PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Teacher preparedness regarding autism spectrum disorder in the Jazan region, Saudi Arabia: a cross-sectional study
items: Odontometric analysis of permanent mandibular first and second premolars in an Indian population using cone beam computed tomography
items: Integrating network pharmacology, molecular docking, and molecular dynamics simulations to explore potential compounds and mechanisms of Coptis chinensis in treating streptococcal infections
items: Anticancer potential of ethanolic sidr leaf extracts against MCF-7 breast cancer cells: phytochemical, nutritional, and antimicrobial profile comparisons of different plant parts
items: Relationship between locomotive syndrome risk test and height and weight in infancy and toddlerhood: a preliminary study
items: Geographic distributions and patterns of co-occurrence among black-bellied and shovel-nosed salamanders (Desmognathus spp.) in the Great Smoky Mountains National Park
items: Establishment and verification of a nomogram model based on the inflammatory indicators of patients with cervical cancer for predicting the risk of their lymph node metastasis
items: Selection of suitable wheat genotypes under thermal stress and complex genotype-environment interaction using stability analyses and selection indices
items: Association of circulating branched-chain amino acids with risk of pre-diabetes: a systematic review and meta-analysis
items: Identification of immunological and prognostic value of SHROOM2 in pan-cancer and experimental verification of its role in promoting malignant phenotypes in breast cancer

Teacher preparedness regarding autism spectrum disorder in the Jazan region, Saudi Arabia: a cross-sectional study
type: item
type: AcademicArticle
description: Background Autism spectrum disorder (ASD) is a multifaceted neurodevelopmental condition marked by distinct behavioral patterns, impaired social interaction, and communication challenges. Early recognition and appropriate intervention are pivotal for improving outcomes. This study aims to comprehensively evaluate the understanding, attitudes, and teaching methodologies of kindergarten and primary school teachers in the Jazan region, Kingdom of Saudi Arabia, regarding children with ASD. Methodology A cross-sectional study was conducted using a multistage cluster random sampling technique. An interview-based questionnaire was administered to kindergarten and primary school teachers in the Jazan region. The target sample size was 800 teachers. Results Among the 870 participating teachers, 87.8% reported lacking prior training on effectively addressing the needs of children with ASD. However, 74.8% demonstrated substantial understanding of the social communication difficulties faced by autistic children, and 76.2% were aware of the attention-related challenges these children encounter. Additionally, 77.7% of participants recognized the pivotal role of open communication between teachers and families in facilitating quality educational experiences and enhancing academic outcomes for students with ASD. Conclusion The study highlights the critical need for targeted training programs to equip teachers with essential skills for supporting students with ASD. These findings underscore the importance of policy interventions to ensure adequate resources and expertise for effectively accommodating the unique needs of students with ASD in mainstream schools.
format: application/pdf
format: text/html
creator: Maged El-Setouhy
creator: Ahmad Y. Alqassim
creator: Mohammad Zaino
creator: Essam A. AlAmeer
creator: Anwar Makeen
creator: Mohammed A. Muaddi
creator: Abdullah A. Alharbi
creator: Renad H. Hamzi
creator: Amaal A. Hamdi
creator: Hanan N. Abu Summah
creator: Norah K. Najmi
creator: Raghad M. Sharahily
creator: Maram A. Zuqayli
creator: Fatimah A. Khubrani
creator: Kholod Wasli
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.20044
publisher: PeerJ Inc.
rights: © 2025 El-Setouhy et al.
abstract: Background Autism spectrum disorder (ASD) is a multifaceted neurodevelopmental condition marked by distinct behavioral patterns, impaired social interaction, and communication challenges. Early recognition and appropriate intervention are pivotal for improving outcomes. This study aims to comprehensively evaluate the understanding, attitudes, and teaching methodologies of kindergarten and primary school teachers in the Jazan region, Kingdom of Saudi Arabia, regarding children with ASD. Methodology A cross-sectional study was conducted using a multistage cluster random sampling technique. An interview-based questionnaire was administered to kindergarten and primary school teachers in the Jazan region. The target sample size was 800 teachers. Results Among the 870 participating teachers, 87.8% reported lacking prior training on effectively addressing the needs of children with ASD. However, 74.8% demonstrated substantial understanding of the social communication difficulties faced by autistic children, and 76.2% were aware of the attention-related challenges these children encounter. Additionally, 77.7% of participants recognized the pivotal role of open communication between teachers and families in facilitating quality educational experiences and enhancing academic outcomes for students with ASD. Conclusion The study highlights the critical need for targeted training programs to equip teachers with essential skills for supporting students with ASD. These findings underscore the importance of policy interventions to ensure adequate resources and expertise for effectively accommodating the unique needs of students with ASD in mainstream schools.
bibliographic citation: El-Setouhy et al. (2025) Teacher preparedness regarding autism spectrum disorder in the Jazan region, Saudi Arabia: a cross-sectional study. PeerJ 13:e20044 https://doi.org/10.7717/peerj.20044
date submitted: 2024-09-04
date accepted: 2025-08-15
issued: 2025-09-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: El-Setouhy
  given name: Maged
author list: Agent
  family name: Alqassim
  given name: Ahmad Y.
author list: Agent
  family name: Zaino
  given name: Mohammad
author list: Agent
  family name: AlAmeer
  given name: Essam A.
author list: Agent
  family name: Makeen
  given name: Anwar
author list: Agent
  family name: Muaddi
  given name: Mohammed A.
author list: Agent
  family name: Alharbi
  given name: Abdullah A.
author list: Agent
  family name: Hamzi
  given name: Renad H.
author list: Agent
  family name: Hamdi
  given name: Amaal A.
author list: Agent
  family name: Abu Summah
  given name: Hanan N.
author list: Agent
  family name: Najmi
  given name: Norah K.
author list: Agent
  family name: Sharahily
  given name: Raghad M.
author list: Agent
  family name: Zuqayli
  given name: Maram A.
author list: Agent
  family name: Khubrani
  given name: Fatimah A.
author list: Agent
  family name: Wasli
  given name: Kholod
doi: 10.7717/peerj.20044
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-26
copyright: ©2025 El-Setouhy et al.
attribution name: El-Setouhy et al.

