PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park
items: Spatially explicit models of density improve estimates of Eastern Bering Sea beluga (Delphinapterus leucas) abundance and distribution from line-transect surveys
items: Morphological, phytochemical, and pharmacological properties of the genus Tamarix in Kazakhstan species: a review
items: Identification and verification of prognostic genes related to zinc homeostasis and zinc transport in breast cancer
items: Unlocking the genomic potential of historical and formalin-fixed specimens: phylogenetic insights from museum-preserved threadfin fishes (Teleostei: Polynemidae)
items: Undernutrition and feeding difficulties among children with disabilities in Zambia: insights for inclusive nutrition strategies
items: Metabolomic and physiological analysis of bud differentiation in dense apple (Malus×domestica Borkh.) orchards following thinning and reshaping
items: Interprofessional collaboration and associated factors among wound, ostomy, and continence nurses: a cross-sectional study in China
items: Optimization of anther culture of awnless triticale
items: Study on the diagnostic potential and molecular mechanism of hsa_circ_0000831 in oral squamous cell carcinoma

Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park
type: item
type: AcademicArticle
description: New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.
format: application/pdf
format: text/html
creator: Sally Kong
creator: Eliana Abrams
creator: Yehuda Binik
creator: Christina Cappelli
creator: Mathew Chu
creator: Taiyo Cornett
creator: Isayah Culbertson
creator: Epifania Garcia
creator: Jada Henry
creator: Kristy Lam
creator: D.B. Lampman
creator: Grace Morenko
creator: Illusion Rivera
creator: Tanasia Swift
creator: Isabella Torres
creator: Rayven Velez
creator: Elliot Waxman
creator: Serena Wessely
creator: Anthony Yuen
creator: Casey K. Lardner
creator: J.L. Weissman
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Biological Oceanography
description: doi:10.7717/peerj.20081
publisher: PeerJ Inc.
rights: © 2025 Kong et al.
abstract: New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.
bibliographic citation: Kong et al. (2025) Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park. PeerJ 13:e20081 https://doi.org/10.7717/peerj.20081
date submitted: 2025-05-13
date accepted: 2025-08-24
issued: 2025-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Sally
author list: Agent
  family name: Abrams
  given name: Eliana
author list: Agent
  family name: Binik
  given name: Yehuda
author list: Agent
  family name: Cappelli
  given name: Christina
author list: Agent
  family name: Chu
  given name: Mathew
author list: Agent
  family name: Cornett
  given name: Taiyo
author list: Agent
  family name: Culbertson
  given name: Isayah
author list: Agent
  family name: Garcia
  given name: Epifania
author list: Agent
  family name: Henry
  given name: Jada
author list: Agent
  family name: Lam
  given name: Kristy
author list: Agent
  family name: Lampman
  given name: D.B.
author list: Agent
  family name: Morenko
  given name: Grace
author list: Agent
  family name: Rivera
  given name: Illusion
author list: Agent
  family name: Swift
  given name: Tanasia
author list: Agent
  family name: Torres
  given name: Isabella
author list: Agent
  family name: Velez
  given name: Rayven
author list: Agent
  family name: Waxman
  given name: Elliot
author list: Agent
  family name: Wessely
  given name: Serena
author list: Agent
  family name: Yuen
  given name: Anthony
author list: Agent
  family name: Lardner
  given name: Casey K.
author list: Agent
  family name: Weissman
  given name: J.L.
doi: 10.7717/peerj.20081
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-30
copyright: ©2025 Kong et al.
attribution name: Kong et al.

Spatially explicit models of density improve estimates of Eastern Bering Sea beluga (Delphinapterus leucas) abundance and distribution from line-transect surveys
type: item
type: AcademicArticle
description: We investigate spatially explicit models and ensemble modeling techniques for estimating animal abundance from line-transect survey data. Spatially explicit models are expected to be statistically more efficient, resulting in more precise abundance estimates, than design-based abundance estimators that rely heavily on assumptions about survey design and realization. Ensemble modeling reduces error by averaging among models, and allows for model selection uncertainty to propagate to the abundance estimator. We develop density surface models using Matérn covariance functions and spline-based smooths for a case study, belugas (Delphinapterus leucas) from the Eastern Bering Sea (EBS) stock. EBS belugas are upper trophic level predators in a rapidly changing ecosystem and are a vital nutritional and cultural resource for Alaska Natives. Effective management of this stock requires regular monitoring to derive accurate and unbiased estimates of abundance. Since 1992, aerial line-transect surveys have been the primary means of surveying and estimating abundance of EBS belugas in the region. We compare EBS beluga abundance estimates for 2017 and 2022 that were derived using post-stratified, design-based abundance estimators with analogous estimates the we derive using spatially explicit and ensemble modeling methods. The estimated precision in the abundance estimates from the individual density surface models (DSMs) and the ensemble average of DSMs is higher than for the design-based estimator in both survey years. The design-based models estimated that there were 12,269 belugas in 2017 (coefficient of variation (CV) = 0.118) and 19,811 belugas within a larger study area in 2022 (CV = 0.343). The ensemble spatial models estimate that there were 11,654 belugas in 2017 (CV = 0.118) and 13,313 belugas in 2022 (CV = 0.216). Among the individual spatially explicit models, abundance estimates range from 11,242 to 11,963 (CV = 0.111 to 0.114) in 2017 and 12,023 to 15,593 (CV = 0.17…
format: application/pdf
format: text/html
creator: Megan C. Ferguson
creator: Paul B. Conn
creator: James T. Thorson
subject: Conservation Biology
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20077
publisher: PeerJ Inc.
