bluuebunny/crossref_metadata_2025_split huggingface dataset:
Description of Rhodobacter flavimaris sp. nov. and proposal of the genera Paenirhodobacter, Sedimentimonas, and Sinirhodobacter as synonyms of Rhodobacter
Authors: Huang Meng-Han , Zhang Dao-Feng , Wang Hong-Chuan , He Wei , Song Xiao-Rui 
Published: October 2024

Two Gram-stain-negative, aerobic, ovoid to short rod-shaped bacterial strains, designated as WL0062T and WL0115, were isolated from coastal zone of the Yellow Sea, Jiangsu Province, PR China, respectively. Strain WL0062T grew optimally at 28 °C, pH 7.0–8.0 and with 1.0–3.0% (w/v) NaCl. Strain WL0115 grew optimally at 28 °C, pH 6.0–7.0 and with 1.0–3.0% (w/v) NaCl. In the bac120 tree, strains WL0062T and WL0115 clustered together with Sedimentimonas flavescens B57T. The respiratory quinone of both strains was ubiquinone-10. The major polar lipids of both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, glycolipid, phosphatidylmonomethylethanolamine, and one unidentified polar lipid. The major fatty acids of strain WL0062T were summed features 8 (C18 : 1
ω6c and/or C18 : 1
ω7c). The major fatty acids of strain WL0115 were summed features 8 (C18 : 1
ω6c and/or C18 : 1
ω7c), C18 : 0, iso-C17 : 1
ω5c and C20 : 4
ω6/9/12/15c (arachidonic acid). The G+C content of genomic DNA of strains WL0062T and WL0115 was 64.0 mol% in both of them. Combined with the analysis of average nucleotide identity, average amino acid identity, and digital DNA–DNA hybridization, strain WL0062T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter flavimaris sp. nov is proposed. The type strain is WL0062T (=MCCC 1K06014T=JCM 34676T=GDMCC 1.2427T). Strain WL0115 (=MCCC 1K07531=JCM 35568=GDMCC 1.3088) should belong to the same species as Sedimentimonas flavescens B57T. In addition, on the basis of phylogenomic relationship and phenotypical characteristics, the genera Paenirhodobacter, Sedimentimonas, and Sinirhodobacter are proposed as synonyms of Rhodobacter.
HLAIIPred: Cross-Attention Mechanism for Modeling the Interaction of HLA Class II Molecules with Peptides
Authors: Haghighatlari Mojtaba , Marze Nick , Seward Robert , Ciarla Andrew , Dhule Santosh , Hindin Rachel , Calderini Jennifer , Keenan Benjamin , Hall-Swan Sarah , Hickling Timothy P. , Bennett Eric , Rai Brajesh , Tourdot Sophie 
Published: October 2024

We introduce HLAIIPred, a deep learning model to predict peptides presented by class II human leukocyte antigens (HLAII) on the surface of antigen presenting cells. HLAIIPred is trained using a Transformer-based neural network and a dataset comprising of HLAII-presented peptides identified by mass spectrometry. In addition to predicting peptide presentation, the model can also provide important insights into peptide-HLAII interactions by identifying core peptide residues that form such interactions. We evaluate the performance of HLAIIPred on three different tasks, peptide presentation in monoallelic samples, immunogenicity prediction of therapeutic antibodies, and neoantigen prioritization for cancer immunotherapy. Additionally, we created a new dataset of biotherapeutics HLAII peptides presented by human dendritic cells. This data is used to develop screening strategies to predict the unwanted immunogenic segments of therapeutic antibodies by HLAII presentation models. HLAIIPred demonstrates superior or equivalent performance when compared to the latest models across all evaluated benchmark datasets. We achieve a 16% increase in prediction of presented peptides compared to the second-best model on a set of unseen peptides presented by less frequent alleles. The model also improves the area under the precision-recall curve by 3% for distinguishing between immunogenic and non-immunogenic antibodies. We show that HLAIIPred can identify epitopes in therapeutic antibodies and prioritize neoantigens with high accuracy.HIGHLIGHTS*We developed a new deep learning model to address the shortcomings of existing models for the prediction of peptides presented by HLAII molecules.*The model is end-to-end and context-free, requiring only a peptide sequence and available HLAII alleles as input.*HLAIIPred outperforms the state-of-the-art models on multiple benchmark datasets.*The model is able to predict the core residues of peptides that interact with HLAIIs.*We created experimental data and developed screening strategies to accurately predict the immunogenic hotspots in therapeutic antibodies.
Double-Blind Randomized Placebo Controlled Trial of aLactobacillusProbiotic Blend in Chronic Obstructive Pulmonary Disease
Authors: Nicola Teodora , Wenger Nancy M. , Evans Michael , Yang Youfeng , Chen Dongquan , Van Der Pol William J. , Walia Amar , Lefkowitz Elliot J. , Wang Jun , LeMoire Ashley , Lin Lois , Morrow Casey , Ambalavanan Namasivayam , Gaggar Amit , Lal Charitharth Vivek 
Published: October 2024

