bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation of a Chlamydia Strain from Lung Tissue Samples in Healthy Chickens Exhibiting Antagonistic Effects on Avian Infectious Bronchitis Virus
Authors: Zhen Miaoxiao 
Published: May 2023

AbstractTo assess the feasibility of isolating Chlamydia strains with antiviral activity against avian infectious bronchitis virus (IBV) from healthy chickens in farms, 58 Chlamydia strains were obtained from 160 lung tissue samples collected across ten chicken farms, yielding an overall isolation rate of 36.25%. SPF chickens co-infected with Chlamydia and IBV were employed for verification, leading to the identification of eight strains (Bi≥ 0.800) with potent antiviral effects against IBV, accounting for 13.79% of the total isolated strains. The top-performing strain, Y17 Chlamydia strain, was selected and subjected to cell co-culture and U-tube experiments with IBV. Results demonstrated that the Y17 Chlamydia strain significantly impeded IBV replication in chicken tracheal epithelial cells (P<0.01) and did not secrete or induce host cells to secrete extracellular metabolites with antagonistic effects on IBV infection in U-tube experiments (P>0.05), suggesting that its antiviral activity was cell-autonomous. Our research highlights the feasibility of isolating Chlamydia strains with antiviral activity against IBV from healthy chickens and suggests that antiviral strains could be widespread, even though their efficacy against viruses is strain-specific. The presence of broad-spectrum antiviral Chlamydia strains may also be possible. Considering the prevalence of Chlamydia strains in vertebrate hosts, along with the fact that some strains are either non-pathogenic or display low toxicity, our findings could offer a fresh perspective on the prevention and treatment of viral infections in vertebrates.
Diversity and Evolution of an Abundant ICEclc-Family of Integrative and Conjugative Elements inPseudomonas aeruginosa
Authors: Benigno Valentina , Carraro Nicolas , Sarton-Lohéac Garance , Romano-Bertrand Sara , Blanc Dominique S. , van der Meer Jan Roelof 
Published: May 2023

AbstractIntegrative and conjugative elements (ICEs) are widespread autonomous mobile DNA, containing the genes necessary for their excision, conjugative transfer, and insertion into a new host cell. ICEs can carry additional genes that are non-essential for their transfer, but that can confer adaptive phenotypes to the host. Our aim here was to better characterize the presence, distribution and evolution of ICEs related to the well-described ICEclcamongPseudomonas aeruginosaclinical isolates, and to understand their potential role in spreading genes with adaptive benefit. We examined a total of 181P. aeruginosagenome sequences obtained from patient or hospital environment isolates. More than 90% of the isolates carried one or more ICEclc-like elements, with different degrees of conservation to the known ICEclc-lifestyle and transfer genes. ICE clones closely matched their host clonal phylogeny, but not exclusively, indicating that both clonal evolution and ICE-horizontal transfer are occurring in the hospital environment. Variable gene regions among the clinicalP. aeruginosaICEclc-type elements were notably enriched for heavy metal resistance genes, toxin-antitoxin systems, potential efflux systems and multidrug resistance proteins, a metalloprotease and for a variety of regulatory systems, but not for specific recognizable antibiotic resistance cassettes. Clonal persistence suggests adaptive benefits of these functional categories; and micro-patterns of gene gain and loss indicate ongoing ICE evolution within theP. aeruginosahosts.
Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization
Authors: Parnell J. Jacob , Vintila Simina , Tang Clara , Wagner Maggie R. , Kleiner Manuel 
Published: May 2023

