PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: gllvm 2.0: fast fitting of advanced ordination methods and joint species distribution models
items: Revisiting the Poison Dart Frog Ameerega ingeri (Anura: Dendrobatidae): external morphology, tadpoles, natural history, distribution, advertisement call, phylogenetic position and conservation
items: Retrospective on decadal progress of the NOAA/NPS ocean noise reference station network
items: Alleviation of cold stress impacts on grapes by the chitosan-salicylic acid nanocomposite (CS-SA NCs) application
items: Human-mediated dispersal of Geniotrigona thoracica (Apidae: Meliponini) colonies promotes high genetic diversity and reduces population structuring in managed populations
items: High abundance of Early Miocene sea cows from Qatar shows repeated evolution of seagrass ecosystem engineers in Eastern Tethys
items: Differential effects of physical activity on cognitive and motor performance in obese young adults
items: Effects of core stability exercises on balance among Chinese children and youth with intellectual disabilities
items: Single-cell RNA-seq reveals breast cancer heterogeneity and identifies TCP1 as a therapeutic target in breast cancer
items: Knowledge, attitude, and practice toward perioperative neurocognitive disorders among healthcare workers in Shandong, China: a cross-sectional study

gllvm 2.0: fast fitting of advanced ordination methods and joint species distribution models
type: item
type: AcademicArticle
description: Background Over the past decade, joint species distribution models (JSDMs) and model-based ordination have emerged as powerful tools for the analysis of community ecology data. Generalized linear latent variable models (GLLVMs) offer a flexible framework for multivariate analysis of a wide range of data types, based on including a small number of latent variables to perform dimension reduction while accounting for residual correlation between species. Fast estimation methods The R package gllvm implements a wide range of GLLVMs, with estimation performed via fast approximate likelihood-based techniques; including the recently proposed extended variational approximation, which is applicable to almost any combination of response type and link function. Since its original development and accompanying software paper, the gllvm package has undergone a significant overhaul, consolidating its place as a general framework for joint modeling of community ecology datasets. Expanded functionalities Some of the key new features of gllvm include model-based constrained and concurrent ordination methods, capacity to account for nested/hierarchical sampling designs, and (phylogenetic) random effects. On top of this, other notable improvements include a great expansion of the response types that it can handle, enhanced capabilities of GLLVM inference, selection and prediction, and an easier-to-use interface for model fitting.
format: application/pdf
format: text/html
creator: Pekka Korhonen
creator: Francis K.C. Hui
creator: Jenni Niku
creator: Sara Taskinen
creator: Bert van der Veen
subject: Bioinformatics
subject: Computational Biology
subject: Ecosystem Science
subject: Statistics
subject: Environmental Impacts
description: doi:10.7717/peerj.20338
publisher: PeerJ Inc.
rights: © 2025 Korhonen et al.
abstract: Background Over the past decade, joint species distribution models (JSDMs) and model-based ordination have emerged as powerful tools for the analysis of community ecology data. Generalized linear latent variable models (GLLVMs) offer a flexible framework for multivariate analysis of a wide range of data types, based on including a small number of latent variables to perform dimension reduction while accounting for residual correlation between species. Fast estimation methods The R package gllvm implements a wide range of GLLVMs, with estimation performed via fast approximate likelihood-based techniques; including the recently proposed extended variational approximation, which is applicable to almost any combination of response type and link function. Since its original development and accompanying software paper, the gllvm package has undergone a significant overhaul, consolidating its place as a general framework for joint modeling of community ecology datasets. Expanded functionalities Some of the key new features of gllvm include model-based constrained and concurrent ordination methods, capacity to account for nested/hierarchical sampling designs, and (phylogenetic) random effects. On top of this, other notable improvements include a great expansion of the response types that it can handle, enhanced capabilities of GLLVM inference, selection and prediction, and an easier-to-use interface for model fitting.
bibliographic citation: Korhonen et al. (2025) gllvm 2.0: fast fitting of advanced ordination methods and joint species distribution models. PeerJ 13:e20338 https://doi.org/10.7717/peerj.20338
date submitted: 2025-05-06
date accepted: 2025-10-13
issued: 2025-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Korhonen
  given name: Pekka
author list: Agent
  family name: Hui
  given name: Francis K.C.
author list: Agent
  family name: Niku
  given name: Jenni
author list: Agent
  family name: Taskinen
  given name: Sara
author list: Agent
  family name: van der Veen
  given name: Bert
doi: 10.7717/peerj.20338
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-12
copyright: ©2025 Korhonen et al.
attribution name: Korhonen et al.