rights: © 2025 Ferguson et al.
abstract: We investigate spatially explicit models and ensemble modeling techniques for estimating animal abundance from line-transect survey data. Spatially explicit models are expected to be statistically more efficient, resulting in more precise abundance estimates, than design-based abundance estimators that rely heavily on assumptions about survey design and realization. Ensemble modeling reduces error by averaging among models, and allows for model selection uncertainty to propagate to the abundance estimator. We develop density surface models using Matérn covariance functions and spline-based smooths for a case study, belugas (Delphinapterus leucas) from the Eastern Bering Sea (EBS) stock. EBS belugas are upper trophic level predators in a rapidly changing ecosystem and are a vital nutritional and cultural resource for Alaska Natives. Effective management of this stock requires regular monitoring to derive accurate and unbiased estimates of abundance. Since 1992, aerial line-transect surveys have been the primary means of surveying and estimating abundance of EBS belugas in the region. We compare EBS beluga abundance estimates for 2017 and 2022 that were derived using post-stratified, design-based abundance estimators with analogous estimates the we derive using spatially explicit and ensemble modeling methods. The estimated precision in the abundance estimates from the individual density surface models (DSMs) and the ensemble average of DSMs is higher than for the design-based estimator in both survey years. The design-based models estimated that there were 12,269 belugas in 2017 (coefficient of variation (CV) = 0.118) and 19,811 belugas within a larger study area in 2022 (CV = 0.343). The ensemble spatial models estimate that there were 11,654 belugas in 2017 (CV = 0.118) and 13,313 belugas in 2022 (CV = 0.216). Among the individual spatially explicit models, abundance estimates range from 11,242 to 11,963 (CV = 0.111 to 0.114) in 2017 and 12,023 to 15,593 (CV = 0.17…
bibliographic citation: Ferguson et al. (2025) Spatially explicit models of density improve estimates of Eastern Bering Sea beluga (Delphinapterus leucas) abundance and distribution from line-transect surveys. PeerJ 13:e20077 https://doi.org/10.7717/peerj.20077
date submitted: 2025-03-28
date accepted: 2025-08-22
issued: 2025-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferguson
  given name: Megan C.
author list: Agent
  family name: Conn
  given name: Paul B.
author list: Agent
  family name: Thorson
  given name: James T.
doi: 10.7717/peerj.20077
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-30
copyright: ©2025 Ferguson et al.
attribution name: Ferguson et al.

Morphological, phytochemical, and pharmacological properties of the genus Tamarix in Kazakhstan species: a review
type: item
type: AcademicArticle
description: The tree-like plants of the genus Tamarix belong to the Tamaricaceae family and predominantly grow in subtropical areas, steppes, and saline soils. These plants exhibit various pharmacological properties, including antioxidant, antidiabetic, anti-inflammatory, and antimicrobial characteristics. The current flora of Kazakhstan also includes 13 Tamarix species. Despite the diversity of the Tamarix taxon, the species discovered in the region have received limited investigation. Therefore, this review analyzed Kazakhstan and international-related scientific studies concerning the morphological, phytochemical, and pharmacological properties of 13 species within the Tamarix genus. The plants’ biological features and potential applications were also comprehensively analyzed. Consequently, this review significantly contributed to botanical science and practical pharmacology. Conservation and sustainable employment of the Tamarix species for medical purposes could also be developed.
format: application/pdf
format: text/html
creator: Arailym Daulbayeva
creator: Gulnara Kadyrbayeva
creator: Kaldanay Kozhanova
creator: Shazlin Shaharudin
creator: Nurgali Rakhymbayev
creator: Zoya Allambergenova
creator: Rabiga Anarbayeva
creator: Urziya Alimova
creator: Aigerim Kantureyeva
creator: Ainash Baidullaeva
creator: Vladimir An
creator: Bakkonat Kydyrbai
subject: Agricultural Science
subject: Plant Science
subject: Taxonomy
subject: Pharmacology
description: doi:10.7717/peerj.20059
publisher: PeerJ Inc.
rights: © 2025 Daulbayeva et al.
abstract: The tree-like plants of the genus Tamarix belong to the Tamaricaceae family and predominantly grow in subtropical areas, steppes, and saline soils. These plants exhibit various pharmacological properties, including antioxidant, antidiabetic, anti-inflammatory, and antimicrobial characteristics. The current flora of Kazakhstan also includes 13 Tamarix species. Despite the diversity of the Tamarix taxon, the species discovered in the region have received limited investigation. Therefore, this review analyzed Kazakhstan and international-related scientific studies concerning the morphological, phytochemical, and pharmacological properties of 13 species within the Tamarix genus. The plants’ biological features and potential applications were also comprehensively analyzed. Consequently, this review significantly contributed to botanical science and practical pharmacology. Conservation and sustainable employment of the Tamarix species for medical purposes could also be developed.
