bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23
Authors: Cane Jennifer , Sanderson Nicholas , Barnett Sophie , Vaughan Ali , Pott Megan , Kapel Natalia , Morgan Marcus , Jesuthasan Gerald , Samuel Reggie , Ehsaan Muhammad , Boothe Hugh , Haduli Eric , Studley Ruth , Rourke Emma , Diamond Ian , Fowler Tom , Watson Conall , Stoesser Nicole , Walker Ann Sarah , Street Teresa , Eyre David 
Published: November 2023

AbstractObjectivesWe evaluated Nanopore sequencing for influenza surveillance.MethodsInfluenza A and B PCR-positive samples from hospital patients in Oxfordshire, UK, and a UK-wide population survey from winter 2022-23 underwent Nanopore sequencing following targeted rt-PCR amplification.ResultsFrom 941 infections, successful sequencing was achieved in 292/388(75%) available Oxfordshire samples: 231(79%) A/H3N2, 53(18%) A/H1N1, and 8(3%) B/Victoria and in 53/113(47%) UK-wide samples. Sequencing was more successful at lower Ct values. Most same-sample replicate sequences had identical haemagglutinin segments (124/141;88%); a subset of samples also Illumina sequenced were very similar to Nanopore sequences.Comparison of Oxfordshire and UK-wide sequences showed frequent inter-regional transmission. Infections were closely-related to 2022-23 vaccine strains. Only one sample had a neuraminidase inhibitor resistance mutation.849/941(90%) Oxfordshire infections were community-acquired. 63/88(72%) potentially healthcare-associated cases shared a hospital ward with ≥1 known infectious case. 33 epidemiologically-plausible transmission links had sequencing data for both source and recipient: 8 were within ≤5 SNPs, of these, 5(63%) involved potential sources that were also hospital-acquired.ConclusionsNanopore influenza sequencing was reproducible and antiviral resistance rare. Inter-regional transmission was common; most infections were genomically similar. Hospital-acquired infections are likely an important source of nosocomial transmission and should be prioritised for infection prevention and control.HighlightsNanopore sequencing is a reproducible tool for influenza surveillanceInter-regional transmission of influenza was common across the UKInfluenza anti-viral resistance was rareIn 1 year most infections were genetically similar, hindering transmission studiesHospital-acquired infections are likely a key source of nosocomial transmission
Occupational biopsychosocial factors associated with neck pain intensity, neck-disability, and sick leave: a cross-sectional study of construction labourers in an African population
Authors: Igwesi-Chidobe Chinonso N , Effiong Excellence , Umunnah Joseph O , Ozumba Benjamin C 
Published: November 2023

AbstractIntroductionThe burden and impact of neck pain is high in African countries including Nigeria. This study investigated the occupational biomechanical and occupational psychosocial factors associated with neck pain intensity, neck disability and sick leave amongst construction labourers in an urban Nigerian population.MethodsThis cross-sectional study measured clinical neck pain outcomes, occupational biomechanical factors, and occupational psychosocial factors. Descriptive, and univariate/multivariate inferential statistical analyses were conducted.ResultsSignificant independent factors associated with neck pain intensity were order and pace of tasks being dependent on others (β= 0.35; p<0.0001); inability to take breaks in addition to scheduled breaks (β= 0.25; p<0.0001); inability to work because of unexpected events (β= 0.21; p<0.0001); inability to control the order and pace of tasks (β= 0.20; p<0.0001); and weight of load (β= 0.17; p<0.0001); accounting for 53% of the variance in neck pain intensity. Significant independent factors associated with neck disability were weight of load (β= 0.30; p<0.0001); duration of load carriage (β= 0.16; p=0.01); working under time pressure/deadlines (β= 0.16; p=0.02); and accounting for 20% of the variance in neck disability. Significant independent factor associated with sick leave was duration of load carriage (β=0.15; p= 0.04), in a non-significant regression model explaining –4% of the variance in sick leave. Addition of pain intensity significantly explained more variance in neck disability (31.0%) but less variance in sick leave (–5%), which was not statistically significant (F (10, 190)= 0.902, p=0.533).ConclusionsOccupational biomechanical factors may be more important than occupational psychosocial factors in explaining neck disability and sick leave. In contrast, occupational psychosocial factors may be more important than occupational biomechanical factors in explaining neck pain intensity in this population in Nigeria.
Job Demands, Social Support, and Burnout among Public Senior High School Teachers, Ghana
Authors: Akutey Richard , Ansah Edward Wilson , Apaak Daniel 
Published: November 2023

