PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Application of intestinal microbiota in marine fish for assessing the toxicity of typical pollutants: a literature review
items: Diagnostic and prognostic implications of growth differentiation factor 15 in heart failure with preserved ejection fraction: a systematic review and meta-analysis
items: Power analyses to inform clutch sampling design to determine the breeding sex ratio in populations with multiple paternity
items: Comparison of the clinical usefulness of CXCL-8 and common clinical tumor markers for esophageal cancer diagnosis
items: Single-particle analysis of small extracellular vesicles from human follicular fluid unveils immunomodulatory PD-L1+ subpopulations and potentially fertility biomarkers
items: Identification of keratinocyte-associated genes for immune characterization and drug response prediction in oral squamous cell carcinoma
items: Sniffin’ sticks smell identification test: exploring measurement properties in an adult Brazilian healthcare professionals sample
items: Retrospective study: the value of GDF-15 and conventional markers in combination for clinical diagnosis of lung cancer
items: Accelerated straw decomposition and mitigated methane emissions via autumn puddling incorporation enhances soil health and yield stability in cold-region rice systems of China
items: Lower limb joints’ contributions to ballet turnout during unipodal and bipodal jumps in fifth position in pre-professional dancers

Application of intestinal microbiota in marine fish for assessing the toxicity of typical pollutants: a literature review
type: item
type: AcademicArticle
description: The widespread diffusion and dilution of pollutants in the ocean lead to prolonged exposure of marine organisms to low-concentration contaminated environments, raising growing concerns about the potential risks associated with chronic low-level pollution. The gut microbiota of fish plays a pivotal role in essential physiological processes, which are critical for host health. Therefore, the key microbes in the gut could serve as valuable biomarkers for assessing the toxic effects of pollutants. This article systematically reviews the structure and functions of marine fish gut microbiota, outlines the primary methodologies for assessing gut microbiota, and highlights the impacts of typical pollutants (including petroleum hydrocarbons, antibiotics, heavy metals, and microplastic) on the composition, functionality, and metabolic activities of marine fish gut microbiota. In the future, integrating multi-technology approaches to investigate the toxic mechanisms of pollutants on gut microbiota and their biodegradation pathways will represent a pivotal direction in marine ecotoxicology research.
format: application/pdf
format: text/html
creator: Yunzhi Feng
creator: Haolong Xu
creator: Guohua Xu
creator: Dong Sun
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Microbiology
subject: Ecotoxicology
description: doi:10.7717/peerj.20248
publisher: PeerJ Inc.
rights: © 2025 Feng et al.
abstract: The widespread diffusion and dilution of pollutants in the ocean lead to prolonged exposure of marine organisms to low-concentration contaminated environments, raising growing concerns about the potential risks associated with chronic low-level pollution. The gut microbiota of fish plays a pivotal role in essential physiological processes, which are critical for host health. Therefore, the key microbes in the gut could serve as valuable biomarkers for assessing the toxic effects of pollutants. This article systematically reviews the structure and functions of marine fish gut microbiota, outlines the primary methodologies for assessing gut microbiota, and highlights the impacts of typical pollutants (including petroleum hydrocarbons, antibiotics, heavy metals, and microplastic) on the composition, functionality, and metabolic activities of marine fish gut microbiota. In the future, integrating multi-technology approaches to investigate the toxic mechanisms of pollutants on gut microbiota and their biodegradation pathways will represent a pivotal direction in marine ecotoxicology research.
bibliographic citation: Feng et al. (2025) Application of intestinal microbiota in marine fish for assessing the toxicity of typical pollutants: a literature review. PeerJ 13:e20248 https://doi.org/10.7717/peerj.20248
date submitted: 2025-06-04
date accepted: 2025-09-25
issued: 2025-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Yunzhi
author list: Agent
  family name: Xu
  given name: Haolong
author list: Agent
  family name: Xu
  given name: Guohua
author list: Agent
  family name: Sun
  given name: Dong
doi: 10.7717/peerj.20248
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-28
copyright: © 2025 Feng et al.
attribution name: Feng et al.

Diagnostic and prognostic implications of growth differentiation factor 15 in heart failure with preserved ejection fraction: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Growth differentiation factor-15 (GDF-15), an emerging biomarker associated with chronic inflammation and oxidative stress, shows potential diagnostic and prognostic significance for heart failure with preserved ejection fraction (HFpEF). This study aimed to assess the diagnostic and prognostic value of GDF-15 in HFpEF. Methods Three databases (PubMed, Scopus, and ScienceDirect) were used to search for relevant literature published before August 6, 2024. Quality assessment was conducted using the Newcastle-Ottawa scale and its adaptation for cross-sectional studies. Statistical analysis was performed using RStudio version 4.4.1. All meta-analyses employed a random-effects model. Sensitivity analysis was conducted using the leave-one-out technique to evaluate the influence of individual studies on pooled estimates. This study protocol was registered in PROSPERO (CRD42024569609). Results A total of 5,696 HFpEF patients were identified from 28,193 individuals across 12 observational studies. GDF-15 levels were consistently elevated in HFpEF patients, with a pooled mean difference (MD) of 647.60 pg/mL (95% CI [148.43–1,146.77]; p = 0.01). Sensitivity analysis confirmed the robustness of this finding, with a slightly higher MD observed when studies involving HFpEF patients with atrial fibrillation were excluded. Qualitative analysis suggested that the overall diagnostic performance of GDF-15 in HFpEF is slightly superior to conventional biomarkers. GDF-15 showed a pooled area under the curve (AUC) of 0.82 (95% CI [0.72–0.91]), indicating good diagnostic accuracy. Additionally, GDF-15 was associated with increased risk of all-cause mortality and heart failure hospitalisation, with pooled hazard ratios (HR) of 1.46 (95% CI [1.30–1.62]; p < 0.01) and 1.76 (95% CI [1.30–2.38]; p < 0.01), respectively. Conclusion GDF-15 demonstrates significant diagnostic and prognostic potential for HFpEF. Elevated GDF-15 levels are associated with increased risk of all-cause mort…
format: application/pdf
format: text/html
creator: Iwan Dakota
creator: Matthew Aldo Wijayanto
creator: Annisa Salsabilla Dwi Nugrahani
creator: Angela Felicia Sunjaya
creator: Shela Rachmayanti
creator: Enny Yuliana Indah
creator: Natasya Naomi
creator: Wilbert Huang
creator: Christopher Daniel Tristan
creator: Mira Fauziah
creator: Hary Sakti Muliawan
creator: Bambang Budi Siswanto
subject: Cardiology
description: doi:10.7717/peerj.20168
publisher: PeerJ Inc.
