bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and application of EpitopeScan, a Python3 toolset for mutation tracking in SARS-CoV-2 immunogenic epitopes
Authors: Kovalenko Alexander , Viatte Sebastien 
Published: May 2024

IntroductionOutbreaks of coronaviruses and especially the recent COVID-19 pandemic emphasize the importance of immunological research in this area to mitigate the effect of future incidents. Bioinformatics approaches are capable of providing multisided insights from virus sequencing data, although currently available software options are not entirely suitable for a specific task of mutation surveillance within immunogenic epitopes of SARS-CoV-2.MethodHere, we describe the development of a mutation tracker, EpitopeScan, a Python3 package with command line and graphical user interface tools facilitating the investigation of the mutation dynamics in SARS-CoV-2 epitopes via analysis of multiple-sequence alignments of genomes over time. We provide an application case by examining three Spike protein-derived immunodominant CD4+ T-cell epitopes restricted by HLA-DRB1*04:01, an allele strongly associated with susceptibility to rheumatoid arthritis (RA). Mutations in these peptides are relevant for immune monitoring of CD4+ T-cell responses against SARS-CoV-2 spike protein in patients with RA. The analysis focused on 2.3 million SARS-CoV-2 genomes sampled in England.ResultsWe detail cases of epitope conservation over time, partial loss of conservation, and complete divergence from the wild type following the emergence of the N969K Omicron-specific mutation in November 2021. The wild type and the mutated peptide represent potential candidates to monitor variant-specific CD4+ T-cell responses. EpitopeScan is available via GitHub repository https://github.com/Aleksandr-biochem/EpitopeScan.
Is there any association between the presence of biomarkers and apical periodontitis? A systematic review
Authors: Matos-Sousa José Mário , Chemelo Victória Santos , Frazão Deborah Ribeiro , Bittencourt Leonardo Oliveira , Moura João Daniel Mendonça de , Mesquita Caio Melo , Marañón-Vásquez Guido , Fagundes Nathalia Carolina Fernandes , Paranhos Luiz Renato , Maia Lucianne Cople , Monteiro Marta Chagas , Lima Rafael Rodrigues 
Published: May 2024

This systematic review aimed to verify whether there is evidence of an association between apical periodontitis and the presence of systemic biomarkers. This study adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses - PRISMA. For this, the acronym PECO was used; population (P) of adult humans exposed (E) to the presence of apical periodontitis, compared (C) to adult humans without apical periodontitis, and the outcome (O) of the presence of biomarkers was observed. The articles were searched in PubMed, Scopus, Web of Science, LILACS, Cochrane Library, OpenGray, and Google Scholar grey databases. Subsequently, studies were excluded based on title, abstract, and full article reading, following the eligibility criteria. The methodological quality of the selected studies was evaluated using the Newcastle-Ottawa qualifier. After exclusion, 656 studies were identified, resulting in 17 final articles that were divided into case-control, cross-sectional, and cohort studies. Eight studies were considered to have a low risk of bias, one had a medium risk of bias, and eight had a high risk of bias. In addition, 12 articles evaluated biomarkers in blood plasma, four evaluated them in saliva, and only one evaluated them in gingival crevicular fluid. The results of these studies indicated an association between apical periodontitis and the systemic presence of biomarkers. These markers are mainly related to inflammation, such as interleukins IL-1, IL-2, and IL-6, oxidative markers, such as nitric oxide and superoxide anions, and immunoglobulins IgG and IgM.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier (CRD42023493959).
Inflammatory activity evaluation in patients with axial spondyloarthritis using MRI relaxometry and mucosal-associated invariant T cells
Authors: Yang Shengsheng , Zheng Yonghong , Chen Xianyuan , Lin Mingui , Dai Xiaomin , Gao Fei , Chen Huangjing , Ma Mingping , Yu Shun 
Published: May 2024

