PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Tryptophan-kynurenine pathway: a possible new mechanism for the prevention and treatment of reproductive system-related diseases
items: Latitudinal variations in morphometric traits and bioenergetic status of adult red squat lobsters Grimothea monodon (H. Milne Edwards, 1837) in the Southeast Pacific Ocean
items: The effect of endoscopic polidocanol carbon dioxide foam for internal hemorrhoids: a retrospective study
items: Enhancing heatstroke prediction accuracy with interpretable machine learning: a multi-center data-driven approach
items: Feeding ecology and trophic interactions of the narrow-barred Spanish Mackerel (Scomberomorus commerson) in the Central Taiwan Strait
items: Does reef crest zone selection influence Acropora palmata (Lamarck, 1816) fragment survival and growth?
items: Status and trends of giant clam populations demonstrate the effectiveness of village-based protection in American Sāmoa
items: Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu)
items: Comparison of quadriceps and hamstring muscle size and strength between young athletes following knee surgery and healthy controls
items: Prevalence of poor sleep quality and its associated factors in patients with concurrent type 2 diabetes mellitus and hypertension

Tryptophan-kynurenine pathway: a possible new mechanism for the prevention and treatment of reproductive system-related diseases
type: item
type: AcademicArticle
description: Tryptophan (Trp) is one of the essential amino acids, and its metabolic pathway is essential for the maintenance of normal human physiological activities. Among them, various metabolites and rate-limiting enzymes of the tryptophan-kynurenine metabolic pathway play important roles in inflammatory responses, immune regulation, energy metabolism, as well as neuroprotective and toxic effects. Abnormalities in tryptophan-kynurenine pathway metabolism thus inevitably lead to numerous pathological changes, such as reproductive disorders. It is noteworthy that the prevention and treatment of reproductive diseases are not currently focused on this pathway. In view of the increasing number of studies that have found abnormalities in the levels of key enzymes and metabolites of tryptophan-kynurenine in reproductive diseases, this article will focus on summarizing the molecular mechanisms and relevance of the pathway in reproductive diseases, as well as proposing new ideas for the prevention and treatment of reproductive diseases, including the use of inhibitors of the pathway and the regulation of tryptophan metabolism in the intestinal flora.
format: application/pdf
format: text/html
creator: Zhongkai Ou
creator: Aixia Xu
creator: Hua Su
creator: Yiting Liu
creator: Jia Li
subject: Biochemistry
subject: Andrology
subject: Gynecology and Obstetrics
subject: Women’s Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.20342
publisher: PeerJ Inc.
rights: © 2025 Ou et al.
abstract: Tryptophan (Trp) is one of the essential amino acids, and its metabolic pathway is essential for the maintenance of normal human physiological activities. Among them, various metabolites and rate-limiting enzymes of the tryptophan-kynurenine metabolic pathway play important roles in inflammatory responses, immune regulation, energy metabolism, as well as neuroprotective and toxic effects. Abnormalities in tryptophan-kynurenine pathway metabolism thus inevitably lead to numerous pathological changes, such as reproductive disorders. It is noteworthy that the prevention and treatment of reproductive diseases are not currently focused on this pathway. In view of the increasing number of studies that have found abnormalities in the levels of key enzymes and metabolites of tryptophan-kynurenine in reproductive diseases, this article will focus on summarizing the molecular mechanisms and relevance of the pathway in reproductive diseases, as well as proposing new ideas for the prevention and treatment of reproductive diseases, including the use of inhibitors of the pathway and the regulation of tryptophan metabolism in the intestinal flora.
bibliographic citation: Ou et al. (2025) Tryptophan-kynurenine pathway: a possible new mechanism for the prevention and treatment of reproductive system-related diseases. PeerJ 13:e20342 https://doi.org/10.7717/peerj.20342
date submitted: 2025-04-22
date accepted: 2025-10-15
issued: 2025-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ou
  given name: Zhongkai
author list: Agent
  family name: Xu
  given name: Aixia
author list: Agent
  family name: Su
  given name: Hua
author list: Agent
  family name: Liu
  given name: Yiting
author list: Agent
  family name: Li
  given name: Jia
doi: 10.7717/peerj.20342
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-17
copyright: ©2025 Ou et al.
attribution name: Ou et al.

Latitudinal variations in morphometric traits and bioenergetic status of adult red squat lobsters Grimothea monodon (H. Milne Edwards, 1837) in the Southeast Pacific Ocean
type: item
type: AcademicArticle
description: Adults of the red squat lobster (Grimothea monodon) present two morphotypes (small-pelagic (SP) and large-benthic (LB)) in their wide geographic distribution range in the Southeastern Pacific Ocean (SEPO). In this marine ecosystem, they are exposed to conspicuous latitudinal variations in oceanographic and physicochemical parameters that affect their nutritional and fitness status. The objective of this study was to determine variations in the bioenergetic condition at the level of morphometric, sexual and biochemical traits of G. monodon, considering a wide spatial scale of their populations’ distribution along a latitudinal gradient (from 9°S to 36°S) in the SEPO. According to the environmental parameters, temperature and dissolved oxygen presented abrupt changes between 15°S–17°S, while chlorophyll and salinity showed a constant reduction along the latitudinal gradient. When environmental parameters were related to the size of the two morphotypes (SP, LB) of G. monodon, some trends of change were observed, while the relative condition factor showed significant differences along the latitudinal gradient. The biochemical condition of SP individuals showed an increasing trend in glucose from Chimbote to Chala, proteins showed abrupt changes in three zones (between Huacho-Lima, Lomitas, and Chala), and lipids showed a notable change between Lima-Cañete. In turn, in LB individual’s increases were recorded in all their biochemical constituents towards high latitudes. A slight variability in fatty acids was observed between SP individuals from the north (Chimbote, Huarmey, Huacho) and SP individuals from the south (Marcona, Chala, Planchada, Mollendo). In addition, significant latitudinal differences were observed in the fatty acids of the two morphotypes (SP, LP). The nutritional condition index (docosahexaenoic acid (DHA)/eicosapentaenoic acid (EPA) ratio) showed significant differences for the locality factor. Our findings revealed conspicuous differences in the bioe…
format: application/pdf
format: text/html
creator: Marco Quispe-Machaca
creator: Maximiliano Zilleruelo
creator: Pepe Espinoza
creator: Gabriela Torres
creator: Ángel Urzúa
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.20339
publisher: PeerJ Inc.
