PeerJ最新文献

{"title":"Prognostic significance of C-reactive protein (CRP) and albumin-based biomarker in patients with breast cancer receiving chemotherapy.","authors":"Susanna Hilda Hutajulu, Yufi Kartika Astari, Meita Ucche, Nyoman Kertia, Yanri Wijayanti Subronto, Dewi Kartikawati Paramita, Lina Choridah, Ericko Ekaputra, Irianiwati Widodo, Suwardjo Suwardjo, Mardiah Suci Hardianti, Kartika Widayati Taroeno-Hariadi, Ibnu Purwanto, Johan Kurnianda","doi":"10.7717/peerj.19319","DOIUrl":"10.7717/peerj.19319","url":null,"abstract":"<p><strong>Background: </strong>Breast cancer patients with similar clinicopathologic characteristics may experience varied outcomes. This urges an increased effort to investigate other prognostic factors. C-reactive protein (CRP)-to-albumin ratio (CAR) is an inflammatory and nutritional biomarker that has been well studied and reported to have an impact on the survival of patients with diverse types of cancer, but limitedly in breast cancer. Therefore, this study aimed to investigate the prognostic significance of CAR in local patients with breast cancer.</p><p><strong>Methods: </strong>This study included 202 stage I-IV breast cancer patients receiving first-line chemotherapy. We calculated inflammatory and nutritional biomarkers including CAR, neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), lymphocyte-to-monocyte ratio (LMR), systemic immune-inflammation index (SII), systemic inflammation response index (SIRI), pan-immune-inflammation value (PIV), and prognostic nutrition index (PNI) before treatment. The Kaplan-Meier with log-rank test and Cox proportional hazard regression were used to analyze the prognostic role of clinicopathologic factors and biomarkers on disease-free survival (DFS), progression-free survival (PFS), and overall survival (OS).</p><p><strong>Results: </strong>The median follow-up period was 46 months (1-77 months). The 3-year DFS and 3-year OS in patients with high CAR (CAR > 1.5) were significantly lower than those with low CAR (CAR ≤ 1.5) (47.0% <i>vs</i> 68.9%, <i>P</i> = 0.022 and 59.5% <i>vs</i> 78.6%, <i>P</i> = 0.009, respectively). Multivariate analysis showed high CAR as prognostic factors for poor DFS (HR 2.10, 95% confidence interval/CI [1.10-3.99], <i>P</i> = 0.023) and OS (HR 2.16, 95% CI [1.27-3.68], <i>P</i> = 0.005), but not for PFS (HR 1.43, 95% CI [0.73-2.80], <i>P</i> = 0.293). In addition, more advanced stage and HER2 positive were correlated with unfavorable DFS and OS, older age predicted poor DFS, and stage was the only prognostic factor of PFS (all <i>P</i> values < 0.05).</p><p><strong>Conclusion: </strong>Besides age, stage, and molecular subtypes that have been widely observed to have impact on the survival of breast cancer patients, CAR was demonstrated as a promising prognostic marker in our local patients. A high CAR at diagnosis was associated with unfavorable DFS and OS, which can aid in identifying patients at risk and guide personalized treatment planning.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19319"},"PeriodicalIF":2.3,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12103165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation and identification of endophytic fungi from <i>Conyza blinii</i> that exhibit antioxidant and antibacterial activities.","authors":"Yujie Jia, Guodong Zhang, Qiqi Xie, Jiwen Tao, Tongliang Bu, Xinyu Zhang, Yirong Xiao, Zhao Chen, Qingfeng Li, Zizhong Tang","doi":"10.7717/peerj.19464","DOIUrl":"10.7717/peerj.19464","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;As a medicinal plant, &lt;i&gt;Conyza blinii&lt;/i&gt; is known to contain a wealth of bioactive constituents, including flavonoids, terpenes, and triterpenoid saponins, which contribute to its anti-inflammatory and anticancer properties. Endophytic fungi, which symbiotically inhabit plant tissues, are recognized for their ability to synthesize bioactive metabolites analogous to those of their hosts. However, the potential of &lt;i&gt;C. blinii&lt;/i&gt;-associated endophytes remains underexplored. This study aims to isolate and characterize phenols-producing endophytic fungi from &lt;i&gt;C. blinii&lt;/i&gt;, evaluate their biological activities, and analyze their chemical components to provide new insights for drug development.