Revisiting the Poison Dart Frog Ameerega ingeri (Anura: Dendrobatidae): external morphology, tadpoles, natural history, distribution, advertisement call, phylogenetic position and conservation
type: item
type: AcademicArticle
description: Many amphibian species have been described based solely on preserved specimens, leaving significant gaps in our understanding of their behavior, natural history, population status, and phylogenetic relationships—factors essential for effective conservation. Ameerega ingeri, a dark poison frog originally believed to be endemic to Colombia, exemplifies this challenge. Described from only four specimens, its coloration in life, ecological traits, and distribution remained poorly understood for decades, leading to taxonomic confusion with closely related species. In this study, we revisit A. ingeri by providing new distribution records that extend its known range, along with detailed morphological and acoustic descriptions, dietary analysis, and population data. By integrating molecular and acoustic data with ecological and natural history observations, we clarify its taxonomic identity and distinguish it from congeners. Furthermore, we assess its conservation status based on updated occurrence and population data, and propose its inclusion in a threat category according to IUCN criteria. Our findings enhance the understanding of dendrobatid diversity and highlight the importance of field-based research on poorly known and potentially threatened species to support informed conservation strategies.
format: application/pdf
format: text/html
creator: Juan C. Diaz-Ricaurte
creator: Alejandro Navarro-Morales
creator: César Malambo
creator: Junner F. González-Ibarra
creator: Yulfreiler Garavito-David
creator: Felipe Silva de Andrade
creator: Mario A. Madrid-Ordoñez
creator: Maykoll J. Parra-Olarte
creator: Diego Huseth Ruiz-Valderrama
creator: Betselene Murcia-Ordoñez
creator: Amanda Varago
creator: Diego J. Santana
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.20078
publisher: PeerJ Inc.
rights: © 2025 Diaz-Ricaurte et al.
abstract: Many amphibian species have been described based solely on preserved specimens, leaving significant gaps in our understanding of their behavior, natural history, population status, and phylogenetic relationships—factors essential for effective conservation. Ameerega ingeri, a dark poison frog originally believed to be endemic to Colombia, exemplifies this challenge. Described from only four specimens, its coloration in life, ecological traits, and distribution remained poorly understood for decades, leading to taxonomic confusion with closely related species. In this study, we revisit A. ingeri by providing new distribution records that extend its known range, along with detailed morphological and acoustic descriptions, dietary analysis, and population data. By integrating molecular and acoustic data with ecological and natural history observations, we clarify its taxonomic identity and distinguish it from congeners. Furthermore, we assess its conservation status based on updated occurrence and population data, and propose its inclusion in a threat category according to IUCN criteria. Our findings enhance the understanding of dendrobatid diversity and highlight the importance of field-based research on poorly known and potentially threatened species to support informed conservation strategies.
bibliographic citation: Diaz-Ricaurte et al. (2025) Revisiting the Poison Dart Frog Ameerega ingeri (Anura: Dendrobatidae): external morphology, tadpoles, natural history, distribution, advertisement call, phylogenetic position and conservation. PeerJ 13:e20078 https://doi.org/10.7717/peerj.20078
date submitted: 2025-01-07
date accepted: 2025-08-22
issued: 2025-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Diaz-Ricaurte
  given name: Juan C.
author list: Agent
  family name: Navarro-Morales
  given name: Alejandro
author list: Agent
  family name: Malambo
  given name: César
author list: Agent
  family name: González-Ibarra
  given name: Junner F.
author list: Agent
  family name: Garavito-David
  given name: Yulfreiler
author list: Agent
  family name: Silva de Andrade
  given name: Felipe
author list: Agent
  family name: Madrid-Ordoñez
  given name: Mario A.
author list: Agent
  family name: Parra-Olarte
  given name: Maykoll J.
author list: Agent
  family name: Ruiz-Valderrama
  given name: Diego Huseth
author list: Agent
  family name: Murcia-Ordoñez
  given name: Betselene
author list: Agent
  family name: Varago
  given name: Amanda
author list: Agent
  family name: Santana
  given name: Diego J.
doi: 10.7717/peerj.20078
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-12
copyright: ©2025 Diaz-Ricaurte et al.
attribution name: Diaz-Ricaurte et al.

Retrospective on decadal progress of the NOAA/NPS ocean noise reference station network
type: item
type: AcademicArticle
description: The National Oceanic and Atmospheric Administration (NOAA), in partnership with the U.S. National Park Service (NPS), established the Ocean Noise Reference Station Network (NRS) in 2014 as a foundational component of NOAA’s Ocean Noise Strategy. This long-term effort aims to characterize baseline ocean ambient sound conditions across diverse marine environments and to inform management of noise impacts on protected species and habitats within U.S. waters. The NRS is now composed of 13 autonomous passive acoustic monitoring stations strategically positioned across the U.S. Exclusive Economic Zone (EEZ), extending from Arctic regions to tropical waters in depths ranging from 33 to 4,790 m. These locations include several National Marine Sanctuaries and National Parks, such as the recently designated Chumash Heritage National Marine Sanctuary off the coast of California. Each station is equipped to continuously sample low-frequency underwater sound at five kHz, enabling the detection of anthropogenic, geophysical, and biological acoustic signals. To date the network has sampled over 72 years of calibrated acoustic data. The spatial breadth and consistent methodology of the NRS allow for comparative acoustic assessments across diverse marine ecosystems. In addition to applied research functions, the NRS has served as a platform for education and training, offering opportunities for students to develop skills for marine science and data analysis. Looking forward, the NRS project team is focused on network expansion, improved data delivery, and broader integration with collaborative scientific initiatives. NRS recordings are being archived in partnership with NOAA’s National Centers for Environmental Information to enhance accessibility and long-term utility. Efforts are underway to develop standardized metadata and summary products to accompany raw audio files, making the data more usable for a wide range of stakeholders in the ocean science community. The NRS is evolvin…
format: application/pdf
format: text/html
creator: Samara M. Haver
creator: Robert P. Dziak
creator: Leila T. Hatch
creator: Joseph Haxel
creator: Christopher Kavanagh
creator: Haru Matsumoto
creator: Megan F. McKenna
creator: Lauren Roche
creator: Sofie M. Van Parijs
creator: Carrie C. Wall
creator: Jason Gedamke
subject: Marine Biology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.20382
publisher: PeerJ Inc.