BackgroundCurrently, there is a lack of an objective quantitative measure to comprehensively evaluate the inflammatory activity of axSpA, which poses certain challenges in accurately assessing the disease activity.ObjectiveTo explore the value of combined-parameter models of sacroiliac joints (SIJs) MRI relaxometry and peripheral blood Mucosal-associated invariant T (MAIT) cells in evaluating the inflammatory activity of axial spondyloarthritis (axSpA).MethodsThis retrospective clinical study included 88 axSpA patients (median age 31.0 (22.0, 41.8) years, 21.6% females) and 20 controls (median age 28.0 (20.5, 49.5) years, 40.0% females). The axSpA group was classified into active subgroup (n=50) and inactive subgroup (n=38) based on ASDAS-CRP. All participants underwent SIJs MRI examination including T1 and T2* mapping, and peripheral blood flow cytometry analysis of MAIT cells (defined as CD3+Vα7.2+CD161+) and their activation markers (CD69). The T1 and T2* values, as were the percentages of MAIT cells and CD69+MAIT cells were compared between different groups. Combined-parameter models were established using logistic regression, and ROC curves were employed to evaluate the diagnostic efficacy.ResultsThe T1 values of SIJs and %CD69+MAIT cells in the axSpA group and its subgroup were higher than the control group (p&lt;0.05), while %MAIT cells were lower than the control group (p&lt;0.05). The T1 values and %CD69+MAIT cells correlated positively, while %MAIT cells correlated negatively, with the ASDAS-CRP (r=0.555, 0.524, -0.357, p&lt;0.001). Between the control and axSpA groups, and between the inactive and active subgroups, the combined-parameter model T1 mapping+%CD69+MAIT cells has the best efficacy (AUC=0.959, 0.879, sensibility=88.6, 70%, specificity=95.0, 94.7%, respectively).ConclusionThe combined-parameter model T1 mapping+%CD69+MAIT cells allows a more accurate evaluation of the level of inflammatory activity.
Prognostic significance of peripheral and tumor-infiltrating lymphocytes in newly diagnosed stage III/IV non-small-cell lung cancer
Authors: Li Fenge , Tian Chong , Wang Yupeng , Wu Huancheng , Jin Mengli , Du Xueming , Yan Jin , Yang Xueling , Yu Haipeng 
Published: May 2024

Background and aimLymphocytes are effector cells that fight cancer by killing tumor cells. Here, we aim to explore the prognostic significance of both peripheral and tumor-infiltrating lymphocytes (TILs) in newly diagnosed stage III/IV non-small-cell lung cancer (NSCLC).Materials and methodsIn total, 105 cases of newly diagnosed stage III/IV NSCLC from July 2017 to October 2022 at the Tianjin Beichen Hospital were retrospectively investigated. Peripheral blood samples at the time of diagnosis and tumor tissue slices from these patients were collected. General peripheral blood cell composition and TILs were measured and analyzed via an automatic blood analyzer and immunofluorescence staining analysis. The overall survival (OS) time of all patients was also obtained and analyzed.ResultsThe median overall survival (mOS) of all patients is 12 months. The 1-, 2-, and 3-year overall survival rates were 60.5, 28.4, and 18.6%, respectively. Peripheral lymphocyte and neutrophil percentages, serum C-reactive protein (CRP) expression, tumor size, and tumor pathology are the prognostic factors of OS for newly diagnosed stage III/IV NSCLC patients. Moreover, patients with high tumor CD4+ and CD8+ T cell infiltration survived significantly longer compared to patients with low tumor CD4+ and CD8+ T cell infiltration (p &lt; 0.0001 and p = 0.011, respectively). Compared to low tumor CD33+ cell infiltration, high tumor CD33+ cell infiltration was associated with worse OS (p = 0.018). High tumor CD8+ T cell infiltration was associated with lower peripheral lymphocyte number, lower serum CRP expression, smaller tumor size, and better tumor pathology (p = 0.012, p = 0.040, p = 0.012, and p = 0.029, respectively).ConclusionIncreased numbers of peripheral lymphocytes, CD33+ cells, CD4+ TILs, and CD8+ TILs were significantly associated with OS in newly diagnosed stage III/IV NSCLC patients, which were positively associated with several basic clinical factors.
Development of the Korean Medicine Core Outcome Set for Facial Palsy: herbal medicine treatment of patients with facial palsy in primary clinics
Authors: Kim Soo-Dam , Kim Sungha , Son Mi Ju , Cha Jiyun , Kim Pyung-Wha , Ko Mi Mi , Jang Soobin , Yang Changsop , Lee Myeong Soo 
Published: May 2024