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;During the study, 20 endophytic fungi were isolated from &lt;i&gt;C. blinii&lt;/i&gt;. The Folin-Ciocalteu method was used to screen for strains capable of producing phenolic compounds. To assess their bioactivity, ethyl acetate extracts of different concentrations were tested for antibacterial and antioxidant activities. Antibacterial activity was evaluated using minimum inhibitory concentration (MIC) determinations, while antioxidant activity was assessed through 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical, 2,2'-Azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical, hydroxyl radical, and superoxide anion radical scavenging assays. Additionally, liquid chromatography-mass spectrometry analysis was conducted to quantify the active components in the extracts.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Among the isolated 20 endophytic fungi, four strains successfully produced phenolic compounds, with the highest total phenolic content of 77.17 ± 1.93 mg milligrams of gallic acid equivalents per gram of extract (GAE/g). All ethyl acetate extracts from the endophytic fungi exhibited good antibacterial and antioxidant properties. Notably, &lt;i&gt;Fusarium circinatum&lt;/i&gt; demonstrated exceptional antioxidant activity, with scavenging rates for DPPH and ABTS radicals reaching 94.28 ± 0.042% and 96.60 ± 0.017%, respectively. The ethyl acetate extract of &lt;i&gt;F. foetens&lt;/i&gt; showed remarkable antibacterial effects against &lt;i&gt;Escherichia coli&lt;/i&gt; and &lt;i&gt;Staphylococcus aureus&lt;/i&gt;, with MIC values as low as 0.5 mg/mL. Furthermore, liquid chromatography-mass spectrometry (LC-MS) analysis revealed that &lt;i&gt;F. foetens&lt;/i&gt; could produce various high-value phenolic compounds, including tyrosol (626.1884 ng/mL) and homovanillic acid (369.15486 ng/mL), which hold potential pharmaceutical value.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Discussion: &lt;/strong&gt;This study isolated 20 endophytic fungi from &lt;i&gt;C. blinii&lt;/i&gt;, discovering that four strains, produced phenolic compounds with strong antioxidant and antimicrobial properties. Among them, &lt;i&gt;F. circinatum&lt;/i&gt; exhibited the highest antioxidant activity. Additionally, the fungi produced bioactive metabolites with potential applications in health care, medicine, and agriculture. These findings highlight the pote","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19464"},"PeriodicalIF":2.3,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correlation of the sperm DNA fragmentation index with semen parameters and its impact on fresh embryo transfer outcomes-a retrospective study.","authors":"Xiao Ju Wan, Meizhen Huang, Min Yu, Tao Ding, Zhihui Huang, Zhiqin Zhang, Xingwu Wu, Jun Tan","doi":"10.7717/peerj.19451","DOIUrl":"10.7717/peerj.19451","url":null,"abstract":"<p><strong>Purpose: </strong>To evaluate the relationships between the sperm DNA fragmentation index (DFI) and semen parameters and its application in fresh embryos <i>via in vitro</i> fertilization and transfer.</p><p><strong>Methods: </strong>A retrospective propensity score matching (PSM) study was conducted on 162 cycles of <i>in vitro</i> fertilization (IVF) or intracytoplasmic sperm injection (ICSI) and fresh embryo transfer (fresh IVF/ICSI-ET) from 2020-2024.</p><p><strong>Results: </strong>Spearman correlation analysis revealed a negative correlation between the sperm DFI and sperm motility (r = -0.44, <i>p</i> = 3.32e-08), forward movement of sperm (r = -0.46, <i>p</i> = 3.25e-09), and normal morphology of sperm (r = -0.25, <i>p</i> = 0.000); there was no correlation between the sperm DFI and male age (r = 0.08, <i>p</i> = 0.31), semen volume (r = -0.15, <i>p</i> = 0.05), sperm concentration (r = -0.16, <i>p</i> = 0.32), or male body mass index (BMI) (r = 0.02, <i>p</i> = 0.98). There were no significant differences in the 2PN fertilization rate (64.98% <i>vs</i>. 67.18%, <i>p</i> = 0.362), D3 high-quality embryo rate (28.34% <i>vs</i>. 23.91%, <i>p</i> = 0.107), biochemical pregnancy rate (71.60% <i>vs</i>. 71.60%, <i>p</i> = 1), clinical pregnancy rate (65.00% <i>vs</i>. 65.00%, <i>p</i> = 1), delivery rate (50.72% <i>vs</i>. 48.44%, <i>p</i> = 0.928), miscarriage rate (7.25% <i>vs</i>. 6.25%, <i>p</i> = 1), or singleton birth weight (3,350 g <i>vs</i>. 3,200 g, <i>p</i> = 0.599) between the normal DFI (DFI < 30%) group and the high DFI (DFI ≥ 30%) group.</p><p><strong>Conclusion: </strong>Sperm DFI is weakly associated with sperm motility, forward movement, and normal sperm morphology, and the correlations are not strong. However, there is no correlation between the sperm DFI and the clinical outcomes of fresh IVF/ICSI-ET.