rights: © 2025 Dakota et al.
abstract: Background Growth differentiation factor-15 (GDF-15), an emerging biomarker associated with chronic inflammation and oxidative stress, shows potential diagnostic and prognostic significance for heart failure with preserved ejection fraction (HFpEF). This study aimed to assess the diagnostic and prognostic value of GDF-15 in HFpEF. Methods Three databases (PubMed, Scopus, and ScienceDirect) were used to search for relevant literature published before August 6, 2024. Quality assessment was conducted using the Newcastle-Ottawa scale and its adaptation for cross-sectional studies. Statistical analysis was performed using RStudio version 4.4.1. All meta-analyses employed a random-effects model. Sensitivity analysis was conducted using the leave-one-out technique to evaluate the influence of individual studies on pooled estimates. This study protocol was registered in PROSPERO (CRD42024569609). Results A total of 5,696 HFpEF patients were identified from 28,193 individuals across 12 observational studies. GDF-15 levels were consistently elevated in HFpEF patients, with a pooled mean difference (MD) of 647.60 pg/mL (95% CI [148.43–1,146.77]; p = 0.01). Sensitivity analysis confirmed the robustness of this finding, with a slightly higher MD observed when studies involving HFpEF patients with atrial fibrillation were excluded. Qualitative analysis suggested that the overall diagnostic performance of GDF-15 in HFpEF is slightly superior to conventional biomarkers. GDF-15 showed a pooled area under the curve (AUC) of 0.82 (95% CI [0.72–0.91]), indicating good diagnostic accuracy. Additionally, GDF-15 was associated with increased risk of all-cause mortality and heart failure hospitalisation, with pooled hazard ratios (HR) of 1.46 (95% CI [1.30–1.62]; p < 0.01) and 1.76 (95% CI [1.30–2.38]; p < 0.01), respectively. Conclusion GDF-15 demonstrates significant diagnostic and prognostic potential for HFpEF. Elevated GDF-15 levels are associated with increased risk of all-cause mort…
bibliographic citation: Dakota et al. (2025) Diagnostic and prognostic implications of growth differentiation factor 15 in heart failure with preserved ejection fraction: a systematic review and meta-analysis. PeerJ 13:e20168 https://doi.org/10.7717/peerj.20168
date submitted: 2025-04-16
date accepted: 2025-09-11
issued: 2025-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dakota
  given name: Iwan
author list: Agent
  family name: Wijayanto
  given name: Matthew Aldo
author list: Agent
  family name: Nugrahani
  given name: Annisa Salsabilla Dwi
author list: Agent
  family name: Sunjaya
  given name: Angela Felicia
author list: Agent
  family name: Rachmayanti
  given name: Shela
author list: Agent
  family name: Indah
  given name: Enny Yuliana
author list: Agent
  family name: Naomi
  given name: Natasya
author list: Agent
  family name: Huang
  given name: Wilbert
author list: Agent
  family name: Tristan
  given name: Christopher Daniel
author list: Agent
  family name: Fauziah
  given name: Mira
author list: Agent
  family name: Muliawan
  given name: Hary Sakti
author list: Agent
  family name: Siswanto
  given name: Bambang Budi
doi: 10.7717/peerj.20168
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-28
copyright: © 2025 Dakota et al.
attribution name: Dakota et al.

Power analyses to inform clutch sampling design to determine the breeding sex ratio in populations with multiple paternity
type: item
type: AcademicArticle
description: In many species, demographic assessments of population viability require an estimate of the number or proportion of breeding adults in a population that are male (the breeding sex ratio). However, this estimate is often difficult to obtain directly in species with multiple paternity when males are difficult to sample. Parentage analysis of breeding females and offspring can produce this estimate by identifying the number of unique males that contribute genetic information to (i.e., sired) a given cohort. There is an added challenge of choosing a sample design with the desired level of confidence to identify all the fathers contributing to a cohort, either at the scale of individual clutches or an entire nesting season, given limited resources. Sampling effort can be defined as the number of offspring sampled per clutch, or the number of clutches sampled per breeding season, depending on the analysis. The minimum number of samples required may depend on the proportions of eggs that different fathers fertilize in a clutch (the paternal contribution mode), the total number of fathers fertilizing a clutch, the proportion of adults available for breeding that are male (the operational sex ratio), and population size. We conducted power analyses to quantify the confidence in identifying all fathers in animal populations with multiple paternity. We simulated sampling a theoretical sea turtle population with a range of population demographics, mating systems, and sampling effort, and used the proportion of 10,000 simulations in which all fathers were identified as a proxy for confidence. At the clutch level, confidence was strongly dependent on the paternal contribution mode, and when it was skewed, it also depended on the total number of fathers contributing and the number of offspring sampled. However, sampling about one third of a clutch was sufficient to identify all fathers with high confidence for most scenarios, unless the paternal contribution mode was extremely ske…
format: application/pdf
format: text/html
creator: Vic Quennessen
creator: Mariana M.B.P. Fuentes
creator: Lisa Komoroske
creator: J. Wilson White
subject: Aquaculture, Fisheries and Fish Science
subject: Computational Biology
subject: Marine Biology
subject: Mathematical Biology
subject: Population Biology
description: doi:10.7717/peerj.20165
publisher: PeerJ Inc.