rights: © 2025
abstract: The National Oceanic and Atmospheric Administration (NOAA), in partnership with the U.S. National Park Service (NPS), established the Ocean Noise Reference Station Network (NRS) in 2014 as a foundational component of NOAA’s Ocean Noise Strategy. This long-term effort aims to characterize baseline ocean ambient sound conditions across diverse marine environments and to inform management of noise impacts on protected species and habitats within U.S. waters. The NRS is now composed of 13 autonomous passive acoustic monitoring stations strategically positioned across the U.S. Exclusive Economic Zone (EEZ), extending from Arctic regions to tropical waters in depths ranging from 33 to 4,790 m. These locations include several National Marine Sanctuaries and National Parks, such as the recently designated Chumash Heritage National Marine Sanctuary off the coast of California. Each station is equipped to continuously sample low-frequency underwater sound at five kHz, enabling the detection of anthropogenic, geophysical, and biological acoustic signals. To date the network has sampled over 72 years of calibrated acoustic data. The spatial breadth and consistent methodology of the NRS allow for comparative acoustic assessments across diverse marine ecosystems. In addition to applied research functions, the NRS has served as a platform for education and training, offering opportunities for students to develop skills for marine science and data analysis. Looking forward, the NRS project team is focused on network expansion, improved data delivery, and broader integration with collaborative scientific initiatives. NRS recordings are being archived in partnership with NOAA’s National Centers for Environmental Information to enhance accessibility and long-term utility. Efforts are underway to develop standardized metadata and summary products to accompany raw audio files, making the data more usable for a wide range of stakeholders in the ocean science community. The NRS is evolvin…
bibliographic citation: Haver et al. (2025) Retrospective on decadal progress of the NOAA/NPS ocean noise reference station network. PeerJ 13:e20382 https://doi.org/10.7717/peerj.20382
date submitted: 2025-08-27
date accepted: 2025-10-22
issued: 2025-12-11
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Haver
  given name: Samara M.
author list: Agent
  family name: Dziak
  given name: Robert P.
author list: Agent
  family name: Hatch
  given name: Leila T.
author list: Agent
  family name: Haxel
  given name: Joseph
author list: Agent
  family name: Kavanagh
  given name: Christopher
author list: Agent
  family name: Matsumoto
  given name: Haru
author list: Agent
  family name: McKenna
  given name: Megan F.
author list: Agent
  family name: Roche
  given name: Lauren
author list: Agent
  family name: Van Parijs
  given name: Sofie M.
author list: Agent
  family name: Wall
  given name: Carrie C.
author list: Agent
  family name: Gedamke
  given name: Jason
doi: 10.7717/peerj.20382
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-11
copyright: ©2025 Haver et al.

Alleviation of cold stress impacts on grapes by the chitosan-salicylic acid nanocomposite (CS-SA NCs) application
type: item
type: AcademicArticle
description: Low temperature is a major abiotic stressor that limits the distribution of various fruit tree species worldwide. In this study, the effects of chitosan-salicylic acid nanocomposite (CS-SA NCs) treatment were evaluated on antioxidant enzyme activity, the antioxidant pool, and membrane stability indices in the grapevine cultivar ‘Flame seedless’ under cold stress conditions. Prolonged exposure to cold, compared to the control, led to a reduction in maximum fluorescence (Fm), variable fluorescence (Fv), the ratio of photochemical to non-photochemical use of light energy in photosystem II (Fv/F0), and the ratio of variable fluorescence to maximum fluorescence (Fv/Fm). Levels of chlorophylls, carotenoids, total soluble protein content, antioxidant enzyme activity, ascorbate, and glutathione activity significantly decreased with increasing cold stress duration. Electrolyte leakage, malondialdehyde, and hydrogen peroxide content increased by 75%, 60%, and 80%, respectively, after 16 hours of cold stress compared to the control. Nanocomposite treatment significantly enhanced antioxidant activity and stabilized membranes under cold stress by reducing electrolyte leakage and malondialdehyde release. Overall, CS-SA NCs act as a biological stimulant and can be effectively used to improve the physiological and biochemical responses of grapevines under cold stress. Further research is needed to gain a comparative understanding of various physiological responses, which will help guide the application of this nanocomposite in extension services and field production systems.
format: application/pdf
format: text/html
creator: Mohammad Ali Aazami
creator: Lamia Vojodi Mehrabani
creator: Mohammad Bagher Hassanpouraghdam
creator: Farzad Rasouli
creator: Gholam Reza Mahdavinia
creator: Sona Skrovankova
creator: Sezai Ercisli
creator: Jiri Mlcek
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20368
publisher: PeerJ Inc.
rights: © 2025 Aazami et al.
