PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Patterns of pre-sleep music use and sleep quality: exploratory survey findings on state anxiety
items: Biological maturation, anthropometric, and physical fitness variables of youth breaking athletes with different competition levels
items: Efflux systems driving resistance and virulence across biological domains
items: Pelvis-Trunk coordination strategies differ a cross preparatory court movement distances during the tennis forehand
items: Mandibular form and function is more disparate in amniotes than in non-amniote tetrapods from the late Palaeozoic
items: Overexpression of ORAOV1 and its association with immunotherapy resistance in hepatocellular carcinoma
items: Resistance of cervical vertebrae in response to muscular stresses in pterosaurs: implications for foraging habits and skeletal pneumatization
items: Microbiome shifts during Fusarium oxysporum and F. solani (syn. Neocosmospora solani)—induced Ligusticum chuanxiong root rot: endophtic bacterial protective responses and fungal pathogenic tendencies
items: Comparative efficacy of different exercise interventions in patients with ankylosing spondylitis: a systematic review and network meta-analysis
items: Coral reefs in the Mahafaly Seascape (SW Madagascar) as potential climate refugia following the 2024 mass bleaching event

Patterns of pre-sleep music use and sleep quality: exploratory survey findings on state anxiety
type: item
type: AcademicArticle
description: Music listening is a widely used self-help approach that may influence psychological and physiological processes associated with sleep. This cross-sectional study explored patterns of pre-sleep music use in relation to psychological distress (state anxiety, mood disturbance, stress) and subjective sleep quality. Adults (N = 269, 52.6% female; Mage = 27.7, SD = 9.0) completed validated self-report measures of sleep quality (the Pittsburgh Sleep Quality Index (PSQI)) and psychological distress. Pre-sleep music use was modestly associated with poorer sleep quality (r = 0.23, p < 0.01). A borderline interaction between state anxiety and music use (β = −0.170, p = 0.050) suggested, but did not confirm, a possible buffering pattern in which the anxiety-sleep association appeared weaker among more frequent music users. No moderation effects were observed for mood or stress. These preliminary findings suggest that pre-sleep music use may reflect a coping-oriented effort among individuals experiencing anxiety. However, given the cross-sectional design, self-report measures, and borderline statistical support, the results should be viewed as descriptive and hypothesis-generating.
format: application/pdf
format: text/html
creator: Andrew Danso
creator: Mareike Ehlert
creator: Friederike Koehler
creator: Rory Kirk
creator: Nandhini Natarajan
creator: Shannon Eilyce Wright
creator: Renee Timmers
creator: Suvi Saarikallio
subject: Health Policy
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
subject: Healthcare Services
description: doi:10.7717/peerj.20444
publisher: PeerJ Inc.
rights: © 2025 Danso et al.
abstract: Music listening is a widely used self-help approach that may influence psychological and physiological processes associated with sleep. This cross-sectional study explored patterns of pre-sleep music use in relation to psychological distress (state anxiety, mood disturbance, stress) and subjective sleep quality. Adults (N = 269, 52.6% female; Mage = 27.7, SD = 9.0) completed validated self-report measures of sleep quality (the Pittsburgh Sleep Quality Index (PSQI)) and psychological distress. Pre-sleep music use was modestly associated with poorer sleep quality (r = 0.23, p < 0.01). A borderline interaction between state anxiety and music use (β = −0.170, p = 0.050) suggested, but did not confirm, a possible buffering pattern in which the anxiety-sleep association appeared weaker among more frequent music users. No moderation effects were observed for mood or stress. These preliminary findings suggest that pre-sleep music use may reflect a coping-oriented effort among individuals experiencing anxiety. However, given the cross-sectional design, self-report measures, and borderline statistical support, the results should be viewed as descriptive and hypothesis-generating.
bibliographic citation: Danso et al. (2025) Patterns of pre-sleep music use and sleep quality: exploratory survey findings on state anxiety. PeerJ 13:e20444 https://doi.org/10.7717/peerj.20444
date submitted: 2025-05-05
date accepted: 2025-10-31
issued: 2025-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Danso
  given name: Andrew
author list: Agent
  family name: Ehlert
  given name: Mareike
author list: Agent
  family name: Koehler
  given name: Friederike
author list: Agent
  family name: Kirk
  given name: Rory
author list: Agent
  family name: Natarajan
  given name: Nandhini
author list: Agent
  family name: Wright
  given name: Shannon Eilyce
author list: Agent
  family name: Timmers
  given name: Renee
author list: Agent
  family name: Saarikallio
  given name: Suvi
doi: 10.7717/peerj.20444
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-26
copyright: © 2025 Danso et al.
attribution name: Danso et al.

Biological maturation, anthropometric, and physical fitness variables of youth breaking athletes with different competition levels
type: item
type: AcademicArticle
description: Purpose This study aimed to analyze differences in anthropometric characteristics and physical fitness performance based on chronological age, maturation status, and competition level among youth breaking athletes. Methods Morphological characteristics and selected physical fitness performances were assessed in 23 male youth breaking athletes (mean age: 14.47 ± 1.99 years). Biological maturity was estimated from anthropometric measures and expressed as age at peak height velocity (APHV) and maturity offset. All athletes were classified into two age groups (U14 and U18), three maturity groups (pre-peak height velocity (PHV), circum-PHV, and post-PHV) and two competition level groups (elite and sub-elite). Independent samples t-tests and analysis of variance (ANOVAs) were employed to examine group differences, and Pearson correlation analysis was conducted to investigate intragroup relationships between morphological and physical fitness variables. Results There was no difference in body fat percentage (P > 0.05) between U14 and U18 in terms of anthropometric measurement indicators. In contrast, significant differences (P < 0.05) were observed in most physical fitness indicators (T-test, standing long jump, 30-m sprint, p ull up and 400-m run), with the U18 athletes showing superior performance. No significant differences were observed between elite and sub-elite youth breaking athletes, except in the one-minute sit-up test (P = 0.028). Significant differences among different maturity groups were found in age (P < 0.01), maturity offset (P < 0.001), height (P < 0.001), body mass (P < 0.001), body mass index (BMI) (P < 0.001), sitting height (P < 0.001), leg length (P = 0.016), T-test (P = 0.029), standing long jump (P = 0.019), 30-m sprint (P = 0.006), 30s bodyweight squat (P = 0.030), and 400-m (P = 0.021). While chronological age and maturity status correlated with multiple physical performance indicators, body fat percentage (P > 0.05) showed no such association. C…
format: application/pdf
format: text/html
creator: Yifan Zhao
creator: Xiaobin Wei
creator: Kewei Zhao
subject: Anatomy and Physiology
subject: Sports Medicine
description: doi:10.7717/peerj.20383
publisher: PeerJ Inc.
