bluuebunny/crossref_metadata_2025_split huggingface dataset:
The causal association between smoking, alcohol consumption and risk of upper urinary calculi: insights from a Mendelian randomization study
Authors: Wang Li , Yin Shan , Li Kun-peng , Bao Er-hao , Wang Jia-hao , Zhu Ping-yu 
Published: December 2023

Background: The causal link between smoking, alcohol consumption, and upper urinary calculi remains uncertain in observational studies due to confounding factors. To uncover potential causal associations, we utilized two-sample univariable and multivariable Mendelian randomization (MR) methods.Methods: Five risk factors related to lifestyles (cigarettes per day, lifetime smoking index, smoking initiation, drinks per week and alcohol intake frequency) were chosen from the Genome-Wide Association Study (GWAS). Upper urinary calculi were obtained from the FinnGen and United Kingdom Biobank consortium. Inverse-variance-weighted (IVW) was mainly used to compute odds ratios (OR) and 95% confidence intervals (Cl). While diligently scrutinizing potential sources of heterogeneity and horizontal pleiotropy via the rigorous utilization of Cochran’s Q test, the MR-PRESSO method, and MR-Egger.Results: The summary OR for upper urinary calculi was 0.6 (IVW 95% CI: 0.49–0.74; p = 1.31 × 10−06) per standard deviation decrease in drinks per week. Interestingly, the genetically predicted alcohol intake frequency was associated with a significantly increased risk upper urinary calculi (OR = 1.27; 95% CI: 1.11–1.45; p = 0.0005). Our study found no association between smoking initiation, the number of cigarettes per day, and the lifetime smoking index and the risk of upper urinary calculi. By adjusting for body mass index and education, estimates of drinks per week remained consistent in multivariate MR analyses, while alcohol intake frequency became non-significant.Conclusion: MR analysis showed that drinks per week was negatively associated with upper urinary calculi, whereas the effect of tobacco on upper urinary calculi was not significant and the detrimental effect of alcohol intake frequency on upper urinary calculi became non-significant after adjusting for BMI and education.
Bendamustine impairs humoral but not cellular immunity to SARS-CoV-2 vaccination in rituximab-treated B-cell lymphoma–affected patients
Authors: Vanni Anna , Salvati Lorenzo , Mazzoni Alessio , Lamacchia Giulia , Capone Manuela , Francalanci Stefania , Kiros Seble Tekle , Cosmi Lorenzo , Puccini Benedetta , Ciceri Manuel , Sordi Benedetta , Rossolini Gian Maria , Annunziato Francesco , Maggi Laura , Liotta Francesco 
Published: December 2023

BackgroundPatients with B-cell lymphoma are a fragile category of subjects, particularly exposed to infections and characterized by an impaired vaccination response due to the disease itself and, even more, to the chemotherapy regimen. For this reason, extensive knowledge of the immune response status of these subjects is of fundamental importance to obtain possible indications for a tailored immunization strategy.MethodsWe enrolled two cohorts of patients with B-cell lymphoma under rituximab treatment or 3–24 months after treatment. In all patients, we evaluated both humoral and cellular immunological memory toward SARS-CoV-2, after standard vaccination and upon one booster dose.ResultsWe observed no Spike-specific IgG production in patients (n = 25) under anti-CD20 treatment, whereas patients (n = 16) vaccinated after the completion of chemotherapy showed a higher humoral response. Evaluating SARS-CoV-2–specific T-cell response, we found that patients in both cohorts had developed robust cellular immunity after vaccination. Of the 21 patients (51%) that experienced a breakthrough SARS-CoV-2 infection, only six patients developed severe disease. Interestingly, these six patients had all been treated with rituximab plus bendamustine. Notably, we observed that Spike-specific IgG levels in patients treated with rituximab plus bendamustine were absent or lower compared with those in patients treated with rituximab plus other chemotherapy, whereas Spike-specific T-cell response was not different based on chemotherapy regiment.DiscussionOur results show that, in patients with B-cell lymphoma under rituximab therapy, anti–SARS-CoV-2 mRNA vaccination induces a weak or absent humoral response but a consistent T-cell response. In addition, chemotherapy regimens with bendamustine further reduce patients’ ability to mount a Spike-specific humoral response even after a long time period from chemotherapy discontinuation. These results provide evidence that different chemotherapeutics display different immunosuppressive properties that could be taken in to account in the choice of the right drug regimen for the right patient. Moreover, they question whether immunocompromised patients, particularly those treated with bendamustine, need interventions to improve vaccine-induced immune response.
A bibliometric analysis on discovering anti-quorum sensing agents against clinically relevant pathogens: current status, development, and future directions
Authors: Peng Bo , Li Yanqun , Yin Jiajia , Ding Wenping , Fazuo Wang , Xiao Zhihui , Yin Hao 
Published: December 2023

