bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual expansion routes likely underlie the present-day population structure in aParnassiusbutterfly across the Japanese Archipelago
Authors: Tamura Hideyuki , Noda Tomoaki , Hayashi Mikiko , Fujii Yuko , Iwata Noriko , Yokota Yuko , Murata Masanori , Tatematsu Chisato , Naka Hideshi , Tera Akio , Ono Katsumi , Yokoi Kakeru , Kato Takanori , Okamoto Tomoko , Tsuchida Koji 
Published: July 2024

AbstractThe Japanese Archipelago, comprising a series of isolated yet interconnected islands, had been geographically separated from the Eurasian continent. The linear topography presents a unique biogeographic context for dispersing organisms from the continent. In this study, we utilized mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) variation to elucidate the dispersal history of the Japanese clouded butterflyParnassius glacialisacross the Japanese Archipelago, including North Island (Hokkaido), Main Island (Honshu) and Shikoku Island. Our analysis of mtDNA (COI, COII) at 1192 base pairs (bps) revealed 49 haplotypes and identified three distinct haplotype groups in the network. These groups correspond geographically to East Japan, West Japan, and Chugoku-Shikoku. The Chugoku-Shikoku group is the most ancient lineage. Interestingly, the Chugoku-Shikoku lineage showed a closer network connection to the East Japan lineage than the geographically proximate West Japan lineage. Divergence time estimates suggest that the Chugoku-Shikoku lineage diverged from the continentalP. glacialisapproximately 3.05 million years ago (MYA). Subsequently, from the Chugoku-Shikoku lineage, the East Japan and West Japan lineages diverged around 1.05 MYA, with the subsequent divergence between the East and West Japan lineages occurring at approximately 0.62 MYA. Based on the 3067 SNP genotypes, population structure analysis revealed five distinct genetic structures within the Japanese Archipelago, indicating geographical differentiation. From the analyses by mtDNA and SNP variations, four primary genetic barriers were identified: between Hokkaido and Honshu, between East and Central Japan, within the Kansai region, and within the Chugoku region. The former three lines corresponded to the Blakiston Line, the Itoigawa-Shizuoka Tectonic Line, and Lake Biwa, respectively. These findings suggest thatP. glacialisdiverged from the continentalP. glacialisand expanded its range across the Japanese Archipelago via the North and South routes, establishing its current distribution.
Evidence for infection ofEucalyptus camaldulensiswith aLeifsoniabacterium in Australia and Syria using high throughput sequencing
Authors: Randles J.W. , Hanold D. , Baumann U. , Borneman A. 
Published: July 2024

ABSTRACTA biotic hypothesis for the eucalypt disease of unknown aetiolgy, Mundulla Yellows (MY), was tested by seeking non-host nucleic acids in affectedEucalyptus camaldulensistrees using high throughput sequencing (HTS). Ten contigs were selected from a pool of nucleic acids unique to diseased trees, and oligonucleotide probes were prepared for specific dot-blot hybridisation assay of these contigs. One of the contigs was found to be associated with a few MY-affected trees collected in South Australia and Western Australia, as well as with similarly affectedE. camaldulensistrees growing in Syria. The probes for this contig represented opposite polarities of the contig, and both hybridised with the same positive samples even after alkali treatment confirming that the contig that they represented was dsDNA. This contig, comprising 766 nt, showed 95% similarity to whole genome shotgun sequence ofLeifsonia xyli. This preliminary microbiome analysis of MY affected trees provides the first evidence that aLeifsoniaspecies may infect eucalypts and that it should be further studied as a potential agent of MY.
Awareness of Intimate Partner Violence among Faith-Based Leaders of Migrant and Refugee Background in New South Wales, Australia
Authors: Kayesa Naomi K. , Ogunsiji Olayide 
Published: July 2024

