PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The acute effects of simulated hypoxic training at different altitudes on oxidative stress and muscle damage in elite long-distance runners
items: Establishment and validation of systemic inflammatory index model and risk assessment of PVT in cirrhosis after splenectomy—a retrospective study
items: In vitro feasibility of bovine and canine whole blood and commercially prepared canine packed red blood cells as a source of xenotransfusion in swine (Sus scrofa domestica)
items: Past agricultural practices explain old field biodiversity and community composition in annually mowed grasslands: a case study of grazing and cultivation legacies in the northeastern United States
items: Deep learning-based fine-grained assessment of aneurysm wall characteristics using 4D-CT angiography
items: Endophytic fungal community composition and function response to strawberry genotype and disease resistance
items: Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes
items: Response surface optimization and flavor determination of fermentation processes of orange peel tea wine
items: Taxonomic and ecologic transitions in Triassic marine bivalve communities
items: Effects of 12-week integrative neuromuscular training on muscular fitness and sex differences in response to intervention in five- to six-year-old preschoolers

The acute effects of simulated hypoxic training at different altitudes on oxidative stress and muscle damage in elite long-distance runners
type: item
type: AcademicArticle
description: Background Understanding the impact of altitude on muscle damage and oxidative stress is essential for optimizing training and recovery strategies for athletes exposed to high-altitude conditions. Therefore, this study aimed to investigate the effects of acute exercise at different altitudes on oxidative stress and muscle damage. Methods A total of twelve elite long-distance runners (mean age: 20.3 ± 1.5 years) from different branches participated in the study. The exercise protocol was the Bruce submaximal treadmill exercise test, which was conducted under three simulated hypoxic conditions (at 1,700 m, 2,450 m, and 3,200 m) and one normoxic condition (sea level). All measurements took place at the same time of the day. After the exercise protocol, 5 ml venous blood samples were taken from the participants, while heart rate and oxygen saturation were monitored at the 3rd, 6th, 9th, and 12th minutes during the exercise. Results Significant altitude-dependent variations were observed in oxidative stress markers, with total oxidant status (TOS) (p = 0.017) and malondialdehyde (MDA) (p < 0.001) levels increasing at higher altitudes, while total antioxidant status (TAS) (p < 0.001) exhibited an elevation and oxidative stress index (OSI) (p < 0.001) demonstrated a decline as altitude increased. However, no significant difference was found in creatine kinase (CK, p = 0.059) levels. Additionally, there were significant differences in the oxygen saturation measurement taken at the 3rd (p < 0.001), 6th (p < 0.001), 9th (p < 0.001), and 12th (p < 0.001), minutes following the exercise session. There was no difference in the pulse measurement taken at the 3rd and 12th minutes, but a difference was observed at the 6th and 9th minutes post-exercise (p < 0.01). Conclusions In conclusion, the study determined that endurance exercises performed under simulated normobaric hypoxia at different altitudes increased TAS and reduced OSI in elite long-distance runners. The increase in TAS…
format: application/pdf
format: text/html
creator: Mücahit Sarikaya
creator: Beyza Öğe
creator: Nuri Mert Embiyaoğlu
creator: Muzaffer Selçuk
creator: Vedat Çınar
creator: Salih Öner
creator: Yıldırım Gökhan Gencer
creator: Mehdi Aslan
creator: Mustafa Sencer Ulema
creator: Yunus Emre Yarayan
creator: Kadir Keskin
creator: Nouf H. Alkhamees
creator: Bodor Bin Sheeha
creator: Gerasimos V. Grivas
creator: Sameer Badri AL-Mhanna
creator: Alexios Batrakoulis
subject: Kinesiology
subject: Metabolic Sciences
subject: Sports Medicine
description: doi:10.7717/peerj.19338
publisher: PeerJ Inc.
rights: © 2025 Sarikaya et al.
abstract: Background Understanding the impact of altitude on muscle damage and oxidative stress is essential for optimizing training and recovery strategies for athletes exposed to high-altitude conditions. Therefore, this study aimed to investigate the effects of acute exercise at different altitudes on oxidative stress and muscle damage. Methods A total of twelve elite long-distance runners (mean age: 20.3 ± 1.5 years) from different branches participated in the study. The exercise protocol was the Bruce submaximal treadmill exercise test, which was conducted under three simulated hypoxic conditions (at 1,700 m, 2,450 m, and 3,200 m) and one normoxic condition (sea level). All measurements took place at the same time of the day. After the exercise protocol, 5 ml venous blood samples were taken from the participants, while heart rate and oxygen saturation were monitored at the 3rd, 6th, 9th, and 12th minutes during the exercise. Results Significant altitude-dependent variations were observed in oxidative stress markers, with total oxidant status (TOS) (p = 0.017) and malondialdehyde (MDA) (p < 0.001) levels increasing at higher altitudes, while total antioxidant status (TAS) (p < 0.001) exhibited an elevation and oxidative stress index (OSI) (p < 0.001) demonstrated a decline as altitude increased. However, no significant difference was found in creatine kinase (CK, p = 0.059) levels. Additionally, there were significant differences in the oxygen saturation measurement taken at the 3rd (p < 0.001), 6th (p < 0.001), 9th (p < 0.001), and 12th (p < 0.001), minutes following the exercise session. There was no difference in the pulse measurement taken at the 3rd and 12th minutes, but a difference was observed at the 6th and 9th minutes post-exercise (p < 0.01). Conclusions In conclusion, the study determined that endurance exercises performed under simulated normobaric hypoxia at different altitudes increased TAS and reduced OSI in elite long-distance runners. The increase in TAS…
bibliographic citation: Sarikaya et al. (2025) The acute effects of simulated hypoxic training at different altitudes on oxidative stress and muscle damage in elite long-distance runners. PeerJ 13:e19338 https://doi.org/10.7717/peerj.19338
date submitted: 2024-12-10
date accepted: 2025-03-27
issued: 2025-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sarikaya
  given name: Mücahit
author list: Agent
  family name: Öğe
  given name: Beyza
author list: Agent
  family name: Embiyaoğlu
  given name: Nuri Mert
author list: Agent
  family name: Selçuk
  given name: Muzaffer
author list: Agent
  family name: Çınar
  given name: Vedat
author list: Agent
  family name: Öner
  given name: Salih
author list: Agent
  family name: Gencer
  given name: Yıldırım Gökhan
author list: Agent
  family name: Aslan
  given name: Mehdi
author list: Agent
  family name: Ulema
  given name: Mustafa Sencer
author list: Agent
  family name: Yarayan
  given name: Yunus Emre
author list: Agent
  family name: Keskin
  given name: Kadir
author list: Agent
  family name: Alkhamees
  given name: Nouf H.
