bluuebunny/crossref_metadata_2025_split huggingface dataset:
A workflow for clinical profiling of BRCA genes in Chilean breast cancer patients via targeted sequencing
Authors: González Evelin , Salinas Rodrigo Moreno , Muñoz Manuel , Herrera Soledad Lantadilla , Morales Mylene Cabrera , Jullian Pastor , Durrels Waleska Ebner , Stari Gonzalo Vigueras , Ramos Javier Anabalón , Miquel Juan Francisco , Jara Lilian , Moraga Carol , Genova Alex 
Published: October 2024

Abstract

Background: Breast cancer (BC) is the leading cause of cancer-related deaths among women globally and in Chile. Mutations in the tumor-suppressor genes BRCA1 and BRCA2 significantly increase the risk of developing cancer, with the probability rising by more than 50%. Identifying pathogenic variants in BRCA1 and BRCA2 is crucial for both diagnosis and treatment. Targeted panels, which focus on medically relevant subsets of genes, have become essential tools in precision oncology. Beyond technical and human resource factors, standardized bioinformatics workflows are essential for the accurate interpretation of results. We developed a robust bioinformatics pipeline, implemented with Nextflow, to process sequencing data from targeted panels to identify germline variants.
Results: We developed an automated and reproducible pipeline using Nextflow for the targeted sequencing of BRCA1/2genes. The pipeline incorporates two variant callers, Strelka and DeepVariant, both of which have demonstrated high performance in detecting germline SNVs and indels. The runtime is efficient, with a median execution time of less than 3 minutes per task. We sequenced and processed 16 samples from breast cancer patients. In our analysis, we identified 8 nonsynonymous mutations in BRCA1 and 9 in BRCA2. Of the total reported germline mutations, 97% were classified as benign, 1% as pathogenic, 1% as of uncertain significance, and 1% as unknown. The allelic frequencies observed in our cohort closely resemble those of Admixed American and South Asian populations, with the greatest divergence observed in comparison to African individuals.
Conclusion: We successfully analyzed the BRCA1and BRCA2 genes in 16 breast cancer patients at a public hospital in Chile. A custom Nextflow pipeline was developed to process the sequencing data and evaluate the pathological significance of the identified genetic variants. By employing multiple variant-calling methodologies, we were able to detect and mitigate potential false positives, thereby enhancing the accuracy and reliability of variant detection through cross-verification. A pathogenic variant was identified in one patient, while benign or likely benign variants were found in the remaining 15. Expanding the number of oncogenes sequenced per patient could improve the detection of actionable variants.
Exploring CO 2 -laser drilling: Potential for Enhanced Mass and Thermal Diffusion in Banana (Musa sapientum) Dehydration
Authors: Silva-Vera Wladimir Enrique , Begoña Giménez , Tian Xiaojing , Romina Abarca O. , Sergio Almonacid A. , Gabriela Sandoval-Hevia. , Ricardo Simpson R. 
Published: October 2024

Abstract

This study addresses the efficacy of CO2-laser drilling as a pre-treatment method to enhance water diffusion in banana slices during air drying, aiming to mitigate the energy and time consumption associated with traditional hot air drying in the food industry. Drilling with CO2-laser resulted in a higher rate of water diffusion, inferred from the higher values in the effective diffusivity coefficient in drilled samples (up to 1.7-fold), attributable to the increased surface area to volume ratio and energy absorption. Consequently, there was a significant reduction in dehydration time, up to 40% (from 169 min in control samples to 102 min in drilled samples). After dehydration process, banana slices drilled at the largest focal distance showed an increased stiffness according to the higher effective Young's modulus and maximum force observed attributable. Therefore, combining CO2-laser drilling with air-drying will represent a promising strategy for reducing dehydration times in the food industry, providing a potential solution for food dehydration.
Gut microbiome community dynamics in captive juvenile chum salmon: the influences of development, diet, and seawater transition
Authors: Ghosh Subrata Kumar , Wong Marty Kwok-Shing , Hyodo Susumu , Hamasaki Koji 
Published: October 2024

