PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Habitat sharing and interspecies interactions in caves used by bats in the Republic of Congo
items: Role of polyethylene glycol to alleviate lead stress in Raphanus sativus
items: A morpho-histological analysis of the exoskeleton of Clathrozoella medeae (Cnidaria, Hydrozoa) reveals insights into the taxonomy of Clathrozoellidae and Hydroidolina
items: The feasibility of virtual reality therapy for upper extremity mobilization during and after intensive care unit admission
items: Identification of crucial extracellular genes as potential biomarkers in newly diagnosed Type 1 diabetes via integrated bioinformatics analysis
items: Efficacy of root canal treatment for autotransplanted third molars: a 6-Year cohort study of 167 teeth in southern China
items: Genetic analysis of Pinna rudis L 1758 (Mollusca, Bivalvia, Pinnidae) in the Northwest Cabo Verde Islands (Central-East Atlantic)
items: Niche-related processes explain phylogenetic structure of acoustic bird communities in Mexico
items: The impact of a disaster medicine clinical training program on medical students’ disaster literacy
items: Clinical characteristics of pathogens in children with community-acquired pneumonia were analyzed via targeted next-generation sequencing detection

Habitat sharing and interspecies interactions in caves used by bats in the Republic of Congo
type: item
type: AcademicArticle
description: Bats play key roles in ecosystem functions and provide services to human populations. There is a need to protect bat populations and to mitigate the risks associated with pathogen spillover. Caves are key habitats for many bat species, which use them as roosting and breeding sites. Caves, bats and their guano also attract many other animals along trophic chains which might favor direct or indirect interspecies interactions. Two caves hosting colonies of insectivorous bats have been investigated in the Republic of Congo to characterize habitat sharing and interactions between bats, humans and animals. We set up a camera-trap monitoring protocol during 19 months at the entrance of and inside each cave. Our results demonstrated the richness and complexity of the species interactions around and within these caves. We identified and/or quantified mainly rodents, but also numerous categories of animals such as insects, birds, reptiles and carnivores using the caves. We investigated the temporal variation in the use of caves and the potential interactions between humans, wild animals and bat colonies. Our study contributes to the understanding of the interface and interactions, for the first time quantified, between cave-dwelling animal species, including humans. This knowledge is important to promote the conservation of cave ecosystems and better understand the ecology of infectious diseases.
format: application/pdf
format: text/html
creator: Morgane Labadie
creator: Serge Morand
creator: Mathieu Bourgarel
creator: Fabien Roch Niama
creator: Guytrich Franel Nguilili
creator: N’Kaya Tobi
creator: Alexandre Caron
creator: Helene De Nys
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.18145
publisher: PeerJ Inc.
rights: © 2025 Labadie et al.
abstract: Bats play key roles in ecosystem functions and provide services to human populations. There is a need to protect bat populations and to mitigate the risks associated with pathogen spillover. Caves are key habitats for many bat species, which use them as roosting and breeding sites. Caves, bats and their guano also attract many other animals along trophic chains which might favor direct or indirect interspecies interactions. Two caves hosting colonies of insectivorous bats have been investigated in the Republic of Congo to characterize habitat sharing and interactions between bats, humans and animals. We set up a camera-trap monitoring protocol during 19 months at the entrance of and inside each cave. Our results demonstrated the richness and complexity of the species interactions around and within these caves. We identified and/or quantified mainly rodents, but also numerous categories of animals such as insects, birds, reptiles and carnivores using the caves. We investigated the temporal variation in the use of caves and the potential interactions between humans, wild animals and bat colonies. Our study contributes to the understanding of the interface and interactions, for the first time quantified, between cave-dwelling animal species, including humans. This knowledge is important to promote the conservation of cave ecosystems and better understand the ecology of infectious diseases.
bibliographic citation: Labadie et al. (2025) Habitat sharing and interspecies interactions in caves used by bats in the Republic of Congo. PeerJ 13:e18145 https://doi.org/10.7717/peerj.18145
date submitted: 2024-01-17
date accepted: 2024-08-30
issued: 2025-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Labadie
  given name: Morgane
author list: Agent
  family name: Morand
  given name: Serge
author list: Agent
  family name: Bourgarel
  given name: Mathieu
author list: Agent
  family name: Niama
  given name: Fabien Roch
author list: Agent
  family name: Nguilili
  given name: Guytrich Franel
author list: Agent
  family name: Tobi
  given name: N’Kaya
author list: Agent
  family name: Caron
  given name: Alexandre
author list: Agent
  family name: De Nys
  given name: Helene
doi: 10.7717/peerj.18145
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-09
copyright: © 2025 Labadie et al.
attribution name: Labadie et al.

