bluuebunny/crossref_metadata_2025_split huggingface dataset:
Equine dermatitis outbreak associated with parapoxvirus
Authors: Virtanen Jenni , Hautala Katja , Utriainen Mira , Dutra Lara , Eskola Katarina , Airas Niina , Uusitalo Ruut , Ahvenainen Ella , Smura Teemu , Sironen Tarja , Vapalahti Olli , Kant Ravi , Virtala Anna-Maija K. , Kinnunen Paula M. 
Published: September 2023

AbstractParapoxviruses (PPV) cause skin and mucous membrane lesions in several animal species, and of the five recognized PPVs, at least three are zoonotic. Equine PPV (EqPPV) is the sixth one initially described in humans in the United States and later in a severely sick horse in Finland in 2013–2015. In 2021–2022, a large-scale pustulo-vesicular pastern dermatitis outbreak occurred in horses all over Finland. This study aimed at analysing the outbreak, identifying and describing the causative agent, describing clinical signs, and searching for risk factors. EqPPV was identified as a probable causative agent and co-infections with several potentially pathogenic and zoonotic bacteria were observed. Histopathologically, suppurative and ulcerative dermatitis was diagnosed. Due to the lack of specific tests for this virus, we developed a novel diagnostic EqPPV-PCR with sensitivity of 10 copies/reaction. Based on a large proportion of the genome sequenced directly from clinical samples, very little variation was detected between the sequences of the case from 2013 and the cases from 2021–2022. Based on an epidemiological survey, the main risk factor for pastern dermatitis was having racehorses. Approximately one third of the horses at each affected stable got clinical dermatitis, manifesting as severe skin lesions. Skin lesions were also occasionally reported in humans, indicating potential zoonotic transmission. Case stables commonly reported attendance in race events before acquiring the disease. Survey also identified differences in practises between case and control stables. Taken together, these results enable a better preparedness, diagnostics, and guidelines for future outbreaks.
Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder Afrotheria
Authors: Tian Ran , Zhang Yaolei , Kang Hui , Zhang Fan , Jin Zhihong , Wang Jiahao , Zhang Peijun , Zhou Xuming , Lanyon Janet M. , Sneath Helen L. , Woolford Lucy , Fan Guangyi , Li Songhai , Seim Inge 
Published: September 2023

AbstractSirenians of the diverse superorder Afrotheria were the first mammals to retransition from land to water and are the sole herbivorous marine mammals, but little is known about the underlying genomic changes. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly and a recent West Indian manatee genome with other afrotherian genomes revealed possible molecular solutions to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functionalin vitroassays confirmed that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans, the only other fully aquatic mammal group. Our analysis also uncovered gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Finally, genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break on the Australian east coast and highlight the need for whole-genome resequencing data from small or isolated dugong populations worldwide for conservation and genetic management.
SARS-CoV-2 Spike amyloid fibrils specifically and selectively accelerates amyloid fibril formation of human prion protein and the amyloid β peptide
Authors: Larsson Johan , Hellstrand Ebba , Hammarström Per , Nyström Sofie 
Published: September 2023

AbstractAn increasing number of reports suggest an association between COVID-19 infection and initiation or acceleration of neurodegenerative diseases (NDs) including Alzheimer’s disease (AD) and Creutzfeldt-Jakob disease (CJD). Both these diseases and several other NDs are caused by conversion of human proteins into a misfolded, aggregated amyloid fibril state. The fibril formation process is self-perpetuating by seeded conversion from preformed fibril seeds. We recently described a plausible mechanism for amyloid fibril formation of SARS-CoV-2 spike protein. Spike-protein formed amyloid fibrils upon cleavage by neutrophil elastase, abundant in the inflammatory response to COVID-19 infection.We here provide evidence of significant Spike-amyloid fibril seeded acceleration of amyloid formation of CJD associated human prion protein (HuPrP) using anin vitroconversion assay. By seeding the HuPrP conversion assay with otherin vitrogenerated disease associated amyloid fibrils we demonstrate that this is not a general effect but a specific feature of spike-amyloid fibrils. We also showed that the amyloid fibril formation of AD associated Aβ1-42 was accelerated by Spike-amyloid fibril seeds. Of seven different 20-amino acid long peptides, Spike532 (532NLVKNKCVNFNFNGLTGTGV551) was most efficient in seeding HuPrP and Spike601 (601GTNTSNQVAVLYQDVNCTEV620) was most effective in seeding Aβ1-42, suggesting substrate dependent selectivity of the cross-seeding activity.Albeit purelyin vitro, our data suggest that cross-seeding by Spike-amyloid fibrils can be implicated in the increasing number of reports of CJD, AD, and possibly other NDs in the wake of COVID-19.
On the estimation of genome-average recombination rates
Authors: Dutheil Julien Y. 
Published: September 2023