author list: Agent
  family name: Sheeha
  given name: Bodor Bin
author list: Agent
  family name: Grivas
  given name: Gerasimos V.
author list: Agent
  family name: AL-Mhanna
  given name: Sameer Badri
author list: Agent
  family name: Batrakoulis
  given name: Alexios
doi: 10.7717/peerj.19338
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-12
copyright: ©2025 Sarikaya et al.
attribution name: Sarikaya et al.

Establishment and validation of systemic inflammatory index model and risk assessment of PVT in cirrhosis after splenectomy—a retrospective study
type: item
type: AcademicArticle
description: Objective The study aimed to create and validate a straightforward nomogram to predict portal vein thrombosis (PVT) in cirrhotic patient post-splenectomy, and investigate the predictive potential of systemic inflammation markers. One objective of the study was to develop a predictive model utilizing these markers to detect high-risk individuals early on. Methods A retrospective analysis was conducted on 184 cases of patients with cirrhosis who underwent splenectomy at The First Affiliated Hospital of University of South China from January 2015 to September 2023. The cohort was randomly divided into training (n = 130) and validation (n = 54) groups. Univariate and multivariate logistic regression analysis was employed to construct the prediction model. The performance of the nomogram was evaluated based on its ability to discriminate, calibrate, and demonstrate clinical utility. Results According to univariate and multivariate logistic regression analysis, we found six prediction indexes of PVT in patients with cirrhosis after splenectomy: postoperative neutrophil-to-lymphocyte ratio (NLR), postoperative derived NLR (dNLR), C-reactive protein to albumin ratio (CAR), portal vein diameter (DPV), platelet change value (PVB), and D-dimer (p-value < 0.05). Our clinical prediction model was created based on the aforementioned risk factors and demonstrated superior predictive power in both the primary cohort (AUC = 0.876) and validation cohort (AUC = 0.817). The calibration curve demonstrated satisfactory agreement between model predictions and actual observations, and the decision curve analysis (DCA) curve indicated high clinical net benefit. Conclusion Postoperative NLR, dNLR, CAR, PVB, DPV, and D-dimer were identified as the independent risk factors of PVT in cirrhotic patients post splenectomy. We had successfully established and validated a novel predictive model with good performance, based on systemic inflammatory indices in predicting PVT in cirrhosis after splenec…
format: application/pdf
format: text/html
creator: Xin Deng
creator: Wenyan Liao
creator: Xinmiao Jiang
creator: Shun Tu
creator: Xiangmin Xie
creator: Yuji Xiao
creator: Wuyao Chen
creator: Huan Zeng
creator: Chengming Ding
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.19254
publisher: PeerJ Inc.
rights: © 2025 Deng et al.
abstract: Objective The study aimed to create and validate a straightforward nomogram to predict portal vein thrombosis (PVT) in cirrhotic patient post-splenectomy, and investigate the predictive potential of systemic inflammation markers. One objective of the study was to develop a predictive model utilizing these markers to detect high-risk individuals early on. Methods A retrospective analysis was conducted on 184 cases of patients with cirrhosis who underwent splenectomy at The First Affiliated Hospital of University of South China from January 2015 to September 2023. The cohort was randomly divided into training (n = 130) and validation (n = 54) groups. Univariate and multivariate logistic regression analysis was employed to construct the prediction model. The performance of the nomogram was evaluated based on its ability to discriminate, calibrate, and demonstrate clinical utility. Results According to univariate and multivariate logistic regression analysis, we found six prediction indexes of PVT in patients with cirrhosis after splenectomy: postoperative neutrophil-to-lymphocyte ratio (NLR), postoperative derived NLR (dNLR), C-reactive protein to albumin ratio (CAR), portal vein diameter (DPV), platelet change value (PVB), and D-dimer (p-value < 0.05). Our clinical prediction model was created based on the aforementioned risk factors and demonstrated superior predictive power in both the primary cohort (AUC = 0.876) and validation cohort (AUC = 0.817). The calibration curve demonstrated satisfactory agreement between model predictions and actual observations, and the decision curve analysis (DCA) curve indicated high clinical net benefit. Conclusion Postoperative NLR, dNLR, CAR, PVB, DPV, and D-dimer were identified as the independent risk factors of PVT in cirrhotic patients post splenectomy. We had successfully established and validated a novel predictive model with good performance, based on systemic inflammatory indices in predicting PVT in cirrhosis after splenec…
bibliographic citation: Deng et al. (2025) Establishment and validation of systemic inflammatory index model and risk assessment of PVT in cirrhosis after splenectomy—a retrospective study. PeerJ 13:e19254 https://doi.org/10.7717/peerj.19254
date submitted: 2024-06-21
date accepted: 2025-03-12
issued: 2025-05-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Xin
author list: Agent
  family name: Liao
  given name: Wenyan
author list: Agent
  family name: Jiang
  given name: Xinmiao
author list: Agent
  family name: Tu
  given name: Shun
author list: Agent
  family name: Xie
  given name: Xiangmin
author list: Agent
  family name: Xiao
  given name: Yuji
author list: Agent
  family name: Chen
  given name: Wuyao
author list: Agent
  family name: Zeng
  given name: Huan
author list: Agent
  family name: Ding
  given name: Chengming
doi: 10.7717/peerj.19254
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-12
copyright: ©2025 Deng et al.