Odontometric analysis of permanent mandibular first and second premolars in an Indian population using cone beam computed tomography
type: item
type: AcademicArticle
description: Background Differences in tooth size across populations can significantly influence dental diagnosis, treatment planning, and forensic identification. Despite its relevance, comprehensive region-specific odontometric data—particularly for the Indian population—remain limited. This study aimed to obtain odontometric measurements of permanent mandibular first and second premolars in the Indian population using cone beam computed tomography (CBCT), and to compare these measurements with Wheeler’s dental morphology standards, focusing on crown length, root length, and total tooth length. Methods In this retrospective study, 300 high-quality CBCT scans were analyzed. Measurements of crown, root, and overall tooth lengths for mandibular first and second premolars were obtained using CS 3D Imaging (Version 3.9.3). A one-sample t-test was performed to compare the mean values with Wheeler’s reference standards. Results Statistically significant differences were observed in all measured dimensions (p < 0.001). For first premolars, crown, root, and total lengths were shorter by 2.3 mm, 1.1 mm, and 3.4 mm, respectively. Second premolars showed reductions of 1.9 mm, 1.2 mm, and 3.0 mm, respectively. Conclusions This odontometric analysis highlights distinct dental morphological characteristics in the Indian population. These findings offer valuable insights for applications in anthropology, evolutionary biology, forensic science, and clinical dentistry.
format: application/pdf
format: text/html
creator: Fiza Hamdulay
creator: Ajinkya M. Pawar
creator: Shivani Singh
creator: Suraj Arora
creator: Luca Testarelli
creator: Asok Mathew
creator: Alexander Maniangat Luke
creator: Mohmed Isaqali Karobari
subject: Anatomy and Physiology
subject: Dentistry
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.20039
publisher: PeerJ Inc.
rights: © 2025 Hamdulay et al.
abstract: Background Differences in tooth size across populations can significantly influence dental diagnosis, treatment planning, and forensic identification. Despite its relevance, comprehensive region-specific odontometric data—particularly for the Indian population—remain limited. This study aimed to obtain odontometric measurements of permanent mandibular first and second premolars in the Indian population using cone beam computed tomography (CBCT), and to compare these measurements with Wheeler’s dental morphology standards, focusing on crown length, root length, and total tooth length. Methods In this retrospective study, 300 high-quality CBCT scans were analyzed. Measurements of crown, root, and overall tooth lengths for mandibular first and second premolars were obtained using CS 3D Imaging (Version 3.9.3). A one-sample t-test was performed to compare the mean values with Wheeler’s reference standards. Results Statistically significant differences were observed in all measured dimensions (p < 0.001). For first premolars, crown, root, and total lengths were shorter by 2.3 mm, 1.1 mm, and 3.4 mm, respectively. Second premolars showed reductions of 1.9 mm, 1.2 mm, and 3.0 mm, respectively. Conclusions This odontometric analysis highlights distinct dental morphological characteristics in the Indian population. These findings offer valuable insights for applications in anthropology, evolutionary biology, forensic science, and clinical dentistry.
bibliographic citation: Hamdulay et al. (2025) Odontometric analysis of permanent mandibular first and second premolars in an Indian population using cone beam computed tomography. PeerJ 13:e20039 https://doi.org/10.7717/peerj.20039
date submitted: 2025-01-15
date accepted: 2025-08-14
issued: 2025-09-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hamdulay
  given name: Fiza
author list: Agent
  family name: Pawar
  given name: Ajinkya M.
author list: Agent
  family name: Singh
  given name: Shivani
author list: Agent
  family name: Arora
  given name: Suraj
author list: Agent
  family name: Testarelli
  given name: Luca
author list: Agent
  family name: Mathew
  given name: Asok
author list: Agent
  family name: Luke
  given name: Alexander Maniangat
author list: Agent
  family name: Karobari
  given name: Mohmed Isaqali
doi: 10.7717/peerj.20039
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-26
copyright: ©2025 Hamdulay et al.
attribution name: Hamdulay et al.

Integrating network pharmacology, molecular docking, and molecular dynamics simulations to explore potential compounds and mechanisms of Coptis chinensis in treating streptococcal infections
type: item
type: AcademicArticle
description: Background Coptis chinensis, a prominent herb in traditional Chinese medicine, is widely utilized for its therapeutic effects against Streptococcus infections, though its precise mechanisms of action remain insufficiently understood. This study aims to clarify the potential mechanisms and active compounds of C. chinensis in the treatment of Streptococcus. Methods Active compounds of C. chinensis were identified using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database, and their potential targets were predicted from multiple public resources. These targets were intersected with streptococcus-related genes to identify overlapping targets, which were then used to construct a protein–protein interaction (PPI) network and screen for key hub genes. To investigate the pharmacological mechanisms, Gene Ontology and KEGG pathway enrichment analyses were performed. Molecular docking was employed to evaluate the binding affinities between active compounds and core target proteins, followed by molecular dynamics simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations to assess binding stability and free energy. Results A total of 24 active compounds were identified, along with 180 overlapping targets related to streptococcal infection. PPI network analysis revealed ten key hub genes, including IL1β, IL6, and MMP9. Enrichment analysis suggested that C. chinensis may inhibit the TLR4/NF-κB inflammatory pathway to modulate host immunity and mediate lipid metabolism reprogramming to restrict pathogen proliferation. Several core targets were also enriched in pathways related to extracellular matrix remodeling and immune regulation, indicating potential indirect effects on host–pathogen interface interactions. Molecular docking and simulation confirmed stable binding between major active ingredients and streptococcus-associated proteins. Conclusion This study provides mechanistic insights into the mul…
format: application/pdf
format: text/html
creator: Wanxiang Qi
creator: Bin Shi
creator: Wenqiang Tang
creator: Jiangyong Zeng
creator: Ma Zhuo
creator: Hongcai Ma
subject: Biochemistry
subject: Computational Biology
subject: Veterinary Medicine
subject: Pharmacology
description: doi:10.7717/peerj.19960
publisher: PeerJ Inc.