Abstract

Background The development of host-associated microbiota evolves from birth to adulthood, with distinct microbial signatures influencing host biological processes. This study aims to analyze how bacterial communities in the digestive tracts of chum salmon are structured during the first 90 days post-hatching (DPH), encompassing the embryonic stage, feeding, and the transition from freshwater to seawater under controlled conditions. Results Gut microbiota was analyzed using high-throughput 16S rRNA gene amplicon sequencing. Our results indicated that bacterial communities were highly dynamic, with significant shifts occurring after feeding began (35 DPH), as diet heavily influenced gut microbiota stability. Upon transferring to seawater, dominant taxa shifted to include Aliivibrio, Colwellia, Bartonella, and Enterococcus, signifying the establishment of a marine microbial population. Core taxa, including Bartonella, Enterococcus, and Acinetobacter, were consistent across almost all fish samples regardless of the freshwater or seawater environment, suggesting these microbes may perform essential functions for the host. Notably, seawater taxa appeared in the gut as fish adapted to the hyperosmotic environment, yet the proportion of diet- and water-derived bacteria declined over time. Conclusions These findings indicate a strong host selection process in community assembly, highlighting the importance of active interactions in shaping gut microbiota, alongside passive environmental uptake. This study provides critical insights into the stability of the gut microbial community during the early development of chum salmon, with implications for aquaculture practices, particularly in hatchery programs, and the potential modification of gut microbiota through probiotics.
Relevance of the oxidative balance score and red cell distribution width/albumin ratio in diabetic retinopathy: A mediation analysis in the NHANES
Authors: Zeng Yining , Zhang Jingqi , Wu Hao , Kang Xinzi , Xiang Junjie , Liu Aonan , Shen Tao , Zhang Tao , Duan Junguo 
Published: October 2024

Abstract

Background: As a comprehensive indicator of the body's overall oxidative stress status, the oxidative balance score (OBS) can reflect the body's antioxidant capacity and is associated with a myriad of diabetes-related complications. The red cell distribution width/albumin ratio (RAR) is recognized as a novel indicator of diabetes-related complications. At present, no studies have yet revealed the relationships among OBS, RAR and diabetic retinopathy (DR). We aimed to elucidate the relationship between OBS and DR risk, and the mediating function of RAR between them.
Methods: A total of 1,961 subjects from the 2005 to 2018 National Health and Nutrition Examination Survey (NHANES) were included in this cross-sectional study. Weighted adjusted multivariate regression analyses were used to evaluate the association between OBS and DR risk. Weighted restricted cubic splines (RCS), mediation analysis and subgroup analysis were used to further elucidate these associations.
Results: According to the multivariate logistic regression model, a significant negative association was found between OBS and DR risk after adjusting for all covariates (OR = 0.96, 95% CI: 0.94-0.99; P=0.007). When OBS were transformed into quartiles, participants in OBS quartile 4 (OR 0.42; 95% CI 0.22-0.80, P=0.009) presented a significantly lower risk of DR than did those in OBS quartile 2 and OBS quartile 3. The RCS results further revealed a nonlinear association between OBS and DR, after adjusting for all covariates (P for nonlinearity <0.01). The results of the subgroup analysis revealed that the association between OBS and DR remained stable over most subgroups (p for interaction >0.05), except for smoking status (p for interaction = 0.017).
Conclusion: OBS is negatively associated with DR. There is a nonlinear relationship between OBS and DR, which may be mediated partly by RAR.
RETRACTED: A Comparison Between the Bowel Ultrasound Score and International Bowel Ultrasound Segmental Activity Score Based on Ileocolonoscopy in Patients with Crohn’s Disease
Authors: Yuksel Ilhami , Cagir Yavuz , Durak Muhammed Bahaddin , Atay Ali , Ergul Mucahit , Ozturk Oguz , Keskin Emir Tugrul , Fedai Ahmet Burak , Ince Muhammed Mustafa , Deniz Erdogan , Kilic Zeki Mesut Yalin 
Published: October 2024

Abstract

The authors have requested that this preprint be removed from Research Square.
High prevalence of hepatitis B virus in TB patients in Kwara State, Nigeria: a call for informed management
Authors: Ilochi Ifeanyichukwu , Awolere Ezekiel , Akanbi Olusola Anuoluwapo , Opaleye Oluyinka Oladele 
Published: October 2024