bibliographic citation: Daulbayeva et al. (2025) Morphological, phytochemical, and pharmacological properties of the genus Tamarix in Kazakhstan species: a review. PeerJ 13:e20059 https://doi.org/10.7717/peerj.20059
date submitted: 2025-02-21
date accepted: 2025-08-19
issued: 2025-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Daulbayeva
  given name: Arailym
author list: Agent
  family name: Kadyrbayeva
  given name: Gulnara
author list: Agent
  family name: Kozhanova
  given name: Kaldanay
author list: Agent
  family name: Shaharudin
  given name: Shazlin
author list: Agent
  family name: Rakhymbayev
  given name: Nurgali
author list: Agent
  family name: Allambergenova
  given name: Zoya
author list: Agent
  family name: Anarbayeva
  given name: Rabiga
author list: Agent
  family name: Alimova
  given name: Urziya
author list: Agent
  family name: Kantureyeva
  given name: Aigerim
author list: Agent
  family name: Baidullaeva
  given name: Ainash
author list: Agent
  family name: An
  given name: Vladimir
author list: Agent
  family name: Kydyrbai
  given name: Bakkonat
doi: 10.7717/peerj.20059
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-30
copyright: ©2025 Daulbayeva et al.
attribution name: Daulbayeva et al.

Identification and verification of prognostic genes related to zinc homeostasis and zinc transport in breast cancer
type: item
type: AcademicArticle
description: Purpose Zinc homeostasis and zinc transporter (ZHT) have been closely associated with the development of various cancers. Therefore, in this study, prognostic genes and their mechanisms related to ZHT in breast cancer (BC) were explored. Patients and methods Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify genes associated with Zinc homeostasis and Zinc transporter-related genes (ZHTGs) in BC. Subsequently, independent prognostic factors and their correlations with clinical features were examined to investigate their association with the prognosis of BC. Finally, we further explored the pathways and immune cells associated with BC prognosis. We also verified gene expression in tissues and cells by quantitative polymerase chain reaction (qPCR). Results In this study, six prognostic genes were identified. Patients were subsequently classified into high-risk and low-risk cohorts based on the median risk score, with the low-risk group presenting superior survival outcomes. Subsequently, riskScore, age, tumor/node/metastasis (T/N/M) stage showed significant associations with the prognosis of BC, and the constructed nomogram demonstrated strong predictive performance. Clinical analysis revealed differences in risk scores among sub-cohorts with different clinical characteristics, such as race (white and others) and T-stage (T1 and T2, T1 and T3). Furthermore, significant disparities were noted in immune cells and immune checkpoints across different risk cohorts. The results of reverse transcription quantitative PCR were basically consistent with the prediction. In addition, the IHC results from the Human Protein Atlas database further validated our prediction. Conclusion We screened six prognosis genes related to ZHT in BC, providing a reference for the prognosis and personalized treatment of BC.
format: application/pdf
format: text/html
creator: Mengxuan Li
creator: Haoyi Zi
creator: Jiajun Ding
creator: Shuai Wang
creator: Yujie Bai
creator: Jianing Sun
creator: Cong Fan
creator: He Chen
creator: Ting Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.20031
publisher: PeerJ Inc.
rights: © 2025 Li et al.
abstract: Purpose Zinc homeostasis and zinc transporter (ZHT) have been closely associated with the development of various cancers. Therefore, in this study, prognostic genes and their mechanisms related to ZHT in breast cancer (BC) were explored. Patients and methods Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify genes associated with Zinc homeostasis and Zinc transporter-related genes (ZHTGs) in BC. Subsequently, independent prognostic factors and their correlations with clinical features were examined to investigate their association with the prognosis of BC. Finally, we further explored the pathways and immune cells associated with BC prognosis. We also verified gene expression in tissues and cells by quantitative polymerase chain reaction (qPCR). Results In this study, six prognostic genes were identified. Patients were subsequently classified into high-risk and low-risk cohorts based on the median risk score, with the low-risk group presenting superior survival outcomes. Subsequently, riskScore, age, tumor/node/metastasis (T/N/M) stage showed significant associations with the prognosis of BC, and the constructed nomogram demonstrated strong predictive performance. Clinical analysis revealed differences in risk scores among sub-cohorts with different clinical characteristics, such as race (white and others) and T-stage (T1 and T2, T1 and T3). Furthermore, significant disparities were noted in immune cells and immune checkpoints across different risk cohorts. The results of reverse transcription quantitative PCR were basically consistent with the prediction. In addition, the IHC results from the Human Protein Atlas database further validated our prediction. Conclusion We screened six prognosis genes related to ZHT in BC, providing a reference for the prognosis and personalized treatment of BC.
bibliographic citation: Li et al. (2025) Identification and verification of prognostic genes related to zinc homeostasis and zinc transport in breast cancer. PeerJ 13:e20031 https://doi.org/10.7717/peerj.20031
date submitted: 2025-04-10
date accepted: 2025-08-13
issued: 2025-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: Mengxuan
author list: Agent
  family name: Zi
  given name: Haoyi
author list: Agent
  family name: Ding
  given name: Jiajun
author list: Agent
  family name: Wang
  given name: Shuai
author list: Agent
  family name: Bai
  given name: Yujie
author list: Agent
  family name: Sun
  given name: Jianing
author list: Agent
  family name: Fan
  given name: Cong
author list: Agent
  family name: Chen
  given name: He
author list: Agent
  family name: Wang
  given name: Ting
doi: 10.7717/peerj.20031
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-30
copyright: ©2025 Li et al.
attribution name: Li et al.