abstract: Low temperature is a major abiotic stressor that limits the distribution of various fruit tree species worldwide. In this study, the effects of chitosan-salicylic acid nanocomposite (CS-SA NCs) treatment were evaluated on antioxidant enzyme activity, the antioxidant pool, and membrane stability indices in the grapevine cultivar ‘Flame seedless’ under cold stress conditions. Prolonged exposure to cold, compared to the control, led to a reduction in maximum fluorescence (Fm), variable fluorescence (Fv), the ratio of photochemical to non-photochemical use of light energy in photosystem II (Fv/F0), and the ratio of variable fluorescence to maximum fluorescence (Fv/Fm). Levels of chlorophylls, carotenoids, total soluble protein content, antioxidant enzyme activity, ascorbate, and glutathione activity significantly decreased with increasing cold stress duration. Electrolyte leakage, malondialdehyde, and hydrogen peroxide content increased by 75%, 60%, and 80%, respectively, after 16 hours of cold stress compared to the control. Nanocomposite treatment significantly enhanced antioxidant activity and stabilized membranes under cold stress by reducing electrolyte leakage and malondialdehyde release. Overall, CS-SA NCs act as a biological stimulant and can be effectively used to improve the physiological and biochemical responses of grapevines under cold stress. Further research is needed to gain a comparative understanding of various physiological responses, which will help guide the application of this nanocomposite in extension services and field production systems.
bibliographic citation: Aazami et al. (2025) Alleviation of cold stress impacts on grapes by the chitosan-salicylic acid nanocomposite (CS-SA NCs) application. PeerJ 13:e20368 https://doi.org/10.7717/peerj.20368
date submitted: 2025-03-18
date accepted: 2025-10-18
issued: 2025-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aazami
  given name: Mohammad Ali
author list: Agent
  family name: Mehrabani
  given name: Lamia Vojodi
author list: Agent
  family name: Hassanpouraghdam
  given name: Mohammad Bagher
author list: Agent
  family name: Rasouli
  given name: Farzad
author list: Agent
  family name: Mahdavinia
  given name: Gholam Reza
author list: Agent
  family name: Skrovankova
  given name: Sona
author list: Agent
  family name: Ercisli
  given name: Sezai
author list: Agent
  family name: Mlcek
  given name: Jiri
doi: 10.7717/peerj.20368
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-11
copyright: ©2025 Aazami et al.
attribution name: Aazami et al.

Human-mediated dispersal of Geniotrigona thoracica (Apidae: Meliponini) colonies promotes high genetic diversity and reduces population structuring in managed populations
type: item
type: AcademicArticle
description: The stingless bee Geniotrigona thoracica is a key managed pollinator in Southeast Asia, valued for its honey, propolis, and colony trade. In Thailand, frequent human-mediated movement of colonies raises concerns about its effects on genetic diversity and population structure. We analysed variation in mitochondrial (COI and 16S rRNA) and nuclear (five microsatellite loci) markers from 70 colonies sampled across 17 meliponaries in seven southern provinces. Microsatellite data revealed high genetic diversity and low nuclear differentiation (K = 1; Fst = 0.0024–0.1219; all P > 0.05), with extensive gene flow (Nm = 3.60–207.83) among provinces. In contrast, mitochondrial markers indicated moderate-to-high differentiation (Fst = 0.619), consistent with mito-nuclear discordance arising from sex-biased. Managed colonies exhibited elevated heterozygosity and allelic richness, likely reflecting admixture from colony exchange, while unique haplotypes in certain provinces suggest introductions from external sources. Significant inbreeding was detected only in Yala, possibly linked to habitat loss and reduced effective population size. Our findings indicate that current meliponicultural practices maintain high genetic diversity in G. thoracica despite mitochondrial structuring, but increasing colony movement between genetically distinct populations may risk erosion of local adaptations, underscoring the need for genetic screening prior to translocation.
format: application/pdf
format: text/html
creator: Orawan Duangphakdee
creator: Ekgachai Jeratthitikul
creator: Pisit Poolprasert
creator: Rujira Pongkitsittiporn
creator: Chama Inson
creator: Atsalek Rattanawannee
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Entomology
subject: Genetics
description: doi:10.7717/peerj.20460
publisher: PeerJ Inc.
rights: © 2025 Duangphakdee et al.
abstract: The stingless bee Geniotrigona thoracica is a key managed pollinator in Southeast Asia, valued for its honey, propolis, and colony trade. In Thailand, frequent human-mediated movement of colonies raises concerns about its effects on genetic diversity and population structure. We analysed variation in mitochondrial (COI and 16S rRNA) and nuclear (five microsatellite loci) markers from 70 colonies sampled across 17 meliponaries in seven southern provinces. Microsatellite data revealed high genetic diversity and low nuclear differentiation (K = 1; Fst = 0.0024–0.1219; all P > 0.05), with extensive gene flow (Nm = 3.60–207.83) among provinces. In contrast, mitochondrial markers indicated moderate-to-high differentiation (Fst = 0.619), consistent with mito-nuclear discordance arising from sex-biased. Managed colonies exhibited elevated heterozygosity and allelic richness, likely reflecting admixture from colony exchange, while unique haplotypes in certain provinces suggest introductions from external sources. Significant inbreeding was detected only in Yala, possibly linked to habitat loss and reduced effective population size. Our findings indicate that current meliponicultural practices maintain high genetic diversity in G. thoracica despite mitochondrial structuring, but increasing colony movement between genetically distinct populations may risk erosion of local adaptations, underscoring the need for genetic screening prior to translocation.
bibliographic citation: Duangphakdee et al. (2025) Human-mediated dispersal of Geniotrigona thoracica (Apidae: Meliponini) colonies promotes high genetic diversity and reduces population structuring in managed populations. PeerJ 13:e20460 https://doi.org/10.7717/peerj.20460
date submitted: 2025-09-02
date accepted: 2025-11-03
issued: 2025-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duangphakdee
  given name: Orawan
author list: Agent
  family name: Jeratthitikul
  given name: Ekgachai
author list: Agent
  family name: Poolprasert
  given name: Pisit
author list: Agent
  family name: Pongkitsittiporn
  given name: Rujira
author list: Agent
  family name: Inson
  given name: Chama
author list: Agent
  family name: Rattanawannee
  given name: Atsalek
doi: 10.7717/peerj.20460
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-10
copyright: ©2025 Duangphakdee et al.
attribution name: Duangphakdee et al.