rights: © 2025 Zhao et al.
abstract: Purpose This study aimed to analyze differences in anthropometric characteristics and physical fitness performance based on chronological age, maturation status, and competition level among youth breaking athletes. Methods Morphological characteristics and selected physical fitness performances were assessed in 23 male youth breaking athletes (mean age: 14.47 ± 1.99 years). Biological maturity was estimated from anthropometric measures and expressed as age at peak height velocity (APHV) and maturity offset. All athletes were classified into two age groups (U14 and U18), three maturity groups (pre-peak height velocity (PHV), circum-PHV, and post-PHV) and two competition level groups (elite and sub-elite). Independent samples t-tests and analysis of variance (ANOVAs) were employed to examine group differences, and Pearson correlation analysis was conducted to investigate intragroup relationships between morphological and physical fitness variables. Results There was no difference in body fat percentage (P > 0.05) between U14 and U18 in terms of anthropometric measurement indicators. In contrast, significant differences (P < 0.05) were observed in most physical fitness indicators (T-test, standing long jump, 30-m sprint, p ull up and 400-m run), with the U18 athletes showing superior performance. No significant differences were observed between elite and sub-elite youth breaking athletes, except in the one-minute sit-up test (P = 0.028). Significant differences among different maturity groups were found in age (P < 0.01), maturity offset (P < 0.001), height (P < 0.001), body mass (P < 0.001), body mass index (BMI) (P < 0.001), sitting height (P < 0.001), leg length (P = 0.016), T-test (P = 0.029), standing long jump (P = 0.019), 30-m sprint (P = 0.006), 30s bodyweight squat (P = 0.030), and 400-m (P = 0.021). While chronological age and maturity status correlated with multiple physical performance indicators, body fat percentage (P > 0.05) showed no such association. C…
bibliographic citation: Zhao et al. (2025) Biological maturation, anthropometric, and physical fitness variables of youth breaking athletes with different competition levels. PeerJ 13:e20383 https://doi.org/10.7717/peerj.20383
date submitted: 2025-05-08
date accepted: 2025-10-22
issued: 2025-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yifan
author list: Agent
  family name: Wei
  given name: Xiaobin
author list: Agent
  family name: Zhao
  given name: Kewei
doi: 10.7717/peerj.20383
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-26
copyright: ©2025 Zhao et al.
attribution name: Zhao et al.

Efflux systems driving resistance and virulence across biological domains
type: item
type: AcademicArticle
description: Background Efflux pumps (EPs) are key contributors to multidrug resistance (MDR) in bacteria, fungi, and cancer cells. These membrane proteins actively extrude a variety of therapeutic agents, reducing their intracellular concentration and thus compromising the efficacy of treatment. Beyond resistance, EPs are also involved in virulence, biofilm formation, immune evasion, and environmental persistence. Aim This review aimed to provide a comprehensive and critical synthesis of the role of efflux pumps in antimicrobial and antitumoral resistance, as well as their contribution to virulence and persistence across biological domains. Methodology A narrative review was conducted following a structured search strategy in PubMed, Scopus, and Web of Science using combinations of terms related to efflux systems, efflux pumps, resistance mechanisms, virulence factors, detection methods, and inhibitors. The review integrates data from in vitro, in silico, and clinical studies, including both classical detection strategies and emerging technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based modulation, biosensors, and microfluidics. Results Efflux pumps from different families (e.g., resistance-nodulation-division (RND), ATP-binding cassette (ABC), major facilitator superfamily (MFS)) are implicated in the active extrusion of antimicrobial agents, facilitating MDR and treatment failure in pathogens such as E. coli, P. aeruginosa, M. tuberculosis, Candida albicans, and cancer cells. EPs also regulate biofilm formation, virulence factor secretion, and metabolic adaptation. Classical methods for detecting efflux (e.g., minimum inhibitory concentration (MIC) shifts with inhibitors, fluorometric assays) have technical limitations, while novel technologies offer improved precision. Several natural and synthetic efflux pump inhibitors (EPIs) have demonstrated efficacy in preclinical studies, yet few have progressed to clinical use due to toxicity a…
format: application/pdf
format: text/html
creator: Pedro Eduardo Almeida da Silva
creator: Andrea Von Groll
creator: Ivy Ramis
creator: Ana Julia Reis
creator: Daniela Ramos
creator: Miguel Viveiros
subject: Microbiology
subject: Mycology
subject: Infectious Diseases
description: doi:10.7717/peerj.20360
publisher: PeerJ Inc.
rights: © 2025 Almeida da Silva et al.