AbstractPurposeIntimate Partner Violence (IPV) is a family violence issue requiring public health system interventions. Migrants and refugees experiencing IPV often rely on their Faith-Based Leaders (FBLs). However, the role of FBLs is under-reported. This study aims to report findings on awareness to IPV among FBLs of migrant and refugee backgrounds.MethodsThis qualitative study engaged 12 FBLs in face-to-face interviews. Thematic analysis revealed three themes namely: Awareness and understanding of IPV; Being the first point of call; Awareness of available services for IPV.ResultsAll FBLs described IPV as relational and identified the different IPV types. Sexual violence did not resonate as IPV by eleven participants. Explanations for being the first point of contact centered around victims’ quest for a win-win outcome and in-accessibility of formal services.ConclusionsIPV specific training, collaboration between FBLs and formal services working with victims of IPV is essential in supporting IPV victims.
Cost per episode of diarrhea and respiratory syncytial virus (RSV) in 128 low- and middle-income countries: how well do disease-specific and WHO-CHOICE estimates align?
Authors: Li Xiao , Bilcke Joke , Asare Ernest O. , Wenger Catherine , Kwon Jiye , Bont Louis , Beutels Philippe , Pitzer Virginia E. 
Published: July 2024

AbstractObjectiveNon-disease-specific WHO-CHOICE unit costs are often used in cost and cost-effectiveness studies in the absence of country-specific data. This study aims to compare reported country-specific disease costs and the corresponding WHO-CHOICE estimates. We use generically defined “diarrhea” (including rotavirus diarrhea) and pathogen-specific “respiratory syncytial virus (RSV)” disease as examples.MethodsWe updated systematic reviews for both diseases in low-income (LICs), lower-middle-income (LMICs) and upper-middle-income (UMICs) countries. Diarrheal (including a sub-analysis of rotavirus-specific) and RSV-specific outpatient and inpatient costs per episode were extracted and compared with WHO-CHOICE estimates in the same countries. If a consistent pattern of under- or over-estimation was identified, we quantified the magnitude of the discrepancy. All costs were updated to 2022 international dollar values.ResultsOut of 1975 new records identified, 23 new cost studies were included. Including previous reviews, we retained 31 diarrhea and 16 RSV studies for comparison. WHO-CHOICE based direct medical costs were similar for diarrheal disease including rotavirus diarrhea, but lower for RSV-related disease. We estimated the cost per episode of diarrhea and RSV in 128 countries. RSV outpatient cost were adjusted by multiplying WHO-CHOICE costs by 6.89 (95% uncertainty interval: 5.58-8.58) in LICs and LMICs and 5.87 (4.95-6.96) in UMICs; RSV inpatient costs were multiplied by 1.43 (1.01-2.01) and 1.36 (0.82-2.27), respectively.ConclusionWHO-CHOICE based costs should be used cautiously. They aligned well with studies for diarrheal disease, but underestimate costs of RSV-related disease. More country- and disease-specific cost data are needed, especially for RSV in LICs.
Long-term consequences of drug usage on the gut microbiome
Authors: Aasmets Oliver , Taba Nele , Krigul Kertu Liis , Andreson Reidar ,   Estonian Biobank Research Team, Org Elin 
Published: July 2024

AbstractMedication usage is a significant contributor to the inter-individual variability in the gut microbiome. However, drugs are often used long-term and repeatedly, a notion yet unaccounted for in microbiome studies, which might lead to underestimating the extent of drug effects. Recently, we and others showed that not only the usage of antibiotics and antidepressants at the time of sampling but also past consumption is associated with the gut microbiome. This effect can be “additive” - the more a drug is used, the stronger the effect on the microbiome. Here, by utilizing electronic health records and the Estonian Microbiome cohort metagenomics dataset (n=2,509), we systematically evaluate the long-term effects of antibiotics and human-targeted medications on the gut microbiome. We show that the past usage of medications is associated with the gut microbiome, and for example, the effects of antibiotics, psycholeptics, antidepressants, proton pump inhibitors, and beta-blockers are detectable several years after usage. Furthermore, by analyzing a subcohort (n=328) with microbiome measured repeatedly, we show that similar changes in the gut microbiome occur after treatment initiation, possibly indicating causal effects.
New job, new habits? A Multilevel Interrupted Time Series analysis of diet, physical activity and sleep changes among young adults starting work for the first time
Authors: Oxenham Alena F , Braune Tanya , van Sluijs Esther , Fairbrother Hannah , Martin Adam , Winpenny Eleanor M 
Published: July 2024