rights: © 2025 Qi et al.
abstract: Background Coptis chinensis, a prominent herb in traditional Chinese medicine, is widely utilized for its therapeutic effects against Streptococcus infections, though its precise mechanisms of action remain insufficiently understood. This study aims to clarify the potential mechanisms and active compounds of C. chinensis in the treatment of Streptococcus. Methods Active compounds of C. chinensis were identified using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database, and their potential targets were predicted from multiple public resources. These targets were intersected with streptococcus-related genes to identify overlapping targets, which were then used to construct a protein–protein interaction (PPI) network and screen for key hub genes. To investigate the pharmacological mechanisms, Gene Ontology and KEGG pathway enrichment analyses were performed. Molecular docking was employed to evaluate the binding affinities between active compounds and core target proteins, followed by molecular dynamics simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations to assess binding stability and free energy. Results A total of 24 active compounds were identified, along with 180 overlapping targets related to streptococcal infection. PPI network analysis revealed ten key hub genes, including IL1β, IL6, and MMP9. Enrichment analysis suggested that C. chinensis may inhibit the TLR4/NF-κB inflammatory pathway to modulate host immunity and mediate lipid metabolism reprogramming to restrict pathogen proliferation. Several core targets were also enriched in pathways related to extracellular matrix remodeling and immune regulation, indicating potential indirect effects on host–pathogen interface interactions. Molecular docking and simulation confirmed stable binding between major active ingredients and streptococcus-associated proteins. Conclusion This study provides mechanistic insights into the mul…
bibliographic citation: Qi et al. (2025) Integrating network pharmacology, molecular docking, and molecular dynamics simulations to explore potential compounds and mechanisms of Coptis chinensis in treating streptococcal infections. PeerJ 13:e19960 https://doi.org/10.7717/peerj.19960
date submitted: 2025-03-31
date accepted: 2025-07-30
issued: 2025-09-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Qi
  given name: Wanxiang
author list: Agent
  family name: Shi
  given name: Bin
author list: Agent
  family name: Tang
  given name: Wenqiang
author list: Agent
  family name: Zeng
  given name: Jiangyong
author list: Agent
  family name: Zhuo
  given name: Ma
author list: Agent
  family name: Ma
  given name: Hongcai
doi: 10.7717/peerj.19960
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-26
copyright: ©2025 Qi et al.
attribution name: Qi et al.

Anticancer potential of ethanolic sidr leaf extracts against MCF-7 breast cancer cells: phytochemical, nutritional, and antimicrobial profile comparisons of different plant parts
type: item
type: AcademicArticle
description: Background Traditional medicine has long utilized natural plants to treat diseases and promote overall health. They have contributed significantly to the creation of modern medications. To supplement existing information, therefore, this current investigation aimed to understand the potential therapeutic properties of the sidr plant against triple negative breast cancer (TNBC) on MCF-7 breast cell line by conducting phytochemical, nutritional, and antimicrobial profile comparisons of different plant parts. Methods Phytochemical analyses involved soluble sugar composition and oxidation profile, whereas nutritional analysis involved the proximate chemical analysis. Additionally, antimicrobial analyses involved six kings of food-borne bacterial strains. Results According to the study, leaves possessed the highest amounts of protein (12.44%) and ash (8.17%), as well as the highest amounts of ascorbic acid and total chlorophyll. On the other hand, pulps exhibited the highest flavonoid concentration in their ethanolic extract and had higher sugar contents. Furthermore, at a dosage of 100 µg/mL, the ethanolic extract of leaves showed potent antimicrobial action and suppressed over 50% of MCF-7 breast cancer cell survival. Conclusions Bioactive components, antioxidant, antimicrobial and nutritional elements of sidr plant appears a promising medicinal candidate to fight breast cancer cells.
format: application/pdf
format: text/html
creator: Roqayah H. Kadi
creator: Nashi K. Alqahtani
creator: Ahmed M. Abdulfattah
creator: Fayez Alsulaimani
creator: Ahmed M. Basri
creator: Reham M. Algheshairy
creator: Hend F. Alharbi
creator: Rokayya Sami
creator: Amal Alyamani
creator: Roua S. Baty
creator: Ruqaiah I. Bedaiwi
creator: Hala M. Abo-Dief
creator: Nahid A. Osman
creator: Nouf H. Alsubhi
creator: Ashwaq M. Al-Nazawi
creator: Manal Malibary
subject: Biochemistry
subject: Food Science and Technology
subject: Nutrition
description: doi:10.7717/peerj.19858
publisher: PeerJ Inc.
rights: © 2025 Kadi et al.
abstract: Background Traditional medicine has long utilized natural plants to treat diseases and promote overall health. They have contributed significantly to the creation of modern medications. To supplement existing information, therefore, this current investigation aimed to understand the potential therapeutic properties of the sidr plant against triple negative breast cancer (TNBC) on MCF-7 breast cell line by conducting phytochemical, nutritional, and antimicrobial profile comparisons of different plant parts. Methods Phytochemical analyses involved soluble sugar composition and oxidation profile, whereas nutritional analysis involved the proximate chemical analysis. Additionally, antimicrobial analyses involved six kings of food-borne bacterial strains. Results According to the study, leaves possessed the highest amounts of protein (12.44%) and ash (8.17%), as well as the highest amounts of ascorbic acid and total chlorophyll. On the other hand, pulps exhibited the highest flavonoid concentration in their ethanolic extract and had higher sugar contents. Furthermore, at a dosage of 100 µg/mL, the ethanolic extract of leaves showed potent antimicrobial action and suppressed over 50% of MCF-7 breast cancer cell survival. Conclusions Bioactive components, antioxidant, antimicrobial and nutritional elements of sidr plant appears a promising medicinal candidate to fight breast cancer cells.