AbstractThis study aimed to investigate the extent to which job demands and social support predict burnout of public senior high school (S.H.S.) teachers in Ghana, and to determine the mediating effect of job resources in the relation between job demands and burnout among these teachers. Employing a quantitative survey, 1028 public S.H.S. teachers were selected using purposive and voluntary sampling methods. A questionnaire adopted from pre-existing standardized instruments yielded composite reliability between 0.94 and 0.98. Data was analyzed using mean, standard deviation, and multiple linear regression. Results revealed a high level of job demands (M = 3.23, SD = 0.43), social support (M = 3.02, SD = 0.54), and burnout (M = 3.33, SD = 0.92) among the teachers. Also, multiple linear regression results indicate that job demands, and social support predict burnout of the teachers. Furthermore, social support is a partial mediator of the effect of job demands on teacher’s burnout. Therefore, perceived high level of burnout is an effect of high levels of job demands, which poses a serious threat to the health and well-being of these teachers and compromises teaching quality in Ghana’s S.H.S. However, this challenge can be prevented or reduced by providing more social support to the teachers. Hence, government, management, and other educational stakeholders need to provide a strong safety leadership in all matters that concerns teacher’s health and safety. The school administrators and teachers are also encouraged to promote social support vertically and horizontally.
Modifiable clinical dental impression methods to obtain whole-mouth and detailed dental traits from vertebrates
Authors: Wibisana Johannes N. , Sallan Ray A. , Ota Towa , Puchenkov Pavel , Kubo Tai , Sallan Lauren 
Published: November 2023

AbstractDental impressions, developed for accurate capture of oral characteristics in human clinical settings, are seldom used in research on non-livestock, non-primate, and especially non-mammalian, vertebrates due to a lack of appropriate tools. Studies of dentitions in most vertebrate species usually require euthanasia and specimen dissection, microCT and other scans with size and resolution tradeoffs, and/or ad-hoc individual impressions or removal of single teeth. These approaches prevent in-vivo studies that factor in growth and other chronological changes and separates teeth from the context of the whole mouth. Here, we describe a non-destructive method for obtaining high resolution dentition-related traits that can be used on both living animals and museum specimens for almost all vertebrates, involving a customizable and printable dental impression tray. This method has repeatedly and accurately capture whole-mouth morphology and detailed features at high resolution in the living non-teleost actinopterygian fish,Polypterus senegalus,in a laboratory setting. It can be used for comparative morphology and to observe temporal changes such as the presence of microwear, tooth replacement rates, and occlusal and morphological changes through ontogeny.Summary statementThis study presents a cheap and customizable method using a printable tray to measure oral morphological traits in vertebrates humanely and accurately.
Alpha9alpha10 knockout mice show altered physiological and behavioral responses to signals in masking noise
Authors: Mondul Jane A. , Burke Kali , Morley Barbara , Lauer Amanda M. 
Published: November 2023

ABSTRACTMedial olivocochlear (MOC) efferents modulate outer hair cell motility through specialized nicotinic acetylcholine receptors to support encoding of signals in noise. Transgenic mice lacking the alpha9 subunits of these receptors (α9KOs) have normal hearing in quiet and noise, but lack classic cochlear suppression effects and show abnormal temporal, spectral, and spatial processing. Mice deficient for both the alpha9 and alpha10 receptor subunits (α9α10KOs) may exhibit more severe MOC-related phenotypes. Like α9KOs, α9α10KOs have normal auditory brainstem response (ABR) thresholds and weak MOC reflexes. Here, we further characterized auditory function in α9α10KO mice. Wildtype and α9α10KO mice had similar ABR thresholds and acoustic startle response (ASR) amplitudes in quiet and noise, and similar frequency and intensity difference sensitivity. α9α10KO mice had larger ABR Wave I amplitudes than wildtypes in quiet and noise, but the noise:quiet amplitude ratio suggested α9α10KOs were more susceptible to masking effects for some stimuli. α9α10KO mice also had larger startle amplitudes in tone backgrounds than wildtypes. Overall, α9α10KO mice had grossly normal auditory function in quiet and noise, though their larger ABR amplitudes and hyperreactive startles suggest some auditory processing abnormalities. These findings contribute to the growing literature showing mixed effects of MOC dysfunction on hearing.
Identification of functional genes underlining growth in large yellow croaker
Authors: Wen Jing , Yue Zhufeng , Ji Jiaojun , Yuan Yingbo , Zhou Meng , Zhang Bo , Zhang Yongjie , Ye Kun , Wang Zhiyong , Jiang Dan , Fang Ming 
Published: November 2023