High abundance of Early Miocene sea cows from Qatar shows repeated evolution of seagrass ecosystem engineers in Eastern Tethys
type: item
type: AcademicArticle
description: Coastal ecosystems that include seagrasses are potential carbon sinks that require strategic conservation of top trophic consumers, such as dugongs, to maintain their function. It is unclear, however, how long seagrass ecosystems have persisted in geologic time because their fossil record is poor, although the record of their associated vertebrate consumers offers useful proxies. Here we describe an area of dense Early Miocene dugongid remains from Qatar. We documented over 172 sites in <1 km2 from one stratigraphic level, including material representing a new species of fossil dugongine dugongid. This taxon is unrelated to coeval Early Miocene dugongids from India and the Eastern Tethys and it is distantly related to extant dugongs, which occupy seagrass habitats of the Persian or Arabian Gulf (hereafter ‘Gulf’) today. The monodominant assemblage in this area likely reflects a single fossil dugongid taxon and matches the ecological diversity and geospatial distribution of modern-day live-dead assemblages in the Gulf. This fossil site from Qatar shows that the Gulf has repeatedly evolved sea cow communities with different taxa over the past 20 million years and coincides with an Early Miocene marine biodiversity hotspot in Arabia, prior to its eastward shift to the Indo-Australian Archipelago where dugongs continue to thrive today.
format: application/pdf
format: text/html
creator: Nicholas D. Pyenson
creator: Ferhan Sakal
creator: Jacques LeBlanc
creator: Jon Blundell
creator: Katherine D. Klim
creator: Christopher D. Marshall
creator: Jorge Velez-Juarbe
creator: Katherine Wolfe
creator: Faisal Al-Naimi
subject: Ecology
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.20030
publisher: PeerJ Inc.
rights: © 2025
abstract: Coastal ecosystems that include seagrasses are potential carbon sinks that require strategic conservation of top trophic consumers, such as dugongs, to maintain their function. It is unclear, however, how long seagrass ecosystems have persisted in geologic time because their fossil record is poor, although the record of their associated vertebrate consumers offers useful proxies. Here we describe an area of dense Early Miocene dugongid remains from Qatar. We documented over 172 sites in <1 km2 from one stratigraphic level, including material representing a new species of fossil dugongine dugongid. This taxon is unrelated to coeval Early Miocene dugongids from India and the Eastern Tethys and it is distantly related to extant dugongs, which occupy seagrass habitats of the Persian or Arabian Gulf (hereafter ‘Gulf’) today. The monodominant assemblage in this area likely reflects a single fossil dugongid taxon and matches the ecological diversity and geospatial distribution of modern-day live-dead assemblages in the Gulf. This fossil site from Qatar shows that the Gulf has repeatedly evolved sea cow communities with different taxa over the past 20 million years and coincides with an Early Miocene marine biodiversity hotspot in Arabia, prior to its eastward shift to the Indo-Australian Archipelago where dugongs continue to thrive today.
bibliographic citation: Pyenson et al. (2025) High abundance of Early Miocene sea cows from Qatar shows repeated evolution of seagrass ecosystem engineers in Eastern Tethys. PeerJ 13:e20030 https://doi.org/10.7717/peerj.20030
date submitted: 2025-05-30
date accepted: 2025-08-13
issued: 2025-12-10
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Pyenson
  given name: Nicholas D.
author list: Agent
  family name: Sakal
  given name: Ferhan
author list: Agent
  family name: LeBlanc
  given name: Jacques
author list: Agent
  family name: Blundell
  given name: Jon
author list: Agent
  family name: Klim
  given name: Katherine D.
author list: Agent
  family name: Marshall
  given name: Christopher D.
author list: Agent
  family name: Velez-Juarbe
  given name: Jorge
author list: Agent
  family name: Wolfe
  given name: Katherine
author list: Agent
  family name: Al-Naimi
  given name: Faisal
doi: 10.7717/peerj.20030
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-10
copyright: ©2025 Pyenson et al.