bibliographic citation: Kadi et al. (2025) Anticancer potential of ethanolic sidr leaf extracts against MCF-7 breast cancer cells: phytochemical, nutritional, and antimicrobial profile comparisons of different plant parts. PeerJ 13:e19858 https://doi.org/10.7717/peerj.19858
date submitted: 2025-03-26
date accepted: 2025-07-16
issued: 2025-09-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kadi
  given name: Roqayah H.
author list: Agent
  family name: Alqahtani
  given name: Nashi K.
author list: Agent
  family name: Abdulfattah
  given name: Ahmed M.
author list: Agent
  family name: Alsulaimani
  given name: Fayez
author list: Agent
  family name: Basri
  given name: Ahmed M.
author list: Agent
  family name: Algheshairy
  given name: Reham M.
author list: Agent
  family name: Alharbi
  given name: Hend F.
author list: Agent
  family name: Sami
  given name: Rokayya
author list: Agent
  family name: Alyamani
  given name: Amal
author list: Agent
  family name: Baty
  given name: Roua S.
author list: Agent
  family name: Bedaiwi
  given name: Ruqaiah I.
author list: Agent
  family name: Abo-Dief
  given name: Hala M.
author list: Agent
  family name: Osman
  given name: Nahid A.
author list: Agent
  family name: Alsubhi
  given name: Nouf H.
author list: Agent
  family name: Al-Nazawi
  given name: Ashwaq M.
author list: Agent
  family name: Malibary
  given name: Manal
doi: 10.7717/peerj.19858
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-26
copyright: ©2025 Kadi et al.
attribution name: Kadi et al.

Relationship between locomotive syndrome risk test and height and weight in infancy and toddlerhood: a preliminary study
type: item
type: AcademicArticle
description: Introduction The Japanese Medical Science Federation’s declaration highlighted that locomotive syndrome (LS) precedes frailty, emphasizing the importance of early intervention beginning in childhood and continuing throughout life. To date, no study has examined the relationship between LS in adults and height and weight during infancy and toddlerhood. As a preliminary investigation, this study aimed to clarify how height and weight during early life stages are related to LS among young adults. Methods In this study, 62 students enrolled at a health sciences university were administered the locomotive syndrome risk test, and their grip strength was measured. Height and weight at birth, at 1 year, and at 3 years of age were obtained from the Maternal and Child Health Handbook. All participants were born via normal delivery. The relationships between the LS risk test results, height, and weight were analyzed using correlation and multivariate analyses. Results Correlation analysis revealed significant associations between height and weight in infancy and toddlerhood and the following variables: two-step length, two-step test value, 25-question geriatric locomotive function scale score, and grip strength. Multiple regression analysis showed a significant relationship between two-step length and height at birth (p = 0.002), and between grip strength and weight at age 3 (p = 0.021). Conclusions A weak-to-moderate relationship was found between LS and height and weight in infancy and toddlerhood. These findings suggest that preventive measures for LS should not be delayed until adulthood; rather, early-life interventions beginning in infancy, toddlerhood, and childhood may be crucial.
format: application/pdf
format: text/html
creator: Shuntaro Tsuji
creator: Tamaki Hirose
creator: Yohei Sawaya
creator: Runa Kawano
creator: Takumi Sugiura
creator: Riona Takimoto
creator: Yuto Nishimura
creator: Masafumi Itokazu
subject: Orthopedics
subject: Rehabilitation
description: doi:10.7717/peerj.20114
publisher: PeerJ Inc.
rights: © 2025 Tsuji et al.
abstract: Introduction The Japanese Medical Science Federation’s declaration highlighted that locomotive syndrome (LS) precedes frailty, emphasizing the importance of early intervention beginning in childhood and continuing throughout life. To date, no study has examined the relationship between LS in adults and height and weight during infancy and toddlerhood. As a preliminary investigation, this study aimed to clarify how height and weight during early life stages are related to LS among young adults. Methods In this study, 62 students enrolled at a health sciences university were administered the locomotive syndrome risk test, and their grip strength was measured. Height and weight at birth, at 1 year, and at 3 years of age were obtained from the Maternal and Child Health Handbook. All participants were born via normal delivery. The relationships between the LS risk test results, height, and weight were analyzed using correlation and multivariate analyses. Results Correlation analysis revealed significant associations between height and weight in infancy and toddlerhood and the following variables: two-step length, two-step test value, 25-question geriatric locomotive function scale score, and grip strength. Multiple regression analysis showed a significant relationship between two-step length and height at birth (p = 0.002), and between grip strength and weight at age 3 (p = 0.021). Conclusions A weak-to-moderate relationship was found between LS and height and weight in infancy and toddlerhood. These findings suggest that preventive measures for LS should not be delayed until adulthood; rather, early-life interventions beginning in infancy, toddlerhood, and childhood may be crucial.
bibliographic citation: Tsuji et al. (2025) Relationship between locomotive syndrome risk test and height and weight in infancy and toddlerhood: a preliminary study. PeerJ 13:e20114 https://doi.org/10.7717/peerj.20114
date submitted: 2025-04-03
date accepted: 2025-08-29
issued: 2025-09-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsuji
  given name: Shuntaro
author list: Agent
  family name: Hirose
  given name: Tamaki
author list: Agent
  family name: Sawaya
  given name: Yohei
author list: Agent
  family name: Kawano
  given name: Runa
author list: Agent
  family name: Sugiura
  given name: Takumi
author list: Agent
  family name: Takimoto
  given name: Riona
author list: Agent
  family name: Nishimura
  given name: Yuto
author list: Agent
  family name: Itokazu
  given name: Masafumi
doi: 10.7717/peerj.20114
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-25
copyright: © 2025 Tsuji et al.
attribution name: Tsuji et al.