attribution name: Deng et al.

In vitro feasibility of bovine and canine whole blood and commercially prepared canine packed red blood cells as a source of xenotransfusion in swine (Sus scrofa domestica)
type: item
type: AcademicArticle
description: Background: Since sourcing porcine blood donors for emergent transfusions to porcine patients is difficult, bovine or canine blood donors might represent alternative sources. The primary objective of this study was to determine the frequency of incompatible major (CMMa) and minor (CMMi) crossmatches by the standard saline agglutination tube method (SSA) between bovine whole blood (bWB) and whole blood from commercial pigs (pWB), and canine universal donor whole blood or commercially-prepared packed red blood cells (pRBCs) with whole blood from companion pigs. A secondary objective was determining the agreement between the reference method (SSA) and a quick slide (QS) method. Methods: Blood was collected from 12 heifers, seven companion pigs, and eight commercial-cross pigs. A0 blood typing was performed for all porcine samples. Bovine blood was pooled into eight bags each containing three crossmatch-compatible individuals. Canine blood included whole blood from three canine blood donors (DEA 1.1, 5, 7 negative, and DEA 4 positive), and three bags each of DEA 1.1 negative and DEA 1.1 positive pRBCs. Crossmatch pairs were performed for bovine-to-porcine (n = 64) and canine-to-porcine (n = 63) samples. Incompatibility was defined as any agglutination or hemolysis on either CMMa and CMMi and reported separately. Complete incompatibility was defined as incompatibility of both CMMa and CMMi on the same pair. Kappa statistics tested the agreement between SSA and QS (significance at P < 0.05). Results: For bWB and pWB, agglutination was observed in 9.4% of CMMa and 100% of CMMi via SSA. Incompatibility on CMMa of bWB was more frequent with porcine blood type “0” (P = 0.0107) than with type “A”, whereas porcine blood group had no effect on CMMi results. All canine-to-porcine CMMa were incompatible with SSA and showed hemolysis severe enough to prevent evaluation of agglutination. The accuracy of QS at detecting incompatibilities was 87.5% in CMMa and 98.4% in CMMi in bovine-…
format: application/pdf
format: text/html
creator: Victoria Diaz
creator: Deanna M. W. Schaefer
creator: Pierre-Yves Mulon
creator: Xiaojuan Zhu
creator: Joe Smith
creator: Luca Giori
creator: Chiara Hampton
subject: Biochemistry
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.19436
publisher: PeerJ Inc.
rights: © 2025 Diaz et al.
abstract: Background: Since sourcing porcine blood donors for emergent transfusions to porcine patients is difficult, bovine or canine blood donors might represent alternative sources. The primary objective of this study was to determine the frequency of incompatible major (CMMa) and minor (CMMi) crossmatches by the standard saline agglutination tube method (SSA) between bovine whole blood (bWB) and whole blood from commercial pigs (pWB), and canine universal donor whole blood or commercially-prepared packed red blood cells (pRBCs) with whole blood from companion pigs. A secondary objective was determining the agreement between the reference method (SSA) and a quick slide (QS) method. Methods: Blood was collected from 12 heifers, seven companion pigs, and eight commercial-cross pigs. A0 blood typing was performed for all porcine samples. Bovine blood was pooled into eight bags each containing three crossmatch-compatible individuals. Canine blood included whole blood from three canine blood donors (DEA 1.1, 5, 7 negative, and DEA 4 positive), and three bags each of DEA 1.1 negative and DEA 1.1 positive pRBCs. Crossmatch pairs were performed for bovine-to-porcine (n = 64) and canine-to-porcine (n = 63) samples. Incompatibility was defined as any agglutination or hemolysis on either CMMa and CMMi and reported separately. Complete incompatibility was defined as incompatibility of both CMMa and CMMi on the same pair. Kappa statistics tested the agreement between SSA and QS (significance at P < 0.05). Results: For bWB and pWB, agglutination was observed in 9.4% of CMMa and 100% of CMMi via SSA. Incompatibility on CMMa of bWB was more frequent with porcine blood type “0” (P = 0.0107) than with type “A”, whereas porcine blood group had no effect on CMMi results. All canine-to-porcine CMMa were incompatible with SSA and showed hemolysis severe enough to prevent evaluation of agglutination. The accuracy of QS at detecting incompatibilities was 87.5% in CMMa and 98.4% in CMMi in bovine-…
bibliographic citation: Diaz et al. (2025) In vitro feasibility of bovine and canine whole blood and commercially prepared canine packed red blood cells as a source of xenotransfusion in swine (Sus scrofa domestica). PeerJ 13:e19436 https://doi.org/10.7717/peerj.19436
date submitted: 2024-11-22
date accepted: 2025-04-16
issued: 2025-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Diaz
  given name: Victoria
author list: Agent
  family name: Schaefer
  given name: Deanna M. W.