rights: © 2025 Quennessen et al.
abstract: In many species, demographic assessments of population viability require an estimate of the number or proportion of breeding adults in a population that are male (the breeding sex ratio). However, this estimate is often difficult to obtain directly in species with multiple paternity when males are difficult to sample. Parentage analysis of breeding females and offspring can produce this estimate by identifying the number of unique males that contribute genetic information to (i.e., sired) a given cohort. There is an added challenge of choosing a sample design with the desired level of confidence to identify all the fathers contributing to a cohort, either at the scale of individual clutches or an entire nesting season, given limited resources. Sampling effort can be defined as the number of offspring sampled per clutch, or the number of clutches sampled per breeding season, depending on the analysis. The minimum number of samples required may depend on the proportions of eggs that different fathers fertilize in a clutch (the paternal contribution mode), the total number of fathers fertilizing a clutch, the proportion of adults available for breeding that are male (the operational sex ratio), and population size. We conducted power analyses to quantify the confidence in identifying all fathers in animal populations with multiple paternity. We simulated sampling a theoretical sea turtle population with a range of population demographics, mating systems, and sampling effort, and used the proportion of 10,000 simulations in which all fathers were identified as a proxy for confidence. At the clutch level, confidence was strongly dependent on the paternal contribution mode, and when it was skewed, it also depended on the total number of fathers contributing and the number of offspring sampled. However, sampling about one third of a clutch was sufficient to identify all fathers with high confidence for most scenarios, unless the paternal contribution mode was extremely ske…
bibliographic citation: Quennessen et al. (2025) Power analyses to inform clutch sampling design to determine the breeding sex ratio in populations with multiple paternity. PeerJ 13:e20165 https://doi.org/10.7717/peerj.20165
date submitted: 2025-02-13
date accepted: 2025-09-11
issued: 2025-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quennessen
  given name: Vic
author list: Agent
  family name: Fuentes
  given name: Mariana M.B.P.
author list: Agent
  family name: Komoroske
  given name: Lisa
author list: Agent
  family name: White
  given name: J. Wilson
doi: 10.7717/peerj.20165
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-28
copyright: ©2025 Quennessen et al.
attribution name: Quennessen et al.

Comparison of the clinical usefulness of CXCL-8 and common clinical tumor markers for esophageal cancer diagnosis
type: item
type: AcademicArticle
description: Background This study aimed to investigate serum CXC motif chemokine ligand 8 (CXCL-8) as a potential biomarker for diagnosing esophageal cancer (EC). Methods Patients diagnosed with EC (n = 141) were enrolled at the Department of Thoracic Surgery, Fujian Medical University Union Hospital, from July through December 2023. Sixty cases were early esophageal cancer (EEC), whereas 81 were advanced (AEC) based on diagnostic criteria. Healthy volunteers (n = 75) were recruited as controls. Serum CXCL-8 levels were quantified using an enzyme-linked immunosorbent assay. Levels of carcinoembryonic antigen (CEA), cytokeratin 19 fragment (Cyfra211), and squamous cell carcinoma antigen (SCC) were assessed using a chemiluminescent microparticle immunoassay. Clinical and pathological attributes of patients with EC were documented and analyzed. Diagnostic efficacies of CXCL-8, CEA, Cyfra211, and SCC for EC were evaluated using receiver operating characteristic (ROC) curves. Results Serum concentrations of CXCL-8, CEA, Cyfra211, and SCC were significantly higher in patients with EC than in controls (P < 0.05). In the EC group, areas under the curves (AUCs) for CXCL-8, CEA, Cyfra211, and SCC were 0.906, 0.707, 0.705, and 0.797, respectively. The combined application of CXCL-8+CEA, CXCL-8+Cyfra211, and CXCL-8+SCC yielded AUCs of 0.931, 0.940, and 0.950, respectively, and was significantly higher than that of the combination of CEA+Cyfra211+SCC (0.854). In EEC, the diagnostic performance of CXCL-8 was similar to that in the EC group. The sensitivity of CXCL-8 was greater than that of CEA, Cyfra211, and SCC alone, and the combination of the three markers (P < 0.05). Conclusions CXCL-8 could be used to distinguish patients with EC from healthy controls, including EEC.
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format: text/html
creator: Pingxia Lu
creator: Baowei Xu
creator: Xinyu Zhang
creator: Cuifeng Zheng
creator: Xianqiang Chen
creator: Junrong Zhang
creator: Yingping Cao
creator: Zhengyuan Huang
subject: Biochemistry
subject: Cell Biology
subject: Oncology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.20079
publisher: PeerJ Inc.
rights: © 2025 Lu et al.
