bluuebunny/crossref_metadata_2025_split huggingface dataset:
Campylobacterinfection of young children in Colombia and its impact on the gastrointestinal environment
Authors: Burcham Zachary M. , Tweedie Jessie L. , Farfán-García AE , Nolan Vikki G. , Donohoe Dallas , Gómez-Duarte Oscar G. , Johnson Jeremiah G. 
Published: May 2024

AbstractCampylobacterinfections are a leading cause of bacterial-derived gastroenteritis worldwide with particularly profound impacts on pediatric patients in low-and-middle income countries. It remains unclear howCampylobacterimpacts these hosts, though it is becoming increasingly evident that it is a multifactorial process that depends on the host immune response, the gastrointestinal microbiota, various bacterial factors, and host nutritional status. Since these factors likely vary between adult and pediatric patients in different regions of the world, it is important that studies define these attributes in well characterized clinical cohorts in diverse settings. In this study, we analyzed the fecal microbiota and the metabolomic and micronutrient profiles of asymptomatic and symptomatic pediatric patients in Colombia that were either infected or uninfected withCampylobacterduring a case-controlled study on acute diarrheal disease. Here, we report that the microbiome ofCampylobacter-infected children only changed in their abundance ofCampylobacterspp. despite the inclusion of children with or without diarrhea. In addition to increasedCampylobacter,computational models were used to identify fecal metabolites that were associated withCampylobacterinfection and found that glucose-6-phosphate and homovanillic acid were the strongest predictors of infection in these pediatric patients, which suggest that colonocyte metabolism are impacted during infection. Despite changes to the fecal metabolome, the concentrations of intestinal minerals and trace elements were not significantly impacted byCampylobacterinfection, but were elevated in uninfected children with diarrhea.ImportanceGastrointestinal infection with pathogenicCampylobacterspecies has long been recognized as a significant cause of human morbidity. Recently, it has been observed that pediatric populations in low-and-middle income countries are uniquely impacted by these organisms in that infected children can be persistently colonized, develop enteric dysfunction, and exhibit reduced development and growth. While the association ofCampylobacterspecies with these long-term effects continues to emerge, the impact of infection on the gastrointestinal environment of these children remains uncharacterized. To address this knowledge gap, our group leveraged clinical samples collected during a previous study on gastrointestinal infections in pediatric patients to examine the fecal microbiota, metabolome, and micronutrient profiles of those infected withCampylobacterspecies, and found that the metabolome was impacted in a way that suggests gastrointestinal cell metabolism is affected during infection, which is some of the first data indicating how gastrointestinal health in these patients may be affected.
Impact of the elderly lung mucosa onMycobacterium tuberculosismetabolic adaptation during infection of alveolar epithelial cells
Authors: Olmo-Fontánez Angélica M. , Allué-Guardia Anna , Garcia-Vilanova Andreu , Glenn Jeremy , Wang Shu-Hua , Merritt Robert E. , Schlesinger Larry S. , Turner Joanne , Wang Yufeng , Torrelles Jordi B. 
Published: May 2024

ABSTRACTBackgroundTuberculosis (TB) is one of the top leading causes of death due to a single infectious agent. Upon infection,Mycobacterium tuberculosis(M.tb) is deposited in the alveoli and encounters the lung mucosa or alveolar lining fluid (ALF). We previously determined that increasedM.tbreplication in human macrophages and alveolar epithelial cells (ATs) is mediated by age-associated changes in human ALF. Here we determine the transcriptional profile ofM.tbwhen exposed to healthy ALF from adult (A-ALF) or elderly (E-ALF) individuals before and during infection of ATs.ResultsPrior to infection, exposure to E-ALF upregulatesM.tbgenes associated with the ESX-4 secretion system, immunomodulatory proteins from the ESX-5 system, and genes encoding phospholipases, phosphatases, and proteases. During infection, E-ALF exposure upregulates keyM.tbgenes from the ESX-5 secretion system, genes associated with PDIMs biosynthesis and transport, and genes linked to bacterial oxidative stress defense mechanisms.ConclusionsThese findings demonstrate how altered ALF in old age can impact the metabolic status ofM.tb, enabling greater adaptation to the host and potentially explainingMtb’s increased survival within host cells. Importantly, we present the first transcriptomic analysis on the impact of the elderly lung mucosa onM.tbpathogenesis during intracellular replication in ATs.
Protection againstClostridioides difficiledisease by a naturally avirulentC. difficilestrain
Authors: Dong Qiwen , Harper Stephen , McSpadden Emma , Son Sophie S. , Allen Marie-Maude , Lin Huaiying , Smith Rita C. , Metcalfe Carolyn , Burgo Victoria , Woodson Che , Sundararajan Anitha , Rose Amber , McMillin Mary , Moran David , Little Jessica , Mullowney Michael , Sidebottom Ashley M. , Shen Aimee , Fortier Louis-Charles , Pamer Eric G. 
Published: May 2024