author list: Agent
  family name: Mulon
  given name: Pierre-Yves
author list: Agent
  family name: Zhu
  given name: Xiaojuan
author list: Agent
  family name: Smith
  given name: Joe
author list: Agent
  family name: Giori
  given name: Luca
author list: Agent
  family name: Hampton
  given name: Chiara
doi: 10.7717/peerj.19436
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-09
copyright: © 2025 Diaz et al.
attribution name: Diaz et al.

Past agricultural practices explain old field biodiversity and community composition in annually mowed grasslands: a case study of grazing and cultivation legacies in the northeastern United States
type: item
type: AcademicArticle
description: The northeastern United States experienced extensive deforestation for agriculture expansion and nearly equal passive reforestation following agriculture abandonment across the region over the past century. Old fields provide critical habitat as grasslands in the Northeast but tend to return to forests without intervention unless land managers implement disturbance regimes to maintain grassland states in the region. The relative importance of past and present disturbances in old field plant communities remains poorly resolved, partly because management varies widely in these systems. This motivated the present case study, which compares two proximate old fields that benefit from long and consistent management practices both before and after agriculture was abandoned in Hanover, NH. One field experienced agricultural disturbances associated with grazing while the other experienced cultivation each for 116 years followed by 50 years of the same annual mowing disturbances after agriculture was abandoned. Diversity was higher, communities more convergent across sub-plots, and woody individuals three times more numerous in the grazed site, while soil texture, type, elevation, and drainage had no discernible impact. The study helps to clarify the different legacies of grazing and cultivation on old field plant community diversity and composition. Despite undergoing 50 years of mowing following agriculture abandonment, the two old fields have divergent communities that are more consistent with the intensity of historic agricultural practices at each site than with any differences in measured soil characteristics. Understanding how agricultural legacies combine with contemporary disturbance regimes to shape successional communities may improve conservation and restoration efforts of grassland habitats and other ecosystems undergoing rapid environmental change, with implications for biodiversity, ecosystem services, and resilience.
format: application/pdf
format: text/html
creator: Alana M. Danieu
creator: Theresa W. Ong
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.19420
publisher: PeerJ Inc.
rights: © 2025 Danieu and Ong
abstract: The northeastern United States experienced extensive deforestation for agriculture expansion and nearly equal passive reforestation following agriculture abandonment across the region over the past century. Old fields provide critical habitat as grasslands in the Northeast but tend to return to forests without intervention unless land managers implement disturbance regimes to maintain grassland states in the region. The relative importance of past and present disturbances in old field plant communities remains poorly resolved, partly because management varies widely in these systems. This motivated the present case study, which compares two proximate old fields that benefit from long and consistent management practices both before and after agriculture was abandoned in Hanover, NH. One field experienced agricultural disturbances associated with grazing while the other experienced cultivation each for 116 years followed by 50 years of the same annual mowing disturbances after agriculture was abandoned. Diversity was higher, communities more convergent across sub-plots, and woody individuals three times more numerous in the grazed site, while soil texture, type, elevation, and drainage had no discernible impact. The study helps to clarify the different legacies of grazing and cultivation on old field plant community diversity and composition. Despite undergoing 50 years of mowing following agriculture abandonment, the two old fields have divergent communities that are more consistent with the intensity of historic agricultural practices at each site than with any differences in measured soil characteristics. Understanding how agricultural legacies combine with contemporary disturbance regimes to shape successional communities may improve conservation and restoration efforts of grassland habitats and other ecosystems undergoing rapid environmental change, with implications for biodiversity, ecosystem services, and resilience.
bibliographic citation: Danieu et al. (2025) Past agricultural practices explain old field biodiversity and community composition in annually mowed grasslands: a case study of grazing and cultivation legacies in the northeastern United States. PeerJ 13:e19420 https://doi.org/10.7717/peerj.19420
date submitted: 2024-12-03
date accepted: 2025-04-14
issued: 2025-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Danieu
  given name: Alana M.
author list: Agent
  family name: Ong
  given name: Theresa W.
doi: 10.7717/peerj.19420
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-09
copyright: © 2025 Danieu and Ong
attribution name: Danieu and Ong

Deep learning-based fine-grained assessment of aneurysm wall characteristics using 4D-CT angiography
type: item
type: AcademicArticle
description: Purpose This study proposes a novel deep learning-based approach for aneurysm wall characteristics, including thin-walled (TW) and hyperplastic-remodeling (HR) regions. Materials and Methods We analyzed fifty-two unruptured cerebral aneurysms employing 4D-computed tomography angiography (4D-CTA) and intraoperative recordings. The TW and HR regions were identified in intraoperative images. The 3D trajectories of observation points on aneurysm walls were processed to compute a time series of 3D speed, acceleration, and smoothness of motion, aiming to evaluate the aneurysm wall characteristics. To facilitate point-level risk evaluation using the time-series data, we developed a convolutional neural network (CNN)—long- short-term memory (LSTM)-based regression model enriched with attention layers. In order to accommodate patient heterogeneity, a patient-independent feature extraction mechanism was introduced. Furthermore, unlabeled data were incorporated to enhance the data-intensive deep model. Results The proposed method achieved an average diagnostic accuracy of 92%, significantly outperforming a simpler model lacking attention. These results underscore the significance of patient-independent feature extraction and the use of unlabeled data. Conclusion This study demonstrates the efficacy of a fine-grained deep learning approach in predicting aneurysm wall characteristics using 4D-CTA. Notably, incorporating an attention-based network structure proved to be particularly effective, contributing to enhanced performance.