AbstractRationaleThe gut-lung axis describes the crosstalk between the gut and lung wherein microbiota in the gut modulate systemic anti-inflammatory and immune responses in the lungs.Objectives:We hypothesized that a blend of probiotic bacteria (Lactobacilli) combined with herbal extracts (resB®) could improve quality of life in COPD patients.MethodsWe conducted a randomized, double-blinded, placebo-controlled study (NCT05523180) evaluating the safety and impact of resB® on quality of life in volunteers with COPD. Participants took two capsules of resB® or placebo orally daily for 12 weeks. The primary endpoint was quality of life changes by Saint George’s Respiratory Questionnaire (SGRQ). In addition to safety, exploratory endpoints included changes in serum and sputum biomarkers as well as sputum and stool microbiome.Measurements and Main ResultsresB® was well tolerated by all participants, with no related adverse events reported. Participants who received resB® had improvement in their SGRQ symptom scores from baseline to final visit (P<0.05), while the change in SGRQ symptom scores in those receiving placebo was not significant. Serum and sputum concentrations of matrix metalloproteinase 9, serum c-reactive protein, and serum interleukin 6 decreased (P<0.05) between baseline and final visit in the resB® group, corresponding with an increase in stoolLactobacilliabundance. Relative abundance ofVeillonellaalso increased in stool and sputum in the resB® group.ConclusionsParticipants with COPD who received resB® improved in respiratory symptoms over a 12-week course. Serum and sputum biomarkers suggest administration of the probiotic and herbal blend reduces inflammation and may thereby attenuate symptoms.
Ethnic Discrimination is Related to Increased Substance Use and Intentions to Use Across Diverse Groups of Adolescents
Authors: Rosales Robert , Veliz Philip , Jardine John , Weigard Alexander , McCabe Sean Esteban 
Published: October 2024

AbstractIntroductionIn recent years, adolescents of color report greater use of selected substances than white adolescents, including alcohol, tobacco, and cannabis. Increased levels of discrimination during the COVID-19 pandemic may have added to the chronic burden associated with increased substance use among adolescents of color. This study assessed the prevalence of substance use (alcohol, tobacco and cannabis) and intentions to use among adolescents by race/ethnicity and assessed associations between discrimination and substance use outcomes across groups.MethodsThe data come from the national panel of 11,868 adolescents in the Adolescent Brain Cognitive Development study (baseline through 4thfollow-up). We tested the prevalence rates of substance use and intentions by race/ethnicity. Multivariable longitudinal analyses tested whether 1) discrimination was connected to substance use and intentions, and 2) whether that relationship differed by race/ethnicity.ResultsWhite adolescents reported the greatest use and curiosity about alcohol. Black adolescents reported the highest rates of being willing to try any of the substances. Hispanic adolescents reported the highest rates of cannabis use. Multiracial adolescents reported the highest rates of tobacco use, curiosity about tobacco, and curiosity about cannabis. Discrimination was found to be associated with greater substance use among all racial/ethnic groups, except Black adolescents for alcohol use and Asian adolescents for alcohol use and tobacco use.ConclusionThis study supports national trends about substance use disparities among adolescents of color. Findings from this study also show that discrimination may explain some of these increased trends through intentions to use substances.
Blood Culture Utilization Optimization: Data-Driven Approaches to Guide Stewardship During Critical Supply Shortages
Authors: Amrollahi Fatemeh , Marshall Nicholas P. , Chang Amy , Deresinski Stanley , Banaei Niaz , Ma Stephen , Chen Jonathan H. 
Published: October 2024

AbstractAmidst the global blood culture bottle shortage, there is an urgent need to reduce unnecessary blood cultures. This study developed BSICalc and BSIScore, data-driven models using electronic health record (EHR) data, to guide blood culture ordering in the emergency department at the point-of-care, enhancing stewardship efforts and supporting clinical decision-making.
SpO2/FiO2Ratio as a Better Metric for Assessment of RBC Transfusion Effectiveness in Non-traumatic Critically Ill Patients with Physiologic Derangements
Authors: Choudhary Tilendra , Smith Geoffrey , Roback John D. , Patel Ravi M. , Josephson Cassandra D. , Kamaleswaran Rishikesan 
Published: October 2024