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19451"},"PeriodicalIF":2.3,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of bacteria on Thai banknotes and coins using MALDI-TOF mass spectrometry and their phenotypic antimicrobial susceptibility profiles.","authors":"Nattamon Niyomdecha, Suwitchaya Sungvaraporn, Arisa Pinmuang, Narissara Mungkornkaew, Thanchira Saita, Waratchaya Rodraksa, Achiraya Phanitmas, Nattapong Yamasamit, Pirom Noisumdaeng","doi":"10.7717/peerj.19465","DOIUrl":"10.7717/peerj.19465","url":null,"abstract":"<p><strong>Background: </strong>The existence and transmission of pathogenic and antibiotic-resistant bacteria through currency banknotes and coins poses a global public health risk. Banknotes and coins are handled by people in everyday life and have been identified as a universal medium for potentially microbial contamination.</p><p><strong>Methods: </strong>To ascertain existence of medically important bacteria, a total of 300 samples including 150 banknotes and 150 coins were randomly collected at onsite retail fresh meat stores, <i>i.e.</i>, pork and chicken, fish, and seafood stores, from nineteen fresh markets distributed across Bangkok, Thailand. An individual banknote or coin was entirely swabbed, and bacterial culture was carried out using tryptic soy agar (TSA), sheep blood agar (SBA) and MacConkey agar (Mac). A colony count was performed and bacterial species identification was conducted using matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry. Phenotypic antimicrobial susceptibility testing was carried out using the Kirby-Bauer disc diffusion methods.</p><p><strong>Results: </strong>The results demonstrated that the bacterial contamination rate was higher on banknotes than on coins (93.33% <i>vs.</i> 30.00%) in all three store types. A substantial number of colonies of >3,000 colony forming units (CFU) was predominantly found in banknotes (70.00%), especially from fish store (83.3%); meanwhile, <1,000 CFU was observed in coin sample (76.67%). MALDI-TOF mass spectrometry could identify 107 bacterial species, most of them were <i>Staphylococcus kloosii</i> (14.02%, 15/107), <i>Staphylococcus saprophyticus</i> (12.15%, 13/107), and <i>Macrococcus caseolyticus</i> (8.41%, 9/107). The prevalence based on genera were <i>Staphylococcus</i> (36.45%, 39/107), <i>Acinetobacter</i> (20.56%, 22/107), and <i>Macrococcus</i> (10.28%, 11/107). Almost all Staphylococcus isolates had low susceptibility to penicillin (21%). Notably, <i>Staphylococcus arlettae</i>, <i>Staphylococcus haemolyticus</i> and <i>M. caseolyticus</i> were multidrug-resistant (MDR). It is notable that none of the staphylococci and macrococci isolates exhibited inducible clindamycin resistance (D-test negative). <i>Escherichia coli</i> and <i>Pseudomonas putida</i> isolates were carbapenem-resistant, and <i>Acinetobacter baumannii</i> isolates were MDR with showing carbapenem resistance.</p><p><strong>Conclusion: </strong>Our data demonstrated a high prevalence of medically important bacteria presented on Thai currency, which may pose a potential risk to human health and food safety. Food vendors and consumers should be educated about the possible cross-contamination of bacteria between the environment, food item, and currency.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19465"},"PeriodicalIF":2.3,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bulk and single-cell RNA sequencing identify prognostic signatures related to FGFBP2⁺ NK cell in hepatocellular carcinoma.","authors":"Yinbing Wu, Huanjun Peng, Guangkang Chen, Yinuo Tu, Xinpei Yu","doi":"10.7717/peerj.19337","DOIUrl":"10.7717/peerj.19337","url":null,"abstract":"<p><strong>Background: </strong>Hepatocellular carcinoma (HCC) is a highly aggressive malignancy. As a specific immune cell subpopulation, FGFBP2⁺ NK cells play a crucial part in immune surveillance of HCC progression. This study set out to identify prognostic signature related to FGFBP2⁺ NK cell in HCC.</p><p><strong>Methods: </strong>Bulk and scRNA-seq data were derived from the public databases. The single cell atlas of HCC and heterogeneity of natural killer (NK) cells were delineated by \"Seurat\" package. Pseudo-time trajectory of FGFBP2⁺ NK cell was constructed by \"Monocle2\" package. Cell-cell interactions were analyzed by \"CellChat\" package. Prognostic signature was screened to develop a RiskScore model, and the prediction robustness was verified. Immune cell infiltration and immunotherapy response were assessed between different risk groups. Drug sensitivity was predicted by \"oncoPredict\" package. The expressions of the prognosis gene signature were detected by <i>in vitro</i> test utilizing HCC cells. The effects of key genes on the proliferative, migratory and invasive capacity of HCC cells were assessed by EdU assay, wound healing and Transwell assay.