bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and genetic diversity of rotavirus in Bangladesh during pre-vaccination period, 1973-2023: a meta-analysis
Authors: Sharif Nadim , Sharif Nazmul , Khan Afsana , Azpíroz Irma Domínguez , Diaz Raquel Martínez , Díez Isabel De la Torre , Parvez Anowar Khasru , Dey Shuvra Kanti 
Published: November 2023

IntroductionRotavirus infection is a major cause of mortality among children under 5 years in Bangladesh. There is lack of integrated studies on rotavirus prevalence and genetic diversity during 1973 to 2023 in Bangladesh.MethodsThis meta-analysis was conducted to determine the prevalence, genotypic diversity and seasonal distribution of rotavirus during pre-vaccination period in Bangladesh. This study included published articles on rotavirus A, rotavirus B and rotavirus C. We used Medline, Scopus and Google Scholar for published articles. Selected literatures were published between 1973 to 2023.ResultsThis study detected 12431 research articles published on rotavirus. Based on the inclusion criteria, 29 of 75 (30.2%) studies were selected. Molecular epidemiological data was taken from 29 articles, prevalence data from 29 articles, and clinical symptoms from 19 articles. The pooled prevalence of rotavirus was 30.1% (95% CI: 22%-45%, p = 0.005). Rotavirus G1 (27.1%, 2228 of 8219) was the most prevalent followed by G2 (21.09%, 1733 of 8219), G4 (11.58%, 952 of 8219), G9 (9.37%, 770 of 8219), G12 (8.48%, 697 of 8219), and G3 (2.79%, 229 of 8219), respectively. Genotype P[8] (40.6%, 2548 of 6274) was the most prevalent followed by P[4] (12.4%, 777 of 6274) and P[6] (6.4%, 400 of 6274), respectively. Rotavirus G1P[8] (19%) was the most frequent followed by G2P [4] (9.4%), G12P[8] (7.2%), and G9P[8], respectively. Rotavirus infection had higher odds of occurrence during December and February (aOR: 2.86, 95% CI: 2.43-3.6, p = 0.001).DiscussionThis is the first meta-analysis including all the studies on prevalence, molecular epidemiology, and genetic diversity of rotavirus from 1973 to 2023, pre-vaccination period in Bangladesh. This study will provide overall scenario of rotavirus genetic diversity and seasonality during pre-vaccination period and aids in policy making for rotavirus vaccination program in Bangladesh. This work will add valuable knowledge for vaccination against rotavirus and compare the data after starting vaccination in Bangladesh.
Response to therapy in Richter syndrome: a systematic review with meta-analysis of early clinical trials
Authors: Sousa-Pimenta Mário , Martins Ângelo , Mariz José Mário , Berraondo Pedro 
Published: November 2023

Introduction and aimsRichter syndrome (RS) represents the clonal evolution of chronic lymphocytic leukemia with histological transformation into a high-grade B cell lymphoma (diffuse large B cell lymphoma - DLBCL) or Hodgkin lymphoma. Considering that RS is an uncommon condition with poor prognosis, few high-quality evidence is available. To overcome this unmet need, this meta-analysis aimed to pool efficacy of early clinical trials in Richter syndrome (DLBCL subtype).MethodsMEDLINE, Scopus and Web of Science were searched up to May of 2023 to identify clinical trials decoying efficacy. The pooled complete response, objective response and intension-to-treat failure rates were calculated by pharmacological categories (classical chemotherapy, immunochemotherapy, immunotherapy, Bruton-tyrosine kinase inhibitors, targeted approaches, cell-based therapies and combinatorial regimens) using the Der-Simonian and Laird random-effects model. The Freeman-Tukey double arcsine method was used to estimate variance and confidence intervals. Heterogeneity was assessed using the I2 method.ResultsOverall, from 1242 studies identified, 30 were included, pooling data from 509 patients. The higher efficacy rates when, cell-based therapies were excluded, were achieved by immunochemotherapeutic regimens followed by combinatorial regimens, with complete response rates of 21.54% (IC95%14.93-28.87) and 23.77% (IC95% 8.70-42.19), respectively. Bispecific antibodies (alone or coupled with a chemotherapy debulking strategy) overtook Bruton tyrosine kinase inhibitors response rates. The latter, although achieving objective response rates above average, presented scarce complete response rates. Checkpoint inhibitors alone usually do not lead to complete responses, but their effectiveness may improve when combined with other agents, unveiling the importance of immune microenvironmental modulation.ConclusionThis is the first meta-analysis of early clinical trials assessing the impact of different therapeutics in RS. By analyzing the pooled efficacy estimates, our work suggests the role of a tailor-made bridging therapy for young patients with RS eligible for allogeneic hematopoietic stem cell transplantation (alloSCT), formally the only curative strategy.
Seasonal iron fluxes and iron cycling in sandy bioirrigated sediments
Authors: Swenson Perger Darci A. , Dwyer Ian P. , Aller Robert C. , Volkenborn Nils , Heilbrun Christina , Wehrmann Laura M. 
Published: November 2023

