PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A green, fast protocol to estimate the accumulation of airborne anthropogenic microfibers in Pittosporum tobira in urban areas: effects of season and rainfall
items: Serum markers for prognostic value of EGFR-TKI in lung adenocarcinoma with bone metastases: a retrospective study
items: Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during stem in tumorous stem mustard
items: Association between urinary incontinence and sarcopenic obesity among middle-aged and older Brazilian women
items: Prolonged growth and extended subadult development in the Tyrannosaurus rex species complex revealed by expanded histological sampling and statistical modeling
items: Phylogenetics within Camassia (Asparagaceae): examining difficult taxonomy and unusual variation using genomic restriction-site-associated DNA sequencing data
items: The simple multivariable model for predicting liver fibrosis in Vietnamese male adults: a combination of Bayesian model averaging and stepwise method
items: Examination of factors affecting insomnia in older victims of the Kumamoto earthquake
items: Genetic diversity and structure of the red squat lobster (Grimothea monodon) in the Humboldt Current Ecosystem using SNP markers
items: Independent effects of mental fatigue and drop height on drop jump performance in American football athletes: an exploration of central-peripheral interaction

A green, fast protocol to estimate the accumulation of airborne anthropogenic microfibers in Pittosporum tobira in urban areas: effects of season and rainfall
type: item
type: AcademicArticle
description: Plastics represent a major organic pollutant, but research focused on their biomonitoring in the air has only recently received attention. In the present work, we investigated the ability of Pittosporum tobira leaves to distinguish different levels of air contamination due to anthropogenic microfibers (MFs) in six urban sites characterized by different land uses (industrial, urban, and green), and the effect of wet/dry season on their accumulation. Moreover, the effect of pouring rain on MFs accumulation was estimated by transplants of P. tobira. Microfiber extraction was done by tape tearing on 1 g composite leaf samples on the leaf surface. In summer, the highest number of MFs were found in the leaves from the industrial site (160), followed by urban ones (84–125), and green parks (48–54). The accumulation of MFs was overall higher in summer than in winter, due to the rain-washing effect in the latter, and the different leaf traits observed in the two seasons. The development of glandular hairs during summer could contribute to increasing the accumulation of MFs observed in this period under conditions of reduced precipitation. In agreement, when comparing MFs fallout on leaves of sheltered and unsheltered transplants after a heavy rainfall, the number counted on the latter was significantly lower, suggesting that precipitations reduce MFs deposition. These findings reinforce the suitability of Pittosporum tobira leaves as a bioindicator for airborne anthropogenic MFs. Moreover, the pronounced seasonal differences, as well as the higher MFs loads during dry summer months, indicate that monitoring sensitivity is enhanced under low-rainfall conditions.
format: application/pdf
format: text/html
creator: Anna Gaglione
creator: Angelo Granata
creator: Fiore Capozzi
creator: Antonio Rallo
creator: Simonetta Giordano
creator: Maria Cristina Sorrentino
creator: Valeria Spagnuolo
subject: Plant Science
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.20558
publisher: PeerJ Inc.
rights: © 2026 Gaglione et al.
abstract: Plastics represent a major organic pollutant, but research focused on their biomonitoring in the air has only recently received attention. In the present work, we investigated the ability of Pittosporum tobira leaves to distinguish different levels of air contamination due to anthropogenic microfibers (MFs) in six urban sites characterized by different land uses (industrial, urban, and green), and the effect of wet/dry season on their accumulation. Moreover, the effect of pouring rain on MFs accumulation was estimated by transplants of P. tobira. Microfiber extraction was done by tape tearing on 1 g composite leaf samples on the leaf surface. In summer, the highest number of MFs were found in the leaves from the industrial site (160), followed by urban ones (84–125), and green parks (48–54). The accumulation of MFs was overall higher in summer than in winter, due to the rain-washing effect in the latter, and the different leaf traits observed in the two seasons. The development of glandular hairs during summer could contribute to increasing the accumulation of MFs observed in this period under conditions of reduced precipitation. In agreement, when comparing MFs fallout on leaves of sheltered and unsheltered transplants after a heavy rainfall, the number counted on the latter was significantly lower, suggesting that precipitations reduce MFs deposition. These findings reinforce the suitability of Pittosporum tobira leaves as a bioindicator for airborne anthropogenic MFs. Moreover, the pronounced seasonal differences, as well as the higher MFs loads during dry summer months, indicate that monitoring sensitivity is enhanced under low-rainfall conditions.
bibliographic citation: Gaglione et al. (2026) A green, fast protocol to estimate the accumulation of airborne anthropogenic microfibers in Pittosporum tobira in urban areas: effects of season and rainfall. PeerJ 14:e20558 https://doi.org/10.7717/peerj.20558
date submitted: 2025-10-10
date accepted: 2025-11-19
issued: 2026-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gaglione
  given name: Anna
author list: Agent
  family name: Granata
  given name: Angelo
author list: Agent
  family name: Capozzi
  given name: Fiore
author list: Agent
  family name: Rallo
  given name: Antonio
author list: Agent
  family name: Giordano
  given name: Simonetta
author list: Agent
  family name: Sorrentino
  given name: Maria Cristina
author list: Agent
  family name: Spagnuolo
  given name: Valeria
doi: 10.7717/peerj.20558
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-01-14
copyright: ©2026 Gaglione et al.
attribution name: Gaglione et al.