abstract: Background Efflux pumps (EPs) are key contributors to multidrug resistance (MDR) in bacteria, fungi, and cancer cells. These membrane proteins actively extrude a variety of therapeutic agents, reducing their intracellular concentration and thus compromising the efficacy of treatment. Beyond resistance, EPs are also involved in virulence, biofilm formation, immune evasion, and environmental persistence. Aim This review aimed to provide a comprehensive and critical synthesis of the role of efflux pumps in antimicrobial and antitumoral resistance, as well as their contribution to virulence and persistence across biological domains. Methodology A narrative review was conducted following a structured search strategy in PubMed, Scopus, and Web of Science using combinations of terms related to efflux systems, efflux pumps, resistance mechanisms, virulence factors, detection methods, and inhibitors. The review integrates data from in vitro, in silico, and clinical studies, including both classical detection strategies and emerging technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based modulation, biosensors, and microfluidics. Results Efflux pumps from different families (e.g., resistance-nodulation-division (RND), ATP-binding cassette (ABC), major facilitator superfamily (MFS)) are implicated in the active extrusion of antimicrobial agents, facilitating MDR and treatment failure in pathogens such as E. coli, P. aeruginosa, M. tuberculosis, Candida albicans, and cancer cells. EPs also regulate biofilm formation, virulence factor secretion, and metabolic adaptation. Classical methods for detecting efflux (e.g., minimum inhibitory concentration (MIC) shifts with inhibitors, fluorometric assays) have technical limitations, while novel technologies offer improved precision. Several natural and synthetic efflux pump inhibitors (EPIs) have demonstrated efficacy in preclinical studies, yet few have progressed to clinical use due to toxicity a…
bibliographic citation: Almeida da Silva et al. (2025) Efflux systems driving resistance and virulence across biological domains. PeerJ 13:e20360 https://doi.org/10.7717/peerj.20360
date submitted: 2025-07-09
date accepted: 2025-10-17
issued: 2025-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almeida da Silva
  given name: Pedro Eduardo
author list: Agent
  family name: Von Groll
  given name: Andrea
author list: Agent
  family name: Ramis
  given name: Ivy
author list: Agent
  family name: Reis
  given name: Ana Julia
author list: Agent
  family name: Ramos
  given name: Daniela
author list: Agent
  family name: Viveiros
  given name: Miguel
doi: 10.7717/peerj.20360
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-26
copyright: ©2025 Almeida da Silva et al.
attribution name: Almeida da Silva et al.

Pelvis-Trunk coordination strategies differ a cross preparatory court movement distances during the tennis forehand
type: item
type: AcademicArticle
description: Objectives To examine the effects of on-court movement distances on pelvis-trunk coordination during forehand strokes. Methods Eighteen male college tennis athletes participated in this study. They performed forehand stroke task at three different preparatory court movement distances (minimum, medium and maximum movement distances). A one-way repeated-measures ANOVA with Statistical Parametric Mapping was used to determine differences in pelvis-trunk coordination in the transverse plane across the three movement distances, and Pearson’s correlation analysis was used to determine the relationships between each of the four pelvis-trunk coordination features on the dominant and non-dominant side and racket speed. Results Significant differences were observed for different movement distances in the non-dominant pelvis-trunk continuous relative phase (CRP) during 23–41% of the acceleration phase (p = 0.016, F2,34 = 5.901) and in the dominant pelvis-trunk CRP during 76–100% of the acceleration phase (p = 0.016, F2,34 = 5.946). For the minimum distance, significant correlations with racket speed were found in the mean CRP (r = − 0.889, p = 0.001) and peak CRP (r = − 0.488, p = 0.04) for the non-dominant side, and the mean CRP (r = − 0.478, p = 0.045) for the dominant side. Regarding medium distances, significant correlations with racket speed were observed for the non-dominant side in the mean CRP (r = − 0.493, p = 0.037), peak CRP (r = − 0.628, p = 0.005), and maximum positive CRP slope (r = 0.477, p = 0.046). For the dominant side, significant correlations with racket speed were noted for peak CRP (r = 0.551, p = 0.018) and maximum positive CRP slope (r = 0.514, p = 0.029). At the maximum distance, significant correlations with racket speed were identified for the dominant side in the maximum positive CRP slope (r = 0.580, p = 0.012) and maximum negative CRP slope (r = 0.566, p = 0.014); however, there was no significant difference in racket speed at impact when approach…
format: application/pdf
format: text/html
creator: Xiangwei Meng
creator: Youngsuk Kim
creator: Shuai Wang
creator: Sukwon Kim
creator: Ming Li
subject: Kinesiology
subject: Computational Science
subject: Biomechanics
description: doi:10.7717/peerj.20321
publisher: PeerJ Inc.
rights: © 2025 Meng et al.