Permeable sediments, which represent more than 50% of the continental shelves, have been largely neglected as a potential source of Fe in current global estimates of benthic dissolved iron (Fed) fluxes. There are open questions regarding the effects of a range of factors on Fed fluxes from these deposits, including seasonal dynamics and the role of bioirrigation. To address these gaps, we performed laboratory-based sediment incubation experiments with muddy sands during summer (21 °C) and winter (7 °C). We used bioirrigation mimics to inject overlying water into the permeable sediment with patterns resembling the bioirrigation activity of the prolific bioturbating polychaete, Clymenella torquata. Newly developed in-line Fe accumulators were used to estimate Fe fluxes with a recirculating set-up. We found high Fed fluxes from sandy sediments, especially in benthic chambers with simulated bioirrigation. In the winter fluxes reached &gt;200 µmol Fed m-2 d-1 at the onset of irrigation and then decreased over the course of a 13-day experiment while in the summer fluxes from irrigated sediments reached &gt;100 µmol Fed m-2 d-1 and remained high throughout a 7-day experiment. Despite different geochemical expressions of Fe-S cycling and resulting porewater Fed concentrations in winter and summer, large Fed fluxes were sustained during both seasons. Solid-phase and porewater concentration profiles showed that maximum concentrations of key constituents, including total solid-phase reactive Fe, and porewater Fed and ammonium, were located closer to the sediment water interface (SWI) in irrigated cores than in non-irrigated cores due to the upward advective transport of dissolved porewater constituents. This upward transport also facilitated Fed fluxes out of the sediments, especially during times of active pumping. Our study demonstrates the potential for large Fed fluxes from sandy sediments in both summer and winter, despite relatively low standing stocks of labile organic matter and porewater Fed. The primary driver of these high fluxes was advective porewater transport, in our study induced by the activity of infaunal organisms. These results suggest that permeable sediments, which dominate shelf regions, must be explicitly considered in global estimates of benthic Fed fluxes, and cannot be simply extrapolated from estimates based on muddy sediments.
Development and validation of a machine learning model integrated with the clinical workflow for early detection of sepsis
Authors: Mahyoub Mohammed A. , Yadav Ravi R. , Dougherty Kacie , Shukla Ajit 
Published: November 2023

BackgroundSepsis is a life-threatening condition caused by a dysregulated response to infection, affecting millions of people worldwide. Early diagnosis and treatment are critical for managing sepsis and reducing morbidity and mortality rates.Materials and methodsA systematic design approach was employed to build a model that predicts sepsis, incorporating clinical feedback to identify relevant data elements. XGBoost was utilized for prediction, and interpretability was achieved through the application of Shapley values. The model was successfully deployed within a widely used Electronic Medical Record (EMR) system.ResultsThe developed model demonstrated robust performance pre-operations, with a sensitivity of 92%, specificity of 93%, and a false positive rate of 7%. Following deployment, the model maintained comparable performance, with a sensitivity of 91% and specificity of 94%. Notably, the post-deployment false positive rate of 6% represents a substantial reduction compared to the currently deployed commercial model in the same health system, which exhibits a false positive rate of 30%.DiscussionThese findings underscore the effectiveness and potential value of the developed model in improving timely sepsis detection and reducing unnecessary alerts in clinical practice. Further investigations should focus on its long-term generalizability and impact on patient outcomes.
The application of artificial intelligence in diabetic retinopathy screening: a Saudi Arabian perspective
Authors: Barakat Abdulaziz A. , Mobarak Omar , Javaid Haroon Ahmed , Awad Mhd Rasheed , Hamweyah Karam , Ouban Abderrahman , Al-Hazzaa Selwa A. F. 
Published: November 2023

