PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Exosome and BCR-ABL mediated molecular alterations in endothelial cells in chronic myeloid leukemia: identification of seven genes and their regulatory network
items: Statistical study of the causes of acacia tree deterioration in the Ha’il region
items: Biostimulant effects of titanium dioxide nanoparticles on germination and initial growth of tomato: evidence of hormesis
items: Experimental tests of habitat preferences in the Comal Springs dryopid beetle, Stygoparnus comalensis
items: Impact of bacterial culture medium on composition and characteristics of Burkholderia pseudomallei extracellular polymeric substances
items: The investigation of fermented food consumption on gastrointestinal symptoms: a cross-sectional study in university students
items: Design and simulation-based evaluation of a novel tracheostomy high-flow therapy device interface: a preclinical study
items: Multiomics analysis reveals flavonoid accumulation and biosynthesis across different cultivation years and localities of Gongronemopsis tenacissima (Dai-Bai-Jie)
items: Experimental assessment of the effects of sustainable landscaping practices on beetles in a new residential land development
items: Diabetes and respiratory diseases as comorbid conditions in COVID-19 patients from Kazakhstan: a retrospective pilot study

Exosome and BCR-ABL mediated molecular alterations in endothelial cells in chronic myeloid leukemia: identification of seven genes and their regulatory network
type: item
type: AcademicArticle
description: Background Chronic myeloid leukemia (CML) progression relies on dynamic crosstalk between leukemic cells and vascular niches. Here, we investigate how exosomes and BCR/ABL overexpression influence endothelial functions, aiming to identify key mediators of leukemia-induced microenvironmental remodeling as potential therapeutic targets. Methods Human umbilical vein endothelial cells (HUVECs) were cultured and divided into four groups: control (Z), treated with K562-derived exosomes (Zexo), BCR-ABL-overexpressing (ZBA), and BCR-ABL-overexpressing with exosome treatment (ZBAexo). Transcriptomic profiling was performed to identify DEGs, followed by functional enrichment and protein–protein interaction network analyses. Gene Set Enrichment Analysis (GSEA) was applied to uncover associated biological pathways. Results Seven specificized expressed genes in ZBAexo group were identified: CAMK2B, CDC25C, SV2A, MND1, CDC20, CLSPN, and GRM1. These genes are involved in cell cycle, DNA replication, and cell adhesion pathways and show significant correlation with the BCR/ABL fusion gene. Expression of these genes was strongly associated with BCR-ABL. Network analysis revealed the potential regulatory roles of transcription factors CREB1 and NFKB1. A competing endogenous RNA (ceRNA) network involving miRNAs (e.g., miR-16-5p, miR-126-5p) and lncRNAs (e.g., AC008124.1, AC064799.2, AGAP11) potentially modulates their expression. Conclusion This study identifies seven novel candidate biomarkers dysregulated in endothelial cells under combined BCR-ABL and exosomal stimulation, shedding light on the molecular crosstalk between leukemic cells and the vascular niche.
format: application/pdf
format: text/html
creator: Zhenglei Shen
creator: Honghua Cao
creator: Yeying Zhou
creator: Wenwen Mao
creator: Kunmei Liu
creator: Jingying Zhu
creator: Ming He
creator: Yunru Mao
creator: Ni Luo
creator: Lei Feng
creator: Heng Le
creator: Liying Song
creator: HuaXian Li
creator: Yasar Mehmood Yousafzai
creator: Asad Zia
creator: Xuezhong Gu
creator: Shiwen Zhang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Hematology
subject: Oncology
description: doi:10.7717/peerj.20371
publisher: PeerJ Inc.
rights: © 2025 Shen et al.
abstract: Background Chronic myeloid leukemia (CML) progression relies on dynamic crosstalk between leukemic cells and vascular niches. Here, we investigate how exosomes and BCR/ABL overexpression influence endothelial functions, aiming to identify key mediators of leukemia-induced microenvironmental remodeling as potential therapeutic targets. Methods Human umbilical vein endothelial cells (HUVECs) were cultured and divided into four groups: control (Z), treated with K562-derived exosomes (Zexo), BCR-ABL-overexpressing (ZBA), and BCR-ABL-overexpressing with exosome treatment (ZBAexo). Transcriptomic profiling was performed to identify DEGs, followed by functional enrichment and protein–protein interaction network analyses. Gene Set Enrichment Analysis (GSEA) was applied to uncover associated biological pathways. Results Seven specificized expressed genes in ZBAexo group were identified: CAMK2B, CDC25C, SV2A, MND1, CDC20, CLSPN, and GRM1. These genes are involved in cell cycle, DNA replication, and cell adhesion pathways and show significant correlation with the BCR/ABL fusion gene. Expression of these genes was strongly associated with BCR-ABL. Network analysis revealed the potential regulatory roles of transcription factors CREB1 and NFKB1. A competing endogenous RNA (ceRNA) network involving miRNAs (e.g., miR-16-5p, miR-126-5p) and lncRNAs (e.g., AC008124.1, AC064799.2, AGAP11) potentially modulates their expression. Conclusion This study identifies seven novel candidate biomarkers dysregulated in endothelial cells under combined BCR-ABL and exosomal stimulation, shedding light on the molecular crosstalk between leukemic cells and the vascular niche.