Unlocking the genomic potential of historical and formalin-fixed specimens: phylogenetic insights from museum-preserved threadfin fishes (Teleostei: Polynemidae)
type: item
type: AcademicArticle
description: DNA sequencing continues to revolutionize our understanding of biodiversity, ecology, and evolution. While analyzing sequence data allows us to address countless questions, most of the world’s vertebrate museum specimens have been historically inaccessible for genetic sampling. This is partially due to the absence of modern genetic samples and/or the impact formalin has on DNA during the preservation of specimen vouchers. Recent studies have shown successful extraction of DNA from historic museum specimens using additional chemicals and/or exposing the sample(s) to heat, with these advances enhancing the possibility of capturing genomic information from type specimens, characterizing genetic diversity within species complexes, and incorporating rare samples into phylogenetic analyses. However, questions remain about the reliability of these data and utility of historic DNA in modern phylogenetic analyses. In this study, we use a commercial extraction kit that targets formalin-fixed, paraffin-embedded samples to successfully extract DNA from historic museum specimens of threadfin fishes (Teleostei: Polynemidae). These specimens represent rare, genetically uncharacterized taxa that have yet to be included in a phylogenetic analysis. Low-depth shotgun sequencing is then used to sequence mitochondrial loci from the historic samples. The resulting sequence data are assembled, validated, and incorporated into a newly generated mitochondrial dataset that is simultaneously analyzed with a previously published ultraconserved-element dataset to construct a phylogenetic framework. We then explore new and previously described morphological variation within this new evolutionary framework for threadfins, identifying several shared characters that warrant revision of the generic-level classification. These findings add to the growing body of literature that demonstrates sequencing historical DNA from museum specimens and analyzing these data with complementary datasets of molecul…
format: application/pdf
format: text/html
creator: Matthew G. Girard
creator: Kevin R. Chovanec
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Evolutionary Studies
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.20029
publisher: PeerJ Inc.
rights: © 2025 Girard and Chovanec
abstract: DNA sequencing continues to revolutionize our understanding of biodiversity, ecology, and evolution. While analyzing sequence data allows us to address countless questions, most of the world’s vertebrate museum specimens have been historically inaccessible for genetic sampling. This is partially due to the absence of modern genetic samples and/or the impact formalin has on DNA during the preservation of specimen vouchers. Recent studies have shown successful extraction of DNA from historic museum specimens using additional chemicals and/or exposing the sample(s) to heat, with these advances enhancing the possibility of capturing genomic information from type specimens, characterizing genetic diversity within species complexes, and incorporating rare samples into phylogenetic analyses. However, questions remain about the reliability of these data and utility of historic DNA in modern phylogenetic analyses. In this study, we use a commercial extraction kit that targets formalin-fixed, paraffin-embedded samples to successfully extract DNA from historic museum specimens of threadfin fishes (Teleostei: Polynemidae). These specimens represent rare, genetically uncharacterized taxa that have yet to be included in a phylogenetic analysis. Low-depth shotgun sequencing is then used to sequence mitochondrial loci from the historic samples. The resulting sequence data are assembled, validated, and incorporated into a newly generated mitochondrial dataset that is simultaneously analyzed with a previously published ultraconserved-element dataset to construct a phylogenetic framework. We then explore new and previously described morphological variation within this new evolutionary framework for threadfins, identifying several shared characters that warrant revision of the generic-level classification. These findings add to the growing body of literature that demonstrates sequencing historical DNA from museum specimens and analyzing these data with complementary datasets of molecul…
bibliographic citation: Girard et al. (2025) Unlocking the genomic potential of historical and formalin-fixed specimens: phylogenetic insights from museum-preserved threadfin fishes (Teleostei: Polynemidae). PeerJ 13:e20029 https://doi.org/10.7717/peerj.20029
date submitted: 2025-05-06
date accepted: 2025-08-13
issued: 2025-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Girard
  given name: Matthew G.
author list: Agent
  family name: Chovanec
  given name: Kevin R.
doi: 10.7717/peerj.20029
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-30
copyright: ©2025 Girard and Chovanec
attribution name: Girard and Chovanec

Undernutrition and feeding difficulties among children with disabilities in Zambia: insights for inclusive nutrition strategies
type: item
type: AcademicArticle
description: Background Understanding the burden of undernutrition in children with disabilities is crucial for designing inclusive nutrition programs and policies. This study aimed to estimate the prevalence of undernutrition and risk for feeding difficulties and describe common feeding practices among children with disabilities living with families in Zambia and receiving services at selected health centers and community-based rehabilitation centers. Methods We analyzed cross-sectional program data from 483 children aged birth to 10 years with reported special healthcare needs, collected between June 2017 and August 2021 at three health centers and ten community-based rehabilitation centers. Data included demographics, weight, height, mid-upper arm circumference (MUAC), hemoglobin concentrations, risk for feeding difficulties, and reported caregiver feeding practices. Undernutrition was assessed using the World Health Organization z-scores for anthropometric measurements, MUAC cut-off points, and anemia criteria. ANOVA and Pearson’s chi-squared tests were used to compare groups. Results More than half of the children were boys (54.2%) and under 5 years old (59.2%). Cerebral palsy was the most common special healthcare need (63.6%), followed by an unspecified “other” category (18.6%). Undernutrition was prevalent, with 62.8% underweight, 68.1% stunted, 22.6% wasted (using MUAC), and 60.5% anemic. Children with cerebral palsy had consistently lower anthropometric z-scores and higher rates of stunting, wasting, and underweight compared to children with other developmental disabilities or special healthcare needs. A risk for feeding difficulties was identified in 89.5% of the children, with common issues including coughing or choking and prolonged mealtimes. Despite these challenges, most caregivers reported practicing responsive feeding techniques at least some of the time. Conclusion These findings highlight the significant risk of undernutrition and feeding difficulties among c…
format: application/pdf
format: text/html
creator: Zeina Makhoul
creator: Julie M. Long
creator: Mulemba Ndonji
creator: Carolyn Moore
creator: Watson Shungu Mwandileya
creator: Edgar Lunda
creator: Kate Miller
creator: Bradley S. Miller
creator: Douglas Taren
subject: Global Health
subject: Nutrition
subject: Pediatrics
description: doi:10.7717/peerj.20023
publisher: PeerJ Inc.
