bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carboplatin-resistance-related DNA damage repair prognostic gene signature and its association with immune infiltration in breast cancer
Authors: Dong Shuwen , Li Anqi , Pan Ruixin , Hong Jin , Wang Zheng , Shen Kunwei 
Published: January 2025

IntroductionBreast cancer is among the most prevalent malignant tumors globally, with carboplatin serving as a standard treatment option. However, resistance often compromises its efficacy. DNA damage repair (DDR) pathways are crucial in determining responses to treatment and are also associated with immune infiltration. This study aimed to identify the DDR genes involved in carboplatin resistance and to elucidate their effects on prognosis, immune infiltration, and drug sensitivity in breast cancer patients.MethodsA 3D-culture model resistant to carboplatin was constructed and sequenced. Co-expressed DDR genes were analyzed to develop a predictive model. Immune infiltration analysis tools were employed to assess the immune microenvironment of patients with varying expression levels of these risk genes. Additionally, drug sensitivity predictions were made to evaluate the efficacy of other DNA damage-related drugs across different risk groups. Molecular assays were performed to investigate the role of the key gene TONSL in breast cancer.ResultsBy integrating data from public database, we established a prognostic signature comprising thirteen DDR genes. Our analysis indicated that this model is associated with immune infiltration patterns in breast cancer patients, particularly concerning CD8+ T cells and NK cells. Additionally, it demonstrated a significant correlation with sensitivity to other DDR-related drugs, suggesting its potential as a biomarker for treatment efficacy. Compared to the control group, TONSL-knockdown cell lines exhibited a diminished response to DNA-damaging agents, marked by a notable increase in DNA damage levels and enhanced drug sensitivity. Furthermore, single-cell analysis revealed elevated TONSL expression in dendritic and epithelial cells, particularly in triple-negative breast cancers.ConclusionsCarboplatin resistance-related DDR genes are associated with prognosis, immune infiltration, and drug sensitivity in breast cancer patients. TONSL may serve as a potential therapeutic target for breast cancer, particularly in triple-negative breast cancer, indicating new treatment strategies for these patients.
Recalibrating the kidney failure risk equation for a Mediterranean European population: reducing age and sex inequality
Authors: Bundó-Luque Daniel , Cunillera-Puértolas Oriol , Cobo-Guerrero Sílvia , Romano José , Arbiol-Roca Ariadna , Domínguez-Alonso José Alberto , Cruzado Josep Maria , Salvador-González Betlem 
Published: January 2025

IntroductionChronic kidney disease (CKD) patients may develop kidney failure (KF), receiving renal replacement therapy (RRT) in some cases. The Kidney Failure Risk Equation (KFRE-4), predicting RRT risk, is widely validated but not in a primary care Mediterranean European population. We aim to recalibrate KFRE-4 accordingly, considering death as a competing risk, to improve performance. Additionally, we recalibrate KFRE-4 for predicting KF, including all patients reaching CKD stage 5, not just those on RRT.MethodsRetrospective cohort study including individuals aged ≥50 years with confirmed glomerular filtration rate (eGFR) &lt;60 mL/min/1.73m2 and measured albumin-to-creatinine ratio (ACR). Dataset was split into training and test sets. New KFRE-4 models were developed in the training set and performance was evaluated in the test set: Base hazard adapted-KFRE (Basic-RRT), Cox reestimation (Cox- RRT), Fine and Gray RRT reestimation (FG-RRT), and Fine and Gray KF reestimation (FG-KF).ResultsAmong 165,371 primary care patients (58.1% female; mean age 78.1 years; mean eGFR 47.3 mL/min/1.73m2, median ACR 10.1 mg/g), original KFRE-4 showed good discrimination but poor calibration, overestimating RRT risk. Basic-RRT showed poorer performance. Cox-RRT and FG-RRT, enhancing the influence of old age and female sex, diminished overprediction. FG-RRT, considering death as a competing risk, resulted the best RRT model. Age and sex had less impact on KF prediction.ConclusionA fully tailored recalibration model diminished RRT overprediction. Considering death as a competing event optimizes performance. Recalibrating for KF prediction offers a more inclusive approach in primary care, addressing the needs of women and elderly.
Development of a prognostic nomogram for ocular melanoma: a SEER population-based study (2000–2021)
Authors: Zheng Miyun , Xu Maodong , You Mengxing , Huang Zhiqing 
Published: January 2025