Serum markers for prognostic value of EGFR-TKI in lung adenocarcinoma with bone metastases: a retrospective study
type: item
type: AcademicArticle
description: Background Lung adenocarcinoma is a prevalent malignancy. Mutations in the epidermal growth factor receptor (EGFR) have introduced novel prospects for targeted therapies. However, the status of EGFR mutations alone may be insufficient to fully predict treatment outcomes. To this end, the present research was performed to evaluate the serum markers associated with epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) treatment in patients with lung adenocarcinoma and bone metastases, specifically focusing on the prognostic value of EGFR-TKI therapy. Methods A retrospective analysis was conducted on 164 patients diagnosed with lung adenocarcinoma and bone metastases at Yunnan Cancer Hospital between January 2019 and December 2020. Clinical and follow-up data were collected, and a Cox regression model was employed to evaluate the combined predictive value of serum markers for survival outcomes. Results The findings revealed that variables identified through Cox regression analysis included age, the neutrophil-to-lymphocyte ratio (NLR), carcinoembryonic antigen (CEA), and Cytokeratin 19 fragment (Cyfra21-1), all exhibiting significance levels of P < 0.05. The Cox model exhibited a c-index of 0.644, and the calibration curve demonstrated satisfactory performance, indicating the moderate predictive capacity of the model. A nomogram was subsequently constructed to visualize these results. Conclusion This research successfully developed a nomogram based on the Cox regression model to predict prognosis and treatment outcomes in patients with lung adenocarcinoma and bone metastases undergoing EGFR-TKI therapy. This facilitates the avoidance of poor treatment outcomes by enabling individualized therapeutic approaches, thereby simplifying the development of the most appropriate treatment plans and ultimately improving patient prognosis.
format: application/pdf
format: text/html
creator: Jiali Li
creator: Shuting Wang
creator: Zhiyong Deng
creator: Lu Zhang
creator: Min Liu
creator: Yunlei Luo
creator: Yunqiu Guo
creator: Pengjie Liu
creator: Chao Liu
subject: Internal Medicine
subject: Oncology
description: doi:10.7717/peerj.20537
publisher: PeerJ Inc.
rights: © 2026 Li et al.
abstract: Background Lung adenocarcinoma is a prevalent malignancy. Mutations in the epidermal growth factor receptor (EGFR) have introduced novel prospects for targeted therapies. However, the status of EGFR mutations alone may be insufficient to fully predict treatment outcomes. To this end, the present research was performed to evaluate the serum markers associated with epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) treatment in patients with lung adenocarcinoma and bone metastases, specifically focusing on the prognostic value of EGFR-TKI therapy. Methods A retrospective analysis was conducted on 164 patients diagnosed with lung adenocarcinoma and bone metastases at Yunnan Cancer Hospital between January 2019 and December 2020. Clinical and follow-up data were collected, and a Cox regression model was employed to evaluate the combined predictive value of serum markers for survival outcomes. Results The findings revealed that variables identified through Cox regression analysis included age, the neutrophil-to-lymphocyte ratio (NLR), carcinoembryonic antigen (CEA), and Cytokeratin 19 fragment (Cyfra21-1), all exhibiting significance levels of P < 0.05. The Cox model exhibited a c-index of 0.644, and the calibration curve demonstrated satisfactory performance, indicating the moderate predictive capacity of the model. A nomogram was subsequently constructed to visualize these results. Conclusion This research successfully developed a nomogram based on the Cox regression model to predict prognosis and treatment outcomes in patients with lung adenocarcinoma and bone metastases undergoing EGFR-TKI therapy. This facilitates the avoidance of poor treatment outcomes by enabling individualized therapeutic approaches, thereby simplifying the development of the most appropriate treatment plans and ultimately improving patient prognosis.
bibliographic citation: Li et al. (2026) Serum markers for prognostic value of EGFR-TKI in lung adenocarcinoma with bone metastases: a retrospective study. PeerJ 14:e20537 https://doi.org/10.7717/peerj.20537
date submitted: 2025-03-17
date accepted: 2025-11-17
issued: 2026-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jiali
author list: Agent
  family name: Wang
  given name: Shuting
author list: Agent
  family name: Deng
  given name: Zhiyong
author list: Agent
  family name: Zhang
  given name: Lu
author list: Agent
  family name: Liu
  given name: Min
author list: Agent
  family name: Luo
  given name: Yunlei
author list: Agent
  family name: Guo
  given name: Yunqiu
author list: Agent
  family name: Liu
  given name: Pengjie
author list: Agent
  family name: Liu
  given name: Chao
doi: 10.7717/peerj.20537
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-01-14
copyright: © 2026 Li et al.
attribution name: Li et al.

Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during stem in tumorous stem mustard
type: item
type: AcademicArticle
description: The Basic Leucine Zipper (bZIP) proteins constitute a large family of transcription factors that play critical roles in plant growth regulation and the expression of resistance genes. However, to date, there have been few reports on the bZIP family in tumorous stem mustard (Brassica juncea var. tumida), an important vegetable crop. In this study, we identified 153 bZIP genes in tumorous stem mustard, which are unevenly distributed across 18 chromosomes and form 13 gene clusters. We systematically investigated their protein characteristics, phylogenetic relationships, gene structures, and conserved motifs. Most bZIP proteins exhibited random coil and α-helix as their predominant secondary structures. Based on RNA-Seq data from our laboratory, we analyzed the expression profiles of bZIP genes during the stem expansion of tumorous stem mustard. Furthermore, qRT-PCR analysis was performed to validate the expression of selected bZIP genes in tumorous stem mustard. The results showed that, compared with the 0 h control (25 °C untreated seedlings), five BjubZIP genes were significantly upregulated and eight were downregulated after 48 h of cold treatment, suggesting their potential involvement in temperature stress regulation in tumorous stem mustard. Under heat-treatment conditions, the transcription levels of BjubZIP111 and BjubZIP070 increased continuously over time, with expression at 48 hours significantly higher than at 12 hours. These findings provide a foundation for further functional research on bZIP genes in tumorous stem mustard, as well as for its breeding and production. Additionally, this study offers a theoretical basis for functional genomics research and the development of new cultivars of tumorous stem mustard.