abstract: Background This study aimed to investigate serum CXC motif chemokine ligand 8 (CXCL-8) as a potential biomarker for diagnosing esophageal cancer (EC). Methods Patients diagnosed with EC (n = 141) were enrolled at the Department of Thoracic Surgery, Fujian Medical University Union Hospital, from July through December 2023. Sixty cases were early esophageal cancer (EEC), whereas 81 were advanced (AEC) based on diagnostic criteria. Healthy volunteers (n = 75) were recruited as controls. Serum CXCL-8 levels were quantified using an enzyme-linked immunosorbent assay. Levels of carcinoembryonic antigen (CEA), cytokeratin 19 fragment (Cyfra211), and squamous cell carcinoma antigen (SCC) were assessed using a chemiluminescent microparticle immunoassay. Clinical and pathological attributes of patients with EC were documented and analyzed. Diagnostic efficacies of CXCL-8, CEA, Cyfra211, and SCC for EC were evaluated using receiver operating characteristic (ROC) curves. Results Serum concentrations of CXCL-8, CEA, Cyfra211, and SCC were significantly higher in patients with EC than in controls (P < 0.05). In the EC group, areas under the curves (AUCs) for CXCL-8, CEA, Cyfra211, and SCC were 0.906, 0.707, 0.705, and 0.797, respectively. The combined application of CXCL-8+CEA, CXCL-8+Cyfra211, and CXCL-8+SCC yielded AUCs of 0.931, 0.940, and 0.950, respectively, and was significantly higher than that of the combination of CEA+Cyfra211+SCC (0.854). In EEC, the diagnostic performance of CXCL-8 was similar to that in the EC group. The sensitivity of CXCL-8 was greater than that of CEA, Cyfra211, and SCC alone, and the combination of the three markers (P < 0.05). Conclusions CXCL-8 could be used to distinguish patients with EC from healthy controls, including EEC.
bibliographic citation: Lu et al. (2025) Comparison of the clinical usefulness of CXCL-8 and common clinical tumor markers for esophageal cancer diagnosis. PeerJ 13:e20079 https://doi.org/10.7717/peerj.20079
date submitted: 2025-02-26
date accepted: 2025-08-24
issued: 2025-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Lu
  given name: Pingxia
author list: Agent
  family name: Xu
  given name: Baowei
author list: Agent
  family name: Zhang
  given name: Xinyu
author list: Agent
  family name: Zheng
  given name: Cuifeng
author list: Agent
  family name: Chen
  given name: Xianqiang
author list: Agent
  family name: Zhang
  given name: Junrong
author list: Agent
  family name: Cao
  given name: Yingping
author list: Agent
  family name: Huang
  given name: Zhengyuan
doi: 10.7717/peerj.20079
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-28
copyright: © 2025 Lu et al.
attribution name: Lu et al.

Single-particle analysis of small extracellular vesicles from human follicular fluid unveils immunomodulatory PD-L1+ subpopulations and potentially fertility biomarkers
type: item
type: AcademicArticle
description: In certain cell systems, small extracellular vesicles bearing PD-L1 (PD-L1+ sEVs) have been shown to suppress T-cell immunity. We investigated whether a distinct profile of PD-L1+ sEVs exists in human follicular fluid (FF), a microenvironment where immune tolerance is crucial for proper follicular development. We characterized the expression and colocalization of CD63, CD81, CD9, and PD-L1 in sEVs derived from FF of women undergoing fertility treatments (n = 10), utilizing single-particle interferometric reflectance imaging sensing combined with single-particle antibody capture and immunofluorescence labeling. Additionally, sEV size distribution was analysed via atomic force microscopy. These integrated techniques revealed that the majority of tetraspanin-expressing EVs in human FF are smaller than 50 nm. Statistical analysis revealed a significant difference in PD-L1 co-expression across CD63, CD81, and CD9, confirming a preferential association of PD-L1 with CD9+ sEVs. Coefficients of variation across the cohort further indicated that PD-L1/CD9 co-expression was the most consistent among patients, suggesting a stable and distinct sEV subpopulation. These findings underscore the potential of PD-L1+ sEVs as biomarkers for immune regulation in reproductive treatments. The discovery of distinct PD-L1+ sEV subpopulations suggests a role in modulating immune responses within the follicular microenvironment. Further studies are warranted to investigate the functional relevance of these vesicles in predicting fertility outcome, promoting local immune tolerance, and facilitating follicular development.
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format: text/html
creator: Barbara Bortot
creator: Roberta Di Florio
creator: Gabriella Zito
creator: Francesco Valle
creator: Marco Brucale
creator: Giuseppe Ricci
creator: Paola Vigano
creator: Stefania Biffi
subject: Biochemistry
subject: Cell Biology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.20057
publisher: PeerJ Inc.
rights: © 2025 Bortot et al.
abstract: In certain cell systems, small extracellular vesicles bearing PD-L1 (PD-L1+ sEVs) have been shown to suppress T-cell immunity. We investigated whether a distinct profile of PD-L1+ sEVs exists in human follicular fluid (FF), a microenvironment where immune tolerance is crucial for proper follicular development. We characterized the expression and colocalization of CD63, CD81, CD9, and PD-L1 in sEVs derived from FF of women undergoing fertility treatments (n = 10), utilizing single-particle interferometric reflectance imaging sensing combined with single-particle antibody capture and immunofluorescence labeling. Additionally, sEV size distribution was analysed via atomic force microscopy. These integrated techniques revealed that the majority of tetraspanin-expressing EVs in human FF are smaller than 50 nm. Statistical analysis revealed a significant difference in PD-L1 co-expression across CD63, CD81, and CD9, confirming a preferential association of PD-L1 with CD9+ sEVs. Coefficients of variation across the cohort further indicated that PD-L1/CD9 co-expression was the most consistent among patients, suggesting a stable and distinct sEV subpopulation. These findings underscore the potential of PD-L1+ sEVs as biomarkers for immune regulation in reproductive treatments. The discovery of distinct PD-L1+ sEV subpopulations suggests a role in modulating immune responses within the follicular microenvironment. Further studies are warranted to investigate the functional relevance of these vesicles in predicting fertility outcome, promoting local immune tolerance, and facilitating follicular development.
bibliographic citation: Bortot et al. (2025) Single-particle analysis of small extracellular vesicles from human follicular fluid unveils immunomodulatory PD-L1+ subpopulations and potentially fertility biomarkers. PeerJ 13:e20057 https://doi.org/10.7717/peerj.20057
date submitted: 2025-05-15
date accepted: 2025-08-17
issued: 2025-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bortot
  given name: Barbara
author list: Agent
  family name: Di Florio
  given name: Roberta
author list: Agent
  family name: Zito
  given name: Gabriella
author list: Agent
  family name: Valle
  given name: Francesco
author list: Agent
  family name: Brucale
  given name: Marco
author list: Agent
  family name: Ricci
  given name: Giuseppe
author list: Agent
  family name: Vigano
  given name: Paola
author list: Agent
  family name: Biffi
  given name: Stefania
doi: 10.7717/peerj.20057
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-28
copyright: ©2025 Bortot et al.
attribution name: Bortot et al.

