical role in the cell antiviral response. Whether PKR can restrict the multiplication of the Old World mammarenavirus lymphocytic choriomeningitis virus (LCMV) and the mechanisms by which LCMV may counteract the antiviral functions of PKR have not yet been investigated. Here we present evidence that LCMV infection results in very limited levels of PKR activation, but LCMV multiplication is enhanced in the absence of PKR. In contrast, infection with a recombinant LCMV with a mutation affecting the 3’-5’ exonuclease (ExoN) activity of the viral nucleoprotein (NP) resulted in robust PKR activation in the absence of detectable levels of dsRNA, which was associated with severely restricted virus multiplication that was alleviated in the absence of PKR. However, pharmacological inhibition of PKR activation resulted in reduced levels of LCMV multiplication. These findings uncovered a complex role of the PKR pathway in LCMV-infected cells involving both pro-and anti- viral activities.IMPORTANCEAs with many other viruses, the prototypic Old World mammarenavirus lymphocytic choriomeningitis virus (LCMV) can interfere with the host cell innate immune response to infection, which includes the double strand (ds)RNA sensor protein kinase receptor (PKR) pathway. A detailed understanding of LCMV-PKR interactions can provide novel insights about mammarenavirus-host cell interactions and facilitate the development of effective antiviral strategies against human pathogenic mammarenaviruses. In the present work, we present evidence that LCMV multiplication is enhanced in PKR- deficient cells, but pharmacological inhibition of PKR activation unexpectedly resulted in severely restricted propagation of LCMV. Likewise, we document a robust PKR activation in LCMV-infected cells in the absence of detectable levels of dsRNA. Our findings have revealed a complex role of the PKR pathway during LCMV infection and uncovered the activation of PKR as a druggable target for the development of antiviral drugs against human pathogenic mammarenaviruses.
Heteroplasmy and tandem repeats reveal adaptation to elevation in the New World Jays (Aves: Corvidae)
Authors: Termignoni-Garcia Flavia , Bougiouri Katia , Edwards Scott V. 
Published: December 2023

ABSTRACTAdvances in high-throughput sequencing (HTS) and bioinformatic tools have enabled the quick and cost-efficient assembly of complete mitochondrial genomes (mitogenomes) in non-model organisms. Consequently, new evidence of heteroplasmy, recombination and paternal leakage in mitogenomes has increased. In this study, we utilized HTS data from whole-genome sequencing to assemble the first complete mitogenomes of nine species of New World Jays (NWJs), covering all genera. We further investigated the evolution of heteroplasmy, tandem repeats (TRs) and signatures of natural selection. Our results showed a molecular shift in the adaptation to low elevation in the NWJs. Among the species studied, we found 10 heteroplasmic sites either containing TRs in the same site or 1 to 300 nucleotides adjacent; one species-specific TR in a transfer RNA (tRNA-P) potentially associated with low elevation; one phylogenetic branch with evidence of episodic positive selection also associated with low elevation; and 5 codon sites with strong support for positive selection. We referred to the heteroplasmy-TR interaction and its possible role with regulation, recombination and paternal leakage in the mitogenomes. Finally, phylogenetic relationships were in agreement with previous studies and we discussed how selective pressure on genes from the oxidative phosphorylation pathway (OXPHOS) may benefit species from low-elevation habitats. Although these findings in the NWJs require further investigation, this study offers promising insights about the evolution of mitogenomes in birds.
The presenilin 1 mutation P436S causes familial Alzheimer’s disease with elevated Aβ43 and atypical clinical manifestations
Authors: Arber Charles , Belder Christopher R.S. , Tomczuk Filip , Gabriele Rebecca , Buhidma Yazead , O’Connor Antoinette , Rice Helen , Lashley Tammaryn , Fox Nick C. , Ryan Natalie S. , Wray Selina 
Published: December 2023

Structured AbstractBACKGROUNDFamilial Alzheimer’s disease (fAD) is heterogeneous in terms of age at onset and clinical presentation. A greater understanding of the pathogenicity of fAD variants and how these contribute to heterogeneity will enhance our understanding of the mechanisms of Alzheimer’s disease more widely. The pathogenicity of the P436S mutation inPSEN1remains unclassified.METHODSTo determine the pathogenicity of thePSEN1P436S mutation, we studied an expanded kindred of 8 affected individuals, with MRI (2 individuals), patient-derived iPSC models (2 donors) and post-mortem histology (1 donor).RESULTSAn autosomal dominant pattern of inheritance of fAD was seen with an average age at symptom onset of 46 years and atypical features including late spastic paraparesis and non-memory led cognitive impairment in some individuals. iPSC models and post- mortem tissue supported high production of Aβ43. PSEN1 peptide maturation was unimpaired, unlike previously reported atypical mutations R278I and E280G. CONCLUSIONS: We confirm that the P436S mutation inPSEN1causes atypical fAD. The location of the mutation in the critical PSEN1 PALP motif may explain the early age of onset despite appropriate protein maturation.
Not only practicing but suffering bullying is correlated with alcohol, tobacco and drugs use results of the Brazilian National School Health Survey (PeNSE 2019)
Authors: Perrotte Giuliana , Baruzzi Marjorie Mastellaro , Castaldelli-Maia João Maurício 
Published: December 2023