AbstractLarge yellow croaker (Larimichthys crocea) is the largest cultured marine fish in China, although its economic benefits are significant, its growth cycle is long and it takes 2 years to market. Identification of genomic variations and genes affecting the growth ofL. croceais of great significance for breeding fast-growing strains by molecular means. We utilized whole genome resequencing to identify a highly effective GWAS locus on chromosome 6 of the genome, and identified some candidate genes that affect growth. This study provides a theoretical basis for analyzing the genetic mechanism of growth traits ofL. croceaand cultivating fast-growing varieties.
CryoENsemble - a Bayesian approach for reweighting biomolecular structural ensembles using heterogeneous cryo-EM maps
Authors: Włodarski Tomasz , Streit Julian O. , Mitropoulou Alkistis , Cabrita Lisa D. , Vendruscolo Michele , Christodoulou John 
Published: November 2023

AbstractCryogenic electron microscopy (cryo-EM) has emerged as a central tool for the determination of structures of complex biological molecules. Accurately characterising the dynamics of such systems, however, remains a challenge. To address this, we introduce cryoENsemble, a method that applies Bayesian reweighing to conformational ensembles derived from molecular dynamics simulations to improve their agreement with cryo-EM data and extract dynamics information. We illustrate the use of cryoENsemble to determine the dynamics of the ribosome-bound state of the co-translational chaperone trigger factor (TF). We also show that cryoENsemble can assist with the interpretation of low-resolution, noisy or unaccounted regions of cryo-EM maps. Notably, we are able to link an unaccounted part of the cryo-EM map to the presence of another protein (methionine aminopeptidase, or MetAP), rather than to the dynamics of TF, and model its TF-bound state. Based on these results, cryoENsemble is expected to find use for challenging heterogeneous cryo-EM maps for various biomolecular systems, especially those encompassing dynamic elements.
Changes in length-at-first return of a sea trout (Salmo trutta) population in northern France
Authors: Josset Quentin , Beaulaton Laurent , Romakkaniemi Atso , Nevoux Marie 
Published: November 2023

AbstractThe resilience of sea trout populations is increasingly concerning, with evidence of major demographic changes in some populations. Based on trapping data and related scale collection, we analysed long-term changes in body length of a sea trout population in the Bresle River, France. From 1984-2022, the length of first-time returning individuals decreased by 1.73 mm.year-1(SD = 0.08), which resulted in the loss ofc.12.3% of mean body length. This decrease results from a decrease in the age at first return, with a gradual loss of the oldest individuals and an increase in the proportion of the youngest. Timing of the return migration advanced drastically, although shorter sea sojourn had little influence on body length. We found little evidence of a decrease in length-at-age, to the exception of the oldest age class, suggesting that growth conditions at sea might not have deteriorated greatly during the study period.
Expression of the MSPDBL2 antigen in a discrete subset ofPlasmodium falciparumschizonts is regulated by GDV1 but not linked to sexual commitment
Authors: Freville Aline , Stewart Lindsay B. , Tetteh Kevin K.A. , Treeck Moritz , Cortes Alfred , Voss Till S. , Tarr Sarah J. , Baker David A. , Conway David J. 
Published: November 2023