AbstractThe rate at which recombination events occur in a population is an indicator of its effective population size and the organism’s reproduction mode. It determines the extent of linkage disequilibrium along the genome and, thereby, the efficacy of both purifying and positive selection. The population recombination rate can be inferred using models of genome evolution in populations. Classical methods based on the patterns of linkage-disequilibrium provide the most accurate estimates, providing large sample sizes are used and the demography of the population is properly accounted for. Here, the capacity of approaches based on the sequentially Markov coalescent (SMC) to infer the genome-average recombination rate from as little as a single diploid genome is examined. SMC approaches provide highly accurate estimates even in the presence of changing population sizes, providing that (1) within genome heterogeneity is accounted for and (2) classical maximum-likelihood optimization algorithms are employed to fit the model. SMC-based estimates proved sensitive to the presence of gene conversion, which leads to an overestimation of the recombination rate if conversion events are frequent. Conversely, methods based on the correlation of heterozygosity succeed in disentangling the rate of crossing over from that of gene conversion events, but only when the population size is constant and the recombination landscape homogeneous. These results call for a convergence of these two methods to obtain accurate and comparable estimates of recombination rates between populations.
Training-dependent gradients of timescales of neural dynamics in the primate prefrontal cortex and their contributions to working memory
Authors: Trepka Ethan , Spitmaan Mehran , Qi Xue-Lian , Constantinidis Christos , Soltani Alireza 
Published: September 2023

AbstractCortical neurons exhibit multiple timescales related to dynamics of spontaneous fluctuations (intrinsic timescales) and response to task events (seasonal timescales) in addition to selectivity to task-relevant signals. These timescales increase systematically across the cortical hierarchy, e.g., from parietal to prefrontal and cingulate cortex, pointing to their role in cortical computations. It is currently unknown whether these timescales depend on training in a specific task and/or are an inherent property of neurons, and whether more fine-grained hierarchies of timescales exist within specific cortical regions. To address these questions, we analyzed single-cell recordings within five subregions of the prefrontal cortex (PFC) of male macaques before and after training on a working-memory task. We found fine-grained but opposite gradients of intrinsic and seasonal timescales that mainly appeared after training. Intrinsic timescales decreased whereas seasonal timescales increased from posterior to anterior subregions within both dorsal and ventral PFC. Moreover, training was accompanied by increases in proportions of neurons that exhibited intrinsic and seasonal timescales. These effects were comparable to the emergence of response selectivity due to training. Finally, task selectivity accompanied opposite neural dynamics such that neurons with task-relevant selectivity exhibited longer intrinsic and shorter seasonal timescales. Notably, neurons with longer intrinsic and shorter seasonal timescales exhibited superior population-level coding, but these advantages extended to the delay period mainly after training. Together, our results provide evidence for plastic, fine-grained gradients of timescales within PFC that can influence both single-cell and population coding, pointing to the importance of these timescales in understanding cognition.Significance statementRecent studies have demonstrated that neural responses exhibit dynamics with different timescales that follow a certain order or hierarchy across cortical areas. While the hierarchy of timescales is consistent across different tasks, it is unknown if these timescales emerge only after training or if they represent inherent properties of neurons. To answer this question, we estimated multiple timescales in neural response across five subregions of the monkeys’ lateral prefrontal cortex before and after training on a working-memory task. Our results provide evidence for fine-grained gradients related to certain neural dynamics. Moreover, we show that these timescales depend on and can be modulated by training in a cognitive task, and contribute to encoding of task-relevant information at single-cell and population levels.
Association of mitochondrial fucosyltransferase TbFUT1 with the assembly of the mitochondrial FoF1-ATP synthase in bloodstream formTrypanosoma brucei
Authors: Duncan Samuel M. , Smithson Laura , Tinti Michele , Vaughan Susan , Ferguson Michael A.J. 
Published: September 2023