abstract: Objectives To examine the effects of on-court movement distances on pelvis-trunk coordination during forehand strokes. Methods Eighteen male college tennis athletes participated in this study. They performed forehand stroke task at three different preparatory court movement distances (minimum, medium and maximum movement distances). A one-way repeated-measures ANOVA with Statistical Parametric Mapping was used to determine differences in pelvis-trunk coordination in the transverse plane across the three movement distances, and Pearson’s correlation analysis was used to determine the relationships between each of the four pelvis-trunk coordination features on the dominant and non-dominant side and racket speed. Results Significant differences were observed for different movement distances in the non-dominant pelvis-trunk continuous relative phase (CRP) during 23–41% of the acceleration phase (p = 0.016, F2,34 = 5.901) and in the dominant pelvis-trunk CRP during 76–100% of the acceleration phase (p = 0.016, F2,34 = 5.946). For the minimum distance, significant correlations with racket speed were found in the mean CRP (r = − 0.889, p = 0.001) and peak CRP (r = − 0.488, p = 0.04) for the non-dominant side, and the mean CRP (r = − 0.478, p = 0.045) for the dominant side. Regarding medium distances, significant correlations with racket speed were observed for the non-dominant side in the mean CRP (r = − 0.493, p = 0.037), peak CRP (r = − 0.628, p = 0.005), and maximum positive CRP slope (r = 0.477, p = 0.046). For the dominant side, significant correlations with racket speed were noted for peak CRP (r = 0.551, p = 0.018) and maximum positive CRP slope (r = 0.514, p = 0.029). At the maximum distance, significant correlations with racket speed were identified for the dominant side in the maximum positive CRP slope (r = 0.580, p = 0.012) and maximum negative CRP slope (r = 0.566, p = 0.014); however, there was no significant difference in racket speed at impact when approach…
bibliographic citation: Meng et al. (2025) Pelvis-Trunk coordination strategies differ a cross preparatory court movement distances during the tennis forehand. PeerJ 13:e20321 https://doi.org/10.7717/peerj.20321
date submitted: 2025-02-13
date accepted: 2025-10-10
issued: 2025-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Meng
  given name: Xiangwei
author list: Agent
  family name: Kim
  given name: Youngsuk
author list: Agent
  family name: Wang
  given name: Shuai
author list: Agent
  family name: Kim
  given name: Sukwon
author list: Agent
  family name: Li
  given name: Ming
doi: 10.7717/peerj.20321
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-26
copyright: ©2025 Meng et al.
attribution name: Meng et al.

Mandibular form and function is more disparate in amniotes than in non-amniote tetrapods from the late Palaeozoic
type: item
type: AcademicArticle
description: Terrestrial tetrapods originated during the Middle Devonian, and the group rapidly diversified throughout the subsequent Carboniferous and Permian periods. Feeding in air rather than water is expected to require changes to tetrapod mandibular form and function. Previous biomechanical studies on jaw evolution, however, found that the increase in functional disparity lagged behind terrestrialisation by approximately 70 Myr, coinciding with the origin of amniotes and herbivory. We expand on a previous dataset composed primarily of non-amniote tetrapods to identify the drivers of this diversification, including representatives of all major amniote clades from the Permo-Carboniferous. First, we measured nine biomechanical traits from 111 tetrapod jaws in medial view. Second, we performed an Elliptical Fourier Analysis on 198 jaws in lateral view and 73 jaws in occlusal view. The first peak in jaw disparity, during the Pennsylvanian, occurs in carnivorous non-amniote tetrapods. However, the jaws of amniotes, particularly those inferred as herbivorous, are consistently more disparate than non-amniote tetrapods from the early Permian, especially in terms of jaw depth, symphysial length and force transmission. Functional and shape disparity of Palaeozoic tetrapod jaws follow a similar pattern that is explained by large-scale faunal turnovers and ecosystem structures.
format: application/pdf
format: text/html
creator: Jasper Ponstein
creator: Mark J. MacDougall
creator: Joep Schaeffer
creator: Christian F. Kammerer
creator: Jörg Fröbisch
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.20243
publisher: PeerJ Inc.
rights: © 2025 Ponstein et al.
abstract: Terrestrial tetrapods originated during the Middle Devonian, and the group rapidly diversified throughout the subsequent Carboniferous and Permian periods. Feeding in air rather than water is expected to require changes to tetrapod mandibular form and function. Previous biomechanical studies on jaw evolution, however, found that the increase in functional disparity lagged behind terrestrialisation by approximately 70 Myr, coinciding with the origin of amniotes and herbivory. We expand on a previous dataset composed primarily of non-amniote tetrapods to identify the drivers of this diversification, including representatives of all major amniote clades from the Permo-Carboniferous. First, we measured nine biomechanical traits from 111 tetrapod jaws in medial view. Second, we performed an Elliptical Fourier Analysis on 198 jaws in lateral view and 73 jaws in occlusal view. The first peak in jaw disparity, during the Pennsylvanian, occurs in carnivorous non-amniote tetrapods. However, the jaws of amniotes, particularly those inferred as herbivorous, are consistently more disparate than non-amniote tetrapods from the early Permian, especially in terms of jaw depth, symphysial length and force transmission. Functional and shape disparity of Palaeozoic tetrapod jaws follow a similar pattern that is explained by large-scale faunal turnovers and ecosystem structures.
bibliographic citation: Ponstein et al. (2025) Mandibular form and function is more disparate in amniotes than in non-amniote tetrapods from the late Palaeozoic. PeerJ 13:e20243 https://doi.org/10.7717/peerj.20243
date submitted: 2025-04-16
date accepted: 2025-09-24
issued: 2025-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ponstein
  given name: Jasper
author list: Agent
  family name: MacDougall
  given name: Mark J.
author list: Agent
  family name: Schaeffer
  given name: Joep
author list: Agent
  family name: Kammerer
  given name: Christian F.
author list: Agent
  family name: Fröbisch
  given name: Jörg
doi: 10.7717/peerj.20243
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-26
copyright: © 2025 Ponstein et al.
attribution name: Ponstein et al.