rights: © 2025 Quispe-Machaca et al.
abstract: Adults of the red squat lobster (Grimothea monodon) present two morphotypes (small-pelagic (SP) and large-benthic (LB)) in their wide geographic distribution range in the Southeastern Pacific Ocean (SEPO). In this marine ecosystem, they are exposed to conspicuous latitudinal variations in oceanographic and physicochemical parameters that affect their nutritional and fitness status. The objective of this study was to determine variations in the bioenergetic condition at the level of morphometric, sexual and biochemical traits of G. monodon, considering a wide spatial scale of their populations’ distribution along a latitudinal gradient (from 9°S to 36°S) in the SEPO. According to the environmental parameters, temperature and dissolved oxygen presented abrupt changes between 15°S–17°S, while chlorophyll and salinity showed a constant reduction along the latitudinal gradient. When environmental parameters were related to the size of the two morphotypes (SP, LB) of G. monodon, some trends of change were observed, while the relative condition factor showed significant differences along the latitudinal gradient. The biochemical condition of SP individuals showed an increasing trend in glucose from Chimbote to Chala, proteins showed abrupt changes in three zones (between Huacho-Lima, Lomitas, and Chala), and lipids showed a notable change between Lima-Cañete. In turn, in LB individual’s increases were recorded in all their biochemical constituents towards high latitudes. A slight variability in fatty acids was observed between SP individuals from the north (Chimbote, Huarmey, Huacho) and SP individuals from the south (Marcona, Chala, Planchada, Mollendo). In addition, significant latitudinal differences were observed in the fatty acids of the two morphotypes (SP, LP). The nutritional condition index (docosahexaenoic acid (DHA)/eicosapentaenoic acid (EPA) ratio) showed significant differences for the locality factor. Our findings revealed conspicuous differences in the bioe…
bibliographic citation: Quispe-Machaca et al. (2025) Latitudinal variations in morphometric traits and bioenergetic status of adult red squat lobsters Grimothea monodon (H. Milne Edwards, 1837) in the Southeast Pacific Ocean. PeerJ 13:e20339 https://doi.org/10.7717/peerj.20339
date submitted: 2024-10-14
date accepted: 2025-10-13
issued: 2025-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quispe-Machaca
  given name: Marco
author list: Agent
  family name: Zilleruelo
  given name: Maximiliano
author list: Agent
  family name: Espinoza
  given name: Pepe
author list: Agent
  family name: Torres
  given name: Gabriela
author list: Agent
  family name: Urzúa
  given name: Ángel
doi: 10.7717/peerj.20339
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-17
copyright: ©2025 Quispe-Machaca et al.
attribution name: Quispe-Machaca et al.

The effect of endoscopic polidocanol carbon dioxide foam for internal hemorrhoids: a retrospective study
type: item
type: AcademicArticle
description: Aim This article aims to explore the effectiveness of polidocanol carbon dioxide foam as a therapy for internal hemorrhoids. Methods A retrospective analysis was conducted on 158 patients who received endoscopic polidocanol foam sclerotherapy for internal hemorrhoids between October 2022 and September 2023. Among the patients, 78 underwent endoscopic polidocanol sclerotherapy with polidocanol air foam (control group), while 80 received polidocanol carbon dioxide foam (study group). The primary outcomes of this study were clinical effect and the incidence of complications 1 month after surgery. Patient self-reports of anal bleeding and anal prolapse served as the foundation for establishing three categories of clinical efficacy criteria. The clinical effect was determined based on the efficacy index, which was employed to assess treatment effectiveness. The occurrence of several postoperative complications was documented, specifically including anal pain, anal swelling, urinary retention, perianal infection, ectopic embolization, and anal edema. Secondary outcomes encompassed the surgical cost, duration of hospital stay, and the administered dosage of polidocanol. Result The treatment success at the end of the sclerotherapy session in the study and control group were 85.0% and 83.3%, respectively (P = 0.829). One month following endoscopic sclerotherapy, the study group exhibited an effective rate of 98.8%, while the control group showed a rate of 98.0%. Compared with the clinical effects one month after surgery of the two groups of patients, postoperative complications, surgical cost, hospitalization time and the dosage of polidocanol, we found 11 patients with anal pain and 12 patients with anal swelling in the control group. Within the study group, three patients experienced anal pain, while four patients presented with anal swelling. The study group exhibited significantly fewer patients with anal pain and anal swelling compared to the control group (P < 0.05), a…
format: application/pdf
format: text/html
creator: Jiahui Xiang
creator: Shichao Li
creator: Tengjiang Yu
creator: Qingfeng Jiang
creator: Xia Jiang
creator: Yong Lan
subject: Clinical Trials
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.20252
publisher: PeerJ Inc.
