bluuebunny/crossref_metadata_2025_split huggingface dataset:
Luteimonas galliterrae sp. nov., isolated from poultry farm soil
Authors: Shen Lei , An Miao-miao , He Xiang-wei , Zhao Guo-zhu 
Published: March 2023

Strain SX5T was isolated from the soil of a poultry farm in Shanxi Province, PR China. The isolate was a Gram-stain-negative, rod-shaped, non-flagellated, and yellow bacterium. Growth occurred at 20–37 °C (optimum, 28 °C), pH 6.0–10.0 (optimum, pH 8.0) and 0–1 % NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SX5T was related to members of the genus

Luteimonas

, and close to

Luteimonas gilva

H23T (97.9 %),

Luteimonas cucumeris

Y4T (97.9 %),

Luteimonas aquatica

RIB1-20T (96.8 %),

Luteimonas notoginsengisoli

SYP-B804T (96.4 %) and

Luteimonas panaciterrae

Gsoil 068T (96.1 %). The major cellular fatty acids of strain SX5T were iso-C16 : 0, iso-C17 : 1
ω9c, iso-C15 : 0 and iso-C11 : 0 3OH. The sole isoprenoid quinone was ubiquinone Q-8, and the major polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Genome analyses revealed that strain SX5T had a genome size of 3.6 Mbp with a G+C content of 65.7 mol% and contained abundant carbohydrate-active enzyme genes and three putative distinct biosynthetic gene clusters, suggesting that it may have great potential to degrade and utilize complex biological organic matter and produce special secondary metabolites. Comparative genomic analyses clearly separated strain SX5T from the known species of the genus

Luteimonas

based on average nucleotide identity and digital DNA–DNA hybridization values below the thresholds for species delineation. Based on its phenotypic, genotypic properties and phylogenetic inference, strain SX5T represents a novel species in the genus

Luteimonas

, for which the name Luteimonas galliterrae sp. nov. is proposed. The type strain is SX5T (=GDMCC 1.2162T=KCTC 82443T=JCM 34401T).
Cytokines as mediators of the associations of prenatal exposure to phenols, parabens, and phthalates with internalizing behaviours at age 3 in boys: a mixture exposure and mediation approach
Authors: Khalfallah Olfa , Barbosa Susana , Phillipat Claire , Slama Remy , Galera Cédric , Heude Barbara , Glaichenhaus Nicolas , Davidovic Laetitia 
Published: March 2023

ABSTRACTChildhood internalizing disorders refer to inwardly focused negative behaviours such as anxiety, depression, and somatic complains. Interactions between psychosocial, genetic, and environmental risk factors adversely impact neurodevelopment and can contribute to internalizing disorders. While prenatal exposure to single endocrine disruptors (ED) is associated with internalizing behaviours in infants, the associations with prenatal exposure to ED in mixture remain poorly addressed. In addition, the biological mediators of ED mixture effects on internalizing behaviours remain unexplored. ED do not only interfere with endocrine function, but also with immune function and inflammatory processes. Based on this body of evidence, we hypothetised that inflammation at birth is a plausible biological pathway through which ED prenatal exposure could operate to influence offspring internalizing behaviours. Based on the EDEN birth cohort, we investigated whether ED mixture exposure increased the odds of internalizing disorders in 459 boy infants at age 3, and whether the pro-inflammatory cytokines IL-1β, IL-6, and TNF-α measured at birth are mediators of this effect. To determine both the joint and individual associations of ED prenatal exposure with infant internalizing behaviours and the possible mediating role of cytokines, we used the counterfactual hierarchical Bayesian Kernel Machine Regression (BKMR) regression-causal mediation analysis. We show that prenatal exposure to a complex ED mixture has limited effects on internalizing behaviours in boys at age 3. We also show that IL-1β, IL-6, and TNF-α are unlikely mediators or suppressors of ED mixture effects on internalizing behaviours. Further studies on larger cohorts are warranted to refine the deleterious effects of ED mixtures on internalizing behaviours and identify possible mediating pathways.
Socio-demographic characteristics associated with COVID-19 vaccination uptake in Switzerland: longitudinal analysis of the CoMix study
Authors: Reichmuth Martina L , Heron Leonie , Riou Julien , Moser André , Hauser Anthony , Low Nicola , Althaus Christian L 
Published: March 2023