rights: © 2025 Makhoul et al.
abstract: Background Understanding the burden of undernutrition in children with disabilities is crucial for designing inclusive nutrition programs and policies. This study aimed to estimate the prevalence of undernutrition and risk for feeding difficulties and describe common feeding practices among children with disabilities living with families in Zambia and receiving services at selected health centers and community-based rehabilitation centers. Methods We analyzed cross-sectional program data from 483 children aged birth to 10 years with reported special healthcare needs, collected between June 2017 and August 2021 at three health centers and ten community-based rehabilitation centers. Data included demographics, weight, height, mid-upper arm circumference (MUAC), hemoglobin concentrations, risk for feeding difficulties, and reported caregiver feeding practices. Undernutrition was assessed using the World Health Organization z-scores for anthropometric measurements, MUAC cut-off points, and anemia criteria. ANOVA and Pearson’s chi-squared tests were used to compare groups. Results More than half of the children were boys (54.2%) and under 5 years old (59.2%). Cerebral palsy was the most common special healthcare need (63.6%), followed by an unspecified “other” category (18.6%). Undernutrition was prevalent, with 62.8% underweight, 68.1% stunted, 22.6% wasted (using MUAC), and 60.5% anemic. Children with cerebral palsy had consistently lower anthropometric z-scores and higher rates of stunting, wasting, and underweight compared to children with other developmental disabilities or special healthcare needs. A risk for feeding difficulties was identified in 89.5% of the children, with common issues including coughing or choking and prolonged mealtimes. Despite these challenges, most caregivers reported practicing responsive feeding techniques at least some of the time. Conclusion These findings highlight the significant risk of undernutrition and feeding difficulties among c…
bibliographic citation: Makhoul et al. (2025) Undernutrition and feeding difficulties among children with disabilities in Zambia: insights for inclusive nutrition strategies. PeerJ 13:e20023 https://doi.org/10.7717/peerj.20023
date submitted: 2024-12-13
date accepted: 2025-08-11
issued: 2025-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Makhoul
  given name: Zeina
author list: Agent
  family name: Long
  given name: Julie M.
author list: Agent
  family name: Ndonji
  given name: Mulemba
author list: Agent
  family name: Moore
  given name: Carolyn
author list: Agent
  family name: Mwandileya
  given name: Watson Shungu
author list: Agent
  family name: Lunda
  given name: Edgar
author list: Agent
  family name: Miller
  given name: Kate
author list: Agent
  family name: Miller
  given name: Bradley S.
author list: Agent
  family name: Taren
  given name: Douglas
doi: 10.7717/peerj.20023
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-30
copyright: ©2025 Makhoul et al.
attribution name: Makhoul et al.

Metabolomic and physiological analysis of bud differentiation in dense apple (Malus×domestica Borkh.) orchards following thinning and reshaping
type: item
type: AcademicArticle
description: Background In China, a majority of apple orchards were initially planted under arboriculture. The branch number increases, causing a deterioration of the canopy light conditions as the trees age. This phenomenon blocks bud differentiation, resulting in yield decrease and deterioration of fruit quality. Thinning and reshaping are effective strategies for addressing these issues. However, the impact of thinning and reshaping remains unclear. This study analyzed the physiological and metabolic aspects of flower bud differentiation following thinning and reshaping of an overcrowded orchard. Methods Physiological and metabolomic analyses were conducted on terminal flower bud samples collected during early (T1) and late (T2) bud differentiation following thinning and reshaping alongside controls CK1 and CK2. Results Sucrose, glucose, fructose, and sorbitol contents in T1 and T2 groups were significantly higher than in CK1 and CK2. Metabolomic analysis revealed significant differences: 60 metabolites (32 up-regulated, 28 down-regulated) in T1 vs CK1 and 51 metabolites (26 up-regulated, 25 down-regulated) in T2 vs CK2. KEGG enrichment analysis revealed that the biosynthesis of secondary metabolites was the most enriched pathway, with the crucial compounds associated with flower bud differentiation. There was an accumulation of coumarin (C05851), eriodictyol (C05631), and histidine (C00135) during both the early and late stages of flower bud differentiation, underscoring their promoting role. In T1 vs CK1, 2-isopropylmalic acid (C02504), (+)-catechin (C09727), and trans-ferulic acid (C01494) were significantly up-regulated, highlighting their potential as metabolic activators. Conversely, 3’,5’-dimethoxy-3,5,7,4’-tetrahydroxyflavone (C11620) and 4-hydroxyphenylpyruvic acid (C01179) decreased, implying divergent regulatory mechanisms. Temporal specificity emerged in T2 vs CK2, with significant upregulation of myricetin (C10107) and isopimpinellin (C02162). In contrast, umbell…
format: application/pdf
format: text/html
creator: Zehua Yang
creator: Tianli Guo
creator: Junqiang Niu
creator: Xiaoning Yin
creator: Ming Ma
subject: Agricultural Science
subject: Bioengineering
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.20011
publisher: PeerJ Inc.