BackgroundQuorum sensing is bacteria’s ability to communicate and regulate their behavior based on population density. Anti-quorum sensing agents (anti-QSA) is promising strategy to treat resistant infections, as well as reduce selective pressure that leads to antibiotic resistance of clinically relevant pathogens. This study analyzes the output, hotspots, and trends of research in the field of anti-QSA against clinically relevant pathogens.MethodsThe literature on anti-QSA from the Web of Science Core Collection database was retrieved and analyzed. Tools such as CiteSpace and Alluvial Generator were used to visualize and interpret the data.ResultsFrom 1998 to 2023, the number of publications related to anti-QAS research increased rapidly, with a total of 1,743 articles and reviews published in 558 journals. The United States was the largest contributor and the most influential country, with an H-index of 88, higher than other countries. Williams was the most productive author, and Hoiby N was the most cited author. Frontiers in Microbiology was the most prolific and the most cited journal. Burst detection indicated that the main frontier disciplines shifted from MICROBIOLOGY, CLINICAL, MOLECULAR BIOLOGY, and other biomedicine-related fields to FOOD, MATERIALS, NATURAL PRODUCTS, and MULTIDISCIPLINARY. In the whole research history, the strongest burst keyword was cystic-fibrosis patients, and the strongest burst reference was Lee and Zhang (2015). In the latest period (burst until 2023), the strongest burst keyword was silver nanoparticle, and the strongest burst reference was Whiteley et al. (2017). The co-citation network revealed that the most important interest and research direction was anti-biofilm/anti-virulence drug development, and timeline analysis suggested that this direction is also the most active. The key concepts alluvial flow visualization revealed seven terms with the longest time span and lasting until now, namely Escherichia coli, virulence, Pseudomonas aeruginosa, virulence factor, bacterial biofilm, gene expression, quorum sensing. Comprehensive analysis shows that nanomaterials, marine natural products, and artificial intelligence (AI) may become hotspots in the future.ConclusionThis bibliometric study reveals the current status and trends of anti-QSA research and may assist researchers in identifying hot topics and exploring new research directions.
Validation of potential RNA biomarkers for prostate cancer diagnosis and monitoring in plasma and urinary extracellular vesicles
Authors: Brokāne Agnese , Bajo-Santos Cristina , Zayakin Pawel , Belovs Alberts , Jansons Juris , Lietuvietis Vilnis , Martens-Uzunova Elena S. , Jenster Guido W. , Linē Aija 
Published: December 2023

Introduction: Prostate cancer (PCa), one of the most prevalent malignancies affecting men worldwide, presents significant challenges in terms of early detection, risk stratification, and active surveillance. In recent years, liquid biopsies have emerged as a promising non-invasive approach to complement or even replace traditional tissue biopsies. Extracellular vesicles (EVs), nanosized membranous structures released by various cells into body fluids, have gained substantial attention as a source of cancer biomarkers due to their ability to encapsulate and transport a wide range of biological molecules, including RNA. In this study, we aimed to validate 15 potential RNA biomarkers, identified in a previous EV RNA sequencing study, using droplet digital PCR.Methods: The candidate biomarkers were tested in plasma and urinary EVs collected before and after radical prostatectomy from 30 PCa patients and their diagnostic potential was evaluated in a test cohort consisting of 20 benign prostate hyperplasia (BPH) and 20 PCa patients’ plasma and urinary EVs. Next, the results were validated in an independent cohort of plasma EVs from 31 PCa and 31 BPH patients.Results: We found that the levels of NKX3-1 (p = 0.0008) in plasma EVs, and tRF-Phe-GAA-3b (p &lt; 0.0001) tRF-Lys-CTT-5c (p &lt; 0.0327), piR-28004 (p = 0.0081) and miR-375-3p (p &lt; 0.0001) in urinary EVs significantly decreased after radical prostatectomy suggesting that the main tissue source of these RNAs is prostate and/or PCa. Two mRNA biomarkers—GLO1 and NKX3-1 showed promising diagnostic potential in distinguishing between PCa and BPH with AUC of 0.68 and 0.82, respectively, in the test cohort and AUC of 0.73 and 0.65, respectively, in the validation cohort, when tested in plasma EVs. Combining these markers in a biomarker model yielded AUC of 0.85 and 0.71 in the test and validation cohorts, respectively. Although the PSA levels in the blood could not distinguish PCa from BPH in our cohort, adding PSA to the mRNA biomarker model increased AUC from 0.71 to 0.76.Conclusion: This study identified two novel EV-enclosed RNA biomarkers–NKX3-1 and GLO1–for the detection of PCa, and highlights the complementary nature of GLO1, NKX3-1 and PSA as combined biomarkers in liquid biopsies of PCa.
The predictive validity of a Brain Care Score for dementia and stroke: data from the UK Biobank cohort
Authors: Singh Sanjula D. , Oreskovic Tin , Carr Sinclair , Papier Keren , Conroy Megan , Senff Jasper R. , Chemali Zeina , Gutierrez-Martinez Leidys , Parodi Livia , Mayerhofer Ernst , Marini Sandro , Nunley Courtney , Newhouse Amy , Ouyang An , Brouwers H. Bart , Westover Brandon , Rivier Cyprien , Falcone Guido , Howard Virginia , Howard George , Pikula Aleksandra , Ibrahim Sarah , Sheth Kevin N. , Yechoor Nirupama , Lazar Ronald M. , Anderson Christopher D. , Tanzi Rudolph E. , Fricchione Gregory , Littlejohns Thomas , Rosand Jonathan 
Published: December 2023