AbstractBackgroundVaccination is an effective strategy to reduce morbidity and mortality from coronavirus disease 2019 (COVID-19). However, the uptake of COVID-19 vaccination has varied across and within countries. Switzerland has had lower levels of COVID-19 vaccination uptake in the general population than many other high-income countries. Understanding the socio-demographic factors associated with vaccination uptake can help to inform future vaccination strategies to increase uptake.MethodsWe conducted a longitudinal online survey in the Swiss population, consisting of six survey waves from June to September 2021. Participants provided information on socio-demographic characteristics, history of testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), social contacts, willingness to be vaccinated, and vaccination status. We used a multivariable Poisson regression model to estimate the adjusted rate ratio (aRR) and 95% confidence intervals (CI) of COVID-19 vaccine uptake.ResultsWe recorded 6,758 observations from 1,884 adults. For the regression analysis, we included 3,513 observations from 1,883 participants. By September 2021, 600 (75%) of 806 study participants had received at least one vaccine dose. Participants who were older, male, and students, had a higher educational level, household income, and number of social contacts, and lived in a household with a medically vulnerable person were more likely to have received at least one vaccine dose. Female participants, those who lived in rural areas and smaller households, and people who perceived COVID-19 measures as being too strict were less likely to be vaccinated. We found no significant association between previous SARS-CoV-2 infections and vaccination uptake.ConclusionsOur results suggest that socio-demographic factors as well as individual behaviours and attitudes played an important role in COVID-19 vaccination uptake in Switzerland. Therefore, appropriate communication with the public is needed to ensure that public health interventions are accepted and implemented by the population. Tailored COVID-19 vaccination strategies in Switzerland that aim to improve uptake should target specific subgroups such as women, people from rural areas or people with lower socio-demographic status.
Neural signatures of risk-taking adaptions across health, bipolar disorder, and lithium treatment
Authors: Scholl Jacqueline , Panchal Priyanka , Nelissen Natalie , Atkinson Lauren Z , Kolling Nils , Saunders Kate EA , Geddes John , Rushworth Matthew FS , Nobre Anna C , Harrison Paul J , Harmer Catherine J 
Published: March 2023

AbstractCognitive and neural mechanisms underlying bipolar disorder (BD) and its treatment are still poorly understood. Here we examined the role of adaptations in risk-taking using a reward- guided decision-making task.We recruited volunteers with high (n=40) scores on the Mood Disorder Questionnaire, MDQ, suspected of high risk for bipolar disorder and those with low-risk scores (n=37). We also recruited patients diagnosed with BD who were assigned (randomized, double-blind) to six weeks of lithium (n=19) or placebo (n=16) after a two-week baseline period (n=22 for FMRI). Participants completed mood ratings daily over 50 (MDQ study) or 42 (BD study) days, as well as a risky decision-making task and functional magnetic resonance imaging. The task measured adaptation of risk taking to past outcomes (increased risk aversion after a previous win vs. loss, ‘outcome history’).While the low MDQ group was risk averse after a win, this was less evident in the high MDQ group and least so in the patients with BD. During fMRI, ‘outcome history’ was linked to medial frontal pole activation at the time of the decision and this activation was reduced in the high risk MDQ vs. the low risk MDQ group. While lithium did not reverse the pattern of BD in the task, nor changed clinical symptoms of mania or depression, it changed reward processing in the dorsolateral prefrontal cortex.Participants’ modulation of risk-taking in response to reward outcomes was reduced as a function of risk for BD and diagnosed BD. These results provide a model for how reward may prime escalation of risk-related behaviours in bipolar disorder and how mood stabilising treatments may work.Key pointsQuestion:Do bipolar disorder and lithium treatment change adaptation of risk-taking over time?Findings:Across an observational study and a randomized controlled trial, we found that while participants modulate their risk taking in a gambling task over time, this was reduced as a function of risk for bipolar disorder. Neurally, this was accompanied by changes in reward memory traces in medial frontal pole.Meaning:The results show that bipolar disorder is linked to a reduction in adaptation of risk- taking to the environment, suggesting a possible computational mechanism and treatment target.
A Large-Scale Proteomics Resource of Circulating Extracellular Vesicles for Biomarker Discovery in Pancreatic Cancer
Authors: Bockorny Bruno , Muthuswamy Lakshmi , Huang Ling , Hadisurya Marco , Lim Christine Maria , Tsai Leo L. , Gill Ritu R. , Wei Jesse L. , Bullock Andrea J. , Grossman Joseph E. , Besaw Robert J. , Narasimhan Supraja , Tao W. Andy , Perea Sofia , Sawhney Mandeep S. , Freedman Steven D. , Hidalgo Manuel , Iliuk Anton , Muthuswamy Senthil K. 
Published: March 2023