bibliographic citation: Shen et al. (2025) Exosome and BCR-ABL mediated molecular alterations in endothelial cells in chronic myeloid leukemia: identification of seven genes and their regulatory network. PeerJ 13:e20371 https://doi.org/10.7717/peerj.20371
date submitted: 2025-05-27
date accepted: 2025-10-20
issued: 2025-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shen
  given name: Zhenglei
author list: Agent
  family name: Cao
  given name: Honghua
author list: Agent
  family name: Zhou
  given name: Yeying
author list: Agent
  family name: Mao
  given name: Wenwen
author list: Agent
  family name: Liu
  given name: Kunmei
author list: Agent
  family name: Zhu
  given name: Jingying
author list: Agent
  family name: He
  given name: Ming
author list: Agent
  family name: Mao
  given name: Yunru
author list: Agent
  family name: Luo
  given name: Ni
author list: Agent
  family name: Feng
  given name: Lei
author list: Agent
  family name: Le
  given name: Heng
author list: Agent
  family name: Song
  given name: Liying
author list: Agent
  family name: Li
  given name: HuaXian
author list: Agent
  family name: Yousafzai
  given name: Yasar Mehmood
author list: Agent
  family name: Zia
  given name: Asad
author list: Agent
  family name: Gu
  given name: Xuezhong
author list: Agent
  family name: Zhang
  given name: Shiwen
doi: 10.7717/peerj.20371
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-17
copyright: ©2025 Shen et al.
attribution name: Shen et al.

Statistical study of the causes of acacia tree deterioration in the Ha’il region
type: item
type: AcademicArticle
description: Acacia trees are vital to arid ecosystems, yet their decline in the Ha’il region of Saudi Arabia poses significant ecological and socio-economic concerns. This study employs a comprehensive statistical approach to identify the environmental and human-induced factors contributing to this deterioration. Data were collected from structured surveys, meteorological records, and satellite imagery. Analytical methods included descriptive statistics, correlation analysis, regression modeling, and chi-square automatic interaction detection (CHAID) classification. Results show that climate change—particularly increased temperatures and erratic rainfall—along with soil degradation, overgrazing, and urban expansion, are key drivers of acacia decline. Regression analysis revealed that drought severity (B = 3.721, p = 0.023) and urban growth (B = 3.365, p = 0.045) significantly predicted deterioration, explaining 17.5% of the variance (adjusted R2 = 0.175). The CHAID model identified urban expansion and overgrazing as critical risk factors, with deterioration scores ranging from 47.1 to 70.1 across subgroups. The study recommends strengthened conservation policies, improved irrigation, expanded protected areas, and increased public awareness to support acacia restoration efforts.
format: application/pdf
format: text/html
creator: Alanazi Talal Abdulrahman
creator: Khudhayr A. Rashedi
creator: Tariq S. Alshammari
subject: Statistics
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.20067
publisher: PeerJ Inc.
rights: © 2025 Abdulrahman et al.
abstract: Acacia trees are vital to arid ecosystems, yet their decline in the Ha’il region of Saudi Arabia poses significant ecological and socio-economic concerns. This study employs a comprehensive statistical approach to identify the environmental and human-induced factors contributing to this deterioration. Data were collected from structured surveys, meteorological records, and satellite imagery. Analytical methods included descriptive statistics, correlation analysis, regression modeling, and chi-square automatic interaction detection (CHAID) classification. Results show that climate change—particularly increased temperatures and erratic rainfall—along with soil degradation, overgrazing, and urban expansion, are key drivers of acacia decline. Regression analysis revealed that drought severity (B = 3.721, p = 0.023) and urban growth (B = 3.365, p = 0.045) significantly predicted deterioration, explaining 17.5% of the variance (adjusted R2 = 0.175). The CHAID model identified urban expansion and overgrazing as critical risk factors, with deterioration scores ranging from 47.1 to 70.1 across subgroups. The study recommends strengthened conservation policies, improved irrigation, expanded protected areas, and increased public awareness to support acacia restoration efforts.
bibliographic citation: Abdulrahman et al. (2025) Statistical study of the causes of acacia tree deterioration in the Ha’il region. PeerJ 13:e20067 https://doi.org/10.7717/peerj.20067
date submitted: 2025-03-07
date accepted: 2025-08-20
issued: 2025-12-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdulrahman
  given name: Alanazi Talal
author list: Agent
  family name: Rashedi
  given name: Khudhayr A.
author list: Agent
  family name: Alshammari
  given name: Tariq S.
doi: 10.7717/peerj.20067
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-17
copyright: © 2025 Abdulrahman et al.
attribution name: Abdulrahman et al.

Biostimulant effects of titanium dioxide nanoparticles on germination and initial growth of tomato: evidence of hormesis
type: item
type: AcademicArticle
description: Background Titanium (Ti) is a beneficial element considered an inorganic biostimulant that may induce hormesis in plants. Supplied as titanium oxide nanoparticles (nTiO2) at appropriate concentrations, it may enhance seed germination, plant vigor, photosynthesis, and abiotic stress tolerance, while increasing nutrient uptake, crop yield and nutritional value. Nonetheless, applied at high concentrations, nTiO2 may trigger detrimental effects in plants. Methods Tomato (Solanum lycopersicum L.) cv. Rio Grande seeds were imbibed in solutions containing 0.0, 52.2, 104.4, 156.6, or 208.8 µM nTiO2. The germination experiment lasted 16 days under controlled conditions in the laboratory (10 h natural light, 21 °C mean temperature, at saturated atmospheric conditions). During the experiment we estimated seed weight increase after imbibition; total germination percentage (TGP); germination speed coefficient (GSC); and the vigor indexes I and II (VI I and II). Seedlings were grown for 30 days after sowing and at the end we measured lengths of stems and roots, number of roots and leaves, moisture content, and fresh and dry biomass weight. In addition, the potential hormetic effect of Ti on length of roots and stems was estimated. Results Applications of 156.6 and 208.8 µM nTiO2 significantly increased vigor index I, root length and total moisture content in leaves, while applying 208.8 µM nTiO2 significantly increased fresh biomass weight of roots. The hormetic analysis revealed that the application of 156.6 µM nTiO2 stimulated the length of roots and stems, with different dose-response curves. Conclusion The application of nTiO2 to tomato seeds improved some germination and plant growth parameters during the initial growth stage, demonstrating its biostimulant effects.