rights: © 2025 Xiang et al.
abstract: Aim This article aims to explore the effectiveness of polidocanol carbon dioxide foam as a therapy for internal hemorrhoids. Methods A retrospective analysis was conducted on 158 patients who received endoscopic polidocanol foam sclerotherapy for internal hemorrhoids between October 2022 and September 2023. Among the patients, 78 underwent endoscopic polidocanol sclerotherapy with polidocanol air foam (control group), while 80 received polidocanol carbon dioxide foam (study group). The primary outcomes of this study were clinical effect and the incidence of complications 1 month after surgery. Patient self-reports of anal bleeding and anal prolapse served as the foundation for establishing three categories of clinical efficacy criteria. The clinical effect was determined based on the efficacy index, which was employed to assess treatment effectiveness. The occurrence of several postoperative complications was documented, specifically including anal pain, anal swelling, urinary retention, perianal infection, ectopic embolization, and anal edema. Secondary outcomes encompassed the surgical cost, duration of hospital stay, and the administered dosage of polidocanol. Result The treatment success at the end of the sclerotherapy session in the study and control group were 85.0% and 83.3%, respectively (P = 0.829). One month following endoscopic sclerotherapy, the study group exhibited an effective rate of 98.8%, while the control group showed a rate of 98.0%. Compared with the clinical effects one month after surgery of the two groups of patients, postoperative complications, surgical cost, hospitalization time and the dosage of polidocanol, we found 11 patients with anal pain and 12 patients with anal swelling in the control group. Within the study group, three patients experienced anal pain, while four patients presented with anal swelling. The study group exhibited significantly fewer patients with anal pain and anal swelling compared to the control group (P < 0.05), a…
bibliographic citation: Xiang et al. (2025) The effect of endoscopic polidocanol carbon dioxide foam for internal hemorrhoids: a retrospective study. PeerJ 13:e20252 https://doi.org/10.7717/peerj.20252
date submitted: 2024-10-31
date accepted: 2025-09-25
issued: 2025-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiang
  given name: Jiahui
author list: Agent
  family name: Li
  given name: Shichao
author list: Agent
  family name: Yu
  given name: Tengjiang
author list: Agent
  family name: Jiang
  given name: Qingfeng
author list: Agent
  family name: Jiang
  given name: Xia
author list: Agent
  family name: Lan
  given name: Yong
doi: 10.7717/peerj.20252
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-17
copyright: © 2025 Xiang et al.
attribution name: Xiang et al.

Enhancing heatstroke prediction accuracy with interpretable machine learning: a multi-center data-driven approach
type: item
type: AcademicArticle
description: Background Heatstroke poses a significant threat to public health, frequently culminating in fatal outcomes. This study aimed to develop and validate an interpretable machine learning (ML) model to forecast heatstroke using clinical and laboratory data. Methods Data were collated from 24 hospitals spanning the years 2021 to 2023, with data from 2021 and 2022 comprising the training datasets and data from 2023 designated for validation. Model efficacy was quantified via the area under the receiver operating characteristic curve (AUROC) and calibration plots. Furthermore, the SHapley Additive exPlanations (SHAP) methodology was employed to elucidate the interpretability of the final model. Results The study encompassed 691 patients, with 176 in the training datasets and 80 in the testing datasets diagnosed with heatstroke. Among the nine ML models assessed, the gradient boosting machine (GBM) model demonstrated superior performance, achieving an AUROC of 0.971 in the training datasets and 0.836 in the testing datasets, and exhibiting substantial net benefits in decision curve analysis. Creatine kinase (CK)-MB was identified as the most impactful variable influencing the GBM model’s efficacy. Conclusion The ML model we developed demonstrates robust predictive capabilities for heatstroke, potentially aiding clinicians in the identification and management of patients at elevated risk.
format: application/pdf
format: text/html
creator: Qingbo Zeng
creator: Xingping Deng
creator: Longping He
creator: Lincui Zhong
creator: Qingwei Lin
creator: Nianqing Zhang
creator: Jingchun Song
subject: Emergency and Critical Care
subject: Public Health
subject: Sports Medicine
description: doi:10.7717/peerj.20377
publisher: PeerJ Inc.
rights: © 2025 Zeng et al.
abstract: Background Heatstroke poses a significant threat to public health, frequently culminating in fatal outcomes. This study aimed to develop and validate an interpretable machine learning (ML) model to forecast heatstroke using clinical and laboratory data. Methods Data were collated from 24 hospitals spanning the years 2021 to 2023, with data from 2021 and 2022 comprising the training datasets and data from 2023 designated for validation. Model efficacy was quantified via the area under the receiver operating characteristic curve (AUROC) and calibration plots. Furthermore, the SHapley Additive exPlanations (SHAP) methodology was employed to elucidate the interpretability of the final model. Results The study encompassed 691 patients, with 176 in the training datasets and 80 in the testing datasets diagnosed with heatstroke. Among the nine ML models assessed, the gradient boosting machine (GBM) model demonstrated superior performance, achieving an AUROC of 0.971 in the training datasets and 0.836 in the testing datasets, and exhibiting substantial net benefits in decision curve analysis. Creatine kinase (CK)-MB was identified as the most impactful variable influencing the GBM model’s efficacy. Conclusion The ML model we developed demonstrates robust predictive capabilities for heatstroke, potentially aiding clinicians in the identification and management of patients at elevated risk.