rights: © 2025 Yang et al.
abstract: Background In China, a majority of apple orchards were initially planted under arboriculture. The branch number increases, causing a deterioration of the canopy light conditions as the trees age. This phenomenon blocks bud differentiation, resulting in yield decrease and deterioration of fruit quality. Thinning and reshaping are effective strategies for addressing these issues. However, the impact of thinning and reshaping remains unclear. This study analyzed the physiological and metabolic aspects of flower bud differentiation following thinning and reshaping of an overcrowded orchard. Methods Physiological and metabolomic analyses were conducted on terminal flower bud samples collected during early (T1) and late (T2) bud differentiation following thinning and reshaping alongside controls CK1 and CK2. Results Sucrose, glucose, fructose, and sorbitol contents in T1 and T2 groups were significantly higher than in CK1 and CK2. Metabolomic analysis revealed significant differences: 60 metabolites (32 up-regulated, 28 down-regulated) in T1 vs CK1 and 51 metabolites (26 up-regulated, 25 down-regulated) in T2 vs CK2. KEGG enrichment analysis revealed that the biosynthesis of secondary metabolites was the most enriched pathway, with the crucial compounds associated with flower bud differentiation. There was an accumulation of coumarin (C05851), eriodictyol (C05631), and histidine (C00135) during both the early and late stages of flower bud differentiation, underscoring their promoting role. In T1 vs CK1, 2-isopropylmalic acid (C02504), (+)-catechin (C09727), and trans-ferulic acid (C01494) were significantly up-regulated, highlighting their potential as metabolic activators. Conversely, 3’,5’-dimethoxy-3,5,7,4’-tetrahydroxyflavone (C11620) and 4-hydroxyphenylpyruvic acid (C01179) decreased, implying divergent regulatory mechanisms. Temporal specificity emerged in T2 vs CK2, with significant upregulation of myricetin (C10107) and isopimpinellin (C02162). In contrast, umbell…
bibliographic citation: Yang et al. (2025) Metabolomic and physiological analysis of bud differentiation in dense apple (Malus×domestica Borkh.) orchards following thinning and reshaping. PeerJ 13:e20011 https://doi.org/10.7717/peerj.20011
date submitted: 2025-02-05
date accepted: 2025-08-08
issued: 2025-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Zehua
author list: Agent
  family name: Guo
  given name: Tianli
author list: Agent
  family name: Niu
  given name: Junqiang
author list: Agent
  family name: Yin
  given name: Xiaoning
author list: Agent
  family name: Ma
  given name: Ming
doi: 10.7717/peerj.20011
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-30
copyright: ©2025 Yang et al.
attribution name: Yang et al.

Interprofessional collaboration and associated factors among wound, ostomy, and continence nurses: a cross-sectional study in China
type: item
type: AcademicArticle
description: Background Wound, ostomy, and continence (WOC) nurses play a crucial role in providing cost-effective and high-quality care for an increasing number of people with acute and chronic wounds. WOC nursing is a multifaceted, evidence-based specialty practice requiring inter-professional collaboration (IPC). IPC is a core competency that ensures comprehensive and holistic wound management, yet few studies have examined IPC among WOC nurses in China. This study aimed to investigate the level and influencing factors of IPC among WOC nurses in China, providing insights into IPC education and intervention. Methods A cross-sectional study was conducted among 247 WOC nurses recruited from various hospitals from January to February 2025. Participants completed an online questionnaire to assess their IPC competency, readiness for interprofessional learning, and work environment. Multiple linear regression was used to determine influencing factors for IPC competency. Results The mean scores for IPC, readiness for inter-professional learning, and work environment were 134.49 ± 10.99, 81.15 ± 6.00, and 127.1 ± 18.78, respectively. A higher level of inter-professional learning readiness (β = 0.46, P < 0.001), a better work environment (β = 0.39, P < 0.001), and being a WOC team leader (β = 0.12, P = 0.008) were associated with a higher level of IPC competency, collectively explaining 55.1% of the total variance. Conclusion WOC nurses showed a generally good level of IPC, but there is still room for improvement. IPC may be effectively improved through optimizing the work environment, strengthening IPC learning, and empowering nurses with leadership responsibilities.
format: application/pdf
format: text/html
creator: Lin Shi
creator: Liqing Yue
creator: Xiaowan Liu
creator: Xueqin Gong
creator: Bingfa Li
subject: Epidemiology
subject: Infectious Diseases
subject: Nursing
subject: Healthcare Services
description: doi:10.7717/peerj.20006
publisher: PeerJ Inc.
rights: © 2025 Shi et al.