ABSTRACTIdentifying critically ill patients who are likely to improve their respiratory physiology following RBC blood transfusion is dynamic and difficult. Current decision tools are over-reliant on hemoglobin transfusion thresholds, without considering respiratory measures that may reflect physiologic effects of anemia and functional responses to RBC transfusion. Further, routine clinical measures to determine transfusion efficacy beyond hemoglobin increment are lacking to identify patients as responders or non-responders. We present a two-center retrospective cohort study aiming to determine a potential biomarker to assess the physiologic response of RBC transfusion for ICU patients. The study was performed with 13,274 eligible admissions at the first center. Another 3,757 from the second center were used for validation purpose. We introduced a comparative analysis of two respiratory measures, SpO2and SpO2/FiO2(SF) ratio, in addition to hemoglobin, to assess individual patient responses to RBC transfusion. A statistical study was performed to analyze the change in these markers before and after the transfusion interval. Based on quantitative statistical analyses, we found SF ratio to be a more effective biomarker than hemoglobin alone for revealing RBC transfusion efficacy. There existed an inverse correlation between pre-transfusion SF and transfusion efficacy. The results were consistent across both centers, revealing generalizability.
Controlled colonization of the human gut with a genetically engineered microbial medicine
Authors: Whitaker Weston R. , Russ Zachary N. , Shepherd Elizabeth Stanley , Popov Lauren M. , Louie Alexander , Lam Kathy , Zong David M. , Gill Clare C. C. , Gehrig Jeanette , Rishi Harneet S. , Tan Jessica A. , Buness Areta , Godoy Janeth , Banta Domenique , Jaidka Sonia , Wilson Katheryne , Flood Jake , Bukshpun Polina , Yocum Richard , Cook David N. , Warsi Tariq , McLean Lachy , Sonnenburg Justin L. , Deloache William C. 
Published: October 2024

AbstractPrecision microbiome programming for therapeutic applications has been limited by challenges in achieving reproducible colonization of the colon. Previously, we used a porphyran prebiotic to create a synthetic niche to engraft engineered bacteria into diverse microbiota in mice. Here we extend that work with biocontainment that links essential gene expression to porphyran presence yielding a platform for controlled colonization and decolonization of humans with engineeredBacteroides. We engineered this chassis with a five-gene oxalate degradation pathway, creating a therapeutic candidate that reduces hyperoxaluria, a cause of kidney stones, in pre-clinical models. Our Phase 1/2a clinical trial demonstrates tunable and reversible engraftment in humans, shows promising oxalate reductions, highlights addressable challenges in this novel modality for therapeutics, and queries key questions in microbiome science.
PET/CT guided tuberculosis treatment shortening: a randomized trial
Authors: Malherbe Stephanus T. , Chen Ray Y. , Yu Xiang , Smith Bronwyn , Liu Xin , Gao Jingcai , Diacon Andreas H. , Dawson Rodney , Tameris Michele , Zhu Hong , Qu Yahong , Jin Hongjian , Pan Shouguo , Dodd Lori E. , Wang Jing , Goldfeder Lisa C. , Cai Ying , Arora Kriti , Vincent Joel , Narunsky Kim , Serole Keboile , Goliath Rene T. , Da Costa Laylah , Taliep Arshad , Aziz Saalikha , Daroowala Remy , Thienemann Friedrich , Mukasa Sandra , Court Richard , Sossen Bianca , Ahlers Petri , Mendelsohn Simon C. , White Lisa , Gouel Aurélie , Lau Chuen-Yen , Hassan Samy , Liang Lili , Duan Hongfei , Moghaddam Gita K. , Paripati Praveen , Lahouar Saher , Harris Michael , Wollenberg Kurt , Jeffrey Brendan , Tartakovsky Mike , Rosenthal Alex , Duvenhage Michael , Armstrong Derek T. , Song Taeksun , Winter Jill , Gao Qian , Via Laura E. , Wilkinson Robert J. , Walzl Gerhard , Barry Clifton E. 
Published: October 2024