AbstractSynthetic microbial communities (SynComs) are a valuable tool to study community assembly patterns, host-microbe interactions, and microbe-microbe interactions in a fully controllable setting. Constructing the SynCom inocula for plant-microbe experiments can be time consuming and difficult because a large number of isolates with different media requirements and growth rates are grown in parallel and mixed to appropriate titers. A potential workaround to assembling fresh SynCom inocula for every experiment could be to pre-make and freeze SynComs on a large scale, creating ready-to-use stock inocula. The objective of this study was to compare the reproducibility, stability, and colonization ability of freshly prepared versus frozen SynCom inocula. We used a community of seven species known to colonize maize roots. The results from inoculation with the frozen SynCom were as consistent as standardizedde novoconstruction of fresh SynCom. Our results indicate that creating frozen SynCom inocula for repeated use in experiments not only saves time, but could also improve cross-experiment reproducibility. Although this approach was only validated with one SynCom, it demonstrates a principle that can be tested for improving approaches in constructing other SynComs.ImportanceSynthetic communities (SynComs) are an invaluable tool to characterize and model plant-microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increases enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of “just add buffer and apply to sterilized seeds or seedlings” and thus can save multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to freshly constructued SynComs and thus allow for large time savings when working with SynComs.
Machine learning uncovers thePseudomonas syringaetranscriptome in microbial communities and during infection
Authors: Bajpe Heera , Rychel Kevin , Lamoureux Cameron R. , Sastry Anand V. , Palsson Bernhard O. 
Published: May 2023

AbstractThe transcriptional regulatory network (TRN) of the phytopathogenPseudomonas syringaepv.tomatoDC3000 regulates its response to environmental stimuli, including interactions with hosts and neighboring bacteria. Despite the importance of transcriptional regulation during these agriculturally-significant interactions, a comprehensive understanding of the TRN ofP. syringaeis yet to be achieved. Here, we collected and decomposed a compendium of public RNA-seq data fromP. syringaeto obtain 45 independently modulated gene sets (iModulons) that quantitatively describe the TRN and its activity state across diverse conditions. Through iModulon analysis, we 1) untangle the complex interspecies interactions betweenP. syringaeand other terrestrial bacteria in cocultures, 2) expand the current understanding of theArabidopsis thaliana-P. syringaeinteraction, and 3) elucidate the AlgU-dependent regulation of flagellar gene expression. The modularized TRN yields a unique understanding of interaction-specific transcriptional regulation inP. syringae.ImportancePseudomonas syringaepv.tomatoDC3000 is a model plant pathogen that infects tomatoes andArabidopsis thaliana. The current understanding of global transcriptional regulation in the pathogen is limited. Here, we applied iModulon analysis to a compendium of RNA-seq data to unravel its transcriptional regulatory network. We characterize each co-regulated gene set, revealing the activity of major regulators across diverse conditions. We provide new insights on the transcriptional dynamics in interactions with the plant immune system and with other bacterial species, such as AlgU-dependent regulation of flagellar genes during plant infection and downregulation of siderophore production in the presence of a siderophore cheater. This study demonstrates the novel application of iModulons in studying temporal dynamics during host-pathogen and microbe-microbe interactions, and reveals specific insights of interest.
In vitromethylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome
Authors: Yang Xiao-cui , Desotell Anthony , Lin Min-Han , Paige Andrew S. , Malinowska Agata , Sun Yadong , Aik Wei Shen , Dadlez Michał , Tong Liang , Dominski Zbigniew 
Published: May 2023

ABSTRACTU7 snRNP is a multi-subunit endonuclease required for 3’ end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 and D2 and instead contains two related proteins, Lsm10 and Lsm11. The remaining five subunits of the U7 heptameric Sm ring, SmE, F, G, B and D3, are shared with the spliceosomal snRNPs. The pathway that assembles the unique ring of U7 snRNP is unknown. Here, we show that a heterodimer of Lsm10 and Lsm11 tightly interacts with the methylosome, a complex of the arginine methyltransferase PRMT5, MEP50 and pICln known to methylate arginines in the C-terminal regions of the Sm proteins B, D1 and D3 during the spliceosomal Sm ring assembly. Both biochemical and Cryo-EM structural studies demonstrate that the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the N-terminal region of Lsm11. Surprisingly, PRMT5 also methylates an N-terminal arginine in SmE, a subunit that does not undergo this type of modification during the biogenesis of the spliceosomal snRNPs. An intriguing possibility is that the unique methylation pattern of Lsm11 and SmE plays a vital role in the assembly of the U7 snRNP.
Lactobacillusmaintains IFNγ homeostasis to promote behavioral stress resilience
Authors: Merchak Andrea R. , Wachamo Samuel , Brown Lucille C. , Thakur Alisha , Moreau Brett , Brown Ryan M. , Rivet-Noor Courtney , Raghavan Tula , Gaultier Alban 
Published: May 2023