IntroductionOcular melanoma (OM) is a rare but lethal subtype of melanoma. This study develops a prognostic nomogram for OM using machine learning and internal validation techniques, aiming to improve prognosis prediction and clinical decision-making.MethodsIndependent prognostic variables were identified using univariate and multivariate COX proportional hazard regression models. Significant variables were then incorporated into the nomogram. The predictive accuracy of the nomogram was evaluated using receiver operating characteristic (ROC) curves, calibration plots, decision curve analysis (DCA), and 10-fold cross-validation. The performance of the nomogram was compared with that of a machine learning model.ResultsThirteen variables, including age, sex, tumor site, histologic subtype, stage, basal diameter size, tumor thickness, liver metastasis, first malignant primary indicator, marital status, and treatment modalities (surgery/radiotherapy/chemotherapy) were identified as independent prognostic factors for overall survival (OS) and were included in the nomogram (all P &lt; 0.05). The nomogram showed a concordance index of 0.712. The areas under the curve (AUC) for predicting 3-, 5-, and 10-year survival rates were 0.749, 0.734, and 0.730, respectively. Calibration plots for 3-, 5-, and 10-year survival were in close agreement with the ideal predictions, and DCA indicated a superior net benefit. The average AUC from 10-fold cross-validation was 0.725. The machine-learning model identified liver metastasis as the most significant predictor of survival, followed by age, radiotherapy, stage, and other factors that were incorporated into the nomogram. The machine-learning model achieved a predictive AUC score of 0.750.ConclusionsA robust nomogram incorporating 13 significant clinicopathological variables was developed. The combined use of ROC curve analysis, calibration plots, DCA, 10-fold cross-validation, and machine learning confirmed the strong predictive performance of the nomogram for survival outcomes in patients with OM.
The trend of phylogenetic and epitope variations of SARS-CoV-2 Omicron sub-lineages in Iran
Authors: Shabani Mehdi , Nejati Ahmad , Yavarian Jila , Sadeghi Kaveh , Zadheidar Sevrin , Ahmadi Akram Sadat , Ghadirali Monire , Zebardast Arghavan , Abedi Adel , Najmi Mohammad Hossein , Shafiei-Jandaghi Nazanin-Zahra , Mokhtari-Azad Talat 
Published: January 2025

IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a significant public health issue worldwide in recent years. The most recently circulating variant of SARS-CoV-2, Omicron, and its rapid evolution into various sub-lineages have raised concerns regarding the effects of the immunity on the virus epitopes, in the human population. The present study evaluated and compared these important variations among different Omicron sub-lineages in Iran.MethodologyFrom October 2023 to August 2024, high coverage whole genome sequences of 49 SARS-CoV-2 strains were subjected to phylogenetic analysis and evaluation of B cell, CD4+, and CD8+ T cell epitopes in Iran National Influenza Centre.ResultsThe phylogenetic tree exhibited eight Nextstrain clades (21L, 22F, 23B, 23H, 23D, 24A, 24B, and 24C) in 48 studied strains, and one recombinant strain (XDK.1). The evaluation of B cell, CD4+, and CD8+ T cell epitopes in all studied strains revealed 31, 65, and 78%, of conservation, respectively. The low B cell epitopes conservation rate among Omicron sub-lineages underscored the escaping from neutralizing humoral immunity. T cell epitopes of the SARS-CoV-2 were considerably preserved across major Omicron sub-lineages. Conservation levels varied based on the epitope class (higher for CD8+ vs. CD4+), protein (higher for non-spike vs. spike), and clades (higher for 21L, 22F, 23B, 23H, 23D, and 24B vs. 24A and 24C).ConclusionHerein, the increased conservation of CD8+ epitopes compared to CD4+ and B cell epitopes is probably attributable to the shorter length of the peptides associated with CD8+ epitopes. The high rate of T-cell epitopes conservation in non-spike proteins among different sub-lineages of the Omicron in this study highlighted the importance of cell-mediated immunity and suggested that non-spike proteins might be more attractive targets for future SARS-CoV-2 vaccines.
Variations in rumen microbiota and host genome impacted feed efficiency in goat breeds
Authors: Rabee Alaa Emara , Abou-souliman Ibrahim , Yousif Ahmed I. , Lamara Mebarek , El-Sherbieny Mohamed A. , Elwakeel Eman Ali , Sallam Ahmed M. 
Published: January 2025