format: application/pdf
format: text/html
creator: Víctor Hugo Carbajal-Vázquez
creator: Libia Iris Trejo-Téllez
creator: Jorge Luis Mejía-Méndez
creator: Josafhat Salinas-Ruiz
creator: Fernando Carlos Gómez-Merino
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20516
publisher: PeerJ Inc.
rights: © 2025 Carbajal-Vázquez et al.
abstract: Background Titanium (Ti) is a beneficial element considered an inorganic biostimulant that may induce hormesis in plants. Supplied as titanium oxide nanoparticles (nTiO2) at appropriate concentrations, it may enhance seed germination, plant vigor, photosynthesis, and abiotic stress tolerance, while increasing nutrient uptake, crop yield and nutritional value. Nonetheless, applied at high concentrations, nTiO2 may trigger detrimental effects in plants. Methods Tomato (Solanum lycopersicum L.) cv. Rio Grande seeds were imbibed in solutions containing 0.0, 52.2, 104.4, 156.6, or 208.8 µM nTiO2. The germination experiment lasted 16 days under controlled conditions in the laboratory (10 h natural light, 21 °C mean temperature, at saturated atmospheric conditions). During the experiment we estimated seed weight increase after imbibition; total germination percentage (TGP); germination speed coefficient (GSC); and the vigor indexes I and II (VI I and II). Seedlings were grown for 30 days after sowing and at the end we measured lengths of stems and roots, number of roots and leaves, moisture content, and fresh and dry biomass weight. In addition, the potential hormetic effect of Ti on length of roots and stems was estimated. Results Applications of 156.6 and 208.8 µM nTiO2 significantly increased vigor index I, root length and total moisture content in leaves, while applying 208.8 µM nTiO2 significantly increased fresh biomass weight of roots. The hormetic analysis revealed that the application of 156.6 µM nTiO2 stimulated the length of roots and stems, with different dose-response curves. Conclusion The application of nTiO2 to tomato seeds improved some germination and plant growth parameters during the initial growth stage, demonstrating its biostimulant effects.
bibliographic citation: Carbajal-Vázquez et al. (2025) Biostimulant effects of titanium dioxide nanoparticles on germination and initial growth of tomato: evidence of hormesis. PeerJ 13:e20516 https://doi.org/10.7717/peerj.20516
date submitted: 2025-03-05
date accepted: 2025-11-12
issued: 2025-12-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carbajal-Vázquez
  given name: Víctor Hugo
author list: Agent
  family name: Trejo-Téllez
  given name: Libia Iris
author list: Agent
  family name: Mejía-Méndez
  given name: Jorge Luis
author list: Agent
  family name: Salinas-Ruiz
  given name: Josafhat
author list: Agent
  family name: Gómez-Merino
  given name: Fernando Carlos
doi: 10.7717/peerj.20516
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-16
copyright: ©2025 Carbajal-Vázquez et al.
attribution name: Carbajal-Vázquez et al.

Experimental tests of habitat preferences in the Comal Springs dryopid beetle, Stygoparnus comalensis
type: item
type: AcademicArticle
description: The Comal Springs dryopid beetle, Stygoparnus comalensis Barr and Spangler (Coleoptera: Dryopidae), is a federally endangered species endemic to three spring systems in central Texas, United States. Improving our understanding of the biology of this species is necessary for making progress towards the goals of its protection: establishing a monitoring program and maintaining captive reproducing populations. A series of experiments were conducted in captivity to empirically examine habitat preferences of S. comalensis while using a similar co-occurring species, Stenelmis sexlineata Sanderson, for comparison. Stygoparnus comalensis had a strong affinity for wood over leaves and rocks and had fuller guts when offered wild-conditioned wood compared with captive-conditioned wood. Adults and larvae of S. sexlineata were also attracted to wood when offered rocks, but did not prefer wood when also offered leaves. Both species responded to light, but responses were light- and species-specific, with S. comalensis avoiding shorter wavelength light and being attracted to longer wavelength light whereas S. sexlineata seemed to hide from all light types. Both species were attracted to conspecifics but not heterospecifics. Stygoparnus comalensis did not exhibit any clear response to flowing water (S. sexlineata was not examined). These results provide insight into the potential adaptations of a spring-endemic beetle species and environmental relationships that can potentially be used for improving monitoring and conservation of wild populations.
format: application/pdf
format: text/html
creator: Matthew R. Pintar
subject: Ecology
subject: Entomology
subject: Freshwater Biology
description: doi:10.7717/peerj.20507
publisher: PeerJ Inc.
rights: © 2025 Pintar
abstract: The Comal Springs dryopid beetle, Stygoparnus comalensis Barr and Spangler (Coleoptera: Dryopidae), is a federally endangered species endemic to three spring systems in central Texas, United States. Improving our understanding of the biology of this species is necessary for making progress towards the goals of its protection: establishing a monitoring program and maintaining captive reproducing populations. A series of experiments were conducted in captivity to empirically examine habitat preferences of S. comalensis while using a similar co-occurring species, Stenelmis sexlineata Sanderson, for comparison. Stygoparnus comalensis had a strong affinity for wood over leaves and rocks and had fuller guts when offered wild-conditioned wood compared with captive-conditioned wood. Adults and larvae of S. sexlineata were also attracted to wood when offered rocks, but did not prefer wood when also offered leaves. Both species responded to light, but responses were light- and species-specific, with S. comalensis avoiding shorter wavelength light and being attracted to longer wavelength light whereas S. sexlineata seemed to hide from all light types. Both species were attracted to conspecifics but not heterospecifics. Stygoparnus comalensis did not exhibit any clear response to flowing water (S. sexlineata was not examined). These results provide insight into the potential adaptations of a spring-endemic beetle species and environmental relationships that can potentially be used for improving monitoring and conservation of wild populations.