AbstractThe geneTbFUT1encodes an essential fucosyltransferase which, unexpectedly, localises to the mitochondrion of the protist parasiteTrypanosoma brucei. The expression ofTbFUT1is required for the maintenance of mitochondrial membrane potential (ΨΔm) in the bloodstream form (BSF) of the parasite, but the precise functions of TbFUT1 are unknown. Here, we demonstrate that depletion of TbFUT1 causes the accumulation of dyskinetoplastid cells; i.e., cells lacking concatenated complexes of mini- and maxicircle kinetoplast DNA (kDNA), the mitochondrial DNA of these organisms. Morphological analysis by serial face block-scanning electron microscopy showed that the dyskinetoplastid mitochondria were otherwise unperturbed with respect to structure and volume. Proteomics analyses showed that TbFUT1 depletion caused a decrease in the steady-state levels of several subunits of the Fo-subcomplex and peripheral stalk components of the mitochondrial FoF1-ATP synthase, as well as a pronounced reduction in mitochondrial ribosomal large subunit (LSU) proteins and more minor reduction in small subunit (SSU) proteins. TbFUT1 was rendered redundant with respect to cell survival and ΨΔm generation upon F1-γWT/L262Pmutation; a mutation that allows the generation of ΨΔm in the absence of mitochondrial translation. Additionally, depletion of TbFUT1 no longer perturbs kDNA replication in these cells, indicating that dyskinetoplasty is a downstream consequence of impaired ΨΔm. Depletion of TbFUT1 in wild type cells leads to the collapse of ΨΔm via a functional FoF1-ATP synthase complex. We therefore conclude these mutants are inhibited in the synthesis of Fo-subcomplex components and, thus, impairing the assembly of functional FoF1-ATP synthase complexes. Curiously, mitochondrial transcript levels exhibit similar changes in abundance after FUT1 ablation in the parental and F1-γWT/L262Pmutants. Further, the ∼5-fold overexpression of TbFUT1 in theTbFUT1conditional knockout mutant under permissive conditions selectively inhibits the formation of the fully RNA-edited A6 transcript by an unknown mechanism, partially suppressing FoF1-ATP synthase assembly in these mutants. Together, these data suggest that mitochondrial fucosylation is essential for the assembly of protein complexes containing kDNA encoded subunits.
SARS-CoV-2 hijacks fragile X mental retardation proteins for efficient infection
Authors: Garvanska Dimitriya H. , Alvarado Rojelio E. , Mundt Filip Oskar , Nilsson Emma , Duel Josephine Kerzel , Coscia Fabian , Lindqvist Richard , Lokugamage Kumari , Johnson Bryan A. , Plante Jessica A. , Morris Dorothea R. , Vu Michelle N. , Estes Leah K. , McLeland Alyssa M. , Walker Jordyn , Crocquet-Valdes Patricia A. , Mendez Blanca Lopez , Plante Kenneth S. , Walker David H. , Weisser Melanie Bianca , Overby Anna K. , Mann Matthias , Menachery Vineet D. , Nilsson Jakob 
Published: September 2023

AbstractViruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1 and FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have attenuated replicationin vitroand have delayed disease onsetin vivo. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins for efficient infection and provides molecular insight to the possible underlying molecular defects in fragile X syndrome.
Resolving the climatic and ecological drivers of geographical gradients in avian sexual selection
Authors: Barber Robert A. , Yang Jingyi , Yang Chenyue , Barker Oonagh , Janicke Tim , Tobias Joseph A. 
Published: September 2023

AbstractSexual selection, one of the central pillars of evolutionary theory, has powerful effects on organismal morphology, behaviour and population dynamics. However, current knowledge about geographical variation in this evolutionary mechanism and its underlying drivers remains highly incomplete, in part because standardized data on the strength of sexual selection is sparse even for well-studied organisms. Here we use information on mating systems – including the incidence of polygamy and extra-pair paternity – to quantify the intensity of sexual selection in 10671 (>99.9%) bird species distributed worldwide. We show that avian sexual selection varies latitudinally, peaking at higher latitudes, although the gradient is reversed in the world’s most sexually selected birds – specialist frugivores – which are strongly associated with tropical forests. Phylogenetic models further reveal that the strength of sexual selection is explained by temperature seasonality coupled with a suite of climate-associated factors, including migration, diet, and territoriality. Overall, these analyses suggest that climatic conditions leading to short, intense breeding seasons, or highly abundant and patchy food resources, increase the potential for polygamy in birds, driving latitudinal gradients in sexual selection. Our findings help to resolve longstanding debates about spatial variation in evolutionary mechanisms linked to reproductive biology, and provide a comprehensive species-level dataset for further studies of selection and phenotypic evolution in the context of global climatic change.
Inhibition of the type IV secretion system from antibiotic-resistantHelicobacter pyloriclinical isolates supports the potential of Cagα as an anti-virulence target
Authors: Oudouhou Flore , Morin Claire , Bouin Mickael , Gaudreau Christiane , Baron Christian 
Published: September 2023