</p><p><strong>Results: </strong>The proportion of NK cell in HCC samples was markedly decreased than that in healthy samples. NK cell was further divided into three cell subpopulations, and FGFBP2⁺ NK cell was associated with the prognosis of HCC patients. Pseudo-time trajectory analysis of FGFBP2⁺ NK cell revealed two differential expression gene clusters. FGFBP2⁺ NK cell exhibited extensive intercellular communication in HCC. Further, eight prognostic signatures were identified, including six \"risk\" genes (<i>UBE2F</i>, <i>AHSA1</i>, <i>PTP4A2</i>, <i>CDKN2D</i>, <i>FTL</i>, <i>RGS2</i>) and two \"protective\" genes (<i>KLF2</i>, <i>GZMH</i>). RiskScore model was established with good prognostic prediction performance. In comparison to low-risk group, high-risk group had poorer prognosis, lower immune cell infiltration, and higher TIDE score. Moreover, 16 drugs showed significant correlation with RiskScore. Additionally, the expressions of <i>GZMH</i> was downregulated while <i>FTL</i>, <i>PTP4A2</i>, <i>UBE2F</i>, <i>CDKN2D</i>, <i>RGS2</i>, and <i>AHSA1</i> were up-regulated in HCC cells. <i>FTL</i> and <i>PTP4A2</i> silencing could suppress the proliferation, migration and invasion abilities of HCC cells.</p><p><strong>Conclusion: </strong>This study identified eight prognostic gene signatures related to FGFBP2⁺ NK cell in HCC, which may serve as potential therapeutic targets for HCC.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19337"},"PeriodicalIF":2.3,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selected Alu methylation levels in the gastric carcinogenesis cascade.","authors":"Jiraroch Meevassana, Chawisa Wanda Vongsuly, Tanchanok Nakbua, Supitcha Kamolratanakul, Pichaya Thitiwanichpiwong, Fardeela Bin-Alee, Somboon Keelawat, Nakarin Kitkumthorn","doi":"10.7717/peerj.19485","DOIUrl":"10.7717/peerj.19485","url":null,"abstract":"<p><strong>Background: </strong>Genome-wide hypomethylation, a common epigenetic change that occurs during cancer development, primarily affects repetitive elements, such as Alu repeats. Consequently, Alu repeats can be used as a surrogate marker of genomic hypomethylation.</p><p><strong>Methods: </strong>In this study, we aimed to investigate the correlation between Alu methylation levels and the multistage course of gastric carcinogenesis.</p><p><strong>Results: </strong>We found that the Alu methylation levels in gastric cancer tissue decreased compared with those in normal gastric tissue, with the change in methylation levels and pattern being most significant between chronic gastritis and intestinal metaplasia. Moreover, Alu methylation levels were not associated with <i>Helicobacter pylori</i> or Epstein-Barr virus infection.</p><p><strong>Conclusions: </strong>Finally, our sensitivity and specificity analyses suggested that Alu methylation level can be used to distinguish gastric cancer tissue from normal tissue. Thus, Alu methylation level shows promise as biomarker for gastric cancer diagnosis.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19485"},"PeriodicalIF":2.3,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interpretable noninvasive diagnosis of tuberculous pleural effusion using LGBM and SHAP: development and clinical application of a machine learning model.","authors":"Bihua Yao, Xingyu Yu, Liannv Qiu, Er-Min Gu, Siyu Mao, Lei Jiang, Jijun Tong, Jianguo Wu","doi":"10.7717/peerj.19411","DOIUrl":"10.7717/peerj.19411","url":null,"abstract":"<p><strong>Background: </strong>Tuberculous pleural effusion (TPE) is a prevalent tuberculosis complication, with diagnosis presenting considerable challenges. Timely and precise identification of TPE is vital for effective patient management and prognosis, yet existing diagnostic methods tend to be invasive, lengthy, and often lack sufficient accuracy. This study seeks to design and validate an interpretable machine learning model based on routine laboratory data to enable noninvasive and rapid TPE diagnosis.