abstract: Background Wound, ostomy, and continence (WOC) nurses play a crucial role in providing cost-effective and high-quality care for an increasing number of people with acute and chronic wounds. WOC nursing is a multifaceted, evidence-based specialty practice requiring inter-professional collaboration (IPC). IPC is a core competency that ensures comprehensive and holistic wound management, yet few studies have examined IPC among WOC nurses in China. This study aimed to investigate the level and influencing factors of IPC among WOC nurses in China, providing insights into IPC education and intervention. Methods A cross-sectional study was conducted among 247 WOC nurses recruited from various hospitals from January to February 2025. Participants completed an online questionnaire to assess their IPC competency, readiness for interprofessional learning, and work environment. Multiple linear regression was used to determine influencing factors for IPC competency. Results The mean scores for IPC, readiness for inter-professional learning, and work environment were 134.49 ± 10.99, 81.15 ± 6.00, and 127.1 ± 18.78, respectively. A higher level of inter-professional learning readiness (β = 0.46, P < 0.001), a better work environment (β = 0.39, P < 0.001), and being a WOC team leader (β = 0.12, P = 0.008) were associated with a higher level of IPC competency, collectively explaining 55.1% of the total variance. Conclusion WOC nurses showed a generally good level of IPC, but there is still room for improvement. IPC may be effectively improved through optimizing the work environment, strengthening IPC learning, and empowering nurses with leadership responsibilities.
bibliographic citation: Shi et al. (2025) Interprofessional collaboration and associated factors among wound, ostomy, and continence nurses: a cross-sectional study in China. PeerJ 13:e20006 https://doi.org/10.7717/peerj.20006
date submitted: 2025-05-07
date accepted: 2025-08-07
issued: 2025-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Lin
author list: Agent
  family name: Yue
  given name: Liqing
author list: Agent
  family name: Liu
  given name: Xiaowan
author list: Agent
  family name: Gong
  given name: Xueqin
author list: Agent
  family name: Li
  given name: Bingfa
doi: 10.7717/peerj.20006
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-30
copyright: ©2025 Shi et al.
attribution name: Shi et al.

Optimization of anther culture of awnless triticale
type: item
type: AcademicArticle
description: Background Compared with traditional breeding methods, anther culture is an effective method for quickly obtaining homozygotes within one generation. The method of cultivating doubled haploid plants derived from the anthers of awnless triticale was studied and optimized. Methods Young awnless triticale spikes were pretreated at 4 °C for 5, 10, 15, 20, or 25 days, respectively, and then the anthers of different treatment days were cultured on cysteine heart blood (CHB) with antibiotics media with four different hormone concentrations, respectively. Results Overall, 15 days was the best low-temperature treatment, and CHB medium containing 1.5 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D) and 1.5 mg/L Kinetin (KT) was the best hormone concentration treatment. The callus induction rate (CIR) was highest (22.20%) for anthers pretreated for 15-days and inoculated on CHB medium containing 1.5 mg/L 2,4-D and 1.5 mg/L KT. The green plantlet differentiation frequency (DFG) was highest (30.20%) for anthers pretreated for 25-days and inoculated on CHB medium containing 0.5 mg/L 2,4-D+0.5 mg/L KT. Green plantlet production (PRG) was highest (4.58%) for anthers which were pretreated for 10-days and inoculated on CHB medium containing 0.5 mg/L 2,4-D+0.5 mg/L KT. The success rate of chromosome doubling for regenerated green plantlets was 52.8%. Nine of the thirteen DH1 plants (the first generation of double haploid plants) had tip and side awns shorter than 5 mm, implying that they may be used for cultivating awnless triticale. Conclusion Triticale anther culture technology was optimized in this work, enabling the rapid breeding of homozygous varieties of awnless triticale and accelerating the breeding of new varieties of awnless triticale.
format: application/pdf
format: text/html
creator: Jun Ma
creator: Fangyuan Zhao
creator: Xinhui Tian
creator: Wenhua Du
subject: Agricultural Science
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.19951
publisher: PeerJ Inc.
rights: © 2025 Ma et al.
abstract: Background Compared with traditional breeding methods, anther culture is an effective method for quickly obtaining homozygotes within one generation. The method of cultivating doubled haploid plants derived from the anthers of awnless triticale was studied and optimized. Methods Young awnless triticale spikes were pretreated at 4 °C for 5, 10, 15, 20, or 25 days, respectively, and then the anthers of different treatment days were cultured on cysteine heart blood (CHB) with antibiotics media with four different hormone concentrations, respectively. Results Overall, 15 days was the best low-temperature treatment, and CHB medium containing 1.5 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D) and 1.5 mg/L Kinetin (KT) was the best hormone concentration treatment. The callus induction rate (CIR) was highest (22.20%) for anthers pretreated for 15-days and inoculated on CHB medium containing 1.5 mg/L 2,4-D and 1.5 mg/L KT. The green plantlet differentiation frequency (DFG) was highest (30.20%) for anthers pretreated for 25-days and inoculated on CHB medium containing 0.5 mg/L 2,4-D+0.5 mg/L KT. Green plantlet production (PRG) was highest (4.58%) for anthers which were pretreated for 10-days and inoculated on CHB medium containing 0.5 mg/L 2,4-D+0.5 mg/L KT. The success rate of chromosome doubling for regenerated green plantlets was 52.8%. Nine of the thirteen DH1 plants (the first generation of double haploid plants) had tip and side awns shorter than 5 mm, implying that they may be used for cultivating awnless triticale. Conclusion Triticale anther culture technology was optimized in this work, enabling the rapid breeding of homozygous varieties of awnless triticale and accelerating the breeding of new varieties of awnless triticale.
bibliographic citation: Ma et al. (2025) Optimization of anther culture of awnless triticale. PeerJ 13:e19951 https://doi.org/10.7717/peerj.19951
date submitted: 2024-12-18
date accepted: 2025-07-29
issued: 2025-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Jun
author list: Agent
  family name: Zhao
  given name: Fangyuan
author list: Agent
  family name: Tian
  given name: Xinhui
author list: Agent
  family name: Du
  given name: Wenhua
doi: 10.7717/peerj.19951
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-30
copyright: ©2025 Ma et al.
attribution name: Ma et al.