IntroductionImproving feed efficiency (FE) is a significant goal in animal breeding programs. Variations in FE and its relationship with rumen microbiota remain poorly understood across different goat breeds.MethodsThis study assessed the influence of the rumen microbiome and host genome on FE in 10 Shami (SH) goats and 10 Zaraibi (ZA) goats, all of which were fed the same diet. The animals were genotyped using the Illumina 65KSNP chip arrays v2, and their rumen bacteria and archaea were investigated using PCR-amplicon sequencing of the 16S rRNA gene.ResultsThe results showed that the ZA goats exhibited higher FE than the SH goats (p &lt; 0.05) and a greater relative abundance (p &lt; 0.05) of rumen bacterial groups that are involved in the degradation of cellulose and hemicelluloses, such as Bacteroidota and Fibrobacterota, along with genera such as Prevotella, Lachnospiraceae AC2044 group, Lachnospiraceae NK3A20 group, and Succiniclasticum, which are linked to carbohydrate and nitrogen metabolism pathways. In addition, breed differences were found to affect the proportions of milk fatty acids. The association analysis identified 26 genome windows containing several putative candidate genes, such as TMEM241, AP4S1, FTO, HYAL2, BBS2, CD52, CRYBG2, PIGV, WDTC1, EEF1A2, GBA2, FNIP1, ACSL6, STARD10, VPS26B, ACAD8, GLB1L3, NRN1L, LCAT, and SLC7A6. These genes contributed to FE traits in Egyptian goats, as they are involved in obesity, metabolism, and the transport of energy, vitamins, fatty acids, proteins, and lipids through diverse biological pathways.DiscussionThis study suggests that specific genetic markers and rumen microbial traits could be used to identify high-efficient individuals in Egyptian goat breeds, and improving breeding strategies for FE.
The impact of bariatric surgery on gut microbiota: a bibliometric analysis of research trends and scientific contributions
Authors: Gong Shuaichang , Zhang Xiabiao , Chen Xiaoliang , Wan Ping , Zhou Longfei , Zhang Jun 
Published: January 2025

BackgroundObesity is a prevalent global disease closely linked to various chronic conditions. Bariatric surgery (BS) is currently recognized as the most effective treatment. Increasing evidence suggests that BS alters the gut microbiota (GM), which plays a crucial role in postoperative weight loss. However, there has been no systematic bibliometric analysis exploring the relationship between BS and GM to date.MethodsWe conducted a literature search on BS and GM from January 1, 1981, to May 25, 2024, within the Web of Science Core Collection (WoSCC). We utilized Excel 2021, VOSviewer 1.6.19, CiteSpace 6.2.R3, and the R package “bibliometrix” 4.3.0, along with the online bibliometric analysis platform (https://bibliometric.com/app), to visualize publishing trends and research hotspots in this field.ResultsA total of 2,542 articles meeting the criteria were included. Since 2015, the rate of publication has significantly accelerated. The United States leads in both the number of publications and average citations per article. The University of São Paulo is the most active institution, whereas the University of Copenhagen has the highest average citation count. Obesity Surgery is the journal with the highest number of publications, and the most prolific author is Karine Clement. Keyword and thematic analyses indicate that “gut microbiota” and “bariatric surgery” are the primary research hotspots for future studies.ConclusionIn summary, this field is garnering increasing attention. Our findings suggest that future research will likely focus on the effects of bariatric surgery on gut microbiota and its biological mechanisms, the role of gut microbiota in the weight loss process, and the development of combined treatments based on gut microbiota.
Bifidobacterium animalis subsp. lactis TG11 ameliorates loperamide-induced constipation in mice by modulating gut microbiota
Authors: Ma Weiwei , Zhao Yiyang , Liu Yuyang , Wang Yanyan , Yu Shuang , Huang Lili 
Published: January 2025