IntroductionFacial palsy (FP) significantly affects the quality of life of patients and poses a treatment challenge in primary healthcare settings. This study aimed to develop a Korean medicine (KM) core outcome set (COS) for FP, with a focus on evaluating the effectiveness of herbal medicine (HM) treatments in KM primary clinics.MethodsOutcomes and effect modifiers related to FP treatments were initially identified through related review articles. Subsequently, experts in the field took part in three rounds of modified Delphi consensus exercises to refine and prioritize these outcomes and effect modifiers. Additionally, primary KM clinicians were involved in a Delphi consensus round to assess the suitability and feasibility of the proposed COS in real-world clinical settings.ResultsThe initial review of related literature identified 44 relevant studies, resulting in an initial selection of 23 outcomes and 10 effect modifiers. The expert consensus process refined these to 8 key outcomes and 6 effect modifiers, which established the foundation of the COS-FP-KM. Subsequently, primary KM clinicians confirmed the practicality and applicability of the COS, endorsing its suitability for use in KM primary clinics.ConclusionThe COS-FP-KM establishes a standardized approach for assessing HM treatment effectiveness in FP patients in KM primary clinics. The COS-FP-KM encourages consistent outcome reporting and enhances patient care quality. Future work should aim to integrate broader stakeholder perspectives to refine and validate the COS further.
Serum neurofilament light chain: a predictive marker for outcomes following mild-to-moderate ischemic stroke
Authors: Xu Chongxi , Yi Tong , Qing Ting , Jiang Yongliang , Yi Xingyang , Xu Jianguo , Ma Junpeng 
Published: May 2024

BackgroundBiomarkers that reflect brain damage or predict functional outcomes may aid in guiding personalized stroke treatments. Serum neurofilament light chain (sNfL) emerges as a promising candidate for fulfilling this role.MethodsThis prospective, observational cohort investigation included 319 acute ischemic stroke (IS) patients. The endpoints were the incidence of early neurological deterioration (END, an elevation of two or more points in the National Institute of Health stroke scale score within a week of hospitalization compared with the baseline) and functional outcome at 3 months (an mRS score of &gt;2 at 3 months was categorized as an unfavorable/poor functional outcome). The association of sNfL, which was assessed within 24 h of admission, with END and unfavorable functional outcomes at follow-up was assessed via multivariate logistic regression, whereas the predictive value of sNfL for unfavorable functional outcomes and END was elucidated by the receiver operating characteristic curve (ROC).ResultsOf 319 IS individuals, 89 (27.90%) suffered from END. sNfL not only reflects the severity of stroke measured by NIHSS score (p &lt; 0.05) but also closely related to the severity of age-related white matter changes. Higher initial NIHSS score, severe white matter lesions, diabetes mellitus, and upregulated sNfL were significant predictors of END. Similarly, the multivariate logistic regression analysis results showed that elevated sNfL, a higher baseline NIHSS score, and severe white matter lesions were substantially linked with unfavorable outcomes for 3 months. Similarly, sNfL was valuable for the prediction of the 3 months of poor outcome (95%CI, 0.504–0.642, p = 0.044). Kaplan–Meier analysis shows that patients with elevated sNfL levels are more likely to reach combined cerebrovascular endpoints (log-rank test p &lt; 0.05).ConclusionThis investigation suggests that sNfL can serve as a valuable biomarker for predicting END and 3-month poor functional outcomes after an IS and has the potential to forecast long-term cardiovascular outcomes.
Correlation between dietary factors and Parkinson’s disease revealed by the analysis of Mendelian randomization
Authors: Zeng Shan , Yusufujiang Aishanjiang , Zhang Chunli , Yang Chen , Li Hongyan 
Published: May 2024