AbstractHelicobacter pyloriresistance to antibiotics is a growing problem and it increasingly leads to treatment failure. While the bacterium is present worldwide, the severity of the clinical outcomes is highly dependent on the geographical origin and genetic characteristics of the strains. One of the major virulence factors identified inH. pyloriis thecagpathogenicity island (cagPAI), which encodes a type IV secretion used to translocate effectors into human cells. Here, we investigated the genetic variability of thecagPAI among 13 antibiotic-resistantH. pyloristrains that were isolated from patient biopsies in Québec. Seven of the clinical strains carried thecagPAI, but only four could be readily cultivated under laboratory conditions. We observed variability of the sequences of CagA and CagL proteins that are encoded by thecagPAI. All clinical isolates induce interleukin-8 secretion and morphological changes upon co-incubation with epithelial gastric cancer cells and two of them produce extracellular T4SS pili. Finally, we demonstrate that molecule 1G2, a small molecule inhibitor of the Cagα protein from the model strainH. pylori26695, reduces interleukin-8 secretion in one of the clinical isolates. Co-incubation with 1G2 also inhibits the assembly of T4SS pili, suggesting a mechanism for its action on T4SS function.
Lipid scrambling is a general feature of protein insertases
Authors: Li Dazhi , Rocha-Roa Cristian , Schilling Matthew A. , Reinisch Karin M. , Vanni Stefano 
Published: September 2023

AbstractGlycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called “scramblases”. These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit-card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place, and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far overlooked role in membrane dynamics as scramblases.
The effect of entrepreneurial leadership traits on corporate sustainable development and firm performance: a resource-based view
Authors: Razzaque Anjum , Lee In , Mangalaraj George 
Published: September 2023

Purpose
This study aims to empirically assess entrepreneurial leadership skills’ role in Corporate Sustainable Development (CSD) and firm performance (FP). This study considers five specific entrepreneurial traits: innovativeness, creativity, analytical thinking, emotional intelligence and passion and motivation. The motivation for this investigation stems from concerns over micro-firms vulnerabilities and small and medium enterprises (SMEs) lacking proper leadership skills. This study is guided by the resource-based view theory and conducted during the pandemic, offering insights into firms operating under constrained conditions.

Design/methodology/approach
Confirmatory factor analysis and structural equation modeling (SEM), were used on survey responses from 321 Bahraini firms. This study’s data collection occurred under environmental uncertainties due to the pandemic and provides a unique context for understanding CSD and entrepreneurial leadership skills under high business/environmental uncertainty.

Findings
The findings reveal that entrepreneurial leadership skills positively impact CSD and firm performance through creativity, passion and motivation. However, innovativeness negatively affects CSD and FP. Furthermore, CSD positively influences firm performance.

Research limitations/implications
Theoretical and practical implications, plus limitations, are also discussed in this study.

Practical implications
Understanding entrepreneurial leadership skills effect on CSD and firm performance in SMEs is important as SEMs are prone to fail in the early years. This study’s findings and its implications help guide SME leaders in furthering their entrepreneurial leadership skills to foster CSD and firm performance.

Originality/value
This study contributes to comprehending the crucial role of entrepreneurial skills, during uncertain times of the pandemic, for SMEs’ survival. It provides valuable insights for firms operating in competitive environments, offering a unique perspective on the required entrepreneurial skills and their effect on CSD and firm performance.
Appraising alternative building technologies adoption in low-cost housing provision to achieving Sustainable Development Goal 11
Authors: Ebekozien Andrew , Aigbavboa Clinton Ohis , Samsurijan Mohamad Shaharudin 
Published: September 2023

PurposeThough alternative building technologies (ABTs) have been encouraged to address accessible and affordable issues in low-cost housing (LCH) provision, their adoption is still overwhelmed with encumbrances. The encumbrances that hinder ABT adoption require an in-depth study, especially in developing countries like Nigeria. However, studies regarding ABT and its role in improving Nigeria's LCH to achieve Sustainable Development Goal (SDG) 11 are scarce. This research investigates encumbrances to ABT adoption in Nigeria's LCH provision and suggests feasible measures to prevent or reduce the encumbrances, thereby improving achieving SDG 11 (sustainable cities and communities).Design/methodology/approachThis research utilised qualitative research and adopted a face-to-face interview as the primary data collection. The interviewees comprised ABT practitioners and end users in Nigeria who were chosen by a convenient sampling technique. The study's data were analysed manually through a thematic approach.FindingsThis study shows that stakeholders should embrace ABT in LCH provision to improve achieving SDG 11 in Nigeria. Also, it clustered the perceived 20 encumbrances to ABT adoption in LCH provision into government/policymaker, housing developers/building contractors, ABT users and ABT manufacturers-related issues in Nigeria's context. This study suggested mechanisms to mitigate encumbrances to ABT adoption in LCH provision, thereby improving achieving SDG 11.Originality/valueThis research adds to the limited literature by analysing ABT adoption encumbrances in Nigeria's LCH provision, which could assist policy formulation for the uptake of ABT in LCH provision and improve achieving Goal 11.