bibliographic citation: Pintar (2025) Experimental tests of habitat preferences in the Comal Springs dryopid beetle, Stygoparnus comalensis. PeerJ 13:e20507 https://doi.org/10.7717/peerj.20507
date submitted: 2025-09-05
date accepted: 2025-11-10
issued: 2025-12-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pintar
  given name: Matthew R.
doi: 10.7717/peerj.20507
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-16
copyright: ©2025 Pintar
attribution name: Pintar

Impact of bacterial culture medium on composition and characteristics of Burkholderia pseudomallei extracellular polymeric substances
type: item
type: AcademicArticle
description: Extracellular polymeric substances (EPS) are essential for maintaining the structural integrity and function of biofilms. In this study, the influence of nutrient composition on biofilm formation and EPS production by Burkholderia pseudomallei was assessed using a quantitative assay after cultivation in brain heart infusion (BHI), Luria-Bertani (LB), and modified Vogel and Bonner medium (MVBM) for 2, 4 and 6 days. Biofilm biomass, the percentage of EPS in the biofilm matrix, and the biochemical composition of EPS were analyzed. The functional groups of EPS were characterized using Fourier transform infrared (FTIR) spectroscopy, while the microstructural features of the EPS were examined using scanning electron microscopy. We found that B. pseudomallei cultured in MVBM exhibited the highest biofilm biomass, despite having the lowest proportion of EPS within the biofilm matrix. In contrast, cultures in LB medium produced the lowest biofilm biomass but contained the highest percentage of EPS. These observations indicate that growth under high carbon/nitrogen (C/N) ratio, as in MVBM, favors biofilm biomass accumulation, whereas low C/N ratio conditions, such as LB and BHI, are associated with a high relative EPS content. Despite these differences, the carbon content of the EPS remained consistent across all media. Notably, the EPS derived from cultures grown in BHI, a nitrogen-rich medium, contained the highest protein content, which corresponded with noticeable amide peaks in FTIR spectra. Collectively, these findings enhance our understanding of how environmental C/N ratios influence B. pseudomallei biofilm development and EPS composition, with implications for bacterial persistence and adaptability in the environment.
format: application/pdf
format: text/html
creator: Suthantip Srithabut
creator: Thotsapol Chaianunporn
creator: Sorujsiri Chareonsudjai
creator: Pisit Chareonsudjai
subject: Biochemistry
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.20488
publisher: PeerJ Inc.
rights: © 2025 Srithabut et al.
abstract: Extracellular polymeric substances (EPS) are essential for maintaining the structural integrity and function of biofilms. In this study, the influence of nutrient composition on biofilm formation and EPS production by Burkholderia pseudomallei was assessed using a quantitative assay after cultivation in brain heart infusion (BHI), Luria-Bertani (LB), and modified Vogel and Bonner medium (MVBM) for 2, 4 and 6 days. Biofilm biomass, the percentage of EPS in the biofilm matrix, and the biochemical composition of EPS were analyzed. The functional groups of EPS were characterized using Fourier transform infrared (FTIR) spectroscopy, while the microstructural features of the EPS were examined using scanning electron microscopy. We found that B. pseudomallei cultured in MVBM exhibited the highest biofilm biomass, despite having the lowest proportion of EPS within the biofilm matrix. In contrast, cultures in LB medium produced the lowest biofilm biomass but contained the highest percentage of EPS. These observations indicate that growth under high carbon/nitrogen (C/N) ratio, as in MVBM, favors biofilm biomass accumulation, whereas low C/N ratio conditions, such as LB and BHI, are associated with a high relative EPS content. Despite these differences, the carbon content of the EPS remained consistent across all media. Notably, the EPS derived from cultures grown in BHI, a nitrogen-rich medium, contained the highest protein content, which corresponded with noticeable amide peaks in FTIR spectra. Collectively, these findings enhance our understanding of how environmental C/N ratios influence B. pseudomallei biofilm development and EPS composition, with implications for bacterial persistence and adaptability in the environment.
bibliographic citation: Srithabut et al. (2025) Impact of bacterial culture medium on composition and characteristics of Burkholderia pseudomallei extracellular polymeric substances. PeerJ 13:e20488 https://doi.org/10.7717/peerj.20488
date submitted: 2025-08-27
date accepted: 2025-11-07
issued: 2025-12-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Srithabut
  given name: Suthantip
author list: Agent
  family name: Chaianunporn
  given name: Thotsapol
author list: Agent
  family name: Chareonsudjai
  given name: Sorujsiri
author list: Agent
  family name: Chareonsudjai
  given name: Pisit
doi: 10.7717/peerj.20488
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-16
copyright: ©2025 Srithabut et al.
attribution name: Srithabut et al.

