bluuebunny/crossref_metadata_2025_split huggingface dataset:
Roles ofspoVFoperon subunits A and B in regulating cell morphology and biofilm formation in the biocontrol agentBacillus subtilis
Authors: Yang Yang , Zhou Yu-Xin , Jia Le-Yao , Song Xin-Yang , Lai Ya-Jie , Wang Su-Yan , Laborda Pedro , Shi Xin-Chi 
Published: January 2025

ABSTRACTEnhanced expression ofspoVFoperon (sporulation initiation factor; dipicolinic acid (DPA) synthase) inBacillus subtilisvegetative cells has been reported to increase host attachment and biocontrol ability. However, how thespoVFoperon regulates these essential biocontrol factors remains unknown. In this study, it was found that the knockout of thespoVFAorspoVFBsubunits, individually (ΔA andΔB), or together (ΔAΔB), decreased DPA biosynthesis, host attachment, nutrient competition ability, and biocontrol efficacy inB. subtilis. Moreover, the cell shape of the knockout strains changed from short rod to spherical. qRT-PCR analysis indicated that thespoVFoperon regulates TCA cycle expression and biofilm formation by balancing the amounts of various transcriptional factors, such as spo0A, SinR, and AbrB, and the cofactor NADPH. The regulatory mechanism of thespoVFoperon inB. subtilisbiofilm-related genes was proposed for the first time.IMPORTANCEBacillus subtilis SpoVFoperon contains thespoVFAorspoVFBsubunits, which are responsible for the dipicolinic acid synthase activity. Dipicolinic acid is an important component ofB. subtilisspores. In this study, the roles ofspoVFAorspoVFBsubunits in the biocontrol abilityB. subtiliswere examined, indicating that thespoVFAsubunit plays a key role inB. subtilisbiofilm formation, cell morphology, growth, and nutrient competition ability. Additionally, the regulatory network connecting thespoVFoperon with biofilm formation-related genes ofB. subtiliswas proposed. The results obtained in this study help to understand key genes involved in the biocontrol ability ofB. subtilis.
Changes in Muscle Activation and Joint Motion During Walking After Transtibial Amputation with Sensory Feedback from Spinal Cord Stimulation: A Case Study
Authors: Bose Rohit , Petersen Bailey A , Sarma Devapratim , Barra Beatrice , Nanivadekar Ameya C , Madonna Tyler J , Liu Monica F , Levy Isaiah , Helm Eric R , Miele Vincent J , Fisher Lee E , Weber Douglas J , Dalrymple Ashley N 
Published: January 2025

ABSTRACTBackgroundThe goal of this study was to examine the effects of spinal cord stimulation (SCS) on muscle activity during walking after lower-limb amputation. Amputation results in a loss of sensory feedback and alterations in gait biomechanics, including co-contractions of antagonist muscles about the knee and ankle, and reduced pelvic obliquity range-of-motion and pelvic drop. SCS can restore sensation in the missing limb, but its effects on muscle activation and gait biomechanics have not been studied in people with lower-limb amputation.MethodsThis case study included a participant with transtibial amputation who was implanted percutaneously with SCS electrodes over the lumbosacral enlargement for 84 days. SCS was used during in-lab experiments to provide somatosensory feedback from the missing limb, relaying a sense of plantar pressure when the prosthesis was in the stance phase of the gait cycle. We used electromyography (EMG) to record muscle activity from the residual and intact limbs, and 3D motion capture to measure pelvic obliquity. EMG signals were recorded during walking with and without SCS at early and late time points across the implant duration.ResultsDuring walking, co-contraction of knee antagonist muscles was reduced following multiple sessions of SCS-mediated sensory restoration. Additionally, the activation of the hip abductor (tensor fasciae latae) muscle increased activity during gait with SCS-mediated sensory restoration, which corresponded to an increase in pelvic obliquity range-of-motion and pelvic drop, towards normal.ConclusionsRestoring sensation in the missing limb using SCS modulated muscle activity during walking leading to improved coordination and pelvic motion in an individual with lower-limb amputation.
PREVALENCE OF HCV AMONG HOUSEHOLD MEMBERS OF HEPATITIS C VIRUS-INFECTED PATIENTS ATTENDING CENTRE UNIVERSITAIRE DE SANTE PUBLIQUE (CUSP) HEALTH CENTER
Authors: Nemeyimana Patrick , Fabrice Uwumuremyi , anselme Ruhumuriza , Pierre Bakunzibake , Mugisha Emmy , Karenzi Valens , Shema Eliah , Kiiza Pascal 
Published: January 2025