ABSTRACTBackgroundBullying and the use of psychoactive substances are prevalent conditions among adolescents that appear to have some connection. However, there is no consensus in the literature regarding the association between being a victim of bullying and using psychoactive substances. Moreover, most analyses of this correlation have taken place in developed countries, possibly not reflecting the reality in Latin America.ObjectiveThis cross-sectional study investigated the association between the use of psychoactive substances and involvement in bullying situations in a representative sample of Brazilian adolescents.MethodsWe used data from the 2019 National School Health Survey (Pesquisa Nacional de Saúde do Escolar), analyzing 123,261 questionnaires from youths aged 13 to 17. Questions about experiencing or engaging in bullying, lifetime use, and recent use (in the last 30 days) of tobacco, hookah, e-cigarettes, other tobacco products, alcohol, and illicit drugs were considered. Responses on the recent use (in the last 30 days) of the following substances were also analyzed: clove cigarettes, straw cigarettes, marijuana, and crack. Multivariate logistic regression models were used to determine correlations, and odds ratios (OR) were calculated.ResultsParticipation in bullying situations, whether as a victim or perpetrator, increases the likelihood of using tobacco cigarette, hookah, e-cigarettes, clove cigarettes, straw cigarettes, alcohol, illicit drugs, marijuana, and crack. The non-involved-in-bullying group has a lower chance of using any analyzed substance, followed by the group that is only a victim. Those with the highest likelihood of use are individuals who engage in bullying exclusively, followed by those who experience both situations.ConclusionIn Brazil, being a victim of bullying is associated with the use of various psychoactive substances. Our results align with findings from Latin America, partially differing from studies in developed countries, highlighting the influence of location in understanding these risk associations.
Non-autonomous cell redox-pairs dictate niche homeostasis in multi-lineage stem populations
Authors: Majhi Olivia , Chhatre Aishwarya , Chaudhary Tanvi , Sinha Devanjan 
Published: December 2023

AbstractReactive oxygen species (ROS), predominantly derived from mitochondrial respiratory complexes, have evolved as key molecules influencing cell fate decisions like maintenance and differentiation. These redox-dependent events are mainly considered to be cell intrinsic in nature, on contrary our observations indicate involvement of these oxygen-derived entities as intercellular communicating agents. In multi-lineageDrosophilagermline, neighbouring Germline Stem Cells (GSCs) and Cystic Stem Cells (CySCs) maintain differential redox thresholds where CySCs by virtue of their higher redox-state regulate physiological ROS levels of germline. Disruption of the intercellular redox equilibrium between the two adjoining stem cell populations results in deregulated niche architecture and loss of GSCs, which was mainly attributed to loss of contact-based receptions and uncontrolled CySC proliferation due to ROS-mediated activation of self-renewing signals. Our observations hint towards the crucial role of intercellular redox gradients originating from somatic progenitors, CySCs in niche stability where they function not only as a source of their own maintenance cues but also serve as non-autonomous redox moderators of germline immortality. Our findings underscore the complexity of niche homeostasis and predicate the importance of intercellular redox communication in understanding stem cell microenvironments.
The black honey bee genome: insights on specific structural elements and a first step towards pan-genomes
Authors: Eynard Sonia E. , Klopp Christophe , Canale-Tabet Kamila , Marande William , Vandecasteele Céline , Roques Céline , Donnadieu Cécile , Boone Quentin , Servin Bertrand , Vignal Alain 
Published: December 2023

AbstractBackgroundThe actual honey bee reference genome, HAv3.1, was produced from a commercial line sample, thought to have a largely dominantApis mellifera ligusticagenetic background.Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pan-genome analyses.ResultsPacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for a re-estimation of the honey recombination rate, over-estimated in some previous studies, due to mis-assemblies resulting in spurious inversions in the older reference genomes. The sequence continuity obtained is very high and the only limit towards continuous chromosome-wide sequences seem to be due to tandem repeat arrays usually longer than 10 kb and belonging to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome, for genotyping two structural variants by a pan-genome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76 % for the two variants respectively.ConclusionsOur new assembly for theApis mellifera melliferahoney bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pan-genomes.
MOBFinder: a tool for MOB typing for plasmid metagenomic fragments based on language model
Authors: Feng Tao , Wu Shufang , Zhou Hongwei , Fang Zhencheng 
Published: December 2023