Overexpression of ORAOV1 and its association with immunotherapy resistance in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality globally. Previous studies have reported that oral cancer overexpression 1 (ORAOV1) is overexpressed in HCC and correlated with poor prognosis, yet its molecular mechanisms remain incompletely understood. In this study, ORAOV1 overexpression was confirmed in HCC tissues via tissue microarray analysis and functionally linked to tumor cell proliferation through a positive correlation with Ki-67 expression in the human HCC cell line MHCC-97L. Bioinformatics analyses using The Cancer Genome Atlas (TCGA) and three Gene Expression Omnibus (GEO) HCC datasets further supported these findings. Multiple mechanisms appear to drive ORAOV1 upregulation, including promoter hypomethylation, amplification of the 11q13 region, and a putative ceRNA network involving AC005332.1, AC012615.1, and hsa-miR-100-5p. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses implicated ORAOV1 in various cellular processes, such as abnormal membrane channel function, extracellular matrix–receptor interactions, IL-17 signaling, and peroxisome proliferator-activated receptor (PPAR) signaling. Co-expression analysis identified significant associations between ORAOV1 and the oncogenes TPCN2 and CCND1. Additionally, ORAOV1 expression correlated with enhanced infiltration of immunosuppressive cells, including regulatory T cells, myeloid-derived suppressor cells, and cancer-associated fibroblasts, as well as upregulation of immune checkpoint markers (PD-1, PD-L1, and CTLA-4). These results indicate that ORAOV1 may modulate the immunosuppressive tumor microenvironment and contribute to resistance against immunotherapy, highlighting its potential as a therapeutic target in HCC.
format: application/pdf
format: text/html
creator: Yuzhen Huang
creator: Ni Yang
creator: Su Wen
creator: Ziwei Fang
creator: Yucong Zhang
creator: Zonghao Qian
creator: Yi Huang
creator: Tiejun Yin
creator: Cuntai Zhang
creator: Le Zhang
subject: Bioinformatics
subject: Genetics
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20390
publisher: PeerJ Inc.
rights: © 2025 Huang et al.
abstract: Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality globally. Previous studies have reported that oral cancer overexpression 1 (ORAOV1) is overexpressed in HCC and correlated with poor prognosis, yet its molecular mechanisms remain incompletely understood. In this study, ORAOV1 overexpression was confirmed in HCC tissues via tissue microarray analysis and functionally linked to tumor cell proliferation through a positive correlation with Ki-67 expression in the human HCC cell line MHCC-97L. Bioinformatics analyses using The Cancer Genome Atlas (TCGA) and three Gene Expression Omnibus (GEO) HCC datasets further supported these findings. Multiple mechanisms appear to drive ORAOV1 upregulation, including promoter hypomethylation, amplification of the 11q13 region, and a putative ceRNA network involving AC005332.1, AC012615.1, and hsa-miR-100-5p. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses implicated ORAOV1 in various cellular processes, such as abnormal membrane channel function, extracellular matrix–receptor interactions, IL-17 signaling, and peroxisome proliferator-activated receptor (PPAR) signaling. Co-expression analysis identified significant associations between ORAOV1 and the oncogenes TPCN2 and CCND1. Additionally, ORAOV1 expression correlated with enhanced infiltration of immunosuppressive cells, including regulatory T cells, myeloid-derived suppressor cells, and cancer-associated fibroblasts, as well as upregulation of immune checkpoint markers (PD-1, PD-L1, and CTLA-4). These results indicate that ORAOV1 may modulate the immunosuppressive tumor microenvironment and contribute to resistance against immunotherapy, highlighting its potential as a therapeutic target in HCC.
bibliographic citation: Huang et al. (2025) Overexpression of ORAOV1 and its association with immunotherapy resistance in hepatocellular carcinoma. PeerJ 13:e20390 https://doi.org/10.7717/peerj.20390
date submitted: 2025-02-10
date accepted: 2025-10-24
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Yuzhen
author list: Agent
  family name: Yang
  given name: Ni
author list: Agent
  family name: Wen
  given name: Su
author list: Agent
  family name: Fang
  given name: Ziwei
author list: Agent
  family name: Zhang
  given name: Yucong
author list: Agent
  family name: Qian
  given name: Zonghao
author list: Agent
  family name: Huang
  given name: Yi
author list: Agent
  family name: Yin
  given name: Tiejun
author list: Agent
  family name: Zhang
  given name: Cuntai
author list: Agent
  family name: Zhang
  given name: Le
doi: 10.7717/peerj.20390
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Huang et al.
attribution name: Huang et al.

Resistance of cervical vertebrae in response to muscular stresses in pterosaurs: implications for foraging habits and skeletal pneumatization
type: item
type: AcademicArticle
description: The necks of pterosaurs were flexible and provided mobility for a relatively long skull. The varied morphologies and levels of pneumatization of their cervical vertebrae reflected differences in biomechanical behavior. Here, we examined the structural resistance of the cervical vertebrae to infer the most advantageous movements during the foraging behaviors of two pterodactyloid pterosaurs. We also examined the relationship between vertebral resistance and the presence of pneumatic foramina on the bone cortex. For this purpose, we analyzed three-dimensional models of the cervical vertebrae of Anhanguera piscator and Azhdarcho lancicollis, which are hypothesized to be aquatic and terrestrial predators, respectively, and employed Finite Element Analysis (FEA) to assess and quantify the stresses experienced by the vertebrae due to the performance of six different movement scenarios. We observed that the shorter vertebrae at the ends of the neck of both species favored the proliferation of larger stresses in these regions, especially in the posterior cervicals of Anhanguera piscator and in the atlas-axis of Azhdarcho lancicollis, and that their taller neural arches aided in absorbing stress. Larger stresses at the ends of the neck are consistent with the interior trabecular reinforcement of the atlas-axis and posterior cervical vertebrae, suggesting a link between biomechanical behavior and the level of pneumatization. Additionally, mechanical requirements may have also influenced the presence, size, and number of pneumatic foramina on the vertebral cortex, as evidenced by the large lateral foramen in Anhanguera piscator and the smaller and more numerous ones bordering the neural canal in Azhdarcho lancicollis. Our inferences corroborate the differences in foraging strategies hypothesized for anhanguerids and azhdarchids. The absorption of stresses resulting from ventral pitching of the head and neck indicates that the cervical vertebrae were well-adapted for making rap…
format: application/pdf
format: text/html
creator: Richard Buchmann
creator: Taissa Rodrigues
subject: Biophysics
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.20388
publisher: PeerJ Inc.