The investigation of fermented food consumption on gastrointestinal symptoms: a cross-sectional study in university students
type: item
type: AcademicArticle
description: Background Fermented foods (FFs) are a valuable source of live microorganisms that can enhance human health, particularly gastrointestinal health, akin to probiotics. This study investigated the relationship between FFs consumption habits and gastrointestinal system findings in university students. Methods A cross-sectional anonymous survey included 546 university students, collecting data on sociodemographic characteristics, the Gastrointestinal Symptom Rating Scale (GSRS), and the Bristol Stool Form Scale (BSFS). FFs consumption habits were recorded using a food frequency questionnaire. Results Results showed that the average GSRS score was 33.66 ± 16.89. According to the BSFS, 15% of students experienced constipation, 72.7% had moderate stool consistency, and 12.3% had diarrhea. Notably, kefir, vinegar, and sourdough bread were never consumed by 56.8%, 44.3%, and 41.9% of students, respectively. Significant differences were found between the frequency of yogurt, kefir, vinegar, cheese, pickle consumption, and gastrointestinal symptoms (p < 0.05). Students with normal stool consistency had fewer dyspepsia, abdominal pain, reflux symptoms, and overall gastrointestinal symptoms than those with constipation (p < 0.05). Conclusion The study concludes that FFs such as yogurt, cheese, pickles, and kefir may offer health benefits, reducing symptoms of reflux, dyspepsia, abdominal pain, and general gastrointestinal issues in young adults.
format: application/pdf
format: text/html
creator: Hande Seven Avuk
creator: Oyku Aydin
creator: Neslihan Kocatepe
creator: Sude Melis Sahin
creator: Irem Akdogan
creator: Eser Cavus
subject: Gastroenterology and Hepatology
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.20479
publisher: PeerJ Inc.
rights: © 2025 Seven Avuk et al.
abstract: Background Fermented foods (FFs) are a valuable source of live microorganisms that can enhance human health, particularly gastrointestinal health, akin to probiotics. This study investigated the relationship between FFs consumption habits and gastrointestinal system findings in university students. Methods A cross-sectional anonymous survey included 546 university students, collecting data on sociodemographic characteristics, the Gastrointestinal Symptom Rating Scale (GSRS), and the Bristol Stool Form Scale (BSFS). FFs consumption habits were recorded using a food frequency questionnaire. Results Results showed that the average GSRS score was 33.66 ± 16.89. According to the BSFS, 15% of students experienced constipation, 72.7% had moderate stool consistency, and 12.3% had diarrhea. Notably, kefir, vinegar, and sourdough bread were never consumed by 56.8%, 44.3%, and 41.9% of students, respectively. Significant differences were found between the frequency of yogurt, kefir, vinegar, cheese, pickle consumption, and gastrointestinal symptoms (p < 0.05). Students with normal stool consistency had fewer dyspepsia, abdominal pain, reflux symptoms, and overall gastrointestinal symptoms than those with constipation (p < 0.05). Conclusion The study concludes that FFs such as yogurt, cheese, pickles, and kefir may offer health benefits, reducing symptoms of reflux, dyspepsia, abdominal pain, and general gastrointestinal issues in young adults.
bibliographic citation: Seven Avuk et al. (2025) The investigation of fermented food consumption on gastrointestinal symptoms: a cross-sectional study in university students. PeerJ 13:e20479 https://doi.org/10.7717/peerj.20479
date submitted: 2025-04-04
date accepted: 2025-11-05
issued: 2025-12-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Seven Avuk
  given name: Hande
author list: Agent
  family name: Aydin
  given name: Oyku
author list: Agent
  family name: Kocatepe
  given name: Neslihan
author list: Agent
  family name: Sahin
  given name: Sude Melis
author list: Agent
  family name: Akdogan
  given name: Irem
author list: Agent
  family name: Cavus
  given name: Eser
doi: 10.7717/peerj.20479
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-16
copyright: ©2025 Seven Avuk et al.
attribution name: Seven Avuk et al.

Design and simulation-based evaluation of a novel tracheostomy high-flow therapy device interface: a preclinical study
type: item
type: AcademicArticle
description: Background High-flow tracheal oxygen (HFTO) does not generate significant positive end-expiratory pressure (PEEP), which may limit its clinical applicability. We designed a novel high-flow tracheal interface (nHFTI) and compared the PEEP and other respiratory parameters it generated with those of the traditional high-flow tracheal interface (tHFTI) across a range of flow rates. Methods We conducted a randomized crossover bench study. A size 8 cuffed tracheostomy tube was connected to the high-flow therapy (HFT) device using two different interfaces. A high-fidelity lung simulator was used to model normal lung mechanics. Gas flow rates were set from 10 to 80 L/min at a gradient of 10 L/min, and the sequence was randomized. At each flow setting, the following parameters were recorded: PEEP, peak inspiratory pressure (PIP), peak expiratory pressure (PEP), end-inspiratory transpulmonary pressure (Ptp-EI), end-expiratory transpulmonary pressure (Ptp-EE), end-inspiratory cardiac pressure (PEIC) and end-expiratory cardiac pressure (PEEC), functional residual capacity (FRC), tidal volume (Vt) and fraction of inspired oxygen (FiO2). Results As the HFT flow rate increased, PEEP increased significantly with both the tHFTI and nHFTI (P < 0.001). Compared with the tHFTI, the nHFTI generated significantly higher PEEP across most flow rates (e.g., 3.4 vs. 1.0 cmH2O at 40 L/min; 7.3 vs. 3.1 cmH2O at 60 L/min, nHFTI vs. tHFTI, mean values). The nHFTI also generated higher PIP, PEP, Ptp-EI, Ptp-EE, PEIC, and PEEC, and resulted in a greater increase in FRC (P < 0.010). Compared with the tHFTI, the nHFTI maintained a relatively constant FiO2 and slightly reduced Vt at the same flow rate level. Conclusions The nHFTI generated a modest level of PEEP, increased FRC and slightly reduced Vt at flow rates of 40–60 L/min. This physiological profile suggests potential for maintaining lung expansion and improving cardiac function in heart failure. Further in vivo studies are needed to evaluate …
format: application/pdf
format: text/html
creator: Anna Hou
creator: Song Mi
creator: Fengwei Jiao
creator: Liming Zhang
creator: Zhaohui Tong
subject: Drugs and Devices
subject: Emergency and Critical Care
subject: Internal Medicine
subject: Respiratory Medicine
description: doi:10.7717/peerj.20445
publisher: PeerJ Inc.