IntroductionThe 21-point Brain Care Score (BCS) was developed through a modified Delphi process in partnership with practitioners and patients to promote behavior changes and lifestyle choices in order to sustainably reduce the risk of dementia and stroke. We aimed to assess the associations of the BCS with risk of incident dementia and stroke.MethodsThe BCS was derived from the United Kingdom Biobank (UKB) baseline evaluation for participants aged 40–69 years, recruited between 2006–2010. Associations of BCS and risk of subsequent incident dementia and stroke were estimated using Cox proportional hazard regressions, adjusted for sex assigned at birth and stratified by age groups at baseline.ResultsThe BCS (median: 12; IQR:11–14) was derived for 398,990 UKB participants (mean age: 57; females: 54%). There were 5,354 incident cases of dementia and 7,259 incident cases of stroke recorded during a median follow-up of 12.5 years. A five-point higher BCS at baseline was associated with a 59% (95%CI: 40-72%) lower risk of dementia among participants aged &lt;50. Among those aged 50–59, the figure was 32% (95%CI: 20-42%) and 8% (95%CI: 2-14%) for those aged &gt;59 years. A five-point higher BCS was associated with a 48% (95%CI: 39-56%) lower risk of stroke among participants aged &lt;50, 52% (95%CI, 47-56%) among those aged 50–59, and 33% (95%CI, 29-37%) among those aged &gt;59.DiscussionThe BCS has clinically relevant and statistically significant associations with risk of dementia and stroke in approximately 0.4 million UK people. Future research includes investigating the feasibility, adaptability and implementation of the BCS for patients and providers worldwide.
Sugarcane/soybean intercropping with reduced nitrogen addition promotes photosynthesized carbon sequestration in the soil
Authors: Zhang Tantan , Tang Hu , Peng Peng , Ge Shiqiang , Liu Yali , Feng Yuanjiao , Wang Jianwu 
Published: December 2023

IntroductionSugarcane/soybean intercropping with reduced nitrogen (N) addition has improved soil fertility and sustainable agricultural development in China. However, the effects of intercropping pattern and N fertilizer addition on the allocation of photosynthesized carbon (C) in plant-soil system were far less understood.MethodsIn this study, we performed an 13CO2 pulse labeling experiment to trace C footprints in plant-soil system under different cropping patterns [sugarcane monoculture (MS), sugarcane/soybean intercropping (SB)] and N addition levels [reduced N addition (N1) and conventional N addition (N2)].Results and discussionOur results showed that compared to sugarcane monoculture, sugarcane/soybean intercropping with N reduced addition increased sugarcane biomass and root/shoot ratio, which in turn led to 23.48% increase in total root biomass. The higher root biomass facilitated the flow of shoot fixed 13C to the soil in the form of rhizodeposits. More than 40% of the retained 13C in the soil was incorporated into the labile C pool [microbial biomass C (MBC) and dissolved organic C (DOC)] on day 1 after labeling. On day 27 after labeling, sugarcane/soybean intercropping with N reduced addition showed the highest 13C content in the MBC as well as in the soil, 1.89 and 1.14 times higher than the sugarcane monoculture, respectively. Moreover, intercropping pattern increased the content of labile C and labile N (alkaline N, ammonium N and nitrate N) in the soil. The structural equation model indicated that the cropping pattern regulated 13C sequestration in the soil mainly by driving changes in labile C, labile N content and root biomass in the soil. Our findings demonstrate that sugarcane/soybean intercropping with reduced N addition increases photosynthesized C sequestration in the soil, enhances the C sink capacity of agroecosystems.
Policy implementation strategies to address rural disparities in access to care for stroke patients
Authors: Rasool Aysha , Bailey Moriah , Lue Brittany , Omeaku Nina , Popoola Adebola , Shantharam Sharada S. , Brown Amanda A. , Fulmer Erika B. 
Published: December 2023