AbstractBackgroundThe workplace is an important determinant of health that people are exposed to for the first-time during adolescence/early adulthood. This study investigates how diet, physical activity, and sleep change as people aged 16-30 years transition into work and whether this varies for different individuals and job types.MethodsMultilevel linear regression models assessed changes in fruit and vegetable intake, sleep duration, and physical activity among 3,302 UK Household Longitudinal Study (UKHLS) participants aged 16-30 years, who started work for the first time between 2015 and 2023. In line with interrupted time series, models assessed behavioural trends in the period before starting work, the immediate effect of starting work, and changes in behaviour over time after employment. Stratified analyses examined differences by selected individual and job characteristics, adjusted for covariates. All analyses were conducted in R v.4.3.2.ResultsSleep duration was stable over the years before and after starting work, but starting work was associated with an immediate reduction in sleep duration (β=-9.74 [95% CI: −16.81 to −2.67], min/night). Physical activity, measured in Metabolic Equivalent Tasks (MET), increased immediately after starting work (β =113.3, [95% CI: 80.49 to 146.11] MET-min/day), but subsequently decreased over time after starting work (β =−26.7, [95% CI: −40.75 to −12.66] MET-min/day/year). The increase in physical activity was greater among men, among those with no degree and among those starting lower socioeconomic classification jobs. Starting a “work from home” job had an immediate negative effect on physical activity (β =−157.81, [-313.07 to - 2.56] MET-min/day), whereas those who worked at their employer’s premises showed an initial increase (β=125.71 [95% CI: 85.79 to 165.63] MET-min/day). Starting work had little influence of fruit and vegetable consumption.ConclusionsThis is the first study to examine how diet, physical activity, and sleep behaviours in young adults change as they start employment in the UK. Starting work is associated with decreased sleep time and increased physical activity, with differences based on sociodemographic and job characteristics. Future research should consider these potential influences of the work environment when developing intervention targets to promote healthy behaviour in the workplace.
Increasing prevalence of bacteriocin carriage in a six-year hospital cohort ofE. faecium
Authors: Garretto Andrea , Dawid Suzanne , Woods Robert 
Published: July 2024

AbstractVancomycin resistant enterococci (VRE) are important pathogens in hospitalized patients, however, the factors involved in VRE colonization of hospitalized patients are not well characterized. Bacteriocins provide a competitive advantage to enterococci in experimental models of colonization, but little is known about bacteriocin content in samples derived from humans and even less is known about their dynamics in the clinical setting. To identify bacteriocins which may be relevant in the transmission of VRE, we present a systematic analysis of bacteriocin content in the genomes of 2,428 patient derivedE. faeciumisolates collected over a six-year period from a single hospital system. We used computational methods to broadly search for bacteriocin structural genes and a functional assay to look for phenotypes consistent with bacteriocin expression. We identified homology to 15 different bacteriocins with two having high presence in this clinical cohort. Bacteriocin 43 (bac43) was found in a total of 58% of isolates, increasing from 8% to 91% presence over the six-year collection period. There was little genetic variation in the bac43 structural or immunity genes across isolates. The enterocin A structural gene was found in 98% of isolates but only 0.3% of isolates had an intact enterocin A gene cluster and displayed a bacteriocin producing phenotype. This study presents a wide survey of bacteriocins from hospital isolates and identified bac43 as highly conserved, increasing in prevalence, and phenotypically functional. This makes bac43 an interesting target for future investigation for a potential role inE. faeciumtransmission.ImportanceWhile enterococci are a normal inhabitant of the human gut, vancomycin-resistantE. faecalisandE. faeciumare urgent public health threats responsible for hospital associated infections. Bacteriocins are ribosomally synthesized antimicrobial proteins and are commonly used by bacteria to provide a competitive advantage in polymicrobial environments. Bacteriocins have the potential be used byE. faeciumto invade and dominate the human gut leading to a greater propensity for transmission. In this work, we explore bacteriocin content in a defined clinically derived population ofE. faeciumusing both genetic and phenotypic studies. We show that one highly active bacteriocin is increasing in prevalence over time and demonstrates great potential relevance toE. faeciumtransmission.
Genetic and Lifestyle Risks for Coronary Artery Disease and Long-Term Risk of Incident Dementia Subtypes
Authors: Sittichokkananon Arisa , Garfield Victoria , Chiesa Scott T. 
Published: July 2024