IntroductionConstipation is a common gastrointestinal disorder that can affect quality of life. Probiotics have garnered substantial attention for their potential to alleviate constipation. This study investigates the preventive effects of Bifidobacterium animalis subsp. lactis TG11 on loperamide-induced constipation in mice.MethodsMice were randomly assigned to normal control (NC), constipation model (CM), and low, medium, and high-dose TG11 treatment groups (LG, MG, HG). From days 1–14, LG, MG, and HG groups received 106, 107, and 108 CFU/mouse of TG11, respectively, while NC and CM groups received saline. On day 14, all groups except NC were administered loperamide (4 mg/kg) orally to induce constipation. Fecal samples were collected for short-chain fatty acid and gut microbiota analyses. Following a 16-hour fasting period, various parameters were assessed on day 15, including intestinal motility, fecal water content, defecation status, gut peptide levels in blood, and mRNA expression levels of SCF and c-kit in colonic tissue.ResultsTG11 significantly enhanced intestinal motility and maintained fecal water content. It normalized blood levels of MTL, SP, SS, ET-1, Gas, and VIP in constipated mice, promoted short-chain fatty acid production, and improved microbial metabolism. TG11 markedly upregulated mRNA expression of SCF and c-kit in colonic tissue. Metagenomic sequencing revealed that TG11 modulated gut microbiota composition, increasing the abundance of beneficial bacteria, particularly Muribaculum_sp. and uncultured_Duncaniella.DiscussionBifidobacterium animalis subsp. lactis TG11 demonstrates efficacy in ameliorating constipation, potentially through modulation of the gut microbiota composition.
Development and internal validation of a nomogram for predicting cognitive impairment after mild ischemic stroke and transient ischemic attack based on cognitive trajectories: a prospective cohort study
Authors: Zhao Panpan , Shi Lin , Zhang Guimei , Wei Chunxiao , Zhai Weijie , Shen Yanxin , Wang Yongchun , Wang Zicheng , Sun Li 
Published: January 2025

IntroductionMany predictive models for cognitive impairment after mild stroke and transient ischemic attack are based on cognitive scales at a certain timepoint. We aimed to develop two easy-to-use predictive models based on longitudinal cognitive trajectories to facilitate early identification and treatment.MethodsThis was a prospective cohort study of 556 patients, followed up every 3 months. Patients with at least two cognitive scales within 2.5 years were included in the latent class growth analysis (LCGA). The patients were categorized into two groups based on the LCGA. First, a difference analysis was performed, and further univariate and stepwise backward multifactorial logistic regression was performed. The results were presented as nomograms, and receiver operating characteristic curve analysis, calibration, decision curve analysis, and cross-validation were performed to assess model performance.ResultsThe LCGA eventually included 255 patients, and the “22” group was selected for further subgroup analysis. Among them, 29.8% were included in the cognitive impairment trajectory. Model 1, which incorporated baseline Montreal Cognitive Assessment, ferritin, age, and previous stroke, achieved an area under the curve (AUC) of 0.973, and model 2, which incorporated age, previous stroke, education, and ferritin, with an AUC of 0.771. Decision curve analysis and cross-validation showed excellent clinical applicability.DiscussionHere, we developed two simple and easy-to-use predictive models of post-stroke cognitive trajectories based on a LCGA, which are presented in the form of nomograms suitable for clinical application. These models provide a basis for early detection and prompt treatment.
Lifetime history of concussion among children and adolescents with attention-deficit/hyperactivity disorder: examining differences stratified by age, medication status, and parent-reported severity
Authors: Maietta Julia E. , Iverson Grant L. , Cook Nathan E. 
Published: January 2025

IntroductionChildren and adolescents with attention-deficit/hyperactivity disorder (ADHD) are more likely to report a lifetime history of concussion compared to those without ADHD. Prior studies have predominantly relied on surveys of youth who self-reported their ADHD status (as opposed to parent report), examined samples with relatively narrow age ranges, and focused on youth athletes. It is unclear if ADHD severity or ADHD medication influences the association between ADHD and greater lifetime history of concussion. We investigated the association between parent-reported ADHD, ADHD severity, and medication status with parent-reported lifetime concussion history in children and adolescents ranging in age from 5 to 17, sampled from the United States general population.MethodsParent reported health data from 33,914 children and adolescents were selected from the 2021 National Survey of Children’s Health. Lifetime history of concussion, current ADHD diagnosed by a healthcare provider, and, for those with current ADHD, ADHD severity (mild or moderate/severe), and current ADHD medication status (yes/no) were reported by parents. A Mantel–Haenszel analysis was used to assess the associations between ADHD and lifetime concussion history across five age groups (ages 5–7, 8–10, 11–13, 14–15, and 16–17). Additional Mantel–Haenszel analyses were used to assess the associations between lifetime history of concussion and ADHD severity as well as medication status across five age groups.ResultsOverall, 6.2% of youth had a parent-reported history of concussion and 12.3% had parent-reported current ADHD. Twice as many youth with ADHD (10.6%) had a parent-reported history of concussion compared to youth without ADHD (5.6%). There were no differences in lifetime concussion history for those with mild (10.9%) versus moderate/severe ADHD (10.3%). Similarly, among those with ADHD, there were no differences in lifetime concussion history for those taking medication (9.9%) versus those not taking medication (11.6%).DiscussionConsistent with previous literature, youth with ADHD had greater lifetime concussion history than youth without ADHD (approximately twice the prevalence in those with ADHD). Contrary to our hypotheses among youth with ADHD, parent-reported ADHD severity and current medication status were not associated with lifetime concussion history.
Radiomics prediction of MGMT promoter methylation in adult diffuse gliomas: a combination of structural MRI, DCE, and DTI
Authors: Liu Yuying , Zhu Zhengyang , Zhou Jianan , Wang Han , Yang Huiquan , Yin Jinfeng , Wang Yitong , Li Xin , Chen Futao , Li Qian , Jiang Zhuoru , Wu Xi , Ge Danni , Zhang Yi , Zhang Xin , Zhang Bing 
Published: January 2025