ABSTRACTPancreatic cancer has the worst prognosis of all common tumors. Earlier cancer diagnosis could increase survival rates and better assessment of metastatic disease could improve patient care. As such, there is an urgent need to develop biomarkers to diagnose this deadly malignancy. Analyzing circulating extracellular vesicles (cEVs) using ‘liquid biopsies’ offers an attractive approach to diagnose and monitor disease status. However, it is important to differentiate EV-associated proteins enriched in patients with pancreatic ductal adenocarcinoma (PDAC) from those with benign pancreatic diseases such as chronic pancreatitis and intraductal papillary mucinous neoplasm (IPMN). To meet this need, we combined the novel EVtrap method for highly efficient isolation of EVs from plasma and conducted proteomics analysis of samples from 124 individuals, including patients with PDAC, benign pancreatic diseases and controls. On average, 912 EV proteins were identified per 100µL of plasma. EVs containing high levels of PDCD6IP, SERPINA12 and RUVBL2 were associated with PDAC compared to the benign diseases in both discovery and validation cohorts. EVs with PSMB4, RUVBL2 and ANKAR were associated with metastasis, and those with CRP, RALB and CD55 correlated with poor clinical prognosis. Finally, we validated a 7-EV protein PDAC signature against a background of benign pancreatic diseases that yielded an 89% prediction accuracy for the diagnosis of PDAC. To our knowledge, our study represents the largest proteomics profiling of circulating EVs ever conducted in pancreatic cancer and provides a valuable open-source atlas to the scientific community with a comprehensive catalogue of novel cEVs that may assist in the development of biomarkers and improve the outcomes of patients with PDAC.
Tuberculosis presentation and outcomes in elderly Hispanics from Tamaulipas, Mexico
Authors: Medrano Belinda A. , Lee Miryoung , Gemeinhardt Gretchen , Rodríguez-Herrera Javier E. , García-Viveros Moncerrato , Restrepo Blanca I. 
Published: March 2023

AbstractOld people are at high risk of developing and dying from pulmonary infections like tuberculosis (TB), but they are few studies and particularly in Hispanics. To address these gaps, we sought to identify host factors associated with TB and adverse treatment outcomes in old Hispanics by conducting a secondary analysis of TB surveillance data from Tamaulipas, Mexico (2006-2013; n=8,381). Multivariable logistic regressions were assessed for the elderly (ELD, ≥65 years) when compared to young (YA, 18 to 39 years) and middle-aged adults (MAA, 40 to 64 years). We found that the ELD had features associated with a less complicated TB (e.g. less extra-pulmonary TB, abandoning of treatment or having drug resistant TB), and yet, were more likely to die during TB treatment (adj-OR 3.9, 95% 2.5, 5.25). Among the elderly, excess alcohol use and low BMI increased their odds of death, while diabetes and BCG vaccination were protective. These data suggest that old people share some, but not all the risk factors for adverse TB treatment outcomes, when compared with younger adults. Furthermore, even though old age in itself is an important predictor of death during TB, the elderly are not prioritized by the World Health Organization for latent TB infection screening and treatment during contact investigations. We propose the inclusion of the elderly as a high-risk group in TB management guidelines.
Synaptic oligomeric tau in Alzheimer’s disease – a potential culprit in the spread of tau pathology through the brain
Authors: Colom-Cadena Martí , Davies Caitlin , Sirisi Sònia , Lee Ji-Eun , Simzer Elizabeth , Tzioras Makis , Querol-Vilaseca Marta , Sánchez-Aced Érika , Chang Ya Yin , Holt Kris , McGeachan Robert , Rose Jamie , Tulloch Jane , Wilkins Lewis , Smith Colin , Andrian Teodora , Belbin Olivia , Pujals Sílvia , Horrocks Mathew H. , Lleó Alberto , Spires-Jones Tara 
Published: March 2023