Differential effects of physical activity on cognitive and motor performance in obese young adults
type: item
type: AcademicArticle
description: The rising prevalence of obesity among young adults presents significant health challenges, particularly due to its adverse effects on cognitive function and physical mobility. This cross-sectional study examined the effects of physical activity on cognitive performance and gait speed in obese individuals aged 18 to 25 years. Seventy-six participants were categorized as either physically active or sedentary based on the Global Physical Activity Questionnaire. All enrolled participants completed the study, and no data were missing. Anthropometric data, including body mass, height, waist circumference, and hip circumference, were collected using standardized procedures. Cognitive assessments included the Trail Making Test, Stroop Color and Word Test, Hand Reaction Time Test, and Logical Memory Test. Gait speed was evaluated using the 10-meter walk test. The physically active group showed significantly better results in logical memory, executive function, and all Stroop test conditions (p < 0.05). No group differences were found in reaction time, Stroop interference score, or gait speed (p > 0.05). These findings suggest that higher physical activity levels are linked to better cognitive performance, highlighting the value of promoting physical activity in young adults with obesity. The lack of observed differences in gait speed and reaction time may indicate that these functions are less sensitive to early changes or require longer periods of inactivity to decline in this population.
format: application/pdf
format: text/html
creator: Piangkwan Sa-nguanmoo
creator: Busaba Chuatrakoon
creator: Puntarik Keawtep
creator: Savitree Thummasorn
creator: Tanawat Thongsukdee
creator: Patimakorn Homjan
creator: Phumiphat Phetcharat
subject: Cognitive Disorders
subject: Kinesiology
subject: Obesity
subject: Mental Health
subject: Rehabilitation
description: doi:10.7717/peerj.20481
publisher: PeerJ Inc.
rights: © 2025 Sa-nguanmoo et al.
abstract: The rising prevalence of obesity among young adults presents significant health challenges, particularly due to its adverse effects on cognitive function and physical mobility. This cross-sectional study examined the effects of physical activity on cognitive performance and gait speed in obese individuals aged 18 to 25 years. Seventy-six participants were categorized as either physically active or sedentary based on the Global Physical Activity Questionnaire. All enrolled participants completed the study, and no data were missing. Anthropometric data, including body mass, height, waist circumference, and hip circumference, were collected using standardized procedures. Cognitive assessments included the Trail Making Test, Stroop Color and Word Test, Hand Reaction Time Test, and Logical Memory Test. Gait speed was evaluated using the 10-meter walk test. The physically active group showed significantly better results in logical memory, executive function, and all Stroop test conditions (p < 0.05). No group differences were found in reaction time, Stroop interference score, or gait speed (p > 0.05). These findings suggest that higher physical activity levels are linked to better cognitive performance, highlighting the value of promoting physical activity in young adults with obesity. The lack of observed differences in gait speed and reaction time may indicate that these functions are less sensitive to early changes or require longer periods of inactivity to decline in this population.
bibliographic citation: Sa-nguanmoo et al. (2025) Differential effects of physical activity on cognitive and motor performance in obese young adults. PeerJ 13:e20481 https://doi.org/10.7717/peerj.20481
date submitted: 2025-07-25
date accepted: 2025-11-05
issued: 2025-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sa-nguanmoo
  given name: Piangkwan
author list: Agent
  family name: Chuatrakoon
  given name: Busaba
author list: Agent
  family name: Keawtep
  given name: Puntarik
author list: Agent
  family name: Thummasorn
  given name: Savitree
author list: Agent
  family name: Thongsukdee
  given name: Tanawat
author list: Agent
  family name: Homjan
  given name: Patimakorn
author list: Agent
  family name: Phetcharat
  given name: Phumiphat
doi: 10.7717/peerj.20481
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-09
copyright: ©2025 Sa-nguanmoo et al.
attribution name: Sa-nguanmoo et al.

Effects of core stability exercises on balance among Chinese children and youth with intellectual disabilities
type: item
type: AcademicArticle
description: Background Children and youth with intellectual disabilities (IDs) are at risk of falls due to balance problems. Objective This study was conducted to assess the effects of six weeks of core stability exercises on balance in this population. Methods Thirty-five participants with IDs from a special school were selected. Static and dynamic balance were assessed by the one-legged stance test (OLS) and lower quarter Y balance test (YBT-LQ), respectively. Results Core stability exercises significantly improved static balance with eyes opened (EO) on firm (FI) ground (t = −5.269, P < 0.001) and dynamic balance in all three directions (left leg: anterior: t = −3.197, P = 0.005; posteromedial: t = − 4.608, P < 0.001; posterolateral: t = −4.706, P < 0.001; right leg: anterior: t = −3.324, P = 0.004; posteromedial: t = −5.614, P < 0.001; posterolateral: t = −5.905, P < 0.001). Conclusions Six weeks of core stability exercises significantly improved the static balance of children and youth with IDs under EO and FI conditions, as well as all three directions of dynamic balance. Future studies with multiple measurement points are warranted to examine the long-term effectiveness of this training on balance in this population.
format: application/pdf
format: text/html
creator: Jing Qi
creator: Yecheng Zhong
creator: Junjie Zhou
creator: Niuniu Li
creator: Yuhang Han
creator: Zehua Dong
creator: Yan Li
creator: Wenhong Xu
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Sports Medicine
description: doi:10.7717/peerj.20454
publisher: PeerJ Inc.
rights: © 2025 Qi et al.