rights: © 2025 Buchmann and Rodrigues
abstract: The necks of pterosaurs were flexible and provided mobility for a relatively long skull. The varied morphologies and levels of pneumatization of their cervical vertebrae reflected differences in biomechanical behavior. Here, we examined the structural resistance of the cervical vertebrae to infer the most advantageous movements during the foraging behaviors of two pterodactyloid pterosaurs. We also examined the relationship between vertebral resistance and the presence of pneumatic foramina on the bone cortex. For this purpose, we analyzed three-dimensional models of the cervical vertebrae of Anhanguera piscator and Azhdarcho lancicollis, which are hypothesized to be aquatic and terrestrial predators, respectively, and employed Finite Element Analysis (FEA) to assess and quantify the stresses experienced by the vertebrae due to the performance of six different movement scenarios. We observed that the shorter vertebrae at the ends of the neck of both species favored the proliferation of larger stresses in these regions, especially in the posterior cervicals of Anhanguera piscator and in the atlas-axis of Azhdarcho lancicollis, and that their taller neural arches aided in absorbing stress. Larger stresses at the ends of the neck are consistent with the interior trabecular reinforcement of the atlas-axis and posterior cervical vertebrae, suggesting a link between biomechanical behavior and the level of pneumatization. Additionally, mechanical requirements may have also influenced the presence, size, and number of pneumatic foramina on the vertebral cortex, as evidenced by the large lateral foramen in Anhanguera piscator and the smaller and more numerous ones bordering the neural canal in Azhdarcho lancicollis. Our inferences corroborate the differences in foraging strategies hypothesized for anhanguerids and azhdarchids. The absorption of stresses resulting from ventral pitching of the head and neck indicates that the cervical vertebrae were well-adapted for making rap…
bibliographic citation: Buchmann et al. (2025) Resistance of cervical vertebrae in response to muscular stresses in pterosaurs: implications for foraging habits and skeletal pneumatization. PeerJ 13:e20388 https://doi.org/10.7717/peerj.20388
date submitted: 2025-07-22
date accepted: 2025-10-24
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buchmann
  given name: Richard
author list: Agent
  family name: Rodrigues
  given name: Taissa
doi: 10.7717/peerj.20388
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Buchmann and Rodrigues
attribution name: Buchmann and Rodrigues

Microbiome shifts during Fusarium oxysporum and F. solani (syn. Neocosmospora solani)—induced Ligusticum chuanxiong root rot: endophtic bacterial protective responses and fungal pathogenic tendencies
type: item
type: AcademicArticle
description: Root rot disease is a globally significant threat to the health of diverse economically important crops. Understanding shifts in the plant microbiome during disease progression can aid in identifying beneficial microbes with disease-resistant potential and developing ecofriendly biocontrol strategies. However, microbiome changes during root rot progression in the medicinal plant Ligusticum chuanxiong remain poorly understood. This study aimed to investigate the response of host-associated microbiomes to pathogen stress (Fusarium oxysporum and F. solani syn. Neocosmospora solani) during L. chuanxiong root rot. The diversity, composition, function, and network interactions of bacterial and fungal communities were examined using high-throughput sequencing and network analysis in healthy rhizomes, healthy layers of diseased rhizomes, rotten layers of diseased rhizomes, and rhizosphere and non-rhizosphere soils. The bacterial diversity decreased as root rot progressed in end ophytic (from 0.72 to 0.38) and rhizosphere soils (from 0.80 to 0.68), whereas the fungal diversity showed no significant changes. The diseased samples were enriched with root rot pathogens and other potential pathogens, such as the soil bacterium Pectobacterium and the soil fungus Gibberella, whereas beneficial taxa, including endophytic Bacillus and Trichoderma, and soil-dwelling Candidatus_Solibacter and Beauveria, were significantly reduced. Notably, in the healthy layers of diseased rhizomes, which represent a “transitional phase”, fungal communities resembled those in rotten tissues with increased pathogenic taxa (e.g., Ceratocystis and Plectosphaerella), whereas bacterial communities were more similar to healthy rhizomes and enriched in beneficial genera (e.g., Microbacterium and Variovorax). Functional prediction indicated suppressed bacterial activity and enhanced fungal saprotrophy in rotten rhizomes. The cross-kingdom network complexity decreased in both endophytic and soil microbial commu…
format: application/pdf
format: text/html
creator: Weiping Gao
creator: Hai Wang
creator: Hongmei Jia
creator: Jianyun Zhang
creator: Zhuyun Yan
creator: Dongmei He
creator: Chuan Zheng
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.20369
publisher: PeerJ Inc.
rights: © 2025 Gao et al.