format: application/pdf
format: text/html
creator: Yuting Deng
creator: Fu Li
creator: Yongfang Xie
creator: Jiaxin Guo
creator: Jianzhong Shu
creator: Rong Qin
creator: Quan Sun
creator: Keman Wu
creator: Feibo Xu
creator: Xiaohong He
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.20518
publisher: PeerJ Inc.
rights: © 2026 Deng et al.
abstract: The Basic Leucine Zipper (bZIP) proteins constitute a large family of transcription factors that play critical roles in plant growth regulation and the expression of resistance genes. However, to date, there have been few reports on the bZIP family in tumorous stem mustard (Brassica juncea var. tumida), an important vegetable crop. In this study, we identified 153 bZIP genes in tumorous stem mustard, which are unevenly distributed across 18 chromosomes and form 13 gene clusters. We systematically investigated their protein characteristics, phylogenetic relationships, gene structures, and conserved motifs. Most bZIP proteins exhibited random coil and α-helix as their predominant secondary structures. Based on RNA-Seq data from our laboratory, we analyzed the expression profiles of bZIP genes during the stem expansion of tumorous stem mustard. Furthermore, qRT-PCR analysis was performed to validate the expression of selected bZIP genes in tumorous stem mustard. The results showed that, compared with the 0 h control (25 °C untreated seedlings), five BjubZIP genes were significantly upregulated and eight were downregulated after 48 h of cold treatment, suggesting their potential involvement in temperature stress regulation in tumorous stem mustard. Under heat-treatment conditions, the transcription levels of BjubZIP111 and BjubZIP070 increased continuously over time, with expression at 48 hours significantly higher than at 12 hours. These findings provide a foundation for further functional research on bZIP genes in tumorous stem mustard, as well as for its breeding and production. Additionally, this study offers a theoretical basis for functional genomics research and the development of new cultivars of tumorous stem mustard.
bibliographic citation: Deng et al. (2026) Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during stem in tumorous stem mustard. PeerJ 14:e20518 https://doi.org/10.7717/peerj.20518
date submitted: 2025-05-05
date accepted: 2025-11-12
issued: 2026-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Yuting
author list: Agent
  family name: Li
  given name: Fu
author list: Agent
  family name: Xie
  given name: Yongfang
author list: Agent
  family name: Guo
  given name: Jiaxin
author list: Agent
  family name: Shu
  given name: Jianzhong
author list: Agent
  family name: Qin
  given name: Rong
author list: Agent
  family name: Sun
  given name: Quan
author list: Agent
  family name: Wu
  given name: Keman
author list: Agent
  family name: Xu
  given name: Feibo
author list: Agent
  family name: He
  given name: Xiaohong
doi: 10.7717/peerj.20518
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-01-14
copyright: ©2026 Deng et al.
attribution name: Deng et al.

Association between urinary incontinence and sarcopenic obesity among middle-aged and older Brazilian women
type: item
type: AcademicArticle
description: Background Urinary incontinence (UI) is a common complaint among middle-aged and older women, associated with many negative impacts in health. The aim of this study was to analyze whether an association exists between UI and sarcopenic obesity (SO) among middle-aged and older women living in northeastern Brazil. The association of UI with sarcopenia or obesity alone was also assessed. Methods In a cross-sectional, analytical study, 531 women living in Santa Cruz and Parnamirim, Rio Grande do Norte state (Brazil), aged between 40 and 80 years, were assessed for the presence of UI in the last 12 months by self-reporting. Waist circumference equal to or greater than 88 cm was considered to classify obesity, while skeletal muscle mass below 5.93 kg/m2, assessed by bioelectrical impedance, classified the presence of sarcopenia. Based on these measurements, the participants were classified into four profiles: neither condition, sarcopenia, obesity, and sarcopenic obesity. Binary logistic regression investigated the association of UI with sarcopenia, obesity, and SO, adjusted for the covariates age, schooling, family income, marital status, hypertension, diabetes, parity, and menopausal status, considering p < 0.05. Results A total of 10.7% had no sarcopenia or obesity, 10.7% had only sarcopenia, 69.7% had only obesity and 8.9% had SO. Obesity alone was associated with a higher odss of UI compared to the group with neither conditions (OR = 1.95; p = 0.025). The associations between UI and sarcopenia alone or combined with obesity were not significant. Conclusion Obesity alone was associated with UI. The results highlight the need for screening UI symptoms among women with abdominal obesity for early detection and timely interventions.
format: application/pdf
format: text/html
creator: Caroline Nayane Alves Medeiros
creator: Ingrid Guerra Azevedo
creator: Sabrina Gabrielle Gomes Fernandes
creator: Álvaro Campos Cavalcanti Maciel
creator: Saionara M.A. Câmara
subject: Epidemiology
subject: Geriatrics
subject: Global Health
subject: Rehabilitation
description: doi:10.7717/peerj.20470
publisher: PeerJ Inc.
rights: © 2026 Medeiros et al.
abstract: Background Urinary incontinence (UI) is a common complaint among middle-aged and older women, associated with many negative impacts in health. The aim of this study was to analyze whether an association exists between UI and sarcopenic obesity (SO) among middle-aged and older women living in northeastern Brazil. The association of UI with sarcopenia or obesity alone was also assessed. Methods In a cross-sectional, analytical study, 531 women living in Santa Cruz and Parnamirim, Rio Grande do Norte state (Brazil), aged between 40 and 80 years, were assessed for the presence of UI in the last 12 months by self-reporting. Waist circumference equal to or greater than 88 cm was considered to classify obesity, while skeletal muscle mass below 5.93 kg/m2, assessed by bioelectrical impedance, classified the presence of sarcopenia. Based on these measurements, the participants were classified into four profiles: neither condition, sarcopenia, obesity, and sarcopenic obesity. Binary logistic regression investigated the association of UI with sarcopenia, obesity, and SO, adjusted for the covariates age, schooling, family income, marital status, hypertension, diabetes, parity, and menopausal status, considering p < 0.05. Results A total of 10.7% had no sarcopenia or obesity, 10.7% had only sarcopenia, 69.7% had only obesity and 8.9% had SO. Obesity alone was associated with a higher odss of UI compared to the group with neither conditions (OR = 1.95; p = 0.025). The associations between UI and sarcopenia alone or combined with obesity were not significant. Conclusion Obesity alone was associated with UI. The results highlight the need for screening UI symptoms among women with abdominal obesity for early detection and timely interventions.