Abstract

Background: Tuberculosis (TB) and chronic hepatitis B virus (HBV) infections are major global health problems, while there currently limited data on HBV infection among TB patients. This study was conducted to determine the prevalence of HBV in tuberculosis patients and evaluate the effect of anti-tuberculosis drugs and HBV infection on the liver.
Methods: Two hundred and fifty-eight samples were collected from TB-positive patients attending selected TB clinics in Kwara State, and 227 patients were followed-up. Participants were assessed at start and after 6 months. Sero-markers for HBV infection was detected using Micropoint 5-panel kit, and liver enzymes were evaluated using Randox Kit following manufacturer’s instructions. Data analysis was done using SPSS Version 22.0.
Results: Of the 258 patients recruited, 227 were followed-up, and 24 (10.5%) had detectable HBsAg/HBeAb/HBcAb or HBsAg. A comparison of initial liver enzymes and at 6months showed significant difference (p≤0.00), and no associations were observed between educational background (X2= 0.425, p=0.547), sex (X2 =0.212, p=0.616) or HBV/TB coinfection. High-risk factors included the use of illicit drugs (OR 95% CI; 2.3, 0.9-5.0), having multiple sexual partners (OR 95% CI; 4.1, 0.9-3.8), having a history of STIs (OR 95% CI; 1.6, 0.7-3.7), and consuming alcohol (OR 95% CI; 1.5, 0.4-4.8).
Conclusion: In this study we found 10.5% prevalence of HBV/TB coinfection which may have led to elevated liver enzymes (ALT and AST), while total bilirubin was only affected when it has progressed to liver failure and cirrhosis. Routine HBV screening is recommended before treatment in TB patients.
Prognostic and Immunological Analysis of Disulfidoptosis-Related Ferroptosis Genes in Lung Adenocarcinoma
Authors: Liu Zichen , Yan Rongdi , Luo Yingxv , Zhang Xin , Zheng Xin 
Published: October 2024

Abstract

Disulfidoptosis, a newly identified form of regulated cell death (RCD), significantly influences the progression of lung adenocarcinoma (LUAD). This study identified 340 ferroptosis-related genes strongly correlated with disulfidoptosis through correlation analysis. By intersecting these genes with those from module genes selected via weighted gene co-expression network analysis (WGCNA), 31 genes were found. In the TCGA-LUAD cohort, Kaplan-Meier(KM) survival analysis initially screened these genes, leading to the selection of 6 Disulfidoptosis-Related Ferroptosis (DRF) genes (IL33, SLC2A1, CDCA3, KIF20A, FANCD2, RRM2) through further screening with Random Forest and SVM-RFE. Based on the expression levels of DRF genes, two distinct groups with differing prognostic and immune characteristics were identified. A machine learning-driven signature (MLS) of 24 DRF-related genes was then constructed using the RSF + SuperPC algorithm and validated in the TCGA-LUAD and GSE31210 datasets. Compared with 77 other signatures, MLS demonstrated superior performance in both datasets. A low MLS score was associated with immune activation, higher tumor mutation burden, and better survival probability. Conversely, a high MLS score correlated with poorer prognosis and reduced potential benefit from immune therapy, although treatments like Doramapimod might still offer benefits. The cell cycle pathway was a key factor distinguishing high from low MLS groups. Overall, MLS shows promise for predicting prognosis in LUAD patients and identifying those who might benefit from immune therapy. Additionally, DRF genes have potential clinical value for diagnosing and treating other cancers, as indicated by pan-cancer analysis. q-PCR experiments targeting select DRF genes confirmed their feasibility as diagnostic markers for LUAD.
Prevalence and Psychosocial Factors Influencing Substance Use Among Students of Abia State Polytechnic: Implication for Policy Makers
Authors: Nwaoru Chiamaka R. , Iloma David O. , Programme Abuja. Charles C. Uwazie Nigeria Field Epidemiology and Labo , Ijere Ignatius N 
Published: October 2024