PurposeTo assess the predictive value of radiomics features extracted from structural MRI, dynamic contrast enhanced (DCE), and diffusion tensor imaging (DTI) in detecting O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation in patients with diffuse gliomas.MethodsRetrospective MRI data of 110 patients were enrolled in this study. The training dataset included 88 patients (mean age 52.84 ± 14.71, 47 females). The test dataset included 22 patients (mean age 50.64 ± 12.58, 12 females). A total of 2,782 radiomic features were extracted from structural MRI, DCE, and DTI within two region of interests (ROIs). Feature section was conducted using Pearson correlation and least absolute shrinkage and selection operator. Principal component analysis was utilized for dimensionality reduction. Support vector machine was employed for model construction. Two radiologists with 1 year and 5 years of experience evaluated the MGMT status in the test dataset as a comparison with the models. The chi-square test and independent samples t-test were used for assessing the statistical differences in patients’ clinical characteristics.ResultsOn the training dataset, the model structural MRI + DCE achieved the highest AUC of 0.906. On the test dataset, the model structural MRI + DCE + DTI achieved the highest AUC of 0.868, outperforming two radiologists.ConclusionThe radiomics models have obtained promising performance in predicting MGMT promoter methylation status. Adding DCE and DTI features can provide extra information to structural MRI in detecting MGMT promoter methylation.
Evaluation of compliance and accuracy in Parkinson’s disease motor symptom tracking: a comparative study of digital and traditional paper diaries using a smartphone application (MyParkinson’s)
Authors: Durmaz Celik Nazli , Yaman Kula Asli , Murat Naci , Kuzu Kumcu Müge , Topal Aydan , Özkan Serhat 
Published: January 2025

Background/objectivesThis study aimed to evaluate compliance and accuracy in comparison with traditional PD diaries for tracking motor symptoms using a new smartphone application (MyParkinson’s) and paper diary strategies. Parkinson’s disease (PD) is a neurodegenerative disorder with progressive motor symptoms. Treatment becomes more challenging as PD progresses, motor complications in the form of wearing-off phenomenon and levodopa-induced dyskinesia develop. Traditional paper diaries and clinical scales used to evaluate patients may be inadequate in assessing whether the patient is “on” or “off,” resulting in less-than-ideal treatment changes.MethodsA randomized crossover design was utilized to examine 22 advanced PD patients who underwent symptomatic assessment with both diaries during two separate 24-h periods seven days apart. The compliance and accuracy of data were assessed by comparing diary entries with the clinical examination notes and WhatsApp queries. LaOerly, patients’ diary preferences were also evaluated.ResultsThe digital diary had significantly beOer compliance and accuracy than the paper diaries, with substantial/almost perfect levels of agreement (κ = 0.615 to 0.818) between logged symptoms and clinical examination notes. 65% of patients preferred the digital diary for follow-ups, and there was no significant difference in ease of use compared to paper diaries.ConclusionDigital diaries are helpful in the clinical management of PD patients as they minimize recall bias and reduce data errors in appropriately selected patients. Our study suggests a broader adoption of digital health technologies in PD management. Still, additional research is necessary to improve the tools and assess long-term patient outcomes.