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format: text/html
creator: Teerawat Kumrai
creator: Takuya Maekawa
creator: Yixuan Chen
creator: Yoshie Sugiyama
creator: Masatoshi Takagaki
creator: Shigeo Yamashiro
creator: Katsumi Takizawa
creator: Tsutomu Ichinose
creator: Fujimaro Ishida
creator: Haruhiko Kishima
subject: Neurology
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
subject: Computational Science
description: doi:10.7717/peerj.19393
publisher: PeerJ Inc.
rights: © 2025 Kumrai et al.
abstract: Purpose This study proposes a novel deep learning-based approach for aneurysm wall characteristics, including thin-walled (TW) and hyperplastic-remodeling (HR) regions. Materials and Methods We analyzed fifty-two unruptured cerebral aneurysms employing 4D-computed tomography angiography (4D-CTA) and intraoperative recordings. The TW and HR regions were identified in intraoperative images. The 3D trajectories of observation points on aneurysm walls were processed to compute a time series of 3D speed, acceleration, and smoothness of motion, aiming to evaluate the aneurysm wall characteristics. To facilitate point-level risk evaluation using the time-series data, we developed a convolutional neural network (CNN)—long- short-term memory (LSTM)-based regression model enriched with attention layers. In order to accommodate patient heterogeneity, a patient-independent feature extraction mechanism was introduced. Furthermore, unlabeled data were incorporated to enhance the data-intensive deep model. Results The proposed method achieved an average diagnostic accuracy of 92%, significantly outperforming a simpler model lacking attention. These results underscore the significance of patient-independent feature extraction and the use of unlabeled data. Conclusion This study demonstrates the efficacy of a fine-grained deep learning approach in predicting aneurysm wall characteristics using 4D-CTA. Notably, incorporating an attention-based network structure proved to be particularly effective, contributing to enhanced performance.
bibliographic citation: Kumrai et al. (2025) Deep learning-based fine-grained assessment of aneurysm wall characteristics using 4D-CT angiography. PeerJ 13:e19393 https://doi.org/10.7717/peerj.19393
date submitted: 2024-12-02
date accepted: 2025-04-08
issued: 2025-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kumrai
  given name: Teerawat
author list: Agent
  family name: Maekawa
  given name: Takuya
author list: Agent
  family name: Chen
  given name: Yixuan
author list: Agent
  family name: Sugiyama
  given name: Yoshie
author list: Agent
  family name: Takagaki
  given name: Masatoshi
author list: Agent
  family name: Yamashiro
  given name: Shigeo
author list: Agent
  family name: Takizawa
  given name: Katsumi
author list: Agent
  family name: Ichinose
  given name: Tsutomu
author list: Agent
  family name: Ishida
  given name: Fujimaro
author list: Agent
  family name: Kishima
  given name: Haruhiko
doi: 10.7717/peerj.19393
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-09
copyright: ©2025 Kumrai et al.
attribution name: Kumrai et al.

Endophytic fungal community composition and function response to strawberry genotype and disease resistance
type: item
type: AcademicArticle
description: Background Utilizating the plant endophytic microbiomes to enhance pathogen resistance in crop production is an emerging alternative method to chemical pesticides. However, research on the composition and role of microbial communities related to perennial fruit plants, such as the strawberry, is still limited. Methods We provide a comprehensive description of the composition and diversity of fungal communities in three niches (root, stem, and leaf) of three strawberry cultivars (‘White Elves’, ‘Tokun’, and ‘Akihime’) using internal transcribed spacer (ITS) rRNA amplicon sequencing and isolation culture methods. In addition, we also evaluated the disease tolerance ability of three strawberry cultivars to Colletotrichum gloeosporioides and Alternaria alternata through pathogenicity testing. Results ‘White Elves’ has stronger resistance to Colletotrichum gloeosporioides, and Alternaria alternata, followed by ‘Tokun’, while ‘Akihime’ has relatively weaker resistance to these pathogens. A total of 258 fungal strains were isolated from healthy strawberry plants and assigned to 34 fungal genera based on morphological and molecular characteristics analysis. Beneficial fungal genera such as Trichoderma and Talaromyces were more prevalent in ‘White Elves’, whereas common pathogenic fungi in strawberry, such as Colletotrichum, Alternaria, and Fusarium, were more prevalent in ‘Akihime’. The composition and diversity of microbial communities vary among genotypes, and resistance to pathogens may play dominant roles in determining the microbial community structure. This study’s results aid the biological control of strawberry fungal diseases and are useful for plant microbiome engineering in strawberry cultivation.
format: application/pdf
format: text/html
creator: Hongjun Yang
creator: Xu Zhang
creator: Rui Wang
creator: Quanzhi Wang
creator: Yuanhua Wang
creator: Geng Zhang
creator: Pengpeng Sun
creator: Bei Lu
creator: Meiling Wu
creator: Zhiming Yan
subject: Biodiversity
subject: Genomics
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.19383
publisher: PeerJ Inc.
rights: © 2025 Yang et al.