AbstractBackgroundMOB typing is a classification scheme that classifies plasmid genomes based on their relaxase gene. The host range of plasmids of different MOB categories are diverse and MOB typing is crucial for investigating the mobilization of plasmid, especially the transmission of resistance genes and virulence factors. However, MOB typing of plasmid metagenomic data is challenging due to the highly fragmented characteristic of metagenomic contigs.ResultsWe developed MOBFinder, an 11-class classifier to classify the plasmid fragments into 10 MOB categories and a non-mobilizable category. We first performed the MOB typing for classifying complete plasmid genomes using the relaxes information, and constructed the artificial benchmark plasmid metagenomic fragments from these complete plasmid genomes whose MOB types are well annotated. Based on natural language models, we used the word vector to characterize the plasmid fragments. Several random forest classification models were trained and integrated for predicting plasmid fragments with different lengths. Evaluating the tool over the benchmark dataset, MOBFinder demonstrates higher performance compared to the existing tool, with an overallaccuracyof approximately 59% higher than the MOB-suite. Moreover, thebalanced accuracy, harmonic meanandF1-scorecould reach 99% in some MOB types. In an application focused on a T2D cohort, MOBFinder offered insights suggesting that the MOBF type might accelerate the antibiotic resistance transmission in patients suffering from T2D.ConclusionsTo the best of our knowledge, MOBFinder is the first tool for MOB tying for plasmid metagenomic fragments. MOBFinder is freely available athttps://github.com/FengTaoSMU/MOBFinder.
Microsomal triglyceride transfer protein is necessary to maintain lipid homeostasis and retinal function
Authors: Grubaugh Catharina R. , Dhingra Anuradha , Prakash Binu , Montenegro Diego , Sparrow Janet R. , Daniele Lauren L. , Curcio Christine A. , Bell Brent A. , Hussain M. Mahmood , Boesze-Battaglia Kathleen 
Published: December 2023

AbstractLipid processing by the retinal pigment epithelium (RPE) is necessary to maintain retinal health and function. Dysregulation of retinal lipid homeostasis due to normal aging or to age-related disease triggers lipid accumulation within the RPE, on Bruch’s membrane (BrM), and in the subretinal space. In its role as a hub for lipid trafficking into and out of the neural retina, the RPE packages a significant amount of lipid into lipid droplets for storage and into apolipoprotein B (apoB)-containing lipoproteins (Blps) for export. Microsomal triglyceride transfer protein (MTP), encoded by theMTTPgene, is essential for Blp assembly. Herein we test the hypothesis that MTP expression in the RPE is essential to maintain lipid balance and retinal function using the newly generatedRPEΔMttpmouse model. Using non-invasive ocular imaging, electroretinography, and histochemical and biochemical analyses we show that genetic deletion ofMttpfrom the RPE results in intracellular lipid accumulation, increased photoreceptor –associated cholesterol deposits and photoreceptor cell death, and loss of rod but not cone function. RPE-specific ablation of Mttp had no significant effect on plasma lipids and lipoproteins. While, apoB was decreased in the RPE, ocular retinoid concentrations remained unchanged. Thus suggesting that RPE MTP is critical for Blp synthesis and assembly but not directly involved in ocular retinoid and plasma lipoprotein metabolism. These studies demonstrate that RPE-specific MTP expression is necessary to establish and maintain retinal lipid homeostasis and visual function.
Research on aerodynamic characteristics of vehicle platoon under crosswind conditions based on Ahmed body
Authors: Luo Jianbin , Li Mingsen , Mi Ke , Liang Zhida , Chen Xiaofeng , Ye Lei , Tie Yuanhao , Xu Song , Zhang Haiguo , Chen Guiguang , Jiang Chunmei 
Published: December 2023

Purpose
The purpose of this paper is to study the aerodynamic characteristics of Ahmed body in longitudinal and lateral platoons under crosswind by computational fluid dynamics simulation. It helps to improve the aerodynamic characteristics of vehicles by providing theoretical basis and engineering direction for the development and progress of intelligent transportation.

Design/methodology/approach
A two-car platoon model is used to compare with the experiment to prove the accuracy of the simulation method. The simplified Ahmed body model and the Reynolds Averaged N-S equation method are used to study the aerodynamic characteristics of vehicles at different distances under cross-winds.