ABSTRACTGlobally, hepatitis C is included in the public health concern. More than 1.4 million deaths are reported. In 170 million who are infected with HCV worldwide,71 million have serious complications. There is a close relationship between hepatitis C infections among family members with one case. Family member’s behaviors and exposure to positive family members without precautions are among the risk factor of getting hepatitis C infection. In Rwanda, the burden of Hepatitis C infections reaches to 4% of infected people. High prevalence of hepatitis C infection can be associated with horizontal transmission among household of positive patients for HCV. In Rwanda no data showing the contribution of horizontal transmission of HCV among household members as one of the risk factors to increase the prevalence of HCV.The objective of this study was to determine the prevalence of HCV among the household members living with HCV positive individual, specifically attending centre universitaire de santé public of BUTARE.The study used a descriptive cross-sectional design to assess the prevalence among 30 families having had positive cases for HCV with 180 sample size. With use of questionnires, HCV risk factors were assessed from our participants and from their responses. Purposive sampling was done for HCV rapid test and positive cases sample were confirmed at university teaching hospital of BUTARE with Elisa.From participants tested, 10.8% were tested positive for HCV counting for the prevalence of our study. Our findings are in line with other same studies conducted in Egypt and Iran revealed that there was 14.1%, which is a bit closer to our finding. we have found that unprotected sex with parnters and marital status between infected cases has a big influence to the high prevelence.Based on the findings from our study, 10.8% of our participants tested positive for HCV due to limited education, awareness, and exposure to contributing risk factors about HCV transmission.
Systematic Prioritisation of AI-Detected Chest X-ray Abnormalities for Optimised Lung Cancer Detection
Authors: Bramley Rhidian , Sharman Anna , Duerden Rebecca , Lyon Sarah , Ryan Melissa , Weber Elodie , Brown Louise , Evison Matthew 
Published: January 2025

AbstractObjectiveThis study aimed to establish a reproducible method for selecting AI-detected chest X-ray (CXR) abnormalities prioritised for urgent reporting to support faster lung cancer diagnosis. By selecting findings informed by cancer prevalence and clinical significance, we sought to maximise detection while maintaining a high negative predictive value (NPV).Materials and MethodsTwo cohorts of CXRs were evaluated: (1) a retrospective cohort of patients with confirmed lung cancer and abnormal CXRs, and (2) a prospective cohort of primary care referred CXRs from seven Greater Manchester trusts, with the AI system in shadow mode. The AI triage system (Annalise Enterprise CXR) evaluated the relative prevalence of 124 abnormalities, and prioritisation strategies were assessed using sensitivity, specificity, positive predictive value (PPV), and NPV.ResultsA total of 1,282 lung cancer patients were included in cohort 1. In cohort 2, the AI system processed 13,802 CXRs. Sensitivity was 95.87% (94.77%-96.97%) in cohort 1, and specificity was 79.11% (78.43%-79.79%) in cohort 2, with an NPV of 99.95%.ConclusionThis study presents a systematic, reproducible method for prioritising AI-detected CXR abnormalities, balancing high sensitivity and NPV while minimising low-risk prioritisation. This approach provides a data-driven alternative to traditional methods relying solely on clinical judgement.
Association between LVEF-1 and Coronary Artery Stenosis and Interventional Treatment Efficacy
Authors: Tang Chao , Yan Bin , Xiong Li , Zhu Yanyu , Ren Jiaxing , Li Xiang , Gu Xiaosong 
Published: January 2025