ABSTRACTBackgroundShared genetic and lifestyle risk factors may underlie the development of both coronary artery disease (CAD) and dementia. This study aimed to examine if an increased genetic risk for CAD is associated with long-term risk of developing all-cause, Alzheimer’s, or vascular dementia, and investigate whether the presence of healthy lifestyle behaviours in the mid-to-late life period may attenuate this risk.MethodsA prospective cohort study of 365,782 participants free from dementia for at least 5 years post-baseline assessment was conducted within the UK Biobank study. Genetic risk was assessed using a genome-wide polygenic risk score (PRS) for CAD, and lifestyle risk using a modified version of the American Heart Association’s Life’s Essential 8 Lifestyle Risk Score (LRS). Primary outcomes were incident all-cause, Alzheimer’s, and vascular dementia diagnoses obtained from linked electronic health records. Secondary outcomes were neuroimaging phenotypes with well-established links to future dementia risk measured in 32,592 participants recalled for MRI imaging.Results8,870 cases of all-cause dementia were observed over a median 13.9-year follow-up. Higher genetic risk for CAD was associated with an elevated risk of all dementia subtypes (HRs = 1.08-1.16; p<0.001 for all). A higher LRS was associated with a modestly increased risk of all-cause dementia (HR = 1.06 [1.04-1.08]; p < 0.001), with this risk likely arising through increased rates of vascular dementia (HR = 1.22 [1.17-1.28]) as no evidence was found for any associations with Alzheimer’s disease (HR = 0.99 [0.95-1.02]; p = 0.535). Individuals with a combination of high genetic and high lifestyle risk scores for CAD were more than twice as likely to develop vascular dementia during long-term follow-up compared to those with low levels of both. This risk was substantially attenuated in those following healthy lifestyle behaviours at baseline, however, regardless of underlying genetic risk (e.g. HR for low vs high lifestyle risk scores = 1.43 [1.12-1.81] vs. 2.16 [1.73-2.69] respectively in individuals with high genetic risk). In a subset of individuals recalled for neuroimaging assessments, those with high genetic and lifestyle risk for CAD demonstrated a 30% greater volume of white matter hyperintensities than those with low risk, while showing little difference in grey matter or hippocampal volumes.ConclusionsIndividuals who are genetically predisposed to developing CAD also face an increased risk of developing dementia in old age. This risk is reduced in those adopting healthy lifestyle behaviours earlier in the lifespan, however, particularly in those at risk from dementia caused by underlying vascular pathology.
WITHDRAWN: Eligibility for thrombolysis and outcome in pediatric acute ischemic stroke
Authors: Briest Romain C. , Bhatia Kartik D , Miteff Christina , Cheung Andrew , Antony Jayne , Ardern-Holmes Simone , Bye Annie , Cardamone Michael , Chan Denise , Dale Russell , Farrar Michelle , Gill Deepak , Gupta Sachin , Johnson Alexandra , Kandula Tejaswi , Lawson John , Manning Nathan , McCann Karlee , McQuinn Alexander , Menezes Manoj P , Miteff Ferdinand , Pillai Sekhar , Sampaio Hugo , Smith Robert L , Subramanian Gopinath M , Teoh Hooi Ling , Troedson Christopher , Webster Richard , Wenderoth Jason , Whitley Justin , Andrews P. Ian 
Published: July 2024

Withdrawal statementThe authors have withdrawn this manuscript because the manuscript has undergone considerable revision, such that this manuscript does not represent the data or interpretation as intended. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
The effect of microbial metabolites from colonic protein fermentation on bacteria-induced cytokine production in dendritic cells
Authors: Xie Zhuqing , Eriksen Danny Blichfeldt , Johnsen Peter Riber , Nielsen Dennis Sandris , Frøkiær Hanne 
Published: July 2024