ContextStroke systems of care (SSOC) promote access to stroke prevention, treatment, and rehabilitation and ensure patients receive evidence-based treatment. Stroke patients living in rural areas have disproportionately less access to emergency medical services (EMS). In the United States, rural counties have a 30% higher stroke mortality rate compared to urban counties. Many states have SSOC laws supported by evidence; however, there are knowledge gaps in how states implement these state laws to strengthen SSOC.ObjectiveThis study identifies strategies and potential challenges to implementing state policy interventions that require or encourage evidence-supported pre-hospital interventions for stroke pre-notification, triage and transport, and inter-facility transfer of patients to the most appropriate stroke facility.DesignResearchers interviewed representatives engaged in implementing SSOC across six states. Informants (n = 34) included state public health agency staff and other public health and clinical practitioners.OutcomesThis study examined implementation of pre-hospital SSOCs policies in terms of (1) development roles, processes, facilitators, and barriers; (2) implementation partners, challenges, and solutions; (3) EMS system structure, protocols, communication, and supervision; and (4) program improvement, outcomes, and sustainability.ResultsChallenges included unequal resource allocation and EMS and hospital services coverage, particularly in rural settings, lack of stroke registry usage, insufficient technologies, inconsistent use of standardized tools and protocols, collaboration gaps across SSOC, and lack of EMS stroke training. Strategies included addressing scarce resources, services, and facilities; disseminating, training on, and implementing standardized statewide SSOC protocols and tools; and utilizing SSOC quality and performance improvement systems and approaches.ConclusionsThis paper identifies several strategies that can be incorporated to enhance the implementation of evidence-based stroke policies to improve access to timely stroke care for all patient populations, particularly those experiencing disparities in rural communities.
DAMPs and alarmin gene expression patterns in aging healthy and diseased mucosal tissues
Authors: Gonzalez O. A. , Kirakodu S. S. , Ebersole J. L. 
Published: December 2023

IntroductionPeriodontitis is delineated by a dysbiotic microbiome at sites of lesions accompanied by a dysregulated persistent inflammatory response that undermines the integrity of the periodontium. The interplay of the altered microbial ecology and warning signals from host cells would be a critical feature for maintaining or re-establishing homeostasis in these tissues.MethodsThis study used a nonhuman primate model (Macaca mulatta) with naturally-occurring periodontitis (n = 34) and experimental ligature-induced periodontitis (n = 36) to describe the features of gene expression for an array of damage-associate molecular patterns (DAMPs) or alarmins within the gingival tissues. The animals were age stratified into: ≤3 years (Young), 7–12 years (Adolescent), 12–15 years (Adult) and 17–23 years (Aged). Gingival tissue biopsies were examined via microarray. The analysis focused on 51 genes representative of the DAMPs/alarmins family of host cell warning factors and 18 genes associated with tissue destructive processed in the gingival tissues. Bacterial plaque samples were collected by curette sampling and 16S rRNA gene sequences used to describe the oral microbiome.ResultsA subset of DAMPs/alarmins were expressed in healthy and naturally-occurring periodontitis tissues in the animals and suggested local effects on gingival tissues leading to altered levels of DAMPs/alarmins related to age and disease. Significant differences from adult healthy levels were most frequently observed in the young and adolescent animals with few representatives in this gene array altered in the healthy aged gingival tissues. Of the 51 target genes, only approximately ⅓ were altered by ≥1.5-fold in any of the age groups of animals during disease, with those increases observed during disease initiation. Distinctive positive and negative correlations were noted with the DAMP/alarmin gene levels and comparative expression changes of tissue destructive molecules during disease across the age groups. Finally, specific correlations of DAMP/alarmin genes and relative abundance of particular microbes were observed in health and resolution samples in younger animals, while increased correlations during disease in the older groups were noted.ConclusionsThus, using this human-like preclinical model of induced periodontitis, we demonstrated the dynamics of the activation of the DAMP/alarmin warning system in the gingival tissues that showed some specific differences based on age.
Attitudes and practices on antibiotic use and its emerging threats among Lebanese dairy veterinarians: a case study from a developing country
Authors: Dankar Iman , Hassan Hussein F. , Serhan Mireille 
Published: December 2023