abstract: Background Children and youth with intellectual disabilities (IDs) are at risk of falls due to balance problems. Objective This study was conducted to assess the effects of six weeks of core stability exercises on balance in this population. Methods Thirty-five participants with IDs from a special school were selected. Static and dynamic balance were assessed by the one-legged stance test (OLS) and lower quarter Y balance test (YBT-LQ), respectively. Results Core stability exercises significantly improved static balance with eyes opened (EO) on firm (FI) ground (t = −5.269, P < 0.001) and dynamic balance in all three directions (left leg: anterior: t = −3.197, P = 0.005; posteromedial: t = − 4.608, P < 0.001; posterolateral: t = −4.706, P < 0.001; right leg: anterior: t = −3.324, P = 0.004; posteromedial: t = −5.614, P < 0.001; posterolateral: t = −5.905, P < 0.001). Conclusions Six weeks of core stability exercises significantly improved the static balance of children and youth with IDs under EO and FI conditions, as well as all three directions of dynamic balance. Future studies with multiple measurement points are warranted to examine the long-term effectiveness of this training on balance in this population.
bibliographic citation: Qi et al. (2025) Effects of core stability exercises on balance among Chinese children and youth with intellectual disabilities. PeerJ 13:e20454 https://doi.org/10.7717/peerj.20454
date submitted: 2025-03-21
date accepted: 2025-10-31
issued: 2025-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Jing
author list: Agent
  family name: Zhong
  given name: Yecheng
author list: Agent
  family name: Zhou
  given name: Junjie
author list: Agent
  family name: Li
  given name: Niuniu
author list: Agent
  family name: Han
  given name: Yuhang
author list: Agent
  family name: Dong
  given name: Zehua
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Xu
  given name: Wenhong
doi: 10.7717/peerj.20454
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-09
copyright: ©2025 Qi et al.
attribution name: Qi et al.

Single-cell RNA-seq reveals breast cancer heterogeneity and identifies TCP1 as a therapeutic target in breast cancer
type: item
type: AcademicArticle
description: Breast cancer is composed of diverse cell populations, and this intratumoral heterogeneity profoundly affects clinical behavior. Here, we leveraged single cell RNA sequencing (scRNA-seq) of 68 breast cancer specimens to dissect tumor heterogeneity at high resolution. Unsupervised clustering identified all major cell types of the tumor microenvironment (TME)—including malignant epithelial cells, fibroblasts, T cells, macrophages, endothelial cells, and others—with striking variability in their proportions across molecular subtypes. For example, a BRCA1-mutant triple-negative breast cancer (TNBC) sample showed dense immune infiltration, whereas an estrogen receptor (ER)-positive tumor was mostly epithelial, consistent with known subtype differences in immunogenicity. We applied inference of copy number variations (inferCNV) to distinguish malignant epithelial cells, identifying ~90,000 tumor cells with significant copy-number aberrations enriched for cancer hallmark pathways. Re-clustering of these malignant cells revealed five discrete subpopulations. Notably, a KRT17-positive subcluster displayed the highest stemness score and a distinctive ETS-family transcription factor (ERG) regulon, suggesting a stem-like phenotype. Using The Cancer Genome Atlas (TCGA) cohort, we found that genes upregulated in this KRT17+ subpopulation, particularly NFKBIA, PDLIM4, and TCP1 stratified patient survival. An 8-gene risk signature derived from the KRT17 program segregated patients into high- and low-risk groups with markedly different outcomes. High-risk tumors were characterized by an immunosuppressive TME enriched in M2-like macrophages, whereas low-risk tumors more often harbored lymphocyte-predominant infiltrates. Focusing on TCP1, a chaperonin subunit upregulated in high-risk tumors, we demonstrate that TCP1 knockdown in breast cancer cell lines substantially impairs cell migration (~50% reduction in wound closure) and invasion (P < 0.01). These findings reveal functionally di…
format: application/pdf
format: text/html
creator: Houman Wu
creator: Haiyang Du
creator: Gao Si
creator: Xuejie Song
creator: Fuchun Si
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.20451
publisher: PeerJ Inc.
rights: © 2025 Wu et al.
abstract: Breast cancer is composed of diverse cell populations, and this intratumoral heterogeneity profoundly affects clinical behavior. Here, we leveraged single cell RNA sequencing (scRNA-seq) of 68 breast cancer specimens to dissect tumor heterogeneity at high resolution. Unsupervised clustering identified all major cell types of the tumor microenvironment (TME)—including malignant epithelial cells, fibroblasts, T cells, macrophages, endothelial cells, and others—with striking variability in their proportions across molecular subtypes. For example, a BRCA1-mutant triple-negative breast cancer (TNBC) sample showed dense immune infiltration, whereas an estrogen receptor (ER)-positive tumor was mostly epithelial, consistent with known subtype differences in immunogenicity. We applied inference of copy number variations (inferCNV) to distinguish malignant epithelial cells, identifying ~90,000 tumor cells with significant copy-number aberrations enriched for cancer hallmark pathways. Re-clustering of these malignant cells revealed five discrete subpopulations. Notably, a KRT17-positive subcluster displayed the highest stemness score and a distinctive ETS-family transcription factor (ERG) regulon, suggesting a stem-like phenotype. Using The Cancer Genome Atlas (TCGA) cohort, we found that genes upregulated in this KRT17+ subpopulation, particularly NFKBIA, PDLIM4, and TCP1 stratified patient survival. An 8-gene risk signature derived from the KRT17 program segregated patients into high- and low-risk groups with markedly different outcomes. High-risk tumors were characterized by an immunosuppressive TME enriched in M2-like macrophages, whereas low-risk tumors more often harbored lymphocyte-predominant infiltrates. Focusing on TCP1, a chaperonin subunit upregulated in high-risk tumors, we demonstrate that TCP1 knockdown in breast cancer cell lines substantially impairs cell migration (~50% reduction in wound closure) and invasion (P < 0.01). These findings reveal functionally di…
bibliographic citation: Wu et al. (2025) Single-cell RNA-seq reveals breast cancer heterogeneity and identifies TCP1 as a therapeutic target in breast cancer. PeerJ 13:e20451 https://doi.org/10.7717/peerj.20451
date submitted: 2025-06-30
date accepted: 2025-10-31
issued: 2025-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wu
  given name: Houman
author list: Agent
  family name: Du
  given name: Haiyang
author list: Agent
  family name: Si
  given name: Gao
author list: Agent
  family name: Song
  given name: Xuejie
author list: Agent
  family name: Si
  given name: Fuchun
doi: 10.7717/peerj.20451
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-09
copyright: © 2025 Wu et al.