</p><p><strong>Methods: </strong>A multicenter prospective study was conducted across China between January 2021 and September 2024, enrolling 963 patients. The derivation cohort, comprising 763 patients, was employed for model training and internal validation, while 200 patients formed the external validation cohort. The model was built upon 18 routine laboratory parameters, including pleural fluid and serum biomarkers, with multiple machine learning (ML) algorithms evaluated. Light gradient boosting machine (LGBM) emerged as the top-performing model. Shapley Additive exPlanations (SHAP) analysis assessed feature importance and interpretability. Model performance was evaluated <i>via</i> area under the curve (AUC) and accuracy metrics.</p><p><strong>Results: </strong>Of the 10 ML models compared, LGBM demonstrated superior performance. Feature importance analysis identified 11 key variables, leading to constructing a highly interpretable LGBM model. The model achieved an AUC of 0.9454 in internal validation and 0.9262 in external validation, showcasing strong robustness and generalizability. SHAP analysis enhanced interpretability by highlighting each feature's contribution to prediction outcomes. This model has since been integrated into clinical practice for noninvasive, rapid TPE diagnosis. During external validation, the model achieved a sensitivity of 0.8600, specificity of 0.9056, positive predictive value of 0.8698, and negative predictive value of 0.8686, underscoring its accuracy across diverse patient cohorts.</p><p><strong>Interpretation: </strong>This interpretable machine learning model offers a noninvasive, accurate solution for early TPE diagnosis, significantly reducing reliance on invasive procedures. The integration of SHAP ensures the model's clinical interpretability, mitigating concerns surrounding the \"black-box\" nature of many machine learning approaches.</p><p><strong>Conclusions: </strong>This interpretable LGBM-based model provides a reliable, noninvasive tool for TPE diagnosis. It supports clinical decision-making with real-time risk assessment and promises broader applicability through future integration into clinical information systems.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19411"},"PeriodicalIF":2.3,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144142986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The chronic effects of change of direction during repeated-sprint training on jumping, sprinting, and change-of-direction abilities in players: a systematic review and meta-analysis.","authors":"Runzhou Kong, Lei Cao, Dongyu Li","doi":"10.7717/peerj.19416","DOIUrl":"10.7717/peerj.19416","url":null,"abstract":"<p><strong>Objectives: </strong>This systematic review and meta-analysis aimed to compare the effects of repeated sprint training with one change of direction (RS-OCOD) and multidirectional changes of direction (RS-MCOD) on players' jumping, sprinting, and change-of-direction (COD) ability.</p><p><strong>Methods: </strong>Following PRISMA guidelines, 15 randomized controlled trials involving 223 players were analyzed. Standardized mean differences (SMD) and 95% confidence intervals (CI) were calculated using fixed- or random-effects models. Heterogeneity (<i>I</i> ² statistic), publication bias (funnel plots and Egger's test), and sensitivity analyses were conducted. Subgroup analyses differentiated RS-OCOD and RS-MCOD outcomes.</p><p><strong>Results: </strong>RS-COD training significantly improved countermovement jump (CMJ) (SMD = -0.68, 95% CI [-1.04 to -0.34]), 20-40 m sprinting ability (SMD = 0.70 [0.39, 1.01]), and COD ability (SMD = 0.77 [0.39, 1.16]). RS-MCOD demonstrated superior effects on 20-40 m sprinting ability (large effect: SMD = 0.97) and COD ability (large effect: SMD = 0.97), while RS-OCOD showed greater benefits for CMJ (large effect: SMD = -0.92). High heterogeneity (<i>I</i> ² > 70%) was observed in 5 m/10 m sprint analyses, attributed to methodological diversity and age variability. Prediction intervals indicated potential overestimation of RS-MCOD effects.</p><p><strong>Conclusion: </strong>RS-OCOD can significantly enhance a player's CMJ ability, while RS-MCOD can notably improve sprinting and COD abilities. These findings advocate for the incorporation of RS-COD into training programs to boost competitive performance. However, the effectiveness of RS-COD may vary based on the number and complexity of directional changes incorporated into the training regimen. Among them, RS-MCOD is prioritized for sports requiring frequent directional changes, whereas RS-OCOD enhances vertical jump performance in explosive sports.