BackgroundThe intricate interplay between dietary habits and the development of Parkinson’s Disease (PD) has long been a subject of scientific inquiry. Mendelian Randomization (MR) emerges as a potent tool, harnessing genetic variants to infer causality in observational data. While evidence links diet to Parkinson’s Disease (PD) etiology, a thorough MR exploration of dietary impacts on PD, particularly involving gut microbiota, is still emerging.MethodsThis research leverages the IEU Open GWAS project’s vast GWAS database1 to address the knowledge gap in understanding diet’s influence on PD, employing a diverse range of dietary variables. Our holistic dataset includes various foods like processed fava beans, bap, red wine, to cheese, reflecting a commitment to untangling dietary complexities in PD etiology. Advancing from initial dietary-PD associations, we innovatively explore the gut microbiota, focusing on Parabacteroides goldsteinii, in relation to bap intake and PD, employing MR. Utilizing weighted median, MR-Egger, and inverse variance weighting methods, we ensure rigorous causality assessments, meticulously mitigating pleiotropy and heterogeneity biases to uphold finding validity.ResultsOur findings indicate red wine (OR: 1.031; 95% CI 1.001–1.062; p = 0.044) and dried fruit consumption (OR: 2.019; 95% CI 1.052–3.875; p = 0.035) correlate with increased PD risk, whereas broad beans (OR: 0.967; 95% CI 0.939–0.996; p = 0.024) and bap intake (OR: 0.922; 95% CI 0.860–0.989; p = 0.023) show protective effects against PD. Employing MR, specifically the IVW method, revealed a significant inverse association between bap intake and gut microbiota, marked by an 8.010-fold decrease in Parabacteroides goldsteinii per standard deviation increase in bap intake (95% CI 1.005–63.818, p = 0.049). Furthermore, a connection between PD and Parabacteroides goldsteinii was observed (OR: 0.810; 95% CI 0.768–0.999; p = 0.049), suggesting a potential microbiota-mediated pathway in PD etiology.ConclusionOur study links dietary habits to PD risk, showing higher PD risk with red wine and dried fruit consumption, and a protective effect from broad beans and bap. Using MR, we found bap intake inversely correlates with Parabacteroides goldsteinii in the gut, suggesting bap influences microbiota. Further, higher Parabacteroides goldsteinii levels correlate with lower PD risk, highlighting a complex interplay of diet, gut microbiome, and neurological health. These insights shed light on potential dietary interventions for PD.
A preliminary investigation of precise visualization, localization, and resection of pelvic lymph nodes in bladder cancer by using indocyanine green fluorescence-guided approach through intracutaneous dye injection into the lower limbs and perineum
Authors: Zhang Yunmeng , Guo Xinyu , Zhang Yueying , Wei Jinzheng , Yan Pengyu , Kang Haiming , Shu Yang , Liu Chao , Yang Xiaofeng 
Published: May 2024

ObjectiveThis study aimed to investigate the feasibility and effectiveness of using indocyanine green (ICG) injected intracutaneously through the lower limbs and perineum for visualized tracking, localization, and qualitative assessment of pelvic lymph nodes (LNs) in bladder cancer to achieve their accurate resection.MethodsFirst, ICG was injected into the LN metastasis model mice lower limbs, and real-time and dynamic in vivo and ex vivo imaging was conducted by using a near-infrared fluorescence imaging system. Additionally, 26 patients with bladder cancer were enrolled and divided into intracutaneous group and transurethral group. A near-infrared fluorescence imaging device with internal and external imaging probes was used to perform real-time tracking, localization, and resection of the pelvic LNs.ResultsThe mice normal LNs and the metastatic LNs exhibited fluorescence. The metastatic LNs showed a significantly higher signal-to-background ratio than the normal LNs (3.9 ± 0.2 vs. 2.0 ± 0.1, p &lt; 0.05). In the intracutaneous group, the accuracy rate of fluorescent-labeled LNs was 97.6%, with an average of 11.3 ± 2.4 LNs resected per patient. Six positive LNs were detected in three patients (18.8%). In the transurethral group, the accuracy rate of fluorescent-labeled LNs was 84.4%, with an average of 8.6 ± 2.3 LNs resected per patient. Two positive LNs were detected in one patient (12.5%).ConclusionFollowing the intracutaneous injection of ICG into the lower limbs and perineum, the dye accumulates in pelvic LNs through lymphatic reflux. By using near-infrared fluorescence laparoscopic fusion imaging, physicians can perform real-time tracking, localization, and precise resection of pelvic LNs.
Comparing time to recovery in wasting treatment: simplified approach vs. standard protocol among children aged 6–59 months in Ethiopia—a cluster-randomized, controlled, non-inferiority trial
Authors: Maru Yetayesh , Tamiru Dessalegn , Baye Kaleab , Chitekwe Stanley , Kifle Yehenew G. , Lailou Arnaud , Belachew Tefera 
Published: May 2024