attribution name: Wu et al.

Knowledge, attitude, and practice toward perioperative neurocognitive disorders among healthcare workers in Shandong, China: a cross-sectional study
type: item
type: AcademicArticle
description: Background Perioperative neurocognitive disorders (PND) refer to neurocognitive abnormalities detected during the perioperative period, currently including postoperative delirium, delayed neurocognitive recovery, postoperative neurocognitive disorder, and both mild and major cognitive impairments. It is a prevalent complication among surgical patients, particularly in older populations. Moreover, PND can have a profound effect on the quality of life for these patients. PND has been previously reported to occur with a prevalence of 10–54% during the first few weeks following surgery, and when persistent at the time of discharge or in the longer term, PND may increase mortality. Therefore, it is of considerable importance for healthcare professionals to accurately identify the occurrence of PND and implement appropriate management measures. This research aims to investigate the knowledge, attitude, and practice (KAP) of healthcare workers concerning perioperative neurocognitive disorders (PND) in Shandong Province, China. Methods This cross-sectional study recruited healthcare workers from twelve hospitals in Shandong Province, China, utilizing self-administered questionnaires distributed between February and May 2025. There are 12 items in the knowledge dimension, and the total score range for this dimension is 0 to 12 points. There are a total of seven items in the attitude dimension, and the total score range for this dimension is 7 to 35 points. There are a total of nine items in the practice dimension, and the total score range for this dimension is from 9 to 45 points. Results The analysis included a total of 309 valid questionnaires, which represents an impressive 87.78% response rate. Among them, a total of 193 doctors (62.5%) and 116 nurses (37.5%) participated in the survey, respectively. The PND knowledge score was 9.14 (SD = 2.85, range = 0–12). The PND attitudes score was 30.89 (SD = 3.81, range = 7–35). The PND practices score was 36.16 (SD = 7.77, range…
format: application/pdf
format: text/html
creator: Ke Zhang
creator: Xuefeng Gu
creator: Xiaoru Li
creator: Honghai Peng
subject: Neuroscience
subject: Cognitive Disorders
subject: Science and Medical Education
description: doi:10.7717/peerj.20450
publisher: PeerJ Inc.
rights: © 2025 Zhang et al.
abstract: Background Perioperative neurocognitive disorders (PND) refer to neurocognitive abnormalities detected during the perioperative period, currently including postoperative delirium, delayed neurocognitive recovery, postoperative neurocognitive disorder, and both mild and major cognitive impairments. It is a prevalent complication among surgical patients, particularly in older populations. Moreover, PND can have a profound effect on the quality of life for these patients. PND has been previously reported to occur with a prevalence of 10–54% during the first few weeks following surgery, and when persistent at the time of discharge or in the longer term, PND may increase mortality. Therefore, it is of considerable importance for healthcare professionals to accurately identify the occurrence of PND and implement appropriate management measures. This research aims to investigate the knowledge, attitude, and practice (KAP) of healthcare workers concerning perioperative neurocognitive disorders (PND) in Shandong Province, China. Methods This cross-sectional study recruited healthcare workers from twelve hospitals in Shandong Province, China, utilizing self-administered questionnaires distributed between February and May 2025. There are 12 items in the knowledge dimension, and the total score range for this dimension is 0 to 12 points. There are a total of seven items in the attitude dimension, and the total score range for this dimension is 7 to 35 points. There are a total of nine items in the practice dimension, and the total score range for this dimension is from 9 to 45 points. Results The analysis included a total of 309 valid questionnaires, which represents an impressive 87.78% response rate. Among them, a total of 193 doctors (62.5%) and 116 nurses (37.5%) participated in the survey, respectively. The PND knowledge score was 9.14 (SD = 2.85, range = 0–12). The PND attitudes score was 30.89 (SD = 3.81, range = 7–35). The PND practices score was 36.16 (SD = 7.77, range…
bibliographic citation: Zhang et al. (2025) Knowledge, attitude, and practice toward perioperative neurocognitive disorders among healthcare workers in Shandong, China: a cross-sectional study. PeerJ 13:e20450 https://doi.org/10.7717/peerj.20450
date submitted: 2025-05-19
date accepted: 2025-10-31
issued: 2025-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ke
author list: Agent
  family name: Gu
  given name: Xuefeng
author list: Agent
  family name: Li
  given name: Xiaoru
author list: Agent
  family name: Peng
  given name: Honghai
doi: 10.7717/peerj.20450
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-09
copyright: ©2025 Zhang et al.
attribution name: Zhang et al.

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