bibliographic citation: Zeng et al. (2025) Enhancing heatstroke prediction accuracy with interpretable machine learning: a multi-center data-driven approach. PeerJ 13:e20377 https://doi.org/10.7717/peerj.20377
date submitted: 2025-05-19
date accepted: 2025-10-20
issued: 2025-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zeng
  given name: Qingbo
author list: Agent
  family name: Deng
  given name: Xingping
author list: Agent
  family name: He
  given name: Longping
author list: Agent
  family name: Zhong
  given name: Lincui
author list: Agent
  family name: Lin
  given name: Qingwei
author list: Agent
  family name: Zhang
  given name: Nianqing
author list: Agent
  family name: Song
  given name: Jingchun
doi: 10.7717/peerj.20377
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-14
copyright: © 2025 Zeng et al.
attribution name: Zeng et al.

Feeding ecology and trophic interactions of the narrow-barred Spanish Mackerel (Scomberomorus commerson) in the Central Taiwan Strait
type: item
type: AcademicArticle
description: Understanding the foraging ecology of marine predators is essential for ecosystem-based fisheries management. This study examined the diet of the narrow-barred Spanish mackerel (Scomberomorus commerson) in the Central Taiwan Strait using stomach content and stable isotope analyses integrated with an isotopic mixing model. A total of 1,733 specimens were collected between January 2017 and March 2022. Stomach content analysis revealed that 79.8% had empty stomachs, while the remainder mainly contained semi-digested fish remains. Among identifiable prey, composition varied by size and season. Sardinella lemuru, Decapterus spp., and Trichiurus spp. dominated the diet of smaller individuals, while larger fish primarily consumed Decapterus spp. and Mene maculata. Sardinella lemuru and Trichiurus spp. were more abundant in summer and autumn–winter, respectively. In the meanwhile, Decapterus spp. remained important year-round. Isotopic analysis further revealed that Sardinella lemuru, Etrumeus micropus, Decapterus macarellus and Penaeidae (Metapenaeopsis barbata) were dominant prey in smaller size classes, while Encrasicholina punctifer, D. macarellus, Evynnis cardinalis, Trichiurus spp. and Uroteuthis spp. were prevalent in intermediate and larger individuals. The estimated trophic position (3.8–4.3; mean = 4.0) confirms that S. commerson functions as a top predator with opportunistic feeding behavior. These findings improve understanding of regional trophic dynamics and support sustainable fisheries management in the Central Taiwan Strait.
format: application/pdf
format: text/html
creator: Li Chi Cheng
creator: Jia Shin He
creator: Chi Chang Lai
creator: Yen Hung Lee
creator: Jinn Shing Weng
creator: Hsing Han Huang
creator: Yi Shu Wu
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.20350
publisher: PeerJ Inc.
rights: © 2025 Cheng et al.
abstract: Understanding the foraging ecology of marine predators is essential for ecosystem-based fisheries management. This study examined the diet of the narrow-barred Spanish mackerel (Scomberomorus commerson) in the Central Taiwan Strait using stomach content and stable isotope analyses integrated with an isotopic mixing model. A total of 1,733 specimens were collected between January 2017 and March 2022. Stomach content analysis revealed that 79.8% had empty stomachs, while the remainder mainly contained semi-digested fish remains. Among identifiable prey, composition varied by size and season. Sardinella lemuru, Decapterus spp., and Trichiurus spp. dominated the diet of smaller individuals, while larger fish primarily consumed Decapterus spp. and Mene maculata. Sardinella lemuru and Trichiurus spp. were more abundant in summer and autumn–winter, respectively. In the meanwhile, Decapterus spp. remained important year-round. Isotopic analysis further revealed that Sardinella lemuru, Etrumeus micropus, Decapterus macarellus and Penaeidae (Metapenaeopsis barbata) were dominant prey in smaller size classes, while Encrasicholina punctifer, D. macarellus, Evynnis cardinalis, Trichiurus spp. and Uroteuthis spp. were prevalent in intermediate and larger individuals. The estimated trophic position (3.8–4.3; mean = 4.0) confirms that S. commerson functions as a top predator with opportunistic feeding behavior. These findings improve understanding of regional trophic dynamics and support sustainable fisheries management in the Central Taiwan Strait.
bibliographic citation: Cheng et al. (2025) Feeding ecology and trophic interactions of the narrow-barred Spanish Mackerel (Scomberomorus commerson) in the Central Taiwan Strait. PeerJ 13:e20350 https://doi.org/10.7717/peerj.20350
date submitted: 2025-05-07
date accepted: 2025-10-15
issued: 2025-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Li Chi
author list: Agent
  family name: He
  given name: Jia Shin
author list: Agent
  family name: Lai
  given name: Chi Chang
author list: Agent
  family name: Lee
  given name: Yen Hung
author list: Agent
  family name: Weng
  given name: Jinn Shing
author list: Agent
  family name: Huang
  given name: Hsing Han
author list: Agent
  family name: Wu
  given name: Yi Shu
doi: 10.7717/peerj.20350
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-14
copyright: © 2025 Cheng et al.
attribution name: Cheng et al.