bibliographic citation: Medeiros et al. (2026) Association between urinary incontinence and sarcopenic obesity among middle-aged and older Brazilian women. PeerJ 14:e20470 https://doi.org/10.7717/peerj.20470
date submitted: 2025-03-28
date accepted: 2025-11-03
issued: 2026-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Medeiros
  given name: Caroline Nayane Alves
author list: Agent
  family name: Azevedo
  given name: Ingrid Guerra
author list: Agent
  family name: Gomes Fernandes
  given name: Sabrina Gabrielle
author list: Agent
  family name: Maciel
  given name: Álvaro Campos Cavalcanti
author list: Agent
  family name: Câmara
  given name: Saionara M.A.
doi: 10.7717/peerj.20470
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-01-14
copyright: ©2026 Medeiros et al.
attribution name: Medeiros et al.

Prolonged growth and extended subadult development in the Tyrannosaurus rex species complex revealed by expanded histological sampling and statistical modeling
type: item
type: AcademicArticle
description: Background Tyrannosaurus rex, one of the most iconic non-avialan dinosaurs, remains a central focus of paleobiological research. Growth modeling suggests T. rex exceeded 8,000 kg within two decades and had a lifespan approaching 30 years. However, this understanding of T. rex growth dynamics is dependent on single-point histological sampling of multiple skeletal elements and lacks specimens encompassing the earliest growth states. Methods We present the most comprehensive histological analysis of Tyrannosaurus ontogeny to date, based on transverse diaphyseal sections of femora and tibiae from 17 individuals ranging from small juveniles to large adults. Four alternative statistical models were tested, differing in the treatment of cortical growth marks, including annulus-like birefringent bands visible only in cross-polarized light. Due to high intraspecies morphological variability, the taxonomic status of many Tyrannosaurus specimens is debated, prompting use of the term “Tyrannosaurus rex species complex” to describe our dataset. Results The best-supported model incorporated all visible growth marks, produced the narrowest confidence bands, and indicated lower maximum growth rates and a delayed attainment of asymptotic size (~35–40 years) compared with earlier estimates. We also find that two immature specimens within the Tyrannosaurus rex species complex are not statistically compatible with the other growth series. Our approach is the first in dinosaur skeletochronology to simultaneously estimate the position of the earliest preserved growth mark across specimens, while fitting sigmoidal curves with simultaneous confidence bands. We find the inclusion of double growth marks and those visible only with cross polarized light provide better statistical model fits and this may have implications for modeling other taxa. Additionally, we find no strong link from extant vertebrates to support the idea that the growth inflection point is biologically significant and cor…
format: application/pdf
format: text/html
creator: Holly N. Woodward
creator: Nathan P. Myhrvold
creator: John R. Horner
subject: Paleontology
subject: Statistics
subject: Histology
description: doi:10.7717/peerj.20469
publisher: PeerJ Inc.
rights: © 2026 Woodward et al.
abstract: Background Tyrannosaurus rex, one of the most iconic non-avialan dinosaurs, remains a central focus of paleobiological research. Growth modeling suggests T. rex exceeded 8,000 kg within two decades and had a lifespan approaching 30 years. However, this understanding of T. rex growth dynamics is dependent on single-point histological sampling of multiple skeletal elements and lacks specimens encompassing the earliest growth states. Methods We present the most comprehensive histological analysis of Tyrannosaurus ontogeny to date, based on transverse diaphyseal sections of femora and tibiae from 17 individuals ranging from small juveniles to large adults. Four alternative statistical models were tested, differing in the treatment of cortical growth marks, including annulus-like birefringent bands visible only in cross-polarized light. Due to high intraspecies morphological variability, the taxonomic status of many Tyrannosaurus specimens is debated, prompting use of the term “Tyrannosaurus rex species complex” to describe our dataset. Results The best-supported model incorporated all visible growth marks, produced the narrowest confidence bands, and indicated lower maximum growth rates and a delayed attainment of asymptotic size (~35–40 years) compared with earlier estimates. We also find that two immature specimens within the Tyrannosaurus rex species complex are not statistically compatible with the other growth series. Our approach is the first in dinosaur skeletochronology to simultaneously estimate the position of the earliest preserved growth mark across specimens, while fitting sigmoidal curves with simultaneous confidence bands. We find the inclusion of double growth marks and those visible only with cross polarized light provide better statistical model fits and this may have implications for modeling other taxa. Additionally, we find no strong link from extant vertebrates to support the idea that the growth inflection point is biologically significant and cor…
bibliographic citation: Woodward et al. (2026) Prolonged growth and extended subadult development in the Tyrannosaurus rex species complex revealed by expanded histological sampling and statistical modeling. PeerJ 14:e20469 https://doi.org/10.7717/peerj.20469
date submitted: 2025-08-29
date accepted: 2025-11-03
issued: 2026-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Woodward
  given name: Holly N.
author list: Agent
  family name: Myhrvold
  given name: Nathan P.
author list: Agent
  family name: Horner
  given name: John R.
doi: 10.7717/peerj.20469
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-01-14
copyright: © 2026 Woodward et al.
attribution name: Woodward et al.