rights: © 2025 Hou et al.
abstract: Background High-flow tracheal oxygen (HFTO) does not generate significant positive end-expiratory pressure (PEEP), which may limit its clinical applicability. We designed a novel high-flow tracheal interface (nHFTI) and compared the PEEP and other respiratory parameters it generated with those of the traditional high-flow tracheal interface (tHFTI) across a range of flow rates. Methods We conducted a randomized crossover bench study. A size 8 cuffed tracheostomy tube was connected to the high-flow therapy (HFT) device using two different interfaces. A high-fidelity lung simulator was used to model normal lung mechanics. Gas flow rates were set from 10 to 80 L/min at a gradient of 10 L/min, and the sequence was randomized. At each flow setting, the following parameters were recorded: PEEP, peak inspiratory pressure (PIP), peak expiratory pressure (PEP), end-inspiratory transpulmonary pressure (Ptp-EI), end-expiratory transpulmonary pressure (Ptp-EE), end-inspiratory cardiac pressure (PEIC) and end-expiratory cardiac pressure (PEEC), functional residual capacity (FRC), tidal volume (Vt) and fraction of inspired oxygen (FiO2). Results As the HFT flow rate increased, PEEP increased significantly with both the tHFTI and nHFTI (P < 0.001). Compared with the tHFTI, the nHFTI generated significantly higher PEEP across most flow rates (e.g., 3.4 vs. 1.0 cmH2O at 40 L/min; 7.3 vs. 3.1 cmH2O at 60 L/min, nHFTI vs. tHFTI, mean values). The nHFTI also generated higher PIP, PEP, Ptp-EI, Ptp-EE, PEIC, and PEEC, and resulted in a greater increase in FRC (P < 0.010). Compared with the tHFTI, the nHFTI maintained a relatively constant FiO2 and slightly reduced Vt at the same flow rate level. Conclusions The nHFTI generated a modest level of PEEP, increased FRC and slightly reduced Vt at flow rates of 40–60 L/min. This physiological profile suggests potential for maintaining lung expansion and improving cardiac function in heart failure. Further in vivo studies are needed to evaluate …
bibliographic citation: Hou et al. (2025) Design and simulation-based evaluation of a novel tracheostomy high-flow therapy device interface: a preclinical study. PeerJ 13:e20445 https://doi.org/10.7717/peerj.20445
date submitted: 2025-03-26
date accepted: 2025-10-31
issued: 2025-12-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Anna
author list: Agent
  family name: Mi
  given name: Song
author list: Agent
  family name: Jiao
  given name: Fengwei
author list: Agent
  family name: Zhang
  given name: Liming
author list: Agent
  family name: Tong
  given name: Zhaohui
doi: 10.7717/peerj.20445
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-16
copyright: ©2025 Hou et al.
attribution name: Hou et al.

Multiomics analysis reveals flavonoid accumulation and biosynthesis across different cultivation years and localities of Gongronemopsis tenacissima (Dai-Bai-Jie)
type: item
type: AcademicArticle
description: Background The dried root of Gongronemopsis tenacissima (Roxb.) S. Reuss, Liede & Meve, traditionally known as Dai-Bai-Jie, is a medicinal plant used by the Dai ethnic group, primarily for detoxification. Due to extensive use, wild resources have become increasingly scarce, prompting domestication efforts in China. However, the accumulation patterns of secondary metabolites—particularly flavonoids, the main detoxifying components—and their biosynthetic mechanisms remain unclear. Methods This study investigated differences in flavonoid accumulation and transcriptional regulation in Dai-Bai-Jie cultivated for one, two, and three years at high altitudes, and three years at low altitudes. Transcriptome and widely targeted metabolome analyses were conducted. A total of 1,495 metabolites were identified using ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS), with 943 showing differential accumulation across the four groups. All flavonoids were classified into six clusters using k-means clustering. Flavonoid levels were generally higher in plants cultivated for two and three years, with total metabolite content also more abundant in these groups. Two-year cultivation was recommended as the optimal harvesting strategy. Results A regulatory relationship was observed between genes such as phenylalanine ammonia-lyase, CYP73A, 4-coumarate: coenzyme A ligase, and flavonol synthase, and the flavonoid components in Dai-Bai-Jie. No significant differences were found in Shannon, Chao1, or abundance coverage estimator (ACE) indices of rhizosphere microorganisms across different cultivation years and locations. Conclusions This study elucidates the mechanisms of flavonoid accumulation and supports the scientific rationale for optimal harvesting years of Dai-Bai-Jie. The findings provide a valuable foundation for guiding large-scale cultivation and reducing reliance on wild resources.