IntroductionDiabetic retinopathy (DR) is the leading cause of preventable blindness in Saudi Arabia. With a prevalence of up to 40% of patients with diabetes, DR constitutes a significant public health burden on the country. Saudi Arabia has not yet established a national screening program for DR. Mounting evidence shows that Artificial intelligence (AI)-based DR screening programs are slowly becoming superior to traditional screening, with the COVID-19 pandemic accelerating research into this topic as well as changing the outlook of the public toward it. The main objective of this study is to evaluate the perception and acceptance of AI in DR screening among eye care professionals in Saudi Arabia.MethodsA cross-sectional study using a self-administered online-based questionnaire was distributed by email through the registry of the Saudi Commission For Health Specialties (SCFHS). 309 ophthalmologists and physicians involved in diabetic eye care in Saudi Arabia participated in the study. Data analysis was done by SPSS, and a value of p &lt; 0.05 was considered significant for statistical purposes.Results54% of participants rated their level of AI knowledge as above average and 63% believed that AI and telemedicine are interchangeable. 66% believed that AI would decrease the workforce of physicians. 79% expected clinical efficiency to increase with AI. Around 50% of participants expected AI to be implemented in the next 5 years.DiscussionMost participants reported good knowledge about AI. Physicians with more clinical experience and those who used e-health apps in clinical practice regarded their AI knowledge as higher than their peers. Perceived knowledge was strongly related to acceptance of the benefits of AI-based DR screening. In general, there was a positive attitude toward AI-based DR screening. However, concerns related to the labor market and data confidentiality were evident. There should be further education and awareness about the topic.
Causal relationship between gut microbiota and immune thrombocytopenia: a Mendelian randomization study of two samples
Authors: Guo Dongmei , Chen Qian , Wang Guojun , Li ChunPu ,   FinnGen consortium
Published: November 2023

BackgroundSome observational studies have shown that immune thrombocytopenia (ITP) is highly associated with the alteration-composition of gut microbiota. However, the causality of gut microbiota on ITP has not yet been determined.MethodsBased on accessible summary statistics of the genome-wide union, the latent connection between ITP and gut microbiota was estimated using bi-directional Mendelian randomization (MR) and multivariable MR (MVMR) analyses. Inverse variance weighted (IVW), weighted median analyses, and MR-Egger regression methods were performed to examine the causal correlation between ITP and the gut microbiota. Several sensitivity analyses verified the MR results. The strength of causal relationships was evaluated using the MR-Steiger test. MVMR analysis was undertaken to test the independent causal effect. MR analyses of reverse direction were made to exclude the potential of reverse correlations. Finally, GO enrichment analyses were carried out to explore the biological functions.ResultsAfter FDR adjustment, two microbial taxa were identified to be causally associated with ITP (PFDR &lt; 0.10), namely Alcaligenaceae (PFDR = 7.31 × 10–2) and Methanobacteriaceae (PFDR = 7.31 × 10–2). In addition, eight microbial taxa were considered as potentially causal features under the nominal significance (P &lt; 0.05): Actinobacteria, Lachnospiraceae, Methanobacteria, Bacillales, Methanobacteriales, Coprococcus2, Gordonibacter, and Veillonella. According to the reverse-direction MR study findings, the gut microbiota was not significantly affected by ITP. There was no discernible horizontal pleiotropy or instrument heterogeneity. Finally, GO enrichment analyses showed how the identified microbial taxa participate in ITP through their underlying biological mechanisms.ConclusionSeveral microbial taxa were discovered to be causally linked to ITP in this MR investigation. The findings improve our understanding of the gut microbiome in the risk of ITP.
Antibiotic prophylaxis and hospitalization of horses subjected to median laparotomy: gut microbiota trajectories and abundance increase of Escherichia
Authors: Kauter Anne , Brombach Julian , Lübke-Becker Antina , Kannapin Dania , Bang Corinna , Franzenburg Sören , Stoeckle Sabita D. , Mellmann Alexander , Scherff Natalie , Köck Robin , Guenther Sebastian , Wieler Lothar H. , Gehlen Heidrun , Semmler Torsten , Wolf Silver A. , Walther Birgit 
Published: November 2023