Findings
When the longitudinal distance x/L = 0.25, the drag coefficients of the middle and trailing cars at β = 30° are improved by about 272% and 160% compared with β = 10°. The side force coefficients of the middle and trailing cars are increased by 50% and 62%. When the lateral distance y/W = 0.25, the side force coefficients of left and middle cars at β = 30° are reduced by 38% and 37.5% compared with β = 10°. However, the side force coefficient of the right car are increased by about 84.3%.

Originality/value
Most of the researches focus on the overtaking process, and there are few researches on the neat lateral platoon. The innovation of this paper is that in addition to studying the aerodynamic characteristics of longitudinal driving, the aerodynamic characteristics of neat lateral driving are also studied, and crosswind conditions are added. The authors hope to contribute to the development of intelligent transportation.
Usability testing of a website through different devices: a task-based approach in a public university setting in Bangladesh
Authors: Yesmin Shamima , Atikuzzaman Md. 
Published: December 2023

Purpose
This study aims to investigate the usability of a public university website for measuring its efficiency, users’ satisfaction or anxiety while searching for and retrieving information through different devices.

Design/methodology/approach
A task-based approach was adopted for the study. Twenty-eight participants were asked to complete 11 information-searching tasks on the website. The participants were divided into two groups. The tasks were carried out by members of each group, using desktop and mobile devices in a rotating fashion. Volunteers observed the participants' actions and recorded information regarding their productivity, time usage (using a timer), satisfaction or annoyance while performing each task. Finally, based on the use of the devices, a comparison was established between the participants' performance accuracy, efficiency and anxiety.

Findings
The study provides an overview of a task-based user experience carried out on the university website using a combination of qualitative and quantitative research methods. According to the results, participants' satisfaction levels were generally high, and their anxiety levels were low while completing the tasks on a mobile device. In comparison to the desktop, it took less time overall to complete all tasks. On the other hand, using a desktop computer (97.1%) resulted in better task completion success rates for participants than using a mobile device (85.7%).

Originality/value
No previous task-based evaluation study of this kind has been conducted to assess the usability of any university website in Bangladesh.
Corporate power purchase agreements and the value of decarbonization
Authors: Hundt Steffen 
Published: December 2023

Purpose
The purpose of this paper is to examine if the announcement of corporate power purchase agreements (PPAs) induce significant effects on the electricity buyers' stock returns.

Design/methodology/approach
This is an event study based on the Fama French Five Factor Model which uses several significance tests and robust regression approaches.

Findings
The announced closing of corporate PPAs induces significant positive abnormal stock returns. This announcement effect is even more pronounced in case of virtual PPAs.

Originality/value
To the best of the author‘s knowledge, this study is the first which explictly investigates the announcement effects of corporate PPAs, which are closed between the owner of the renewable energy asset and the institutional end consumer. In addition, this study extends the event study approach by robust regression methods.
Assessing subjective career success: the role of career commitment, career resilience and self-efficacy: a evidence from hospitality industry
Authors: Bhawna Bhawna , Sharma Sanjeev Kumar , Akram Umair 
Published: December 2023

Purpose
This study aims to examine how career commitment (CC) affects hospitality employees perceived subjective career success (SCS) using a serial mediation system that uses career resilience (CR) behaviour and self-efficacy (SE) as serial mediators.

Design/methodology/approach
To examine the proposed relationships, a comprehensive theoretical serial mediation model was constructed. The proposed hypotheses were tested on a sample of 316 hospitality employees from India using regression analysis (Process Macro Model 6) with 5,000 bootstrapping at 95% confidence interval.

Findings
The regression analysis confirmed a strong, positive relationship between CC and SCS. It also highlighted a significant indirect effect, involving a serial mediation through CR and SE, demonstrating how CC influences SCS.

Research limitations/implications
Drawing from three prominent theories – career self-determination theory (CSDT), career construction theory (CCT) and the contextual action theory of career development (CATCD), this research underscores the importance of fostering career-committed behaviour among employees and advocating for strategic career development initiatives. Understanding CC elements may help firms retain and encourage individuals, which can boost job satisfaction and performance. Importantly, the results advocate for the implementation of targeted career development strategies and the promotion of career-committed behaviour within hospitality organisations. This, in turn, fosters resilience and competence, ultimately contributing to individual career success and organisational excellence.

Originality/value
A serial mediation model with CR and SE introduces a fresh perspective that, to the best of the authors’ knowledge, has not been extensively explored in previous research examining the relationship between CC and SCS.