Does reef crest zone selection influence Acropora palmata (Lamarck, 1816) fragment survival and growth?
type: item
type: AcademicArticle
description: In this study, we evaluated the effects of the crest zones on the survival and growth of Acropora palmata fragments in four sites differentially impacted by multiple natural and anthropogenic stressors. The crests are in the northwest (Playa Baracoa and Rincón de Guanabo) and the south-central region (El Peruano and Mariflores in Jardines de la Reina National Park) of Cuba. We established a field-based experiment with 50 fragments placed in each crest, 25 fragments in the back crest zone and 25 in the fore crest zone, parallel to the shoreline. The water flow intensity was estimated in both crest zones, using the dissolution of plaster discs as an indicator. The survival and growth of fragments were significantly influenced by site-specific and microhabitat conditions. The survival of the A. palmata fragments was high (survival probability: >0.6) in all four crests. Fragments placed in the fore crest zone (p = 0.02) exhibited higher survival than those in the back crest zone. The growth rates were slower (−1.5 to 7.3 cm year−1) than those previously recorded for wild A. palmata colonies and were negatively affected (estimate = −6.1; p = 0.004) in the fore crest zone. The dissolution of the plaster discs did not indicate a marked gradient of water flow between the crest zones, during April and June, but it was significantly higher (p = 0.03) in the fore crest zone in December at El Peruano and Mariflores crests, indicating temporal variations during the monitoring periods. The dissolution of plaster discs, as a proxy for water flow, did not have a significant effect on fragment survival between zones. However, when the dissolution was below approximately 68%, growth declined slightly; above this threshold, growth increased, possibly by higher inferred water flow. At higher levels of water flow (dissolution of the plaster discs), the positive effect of temperature on growth was attenuated (p = 0.007), suggesting that under strong water flow heat may be dissipated. The…
format: application/pdf
format: text/html
creator: Amanda Ramos Romero
creator: Patricia González-Díaz
creator: Gabriela Aguilera Pérez
creator: Anastazia T. Banaszak
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.20303
publisher: PeerJ Inc.
rights: © 2025 Ramos Romero et al.
abstract: In this study, we evaluated the effects of the crest zones on the survival and growth of Acropora palmata fragments in four sites differentially impacted by multiple natural and anthropogenic stressors. The crests are in the northwest (Playa Baracoa and Rincón de Guanabo) and the south-central region (El Peruano and Mariflores in Jardines de la Reina National Park) of Cuba. We established a field-based experiment with 50 fragments placed in each crest, 25 fragments in the back crest zone and 25 in the fore crest zone, parallel to the shoreline. The water flow intensity was estimated in both crest zones, using the dissolution of plaster discs as an indicator. The survival and growth of fragments were significantly influenced by site-specific and microhabitat conditions. The survival of the A. palmata fragments was high (survival probability: >0.6) in all four crests. Fragments placed in the fore crest zone (p = 0.02) exhibited higher survival than those in the back crest zone. The growth rates were slower (−1.5 to 7.3 cm year−1) than those previously recorded for wild A. palmata colonies and were negatively affected (estimate = −6.1; p = 0.004) in the fore crest zone. The dissolution of the plaster discs did not indicate a marked gradient of water flow between the crest zones, during April and June, but it was significantly higher (p = 0.03) in the fore crest zone in December at El Peruano and Mariflores crests, indicating temporal variations during the monitoring periods. The dissolution of plaster discs, as a proxy for water flow, did not have a significant effect on fragment survival between zones. However, when the dissolution was below approximately 68%, growth declined slightly; above this threshold, growth increased, possibly by higher inferred water flow. At higher levels of water flow (dissolution of the plaster discs), the positive effect of temperature on growth was attenuated (p = 0.007), suggesting that under strong water flow heat may be dissipated. The…
bibliographic citation: Ramos Romero et al. (2025) Does reef crest zone selection influence Acropora palmata (Lamarck, 1816) fragment survival and growth?. PeerJ 13:e20303 https://doi.org/10.7717/peerj.20303
date submitted: 2025-04-07
date accepted: 2025-10-07
issued: 2025-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramos Romero
  given name: Amanda
author list: Agent
  family name: González-Díaz
  given name: Patricia
author list: Agent
  family name: Aguilera Pérez
  given name: Gabriela
author list: Agent
  family name: Banaszak
  given name: Anastazia T.
doi: 10.7717/peerj.20303
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-14
copyright: ©2025 Ramos Romero et al.
attribution name: Ramos Romero et al.

Status and trends of giant clam populations demonstrate the effectiveness of village-based protection in American Sāmoa
type: item
type: AcademicArticle
description: Giant clams (subfamily Tridacninae) serve diverse ecological functions in coral reef ecosystems but have experienced severe populatiaon declines across much of their native ranges. Continued overharvesting, habitat degradation, and climate change impacts reinforce the need for updated population assessments and have prompted consideration for endangered species status. Here, we report a territory-wide evaluation of giant clam populations in American Sāmoa, integrating historical data (1994/95, 2002, and 2018) with new surveys conducted from 2022 to 2024 to assess the population status of these ecologically important bivalves. Using belt transects (50 m × 2 m at 10 m depth), we examined clam densities, size-class distributions, species composition, and population trends across six islands—Tutuila, Aunuʻu, Ofu, Olosega, Taʻū, and Muliāva. This study added 264 transects to the historical dataset and showed population densities of giant clams varied among islands but have remained relatively consistent over time. Using univariate and factorial ANOVAs of giant clam abundance and size data, we assessed spatial and temporal variation across American Sāmoa, and our analyses tested for effects of island, year, protection status, and their interactions. The lowest recent clam densities (83.5 individuals per hectare in 2022) were observed on the main island of Tutuila, where 98% of residents live. Mean clam density on Tutuila has increased from 14.1/ha in 1994/95, but the island has considerable variation amongst locations. Remote islands, such as Taʻū and Muliāva, showed higher densities, up to 812 and 1,166/ha, respectively. Most (96.7%) of giant clams found on transects were identified as Tridacna maxima, with infrequent occurrences of the cryptic species T. squamosa and T. noae, primarily within specific, village-managed protected areas. On Tutuila, surveys sites included a variety of jurisdictions and levels of management, with village protected areas and remote sites sup…
format: application/pdf
format: text/html
creator: Paolo Marra-Biggs
creator: Eric K. Brown
creator: Domingo Galgo Ochavillo
creator: Alison L. Green
creator: Alice Lawrence
creator: Carlos Tramonte
creator: Valentine Vaeoso
creator: Ian Moffitt
creator: Kersten Schnurle
creator: Nury Molina
creator: Robert J. Toonen
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
subject: Science Policy
description: doi:10.7717/peerj.20290
publisher: PeerJ Inc.