Geographic distributions and patterns of co-occurrence among black-bellied and shovel-nosed salamanders (Desmognathus spp.) in the Great Smoky Mountains National Park
type: item
type: AcademicArticle
description: The southern Appalachian Mountains are a global hotspot for salamander diversity. Recent taxonomic revisions driven by a growing understanding of cryptic diversity and advancements in genomic technology have increased the number of described species in the area significantly, raising questions about biogeography and community structure. Recently described species in the Desmognathus quadramaculatus-marmoratus complex are morphologically cryptic but diagnosable by mitochondrial DNA. The complex includes multiple species within each of two distinct ecomorphs, the highly aquatic ‘shovel-nosed’ (SN) ecomorph and the semi-aquatic ‘black-bellied’ (BB) ecomorph. Here, we use mitochondrial DNA and Bayesian phylogenetic analysis to clarify distributions and patterns of co-occurrence of recently described species in the Great Smoky Mountains. We present new data showing more extensive co-occurrence of two cryptic species of the black-bellied ecomorph than previously recognized. Our results are also consistent with earlier work indicating shared variation between ecomorphs within one clade. In addition, we identified a divergent mitochondrial lineage of the shovel-nosed ecomorph related to D. aureatus, a species not previously known to inhabit the Great Smoky Mountains. These results reveal a more complex and diverse assemblage of ecomorphs than previously recognized in this hotspot of salamander diversity.
format: application/pdf
format: text/html
creator: Aidan Shaw
creator: Rebecca Chastain
creator: Benjamin M. Fitzpatrick
subject: Biodiversity
subject: Taxonomy
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.20110
publisher: PeerJ Inc.
rights: © 2025 Shaw et al.
abstract: The southern Appalachian Mountains are a global hotspot for salamander diversity. Recent taxonomic revisions driven by a growing understanding of cryptic diversity and advancements in genomic technology have increased the number of described species in the area significantly, raising questions about biogeography and community structure. Recently described species in the Desmognathus quadramaculatus-marmoratus complex are morphologically cryptic but diagnosable by mitochondrial DNA. The complex includes multiple species within each of two distinct ecomorphs, the highly aquatic ‘shovel-nosed’ (SN) ecomorph and the semi-aquatic ‘black-bellied’ (BB) ecomorph. Here, we use mitochondrial DNA and Bayesian phylogenetic analysis to clarify distributions and patterns of co-occurrence of recently described species in the Great Smoky Mountains. We present new data showing more extensive co-occurrence of two cryptic species of the black-bellied ecomorph than previously recognized. Our results are also consistent with earlier work indicating shared variation between ecomorphs within one clade. In addition, we identified a divergent mitochondrial lineage of the shovel-nosed ecomorph related to D. aureatus, a species not previously known to inhabit the Great Smoky Mountains. These results reveal a more complex and diverse assemblage of ecomorphs than previously recognized in this hotspot of salamander diversity.
bibliographic citation: Shaw et al. (2025) Geographic distributions and patterns of co-occurrence among black-bellied and shovel-nosed salamanders (Desmognathus spp.) in the Great Smoky Mountains National Park. PeerJ 13:e20110 https://doi.org/10.7717/peerj.20110
date submitted: 2025-03-25
date accepted: 2025-08-29
issued: 2025-09-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shaw
  given name: Aidan
author list: Agent
  family name: Chastain
  given name: Rebecca
author list: Agent
  family name: Fitzpatrick
  given name: Benjamin M.
doi: 10.7717/peerj.20110
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-25
copyright: © 2025 Shaw et al.
attribution name: Shaw et al.

Establishment and verification of a nomogram model based on the inflammatory indicators of patients with cervical cancer for predicting the risk of their lymph node metastasis
type: item
type: AcademicArticle
description: Based on inflammatory indicators, this study aimed to predict the risk of lymph node metastasis (LNM) in patients with cervical squamous cell carcinoma (CSCC) and establish a predictive nomogram model. Methods This retrospective study analyzed the clinical data of 194 patients with stage IA2-IIA2 who underwent surgery at Hebei General Hospital (between January 2017 and August 2023). Patients were divided into two groups based on the presence of LNM or not. Clinical data of the participants were gathered and analyzed to compare the two groups. Logistic regression analysis was used to analyze the factors influencing LNM in patients with CSCC. R software was used to construct a nomogram model to predict LNM in patients with CSCC, and its accuracy was verified. Results Squamous cell carcinoma antigen (SCC-Ag) level, D-dimer level, platelet (PLT) count, and platelet-to-lymphocyte ratio (PLR) index were significantly higher in patients with LNM than in those without LNM (P < 0.05). There was a significant association between lymph vascular space invasion (LVSI) in patients with CSCC and their LNM (P < 0.05). Logistic regression analysis showed that SCC-Ag, PLR, and LVSI in patients with CSCC were independent risk factors for LNM (P < 0.05). A predictive nomogram model was constructed, and the prediction probability was consistent with the actual observed value (Hosmer–Lemeshow P = 0.313). Analyses using the receiver operating characteristic (ROC) curve revealed that the combination of the SCC-Ag, PLR, and LVSI values of patients with CSCC significantly improved the diagnostic efficiency of their LNM (AUC = 0.792, P < 0.001). Conclusion Establishing a nomogram model based on preoperative inflammatory indicators of patients with CSCC can accurately predict the risk of LNM, providing evidence for implementing a clinical diagnosis and treatment scheme.