Phylogenetics within Camassia (Asparagaceae): examining difficult taxonomy and unusual variation using genomic restriction-site-associated DNA sequencing data
type: item
type: AcademicArticle
description: Premise Diversification of Camassia (Asparagaceae) in North America has shaped variety in morphological, ecological, and reproductive traits, and resulted in a classification with ambiguity in taxon boundaries, including numerous putative subspecies. Phylogenetic analyses of restriction-site-associated DNA sequences (RADseq) allowed new insights into its evolution and taxonomy, enhancing understanding of basal relationships, geographic patterns, taxonomic boundaries, and potential new species. Methods A total of 157 individuals in 71 populations across all 15 putative taxa of Camassia and 42 outgroup individuals in 21 populations from Hastingsia and Chlorogalum were sampled and genomic libraries were generated using the modified single-digest RADseq method known as multiplexed shotgun genotyping. Assembly in ipyrad included targeted comparisons across a range of parameters that influence homology assessment and amount of missing data, with analysis of the set of resulting datasets in RAxML and SVDquartets followed by comparison and summary across the sets of trees. Results and Conclusions Increasing the number of sampled loci improved phylogenetic signal despite concurrent increases in missing data. Each taxon was generally cohesive on the phylogenies, but some species and subspecies were not monophyletic. Results suggest that there was an early separation of C. howellii and C. leichtlinii from the rest of the genus during diversification. Different analysis parameters supported either a clade of both species as sister to the remainder of the genus, or C. howellii alone as sister. Relationships among all relatively deep clades within the genus were well supported. Within species, C. leichtlinii had particularly robust support for relationships compared to others in Camassia, and geographic patterns corresponding to the diversification of some subclades were resolved. The eight subspecies of C. quamash largely formed two main clades. Although most subspecies showed s…
format: application/pdf
format: text/html
creator: Jenny K. Archibald
creator: Susan R. Kephart
creator: Patrick J. Monnahan
creator: Kathryn E. Theiss
creator: Theresa M. Culley
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.20438
publisher: PeerJ Inc.
rights: © 2026 Archibald et al.
abstract: Premise Diversification of Camassia (Asparagaceae) in North America has shaped variety in morphological, ecological, and reproductive traits, and resulted in a classification with ambiguity in taxon boundaries, including numerous putative subspecies. Phylogenetic analyses of restriction-site-associated DNA sequences (RADseq) allowed new insights into its evolution and taxonomy, enhancing understanding of basal relationships, geographic patterns, taxonomic boundaries, and potential new species. Methods A total of 157 individuals in 71 populations across all 15 putative taxa of Camassia and 42 outgroup individuals in 21 populations from Hastingsia and Chlorogalum were sampled and genomic libraries were generated using the modified single-digest RADseq method known as multiplexed shotgun genotyping. Assembly in ipyrad included targeted comparisons across a range of parameters that influence homology assessment and amount of missing data, with analysis of the set of resulting datasets in RAxML and SVDquartets followed by comparison and summary across the sets of trees. Results and Conclusions Increasing the number of sampled loci improved phylogenetic signal despite concurrent increases in missing data. Each taxon was generally cohesive on the phylogenies, but some species and subspecies were not monophyletic. Results suggest that there was an early separation of C. howellii and C. leichtlinii from the rest of the genus during diversification. Different analysis parameters supported either a clade of both species as sister to the remainder of the genus, or C. howellii alone as sister. Relationships among all relatively deep clades within the genus were well supported. Within species, C. leichtlinii had particularly robust support for relationships compared to others in Camassia, and geographic patterns corresponding to the diversification of some subclades were resolved. The eight subspecies of C. quamash largely formed two main clades. Although most subspecies showed s…
bibliographic citation: Archibald et al. (2026) Phylogenetics within Camassia (Asparagaceae): examining difficult taxonomy and unusual variation using genomic restriction-site-associated DNA sequencing data. PeerJ 14:e20438 https://doi.org/10.7717/peerj.20438
date submitted: 2025-07-24
date accepted: 2025-10-31
issued: 2026-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Archibald
  given name: Jenny K.
author list: Agent
  family name: Kephart
  given name: Susan R.
author list: Agent
  family name: Monnahan
  given name: Patrick J.
author list: Agent
  family name: Theiss
  given name: Kathryn E.
author list: Agent
  family name: Culley
  given name: Theresa M.
doi: 10.7717/peerj.20438
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-01-14
copyright: ©2026 Archibald et al.
attribution name: Archibald et al.

The simple multivariable model for predicting liver fibrosis in Vietnamese male adults: a combination of Bayesian model averaging and stepwise method
type: item
type: AcademicArticle
description: Background Liver fibrosis is a significant health burden in Vietnamese male adults, driven by high rates of hepatitis B and hepatitis C, excessive alcohol consumption, and genetic and environmental factors. Despite progress in diagnostic tools, there is a pressing need for cost-effective screening methods tailored to this high-risk group, particularly in resource-limited settings. Methods This study enrolled 952 Vietnamese male adults over 40 years old undergoing FibroScan, excluding those with conditions affecting test accuracy. Data on demographics, clinical history, and anthropometrics were collected, and fibrosis stages were classified using the METAVIR system. Model development combined Bayesian model averaging and forward stepwise methods, with predictive performance validated via receiver operating characteristic (ROC) analysis and area under the curve (AUC) estimation in the R environment. Results Among 952 male participants, the prevalence of liver fibrosis was 19.9%, with most cases classified as mild (F1). Multivariate analysis identified significant risk factors, including advanced age (odds ratio (OR) = 1.6; 95% confidence interval (CI) [1.02–2.51]), alcohol abuse (OR = 4.44; 95% CI [2.65–7.42]), hepatitis B (OR = 6.76; 95% CI [3.14–14.54], hepatitis C (OR = 33.04; 95% CI [5.26–207.42]), family history of cirrhosis (OR = 16.14; 95% CI [3.28–79.55]), and hepatic steatosis (OR = 4.02; 95% CI [2.57–6.28]). The predictive model demonstrated good discriminative performance with an AUC of 0.769 (95% CI [0.734–0.800]) and showed satisfactory calibration through bootstrap resampling, indicating close agreement between predicted and observed risks. Conclusion The current prevalence of liver fibrosis among Vietnamese male adults was found to be 19.9%, and the developed risk prediction model effectively identifies high-risk individuals, enabling early diagnosis and targeted prevention, particularly in resource-limited settings. However, the lack of external valida…
format: application/pdf
format: text/html
creator: Nghia Nhu Nguyen
creator: Bao The Nguyen
creator: Huyen Thi Ngoc Le
creator: Hoang Nhat Dang
creator: Hao Minh Pham
creator: Duong Dai Ngo
creator: Duy Khanh Tran Nguyen
creator: Tam Thai Thanh Tran
creator: Hung Thanh Kim
creator: Tan Ngoc Huynh Mai
subject: Epidemiology
subject: Evidence Based Medicine
subject: Gastroenterology and Hepatology
subject: Internal Medicine
subject: Public Health
description: doi:10.7717/peerj.20435
publisher: PeerJ Inc.