AbstractThe gut microbiome consists of the trillions of bacteria, fungi, and viruses that inhabit the digestive tract. These communities are sensitive to disruption from environmental exposures ranging from diet changes to illness. Disruption of the community of lactic acid producing bacteria,Lactobaccillacea, has been well documented in mood disorders and stress exposure. In fact, oral supplement with manyLactobacillusspecies can ameliorate these effects, preventing depression- and anxiety-like behavior. Here, for the first time, we utilize a gnotobiotic mouse colonized with the Altered Schaedler Flora to remove the two native species ofLactobaccillacea. Using this novel microbial community, we found that theLactobacillusspecies themselves, and not the disrupted microbial communities are protective from environmental stressors. Further, we determine thatLactobaccillaceaare maintaining homeostatic IFNγ levels which are mediating these behavioral and circuit level responses. By utilizing the Altered Schaedler Flora, we have gained new insight into how probiotics influence behavior and give novel methods to study potential therapies developed to treat mood disorders.
Behavioral Classification of Sequential Neural Activity Using Time Varying Recurrent Neural Networks
Authors: Zhang Yongxu , Mitelut Catalin , Arpin David J. , Vaillancourt David , Murphy Timothy , Saxena Shreya 
Published: May 2023

ABSTRACTShifts in data distribution across time can strongly affect early classification of time-series data. When decoding behavior from neural activity, early detection of behavior may help in devising corrective neural stimulation before the onset of behavior. Recurrent Neural Networks (RNNs) are common models for sequence data. However, standard RNNs are not able to handle data with temporal distributional shifts to guarantee robust classification across time. To enable the network to utilize all temporal features of the neural input data, and to enhance the memory of an RNN, we propose a novel approach: RNNs with time-varying weights, here termed Time-Varying RNNs (TV-RNNs). These models are able to not only predict the class of the time-sequence correctly but also lead to accurate classification earlier in the sequence than standard RNNs. In this work, we focus on early sequential classification of brain-wide neural activity across time using TV-RNNs applied to a variety of neural data from mice and humans, as subjects perform motor tasks. Finally, we explore the contribution of different brain regions on behavior classification using SHapley Additive exPlanation (SHAP) value, and find that the somatosensory and premotor regions play a large role in behavioral classification.
Mammalian orthoreovirus infection in human epidermal growth factor receptor 2 positive (HER2+) breast cancer cells
Authors: Jandick Nicole A. , Kirner Nicolette , Miller Cathy L. 
Published: May 2023

AbstractMammalian orthoreovirus (MRV) is a clinically benign oncolytic virus which has been investigated for use in multiple cancer types, including breast cancer (BC). In human clinical trials, MRV has been shown to be safe, and multiple BC patients have shown partial responses to intratumoral and intravenous virus delivery. Combination therapies inclusive of MRV and current FDA approved BC chemotherapies are being investigated to target metastatic, early BC, and triple negative BC. Though MRV is being tested clinically, we still do not fully understand the highly variable patient responses to MRV therapy. One of the most aggressive BC subtypes is HER2+ BC, in which human epidermal growth factor receptor 2 (HER2) is dysregulated, resulting in increased growth, survival, and metastasis of cancer cells. FDA approved therapies, trastuzumab and pertuzumab, target HER2 to prevent signaling of the phosphoinositide 3-kinase (PI3K) pathway. However, recent findings show that accumulation of hypoxia inducible factor-1 alpha (HIF-1α) in HER2+ BC cells contributes to trastuzumab resistance. In this work, we provide evidence that MRV infects, replicates in, and kills HER2 overexpressing cells. MRV infection is also found to have variable effects on signaling pathways that activate or are activated by HER2 expression. Finally, we show that MRV reduces HIF-1α accumulation in all the cell lines tested, including a HER2+ BC cell line. These studies provide further evidence that MRV holds promise for use in conjunction with trastuzumab to treat HER2+ BC patients.
Mpox diagnosis history, behavioural risk modification, and vaccination uptake in gay, bisexual, and other men who have sex with men in the UK: findings from a large, online community cross-sectional survey (RiiSH-Mpox) undertaken November/December 2022
Authors: Ogaz Dana , Enayat Qudsia , Brown Jack RG , Phillips Dawn , Wilkie Ruth , Jayes Danielle , Reid David , Hughes Gwenda , Mercer Catherine H , Saunders John , Mohammed Hamish 
Published: May 2023