format: application/pdf
format: text/html
creator: Liyun Song
creator: Kaiyun Qin
creator: Suning Bai
creator: Qi Wu
creator: Jing Zhao
creator: Jie Qi
creator: Junmei Zhang
creator: Yazhuo Wang
creator: Yuan Zhang
creator: Ren Xu
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.20069
publisher: PeerJ Inc.
rights: © 2025 Song et al.
abstract: Based on inflammatory indicators, this study aimed to predict the risk of lymph node metastasis (LNM) in patients with cervical squamous cell carcinoma (CSCC) and establish a predictive nomogram model. Methods This retrospective study analyzed the clinical data of 194 patients with stage IA2-IIA2 who underwent surgery at Hebei General Hospital (between January 2017 and August 2023). Patients were divided into two groups based on the presence of LNM or not. Clinical data of the participants were gathered and analyzed to compare the two groups. Logistic regression analysis was used to analyze the factors influencing LNM in patients with CSCC. R software was used to construct a nomogram model to predict LNM in patients with CSCC, and its accuracy was verified. Results Squamous cell carcinoma antigen (SCC-Ag) level, D-dimer level, platelet (PLT) count, and platelet-to-lymphocyte ratio (PLR) index were significantly higher in patients with LNM than in those without LNM (P < 0.05). There was a significant association between lymph vascular space invasion (LVSI) in patients with CSCC and their LNM (P < 0.05). Logistic regression analysis showed that SCC-Ag, PLR, and LVSI in patients with CSCC were independent risk factors for LNM (P < 0.05). A predictive nomogram model was constructed, and the prediction probability was consistent with the actual observed value (Hosmer–Lemeshow P = 0.313). Analyses using the receiver operating characteristic (ROC) curve revealed that the combination of the SCC-Ag, PLR, and LVSI values of patients with CSCC significantly improved the diagnostic efficiency of their LNM (AUC = 0.792, P < 0.001). Conclusion Establishing a nomogram model based on preoperative inflammatory indicators of patients with CSCC can accurately predict the risk of LNM, providing evidence for implementing a clinical diagnosis and treatment scheme.
bibliographic citation: Song et al. (2025) Establishment and verification of a nomogram model based on the inflammatory indicators of patients with cervical cancer for predicting the risk of their lymph node metastasis. PeerJ 13:e20069 https://doi.org/10.7717/peerj.20069
date submitted: 2025-05-07
date accepted: 2025-08-21
issued: 2025-09-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Liyun
author list: Agent
  family name: Qin
  given name: Kaiyun
author list: Agent
  family name: Bai
  given name: Suning
author list: Agent
  family name: Wu
  given name: Qi
author list: Agent
  family name: Zhao
  given name: Jing
author list: Agent
  family name: Qi
  given name: Jie
author list: Agent
  family name: Zhang
  given name: Junmei
author list: Agent
  family name: Wang
  given name: Yazhuo
author list: Agent
  family name: Zhang
  given name: Yuan
author list: Agent
  family name: Xu
  given name: Ren
doi: 10.7717/peerj.20069
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-25
copyright: ©2025 Song et al.
attribution name: Song et al.

Selection of suitable wheat genotypes under thermal stress and complex genotype-environment interaction using stability analyses and selection indices
type: item
type: AcademicArticle
description: Thermal stress is a consequence of climate change that threatens food security, causes plant tissue damage, and harms crop production, particularly during the pollination and fertilization period and in grain-filling stages negatively impacting the number of grains, grain size, and quality. Genotype-environment interaction (GEN: ENV) complicates the selection of optimal wheat genotypes due to the complex genetic basis of yield under varying conditions. Diversified approaches were put forth in response to the pressing demand for simultaneous enhancements in high-yield performance combined with stability. This study investigates the selection of ideal wheat genotypes under thermal stress and complex GEN: ENV using stability analyses and selection indices to assess genotype performance and stability. Twenty wheat genotypes were evaluated across optimal conditions (OC) and thermal stress conditions (TSC) over three growing seasons with six ENVs. Results demonstrated significant GEN: ENV, revealing genetic variations in thermal tolerance. The additive main effects and multiplicative interaction (AMMI2) biplot indicated a combined variance of 99.00%, and eleven genotypes showed stable grain yield (GY) with six ENVs, three (G05, G09, and G17) were more stable. The G04, G05, G06, G09, and G18 genotypes were chosen for GY as perfect (stable and high-performance) genotypes by weighted average of absolute scores biplot (WAASB) and were also identified as the best genotypes group by WAASB-GY, with the exception of G18. Ten selection indices showed significant positive associations under GYoc and GYtsc, so they can be leveraged to detect the genotype’s high yield of GYtsc indirectly. The heritability, accuracy, and rgen: env values for most indices were high, indicating a major role of the genotypic effect in their inheritance, with the exception of the stress-non-stress production index (SNPI) index. Out of the five that were examined by WAASB, G04, G05, G06, and G09 were the t…
format: application/pdf
format: text/html
creator: Abdelhalim Ghazy
creator: Walid Ben Romdhane
creator: Majed Alotaibi
creator: Abdullah Al-Doss
creator: Omar Dahrog
creator: Nasser Al-Suhaibani
creator: Abdullah Ibrahim
creator: Adel M. Al-Saif
creator: Khalid A. Al-Gaadi
creator: Ahmed M. Zeyada
creator: Khalid F. Almutairi
creator: Ibrahim Al-Ashkar
subject: Agricultural Science
subject: Plant Science
subject: Climate Change Biology
subject: Environmental Impacts
subject: Population Biology
description: doi:10.7717/peerj.20061
publisher: PeerJ Inc.
rights: © 2025 Ghazy et al.