abstract: Root rot disease is a globally significant threat to the health of diverse economically important crops. Understanding shifts in the plant microbiome during disease progression can aid in identifying beneficial microbes with disease-resistant potential and developing ecofriendly biocontrol strategies. However, microbiome changes during root rot progression in the medicinal plant Ligusticum chuanxiong remain poorly understood. This study aimed to investigate the response of host-associated microbiomes to pathogen stress (Fusarium oxysporum and F. solani syn. Neocosmospora solani) during L. chuanxiong root rot. The diversity, composition, function, and network interactions of bacterial and fungal communities were examined using high-throughput sequencing and network analysis in healthy rhizomes, healthy layers of diseased rhizomes, rotten layers of diseased rhizomes, and rhizosphere and non-rhizosphere soils. The bacterial diversity decreased as root rot progressed in end ophytic (from 0.72 to 0.38) and rhizosphere soils (from 0.80 to 0.68), whereas the fungal diversity showed no significant changes. The diseased samples were enriched with root rot pathogens and other potential pathogens, such as the soil bacterium Pectobacterium and the soil fungus Gibberella, whereas beneficial taxa, including endophytic Bacillus and Trichoderma, and soil-dwelling Candidatus_Solibacter and Beauveria, were significantly reduced. Notably, in the healthy layers of diseased rhizomes, which represent a “transitional phase”, fungal communities resembled those in rotten tissues with increased pathogenic taxa (e.g., Ceratocystis and Plectosphaerella), whereas bacterial communities were more similar to healthy rhizomes and enriched in beneficial genera (e.g., Microbacterium and Variovorax). Functional prediction indicated suppressed bacterial activity and enhanced fungal saprotrophy in rotten rhizomes. The cross-kingdom network complexity decreased in both endophytic and soil microbial commu…
bibliographic citation: Gao et al. (2025) Microbiome shifts during Fusarium oxysporum and F. solani (syn. Neocosmospora solani)—induced Ligusticum chuanxiong root rot: endophtic bacterial protective responses and fungal pathogenic tendencies. PeerJ 13:e20369 https://doi.org/10.7717/peerj.20369
date submitted: 2025-06-13
date accepted: 2025-10-18
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Gao
  given name: Weiping
author list: Agent
  family name: Wang
  given name: Hai
author list: Agent
  family name: Jia
  given name: Hongmei
author list: Agent
  family name: Zhang
  given name: Jianyun
author list: Agent
  family name: Yan
  given name: Zhuyun
author list: Agent
  family name: He
  given name: Dongmei
author list: Agent
  family name: Zheng
  given name: Chuan
doi: 10.7717/peerj.20369
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Gao et al.
attribution name: Gao et al.

Comparative efficacy of different exercise interventions in patients with ankylosing spondylitis: a systematic review and network meta-analysis
type: item
type: AcademicArticle
description: Background Exercise interventions have been widely applied as an adjunctive treatment for ankylosing spondylitis (AS), effectively alleviating pain, improving function, and enhancing quality of life. However, the efficacy of different exercise modalities remains inconclusive. This study aims to systematically compare the effects of various exercise interventions on clinical outcomes in AS patients using a network meta-analysis (NMA) to determine the optimal exercise regimen. Methods A comprehensive search was performed across six databases to identify studies assessing the impact of exercise interventions on AS. The primary outcomes analyzed included the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Functional Index (BASFI), Bath Ankylosing Spondylitis Metrology Index (BASMI), and Ankylosing Spondylitis Quality of Life (ASQoL). A network meta-analysis was conducted using the frequentist approach in STATA 18.0, while effect publication bias analysis used Review Manager 5.4. Results Forty-eight studies involving 3,140 participants were included, published between 2002 and 2024. Compared to the control group, all exercise interventions demonstrated varying degrees of benefit in improving BASDAI, BASFI, BASMI, and ASQoL scores. For BASDAI, the Aquatic Stretching Exercise (ASE) (−1.42, 95% CI [−2.51 to −0.33]), Land Aerobic Exercise (LAE) (−0.94, 95% CI [−1.41 to −0.47]), and Land Stretching Exercise (LSE) (−0.49, 95% CI [−0.94 to −0.04]) exhibited significant symptom relief, with ASE ranking highest (surface under the cumulative ranking curve (SUCRA) = 85.5). For BASFI, statistically significant improvements were observed with the Aquatic Aerobic Exercise (AAE) (−0.90, 95% CI [−1.50 to −0.29]), ASE (−1.74, 95% CI [−2.45 to −1.04]), LAE (−0.74, 95% CI [−1.05 to −0.43]), LSE (−0.54, 95% CI [−0.81 to −0.27]), and Muscle Exercise (ME) (−0.48, 95% CI [−0.83 to −0.13]). ASE had the highest SUCRA ranking (99.6). For BASMI, ASE (−1.06,…
format: application/pdf
format: text/html
creator: Lingkui Kong
creator: Chuanwen Yu
creator: Chaoxin Wang
creator: Zhanpeng Meng
subject: Evidence Based Medicine
subject: Kinesiology
subject: Sports Injury
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.20336
publisher: PeerJ Inc.
rights: © 2025 Kong et al.
abstract: Background Exercise interventions have been widely applied as an adjunctive treatment for ankylosing spondylitis (AS), effectively alleviating pain, improving function, and enhancing quality of life. However, the efficacy of different exercise modalities remains inconclusive. This study aims to systematically compare the effects of various exercise interventions on clinical outcomes in AS patients using a network meta-analysis (NMA) to determine the optimal exercise regimen. Methods A comprehensive search was performed across six databases to identify studies assessing the impact of exercise interventions on AS. The primary outcomes analyzed included the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Functional Index (BASFI), Bath Ankylosing Spondylitis Metrology Index (BASMI), and Ankylosing Spondylitis Quality of Life (ASQoL). A network meta-analysis was conducted using the frequentist approach in STATA 18.0, while effect publication bias analysis used Review Manager 5.4. Results Forty-eight studies involving 3,140 participants were included, published between 2002 and 2024. Compared to the control group, all exercise interventions demonstrated varying degrees of benefit in improving BASDAI, BASFI, BASMI, and ASQoL scores. For BASDAI, the Aquatic Stretching Exercise (ASE) (−1.42, 95% CI [−2.51 to −0.33]), Land Aerobic Exercise (LAE) (−0.94, 95% CI [−1.41 to −0.47]), and Land Stretching Exercise (LSE) (−0.49, 95% CI [−0.94 to −0.04]) exhibited significant symptom relief, with ASE ranking highest (surface under the cumulative ranking curve (SUCRA) = 85.5). For BASFI, statistically significant improvements were observed with the Aquatic Aerobic Exercise (AAE) (−0.90, 95% CI [−1.50 to −0.29]), ASE (−1.74, 95% CI [−2.45 to −1.04]), LAE (−0.74, 95% CI [−1.05 to −0.43]), LSE (−0.54, 95% CI [−0.81 to −0.27]), and Muscle Exercise (ME) (−0.48, 95% CI [−0.83 to −0.13]). ASE had the highest SUCRA ranking (99.6). For BASMI, ASE (−1.06,…
bibliographic citation: Kong et al. (2025) Comparative efficacy of different exercise interventions in patients with ankylosing spondylitis: a systematic review and network meta-analysis. PeerJ 13:e20336 https://doi.org/10.7717/peerj.20336
date submitted: 2025-04-18
date accepted: 2025-10-13
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Lingkui
author list: Agent
  family name: Yu
  given name: Chuanwen
author list: Agent
  family name: Wang
  given name: Chaoxin
author list: Agent
  family name: Meng
  given name: Zhanpeng
doi: 10.7717/peerj.20336
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Kong et al.