IntroductionHorse clinics are hotspots for the accumulation and spread of clinically relevant and zoonotic multidrug-resistant bacteria, including extended-spectrum β-lactamase producing (ESBL) Enterobacterales. Although median laparotomy in cases of acute equine colic is a frequently performed surgical intervention, knowledge about the effects of peri-operative antibiotic prophylaxis (PAP) based on a combination of penicillin and gentamicin on the gut microbiota is limited.MethodsWe collected fecal samples of horses from a non-hospitalized control group (CG) and from horses receiving either a pre-surgical single-shot (SSG) or a peri-operative 5-day (5DG) course of PAP. To assess differences between the two PAP regimens and the CG, all samples obtained at hospital admission (t0), on days three (t1) and 10 (t2) after surgery, were screened for ESBL-producing Enterobacterales and subjected to 16S rRNA V1–V2 gene sequencing.ResultsWe included 48 samples in the SSG (n = 16 horses), 45 in the 5DG (n = 15), and 20 in the CG (for t0 and t1, n = 10). Two samples of equine patients receiving antibiotic prophylaxis (6.5%) were positive for ESBL-producing Enterobacterales at t0, while this rate increased to 67% at t1 and decreased only slightly at t2 (61%). Shannon diversity index (SDI) was used to evaluate alpha-diversity changes, revealing there was no significant difference between horses suffering from acute colic (5DG, SDImean of 5.90, SSG, SDImean of 6.17) when compared to the CG (SDImean of 6.53) at t0. Alpha-diversity decreased significantly in both PAP groups at t1, while at t2 the onset of microbiome recovery was noticed. Although we did not identify a significant SDImean difference with respect to PAP duration, the community structure (beta-diversity) was considerably restricted in samples of the 5DG at t1, most likely due to the ongoing administration of antibiotics. An increased abundance of Enterobacteriaceae, especially Escherichia, was noted for both study groups at t1.ConclusionColic surgery and PAP drive the equine gut microbiome towards dysbiosis and reduced biodiversity that is accompanied by an increase of samples positive for ESBL-producing Enterobacterales. Further studies are needed to reveal important factors promoting the increase and residency of ESBL-producing Enterobacterales among hospitalized horses.
A novel endophytic fungus strain of Cladosporium: its identification, genomic analysis, and effects on plant growth
Authors: Yang Nan , Zhang Wenbin , Wang Dan , Cao Dingding , Cao Yanyu , He Weihong , Lin Ziting , Chen Xiaofeng , Ye Guiping , Chen Zhiming , Chen Jianjun , Wei Xiangying 
Published: November 2023

IntroductionEndophytic microorganisms are bacteria or fungi that inhabit plant internal tissues contributing to various biological processes of plants. Some endophytic microbes can promote plant growth, which are known as plant growth-promoting endophytes (PGPEs). There has been an increasing interest in isolation and identification of PGPEs for sustainable production of crops. This study was undertaken to isolate PGPEs from roots of a halophytic species Sesuvium portulacastrum L. and elucidate potential mechanisms underlying the plant growth promoting effect.MethodsSurface-disinfected seeds of S. portulacastrum were germinated on an in vitro culture medium, and roots of some germinated seedlings were contaminated by bacteria and fungi. From the contamination, an endophytic fungus called BF-F (a fungal strain isolated from bacterial and fungal contamination) was isolated and identified. The genome of BF-F strain was sequenced, its genome structure and function were analyzed using various bioinformatics software. Additionally, the effect of BF-F on plant growth promotion were investigated by gene cluster analyses.ResultsBased on the sequence homology (99%) and phylogenetic analysis, BF-F is likely a new Cladosporium angulosum strain or possibly a new Cladosporium species that is most homologous to C. angulosum. The BF-F significantly promoted the growth of dicot S. portulacastrum and Arabidopsis as well as monocot rice. Whole genome analysis revealed that the BF-F genome has 29,444,740 bp in size with 6,426 annotated genes, including gene clusters associated with the tryptophan synthesis and metabolism pathway, sterol synthesis pathway, and nitrogen metabolism pathway. BF-F produced indole-3-acetic acid (IAA) and also induced the expression of plant N uptake related genes.DiscussionOur results suggest that BF-F is a novel strain of Cladosporium and has potential to be a microbial fertilizer for sustainable production of crop plants. The resulting genomic information will facilitate further investigation of its genetic evolution and its function, particularly mechanisms underlying plant growth promotion.
A global bibliometric and visualized analysis of bacterial biofilm eradication from 2012 to 2022
Authors: Wang Tao , Zhang Rui , Chen Zhiling , Cao Peipei , Zhou Qionglin , Wu Qiang 
Published: November 2023