abstract: Background Utilizating the plant endophytic microbiomes to enhance pathogen resistance in crop production is an emerging alternative method to chemical pesticides. However, research on the composition and role of microbial communities related to perennial fruit plants, such as the strawberry, is still limited. Methods We provide a comprehensive description of the composition and diversity of fungal communities in three niches (root, stem, and leaf) of three strawberry cultivars (‘White Elves’, ‘Tokun’, and ‘Akihime’) using internal transcribed spacer (ITS) rRNA amplicon sequencing and isolation culture methods. In addition, we also evaluated the disease tolerance ability of three strawberry cultivars to Colletotrichum gloeosporioides and Alternaria alternata through pathogenicity testing. Results ‘White Elves’ has stronger resistance to Colletotrichum gloeosporioides, and Alternaria alternata, followed by ‘Tokun’, while ‘Akihime’ has relatively weaker resistance to these pathogens. A total of 258 fungal strains were isolated from healthy strawberry plants and assigned to 34 fungal genera based on morphological and molecular characteristics analysis. Beneficial fungal genera such as Trichoderma and Talaromyces were more prevalent in ‘White Elves’, whereas common pathogenic fungi in strawberry, such as Colletotrichum, Alternaria, and Fusarium, were more prevalent in ‘Akihime’. The composition and diversity of microbial communities vary among genotypes, and resistance to pathogens may play dominant roles in determining the microbial community structure. This study’s results aid the biological control of strawberry fungal diseases and are useful for plant microbiome engineering in strawberry cultivation.
bibliographic citation: Yang et al. (2025) Endophytic fungal community composition and function response to strawberry genotype and disease resistance. PeerJ 13:e19383 https://doi.org/10.7717/peerj.19383
date submitted: 2024-12-10
date accepted: 2025-04-07
issued: 2025-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Yang
  given name: Hongjun
author list: Agent
  family name: Zhang
  given name: Xu
author list: Agent
  family name: Wang
  given name: Rui
author list: Agent
  family name: Wang
  given name: Quanzhi
author list: Agent
  family name: Wang
  given name: Yuanhua
author list: Agent
  family name: Zhang
  given name: Geng
author list: Agent
  family name: Sun
  given name: Pengpeng
author list: Agent
  family name: Lu
  given name: Bei
author list: Agent
  family name: Wu
  given name: Meiling
author list: Agent
  family name: Yan
  given name: Zhiming
doi: 10.7717/peerj.19383
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-09
copyright: ©2025 Yang et al.
attribution name: Yang et al.

Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes
type: item
type: AcademicArticle
description: Background Tropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (Tillandsia multicaulis) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico. Methods We used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (Austrophorocera sp., Tachinidae, and Copestylum sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis. Results The bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by Copestylum and Austrophorocera larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks. Conclusions Our data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank.
format: application/pdf
format: text/html
creator: Rodolfo Martínez-Mota
creator: Antonio Acini Vásquez-Aguilar
creator: Dolores Hernández-Rodríguez
creator: Emilio A. Suárez-Domínguez
creator: Thorsten Krömer
subject: Ecology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.19376
publisher: PeerJ Inc.
rights: © 2025 Martínez-Mota et al.
abstract: Background Tropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (Tillandsia multicaulis) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico. Methods We used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (Austrophorocera sp., Tachinidae, and Copestylum sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis. Results The bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by Copestylum and Austrophorocera larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks. Conclusions Our data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank.
bibliographic citation: Martínez-Mota et al. (2025) Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes. PeerJ 13:e19376 https://doi.org/10.7717/peerj.19376
date submitted: 2024-08-26
date accepted: 2025-04-07
issued: 2025-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez-Mota
  given name: Rodolfo
author list: Agent
  family name: Vásquez-Aguilar
  given name: Antonio Acini
author list: Agent
  family name: Hernández-Rodríguez
  given name: Dolores
author list: Agent
  family name: Suárez-Domínguez
  given name: Emilio A.
author list: Agent
  family name: Krömer
  given name: Thorsten
doi: 10.7717/peerj.19376
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-09
copyright: © 2025 Martínez-Mota et al.
attribution name: Martínez-Mota et al.

Response surface optimization and flavor determination of fermentation processes of orange peel tea wine
type: item
type: AcademicArticle
description: Background In this study, Xinyang Maojian tea and orange peel were used as raw materials to brew health wine with orange and tea flavors. Methods Based on a single factor, the response surface method was used to optimize the fermentation of orange peel tea wine. Material volume ratio, yeast addition, fermentation temperature, fermentation time, and sucrose addition were used as the single-factor variables. The fermentation conditions of orange peel tea wine obtained by this method provide a theoretical basis for the development and utilization of tea wine and orange peel, which can promote the development of the tea wine market. Results The results showed that the material volume ratio of orange peel juice to tea juice was 1:3, the yeast addition amount was 4.9%, the fermentation temperature was 29 °C, the fermentation time was 7 d, and the sucrose addition amount was 29%. The main change indexes in the fermentation process of orange peel tea wine were determined, and the results were consistent with the fermentation law of orange peel tea wine. The contents of total flavonoids and total phenols in orange peel tea wine were 0.48 and 2.32 mg/mL, respectively, and were obtained using spectrophotometry and the Folin–Ciocalteu (F–C) method. The scavenging rate of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals was 90.8%, and the scavenging rate of ·OH radicals was 77.3%. A total of 26 flavor compounds were detected by gas chromatography-mass spectrometry (GC-MS). The main aroma compounds were ethanol, 3-methyl-1-butanol, 2-methyl-1-propanol, phenylethyl alcohol, acetic acid, n-hexadecanoic acid, 2,4-di-tert-butylphenol, and other compounds. Conclusion The resulting orange peel tea wine was transparent, yellow in color, harmonious in flavor, and had certain health benefits, including strong antioxidant properties. The results of this study provide the theoretical basis for the research and development of tea wine.