SummaryIn Alzheimer’s disease (AD), fibrillar tau pathology accumulates and spreads through the brain and synapses are lost. Evidence from mouse models indicates that tau spreads trans-synaptically from pre- to postsynapses and that oligomeric tau is synaptotoxic, but data on synaptic tau in human brain is scarce. Here we used sub-diffraction-limit microscopy to study synaptic tau accumulation in post-mortem temporal and occipital cortices of human AD and control donors. Oligomeric tau is present in both pre- and postsynaptic terminals even in areas without abundant fibrillar tau deposition. Further, there is a higher proportion of oligomeric tau compared to phosphorylated or misfolded tau found at synaptic terminals. These data suggest that accumulation of oligomeric tau in synapses is an early event in disease pathogenesis, and that tau pathology may progress through the brain via trans-synaptic spread in human disease. Thus, specifically reducing oligomeric tau at synapses may be a promising therapeutic strategy for AD.
Sedentary lifestyle, Physical Activity, and Gastrointestinal Diseases: Evidence from Mendelian Randomization Analysis
Authors: Chen Jie , Ruan Xixian , Fu Tian , Lu Shiyuan , Gill Dipender , He Zixuan , Burgess Stephen , Giovannucci Edward L , Larsson Susanna C. , Deng Minzi , Yuan Shuai , Li Xue 
Published: March 2023

AbstractObjectivesThe causal associations of physical activity and sedentary behavior with the risk of gastrointestinal disease is unclear. We performed a Mendelian randomization analysis to examine these associations.MethodsGenetic instruments associated with leisure screen time (LST, an indicator of a sedentary lifestyle) and moderate-to-vigorous intensity physical activity (MVPA) at the genome-wide significance (P<5×10−8) level were selected from a genome-wide association study (N<703,901). Summary statistics for gastrointestinal diseases were obtained from the UK Biobank study (N>330,000), the FinnGen study (N>220,000), and large consortia. Multivariable MR analyses were conducted for genetically determined LST with adjustment for MVPA and vice versa. We also performed multivariable MR with adjustment for genetically proxied smoking, body mass index (BMI), fasting insulin, and type 2 diabetes for both exposures.ResultsGenetically proxied longer LST was associated with increased risk of gastrointestinal reflux, gastric ulcer, duodenal ulcer, chronic gastritis, irritable bowel disease, diverticular disease, Crohn’s disease, non-alcoholic fatty liver disease, alcoholic liver disease, cholecystitis, cholelithiasis, acute pancreatitis, chronic pancreatitis, and acute appendicitis. Most associations remained after adjustment for genetic liability to MVPA. Genetic liability to MVPA was associated with decreased risk of gastroesophageal reflux, gastric ulcer, chronic gastritis, irritable bowel syndrome, cholelithiasis, and acute pancreatitis. The associations attenuated albeit directionally remained after adjusting for genetically predicted LST. Multivariable MR analysis found that BMI and type 2 diabetes mediated the associations of LST and MVPA with several gastrointestinal diseases.ConclusionThe study suggests that a sedentary lifestyle may play a causal role in the development of many gastrointestinal diseases.
Air pollution and out-of-hospital cardiac arrest risk
Authors: Moderato L. , Aschieri D. , Lazzeroni D. , Rossi L. , Bricoli S. , Biagi A. , Ferraro S. , Binno S.M. , Monello A. , Pelizzoni V. , Sticozzi C. , Zanni A. , Magnani G. , Gurgoglione F.L. , Capucci A. , Nani S. , Montone R.A. , Ardissino D. , Nicolini F. , Niccoli G. 
Published: March 2023

ABSTRACTBackgroundGlobally nearly 20% of cardiovascular disease deaths were attributable to air pollution. Out-of-hospital cardiac arrest (OHCA) represents a major public health problem, therefore, the identification of novel OHCA triggers is of crucial relevance. The aim of the study was to evaluate the association between air pollution (short-, mid-and long-term exposure) and out-of-hospital cardiac arrest (OHCA) risk, during a 7 years-period from a highly polluted urban area with a high density of automated external defibrillators (AEDs).Methods and resultsOHCA were prospectively collected from the “Progetto Vita Database” between 01/01/2010 to 31/12/2017; day-by-day air pollution levels were extracted from the Environmental Protection Agency (ARPA) stations. Electrocardiograms of OHCA interventions were collected from the AEDs data cards. Day-by-day particulate matter (PM) 2.5 and 10, ozone (O3), carbon monoxide (CO) and nitrogen dioxide (NO2) levels were measured. A total of 880 OHCAs occurred in 748 days. A significantly increased in OHCA risk with the progressive increase in PM 2.5, PM 10, CO and NO2 levels was found. After adjustment for temperature and seasons, a 9% and 12% increase of OHCA risk for each 10 μg/m3 increase of PM 10 (p< 0.0001) and PM 2.5 (p< 0.0001) levels was found. Air pollutants levels were associated with both asystole and shockable rhythm risk while no correlation was found with pulseless electrical activity.ConclusionsShort-term and mid-term exposure to PM 2.5 and PM 10 is independently associated with the risk of OHCA due to asystole or shockable rhythm.
Validation of a Non-invasive Prenatal Test for Fetal RhD, C, c, E, Kell and FyA Antigens
Authors: Alford Brian , Landry Brian P. , Hou Sarah , Bower Xavier , Bueno Anna M. , Chen Drake , Husic Brooke , Cantonwine David E. , McElrath Thomas F. , Carozza Jaqueline , Wynn Julia , Hoskovec Jennifer , Gray Kathryn J. 
Published: March 2023