rights: © 2025 Marra-Biggs et al.
abstract: Giant clams (subfamily Tridacninae) serve diverse ecological functions in coral reef ecosystems but have experienced severe populatiaon declines across much of their native ranges. Continued overharvesting, habitat degradation, and climate change impacts reinforce the need for updated population assessments and have prompted consideration for endangered species status. Here, we report a territory-wide evaluation of giant clam populations in American Sāmoa, integrating historical data (1994/95, 2002, and 2018) with new surveys conducted from 2022 to 2024 to assess the population status of these ecologically important bivalves. Using belt transects (50 m × 2 m at 10 m depth), we examined clam densities, size-class distributions, species composition, and population trends across six islands—Tutuila, Aunuʻu, Ofu, Olosega, Taʻū, and Muliāva. This study added 264 transects to the historical dataset and showed population densities of giant clams varied among islands but have remained relatively consistent over time. Using univariate and factorial ANOVAs of giant clam abundance and size data, we assessed spatial and temporal variation across American Sāmoa, and our analyses tested for effects of island, year, protection status, and their interactions. The lowest recent clam densities (83.5 individuals per hectare in 2022) were observed on the main island of Tutuila, where 98% of residents live. Mean clam density on Tutuila has increased from 14.1/ha in 1994/95, but the island has considerable variation amongst locations. Remote islands, such as Taʻū and Muliāva, showed higher densities, up to 812 and 1,166/ha, respectively. Most (96.7%) of giant clams found on transects were identified as Tridacna maxima, with infrequent occurrences of the cryptic species T. squamosa and T. noae, primarily within specific, village-managed protected areas. On Tutuila, surveys sites included a variety of jurisdictions and levels of management, with village protected areas and remote sites sup…
bibliographic citation: Marra-Biggs et al. (2025) Status and trends of giant clam populations demonstrate the effectiveness of village-based protection in American Sāmoa. PeerJ 13:e20290 https://doi.org/10.7717/peerj.20290
date submitted: 2025-05-19
date accepted: 2025-10-03
issued: 2025-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marra-Biggs
  given name: Paolo
author list: Agent
  family name: Brown
  given name: Eric K.
author list: Agent
  family name: Ochavillo
  given name: Domingo Galgo
author list: Agent
  family name: Green
  given name: Alison L.
author list: Agent
  family name: Lawrence
  given name: Alice
author list: Agent
  family name: Tramonte
  given name: Carlos
author list: Agent
  family name: Vaeoso
  given name: Valentine
author list: Agent
  family name: Moffitt
  given name: Ian
author list: Agent
  family name: Schnurle
  given name: Kersten
author list: Agent
  family name: Molina
  given name: Nury
author list: Agent
  family name: Toonen
  given name: Robert J.
doi: 10.7717/peerj.20290
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-14
copyright: ©2025 Marra-Biggs et al.
attribution name: Marra-Biggs et al.

Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu)
type: item
type: AcademicArticle
description: Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies on multiple lines of evidence, including phylogenetic trees and metrics like the percentage of conserved proteins (POCP). POCP is widely used, but requires benchmarking in terms of both, computation and accuracy. We used 2,358,466 pairwise comparisons of proteomes derived from 4,767 genomes across 35 families to systematically assess POCP calculation and percentage of conserved proteins with unique matches (POCPu) which considers unique matches only. Both methods are 20x faster than the reference BLASTP when using the very-sensitive setting of DIAMOND. However, POCPu differentiates better within-genus from between-genera values, which improves bacterial genus assignment. This work facilitates comparative analysis of an increasingly larger number of genomes, providing a reliable metric to support genus delineation. The findings suggest that specific POCPu thresholds deviating from the reference 50% value are needed for certain families.
format: application/pdf
format: text/html
creator: Charlie Pauvert
creator: Thomas C.A. Hitch
creator: Thomas Clavel
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Taxonomy
subject: Data Science
description: doi:10.7717/peerj.20259
publisher: PeerJ Inc.
rights: © 2025 Pauvert et al.
abstract: Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies on multiple lines of evidence, including phylogenetic trees and metrics like the percentage of conserved proteins (POCP). POCP is widely used, but requires benchmarking in terms of both, computation and accuracy. We used 2,358,466 pairwise comparisons of proteomes derived from 4,767 genomes across 35 families to systematically assess POCP calculation and percentage of conserved proteins with unique matches (POCPu) which considers unique matches only. Both methods are 20x faster than the reference BLASTP when using the very-sensitive setting of DIAMOND. However, POCPu differentiates better within-genus from between-genera values, which improves bacterial genus assignment. This work facilitates comparative analysis of an increasingly larger number of genomes, providing a reliable metric to support genus delineation. The findings suggest that specific POCPu thresholds deviating from the reference 50% value are needed for certain families.