AbstractClostridioides difficile (C. difficile)strains belonging to the epidemic BI/NAP1/027 (RT027) group have been associated with increased transmissibility and disease severity. In addition to the major toxin A and toxin B virulence factors, RT027 strains also encode the CDT binary toxin. Our lab previously identified a toxigenic RT027 isolate, ST1-75, that is avirulent in mice despite densely colonizing the colon. Here, we show that co-infecting mice with the avirulent ST1-75 and virulent R20291 strains protects mice from colitis due to rapid clearance of the virulent strain and persistence of the avirulent strain. Although avirulence of ST1-75 is due to a mutation in thecdtRgene, which encodes a response regulator that modulates the production of all threeC. difficiletoxins, the ability of ST1-75 to protect against acute colitis is not directly attributable to thecdtRmutation. Metabolomic analyses indicate that the ST1-75 strain depletes amino acids more rapidly than the R20291 strain and supplementation with amino acids ablates ST1-75’s competitive advantage, suggesting that the ST1-75 strain limits the growth of virulent R20291 bacteria by amino acid depletion. Since the germination kinetics and sensitivity to the co-germinant glycine are similar for the ST1-75 and R20291 strains, our results identify the rapidity ofin vivonutrient depletion as a mechanism providing strain-specific, virulence-independent competitive advantages to different BI/NAP1/027 strains. They also suggest that the ST1-75 strain may, as a biotherapeutic agent, enhance resistance to CDI in high-risk patients.ImportanceClostridioides difficileinfections (CDI) are prevalent in healthcare settings and are associated with high recurrence rates. Therapies to prevent CDI, including recent FDA-approved live biotherapeutic products, are costly and have not been used to prevent primary infections. While a nontoxigenicC. difficilestrain (NTCD-M3) protects against virulent CDI in animals and reduced CDI recurrence in a phase 2 clinical trial, protection against CDI recurrence in humans was variable and required high doses of the nontoxigenic strain. Here we show that an avirulentC. difficileisolate, ST1-75, efficiently outcompetes virulentC. difficilestrains in mice when co-infected at a 1:1 ratio. Our data suggest that inter-strain competition results from ST1-75’s more rapid depletion of amino acids than the virulent R20291 strain. Our study identifies inter-strain nutrient depletion as a potentially exploitable mechanism to reduce the incidence of CDI.
Chronic abolition of evoked vesicle release from layer 5 projection neurons disrupts the laminar distribution of parvalbumin interneurons in the adult cortex
Authors: Szabó Florina P , Sigutova Veronika , Schneider Anna M , Hoerder-Suabedissen Anna , Molnár Zoltán 
Published: May 2024

AbstractEstablishing precisely built neuronal networks during cortical development requires appropriate proportions of glutamatergic and GABAergic neurons. Developmental disturbances in pyramidal neuron activity can impede the development of GABAergic neurons with long-lasting effects on inhibitory networks. However, the role of deep-layer pyramidal neurons in instructing the development and distribution of GABAergic neurons remains unknown. To unravel the role of deep-layer pyramidal neuron activity in orchestrating the spatial and laminar organisation of parvalbumin neurons, we selectively manipulated the activity of projection neurons in layer 5 of the cortex. By ablating SNAP25 from subsets of glutamatergic L5 projection neurons across the cortical mantle, we abolished Ca2+-dependent vesicle release from Rbp4-Cre+ pyramidal neurons. We explored thelocal(location of the cell bodies) and theglobal(subcortical projection sites) effects of chronically silencing cortical L5 neurons on parvalbumin interneurons. We found that the chronic cessation of vesicle release from L5 projection neurons left the density, distribution, and developmental trajectory of cortical and subcortical PV neurons intact during the second and third postnatal week; however, it resulted in the reorganisation of the laminar distribution of cortical PV neurons in layer 4 of S1 in the adult cortex. The abolition of evoked vesicle release from L5 also affected the perineuronal nets in the adult motor cortex and revealed a significant decrease in the density of VVA+ and PV-VVA+ cells in L5 of M1 at 3 months of age. The alterations in the laminar arrangement of VVA+ neurons may imply that Ca2+-dependent synaptic transmission from L5 may control PNN density in adult networks. We also discovered that the absence of L5 activity only had a transient effect on the morphology of striatal PV neurons. The correlation between PV and VVA neurons was contingent on brain regions and cortical layers, therefore the link between the perineuronal net and PV neurons is significantly more intricate than previously believed. The present study will aid our understanding of the bidirectional relationship between deep-layer pyramidal cells and GABAergic neurons while uncovering the long-term effects of chronically disrupting pyramidal neurons on inhibitory networks.
Exploring the Efficacy and Potential of Large Language Models for Depression: A Systematic Review
Authors: Omar Mahmud , Levkovich Inbar 
Published: May 2024