ABSTRACTThePlasmodium falciparummerozoite surface protein MSPDBL2 is a polymorphic antigen targeted by acquired immune responses, and normally expressed in only a minority of mature schizonts. The potential relationship of MSPDBL2 to sexual commitment is examined, as variablemspdbl2transcript levels and proportions of MSPDBL2-positive mature schizonts in clinical isolates have previously correlated with levels of many sexual stage parasite gene transcripts, although not with the master regulatorap2-g. It is demonstrated that conditional overexpression of GDV1, which promotes sexual commitment, also substantially increases the proportion of MSPDBL2-positive schizonts in culture. Conversely, truncation of thegdv1gene is shown to prevent any expression of MSPDBL2. However, across diverseP. falciparumcultured lines the variable proportions of MSPDBL2 positivity in schizonts does not correlate significantly with variable gametocyte conversion rates, indicating it is not involved in sexual commitment. Confirming this, examining a line with endogenous HA-tagged AP2-G showed that the individual schizonts expressing MSPDBL2 are mostly different to those expressing AP2-G. Using a selection-linked integration system, modifiedP. falciparumlines were engineered to express an intact or disrupted version of MSPDBL2, showing the protein is not required for sexual commitment or early gametocyte development. Asexual parasite multiplication rates were also not affected by expression of either intact or disrupted MSPDBL2 in a majority of schizonts. Occurring alongside sexual commitment, the role of the discrete MSPDBL2-positive schizont subpopulation requires further investigation in natural infections where it is under immune selection.
From Sequence to Significance: A Thorough Investigation of the Distinctive Genome Traits Uncovered inC. werkmaniistrain NIB003
Authors: Hossain Mohammad Uzzal , Tanvir Neyamat Khan , Chowdhury Zeshan Mahmud , Rahman A.B.Z Naimur , Hossain Md. Shahadat , Dey Shajib , Bhattacharjee Arittra , Ahmed Ishtiaqe , Hashem Abu , Das Keshob Chandra , Keya Chaman Ara , Salimullah Md. 
Published: November 2023

AbstractCitrobacter werkmanii(C. werkmanii) is an opportunistic bacterium that has received very little investigation in Bangladesh, even though it is thought to be capable of causing diseases including diarrhea and urinary tract infections. Therefore, the present study focuses on the exploration of genomic features, including antibiotic resistance genes, virulent genes, and their distinctive nature in the pathogenesis of diseases. A complete genome was sequenced for the first time in Bangladesh after the morphological, biochemical and molecular identification of this bacteria. A total of 47,65,861 nucleotide base pairs makes up the genome, which contains 4669 genes, and many of the protein-coding genes can be classified into various ontological frameworks, including COG and KEGG pathways. Notably,C. werkmaniihas the capability to have interactions withEscherichia coli, Salmonella,andKlebsiellawhile they possess the same domains and motifs, indicating a causal role in the development of diarrhea. Furthermore, the Bangladeshi isolate ofC. werkmaiihas observed genetic heterogeneity when compared to other strains ofC. werkmanii: C. werkmanii FDAARGOS_616, C. werkmanii LCU-V21, andC. werkmanii BF-6. This identified genetic variation of sequencedC. werkmaniicould drive the functional aberration in body homeostasis of bacteria. Later, molecular dynamics studies have proven the impact of their genetic variation on the protein structure, as indicated by the SASA, RMSD, Rg, and RMSF values. Finally, the findings ofC. werkmaniifrom the sequenced genome might provide us with a better understanding ofC. werkmaniiand their possible role as opportunistic bacteria in diseases including diarrhea and urinary tract infections.
LightMHC: A Light Model for pMHC Structure Prediction with Graph Neural Networks
Authors: Delaunay Antoine P. , Fu Yunguan , Gorbushin Nikolai , McHardy Robert , Djermani Bachir A. , Copoiu Liviu , Rooney Michael , Lang Maren , Tovchigrechko Andrey , Şahin Uğur , Beguir Karim , Carranza Nicolas Lopez 
Published: November 2023

AbstractThe peptide-major histocompatibility complex (pMHC) is a crucial protein in cell-mediated immune recognition and response. Accurate structure prediction is potentially beneficial for protein interaction prediction and therefore helps immunotherapy design. However, predicting these structures is challenging due to the sequential and structural variability. In addition, existing pre-trained models such as AlphaFold 2 require expensive computation thus inhibiting high throughputin silicopeptide screening. In this study, we propose LightMHC: a lightweight model (2.2M parameters) equipped with attention mechanisms, graph neural networks, and convolutional neural networks. LightMHC predicts full-atom pMHC structures from amino-acid sequences alone, without template structures. The model achieved comparable or superior performance to AlphaFold 2 and ESMFold (93M and 15B parameters respectively), with five-fold acceleration (6.65 seconds/sample for LightMHC versus 36.82 seconds/sample for AlphaFold 2), potentially offering a valuable tool for immune protein structure prediction and immunotherapy design.
Intricate mechanism (s) of substrate specificity and loss of function on disease mutation (K211N) of Parkin
Authors: Lenka Dipti Ranjan , Chaurasiya Shradha , Kumar Atul 
Published: November 2023