Study on the diagnostic potential and molecular mechanism of hsa_circ_0000831 in oral squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Circular RNA (circRNA) are a new class of non-coding RNAs that are involved in the molecular pathology of cancer. This study aims to screen and validate key circRNAs with diagnostic potential in o ral squamous cell carcinoma (OSCC), and explore their possible molecular mechanism. Methods This study first integrated the GSE131182 dataset with clinically obtained OSCC sample data and used the limma package to identify differentially expressed circular RNAs (DEcircRNAs). Subsequently, circRNAs associated with head and neck squamous cell carcinoma were identified using CircNet2.0 and intersected with the differentially expressed circRNAs to determine the key circRNA. The diagnostic value of the key circRNA was evaluated using receiver operating characteristic (ROC) curves, followed by functional validation through in vitro assays including cell counting kit-8 (CCK-8), wound healing, transwell assay, and flow cytometry. Finally, target microRNAs (miRNAs) were predicted using CircNet2.0 and miRDB, a ceRNA network was constructed, and functional enrichment analysis of target genes was performed using Metascape tool. Results A total of 318 and 46 differentially expressed circRNAs (DEcircRNAs) were identified from the GSE131182 dataset and clinical samples, respectively. Through intersection analysis, the key circRNA hsa_circ_0000831 was identified. hsa_circ_0000831 was upregulated in OSCC samples, and ROC curve analysis indicated its high diagnostic performance. In vitro experiments showed that inhibition of hsa_circ_0000831 significantly reduced OSCC cell viability, migration, and invasion, while markedly enhancing apoptosis. ceRNA network analysis predicted that hsa_circ_0000831 targets five miRNAs (including hsa-miR-136-5p, hsa-miR-100-3p, hsa-miR-144-5p, hsa-miR-149-5p and hsa-miR-214-5p), with the associated target genes mainly enriched in cancer-related pathways. Conclusion This work offer s a novel foundation for the early identification of OSCC and provid…
format: application/pdf
format: text/html
creator: Ting Liu
creator: Xiaoze Chen
creator: Shigeng Lin
creator: Qitao Wen
creator: Wei Deng
creator: Daiying Huang
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.20082
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Background Circular RNA (circRNA) are a new class of non-coding RNAs that are involved in the molecular pathology of cancer. This study aims to screen and validate key circRNAs with diagnostic potential in o ral squamous cell carcinoma (OSCC), and explore their possible molecular mechanism. Methods This study first integrated the GSE131182 dataset with clinically obtained OSCC sample data and used the limma package to identify differentially expressed circular RNAs (DEcircRNAs). Subsequently, circRNAs associated with head and neck squamous cell carcinoma were identified using CircNet2.0 and intersected with the differentially expressed circRNAs to determine the key circRNA. The diagnostic value of the key circRNA was evaluated using receiver operating characteristic (ROC) curves, followed by functional validation through in vitro assays including cell counting kit-8 (CCK-8), wound healing, transwell assay, and flow cytometry. Finally, target microRNAs (miRNAs) were predicted using CircNet2.0 and miRDB, a ceRNA network was constructed, and functional enrichment analysis of target genes was performed using Metascape tool. Results A total of 318 and 46 differentially expressed circRNAs (DEcircRNAs) were identified from the GSE131182 dataset and clinical samples, respectively. Through intersection analysis, the key circRNA hsa_circ_0000831 was identified. hsa_circ_0000831 was upregulated in OSCC samples, and ROC curve analysis indicated its high diagnostic performance. In vitro experiments showed that inhibition of hsa_circ_0000831 significantly reduced OSCC cell viability, migration, and invasion, while markedly enhancing apoptosis. ceRNA network analysis predicted that hsa_circ_0000831 targets five miRNAs (including hsa-miR-136-5p, hsa-miR-100-3p, hsa-miR-144-5p, hsa-miR-149-5p and hsa-miR-214-5p), with the associated target genes mainly enriched in cancer-related pathways. Conclusion This work offer s a novel foundation for the early identification of OSCC and provid…
bibliographic citation: Liu et al. (2025) Study on the diagnostic potential and molecular mechanism of hsa_circ_0000831 in oral squamous cell carcinoma. PeerJ 13:e20082 https://doi.org/10.7717/peerj.20082
date submitted: 2025-05-26
date accepted: 2025-08-24
issued: 2025-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Ting
author list: Agent
  family name: Chen
  given name: Xiaoze
author list: Agent
  family name: Lin
  given name: Shigeng
author list: Agent
  family name: Wen
  given name: Qitao
author list: Agent
  family name: Deng
  given name: Wei
author list: Agent
  family name: Huang
  given name: Daiying
doi: 10.7717/peerj.20082
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-09-29
copyright: ©2025 Liu et al.
attribution name: Liu et al.

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