BackgroundTo deeply explore the dynamic trends, focal points and emerging topics of bacterial biofilm eradication field and provide novel insights for prospective research endeavors, the first global bibliometric and visualized analysis of the field was employed in this study.MethodsThe study meticulously curated articles and reviews concentrating on biofilm eradication from the Web of Science Core Collection (WoSCC) and identified literature published in 2012–2022 for further analysis, and the bibliometric and visualized analysis was performed to elucidate a clustering pattern in the domain with tools mainly including CiteSpace and VOSviewer.Results15,503 authors affiliated with 2,397 institutions spanning 96 countries or regions contributed to a corpus of 3,201 articles, containing 7,005 keywords. The USA emerged as a commanding vanguard in exploring the antibiofilm strategies and displaying pioneering initiatives within this sphere. The Chinese Academy of Sciences (CAS) emerged as the most prolific source of publications. Noteworthy among authors, Pandian Shunmugiah Karutha secured the lead in article contributions as well as co-citations while Deng Le with his team is poised to become a dominant influence in the future. Despite that, the extent of collaborative engagement across different institutions and authors appeared to fall short of its potential. Frontiers in Microbiology led the discourse by publishing a substantial body of articles and standing as the most recurrently co-cited publication. The most influential research domains encompassed “bacterial biofilm formation, “photodynamic therapy” and “phage therapy.” Recent trends and forefronts concentrate on intensifying research into facilitating the shift of multiple strategies for biofilm eradication from controlled lab settings or animal studies to real-world clinical environments.ConclusionFundamentally, this study presents a comprehensive scrutiny and reveals that the realm of bacterial biofilm eradication is undergoing rapid evolution, with even greater expansion anticipated in the times ahead. Subsequent scholars should emphasize the augmentation of collaborative efforts and focus their energies on emerging topics, thus contributing to break through current barriers in transitioning biofilm eradication strategies from the “fundamental” stage to “practical” application.
Leaf, root, and soil microbiomes of an invasive plant, Ardisia crenata, differ between its native and exotic ranges
Authors: Nakamura Naoto , Toju Hirokazu , Kitajima Kaoru 
Published: November 2023

IntroductionEcological underpinnings of the invasion success of exotic plants may be found in their interactions with microbes, either through the enemy release hypothesis and the enhanced mutualism hypothesis. Whereas recent high-throughput sequencing techniques have significantly expanded our understanding of plant-associated microbiomes and their functional guilds, few studies to date have used these techniques to compare the microbiome associated with invasive plants between their native and exotic ranges.MethodsWe extracted fungal and bacterial DNA within leaf endosphere, root endosphere and soil of an invasive plant, Ardisia crenata, sampled from their native range Japan and exotic range Florida, USA. Using Illumina sequencing data, we compared microbial community compositions and diversity between the native and exotic ranges, and tested whether abundance of pathogenic or mutualistic microbes differ between the native or exotic ranges in accordance to the enemy release hypothesis or the enhanced mutualism hypothesis.ResultsFungal and bacterial community compositions differed among leaves, roots and soil, and between the native and exotic ranges. Despite a higher microbial diversity in the soil in the exotic range than in the native range, the microbial diversity within leaf and root was lower in the exotic range compared to the native range. In addition, leaves in the native range harbored a greater number of plant pathogenic fungi compared to those in the exotic range.DiscussionThese patterns suggest plant controls over what microbes become associated with leaves and roots. The higher abundance of leaf pathogenic fungi, including the pathogen which is known to cause specific disease in A. crenata in the exotic range than in the native range, support the enemy release hypothesis and highlighted potential importance of examining microbial communities both above- and below-ground.