abstract: Thermal stress is a consequence of climate change that threatens food security, causes plant tissue damage, and harms crop production, particularly during the pollination and fertilization period and in grain-filling stages negatively impacting the number of grains, grain size, and quality. Genotype-environment interaction (GEN: ENV) complicates the selection of optimal wheat genotypes due to the complex genetic basis of yield under varying conditions. Diversified approaches were put forth in response to the pressing demand for simultaneous enhancements in high-yield performance combined with stability. This study investigates the selection of ideal wheat genotypes under thermal stress and complex GEN: ENV using stability analyses and selection indices to assess genotype performance and stability. Twenty wheat genotypes were evaluated across optimal conditions (OC) and thermal stress conditions (TSC) over three growing seasons with six ENVs. Results demonstrated significant GEN: ENV, revealing genetic variations in thermal tolerance. The additive main effects and multiplicative interaction (AMMI2) biplot indicated a combined variance of 99.00%, and eleven genotypes showed stable grain yield (GY) with six ENVs, three (G05, G09, and G17) were more stable. The G04, G05, G06, G09, and G18 genotypes were chosen for GY as perfect (stable and high-performance) genotypes by weighted average of absolute scores biplot (WAASB) and were also identified as the best genotypes group by WAASB-GY, with the exception of G18. Ten selection indices showed significant positive associations under GYoc and GYtsc, so they can be leveraged to detect the genotype’s high yield of GYtsc indirectly. The heritability, accuracy, and rgen: env values for most indices were high, indicating a major role of the genotypic effect in their inheritance, with the exception of the stress-non-stress production index (SNPI) index. Out of the five that were examined by WAASB, G04, G05, G06, and G09 were the t…
bibliographic citation: Ghazy et al. (2025) Selection of suitable wheat genotypes under thermal stress and complex genotype-environment interaction using stability analyses and selection indices. PeerJ 13:e20061 https://doi.org/10.7717/peerj.20061
date submitted: 2025-03-10
date accepted: 2025-08-19
issued: 2025-09-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ghazy
  given name: Abdelhalim
author list: Agent
  family name: Ben Romdhane
  given name: Walid
author list: Agent
  family name: Alotaibi
  given name: Majed
author list: Agent
  family name: Al-Doss
  given name: Abdullah
author list: Agent
  family name: Dahrog
  given name: Omar
author list: Agent
  family name: Al-Suhaibani
  given name: Nasser
author list: Agent
  family name: Ibrahim
  given name: Abdullah
author list: Agent
  family name: Al-Saif
  given name: Adel M.
author list: Agent
  family name: Al-Gaadi
  given name: Khalid A.
author list: Agent
  family name: Zeyada
  given name: Ahmed M.
author list: Agent
  family name: Almutairi
  given name: Khalid F.
author list: Agent
  family name: Al-Ashkar
  given name: Ibrahim
doi: 10.7717/peerj.20061
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-25
copyright: ©2025 Ghazy et al.
attribution name: Ghazy et al.

Association of circulating branched-chain amino acids with risk of pre-diabetes: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective Recent investigations have looked at the systemic concentrations of branched-chain amino acids (BCAA), which they consider prospective indicators for health conditions and the likelihood of chronic diseases. To elucidate the equivocal link between systemic BCAA concentrations and prediabetes, our study undertook a meta-analytical investigation. Materials and Methods Electronic databases were comprehensively searched in April 2024, and the study quality evaluation relied on the Newcastle-Ottawa Scale (NOS). The I2 statistic was used for heterogeneity assessment, and data analysis relied on Review Manager 5.4 and Stata 12.0. Standard mean difference (SMD) was used as the effect size to account for varying units of measurement across the included studies. Sensitivity assessment was instituted to evaluate result tenacity, and subgroup examinations were concomitantly carried out, with funnel plots, Egger’s regression analysis, and Begg’s rank-correlation methodology deployed to discern publication bias. PROSPERO registration (CRD42024572760) validates this review’s protocol compliance. Results Meta-analysis was conducted on 15 studies that involved 3,849 participants. Most individuals were over 40 years old. The prediabetes (PreDM) group exhibited significantly elevated levels of valine (Val) (SMD = 0.29; 95% confidence interval (CI) [0.14–0.45]; P = 0.0002), leucine (Leu) (SMD = 0.34; 95% CI [0.18–0.49]; P < 0.0001), and isoleucine (Ile) (SMD = 0.24; 95% CI [0.15–0.32]; P < 0.00001) compared to controls. Affirming the soundness of the results, sensitivity analysis indicated the lack of significant publication bias. Conclusions This meta-analysis supports the hypothesis that circulating BCAA levels increase in PreDM, suggesting that measuring BCAA levels could be investigated as a potential biomarker for the diagnosis of PreDM and a target for its treatment.
format: application/pdf
format: text/html
creator: Yu Wang
creator: Jiang-Hong Xiao
creator: Xi-Mei Zhang
creator: Wen-Xiao Wang
creator: Qiao Zhang
creator: Yu-Ping Tang
creator: Shi-Jun Yue
subject: Molecular Biology
subject: Diabetes and Endocrinology
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.20054
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Objective Recent investigations have looked at the systemic concentrations of branched-chain amino acids (BCAA), which they consider prospective indicators for health conditions and the likelihood of chronic diseases. To elucidate the equivocal link between systemic BCAA concentrations and prediabetes, our study undertook a meta-analytical investigation. Materials and Methods Electronic databases were comprehensively searched in April 2024, and the study quality evaluation relied on the Newcastle-Ottawa Scale (NOS). The I2 statistic was used for heterogeneity assessment, and data analysis relied on Review Manager 5.4 and Stata 12.0. Standard mean difference (SMD) was used as the effect size to account for varying units of measurement across the included studies. Sensitivity assessment was instituted to evaluate result tenacity, and subgroup examinations were concomitantly carried out, with funnel plots, Egger’s regression analysis, and Begg’s rank-correlation methodology deployed to discern publication bias. PROSPERO registration (CRD42024572760) validates this review’s protocol compliance. Results Meta-analysis was conducted on 15 studies that involved 3,849 participants. Most individuals were over 40 years old. The prediabetes (PreDM) group exhibited significantly elevated levels of valine (Val) (SMD = 0.29; 95% confidence interval (CI) [0.14–0.45]; P = 0.0002), leucine (Leu) (SMD = 0.34; 95% CI [0.18–0.49]; P < 0.0001), and isoleucine (Ile) (SMD = 0.24; 95% CI [0.15–0.32]; P < 0.00001) compared to controls. Affirming the soundness of the results, sensitivity analysis indicated the lack of significant publication bias. Conclusions This meta-analysis supports the hypothesis that circulating BCAA levels increase in PreDM, suggesting that measuring BCAA levels could be investigated as a potential biomarker for the diagnosis of PreDM and a target for its treatment.