AbstractWe developed and validated a next generation sequencing (NGS) based NIPT assay using quantitative counting template (QCT) technology to detect RhD, C, c, E, Kell, and Fyafetal antigen genotypes in the diverse U.S. population. The assay quantifies paternally derived fetal antigen cell-free DNA molecules after calibration to fetal fraction and a reference gene. The assay correctly determined fetal antigen status for 1061 preclinical samples with an analytical sensitivity of 100% (95% CI: 99-100%) and analytical specificity of 100% (95% CI: 99-100%). The assay showed a clear separation between antigen detected and not detected for 15,939 clinical plasma samples in a general population setting, with an estimated clinical sensitivity of 99.6%-100%. The precision of the assay in which two replicate plasma samples were independently analyzed was 99.9% for 1683 clinical samples. Moreover, a fetal antigen determination could be made for samples withRHDΨ, a variant more common among RhD-negative Black individuals. The NIPT results were 100% concordant with neonatal antigen genotype/serology for 23 RhD negative pregnant individuals and 12 other antigen evaluations in 4 alloimmunized pregnant individuals. This NGS-based fetal antigen NIPT assay had excellent performance in a validation study of samples from a diverse U.S. population for fetal fractions as low as 1.1% and as early as 10 weeks of gestation, without the need for a sample from the biological partner. Implementation of NIPT for the detection of fetal antigen in RhD-negative and alloimmunized pregnant individuals will streamline care and reduce unnecessary treatment, monitoring and patient anxiety.
Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives
Authors: Burgarella Concetta , Brémaud Marie-Fleur , Hirschheydt Gesa Von , Viader Veronique , Ardisson Morgane , Santoni Sylvain , Ranwez Vincent , Navascués Miguel , David Jacques , Glémin Sylvain 
Published: March 2023

AbstractHow and why genetic diversity varies among species is a long-standing question in evolutionary biology. Life history traits have been shown to explain a large part of observed diversity. Among them, mating systems have one of the strongest impacts on genetic diversity, with selfing species usually exhibiting much lower diversity than outcrossing relatives. Theory predicts that a high rate of selfing amplifies selection at linked sites, reducing genetic diversity genome wide, but frequent bottlenecks and rapid population turn-over could also explain low genetic diversity in selfers. However, how linked selection varies with mating systems and whether it is sufficient to explain the observed difference between selfers and outcrossers has never been tested. Here, we used theAegilops/Triticumgrass species, a group characterized by contrasted mating systems (from obligate out-crossing to high selfing) and marked recombination rate variation across the genome, to quantify the effects of mating system and linked selection on patterns of neutral and selected polymorphism. By analyzing phenotypic and transcriptomic data of 13 species, we show that selfing strongly affects genetic diversity and the efficacy of selection by amplifying the intensity of linked selection genome wide. In particular, signatures of adaptation were only found in the highly recombining regions in outcrossing species. These results bear implications for the evolution of mating systems and more generally for our understanding of the fundamental drivers of genetic diversity.
Modelling the Dynamics of Senescence Spread
Authors: Martin Lucy , Schumacher Linus , Chandra Tamir 
Published: March 2023

AbstractCellular senescence is a cell surveillance mechanism that arrests the cell cycle in damaged cells. The senescent phenotype can spread from cell to cell through paracrine and juxtacrine signalling, but the dynamics of this process are not well understood. Although senescent cells are important in ageing, wound healing, and cancer, it is unclear how the spread of senescence is contained in senescent lesions. In the absence of the immune system, senescence could theoretically spread infinitely from one cell to another, but this contradicts experimental evidence. To investigate this issue, we developed both a minimal mathematical model and a stochastic simulation of senescence spread. Our results suggest that differences in the number of signalling molecules secreted between subtypes of senescent cells can limit the spread of senescence. We found that dynamic, timedependent paracrine signalling prevents the uncontrolled spread of senescence and we demonstrate how model parameters can be determined using Bayesian inference in a proposed experiment.