Identification of keratinocyte-associated genes for immune characterization and drug response prediction in oral squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Oral squamous cell carcinoma (OSCC) is one of the most frequent types of head and neck tumor. Keratinocytes play a crucial part in tumor cell growth but their role in OSCC remains unknown. Methods We obtained single-cell RNA sequencing (scRNA-seq) data and bulk RNA sequencing data of OSCC from the Gene Expression Omnibus (GEO) database and utilized the Seurat package for quality control, downscaling, and clustering of the scRNA-seq data. The CellChat package was utilized to develop a ligand-receptor network of keratinocytes. Subsequently, high-dimensional weighted gene co-expression network analysis (hdWGCNA) and differential expression analysis were employed to identify keratinocyte-related gene modules and obtain hub genes. The predictive value of the hub genes was assessed by constructing a diagnostic model, and the CIBERSORT and ESTIMATE algorithms were utilized to analyze the correlation between immune infiltration and the diagnostic model. Finally, the mRNA expressions of the screened genes were measured, and their effects on the proliferation, migration, and invasion ability of OSCC cells were explored using in vitro models. Results We identified eight major cellular subpopulations including T cells and keratinocytes. Cellular communication revealed that keratinocytes may have close mutual communication with macrophages, fibroblasts, and endothelial cells. The hdWGCNA screening classified nine keratinocyte-related modules and 50 hub genes were extracted, among them KRT6B, KRT16, CSTB, and CSTA were identified as differentially expressed keratinocyte-related genes. A nomogram was developed, and KRT16, CSTA, and CSTB were determined as highly effective genes for the diagnosis of OSCC. Immune infiltration analysis revealed that StromalScore, ImmuneScore and ESTIMATEScore, were negatively linked to CSTA and CSTB but positively correlated with KRT16. Finally, in vitro experiments showed that the viability, migration, and invasion of OSCC cells were mark…
format: application/pdf
format: text/html
creator: Jinyu Huang
creator: Yijing Li
creator: Weiyi Lin
creator: Zhiqin Wu
creator: Shanshan Si
creator: Dalong Shu
subject: Biochemistry
subject: Cell Biology
subject: Genetics
description: doi:10.7717/peerj.19953
publisher: PeerJ Inc.
rights: © 2025 Huang et al.
abstract: Background Oral squamous cell carcinoma (OSCC) is one of the most frequent types of head and neck tumor. Keratinocytes play a crucial part in tumor cell growth but their role in OSCC remains unknown. Methods We obtained single-cell RNA sequencing (scRNA-seq) data and bulk RNA sequencing data of OSCC from the Gene Expression Omnibus (GEO) database and utilized the Seurat package for quality control, downscaling, and clustering of the scRNA-seq data. The CellChat package was utilized to develop a ligand-receptor network of keratinocytes. Subsequently, high-dimensional weighted gene co-expression network analysis (hdWGCNA) and differential expression analysis were employed to identify keratinocyte-related gene modules and obtain hub genes. The predictive value of the hub genes was assessed by constructing a diagnostic model, and the CIBERSORT and ESTIMATE algorithms were utilized to analyze the correlation between immune infiltration and the diagnostic model. Finally, the mRNA expressions of the screened genes were measured, and their effects on the proliferation, migration, and invasion ability of OSCC cells were explored using in vitro models. Results We identified eight major cellular subpopulations including T cells and keratinocytes. Cellular communication revealed that keratinocytes may have close mutual communication with macrophages, fibroblasts, and endothelial cells. The hdWGCNA screening classified nine keratinocyte-related modules and 50 hub genes were extracted, among them KRT6B, KRT16, CSTB, and CSTA were identified as differentially expressed keratinocyte-related genes. A nomogram was developed, and KRT16, CSTA, and CSTB were determined as highly effective genes for the diagnosis of OSCC. Immune infiltration analysis revealed that StromalScore, ImmuneScore and ESTIMATEScore, were negatively linked to CSTA and CSTB but positively correlated with KRT16. Finally, in vitro experiments showed that the viability, migration, and invasion of OSCC cells were mark…
bibliographic citation: Huang et al. (2025) Identification of keratinocyte-associated genes for immune characterization and drug response prediction in oral squamous cell carcinoma. PeerJ 13:e19953 https://doi.org/10.7717/peerj.19953
date submitted: 2025-05-14
date accepted: 2025-07-29
issued: 2025-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Jinyu
author list: Agent
  family name: Li
  given name: Yijing
author list: Agent
  family name: Lin
  given name: Weiyi
author list: Agent
  family name: Wu
  given name: Zhiqin
author list: Agent
  family name: Si
  given name: Shanshan
author list: Agent
  family name: Shu
  given name: Dalong
doi: 10.7717/peerj.19953
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-28
copyright: ©2025 Huang et al.
attribution name: Huang et al.