AbstractSix months of chemotherapy using current agents is standard of care for pulmonary, drug-sensitive tuberculosis (TB), even though some are believed to be cured more rapidly and others require longer therapy. Understanding what factors determine the length of treatment required for durable cure in individual patients would allow individualization of treatment durations, provide better clinical tools to determine the of appropriate duration of new regimens, as well as reduce the cost of large Phase III studies to determine the optimal combinations to use in TB control programs. We conducted a randomized clinical trial in South Africa and China that recruited 704 participants with newly diagnosed, drug-sensitive pulmonary tuberculosis and stratified them based on radiographic disease characteristics as assessed by FDG PET/CT scan readers. Participants with less extensive disease (N=273) were randomly assigned to complete therapy after four months or continue receiving treatment for six months. Amongst participants who received four months of therapy, 17 of 141 (12.1%) experienced unfavorable outcomes compared to only 2 of 132 (1.5%) who completed six months of treatment (treatment success 98.4% in B, 86.7% in C (difference -11.7%, 95% CI, -18.2%, -5.3%)). In the non-randomized arm that included participants with more extensive disease, only 8 of 248 (3.2%) experienced unfavorable outcomes. Total cavity volume and total lesion glycolysis at week 16 were significantly associated with risk of unfavorable outcome in the randomized participants. Based on PET/CT scans at TB recurrence, bacteriological relapses (confirmed by whole genome sequencing) predominantly occurred in the same active cavities originally present at baseline. Automated segmentation of the serial PET/CT scans was later performed, and machine-learning was used to classify participants according to their likelihood of relapse, allowing the development of predictive models with good performance based on CT, PET, microbiological and clinical characteristics. These results open the possibility for more efficient studies of future TB treatment regimens.
Data Missingness in Digital Phenotyping: Implications for Clinical Inference and Decision-Making
Authors: Shen Joanna , Abdelkader Kareem , Isaac Zacharia , Sarno Danielle , Kurz Jennifer , Silbersweig David , Onnela Jukka-Pekka , Barron Daniel 
Published: October 2024

AbstractBackgroundDigital phenotyping, the use of personal digital devices to capture and categorize real-world behavioral and physiological data, holds great potential for complementing traditional clinical assessments. However, missing data remains a critical challenge in this field, especially in longitudinal studies where missingness might obscure clinically relevant insights.ObjectiveThis paper examines the impact of data missingness on digital phenotyping clinical research, proposes a framework for reporting and accounting for data missingness, and explores its implications for clinical inference and decision-making.MethodsWe analyzed digital phenotyping data from a study involving 85 patients with chronic musculoskeletal pain, focusing on active (PROMIS-29 survey responses) and passive (accelerometer and GPS measures) data collected via the Beiwe Research Platform. We assessed data completeness and missingness at different timescales (day, hour, and minute levels), examined the relationship between data missingness and accelerometer measures and imputed GPS summary statistics, and studied the stability of regression models across varying levels of data missingness. We further investigated the association between functional status and day-level data missingness in PROMIS-29 subscores.ResultsData completeness showed substantial variability across timescales. Accelerometer-based cadence and imputed GPS-based home time and number of significant locations were generally robust to varying levels of data missingness. However, the stability of regression models was affected at higher thresholds (40% for cadence and 60% for home time). We also identified patterns wherein data missingness was associated with functional status.ConclusionData missingness in clinical digital phenotyping studies impacts individual- and group-level analyses. Given these results, we recommend that studies account for and report data at multiple timescales (we recommend day, hour, and minute-level where possible), depending on the clinical goals of data collection. We propose a modified framework for categorizing missingness mechanisms in digital phenotyping, emphasizing the need for clinically relevant reporting and interpretation of missing data. Our framework highlights the importance of integrating clinical with statistical expertise, specifically to ensure that imputing missing data does not obscure but helps capture clinically meaningful changes in functional status.
Metabolic alterations in Crohn’s disease: A Systematic Review
Authors: Dev Atul , Kahlon Sartajdeep , Ruiz Jonathan Javier , Kushwaha Avinash Chandra , Van Noord Megan G. , Adams Sean H. , Barrett Kim Elaine , Arkin Adam Paul , Dave Maneesh 
Published: October 2024