rights: © 2026 Nguyen et al.
abstract: Background Liver fibrosis is a significant health burden in Vietnamese male adults, driven by high rates of hepatitis B and hepatitis C, excessive alcohol consumption, and genetic and environmental factors. Despite progress in diagnostic tools, there is a pressing need for cost-effective screening methods tailored to this high-risk group, particularly in resource-limited settings. Methods This study enrolled 952 Vietnamese male adults over 40 years old undergoing FibroScan, excluding those with conditions affecting test accuracy. Data on demographics, clinical history, and anthropometrics were collected, and fibrosis stages were classified using the METAVIR system. Model development combined Bayesian model averaging and forward stepwise methods, with predictive performance validated via receiver operating characteristic (ROC) analysis and area under the curve (AUC) estimation in the R environment. Results Among 952 male participants, the prevalence of liver fibrosis was 19.9%, with most cases classified as mild (F1). Multivariate analysis identified significant risk factors, including advanced age (odds ratio (OR) = 1.6; 95% confidence interval (CI) [1.02–2.51]), alcohol abuse (OR = 4.44; 95% CI [2.65–7.42]), hepatitis B (OR = 6.76; 95% CI [3.14–14.54], hepatitis C (OR = 33.04; 95% CI [5.26–207.42]), family history of cirrhosis (OR = 16.14; 95% CI [3.28–79.55]), and hepatic steatosis (OR = 4.02; 95% CI [2.57–6.28]). The predictive model demonstrated good discriminative performance with an AUC of 0.769 (95% CI [0.734–0.800]) and showed satisfactory calibration through bootstrap resampling, indicating close agreement between predicted and observed risks. Conclusion The current prevalence of liver fibrosis among Vietnamese male adults was found to be 19.9%, and the developed risk prediction model effectively identifies high-risk individuals, enabling early diagnosis and targeted prevention, particularly in resource-limited settings. However, the lack of external valida…
bibliographic citation: Nguyen et al. (2026) The simple multivariable model for predicting liver fibrosis in Vietnamese male adults: a combination of Bayesian model averaging and stepwise method. PeerJ 14:e20435 https://doi.org/10.7717/peerj.20435
date submitted: 2025-05-20
date accepted: 2025-10-30
issued: 2026-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nguyen
  given name: Nghia Nhu
author list: Agent
  family name: Nguyen
  given name: Bao The
author list: Agent
  family name: Le
  given name: Huyen Thi Ngoc
author list: Agent
  family name: Dang
  given name: Hoang Nhat
author list: Agent
  family name: Pham
  given name: Hao Minh
author list: Agent
  family name: Ngo
  given name: Duong Dai
author list: Agent
  family name: Nguyen
  given name: Duy Khanh Tran
author list: Agent
  family name: Tran
  given name: Tam Thai Thanh
author list: Agent
  family name: Kim
  given name: Hung Thanh
author list: Agent
  family name: Mai
  given name: Tan Ngoc Huynh
doi: 10.7717/peerj.20435
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-01-14
copyright: ©2026 Nguyen et al.
attribution name: Nguyen et al.

Examination of factors affecting insomnia in older victims of the Kumamoto earthquake
type: item
type: AcademicArticle
description: Objective Post-disaster survivors are prone to increased risks related to mental disorders such as insomnia and depression. In addition, it has been recently noted that elderly people have difficulty falling asleep and waking up in the middle of the night, decreasing sleep efficiency. Therefore, there is a need to understand the actual situation of insomnia among the older persons affected after the earthquake and consider appropriate support. However, the actual situation after the Kumamoto earthquake in 2016 has not been clarified. Therefore, this study aimed to examine the factors affecting insomnia among the older adults affected by the Kumamoto earthquake. Methods The study included 4,758 persons (2,010 men and 2,748 women; mean age 75.36 ± 7.33 years) aged 65 years or older among those who had moved out of temporary housing in Kumamoto City. The survey was a self-administered questionnaire sent by mail. The independence of each variable was confirmed using the χ2 test. Binomial logistic regression analysis was used to examine factors influencing insomnia. Results Persons significantly more likely to report insomnia had the following characteristics: age ≥ 75, no exercise habits, not eating three times a day, no appetite, eating alone, not participating in community activities, not knowing information about community activities, no one to talk to, no family to talk to, and no coworkers to talk to. Conversely, those less likely to fall into the insomnia category had the following attributes: men, those who had no employers, those who consulted friends, those who consulted a medical institution, those who consulted a care welfare office, and those who consulted city hall. Additionally, the respondents were more likely to report insomnia when they moved out of the community. Discussion Support for insomnia requires both informal supports to prevent isolation based on mutual community support and formal support for those suspected of insomnia.
format: application/pdf
format: text/html
creator: Yumie Kanamori
creator: Tomonori Samiso
creator: Ayako Ide-Okochi
subject: Health Policy
subject: Nursing
subject: Public Health
subject: Mental Health
subject: Healthcare Services
description: doi:10.7717/peerj.20584
publisher: PeerJ Inc.