AbstractParkin mutations lead to the early onset of Parkinson’s disease. PINK1-mediated phosphorylation of its substrates Ubiquitin (Ub)-like proteins (NEDD8, Ubiquitin) and Ubiquitin-like (Ubl) domain activate autoinhibited Parkin. Substrate specificity on Parkin and the cause of loss of function in disease mutation K211N remain elusive. Herein, we determine the first crystal structure of human Parkin bound with phospho(p)-NEDD8 and establish the mechanism of substrate specificity on Parkin. RING0 pocket is specific for pUbl and does not bind with pUb/pNEDD8. In contrast, pNEDD8 has evolved to bind robustly in the RING1 pocket and shows higher activation of Parkin compared to pUb. Also, the binding of activators in the RING1 and RING0 pockets of Parkin leads to a distinct extent of RING2 displacement during Parkin activation. Furthermore, the crystal structure of pNEDD8-bound Parkin K211N reveals novel conformational changes due to N211 that lock RING2 with RING0 to inhibit Parkin activity without losing pNEDD8/pUb binding. This study would help design small-molecule Parkin activators against Parkinson’s disease.
The CD36 scavenger receptor Bez regulates lipid redistribution from fat body to oocytes in Drosophila
Authors: Carrera Pilar , Odenthal Johanna , Risse Katharina S. , Jung Yerin , Kuerschner Lars , Bülow Margret H. 
Published: November 2023

AbstractClass B scavenger receptors of the CD36 family are important for lipid mobilization from mammalian adipose tissue. This protein family has 3 members in mammals, but 14 inDrosophila melanogaster. Lipid distribution inDrosophilais mediated by homologs of the LDL receptors, while little is known about the function of scavenger receptors for this process in invertebrates. Here we unravel a role for the so far uncharacterized scavenger receptor Bez in lipid export fromDrosophilaadipocytes. Bez shares the lipid binding residue with CD36 and is expressed at the plasma membrane of the embryonic, larval and adult fat body. Bez loss-of-function lowers the organismal content of storage lipids while they accumulate in the fat body, concomitant with female sterility and degeneration of ovaries. Using an alkyne-labeled fatty acid tracer, we demonstrate that Bez interacts with the apoB homolog Lipophorin at the plasma membrane of adipocytes, thereby enabling lipid transfer. Our study shows how a scavenger receptor interacts with lipoproteins to distribute storage lipids from the fat body to the ovaries and thereby contributes to the metabolic control of development.
Role ofugtgenes in detoxification and glycosylation of 1-hydroxy phenazine (1-HP) inCaenorhabditis elegans
Authors: Asif Muhammad Zaka , Nocilla Kelsey A. , Ngo Li T. , Shah Man K. , Smadi Yosef , Hafeez Zaki A. , Parnes Michael , Manson Allie , Glushka John , Leach Franklin E. , Edison Arthur S. 
Published: November 2023

ABSTRACTCaenorhabditis elegansis an ideal model organism to study the xenobiotic detoxification pathways of various natural and synthetic toxins. One toxin shown to cause death inC. elegansis 1-hydroxyphenazine (1-HP), a molecule produced by the bacteriumPseudomonas aeruginosa.We previously showed that the median lethal dose (LD50) for 1-HP inC elegansis 179 μM in PD1074 and between 150-200 μM in N2 (C. eleganslab strain). We also showed thatC. elegansdetoxifies 1-HP by glycosylation by adding one, two, or three glucose molecules in N2 worms. This study tested whether UDP-glycosyltransferase (ugt)genes play a role in 1-HP detoxification. We show thatugt-23andugt-49 knockout mutants are more sensitive to 1-HP. Our data also show thatugt-23knockout mutants produce reduced amounts of the trisaccharide sugars, while theugt-49knockout mutants produce reduced amounts of all 1-HP derivatives except for the glucopyranosyl product. We have also characterized the structure of the trisaccharide sugar phenazine structures made byC. elegansand show that one of the sugar modifications contains an N-acetylglucosamine (GlcNAc) in place of glucose. This implies broad specificity regarding UGT function and the role of genes other thanogt-1in adding GlcNAc, at least in small-molecule detoxification.