bibliographic citation: Pauvert et al. (2025) Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu). PeerJ 13:e20259 https://doi.org/10.7717/peerj.20259
date submitted: 2025-08-04
date accepted: 2025-09-29
issued: 2025-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pauvert
  given name: Charlie
author list: Agent
  family name: Hitch
  given name: Thomas C.A.
author list: Agent
  family name: Clavel
  given name: Thomas
doi: 10.7717/peerj.20259
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-14
copyright: ©2025 Pauvert et al.
attribution name: Pauvert et al.

Comparison of quadriceps and hamstring muscle size and strength between young athletes following knee surgery and healthy controls
type: item
type: AcademicArticle
description: Objectives This study compared the size and strength of the quadriceps and hamstring muscles in young athletes who had undergone previous knee surgery (POST) to sex- and age- matched, healthy controls (SAM). Methods A total of 18 (nine POST and nine SAM) participants volunteered to participate in the study’s procedures. Of the nine POST participants, six had underwent anterior cruciate ligament reconstruction, two underwent medial patellofemoral ligament reconstruction and one had undergone patellar tendon repair. Maximal voluntary isometric contractions assessed absolute strength (MVICABS) of the quadriceps and hamstrings. Muscle size was quantified as muscle cross-sectional area (mCSA) from panoramic ultrasound images. Relative strength (MVICREL) was calculated as a ratio of strength to muscle size. Separate 2-way mixed-factorial analyses of variance leg (operative or non-dominant (O-ND) vs. non-operative or dominant (NO-D)) and group (POST vs. SAM) assessed statistical differences at p ≤ 0.05. Results There were no significant two-way interactions (p-range: 0.142–0.74) for any variables. Further, there were no significant main effects for the quadriceps (p-range: 0.127–0.605) nor was there a main effect for leg in any hamstrings variables (p-range: 0.126–0.367). However, the POST group had greater MVICABS and MVICREL than SAM for the hamstrings by 69.8 ± 30.7 N (p = 0.037) and 2.21 ± 1.02 N cm−2 (p = 0.045). Conclusions These findings indicate that there was no difference in quadriceps muscle strength or size between the POST and SAM groups. However, the POST group had greater hamstrings strength than SAM yet no differences in muscle size. These results suggest that the rehabilitation program may have been effective in restoring quadriceps function and enhancing hamstrings strength in young athletes following knee surgery. However, future studies should continue to elucidate the physiological effects of knee surgeries in larger, more diverse samples to attenuate …
format: application/pdf
format: text/html
creator: Christopher J. Cleary
creator: Isaiah G. Roepe
creator: Christopher D. Bernard
creator: Traci Smiley
creator: John K. Veazey
creator: Kyle A. Martin
creator: Megan Bechtold
creator: Bryan G. Vopat
creator: Ashley A. Herda
subject: Kinesiology
subject: Orthopedics
subject: Sports Injury
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.20330
publisher: PeerJ Inc.
rights: © 2025 Cleary et al.
abstract: Objectives This study compared the size and strength of the quadriceps and hamstring muscles in young athletes who had undergone previous knee surgery (POST) to sex- and age- matched, healthy controls (SAM). Methods A total of 18 (nine POST and nine SAM) participants volunteered to participate in the study’s procedures. Of the nine POST participants, six had underwent anterior cruciate ligament reconstruction, two underwent medial patellofemoral ligament reconstruction and one had undergone patellar tendon repair. Maximal voluntary isometric contractions assessed absolute strength (MVICABS) of the quadriceps and hamstrings. Muscle size was quantified as muscle cross-sectional area (mCSA) from panoramic ultrasound images. Relative strength (MVICREL) was calculated as a ratio of strength to muscle size. Separate 2-way mixed-factorial analyses of variance leg (operative or non-dominant (O-ND) vs. non-operative or dominant (NO-D)) and group (POST vs. SAM) assessed statistical differences at p ≤ 0.05. Results There were no significant two-way interactions (p-range: 0.142–0.74) for any variables. Further, there were no significant main effects for the quadriceps (p-range: 0.127–0.605) nor was there a main effect for leg in any hamstrings variables (p-range: 0.126–0.367). However, the POST group had greater MVICABS and MVICREL than SAM for the hamstrings by 69.8 ± 30.7 N (p = 0.037) and 2.21 ± 1.02 N cm−2 (p = 0.045). Conclusions These findings indicate that there was no difference in quadriceps muscle strength or size between the POST and SAM groups. However, the POST group had greater hamstrings strength than SAM yet no differences in muscle size. These results suggest that the rehabilitation program may have been effective in restoring quadriceps function and enhancing hamstrings strength in young athletes following knee surgery. However, future studies should continue to elucidate the physiological effects of knee surgeries in larger, more diverse samples to attenuate …
bibliographic citation: Cleary et al. (2025) Comparison of quadriceps and hamstring muscle size and strength between young athletes following knee surgery and healthy controls. PeerJ 13:e20330 https://doi.org/10.7717/peerj.20330
date submitted: 2025-04-17
date accepted: 2025-10-13
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cleary
  given name: Christopher J.
author list: Agent
  family name: Roepe
  given name: Isaiah G.
author list: Agent
  family name: Bernard
  given name: Christopher D.
author list: Agent
  family name: Smiley
  given name: Traci
author list: Agent
  family name: Veazey
  given name: John K.
author list: Agent
  family name: Martin
  given name: Kyle A.
author list: Agent
  family name: Bechtold
  given name: Megan
author list: Agent
  family name: Vopat
  given name: Bryan G.
author list: Agent
  family name: Herda
  given name: Ashley A.
doi: 10.7717/peerj.20330
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 Cleary et al.
attribution name: Cleary et al.