format: application/pdf
format: text/html
creator: Yanbo Liu
creator: Liu Mengge
creator: Pengpeng Zhang
creator: Wenxi Liu
creator: Chong Yang
creator: Jiayi Cui
creator: Haideng Li
creator: Chunmei Pan
subject: Biochemistry
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.19357
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Background In this study, Xinyang Maojian tea and orange peel were used as raw materials to brew health wine with orange and tea flavors. Methods Based on a single factor, the response surface method was used to optimize the fermentation of orange peel tea wine. Material volume ratio, yeast addition, fermentation temperature, fermentation time, and sucrose addition were used as the single-factor variables. The fermentation conditions of orange peel tea wine obtained by this method provide a theoretical basis for the development and utilization of tea wine and orange peel, which can promote the development of the tea wine market. Results The results showed that the material volume ratio of orange peel juice to tea juice was 1:3, the yeast addition amount was 4.9%, the fermentation temperature was 29 °C, the fermentation time was 7 d, and the sucrose addition amount was 29%. The main change indexes in the fermentation process of orange peel tea wine were determined, and the results were consistent with the fermentation law of orange peel tea wine. The contents of total flavonoids and total phenols in orange peel tea wine were 0.48 and 2.32 mg/mL, respectively, and were obtained using spectrophotometry and the Folin–Ciocalteu (F–C) method. The scavenging rate of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals was 90.8%, and the scavenging rate of ·OH radicals was 77.3%. A total of 26 flavor compounds were detected by gas chromatography-mass spectrometry (GC-MS). The main aroma compounds were ethanol, 3-methyl-1-butanol, 2-methyl-1-propanol, phenylethyl alcohol, acetic acid, n-hexadecanoic acid, 2,4-di-tert-butylphenol, and other compounds. Conclusion The resulting orange peel tea wine was transparent, yellow in color, harmonious in flavor, and had certain health benefits, including strong antioxidant properties. The results of this study provide the theoretical basis for the research and development of tea wine.
bibliographic citation: Liu et al. (2025) Response surface optimization and flavor determination of fermentation processes of orange peel tea wine. PeerJ 13:e19357 https://doi.org/10.7717/peerj.19357
date submitted: 2024-07-02
date accepted: 2025-04-02
issued: 2025-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yanbo
author list: Agent
  family name: Mengge
  given name: Liu
author list: Agent
  family name: Zhang
  given name: Pengpeng
author list: Agent
  family name: Liu
  given name: Wenxi
author list: Agent
  family name: Yang
  given name: Chong
author list: Agent
  family name: Cui
  given name: Jiayi
author list: Agent
  family name: Li
  given name: Haideng
author list: Agent
  family name: Pan
  given name: Chunmei
doi: 10.7717/peerj.19357
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-09
copyright: © 2025 Liu et al.
attribution name: Liu et al.

Taxonomic and ecologic transitions in Triassic marine bivalve communities
type: item
type: AcademicArticle
description: The Permian–Triassic mass extinction was a pivotal event in shaping marine benthic ecosystems, leading to the rise of mollusks such as bivalves and gastropods as representatives of the Modern Evolutionary Fauna. However, the detailed changes in the ecological structure of marine benthic communities throughout the Triassic remain underexplored, particularly the interrelationship between taxonomic and ecological diversities. Here, we present a study on the Triassic bivalve communities from the typical shallow marine facies in South China to document regional evolutionary patterns and explore how these patterns connect to the global trends. Broad congruence in the timing of taxonomic and ecological changes was observed through the Triassic in South China. However, both the South China materials and global data revealed a decoupling of taxonomic and ecological diversities. Substantial variability in taxonomic richness was observed alongside stable ecological diversity. Taxonomic recovery occurred early in the Early Triassic, whereas ecological diversity fully recovered only in the Middle Triassic. The Carnian stage represents a significant transition in ecosystem structure, characterized by a shift towards infaunal dominance and the expansion of habitat depth.
format: application/pdf
format: text/html
creator: Xue Miao
creator: Jinnan Tong
creator: Yunfei Huang
creator: Shiyan Zhang
creator: Peishan Li
creator: Yiran Cao
creator: Daoliang Chu
creator: Wolfgang Kiessling
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.19237
publisher: PeerJ Inc.
rights: © 2025 Miao et al.
abstract: The Permian–Triassic mass extinction was a pivotal event in shaping marine benthic ecosystems, leading to the rise of mollusks such as bivalves and gastropods as representatives of the Modern Evolutionary Fauna. However, the detailed changes in the ecological structure of marine benthic communities throughout the Triassic remain underexplored, particularly the interrelationship between taxonomic and ecological diversities. Here, we present a study on the Triassic bivalve communities from the typical shallow marine facies in South China to document regional evolutionary patterns and explore how these patterns connect to the global trends. Broad congruence in the timing of taxonomic and ecological changes was observed through the Triassic in South China. However, both the South China materials and global data revealed a decoupling of taxonomic and ecological diversities. Substantial variability in taxonomic richness was observed alongside stable ecological diversity. Taxonomic recovery occurred early in the Early Triassic, whereas ecological diversity fully recovered only in the Middle Triassic. The Carnian stage represents a significant transition in ecosystem structure, characterized by a shift towards infaunal dominance and the expansion of habitat depth.