AbstractMpox cases, first identified as part of the multi-country outbreak in May 2022, rapidly fell in the UK from September 2022. Public health responses included community-coordinated messaging and a targeted mpox vaccination in eligible gay, bisexual, and other men who have sex with men (GBMSM). Using data from an online, community survey of GBMSM (November/December 2022), we examined self-reported mpox diagnoses, behavioural risk modification, and mpox vaccination offer and uptake (≥1 dose). Thirty-five participants (2.6%, 35/1,333) were ever mpox test positive; half (53%, 707/1,333) reported behaviour modification to avoid mpox. In GBMSM considered vaccine eligible, uptake was 69% (95% CI: 65%-72%, 601/875) or 92% (95% CI: 89%-94%, 601/655) in those eligible and offered. GBMSM self-identifying as bisexual, those with lower educational qualifications, and those unemployed were less likely to be vaccinated. Equitable mpox vaccine offer and provision is needed to minimise the risk of future outbreaks and mpox-related health inequalities.
Diagnosis coding of Chronic Kidney Disease in Type 2 Diabetes in UK primary care
Authors: Sisk Rose , Cameron Rory , Tahir Waqas , Sammut-Powell Camilla 
Published: May 2023

1.AbstractBackgroundType 2 diabetes (T2D) is a leading cause of both chronic kidney disease (CKD) and onward progression to end stage renal disease. Timely diagnosis coding of CKD in patients with T2D could lead to improvements in quality of care and patient outcomes.AimTo assess the consistency between estimated glomerular filtration rate (eGFR) based evidence of CKD and CKD diagnosis coding in UK primary care.Design and SettingA retrospective analysis of electronic health record data in a cohort of people with type 2 diabetes from 60 primary care centres within England between 2012 and 2022.MethodWe estimated the incidence rate of CKD per 100 person-years using eGFR-based CKD and diagnosis codes. Logistic regression was applied to establish which attributes were associated with diagnosis coding. Time from eGFR-based CKD to entry of a diagnosis code was summarised using the median and interquartile range.ResultsThe overall incidence of CKD was 2.32 (95% CI: 2.24, 2.41) and significantly different between eGFR-based criteria and diagnosis codes: 1.98 (95% CI: 1.90, 2.05) vs 1.06 (95% CI: 1.00, 1.11) respectively; p<0.001. Only 46% of CKD incidences identified using eGFR-based criteria had a corresponding diagnosis code. Younger patients, patients with a higher severity CKD stage, and patients with an observed urine-albumin-to-creatinine ratio were more likely to have a diagnosis code.ConclusionDiagnosis coding of patients with eGFR-based evidence of CKD in UK primary care is poor within patients with type 2 diabetes, despite CKD being a well-known complication of diabetes.2.How this fits inType 2 diabetes is a recognised cause of chronic kidney disease (CKD), and early identification and management of CKD can reduce the risk of progression and related complications. Diagnosis coding of CKD is associated with better patient outcomes, yet we have observed that less than half of patients with type 2 diabetes who meet eGFR-based criteria for stage 3-5 CKD have a CKD diagnosis code in their primary care record. There is a need to understand why CKD diagnosis coding practices are subpar in primary care and this research acts as a call-to-action to improve.
Phase relations of interneuronal activity relative to theta rhythm
Authors: Mysin Ivan 
Published: May 2023