AbstractBackgroundMyocardial ischemia leads to a decrease in the speed and intensity of myocardial tissue contraction. In the early stages, this cardiac dysfunction is difficult to be detected by conventional echocardiography methods.ObjectiveFirst-phase left ventricular ejection fraction (LVEF-1) serves as a sensitive indicator for evaluating myocardial contractility. The aim of this study was to assess the decreased cardiac function caused by myocardial ischemia and its improvement following interventional treatment, as measured by LVEF-1.Methods207 patients were enrolled. Based on the results of the angiography, they were categorized into three groups: mild, moderate, and severe. The LVEF-1, Gensini score and other clinical data were compared among these groups. Furthermore, logistic regression analysis was used to analyze the relationship between LVEF-1 and coronary artery stenosis, as well as factors associated with improvement in LVEF-1 following interventional treatment using linear regression.ResultsThe LVEF-1 of patients in the 3 groups were 29.6 (28.2, 31.7) %, 27.8 (27.0, 28.6) %, and 25.2 (23.6, 26.5) % (p<0.001). There was a negative relationship between LVEF-1 and the Gensini score (r=-0.694, p<0.001), as well as between LVEF-1 and BNP (r=-0.244, p<0.001). LVEF-1 was identified as an independent predictor for coronary artery stenosis ≥50% or ≥70%. A cutoff value of 26.9% for LVEF-1 had a sensitivity of 89.5% and specificity of 83.9% for predicting the coronary artery stenosis ≥70%. Following intervention, LVEF-1 increased from 24.70 (23.30, 26.32) % to 28.10 (26.80, 29.92) % in 82 patients. Stent diameter was identified as an independent factor influencing the improvement in LVEF-1 post-intervention.ConclusionsLVEF-1 is negatively correlated with the severity of coronary artery stenosis, and it increases after receiving coronary artery intervention therapy, suggesting that LVEF-1 can serve as a new indicator to evaluate the severity of coronary artery stenosis and the efficacy of interventional treatment.
Applicability of a short form of the Speech, Spatial and Qualities of Hearing Scale in 97 individuals with Menière’s disease in a multicenter registry
Authors: Spiegel Jennifer L. , Lehnert Bernhard , Schuller Laura , Adler Irina , Rader Tobias , Brzoska Tina , Weiss Bernhard G. , Canis Martin , Busch Chia-Jung , Ihler Friedrich 
Published: January 2025

AbstractBACKGROUNDMenière’s Disease (MD) is a debilitating disorder with episodic and variable ear symptoms. Diagnosis can be challenging and evidence for a psychometric instrument to assess subjective impairment of hearing and the associated burden in daily life is currently lacking.OBJECTIVETo evaluate a short form of the Speech, Spatial and Qualities of Hearing Scale (SSQ) for hearing-related disability in MD.METHODSData was collected from a multicenter prospective patient registry for long-term follow up of MD patients. Hearing was assessed by pure tone and speech audiometry. The SSQ was applied in a version with 17 items.RESULTS97 consecutive patients with unilateral MD had a mean age of 56.2 ± 5.0 years. 55 individuals (57.3%) were female, 72 (75.0%) were categorized as definite MD. Average total score of the SSQ was 6.0 ± 2.1. Cronbach’s alpha for internal consistency was 0.960 for the total score. We did not observe undue floor or ceiling effects. SSQ values showed a negative correlation with hearing thresholds and a positive correlation with speech recognition scores.CONCLUSIONSThe short form of the SSQ provides insight into hearing-specific disability in patients with MD. Thereby, it may be informative regarding disease stage and rehabilitation needs.
Investigating the genetic relationship between vitamin B12 deficiency and Parkinson’s disease
Authors: Dering Raphael , Onvumere Margarita , Liu Lang , Huot Philippe , Gan-Or Ziv , Senkevich Konstantin 
Published: January 2025