bibliographic citation: Miao et al. (2025) Taxonomic and ecologic transitions in Triassic marine bivalve communities. PeerJ 13:e19237 https://doi.org/10.7717/peerj.19237
date submitted: 2024-09-18
date accepted: 2025-03-10
issued: 2025-05-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miao
  given name: Xue
author list: Agent
  family name: Tong
  given name: Jinnan
author list: Agent
  family name: Huang
  given name: Yunfei
author list: Agent
  family name: Zhang
  given name: Shiyan
author list: Agent
  family name: Li
  given name: Peishan
author list: Agent
  family name: Cao
  given name: Yiran
author list: Agent
  family name: Chu
  given name: Daoliang
author list: Agent
  family name: Kiessling
  given name: Wolfgang
doi: 10.7717/peerj.19237
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-09
copyright: ©2025 Miao et al.
attribution name: Miao et al.

Effects of 12-week integrative neuromuscular training on muscular fitness and sex differences in response to intervention in five- to six-year-old preschoolers
type: item
type: AcademicArticle
description: Objectives This study examined the effects of a 12-week integrative neuromuscular training (INT) program on muscular fitness in male and female five- to six-year-old preschoolers. Methods Thirty preschoolers were randomly assigned to either an experimental group (EG; n = 15; age = 5.3 ± 0.5 years, body height = 115.3 ± 5.2 cm, body mass = 20.7 ± 2.6 kg) or a control group (CG; n = 15; age = 5.2 ± 0.4 years, body height = 118.5 ± 4.9 cm, body mass = 22.6 ± 2.7 kg) participating in a 12-week INT program and regular physical education classes three times per week, respectively. Upper extremity maximal strength (grip strength test) and power (tennis ball throwing test), core endurance strength (one-minute sit-up test), and lower extremity power (standing long jump test) were assessed at the baseline (T0), Week 6 (T6), and Week 12 (T12). Data were analyzed using an independent samples T-test and a two-way repeated-measures ANOVA. Results Significant interaction effects between the EG and CG were observed for grip strength, tennis ball throws, one-minute sit-ups, and standing long jumps (p < 0.001). Relative to the CG, the EG demonstrated significant improvements in all muscular fitness at T6 and T12 (p < 0.05). However, no significant interaction was found between the time and the sex (p > 0.05). Conclusions These findings suggested that a 12-week INT program can more effectively enhance the muscular fitness of 5–6-year-old preschoolers compared to regular physical education classes, serving as an effective and efficient supplement to physical education for this age group. Furthermore, there is no evidence of sex -specific differences in the development of muscular fitness among 5–6-year-old preschoolers under the INT program.
format: application/pdf
format: text/html
creator: Zhihai Wang
creator: Jiayu Zang
creator: Zhaohong Wang
creator: Daniel T.P. Fong
creator: Dan Wang
subject: Kinesiology
subject: Pediatrics
subject: Public Health
subject: Sports Medicine
description: doi:10.7717/peerj.19417
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Objectives This study examined the effects of a 12-week integrative neuromuscular training (INT) program on muscular fitness in male and female five- to six-year-old preschoolers. Methods Thirty preschoolers were randomly assigned to either an experimental group (EG; n = 15; age = 5.3 ± 0.5 years, body height = 115.3 ± 5.2 cm, body mass = 20.7 ± 2.6 kg) or a control group (CG; n = 15; age = 5.2 ± 0.4 years, body height = 118.5 ± 4.9 cm, body mass = 22.6 ± 2.7 kg) participating in a 12-week INT program and regular physical education classes three times per week, respectively. Upper extremity maximal strength (grip strength test) and power (tennis ball throwing test), core endurance strength (one-minute sit-up test), and lower extremity power (standing long jump test) were assessed at the baseline (T0), Week 6 (T6), and Week 12 (T12). Data were analyzed using an independent samples T-test and a two-way repeated-measures ANOVA. Results Significant interaction effects between the EG and CG were observed for grip strength, tennis ball throws, one-minute sit-ups, and standing long jumps (p < 0.001). Relative to the CG, the EG demonstrated significant improvements in all muscular fitness at T6 and T12 (p < 0.05). However, no significant interaction was found between the time and the sex (p > 0.05). Conclusions These findings suggested that a 12-week INT program can more effectively enhance the muscular fitness of 5–6-year-old preschoolers compared to regular physical education classes, serving as an effective and efficient supplement to physical education for this age group. Furthermore, there is no evidence of sex -specific differences in the development of muscular fitness among 5–6-year-old preschoolers under the INT program.
bibliographic citation: Wang et al. (2025) Effects of 12-week integrative neuromuscular training on muscular fitness and sex differences in response to intervention in five- to six-year-old preschoolers. PeerJ 13:e19417 https://doi.org/10.7717/peerj.19417
date submitted: 2024-12-19
date accepted: 2025-04-10
issued: 2025-05-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhihai
author list: Agent
  family name: Zang
  given name: Jiayu
author list: Agent
  family name: Wang
  given name: Zhaohong
author list: Agent
  family name: Fong
  given name: Daniel T.P.
author list: Agent
  family name: Wang
  given name: Dan
doi: 10.7717/peerj.19417
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-08
copyright: ©2025 Wang et al.
attribution name: Wang et al.

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