AbstractBackground and ObjectiveDepression is a substantial public health issue, with global ramifications. While initial literature reviews explored the intersection between artificial intelligence (AI) and mental health, they have not yet critically assessed the specific contributions of Large Language Models (LLMs) in this domain. The objective of this systematic review was to examine the usefulness of LLMs in diagnosing and managing depression, as well as to investigate their incorporation into clinical practice.MethodsThis review was based on a thorough search of the PubMed, Embase, Web of Science, and Scopus databases for the period January 2018 through March 2024. The search used PROSPERO and adhered to PRISMA guidelines. Original research articles, preprints, and conference papers were included, while non-English and non-research publications were excluded. Data extraction was standardized, and the risk of bias was evaluated using the ROBINS-I, QUADAS-2, and PROBAST tools.ResultsOur review included 34 studies that focused on the application of LLMs in detecting and classifying depression through clinical data and social media texts. LLMs such as RoBERTa and BERT demonstrated high effectiveness, particularly in early detection and symptom classification. Nevertheless, the integration of LLMs into clinical practice is in its nascent stage, with ongoing concerns about data privacy and ethical implications.ConclusionLLMs exhibit significant potential for transforming strategies for diagnosing and treating depression. Nonetheless, full integration of LLMs into clinical practice requires rigorous testing, ethical considerations, and enhanced privacy measures to ensure their safe and effective use.A visual abstract
Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh
Authors: Carnegie L. , McCrone J.T. , du Plessis L. , Hasan M. , Ali M.Z. , Begum R. , Hassan M.Z. , Islam S. , Rahman M.H. , Uddin A.S.M. , Sarker M.S. , Das T. , Hossain M. , Khan M. , Razu M.H. , Akram A. , Arina S. , Hoque E. , Molla M.M.A. , Nafisaa T. , Angra P. , Rambaut A. , Pullan S.T. , Osman K.L , Hoque M.A. , Biswas P. , Flora M.S. , Raghwani J. , Fournié G. , Samad M.A. , Hill S.C. 
Published: May 2024

AbstractBackgroundGenomic epidemiology has helped reconstruct the global and regional movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is still a lack of understanding of SARS-CoV-2 spread in some of the world’s least developed countries (LDCs).MethodsTo begin to address this disparity, we studied the transmission dynamics of the virus in Bangladesh during the country’s first COVID-19 wave by analysing case reports and whole-genome sequences from all eight divisions of the country.ResultsWe detected >50 virus introductions to the country during the period, including during a period of national lockdown. Additionally, through discrete phylogeographic analyses, we identified that geographical distance and population -density and/or -size influenced virus spatial dispersal in Bangladesh.ConclusionsOverall, this study expands our knowledge of SARS-CoV-2 genomic epidemiology in Bangladesh, shedding light on crucial transmission characteristics within the country, while also acknowledging resemblances and differences to patterns observed in other nations.
A cooperatively breeding mouse shows flexible use of its vocal repertoire according to social context
Authors: Perrier Léo , de Witasse-Thézy Aude , Pradeau Aurélie , Schradin Carsten , Greenfield Michael D. , Mathevon Nicolas , Levréro Florence 
Published: May 2024

AbstractMice exchange information using chemical, visual and acoustic signals. Long ignored, mouse ultrasonic communication is now considered to be an important aspect of their social life, transferring information such as individual identity or stress levels. However, whether and how mice modulate their acoustic communications is largely unknown. Here we show that a wild mouse species with a complex social system controls its vocal production both qualitatively and quantitatively, depending on social context. We found that the African striped mouseRhabdomys pumilio, a cooperatively breeding species, has a vocal repertoire consisting of seven call types, which it uses differently depending on whether the individuals encounter another mouse that is familiar, unfamiliar, of the same or different sex. Familiar individuals, whether of the same or different sex, vocalize more than two unfamiliar same-sex individuals. The greatest diversity of vocalisations is recorded when a female and a male first encounter, suggesting that certain calls are reserved for courtship. Our results highlight that familiar mice alternate their vocalisations (turn-taking) while unfamiliar individuals tend to overlap one another. These observations suggest that African striped mice control the production and temporal dynamics of their vocalisations, addressing targeted information to specific receivers via the acoustic channel.
First genome assembly of the order Strepsiptera using PacBio HiFi reads reveals a miniature genome
Authors: Castaño María Isabel , Ye Xinhai , Uy Floria MK 
Published: May 2024