Sniffin’ sticks smell identification test: exploring measurement properties in an adult Brazilian healthcare professionals sample
type: item
type: AcademicArticle
description: Introduction Olfactory evaluation has gained significant attention in both neurological and otorhinolaryngological assessments, particularly following the COVID-19 pandemic where SARS-CoV-2 infection emerged as a frequent cause of chemosensory dysfunction. The Sniffin’ Sticks identification test is a widely used screening tool for olfactory function. This study aimed to investigate the psychometric properties, specifically validity evidence based on internal structure (unidimensionality) and relations to other variables (demographic effects), of the 16-item Sniffin’ Sticks odor identification test (SS-16) in a homogeneous sample of highly educated young and middle-aged Brazilian adults, while exploring item-specific demographic effects. Methods A prospective observational cross-sectional study was conducted on 144 highly educated adults. The SS-16 was administered using the ‘Odor-on-lines’ paradigm. Rasch analysis assessed person-item mapping and fit statistics, while multiple regression analyses determined the effects of age, sex, and education on both overall and item-specific performance. Results Rasch analysis supported the unidimensionality of the SS-16. Item difficulty varied, with peppermint, cinnamon, and fish being easiest to identify, while apple, turpentine, and liquorice were the most challenging. Item-level analyses revealed specific demographic influences: older age was associated with poorer identification of coffee (β = −0.05, p = 0.021) and cloves (β = −0.123, p = 0.001); female sex was associated with significantly better identification of rose (β = 1.15, p = 0.026); and higher education level positively impacted identification of cloves and anise (β = 0.122, p = 0.011). These item-specific effects suggest potential differential age-related vulnerability for certain odorants, possible hormonal influences on floral odor detection, and educational effects potentially linked to semantic processing of complex aromas. Smell identification capacity was c…
format: application/pdf
format: text/html
creator: Pedro Renato de Paula Brandão
creator: Danilo Assis Pereira
creator: Diógenes Diego de Carvalho Bispo
creator: Felipe von Glehn
creator: Laura Silveira-Moriyama
creator: Simoneide Souza Titze-de-Almeida
creator: Marcio Nakanishi
creator: Felipe Saldanha-Araujo
creator: Enrique Roberto Arganaraz
creator: Adriana Pinheiro Ribeiro
creator: Agda Lima dos Santos
creator: Ricardo Titze-de-Almeida
subject: Neurology
subject: Otorhinolaryngology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.19733
publisher: PeerJ Inc.
rights: © 2025 Brandão et al.
abstract: Introduction Olfactory evaluation has gained significant attention in both neurological and otorhinolaryngological assessments, particularly following the COVID-19 pandemic where SARS-CoV-2 infection emerged as a frequent cause of chemosensory dysfunction. The Sniffin’ Sticks identification test is a widely used screening tool for olfactory function. This study aimed to investigate the psychometric properties, specifically validity evidence based on internal structure (unidimensionality) and relations to other variables (demographic effects), of the 16-item Sniffin’ Sticks odor identification test (SS-16) in a homogeneous sample of highly educated young and middle-aged Brazilian adults, while exploring item-specific demographic effects. Methods A prospective observational cross-sectional study was conducted on 144 highly educated adults. The SS-16 was administered using the ‘Odor-on-lines’ paradigm. Rasch analysis assessed person-item mapping and fit statistics, while multiple regression analyses determined the effects of age, sex, and education on both overall and item-specific performance. Results Rasch analysis supported the unidimensionality of the SS-16. Item difficulty varied, with peppermint, cinnamon, and fish being easiest to identify, while apple, turpentine, and liquorice were the most challenging. Item-level analyses revealed specific demographic influences: older age was associated with poorer identification of coffee (β = −0.05, p = 0.021) and cloves (β = −0.123, p = 0.001); female sex was associated with significantly better identification of rose (β = 1.15, p = 0.026); and higher education level positively impacted identification of cloves and anise (β = 0.122, p = 0.011). These item-specific effects suggest potential differential age-related vulnerability for certain odorants, possible hormonal influences on floral odor detection, and educational effects potentially linked to semantic processing of complex aromas. Smell identification capacity was c…
bibliographic citation: Brandão et al. (2025) Sniffin’ sticks smell identification test: exploring measurement properties in an adult Brazilian healthcare professionals sample. PeerJ 13:e19733 https://doi.org/10.7717/peerj.19733
date submitted: 2024-11-14
date accepted: 2025-06-20
issued: 2025-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brandão
  given name: Pedro Renato de Paula
author list: Agent
  family name: Pereira
  given name: Danilo Assis
author list: Agent
  family name: Bispo
  given name: Diógenes Diego de Carvalho
author list: Agent
  family name: von Glehn
  given name: Felipe
author list: Agent
  family name: Silveira-Moriyama
  given name: Laura
author list: Agent
  family name: Titze-de-Almeida
  given name: Simoneide Souza
author list: Agent
  family name: Nakanishi
  given name: Marcio
author list: Agent
  family name: Saldanha-Araujo
  given name: Felipe
author list: Agent
  family name: Arganaraz
  given name: Enrique Roberto
author list: Agent
  family name: Ribeiro
  given name: Adriana Pinheiro
author list: Agent
  family name: Santos
  given name: Agda Lima dos
author list: Agent
  family name: Titze-de-Almeida
  given name: Ricardo
doi: 10.7717/peerj.19733
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-28
copyright: © 2025 Brandão et al.
attribution name: Brandão et al.

Retrospective study: the value of GDF-15 and conventional markers in combination for clinical diagnosis of lung cancer
type: item
type: AcademicArticle
description: Lung cancer is a leading cause of morbidity and mortality worldwide, and effective biomarkers for its screening and monitoring are still lacking. This study aims to assess the diagnostic value of Growth Differentiation Factor 15 (GDF15) in lung cancer and its subtypes, compared to conventional biomarkers, to evaluate its potential as a predictive biomarker for lung cancer screening and monitoring. GDF15 levels were measured and analyzed in different subtypes of lung cancer and non-tumor controls. The correlation between GDF15 and the expression of eight conventional biomarkers was assessed by analyzing serum GDF15 levels in the markersnormal groups and the markershigh groups. The superiority of GDF15 in screening and monitoring of lung cancer was confirmed using the receiver operating characteristic (ROC) curve analysis of GDF15, alongside conventional biomarkers. Serum GDF15 levels were significantly higher in all subtypes of lung cancer compared with non-tumor controls, showing significant correlations with the levels of conventional biomarkers. ROC curve analysis demonstrated that GDF15 has superior sensitivity and specificity over conventional biomarkers, highlighting its potential as a promising diagnostic biomarker for lung cancer. GDF15 shows strong potential as a diagnostic tool for lung cancer, outperforming conventional markers. It presents a promising new biomarker for lung cancer monitoring and diagnosis.