format: application/pdf
format: text/html
creator: Mengqi Wang
creator: Yunxia Gu
creator: Liming Shan
creator: Chunyu Li
creator: Ertai Yuan
creator: Ge Li
creator: Xiaoli Liu
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.20439
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Background The dried root of Gongronemopsis tenacissima (Roxb.) S. Reuss, Liede & Meve, traditionally known as Dai-Bai-Jie, is a medicinal plant used by the Dai ethnic group, primarily for detoxification. Due to extensive use, wild resources have become increasingly scarce, prompting domestication efforts in China. However, the accumulation patterns of secondary metabolites—particularly flavonoids, the main detoxifying components—and their biosynthetic mechanisms remain unclear. Methods This study investigated differences in flavonoid accumulation and transcriptional regulation in Dai-Bai-Jie cultivated for one, two, and three years at high altitudes, and three years at low altitudes. Transcriptome and widely targeted metabolome analyses were conducted. A total of 1,495 metabolites were identified using ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS), with 943 showing differential accumulation across the four groups. All flavonoids were classified into six clusters using k-means clustering. Flavonoid levels were generally higher in plants cultivated for two and three years, with total metabolite content also more abundant in these groups. Two-year cultivation was recommended as the optimal harvesting strategy. Results A regulatory relationship was observed between genes such as phenylalanine ammonia-lyase, CYP73A, 4-coumarate: coenzyme A ligase, and flavonol synthase, and the flavonoid components in Dai-Bai-Jie. No significant differences were found in Shannon, Chao1, or abundance coverage estimator (ACE) indices of rhizosphere microorganisms across different cultivation years and locations. Conclusions This study elucidates the mechanisms of flavonoid accumulation and supports the scientific rationale for optimal harvesting years of Dai-Bai-Jie. The findings provide a valuable foundation for guiding large-scale cultivation and reducing reliance on wild resources.
bibliographic citation: Wang et al. (2025) Multiomics analysis reveals flavonoid accumulation and biosynthesis across different cultivation years and localities of Gongronemopsis tenacissima (Dai-Bai-Jie). PeerJ 13:e20439 https://doi.org/10.7717/peerj.20439
date submitted: 2025-02-05
date accepted: 2025-10-31
issued: 2025-12-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Mengqi
author list: Agent
  family name: Gu
  given name: Yunxia
author list: Agent
  family name: Shan
  given name: Liming
author list: Agent
  family name: Li
  given name: Chunyu
author list: Agent
  family name: Yuan
  given name: Ertai
author list: Agent
  family name: Li
  given name: Ge
author list: Agent
  family name: Liu
  given name: Xiaoli
doi: 10.7717/peerj.20439
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-16
copyright: ©2025 Wang et al.
attribution name: Wang et al.

Experimental assessment of the effects of sustainable landscaping practices on beetles in a new residential land development
type: item
type: AcademicArticle
description: As cities sprawl globally, the need for sustainable landscaping practices becomes more critical for addressing issues like water conservation, soil health, and local biodiversity. Beetles are valuable environmental indicators of insect habitat quality and are ecologically important. Here we experimentally assessed the response of ground-active beetle communities to sustainable landscaping practices (i.e., drought-tolerant native plants, reduced irrigation, and compost-amended soils) in an ongoing suburban development in Central Florida, one of the fastest growing regions in the USA. We assessed beetle activity density, diversity, and ecological functionality during the wet and dry seasons using pitfall traps, a well-tested technique for sampling ground arthropods. We hypothesized that the reduced compaction and better moisture retention of compost-amended soil would create better conditions for soil-dwelling beetles that use soil for egg deposition and larval development. We also hypothesized that plant growth-form traits would affect the spatial distribution of beetles within the experimental plots. Finally, we hypothesized that irrigation treatments would not affect beetle communities which are adapted to the region’s seasonal rainfall patterns. Results showed that beetle species richness positively correlated with percent cover of native ground cover forbs, and that beetle activity density tended to decline with increasing pine straw mulch coverage. Warmer soils enhanced both richness and activity density, while both of these metrics exhibited a hump-shaped pattern relative to soil moisture, peaking at intermediate levels. Trait-environment relationships revealed that beetle traits, including diet, body size, and larval substrate use, varied with microclimatic conditions. Trait diversity rose with species richness but plateaued due to trait saturation, while uneven trait distribution suggested filtering and niche separation driven by short-term climatic condition…
format: application/pdf
format: text/html
creator: Alessandra Pandolfi
creator: Patrick J. Bohlen
creator: Basil V. Iannone III
creator: Brooke L. Moffis
creator: Paul E. Skelley
creator: David G. Jenkins
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Natural Resource Management
description: doi:10.7717/peerj.20415
publisher: PeerJ Inc.
rights: © 2025 Pandolfi et al.
abstract: As cities sprawl globally, the need for sustainable landscaping practices becomes more critical for addressing issues like water conservation, soil health, and local biodiversity. Beetles are valuable environmental indicators of insect habitat quality and are ecologically important. Here we experimentally assessed the response of ground-active beetle communities to sustainable landscaping practices (i.e., drought-tolerant native plants, reduced irrigation, and compost-amended soils) in an ongoing suburban development in Central Florida, one of the fastest growing regions in the USA. We assessed beetle activity density, diversity, and ecological functionality during the wet and dry seasons using pitfall traps, a well-tested technique for sampling ground arthropods. We hypothesized that the reduced compaction and better moisture retention of compost-amended soil would create better conditions for soil-dwelling beetles that use soil for egg deposition and larval development. We also hypothesized that plant growth-form traits would affect the spatial distribution of beetles within the experimental plots. Finally, we hypothesized that irrigation treatments would not affect beetle communities which are adapted to the region’s seasonal rainfall patterns. Results showed that beetle species richness positively correlated with percent cover of native ground cover forbs, and that beetle activity density tended to decline with increasing pine straw mulch coverage. Warmer soils enhanced both richness and activity density, while both of these metrics exhibited a hump-shaped pattern relative to soil moisture, peaking at intermediate levels. Trait-environment relationships revealed that beetle traits, including diet, body size, and larval substrate use, varied with microclimatic conditions. Trait diversity rose with species richness but plateaued due to trait saturation, while uneven trait distribution suggested filtering and niche separation driven by short-term climatic condition…
bibliographic citation: Pandolfi et al. (2025) Experimental assessment of the effects of sustainable landscaping practices on beetles in a new residential land development. PeerJ 13:e20415 https://doi.org/10.7717/peerj.20415
date submitted: 2025-06-19
date accepted: 2025-10-28
issued: 2025-12-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pandolfi
  given name: Alessandra
author list: Agent
  family name: Bohlen
  given name: Patrick J.