IntroductionThis study aimed to explore how veterinarians (vets) rationalized their prescribing decisions for antimicrobial (AM) uses, the barriers they perceived to implement proper farm management in Lebanon, and the consecutive threats that might arise concerning the emergent spread of antimicrobial resistance in animals and the population.MethodsAmid the COVID-19 pandemic, phone call interviews were conducted with 34 veterinarians working in different demographic regions across the country. Data were analyzed qualitatively using an inductive thematic analysis.Results and discussionThe majority of veterinarians called for responsible antibiotic use. The prescribing decision of veterinarians was based mainly on suspected disease from field examination, farmer’s reports via phone calls, and the ability of the farmer to cover antibiotic costs. Very few veterinarians referred to laboratory diagnosis before prescribing a specific AM due to many obstacles. This study uncovered the absence of a trust relationship between veterinarians and farmers in Lebanon. Veterinarians provided different insights into farming practices, reflecting that farmers, in general, lack proper knowledge and implementation of farm management and that they mainly treat the herd on their own, especially in light of the current unprecedented economic crisis that Lebanon has been facing in the last three years. Above all, veterinarians revealed that AM resistance in Lebanon is markedly spreading, which calls for a serious and instantaneous set of governmental policies and regulations.
Rice (Oryza sativa L.) Grain Size, Shape, and Weight-Related QTLs Identified Using GWAS with Multiple GAPIT Models and High-Density SNP Chip DNA Markers
Authors: Kabange Nkulu Rolly , Dzorkpe Gamenyah Daniel , Park Dong-Soo , Kwon Youngho , Lee Sais-Beul , Lee So-Myeong , Kang Ju-Won , Jang Seong-Gyu , Oh Ki-Won , Lee Jong-Hee 
Published: December 2023

This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint-strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK)), Fixed and random model Circulating Probability Uniform (FarmCPU), Settlement of MLM Under Progressive Exclusive Relationship (SUPER), and General Linear Model (GLM)]–High-Density SNP Chip DNA Markers (60,461) to conduct a Genome-Wide Association Study (GWAS). GWAS was performed using genotype and grain-related phenotypes of 143 recombinant inbred lines (RILs). Data show that parental lines (Ilpum and Tung Tin Wan Hein 1, TTWH1, Oryza sativa L., ssp. japonica and indica, respectively) exhibited divergent phenotypes for all analyzed grain traits), which was reflected in their derived population. GWAS results revealed the association between seven SNP Chip makers and QTLs for grain length, co-detected by all GAPIT models on chromosomes (Chr) 1–3, 5, 7, and 11, were qGL1-1BFSG (AX-95918134, Chr1: 3,820,526 bp) explains 65.2–72.5% of the phenotypic variance explained (PVE). In addition, qGW1-1BFSG (AX-273945773, Chr1: 5,623,288 bp) for grain width explains 15.5–18.9% of PVE. Furthermore, BLINK or FarmCPU identified three QTLs for grain thickness independently, and explain 74.9% (qGT1Blink, AX-279261704, Chr1: 18,023,142 bp) and 54.9% (qGT2-1Farm, AX-154787777, Chr2: 2,118,477 bp) of the observed PVE. For the grain length-to-width ratio (LWR), the qLWR2BFSG (AX-274833045, Chr2: 10,000,097 bp) explains nearly 15.2–32% of the observed PVE. Likewise, the major QTL for thousand-grain weight (TGW) was detected on Chr6 (qTGW6BFSG, AX-115737727, 28,484,619 bp) and explains 32.8–54% of PVE. The qTGW6BFSG QTL coincides with qGW6-1Blink for grain width and explained 32.8–54% of PVE. Putative candidate genes pooled from major QTLs for each grain trait have interesting annotated functions that require functional studies to elucidate their function in the control of grain size, shape, or weight in rice. Genome selection analysis proposed makers useful for downstream marker-assisted selection based on genetic merit of RILs.