Abstract

The issue of drug use has escalated into a critical global concern, demanding immediate attention from researchers, policymakers, and stakeholders. The widespread misuse of drugs among students is becoming increasingly problematic and a health concern in many countries, including Nigeria. This study's objective is to assess the prevalence and psychosocial factors responsible for substance use among undergraduate students of Abia State Polytechnic. The findings of this study have significant implications for the broader public health and education systems, as they highlight the urgent need for intervention programs to address the high prevalence of drug use among students.
Method: The study adopted a snowball sampling design to recruit four hundred and seventy-two (472) students from the five (5) schools that comprise all the Abia State Polytechnic Departments. A study-developed questionnaire called Substance Use and Psychosocial Factors Checklist (SUPSF) was adopted from DUDIT and AUDIT and validated. Three hypotheses were advanced, and data was analyzed via IBM SPSS-23.
Results: Descriptive results showed a high prevalence of psychoactive substance use among undergraduate students, with the highest substance being Marijuana, with a prevalence of 71.61%. Multi-linear regression revealed that psychosocial factors significantly predicted the criterion variable (β= -.66; t = -19.02; p<0.05). Also, among the demographic variables, age was the best predictor of psychoactive substance use, with 17.1% out of the 19.6% combined variance, F(1,471) = 97.03, p<0.05.
Conclusion: In line with the findings, we concluded that the school's management should, as a matter of urgency, introduce drug test programs. These programs can help identify students at risk of substance use early, allowing for timely intervention. We stress the need for the establishment of a functional counseling unit and course advisers to address possible psychosocial factors that may pressure a student into using psychoactive substances. The need for these intervention programs is crucial, and their successful implementation could significantly reduce the high prevalence of drug use among students, offering hope for a healthier future.
Navigating Power Dynamics in Acute Care: Enhancing Nursing Autonomy and Implementing Evidence-Based Practice Through Interprofessional Collaboration
Authors: Ominyi Jude , Beryl Nwedu Aaron , Agom David A 
Published: October 2024

Abstract

Aim: This study explores the impact of power dynamics between nurses and physicians in acute care settings, focusing on how these dynamics influence nursing autonomy and the implementation of Evidence-Based Practices (EBPs). It aims to identify strategies that promote interprofessional collaboration, enhance nurse leadership, and support shared decision-making to improve patient outcomes.
Design: An exploratory qualitative methodological approach grounded in the philosophy of social constructivism was utilised in this study.
Methods: Data were collected through non-participant observations, semi-structured interviews, and document analysis across two large NHS acute care hospitals in the Midlands. Thematic analysis, following Braun and Clarke’s framework, was used to identify key themes related to hierarchical barriers, nursing autonomy, and interprofessional collaboration. The participants included 37 staff nurses, ward managers, nurse managers, and physicians.
Findings: The study revealed that hierarchical power imbalances, particularly medical dominance, significantly limit nursing autonomy and hinder EBP implementation. Nurses reported limited decision-making authority and were often excluded from critical care discussions. However, interprofessional collaboration, leadership development, and shared governance models were identified as effective strategies to reduce these power imbalances. Nurses who engaged in leadership training and participated in nurse-led initiatives experienced increased autonomy and reported improved patient care outcomes.
Conclusion: Power imbalances hinder the implementation of EBPs by nurses in acute care settings. Enhancing nursing leadership, promoting interprofessional collaboration, and adopting shared governance models can empower nurses, improve autonomy, and enhance patient outcomes.
Impact: The findings highlight the importance for healthcare organisations to invest in nursing leadership development, implement collaborative governance models, and foster interprofessional teamwork to support EBP implementation and improve patient care quality.
Reporting Method: The study adheres to the Consolidated Criteria for Reporting Qualitative Research (COREQ) guidelines.
Patient/Public Contributions: Patients and the public were not directly involved in this study. However, the study’s focus on nurse-led initiatives has significant implications for improving patient care quality.
The impact of fused deposition modeling nozzle types on the structure of 3D printed fibers
Authors: Diak Viktorija , Diak Andrii 
Published: October 2024

Abstract

When engaging in polymer printing, the structure and quality of 3D printed samples are contingent upon numerous adjustable parameters. The focus of this paper is to examine the disparities in the capabilities of 3D printer head nozzles employing fused deposition modeling (FDM) technology, while also considering the influence of software/technical methods that regulate filament extrusion. The study in question delves into the intricacies of how the structure/material of said nozzles (including composite variations) impact their performance, ability to print abrasive materials, and danger of clogging. The primary objective of this research endeavor is to attain the thinnest possible thickness of the printed fiber for each respective material (PLA and TPU-CF). Additionally, the shape of cross-section, uniformity of the fiber, distance to the print bed, and instances of breakage are taken into account. It is worth noting that the refinement of the fiber structure frequently correlates with the temperature range during filament extrusion, thereby affecting its flowability. It has also been substantiated that there are techniques that effectively assist in achieving finer structures that are unobtainable through standard printing methods. The acquired results are classified to facilitate the understanding of the connections between different nozzle types and printing parameters, while also highlighting their optimal performance regarding fine detail and quality. In essence, the findings have reassured that the adjustment and balance of the entire system in attaining the established objectives wield a significantly greater influence than individual components.
Pemanfaatan Teknologi dalam Pembelajaran di PAUD Kelompok Usia 2-3 Tahun di Labschool UNNES
Authors: Choirunnisa Silvya , Muyasaroh Ulya , Farda Aniqotul , Hartati Yuni Setya , Umiyati Umiyati 
Published: October 2024