AbstractIntroductionEpidemiological studies suggest that patients with Parkinson’s disease (PD) may have lower levels of vitamin B12 compared to healthy controls, and it was proposed that PD patients could benefit from vitamin B12 supplementation. Functional studies have shown that B12 could modify LRRK2 activity and may directly interact with alpha-synuclein. This study aimed to investigate the role of common and rare variants in genes related to B12 metabolism and assess the potential causal relationships between B12 levels and PD risk, age-at-onset, and motor/cognitive progression.MethodsWe investigated the association between common and rare variants in genes involved in vitamin B12 metabolism. Rare variants (minor allele frequency < 0.01) were analyzed using the optimal sequence kernel association test (SKAT-O) in 4,815 PD patients and 65,607 controls from two independent cohorts. We constructed pathway-specific polygenic risk scores (PRS) for genes essential to B12 metabolism and for genes identified in previous genome-wide association studies (GWAS) on B12 metabolism. Mendelian randomization and genetic correlation analyses were applied to explore the relationship between vitamin B12 levels and PD risk, age-at-onset, and disease progression.ResultsOur analysis showed no associations between common variants of genes crucial in B12 metabolism and PD. Pathway PRS identified nominal association between B12-related genes and PD (OR = 1.061, 95% CI: 1.004–1.121, p = 0.038), which did not survive Bonferroni correction. In the rare variants analysis, we identified a significant association between variants with high CADD scores in theCUBNgene (P=6.07E-05; Pfdr=0.005) in the AMP-PD cohort, driven by the benign variant p.G3114S (OR=3.3; p=3.56E-05); however, this was not validated in the meta-analysis. We did not identify a potentially causal relationship between vitamin B12 levels and the risk, age-at-onset, or progression of PD. Additionally, no genetic correlation was observed between vitamin B12 and PD risk or age-at-onset GWASs.ConclusionOverall, our analyses indicate lack of genetic link between B12 levels or metabolism and PD.
LUKB DT: A Web Tool for Quick and Efficient Identification of Disease Trajectories
Authors: Li Xiangnan , Zhang Hui , Jiang Shuai , Gao Baocai , Hu Zixin 
Published: January 2025

AbstractAs the volume of electronic medical data grows, understanding disease progression and identifying risk factors have become central to public health research. Disease trajectories provide valuable insights into disease progression and risk factors. LUKB DT (LUKB Disease Trajectories) is a user-friendly web tool designed to facilitate disease trajectory analysis using electronic medical records (EMR), particularly the UK Biobank data. LUKB DT processes EMR data, including patient ID, disease diagnoses, corresponding timestamps, and other relevant variables, combining Cox regression, binomial tests, and conditional logistic regression to identify disease trajectories. This tool offers a quick and efficient way to prepare and analyze disease trajectories, contributing to the expanding field of disease trajectory research and providing valuable insights for risk factor identification and disease progression studies. Detailed deployment and usage can be found in the Supplementary Material.LUKB DT is freely available athttps://github.com/HaiGenBuShang/LUKB.
Approaches for measuring socioeconomic status in health studies in Sub-Saharan Africa: a scoping review
Authors: Yopa Daniele Sandra , Kiki Gbetogo Maxime , Ngangue Patrice , Ngoufack Marie Nicole , Lekelem Dongmo Gilles Protais , Mbang Massom Douglas , Amvella Priscillia Anya , Bongwong Tamfon Brian , Chichom-Mefire Alain , Juillard Catherine , Hubbard Alan , Nguefack-Tsague Georges 
Published: January 2025

AbstractBackgroundSocioeconomic status (SES) is essential for determining a person or community’s position about certain social and economic characteristics. This is particularly important in sub-Saharan Africa, where health disparities are pronounced. We conducted a scoping review to explore approaches used in health studies to measure socio-economic status in the sub-Saharan region.MethodsA comprehensive literature search covering January 2012 to June 2024 was conducted in five databases: PubMed, EMBASE, CIHNAL, Web of Science, and African Index Medicus. All studies in sub-Saharan Africa focused on health-related socioeconomic status were included, regardless of study methodology. Three peer reviewers independently evaluated the selected articles according to inclusion and exclusion criteria. Discrepancies between reviewers were resolved through a consensus meeting. The review protocol was registered on the Open Science Framework (OSF,OSF.IO/7NGX3).ResultsThe initial search yielded 19,669 articles. At the end of the screening process, 65 articles were analysed. Cross-sectional studies have been widely used. South Africa (13.4%) and Kenya (11%) were the most represented countries. Maternal, neonatal, and infant/juvenile health was the most covered theme (31%). The review identified 12 categories of SES measurement methods, with the asset-based wealth index being the most widespread (61.9%). Principal component analysis (PCA) is the primary analytical method used to calculate this index (57.7%).ConclusionsThis scoping review identified the asset-based wealth index as the most frequently used and provided essential elements for pooling different SES calculation methodologies to reach a consensus. Using SES to improve interventions is important to limit African health disparities.
PERFORMANCE OF FOUR NEWLY RELEASED CASSAVA VARIETIES IN A FALLOWED LAND OVER TWO FARMING SEASONS
Authors: Ossai C. O. , Ojobor S. A. , Ogwuche T. O. , Akpeji S. C. , Alama I. S. , Diebiru-Ojo E. M. 
Published: January 2025