AbstractBackgroundCrohn’s disease (CD) is a chronic inflammatory disorder of the gastrointestinal tract with an unknown etiology. Several studies have identified dysregulated metabolites in patients with CD. However, there is significant variability in the metabolites found to be dysregulated across these studies, making it unclear whether a comprehensive, disease-specific metabolic signature for CD exists.ObjectiveTo analyze Crohn’s disease-specific metabolomic studies and available datasets to identify a comprehensive signature of dysregulated metabolites and metabolic pathways implicated in human CD.DesignA comprehensive systematic review was conducted using Medline and Embase databases to identify studies (from inception to May 2024) that employed analytical chemistry techniques to quantify metabolites in various biological samples from Crohn’s disease patients and non-IBD controls. Metabolites that were significantly altered in Crohn’s patients and reported in at least two studies were included for further analysis.ResultsThe systematic search identified 3,632 studies, with 88 selected for data extraction. Across these studies, 79 metabolites were consistently reported as significantly altered in Crohn’s disease (CD) patients in two or more studies. These metabolites form a distinct metabolic signature that differentiates CD patients from non-IBD controls, highlighting their relevance in the pathophysiology of the disease.ConclusionThis systematic review presents a comprehensive and well-defined signature of dysregulated metabolites across various biological samples and provides detailed insight into the perturbed metabolic pathways involved in CD.
Impacts of vaccination on the variant selection of SARS-CoV-2 and the subsequent case hospitalization rate: insights from the first U.S. Omicron wave
Authors: Liang Jingbo , Ding Zhaojun , Zhang Qingpeng , Yuan Hsiang-Yu 
Published: October 2024

AbstractBackgroundCOVID-19 vaccines, while providing protection against hospitalization, could inadvertently increase selection pressure on new immune-escape variants, impacting case hospitalization rate (CHR).MethodsUsing epidemiological and genomic sequence data, we calculated daily state-level CHR and the proportion of Omicron mutations in the United States during the first Omicron wave (between December 11, 2021, and March 22, 2022). We derived mathematical formulas to link evolution responses to an increasing population immunity with lagged regression models. Using mediation analysis, together with generalized linear mixed models and distributed lag nonlinear models, we assessed how natural selection, shaped by vaccine coverage, impacts CHR.ResultsThe model showed that increasing vaccination coverage from 45% to 70% contributed to a reduction in CHR from 5.8% to 4.4%. Part of the reduction resulted from direct vaccine protection (OR: 0.85, p-value=0.012). However, the higher vaccination coverage was correlated with a 20% increase in the proportion of BA.1/BA.1.1-associated mutations. As the Omicron variants were less severe than their predecessors (Delta), CHR further reduced (OR: 0.87, p-value<0.001). Marginally, this could reduce CHR from 5.8% to 5.1% via the adaptation of Omicron variants as marginal effect without accounting for direct vaccine protection.ConclusionsThe study offers new insight into vaccine strategies for reducing hospitalization risk by shortening [or maintaining] the circulation of more [or less] virulent variants among infectious diseases. Continuous monitoring of variant evolution, including their virulence, is critical.
The Arabidopsis RNA-binding protein SGS3 is recruited to the chromatin remodeler CHR11 to promote siRNA production from protein-coding genes
Authors: Elmayan Taline , Blein Thomas , Elvira-Matelot Emilie , Masson Ivan Le , Christ Aurélie , Bouteiller Nathalie , Crespi Martin D. , Vaucheret Hervé 
Published: October 2024

AbstractIn plants, aberrant RNAs produced by endogenous genes or transgenes are normally degraded by the nuclear and cytosolic RNA quality control (RQC) pathways. Under certain biotic or abiotic stresses, RQC is impaired, and aberrant RNAs are converted into siRNAs that initiate post-transcriptional gene silencing (PTGS) in the cytosol. How aberrant RNAs are selected and brought to the cytoplasm is not known. Here we show that the RNA-binding protein SUPPRESSOR OF GENE SILENCING (SGS)3 shuttles between the cytosol and the nucleus where it associates with the ISWI-like CHROMATIN REMODELER (CHR)11. CHR11 binds to transgenes prone to trigger PTGS. Knocking downCHR11and its paralogCHR17strongly reduces transgene PTGS, suggesting that SGS3 recruitment by CHR11/17 facilitates PTGS initiation. CHR11 is also enriched at endogenous protein-coding genes (PCGs) producing nat-siRNAs and va-siRNAs under biotic or abiotic stresses, and this production is reduced inchr11 chr17double mutants at genome-wide level. Moreover, impairing CHR11 and CHR17 rescues the lethal phenotype caused by the massive production of siRNAs from PCGs in RQC-deficient mutants. We propose that SGS3 recruitment by CHR11/17 allows exporting RNAs to the cytosol to initiate the production of siRNAs.One Sentence SummaryThe plant PTGS component SGS3 is recruited by the chromatin remodeler CHR11 to select nuclear RNAs for export to the cytosol and siRNA production.