AbstractThe theta rhythm plays a crucial role in synchronizing neural activity during attention and memory processes. However, the mechanisms behind the formation of neural activity during theta rhythm generation remain unknown. To address this, we propose a mathematical model that explains the distribution of interneurons in the CA1 field during the theta rhythm phase. Our model consists of a network of seven types of interneurons in the CA1 field that receive inputs from the CA3 field, entorhinal cortex, and local pyramidal neurons in the CA1 field. By adjusting the parameters of the connections in the model. We demonstrate that it is possible to replicate the experimentally observed phase relations between interneurons and the theta rhythm. Our model predicts that populations of interneurons receive unimodal excitation and inhibition with coinciding peaks, and that excitation dominates to determine the firing dynamics of interneurons.
Consumer decisions toward halal purchase before and during COVID-19 pandemic: a grey relational analysis approach
Authors: Lee Tzong-Ru , Lin Yong-Shun , Kassim Erne Suzila , Sebastian Stephanie 
Published: May 2023

PurposeThe main objective of this research is to investigate the factors that influence consumer purchase decisions for halal products before and during the COVID-19 pandemic, based on the Engel-Kollat-Blackwell (EKB) theory.Design/methodology/approachThe research was conducted as a survey. The influencing factors were determined based on the grey relational analysis (GRA) approach.FindingsThe findings indicate before the COVID-19 pandemic, consumers mainly purchased halal products based on four key factors: purchasing experience, certification label, Internet searches and past consumption experience. However, during the pandemic, the ranking and factors have changed to six indicators, which are past consumption experience, purchasing experience, certification labels, standardized specifications, Internet searches and halal certification labels.Research limitations/implicationsThe study was limited by the sample size and geographical area. Nevertheless, the findings could be further explored by expanding related theories toward understand human decisions based on spiritual beliefs.Practical implicationsThe findings of this study have important implications for research, practice and society. Understanding the factors influencing halal purchase decisions before and during the pandemic can help businesses, policymakers and halal certification bodies to better cater to consumers' needs and preferences and ensure the continued growth and development of the halal industry.Originality/valueThis study evaluates halal purchasing decisions between periods of certainty and uncertainty by using the GRA. Changes in halal consumption and purchase decisions in response to COVID-19 pandemic have become an emerging topic of discovery. The study addresses the gap in the literature regarding changes in consumer decision pattern.
Pabiben.com – integrating Gandhian philosophies for business growth
Authors: Nagori Viral 
Published: May 2023

Learning outcomes
The learning outcomes are as follows: to strike a balance between business growth and keeping the core Gandhian philosophies intact; to evaluate the relevance of Gandhian philosophy in the age of the digital era, especially for the grassroots enterprises; and to identify the leadership characteristics demonstrated by Pabiben from the lens of servant-leadership theory.

Case overview/synopsis
The case describes the journey of a grassroots-based rural women entrepreneur, Pabibben, who had created an artisan's enterprise and rural business model based on Gandhian philosophies. The case focuses on whether Gandhian philosophies are still relevant in today's time for business growth. The case appeals to the academic fraternity, budding entrepreneurs, social sector start-ups and practitioners who believe in the inclusive and holistic growth of an individual, community, society and the nation.
The case is about the dilemma of how to grow a business ethically and balance economic and social gain. Pabiben used Gandhian philosophies as a set of values to make decisions and set policies for her business. Pabiben wanted to grow her business and expand her e-commerce portal “Pabiben.com” for other artisans to display, promote and sell their products to the global communities. She had to decide on the following:
1. Should she sell other artisans' products under “Pabiben.com”?
2. Should she allow other artisans to create their own identity on the portal and help the artisans' community grow?
3. Are Gandhian philosophies still relevant in today’s time for business growth?