IntroductionWasting occurs when the body's nutritional needs are unmet due to insufficient intake or illness. It represents a significant global challenge, with approximately 45 million infants and children under 5 years of age suffering from wasting in 2022.MethodsA cluster-randomized, controlled, non-inferiority trial was conducted in three regions of Ethiopia. A non-inferiority margin of 15%, along with a recovery rate of 90% and a minimum acceptable recovery rate of 75%, were considered alongside an intra-cluster correlation coefficient of 0.05 and an anticipated loss to follow-up of 10% in determining the total sample size of 1,052 children. Children with severe acute malnutrition (SAM) in the simplified group received two sachets of ready-to-use therapeutic food (RUTF) daily, while the standard group received RUTF based on their body weight. For moderate acute malnutrition (MAM) cases, the simplified group received one sachet of RUTF, whereas the standard group received one sachet of ready-to-use supplementary food daily. A non-parametric Kaplan–Meir curve was utilized to compare the survival time to recovery.ResultsA total of 1,032 data points were gathered. For SAM cases, the average length of stay was 8.86 (±3.91) weeks for the simplified protocol and 8.26 (±4.18) weeks for the standard protocol (P = 0.13). For MAM cases, the average length of stay was 8.18 (±2.96) weeks for the simplified approach and 8.32 (±3.55) weeks for the standard protocol (P = 0.61). There was no significant difference (P = 0.502) observed between the simplified protocol [8 weeks, interquartile range (IQR): 7.06–8.94] and the standard protocol [9 weeks (IQR: 8.17–9.83)] among children with SAM on the median time to cure. There was no significant difference (P = 0.502) in the time to cure between the simplified approach [8 weeks (IQR: 7.53–8.47)] and the standard protocol [8 weeks (IQR: 7.66–8.34)] among children with MAM. The survival curves displayed similarity, with the log-rank test not showing significance (P &gt; 0.5), indicating the non-inferiority of the simplified approach for cure time.ConclusionThe findings showed that the simplified and standard protocols demonstrated no significant differences in terms of the average duration of stay and time required for recovery.
Clinical Trial Registrationhttps://pactr.samrc.ac.za/, Identifier (PACTR202202496481398).
Deleterious effects of polypropylene released from paper cups on blood profile and liver tissue of Clarias gariepinus: bioremediation using Spirulina
Authors: Eid Zainab , Mahmoud Usama M. , Sayed Alaa El-Din H. 
Published: May 2024

Despite numerous studies on microplastics, the biological impacts of polypropylene microplastics (PP-MPs) and its toxicity on freshwater fish have yet to be fully revealed. The purpose of this research was to look at the potentially harmful effects of PP-MPs in freshwater African catfish Clarias gariepinus and bioremediation using Spirulina. After acclimatization to laboratory conditions, 108 fish (125 ± 3 gm and 27 ± 2 cm) were assigned into triplicate six experimental groups (12 fish/group), a control group, Spirulina group (SP), PP-MP-treated groups (0.14 and 0.28 mg/l PP-MPs), and PP-MP + Spirulina-treated groups (0.14 mg/l PP-MPs + 200 mg/L SP and 0.28 mg/l PP-MPs +200 mg/L SP) for 15-day exposure and 45-day recovery after that. The hematological parameters exhibiting significance (RBCs, Hct, Hb, and MCV) or non-significance (MCH and MCHC) either decreased with the increase in PP-MP doses from 0.0 in the control to 0.28 mg/L red blood cells (RBCs), hematocrit (Hct), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), hemoglobin (Hb) and platelets or increased with such an increase in doses (mean corpuscular volume (MCV)). The liver enzyme activity, aspartate aminotransferase (AST), alkaline phosphatase (ALP), and alanine aminotransferase (ALT) exhibited non-significant (p ≥ 0.05) or significant (p &lt; 0.05) increases in (0.14 and 0.28 mg/L) PP-MP-exposed groups, respectively, except ALP. Furthermore, there was a significant (p &lt; 0.05) or non-significant (p ≥ 0.05) increase in 0.14 and 0.28 mg/l PP-MP +200 mg/L-exposure groups, respectively, compared to the control group and the same exposure group without Spirulina. In comparison to the control group, PP-MPs (0.14 and 0.28 mg/L) induced a significant (p &lt; 0.05) increase in the percentage of poikilocytosis and nuclear abnormalities of RBCs. The liver tissue from fish exposed to PP-MPs exhibited varying degrees of pathological changes. These results indicated that these pathological changes increased with PP-MP concentration, suggesting that the effect of PP-MPs was dose-dependent. After 45 days of recovery under normal conditions, it was obvious that there was a significant improvement in the percentage of poikilocytosis and nuclear abnormalities of RBCs, as well as a non-significant improvement in hemato-biochemical parameters and liver tissue.