author list: Agent
  family name: Iannone III
  given name: Basil V.
author list: Agent
  family name: Moffis
  given name: Brooke L.
author list: Agent
  family name: Skelley
  given name: Paul E.
author list: Agent
  family name: Jenkins
  given name: David G.
doi: 10.7717/peerj.20415
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-16
copyright: ©2025 Pandolfi et al.
attribution name: Pandolfi et al.

Diabetes and respiratory diseases as comorbid conditions in COVID-19 patients from Kazakhstan: a retrospective pilot study
type: item
type: AcademicArticle
description: Background Diabetes and respiratory diseases are prevalent in Central Asia, and their prevention represents an opportunity to increase life expectancy in the region, especially in Kazakhstan. This study aims to analyze trends in the prevalence of diabetes and respiratory diseases as comorbidities in patients with recent COVID-19 infections, based on the information obtained from several clinics in Almaty, Kazakhstan. Methods This study was conducted as a cross-sectional analysis using de-identified electronic medical records from a multidisciplinary hospital in Almaty, Kazakhstan. Adults hospitalized with laboratory-confirmed COVID-19 during 2021–2022 were included (N = 292; mean age 55 years, range 18–91). Continuous variables were summarized with means and standard deviations, and categorical variables with counts and percentages. Data extraction and statistical analyses were performed in September–December 2023. Results The mortality rate was higher among patients with pneumonia (16.8%) compared to chronic bronchitis (10.6%). We identified a high level of comorbidity with diabetes (35.3% in the 45–59 age group) and chronic respiratory disease (37.9% in the same group). Discussion The mortality and comorbidity rates for hospitalized patients with recent COVID-19 infections in Almaty were high in comparison to other middle-income countries. These findings underscore the need for targeted early prevention strategies and public health interventions to address the rising burden of chronic diseases in Kazakhstan, particularly among middle-aged adults.
format: application/pdf
format: text/html
creator: Karlygash Tazhibayeva
creator: Zinat Abdrakhmanova
creator: Ariel Shensa
creator: Aizhan Raushanova
creator: Assel Sadykova
creator: Natalya Glushkova
creator: Saltanat Mamyrbekova
creator: Zhanar Zhagiparova
creator: Arailym Beisbekova
creator: Faina Linkov
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Public Health
subject: Respiratory Medicine
subject: COVID-19
description: doi:10.7717/peerj.20413
publisher: PeerJ Inc.
rights: © 2025 Tazhibayeva et al.
abstract: Background Diabetes and respiratory diseases are prevalent in Central Asia, and their prevention represents an opportunity to increase life expectancy in the region, especially in Kazakhstan. This study aims to analyze trends in the prevalence of diabetes and respiratory diseases as comorbidities in patients with recent COVID-19 infections, based on the information obtained from several clinics in Almaty, Kazakhstan. Methods This study was conducted as a cross-sectional analysis using de-identified electronic medical records from a multidisciplinary hospital in Almaty, Kazakhstan. Adults hospitalized with laboratory-confirmed COVID-19 during 2021–2022 were included (N = 292; mean age 55 years, range 18–91). Continuous variables were summarized with means and standard deviations, and categorical variables with counts and percentages. Data extraction and statistical analyses were performed in September–December 2023. Results The mortality rate was higher among patients with pneumonia (16.8%) compared to chronic bronchitis (10.6%). We identified a high level of comorbidity with diabetes (35.3% in the 45–59 age group) and chronic respiratory disease (37.9% in the same group). Discussion The mortality and comorbidity rates for hospitalized patients with recent COVID-19 infections in Almaty were high in comparison to other middle-income countries. These findings underscore the need for targeted early prevention strategies and public health interventions to address the rising burden of chronic diseases in Kazakhstan, particularly among middle-aged adults.
bibliographic citation: Tazhibayeva et al. (2025) Diabetes and respiratory diseases as comorbid conditions in COVID-19 patients from Kazakhstan: a retrospective pilot study. PeerJ 13:e20413 https://doi.org/10.7717/peerj.20413
date submitted: 2025-07-11
date accepted: 2025-10-28
issued: 2025-12-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tazhibayeva
  given name: Karlygash
author list: Agent
  family name: Abdrakhmanova
  given name: Zinat
author list: Agent
  family name: Shensa
  given name: Ariel
author list: Agent
  family name: Raushanova
  given name: Aizhan
author list: Agent
  family name: Sadykova
  given name: Assel
author list: Agent
  family name: Glushkova
  given name: Natalya
author list: Agent
  family name: Mamyrbekova
  given name: Saltanat
author list: Agent
  family name: Zhagiparova
  given name: Zhanar
author list: Agent
  family name: Beisbekova
  given name: Arailym
author list: Agent
  family name: Linkov
  given name: Faina
doi: 10.7717/peerj.20413
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-16
copyright: ©2025 Tazhibayeva et al.
attribution name: Tazhibayeva et al.

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