rights: © 2026 Kanamori et al.
abstract: Objective Post-disaster survivors are prone to increased risks related to mental disorders such as insomnia and depression. In addition, it has been recently noted that elderly people have difficulty falling asleep and waking up in the middle of the night, decreasing sleep efficiency. Therefore, there is a need to understand the actual situation of insomnia among the older persons affected after the earthquake and consider appropriate support. However, the actual situation after the Kumamoto earthquake in 2016 has not been clarified. Therefore, this study aimed to examine the factors affecting insomnia among the older adults affected by the Kumamoto earthquake. Methods The study included 4,758 persons (2,010 men and 2,748 women; mean age 75.36 ± 7.33 years) aged 65 years or older among those who had moved out of temporary housing in Kumamoto City. The survey was a self-administered questionnaire sent by mail. The independence of each variable was confirmed using the χ2 test. Binomial logistic regression analysis was used to examine factors influencing insomnia. Results Persons significantly more likely to report insomnia had the following characteristics: age ≥ 75, no exercise habits, not eating three times a day, no appetite, eating alone, not participating in community activities, not knowing information about community activities, no one to talk to, no family to talk to, and no coworkers to talk to. Conversely, those less likely to fall into the insomnia category had the following attributes: men, those who had no employers, those who consulted friends, those who consulted a medical institution, those who consulted a care welfare office, and those who consulted city hall. Additionally, the respondents were more likely to report insomnia when they moved out of the community. Discussion Support for insomnia requires both informal supports to prevent isolation based on mutual community support and formal support for those suspected of insomnia.
bibliographic citation: Kanamori et al. (2026) Examination of factors affecting insomnia in older victims of the Kumamoto earthquake. PeerJ 14:e20584 https://doi.org/10.7717/peerj.20584
date submitted: 2025-02-23
date accepted: 2025-11-24
issued: 2026-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kanamori
  given name: Yumie
author list: Agent
  family name: Samiso
  given name: Tomonori
author list: Agent
  family name: Ide-Okochi
  given name: Ayako
doi: 10.7717/peerj.20584
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-01-13
copyright: ©2026 Kanamori et al.
attribution name: Kanamori et al.

Genetic diversity and structure of the red squat lobster (Grimothea monodon) in the Humboldt Current Ecosystem using SNP markers
type: item
type: AcademicArticle
description: The Humboldt Current Ecosystem (HCE) presents a wide variability of environmental and geographic conditions that play an important role in marine invertebrates, modulating variations not only in their behavior, physiology and morphology; but also changes in their patterns of genetic differentiation. Therefore, it is necessary to characterize genetic diversity and structure to develop management and conservation strategies in commercially important invertebrates such as the red squat lobster Grimothea monodon, which in the HCE presents two highly contrasting morphotypes and/or lifestyles (pelagic vs. benthic). The objective of the present study was to evaluate the diversity, structure, and genetic connectivity of the G. monodon population along the latitudinal gradient in the HCE using single nucleotide polymorphism (SNP) markers. Low heterozygosity (0.05 ± 0.1) and similar allelic richness among all studied populations (∼1.09) were observed. However, a slightly higher inbreeding was recorded in individuals from the Concepción population. At the level of genetic structure, using LEA and STRUCTURE, it is confirmed that G. monodon is a single population unit between the pelagic and benthic morphotypes, and that the difference observed in the discriminant analysis of principal components (DPCA) is due to the geographic distance (isolation by distance) between the extreme southern locations of the HCE (Constitución-Concepción: verified by Analysis of Molecular Variance (AMOVA) and Mantel test). The slight difference observed mainly in Concepción is due to inbreeding, however, this tends to be very low due to the high genetic flow explained by the prolonged development time of their planktonic larvae, which can positively influence an optimal recovery of their natural populations along the latitudinal gradient. This study emphasizes that the slight genetic differentiation of G. monodon could be due only to its wide geographic distribution range, generating only intra-popu…
format: application/pdf
format: text/html
creator: Marco Quispe-Machaca
creator: Carlos Muñoz-Ramírez
creator: Antonio Brante
creator: Pepe Espinoza
creator: Maximiliano Zilleruelo
creator: Gabriela Torres
creator: Ángel Urzúa
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.20580
publisher: PeerJ Inc.
rights: © 2026 Quispe-Machaca et al.
abstract: The Humboldt Current Ecosystem (HCE) presents a wide variability of environmental and geographic conditions that play an important role in marine invertebrates, modulating variations not only in their behavior, physiology and morphology; but also changes in their patterns of genetic differentiation. Therefore, it is necessary to characterize genetic diversity and structure to develop management and conservation strategies in commercially important invertebrates such as the red squat lobster Grimothea monodon, which in the HCE presents two highly contrasting morphotypes and/or lifestyles (pelagic vs. benthic). The objective of the present study was to evaluate the diversity, structure, and genetic connectivity of the G. monodon population along the latitudinal gradient in the HCE using single nucleotide polymorphism (SNP) markers. Low heterozygosity (0.05 ± 0.1) and similar allelic richness among all studied populations (∼1.09) were observed. However, a slightly higher inbreeding was recorded in individuals from the Concepción population. At the level of genetic structure, using LEA and STRUCTURE, it is confirmed that G. monodon is a single population unit between the pelagic and benthic morphotypes, and that the difference observed in the discriminant analysis of principal components (DPCA) is due to the geographic distance (isolation by distance) between the extreme southern locations of the HCE (Constitución-Concepción: verified by Analysis of Molecular Variance (AMOVA) and Mantel test). The slight difference observed mainly in Concepción is due to inbreeding, however, this tends to be very low due to the high genetic flow explained by the prolonged development time of their planktonic larvae, which can positively influence an optimal recovery of their natural populations along the latitudinal gradient. This study emphasizes that the slight genetic differentiation of G. monodon could be due only to its wide geographic distribution range, generating only intra-popu…
bibliographic citation: Quispe-Machaca et al. (2026) Genetic diversity and structure of the red squat lobster (Grimothea monodon) in the Humboldt Current Ecosystem using SNP markers. PeerJ 14:e20580 https://doi.org/10.7717/peerj.20580
date submitted: 2025-04-22
date accepted: 2025-11-22
issued: 2026-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quispe-Machaca
  given name: Marco
author list: Agent
  family name: Muñoz-Ramírez
  given name: Carlos
author list: Agent
  family name: Brante
  given name: Antonio
author list: Agent
  family name: Espinoza
  given name: Pepe
author list: Agent
  family name: Zilleruelo
  given name: Maximiliano
author list: Agent
  family name: Torres
  given name: Gabriela
author list: Agent
  family name: Urzúa
  given name: Ángel
doi: 10.7717/peerj.20580
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-01-13
copyright: ©2026 Quispe-Machaca et al.