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19416"},"PeriodicalIF":2.3,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intrinsic factors behind long COVID: exploring the role of nucleocapsid protein in thrombosis.","authors":"Ahmed Eltayeb, Muhamed Adilović, Maryam Golzardi, Altijana Hromić-Jahjefendić, Alberto Rubio-Casillas, Vladimir N Uversky, Elrashdy M Redwan","doi":"10.7717/peerj.19429","DOIUrl":"10.7717/peerj.19429","url":null,"abstract":"<p><p>COVID-19, caused by the SARS-CoV-2, poses significant global health challenges. A key player in its pathogenesis is the nucleocapsid protein (NP), which is crucial for viral replication and assembly. While NPs from other coronaviruses, such as SARS-CoV and MERS-CoV, are known to increase inflammation and cause acute lung injury, the specific effects of the SARS-CoV-2 NP on host cells remain largely unexplored. Recent findings suggest that the NP acts as a pathogen-associated molecular pattern (PAMP) that binds to Toll-like receptor 2 (TLR2), activating NF-<i>κ</i>B (nuclear factor kappa-light-chain-enhancer of activated B cells) and MAPK (mitogen-activated protein kinase) signaling pathways. This activation is particularly pronounced in severe COVID-19 cases, leading to elevated levels of soluble ICAM-1 (intercellular adhesion molecule 1) and VCAM-1 (vascular cell adhesion molecule 1), which contribute to endothelial dysfunction and multiorgan damage. Furthermore, the NP is implicated in hyperinflammation and thrombosis-key factors in COVID-19 severity and long COVID. Its potential to bind with MASP-2 (mannan-binding lectin serine protease 2) may also be linked to persistent symptoms in long COVID patients. Understanding these mechanisms, particularly the role of the NP in thrombosis, is essential for developing targeted therapies to manage both acute and chronic effects of COVID-19 effectively. This comprehensive review aims to elucidate the multifaceted roles of the NP, highlighting its contributions to viral pathogenesis, immune evasion, and the exacerbation of thrombotic events, thereby providing insights into potential therapeutic targets for mitigating the severe and long-term impacts of COVID-19.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19429"},"PeriodicalIF":2.3,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the effect of the triglyceride-glucose index on bone metabolism in prepubertal children, a retrospective study: insights from traditional methods and machine-learning-based bone remodeling prediction.","authors":"Shunshun Cao, Aolei Chen, Botian Song, Yangyang Hu","doi":"10.7717/peerj.19483","DOIUrl":"10.7717/peerj.19483","url":null,"abstract":"<p><strong>Background: </strong>Childhood obesity poses a significant risk to bone health, but the impact of insulin resistance (IR) on bone metabolism in prepubertal children, as assessed by the triglyceride-glucose (TyG) index, remains underexplored. Bone turnover markers (BTMs) provide a non-invasive method for evaluating bone remodeling, but their relationship to obesity-related metabolic changes requires further study.</p><p><strong>Methods: </strong>In this retrospective study of 332 prepubertal children (163 boys and 169 girls), we used multivariate linear regression and five machine learning (ML) algorithms to explore the association between the TyG index and BTMs, including β-C-terminal telopeptide of type 1 collagen (β-CTx), total procollagen type 1 N-terminal propeptide (T-P1NP), and N-terminal mid-fragment of osteocalcin (N-MID). The categorical boosting (CatBoost) models selected based on optimal performance metrics were interpreted using SHapley Additive exPlanation (SHAP) analysis to identify key features affecting prediction.</p><p><strong>Results: </strong>The TyG index was negatively correlated with β-CTx, T-P1NP, and N-MID levels (<i>P</i> < 0.05), with a dose-response effect. The CatBoost model showed higher predictive accuracy and robustness, with the area under the receiver operating characteristic curve (AUROC) values of 0.782 (95% CI [0.68-0.885]), 0.789 (95% CI [0.691-0.874]), and 0.727 (95% CI [0.619-0.827]) for β-CTx, T-P1NP, and N-MID predictions, respectively. The SHAP analysis highlighted body mass index (BMI) and HbA1c as the key predictors.</p><p><strong>Conclusions: </strong>The TyG index is a reliable predictor of bone metabolic disorders in prepubertal obese children, and the interpretable CatBoost model provides a cost-effective tool for early intervention. This study has important implications for prevention strategies for disorders of bone metabolism in prepubertal obese children to reduce the risk of skeletal fragility in adulthood or old age.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"13 ","pages":"e19483"},"PeriodicalIF":2.3,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}