format: application/pdf
format: text/html
creator: Jingru Ni
creator: Xiaohe Hao
creator: Yongkang Wu
creator: Cuiping Mao
creator: Limin Niu
creator: Heng Liu
creator: Qinghai Lin
subject: Epidemiology
subject: Oncology
subject: Respiratory Medicine
subject: Translational Medicine
description: doi:10.7717/peerj.20281
publisher: PeerJ Inc.
rights: © 2025 Ni et al.
abstract: Lung cancer is a leading cause of morbidity and mortality worldwide, and effective biomarkers for its screening and monitoring are still lacking. This study aims to assess the diagnostic value of Growth Differentiation Factor 15 (GDF15) in lung cancer and its subtypes, compared to conventional biomarkers, to evaluate its potential as a predictive biomarker for lung cancer screening and monitoring. GDF15 levels were measured and analyzed in different subtypes of lung cancer and non-tumor controls. The correlation between GDF15 and the expression of eight conventional biomarkers was assessed by analyzing serum GDF15 levels in the markersnormal groups and the markershigh groups. The superiority of GDF15 in screening and monitoring of lung cancer was confirmed using the receiver operating characteristic (ROC) curve analysis of GDF15, alongside conventional biomarkers. Serum GDF15 levels were significantly higher in all subtypes of lung cancer compared with non-tumor controls, showing significant correlations with the levels of conventional biomarkers. ROC curve analysis demonstrated that GDF15 has superior sensitivity and specificity over conventional biomarkers, highlighting its potential as a promising diagnostic biomarker for lung cancer. GDF15 shows strong potential as a diagnostic tool for lung cancer, outperforming conventional markers. It presents a promising new biomarker for lung cancer monitoring and diagnosis.
bibliographic citation: Ni et al. (2025) Retrospective study: the value of GDF-15 and conventional markers in combination for clinical diagnosis of lung cancer. PeerJ 13:e20281 https://doi.org/10.7717/peerj.20281
date submitted: 2025-01-03
date accepted: 2025-10-01
issued: 2025-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Ni
  given name: Jingru
author list: Agent
  family name: Hao
  given name: Xiaohe
author list: Agent
  family name: Wu
  given name: Yongkang
author list: Agent
  family name: Mao
  given name: Cuiping
author list: Agent
  family name: Niu
  given name: Limin
author list: Agent
  family name: Liu
  given name: Heng
author list: Agent
  family name: Lin
  given name: Qinghai
doi: 10.7717/peerj.20281
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-27
copyright: © 2025 Ni et al.
attribution name: Ni et al.

Accelerated straw decomposition and mitigated methane emissions via autumn puddling incorporation enhances soil health and yield stability in cold-region rice systems of China
type: item
type: AcademicArticle
description: This study discusses two challenges to rice production in China’s cold growing regions: the slow decomposition of straw due to low temperatures in the winter, and the environmental threats—concentrated methane emissions and soil reduction stress—associated with incorporation in the spring. To address these issues, a field experiment was conducted over two years (2022–2023) in paddy fields in central Jilin Province. The outcomes of three treatments were compared: no straw return (CK), puddling with water to promote straw incorporation in the spring (T1), and puddling with water to promote straw incorporation in the autumn (T2). The results demonstrated that T2 significantly enhanced the straw decomposition rate compared to T1 by extending the decomposition period, resulting in a 2.9% increase in straw weight loss after incorporation and a reduction in total methane emissions by 32.3%. T2 produced a smaller decline in soil redox potential, thereby alleviating soil reduction stress. Compared to CK, T2 significantly increased the levels of nitrogen, phosphorus , and calcium in the soil. T2 also maintained greater root activity and higher stem numbers than T1. While the grain yield under T2 did not differ significantly from that of CK, the yield under T1 was significantly reduced by 12.7%. Thus, incorporating puddling in autumn accelerates straw decomposition, reduces summer methane peaks, alleviates soil stress, enhances nutrient supply, and stabilizes yields. This makes it a sustainable strategy for managing straw in cold-region rice systems.
format: application/pdf
format: text/html
creator: Bing He
creator: Yonglin Si
creator: Chao Li
creator: Limin Wang
subject: Agricultural Science
subject: Ecology
subject: Soil Science
subject: Environmental Impacts
description: doi:10.7717/peerj.20264
publisher: PeerJ Inc.
rights: © 2025 He et al.
abstract: This study discusses two challenges to rice production in China’s cold growing regions: the slow decomposition of straw due to low temperatures in the winter, and the environmental threats—concentrated methane emissions and soil reduction stress—associated with incorporation in the spring. To address these issues, a field experiment was conducted over two years (2022–2023) in paddy fields in central Jilin Province. The outcomes of three treatments were compared: no straw return (CK), puddling with water to promote straw incorporation in the spring (T1), and puddling with water to promote straw incorporation in the autumn (T2). The results demonstrated that T2 significantly enhanced the straw decomposition rate compared to T1 by extending the decomposition period, resulting in a 2.9% increase in straw weight loss after incorporation and a reduction in total methane emissions by 32.3%. T2 produced a smaller decline in soil redox potential, thereby alleviating soil reduction stress. Compared to CK, T2 significantly increased the levels of nitrogen, phosphorus , and calcium in the soil. T2 also maintained greater root activity and higher stem numbers than T1. While the grain yield under T2 did not differ significantly from that of CK, the yield under T1 was significantly reduced by 12.7%. Thus, incorporating puddling in autumn accelerates straw decomposition, reduces summer methane peaks, alleviates soil stress, enhances nutrient supply, and stabilizes yields. This makes it a sustainable strategy for managing straw in cold-region rice systems.