AbstractTwisted-wing insects (Strepsiptera) are an enigmatic order of parasites with unusual life histories and striking sexual dimorphism. Males emerge from hosts as free-living winged adults, while females from most species remain as endoparasites that retain larval traits. Due to scarce genomic data and phylogenetic controversies, Strepsiptera was only recently placed as the closest living relative to beetles (Coleoptera). Here, we report the first PacBio HiFi genome assembly of the strepsipteranXenos peckii(Xenidae). Thisde novoassembly size is 72.1 Mb, with a BUSCO score of 87.4%, N50 of 7.3 Mb, 23.4% GC content and 38.41% repeat content. We identified 8 contigs that contain > 75% of the assembly and reflect the haploid chromosome number reported from karyotypic data, and 3 contigs that exhibit sex chromosome coverage patterns. Additionally, the mitochondrial genome is 16,111 bp long and has 34 genes. This long-read assembly for Strepsiptera reveals a miniature genome and provides a unique tool to understand complex genome evolution associated with a parasitic lifestyle and extreme sexual dimorphism.
Stability of plane Couette flow with constant wall transpiration
Authors: Sun W. , Yalcin A. , Oberlack M. 
Published: May 2024

Plane Couette flow with constant wall transpiration, i.e., constant blowing from below and constant suction from above, is a solution of the Navier-Stokes equations in terms of exponentials. It is characterized by two Reynolds numbers Re and ReV, where Re parametrizes the moving wall and ReV describes the influence of the transpiration. For this flow the modified Orr-Sommerfeld equation admits one of the very few exact solutions in terms of hypergeometric functions. Based on this, we solve the stability problem, though for the main part focus on temporal stability. For small wall-transpiration rates up to ReV≃6.71, the flow remains unconditionally stable, analogous to the classical Couette flow for arbitrary Reynolds numbers Re. By further increasing ReV an instability sets in and a minimum critical Reynolds number of Re=668350.491 is reached at ReV=9.799. Hence, around this point, the destabilizing effect of blowing outweighs the stabilizing effect of suction. By further increasing the transpiration rate beyond this point, the corresponding critical Reynolds number Re increases again and continues to grow. This limiting case is accompanied by the development of a strong boundary-layer-like velocity profile near the upper wall and the flow transitions to the asymptotic suction boundary layer (ASBL). Thus, the present analysis comprises the whole range from classical Couette flows extended by transpiration to the ASBL, which is known to have a strongly stabilizing effect.

Published by the American Physical Society
2024
Blending logics with performance management systems in an NGO setting
Authors: Thambar Paul J. , Ferreira Aldónio , Thoradeniya Prabanga 
Published: May 2024

PurposeThis study aims to examine the role of performance management systems (PMSs) in enabling logic blending to manage institutional complexity and tensions arising from coexisting institutional logics.Design/methodology/approachThis research uses a case study of an Australian non-government organisation (NGO) operating in an institutional field dominated by the state government, in which policy reform jolted the balance between institutional logics. Data was collected through semi-structured interviews, archival documents and observations.FindingsWe find the policy reform required the NGO to transform from a wholly care focus to accommodate a more balanced approach with a focus on care coupled with efficiency, outcome delivery and performance measurement. The NGO responded by revising its purpose, strategy and operational model and by seeking to address the imperatives of two dominant and often competing care and managerial logics. We find this was achieved through logic blending, in which PMSs played a pivotal role, with the formalisation and collaboration processes mobilising different elements of PMSs, mobilising some elements differently or not mobilising some elements at all.Originality/valueThis study highlights the central role of PMSs in managing tensions between and the complexity arising from coexisting institutional logics through logic blending, a form of enduring compromise. This study extends the accounting logics and performance management literature by developing the understanding of what constitutes logic blending and how it is distinct from other forms of compromise.
Effect of team identification on employee constructive deviance: the role of moral justification and environmental instability
Authors: Liu Tingting , Shao Danping , Li Yulei , Liu Chang-E , He Wei 
Published: May 2024

Purpose
Despite an emerging interest in constructive deviance, the exploration of its antecedents is still limited, particularly from an ethical perspective. This study aims to uses moral disengagement theory to investigate how team identification, moral justification and team environmental instability interact to affect employee constructive deviance.

Design/methodology/approach
With survey data collected in two waves from 315 employees of 49 work teams in five service companies in China, this study develops four hypotheses and tests them through hierarchical linear model.

Findings
The survey results support the complete mediating effect of moral justification on the positive impact of team identification on constructive deviance. They also confirm the moderating effect of environmental instability on the relationship between team identification, moral justification and constructive deviance.

Originality/value
This study explores the sources of constructive deviance at team level from the ethical decision-making perspective and reveals the mechanism and contingency factors in the relationship between identity and constructive deviance. In practice, the study findings imply that managers should encourage their employees to cultivate their identification with their team and align their moral justification with the team’s norms especially when the team faces turbulent environment.