ABSTRACTCassava (Manihot esculentaCrantz) is an important crop for humans due to its staple and industrial values. Currently the demand is more than the supply as the current output falls below the expected. This necessitated the breeding of superior genotypes that are high yielding. These superior genotypes also requires a fertile soil for optimum production. However, this has been primarily achieved through the application of inorganic manures. It is then important to evaluate four newly released cassava varieties in an organically enriched soil relative to the local best variety. Four newly released cassava varieties, Hope, Obasanjo2, Baba 70, and Game changer, and one Local Best (LB) was planted in 5-years fallowed farm lands at three plots (A, B and C) for 2 seasons. It was a three-way factorial (5-varieties*3-farms*2-seasons) arranged in a randomized complete block design and replicated three times. Data were taken on the Fresh Tuber Weight (FTW) and Stem Height (SH) per variety, and pre and post soil status. Data were analyzed using analysis of variance, while differences in varietal means were separated using least significant differences at 5% level of significance. The FTW and SH differed significantly across varieties, years and interaction between variety, farms and year, and ranged from 19.2±0.5 (LB) to 41.0±0.5 (Obasanjo2), 32.1±0.4 (farm C) to 34.1±0.4 (farm A), 30.4±0.3 (year two) to 35.0±0.3 (year one), and the interactions between variety and year, farms and year, and variety, year and farms were significant. The soil macro and micro elements declined in the post relative to the pre status. The yield obtained from the improved varieties almost doubled the local best and yield declined in the second season.
A Multidisciplinary Theoretical Framework for Enhancing Scientific Writing: A Validated Model for Supporting Young Researchers
Authors: Köpeczi-Bócz Tamás 
Published: January 2025

AbstractThis study investigates multidisciplinary innovation in the teaching of scientific writing, focusing on the development of a theoretical framework and its experimental validation. The framework integrates logical thinking, creativity, and adaptability to enhance scientific writing skills and communication competencies. The experiment involved a four-semester university program guiding students from creative writing to complex scientific article production within diverse multidisciplinary contexts. The proposed methodology is also applicable in research institutions, corporate training programs, and other roles requiring proficiency in multidisciplinary scientific writing.The findings demonstrate that the framework significantly improved students’ reasoning, structured thinking, and innovation capabilities, enabling them to present novel ideas effectively in academic settings. A key outcome of the program was the advancement of metacognitive awareness, supported by AI tools, allowing students to critically evaluate and refine their work. Additionally, the study highlighted the role of AI in enhancing the structural and stylistic quality of scientific writing while addressing ethical considerations.The sequential design of the methodology and the multidisciplinary environment fostered knowledge exchange among students from various disciplines, preserving the unique attributes of each field. The five-step analysis framework, used to compare the outcomes of experimental and control groups, revealed statistically significant advantages for students participating in the methodological program. This research underscores the importance of multidisciplinary approaches for advancing 21st-century scientific literacy and emphasizes the global adaptability of such innovative programs.
High-quality genome assemblies of 152 root commensal bacteria from the model legumeLotus japonicus
Authors: Gómez-Repollés Adrián , Villa-Rodriguez Eber , Ferguson Shaun , Radutoiu Simona 
Published: January 2025

AbstractBacterial culture collections represent a valuable tool for mechanistic understanding of microbiome assemblies and are increasingly used to assemble tailored synthetic communities to characterize their microbe-microbe interactions and those with the environment. Given the size of these collections, short-read sequencing is primarily used to capture the encoded genetic information. Whilst sufficient for many microbiome studies, this approach is not amenable for understanding bacterial genome evolution or detailed genetic analyses at the entire genome level. Here we report the assembly of 152 full bacterial genomes from theLj-SPHERE, theLotus japonicuscollection of root commensals. We performed long-read sequencing using Oxford Nanopore technology and used this together with pre-existing Illumina sequences tode novoassemble these into high quality genomes with improved contiguity and quality. These genomes now provide a solid platform for detailed, mechanistic understanding of microbiome assembly, dynamics and evolution in plants.