bibliographic citation: He et al. (2025) Accelerated straw decomposition and mitigated methane emissions via autumn puddling incorporation enhances soil health and yield stability in cold-region rice systems of China. PeerJ 13:e20264 https://doi.org/10.7717/peerj.20264
date submitted: 2025-07-08
date accepted: 2025-09-29
issued: 2025-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Bing
author list: Agent
  family name: Si
  given name: Yonglin
author list: Agent
  family name: Li
  given name: Chao
author list: Agent
  family name: Wang
  given name: Limin
doi: 10.7717/peerj.20264
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-27
copyright: ©2025 He et al.
attribution name: He et al.

Lower limb joints’ contributions to ballet turnout during unipodal and bipodal jumps in fifth position in pre-professional dancers
type: item
type: AcademicArticle
description: Turnout, a large external rotation of the lower limb joints, is a key element of jumps and of other postures in classical ballet technique. Correct transverse-plane alignment of body segments in turnout is critical to reduce technical errors and injury risk. Although many studies have examined turnout in static positions, there is a need for a deeper understanding of this element dynamically, particularly during uni- and bipodal jumps with body displacements in fifth position. Such insights could help improve the technique and the training protocols. This study investigated the external rotations of the hip, knee, and ankle in turnout during three phases (preparation, flight, and landing) of two jumps with displacement performed in the fifth position: one unipodal, the Sissone Ouvert, and one bipodal, the Assemblé Dessus. Twenty-eight pre-professional ballet dancers were analyzed with 10.9 ± 3.2 years of ballet practice, 12.4 ± 2.7 hours of weekly training and a passive hip external rotation (static turnout) of 53.9 ± 10.1 deg. The dancers were instrumented with 16 skin-markers according to the Plug-in-Gait protocol and an eight-camera motion analysis system recorded lower limb kinematics in the transverse plane of the self-selected leg. Temporal profiles of joint angles were time normalized and the external rotation peak of hip, ankle, and knee were compared across phases and joints by repeated measures analysis of variance (ANOVAs) and Newman–Keuls post hoc (p < 0.05). The external rotation peak of the ankle, knee, and hip differed across phases (p < 0.001) for both jumps. In the Assemblé, hip and knee rotation peaks exhibited a similar behavior between the preparation and flight, while the ankle reached its highest peak at landing (p = 0.022). In the Sissone’s preparation, knee and ankle peaks showed significantly greater rotation compared to hip (p < 0.001), whereas in the flight, the hip exhibited the highest rotation compared to the other joints (p < 0.001). T…
format: application/pdf
format: text/html
creator: Luciana C. Manfrim
creator: Maria Isabel V. Orselli
creator: Bianca M. Portela
creator: Matheus O. Moutinho
creator: Paolo Caravaggi
creator: Isabel C.N. Sacco
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.20263
publisher: PeerJ Inc.
rights: © 2025 Manfrim et al.
abstract: Turnout, a large external rotation of the lower limb joints, is a key element of jumps and of other postures in classical ballet technique. Correct transverse-plane alignment of body segments in turnout is critical to reduce technical errors and injury risk. Although many studies have examined turnout in static positions, there is a need for a deeper understanding of this element dynamically, particularly during uni- and bipodal jumps with body displacements in fifth position. Such insights could help improve the technique and the training protocols. This study investigated the external rotations of the hip, knee, and ankle in turnout during three phases (preparation, flight, and landing) of two jumps with displacement performed in the fifth position: one unipodal, the Sissone Ouvert, and one bipodal, the Assemblé Dessus. Twenty-eight pre-professional ballet dancers were analyzed with 10.9 ± 3.2 years of ballet practice, 12.4 ± 2.7 hours of weekly training and a passive hip external rotation (static turnout) of 53.9 ± 10.1 deg. The dancers were instrumented with 16 skin-markers according to the Plug-in-Gait protocol and an eight-camera motion analysis system recorded lower limb kinematics in the transverse plane of the self-selected leg. Temporal profiles of joint angles were time normalized and the external rotation peak of hip, ankle, and knee were compared across phases and joints by repeated measures analysis of variance (ANOVAs) and Newman–Keuls post hoc (p < 0.05). The external rotation peak of the ankle, knee, and hip differed across phases (p < 0.001) for both jumps. In the Assemblé, hip and knee rotation peaks exhibited a similar behavior between the preparation and flight, while the ankle reached its highest peak at landing (p = 0.022). In the Sissone’s preparation, knee and ankle peaks showed significantly greater rotation compared to hip (p < 0.001), whereas in the flight, the hip exhibited the highest rotation compared to the other joints (p < 0.001). T…
bibliographic citation: Manfrim et al. (2025) Lower limb joints’ contributions to ballet turnout during unipodal and bipodal jumps in fifth position in pre-professional dancers. PeerJ 13:e20263 https://doi.org/10.7717/peerj.20263
date submitted: 2025-05-30
date accepted: 2025-09-29
issued: 2025-10-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Manfrim
  given name: Luciana C.
author list: Agent
  family name: Orselli
  given name: Maria Isabel V.
author list: Agent
  family name: Portela
  given name: Bianca M.
author list: Agent
  family name: Moutinho
  given name: Matheus O.
author list: Agent
  family name: Caravaggi
  given name: Paolo
author list: Agent
  family name: Sacco
  given name: Isabel C.N.
doi: 10.7717/peerj.20263
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-27
copyright: ©2025 Manfrim et al.
attribution name: Manfrim et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359