bibliographic citation: Wang et al. (2025) Association of circulating branched-chain amino acids with risk of pre-diabetes: a systematic review and meta-analysis. PeerJ 13:e20054 https://doi.org/10.7717/peerj.20054
date submitted: 2024-12-17
date accepted: 2025-08-17
issued: 2025-09-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Xiao
  given name: Jiang-Hong
author list: Agent
  family name: Zhang
  given name: Xi-Mei
author list: Agent
  family name: Wang
  given name: Wen-Xiao
author list: Agent
  family name: Zhang
  given name: Qiao
author list: Agent
  family name: Tang
  given name: Yu-Ping
author list: Agent
  family name: Yue
  given name: Shi-Jun
doi: 10.7717/peerj.20054
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-25
copyright: ©2025 Wang et al.
attribution name: Wang et al.

Identification of immunological and prognostic value of SHROOM2 in pan-cancer and experimental verification of its role in promoting malignant phenotypes in breast cancer
type: item
type: AcademicArticle
description: Objective This study aimed to investigate the relationship between Shroom Family Member 2 (SHROOM2) expression and immune features, survival outcomes, and tumor mutational burden (TMB) across various cancer types, as well as its impact on the aggressive behavior of breast cancer (BC). Methods RNA sequencing and clinical survival data were retrieved from the TCGA-BRCA and TCGA-PANCANCER datasets within The Cancer Genome Atlas (TCGA) database. Survival analyses were performed to assess the association between SHROOM2 expression and clinical outcomes across different cancer types. Gene set enrichment analysis (GSEA) was applied to identify potential mechanisms associated with differentially expressed genes in BC. Spearman correlation and Wilcoxon tests were used to evaluate the relationships between SHROOM2 levels and immune characteristics, TMB, or drug sensitivity. Additionally, the effects of SHROOM2 on BC cells were assessed through reverse transcription-quantitative polymerase chain reaction (PCR), cell counting kit-8 (CCK-8) assay, transwell assay, and wound healing assay. Results SHROOM2 was overexpressed in a range of cancers, and its upregulation was associated with poor clinical outcomes. It was significantly correlated with immunomodulators, immune checkpoints, and immune cell infiltration in pan-cancer. Moreover, it showed an association with TMB and drug sensitivity in BC. Increased SHROOM2 expression enhanced the proliferative, migratory, and invasive capabilities of BC cells in vitro. Conclusion High SHROOM2 expression is linked to poor prognosis in BC, supporting its potential as both an immunological and predictive biomarker.
format: application/pdf
format: text/html
creator: Yaya Wang
creator: Yuechao Ren
creator: Xiaoyan Zheng
creator: Yan Wang
creator: Haoqi Wang
creator: Xi Zhang
creator: Sainan Li
subject: Bioinformatics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.20051
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Objective This study aimed to investigate the relationship between Shroom Family Member 2 (SHROOM2) expression and immune features, survival outcomes, and tumor mutational burden (TMB) across various cancer types, as well as its impact on the aggressive behavior of breast cancer (BC). Methods RNA sequencing and clinical survival data were retrieved from the TCGA-BRCA and TCGA-PANCANCER datasets within The Cancer Genome Atlas (TCGA) database. Survival analyses were performed to assess the association between SHROOM2 expression and clinical outcomes across different cancer types. Gene set enrichment analysis (GSEA) was applied to identify potential mechanisms associated with differentially expressed genes in BC. Spearman correlation and Wilcoxon tests were used to evaluate the relationships between SHROOM2 levels and immune characteristics, TMB, or drug sensitivity. Additionally, the effects of SHROOM2 on BC cells were assessed through reverse transcription-quantitative polymerase chain reaction (PCR), cell counting kit-8 (CCK-8) assay, transwell assay, and wound healing assay. Results SHROOM2 was overexpressed in a range of cancers, and its upregulation was associated with poor clinical outcomes. It was significantly correlated with immunomodulators, immune checkpoints, and immune cell infiltration in pan-cancer. Moreover, it showed an association with TMB and drug sensitivity in BC. Increased SHROOM2 expression enhanced the proliferative, migratory, and invasive capabilities of BC cells in vitro. Conclusion High SHROOM2 expression is linked to poor prognosis in BC, supporting its potential as both an immunological and predictive biomarker.
bibliographic citation: Wang et al. (2025) Identification of immunological and prognostic value of SHROOM2 in pan-cancer and experimental verification of its role in promoting malignant phenotypes in breast cancer. PeerJ 13:e20051 https://doi.org/10.7717/peerj.20051
date submitted: 2025-02-24
date accepted: 2025-08-17
issued: 2025-09-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yaya
author list: Agent
  family name: Ren
  given name: Yuechao
author list: Agent
  family name: Zheng
  given name: Xiaoyan
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Wang
  given name: Haoqi
author list: Agent
  family name: Zhang
  given name: Xi
author list: Agent
  family name: Li
  given name: Sainan
doi: 10.7717/peerj.20051
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-25
copyright: ©2025 Wang et al.
attribution name: Wang et al.

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