AbstractScopeCompared to the well-defined immune-modulating effect of butyrate, the knowledge of other metabolites from colonic protein fermentation is limited.Methods and resultsThe effect of protein-derived metabolites (valerate, branched-chain fatty acids, ammonium, phenol, p-Cresol, indole, and H2S) on cytokine production in murine bone marrow-derived dendritic cells (BMDCs) stimulated with LPS,Lactobacillus acidophilusNCFM, orStaphylococcus aureusUSA300 was investigated. The metabolites modulated the cytokine profile differently and depended on the specific microbial stimulus with short-chain fatty acids (SCFAs) exhibiting the strongest effects and no toxicity. After short-term treatment, SCFAs affected the cytokine profile similar to but weaker than butyrate, reflected by inhibition of IL-12p70 and IL-10 but enhanced IL-23 (LPS andS. aureusUSA300) and IL-1β production. Compared to valerate, butyrate exhibited a stronger and more prompt effect on cytokine gene expression without influencing reactive oxygen species (ROS) formation. Oppositely, long-term treatment with the two SCFAs resulted in similar anti-inflammatory effects, i.e. abrogation of LPS-induced IL-12 and enhancement of IL-10 and the expression of aryl hydrocarbon receptor (Ahr) and LPS-stimulated dual specificity phosphatase 1 (Dusp1).ConclusionOur data reveals immune-modulating effects of various protein fermentation metabolites, and valerate in specific holds activities resembling but not identical to butyrate.
Cell-scale gene-expression measurements inVibrio choleraebiofilms reveal spatiotemporal patterns underlying development
Authors: Johnson Grace E. , Fei Chenyi , Wingreen Ned S. , Bassler Bonnie L. 
Published: July 2024

AbstractBacteria commonly exist in multicellular, surface-attached communities called biofilms. Biofilms are central to ecology, medicine, and industry. TheVibrio choleraepathogen forms biofilms from single founder cells that, via cell division, mature into three-dimensional structures with distinct, yet reproducible, regional architectures. To define mechanisms underlying biofilm developmental transitions, we establish a single-molecule fluorescence in situ hybridization (smFISH) approach that enables accurate quantitation of spatiotemporal gene-expression patterns in biofilms at cell-scale resolution. smFISH analyses ofV. choleraebiofilm regulatory and structural genes demonstrate that, as biofilms mature, overall matrix gene expression decreases, and simultaneously, a pattern emerges in which matrix gene expression becomes largely confined to peripheral biofilm cells. Both quorum sensing and c-di-GMP-signaling are required to generate the proper temporal pattern of matrix gene expression. Quorum sensing autoinducer levels are uniform across the biofilm, and thus, c-di-GMP-signaling alone sets the regional matrix gene expression pattern. The smFISH strategy provides insight into mechanisms conferring particular fates to individual biofilm cells.
Exploring Harmala Alkaloids as Novel Antimalarial Agents againstPlasmodium falciparumthrough Bioinformatics Approaches
Authors: Dipto Kaushik Zaman , Shariar Raiyan , Saha Chinmoy Kumar , Huzaifa Abir , Robin Tanjin Barketullah , Patil Rajesh B. , Alam Md. Tamzidul , Rafi Md. Irfan Habib , Faruk Ashraf Zaman , Moin Abu Tayab , Zinnah Kazi Md. Ali , Hasanuzzaman Md. , Islam Tofazzal 
Published: July 2024

AbstractMalaria, caused by thePlasmodium falciparum, remains a significant global health challenge, with Plasmodium falciparum accounting for approximately 50% of cases and posing a considerable threat. Despite advances in control measures, malaria continues to cause an estimated one million deaths annually. The complex lifecycle ofP. falciparum, involving both vertebrate hosts and Anopheles mosquitoes, complicates eradication efforts. The parasite’s resistance to existing antimalarial drugs, along with medication toxicity, necessitates innovative therapeutic approaches.Recent research has revealed that harmine, an alkaloid produced by an endophytic gut bacterium of Anopheles mosquitoes, can impede the transmission of the malarial parasite to humans by inhibiting a crucial life stage. This study investigates harmala alkaloids, sourced from plants and bacteria such asPeganum harmala, as potential alternatives to conventional antimalarial drugs. Notably, harmine and harmaline have shown promising antimalarial activity by inhibiting the essential enzyme protein kinase 4 (PK4), which is vital for the parasite’s survival. These compounds exhibit lower toxicity, effectively inhibiting both the blood stage growth and transmission of the parasite. Using in silico methodologies, including ADME analysis, molecular docking, MD simulation, and toxicity analysis, this study identifies harmala alkaloids as potential inhibitors against crucialP. falciparumproteins. Targeting proteins essential for the parasite’s survival, similar to established drugs like pfCRT protein, lays the foundation for developing effective antimalarial treatments. The comprehensive screening of harmala alkaloid molecules opens avenues for the pharmaceutical industry to tackle challenges related to drug resistance and toxicity, offering a promising route for the biorational management of malaria.