attribution name: Kong et al.

Coral reefs in the Mahafaly Seascape (SW Madagascar) as potential climate refugia following the 2024 mass bleaching event
type: item
type: AcademicArticle
description: The southwesternmost coast of Madagascar, including the Mahafaly seascape, is home to some of the country’s most ecologically and culturally important coral reefs, which remain largely understudied. These ecosystems are facing growing pressure from a panel of disturbances, with climate-induced events such as marine heatwaves being among of the causes of coral bleaching. The decline of these reefs can directly threaten the livelihoods of the local communities, who depend heavily on the resources they provide. In this context, understanding how different disturbances impact coral reef condition and recovery is critical for developing effective management strategies and conservation for this vulnerable region. This study investigates coral bleaching dynamics in the Mahafaly seascape during and after the fourth mass coral bleaching event in 2024. Six reef locations within locally managed marine areas were surveyed, comprising a total of 11 stations, with 20 one-square-meter quadrats randomly deployed at each station during each sampling period. Average hard coral densities of 18.3 and 19.3 colonies m−2 were recorded during and after the event, respectively. Bleaching prevalence peaked during the event, affecting 38.8% of coral colonies, with a marked decrease to 6.0% afterward. However, coral mortality remained relatively low across the entire seascape, with a slight post-bleaching increase in dead colonies (+3.5%). Northern sites experienced the highest thermal stress, with Beheloke and Besambay reefs being the most susceptible to bleaching, whereas Ambola exhibited remarkable resilience. In the south, Ambohibola showed low vulnerability, Lembehitake moderate susceptibility, and Itampolo the highest bleaching prevalence despite lower thermal stress. Taxa-specific patterns were also evident, with thermally sensitive branching genera being most affected, contrasting with the relative tolerance of massive and encrusting corals. The heterogeneous coral bleaching patterns o…
format: application/pdf
format: text/html
creator: Mahery Randrianarivo
creator: Solotahiana Rakotomanga
creator: Fanja Razafindramasy
creator: Danny Kornelio Ravelojaona
creator: Tahiry Ranaivoson
creator: Domoina Rakotomalala
creator: Rémi Ratsimbazafy
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.20319
publisher: PeerJ Inc.
rights: © 2025 Randrianarivo et al.
abstract: The southwesternmost coast of Madagascar, including the Mahafaly seascape, is home to some of the country’s most ecologically and culturally important coral reefs, which remain largely understudied. These ecosystems are facing growing pressure from a panel of disturbances, with climate-induced events such as marine heatwaves being among of the causes of coral bleaching. The decline of these reefs can directly threaten the livelihoods of the local communities, who depend heavily on the resources they provide. In this context, understanding how different disturbances impact coral reef condition and recovery is critical for developing effective management strategies and conservation for this vulnerable region. This study investigates coral bleaching dynamics in the Mahafaly seascape during and after the fourth mass coral bleaching event in 2024. Six reef locations within locally managed marine areas were surveyed, comprising a total of 11 stations, with 20 one-square-meter quadrats randomly deployed at each station during each sampling period. Average hard coral densities of 18.3 and 19.3 colonies m−2 were recorded during and after the event, respectively. Bleaching prevalence peaked during the event, affecting 38.8% of coral colonies, with a marked decrease to 6.0% afterward. However, coral mortality remained relatively low across the entire seascape, with a slight post-bleaching increase in dead colonies (+3.5%). Northern sites experienced the highest thermal stress, with Beheloke and Besambay reefs being the most susceptible to bleaching, whereas Ambola exhibited remarkable resilience. In the south, Ambohibola showed low vulnerability, Lembehitake moderate susceptibility, and Itampolo the highest bleaching prevalence despite lower thermal stress. Taxa-specific patterns were also evident, with thermally sensitive branching genera being most affected, contrasting with the relative tolerance of massive and encrusting corals. The heterogeneous coral bleaching patterns o…
bibliographic citation: Randrianarivo et al. (2025) Coral reefs in the Mahafaly Seascape (SW Madagascar) as potential climate refugia following the 2024 mass bleaching event. PeerJ 13:e20319 https://doi.org/10.7717/peerj.20319
date submitted: 2025-03-18
date accepted: 2025-10-09
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Randrianarivo
  given name: Mahery
author list: Agent
  family name: Rakotomanga
  given name: Solotahiana
author list: Agent
  family name: Razafindramasy
  given name: Fanja
author list: Agent
  family name: Ravelojaona
  given name: Danny Kornelio
author list: Agent
  family name: Ranaivoson
  given name: Tahiry
author list: Agent
  family name: Rakotomalala
  given name: Domoina
author list: Agent
  family name: Ratsimbazafy
  given name: Rémi
doi: 10.7717/peerj.20319
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Randrianarivo et al.
attribution name: Randrianarivo et al.

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