Prevalence of poor sleep quality and its associated factors in patients with concurrent type 2 diabetes mellitus and hypertension
type: item
type: AcademicArticle
description: Background The coexistence of type 2 diabetes mellitus (T2DM) and hypertension can impair sleep quality, potentially leading to a wide range of adverse health outcomes. Therefore, this study aimed to evaluate sleep quality and its associated factors in patients with concurrent T2DM and hypertension in Hunan, China. Methods This cross-sectional study recruited patients with concurrent T2DM and hypertension who visited the Department of Endocrinology at the First People’s Hospital of Ruanjiang City, Hunan Province, China, between July 2022 and February 2023. Trained investigators conducted face-to-face interviews to collect data on sociodemographic, lifestyle, and disease-related factors, and assessed anxiety and sleep quality using the Generalized Anxiety Disorder-7 scale and the Pittsburgh Sleep Quality Index, respectively. Multivariable logistic regression analysis was performed to identify factors independently associated with sleep quality. A receiver operating characteristic (ROC) curve was generated to evaluate the predictive ability of the model, and the Hosmer–Lemeshow test was used to assess model calibration. Subgroup analyses were conducted by sex, educational level, and number of T2DM complications to test model robustness. Results A total of 475 patients with concurrent T2DM and hypertension were included. The prevalence of poor sleep quality was 59.4% (95% confidence interval (CI) [54.9%–63.9%]). Multivariable logistic regression analysis showed that advanced age (adjusted odds ratio (aOR) = 2.12, 95% CI [1.29–3.48]), history of stroke (aOR = 2.16, 95% CI [1.15–4.06]), and anxiety (aOR = 4.24, 95% CI [2.58–6.98]) were associated with higher odds of poor sleep quality. Regular physical activity was associated with lower odds (aOR = 0.53, 95% CI [0.34–0.84]). The area under the receiver operating characteristic (ROC) curve was 0.776 (95% CI [0.735–0.818]), and the Hosmer–Lemeshow test (P = 0.260) indicated good model calibration. Subgroup analyses yielded…
format: application/pdf
format: text/html
creator: Ziling Feng
creator: Hongying Liu
creator: Ni Xiong
creator: Leyao Tang
creator: Wenjie Dai
creator: Fang Yang
subject: Anthropology
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.20325
publisher: PeerJ Inc.
rights: © 2025 Feng et al.
abstract: Background The coexistence of type 2 diabetes mellitus (T2DM) and hypertension can impair sleep quality, potentially leading to a wide range of adverse health outcomes. Therefore, this study aimed to evaluate sleep quality and its associated factors in patients with concurrent T2DM and hypertension in Hunan, China. Methods This cross-sectional study recruited patients with concurrent T2DM and hypertension who visited the Department of Endocrinology at the First People’s Hospital of Ruanjiang City, Hunan Province, China, between July 2022 and February 2023. Trained investigators conducted face-to-face interviews to collect data on sociodemographic, lifestyle, and disease-related factors, and assessed anxiety and sleep quality using the Generalized Anxiety Disorder-7 scale and the Pittsburgh Sleep Quality Index, respectively. Multivariable logistic regression analysis was performed to identify factors independently associated with sleep quality. A receiver operating characteristic (ROC) curve was generated to evaluate the predictive ability of the model, and the Hosmer–Lemeshow test was used to assess model calibration. Subgroup analyses were conducted by sex, educational level, and number of T2DM complications to test model robustness. Results A total of 475 patients with concurrent T2DM and hypertension were included. The prevalence of poor sleep quality was 59.4% (95% confidence interval (CI) [54.9%–63.9%]). Multivariable logistic regression analysis showed that advanced age (adjusted odds ratio (aOR) = 2.12, 95% CI [1.29–3.48]), history of stroke (aOR = 2.16, 95% CI [1.15–4.06]), and anxiety (aOR = 4.24, 95% CI [2.58–6.98]) were associated with higher odds of poor sleep quality. Regular physical activity was associated with lower odds (aOR = 0.53, 95% CI [0.34–0.84]). The area under the receiver operating characteristic (ROC) curve was 0.776 (95% CI [0.735–0.818]), and the Hosmer–Lemeshow test (P = 0.260) indicated good model calibration. Subgroup analyses yielded…
bibliographic citation: Feng et al. (2025) Prevalence of poor sleep quality and its associated factors in patients with concurrent type 2 diabetes mellitus and hypertension. PeerJ 13:e20325 https://doi.org/10.7717/peerj.20325
date submitted: 2025-05-16
date accepted: 2025-10-13
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Ziling
author list: Agent
  family name: Liu
  given name: Hongying
author list: Agent
  family name: Xiong
  given name: Ni
author list: Agent
  family name: Tang
  given name: Leyao
author list: Agent
  family name: Dai
  given name: Wenjie
author list: Agent
  family name: Yang
  given name: Fang
doi: 10.7717/peerj.20325
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 Feng et al.
attribution name: Feng et al.

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