attribution name: Quispe-Machaca et al.

Independent effects of mental fatigue and drop height on drop jump performance in American football athletes: an exploration of central-peripheral interaction
type: item
type: AcademicArticle
description: Background This study aimed to investigate the effects of mental fatigue (MF) and different drop heights on the athletic performance of American football players executing the drop jump (DJ) movement. Methods Twelve male American football athletes were selected as subjects. The Vicon infrared three-dimensional motion capture and analysis system, Kistler three-dimensional force platform, and other instruments were used. MF was induced through a Stroop task, and the DJ performance of the subjects was tested at drop heights of 30 cm, 40 cm, and 50 cm. A 2 × 3 repeated measures analysis of variance was employed. Results Regarding different jump heights, both under MF and baseline conditions, 40 cm and 50 cm heights resulted in lower jump heights compared to the 30 cm height (p = 0.002, p = 0.008); in terms of the rate of force development (RFD) metric, both under MF and baseline conditions, 40 cm and 50 cm heights showed lower RFD compared to the 30 cm height (p < 0.001); in the average power output metric, compared to the baseline, MF resulted in lower average power output across different drop heights (p < 0.001); in the reactive strength index (RSI) metric, compared to the baseline, MF resulted in lower RSI across different drop heights (p = 0.001), and compared to the 30 cm height, 40 cm and 50 cm heights showed lower RSI (p = 0.004, p = 0.008); in the Reactive Strength Ratio (RSR) metric, compared to the baseline, MF resulted in lower RSR across different drop heights (p = 0.001); in the Kleg metric, compared to the 30 cm height, 40 cm and 50 cm heights showed higher Kleg (p = 0.001, p = 0.008). Conclusions Under MF conditions, athletes’ performance in average power output, RSI, and RSR declined, suggesting a reduction in central nervous system efficiency. Additionally, increasing the drop height to 40 cm or above significantly reduced jump height and RFD, and increased Kleg. However, no interactive effects between MF and drop height were observed.
format: application/pdf
format: text/html
creator: Zilong Wang
creator: Ziqi Feng
creator: Mengya Lu
creator: Jing Sun
creator: Tao Liu
creator: Qiuxia Zhang
creator: Xiangdong Wang
subject: Kinesiology
subject: Biomechanics
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.20574
publisher: PeerJ Inc.
rights: © 2026 Wang et al.
abstract: Background This study aimed to investigate the effects of mental fatigue (MF) and different drop heights on the athletic performance of American football players executing the drop jump (DJ) movement. Methods Twelve male American football athletes were selected as subjects. The Vicon infrared three-dimensional motion capture and analysis system, Kistler three-dimensional force platform, and other instruments were used. MF was induced through a Stroop task, and the DJ performance of the subjects was tested at drop heights of 30 cm, 40 cm, and 50 cm. A 2 × 3 repeated measures analysis of variance was employed. Results Regarding different jump heights, both under MF and baseline conditions, 40 cm and 50 cm heights resulted in lower jump heights compared to the 30 cm height (p = 0.002, p = 0.008); in terms of the rate of force development (RFD) metric, both under MF and baseline conditions, 40 cm and 50 cm heights showed lower RFD compared to the 30 cm height (p < 0.001); in the average power output metric, compared to the baseline, MF resulted in lower average power output across different drop heights (p < 0.001); in the reactive strength index (RSI) metric, compared to the baseline, MF resulted in lower RSI across different drop heights (p = 0.001), and compared to the 30 cm height, 40 cm and 50 cm heights showed lower RSI (p = 0.004, p = 0.008); in the Reactive Strength Ratio (RSR) metric, compared to the baseline, MF resulted in lower RSR across different drop heights (p = 0.001); in the Kleg metric, compared to the 30 cm height, 40 cm and 50 cm heights showed higher Kleg (p = 0.001, p = 0.008). Conclusions Under MF conditions, athletes’ performance in average power output, RSI, and RSR declined, suggesting a reduction in central nervous system efficiency. Additionally, increasing the drop height to 40 cm or above significantly reduced jump height and RFD, and increased Kleg. However, no interactive effects between MF and drop height were observed.
bibliographic citation: Wang et al. (2026) Independent effects of mental fatigue and drop height on drop jump performance in American football athletes: an exploration of central-peripheral interaction. PeerJ 14:e20574 https://doi.org/10.7717/peerj.20574
date submitted: 2025-04-22
date accepted: 2025-11-20
issued: 2026-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zilong
author list: Agent
  family name: Feng
  given name: Ziqi
author list: Agent
  family name: Lu
  given name: Mengya
author list: Agent
  family name: Sun
  given name: Jing
author list: Agent
  family name: Liu
  given name: Tao
author list: Agent
  family name: Zhang
  given name: Qiuxia
author list: Agent
  family name: Wang
  given name: Xiangdong
doi: 10.7717/peerj.20574
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-01-13
copyright: ©2026 Wang et al.
attribution name: Wang et al.

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