Pendidikan hingga kini masih dipercaya sebagai media yang sangat ampuh dalam membangun kecerdasan sekaligus keperibadian anak manusia menjadi lebih baik. Pemanfaatan Teknologi dalam Pembelajaran di PAUD ini menjadi sarana dalam meningkatkan stimulasi perkembangan anak secara optimal. Tujuan penelitian ini untuk mendapatkan informasi mengenai pemanfaatan teknologi dalam pembelajaran di PAUD kelompom usia 2-3 tahun. Metode penelitian pendekatan kualitataif, jenis penelitian ini adalah penelitian deskriptif. Berdasarkan hasil penelitian,seiring dengan perkembangan zaman dan teknologi, saat ini banyak aplikasi-aplikasi yang bisa digunakan dalam proses belajar mengajar anak usia dini. Seperti canva, PPT, capcut dan lain lain bahkan ada beragam game edukasi menarik yang dapat guru gunakan pada saat proses belajarengajar.Aplikasi aplikasi tersebut sangat berguna apabila bisa dioperasikan dengan baik.
Chlorine dosage management in drinking water systems: comparing Bayesian optimization to evolutionary algorithms
Authors: Moeini Mohammadreza , Abokifa Ahmed 
Published: October 2024

ABSTRACT
To maintain a sufficient chlorine residual in water distribution systems (WDSs), chlorine dosage needs to be regulated. The majority of previous studies that aimed to optimize chlorine dosage in WDSs considered single-species water quality (WQ) models featuring chlorine decay with simple reaction kinetics. Recent efforts have proposed using multi-species water quality (MS-WQ) models to account for chlorine interactions with various chemical and microbiological species, thus providing a comprehensive and accurate evaluation of the WQ within WDSs. Nevertheless, the key challenge of implementing MS-WQ models within optimization frameworks is their high computational cost and poor scalability for larger WDSs. Furthermore, previous optimization studies generally relied on evolutionary algorithms (EAs), which require conducting a significant number of WQ simulations. Bayesian optimization (BO) has been recently suggested as an efficient alternative to EAs for the optimization of computationally expensive functions. This study aims to present a systematic comparison between BO and other widely used EAs for the optimization of MS-WQ in WDSs. A case study featuring a real-life, midsized benchmark WDS was implemented to comprehensively evaluate all three optimization techniques. The results revealed that BO is notably more computationally efficient and less sensitive to changes in the constraints than EAs.
Modeling phosphorus transport in soil columns amended with polyaluminum chloride and anionic polyacrylamide water treatment residuals: Implications for stormwater bioretention systems
Authors: Wang Li , Duan Runbin 
Published: October 2024

ABSTRACT

Understanding phosphorus transport in soil columns amended with polyaluminum chloride and anionic polyacrylamide water treatment residuals (PAC-APAM WTRs) is crucial for the effective recycling of PAC-APAM WTRs into traditional soil-based stormwater bioretention systems. Phosphorus transport in columns containing three distinct soil types amended with PAC-APAM WTRs under saturated steady-state flow conditions was effectively modeled using three different models: the convection-dispersion equation (CDE) model with linear isotherm, the CDE model with Langmuir isotherm, and the chemical non-equilibrium two-site model (TSM). In Soils 1 and 2, amended with PAC-APAM WTRs, the primary mechanism governing phosphorus transport transitioned from instantaneous adsorption to two-site adsorption as flow rate increased. In contrast, Soil 3 amended with PAC-APAM WTRs was predominantly governed by two-site adsorption throughout the experiments. An increase in flow rate reduced the solid–liquid distribution coefficient and the fraction of equilibrium adsorption sites, resulting in decreased phosphorus adsorption and increased phosphorus mobility. This study strongly recommends the selection of soil amended with PAC-APAM WTRs that exhibits higher instantaneous phosphorus adsorption. Additionally, this study emphasizes the importance of appropriately designing the depth of the ponding layer, utilizing the TSM model, and refining modeling techniques to optimize phosphorus retention and mitigate pollution risks in stormwater management.