Role of polyethylene glycol to alleviate lead stress in Raphanus sativus
type: item
type: AcademicArticle
description: The continuous contamination of heavy metals (HMs) in our ecosystem due to industrialization, urbanization and other anthropogenic activities has become a serious environmental constraint to successful crop production. Lead (Pb) toxicity causes ionic, oxidative and osmotic injuries which induce various morphological, physiological, metabolic and molecular abnormalities in plants. Polyethylene glycol (PEG) is widely used to elucidate drought stress induction and alleviation mechanisms in treated plants. Some recent studies have unveiled the potential of PEG in regulating plant growth and developmental procedures including seed germination, root and shoot growth and alleviating the detrimental impacts of abiotic stresses in plants. Therefore, the current study aimed to assess the effects of seed priming with various concentrations (10%, 20%, 30% and 40%) of PEG on the growth and development of radish plants growing under Pb stress (75 mg/kg soil). Lead toxicity reduced root growth (32.89%), shoot growth (32.81%), total chlorophyll (56.25%) and protein content (58.66%) in treated plants. Similarly, plants showed reduced biomass production of root (35.48%) and shoot (31.25%) under Pb stress, while 30% PEG seed priming enhanced biomass production of root (28.57%) and shoot (35.29%) under Pb contaminated regimes. On the other hand, seedlings obtained from 30% PEG priming demonstrated a notable augmentation in the concentrations of photosynthetic pigments, antioxidative activity and biomass accumulation of the plants. PEG-treated plants showed modulations in the enzymatic activities of peroxidase (PO), catalase (CAT) and superoxide dismutase (SOD). These changes collectively played a role in mitigating the adverse effects of Pb on plant physiology. Our data revealed that PEG interceded stress extenuation encompasses numerous regulatory mechanisms including scavenging of ROS through antioxidant and non-antioxidants, improved photosynthetic activity and appropriate nutrition…
format: application/pdf
format: text/html
creator: Muhammad Sajid
creator: Shakil Ahmed
creator: Rehana Sardar
creator: Aamir Ali
creator: Nasim Ahmad Yasin
subject: Agricultural Science
subject: Plant Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.18147
publisher: PeerJ Inc.
rights: © 2025 Sajid et al.
abstract: The continuous contamination of heavy metals (HMs) in our ecosystem due to industrialization, urbanization and other anthropogenic activities has become a serious environmental constraint to successful crop production. Lead (Pb) toxicity causes ionic, oxidative and osmotic injuries which induce various morphological, physiological, metabolic and molecular abnormalities in plants. Polyethylene glycol (PEG) is widely used to elucidate drought stress induction and alleviation mechanisms in treated plants. Some recent studies have unveiled the potential of PEG in regulating plant growth and developmental procedures including seed germination, root and shoot growth and alleviating the detrimental impacts of abiotic stresses in plants. Therefore, the current study aimed to assess the effects of seed priming with various concentrations (10%, 20%, 30% and 40%) of PEG on the growth and development of radish plants growing under Pb stress (75 mg/kg soil). Lead toxicity reduced root growth (32.89%), shoot growth (32.81%), total chlorophyll (56.25%) and protein content (58.66%) in treated plants. Similarly, plants showed reduced biomass production of root (35.48%) and shoot (31.25%) under Pb stress, while 30% PEG seed priming enhanced biomass production of root (28.57%) and shoot (35.29%) under Pb contaminated regimes. On the other hand, seedlings obtained from 30% PEG priming demonstrated a notable augmentation in the concentrations of photosynthetic pigments, antioxidative activity and biomass accumulation of the plants. PEG-treated plants showed modulations in the enzymatic activities of peroxidase (PO), catalase (CAT) and superoxide dismutase (SOD). These changes collectively played a role in mitigating the adverse effects of Pb on plant physiology. Our data revealed that PEG interceded stress extenuation encompasses numerous regulatory mechanisms including scavenging of ROS through antioxidant and non-antioxidants, improved photosynthetic activity and appropriate nutrition…
bibliographic citation: Sajid et al. (2025) Role of polyethylene glycol to alleviate lead stress in Raphanus sativus. PeerJ 13:e18147 https://doi.org/10.7717/peerj.18147
date submitted: 2024-07-01
date accepted: 2024-08-30
issued: 2025-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sajid
  given name: Muhammad
author list: Agent
  family name: Ahmed
  given name: Shakil
author list: Agent
  family name: Sardar
  given name: Rehana
author list: Agent
  family name: Ali
  given name: Aamir
author list: Agent
  family name: Yasin
  given name: Nasim Ahmad
doi: 10.7717/peerj.18147
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-09
copyright: ©2025 Sajid et al.
attribution name: Sajid et al.

A morpho-histological analysis of the exoskeleton of Clathrozoella medeae (Cnidaria, Hydrozoa) reveals insights into the taxonomy of Clathrozoellidae and Hydroidolina
type: item
type: AcademicArticle
description: The taxonomic complexity of the families Clathrozoidae and Clathrozoellidae, rooted in early 20th-century hydroid descriptions, highlights the need for comprehensive and detailed morphological analyses. This study aimed to elucidate the histology of the polypoid stage of Clathrozoella medeae Peña Cantero, Vervoort & Watson, 2003, with a particular emphasis on its exoskeletal structure. Specimens from the National Museum of Natural History were examined histologically using different staining techniques. The results revealed a three-layered mesoglea, diverse gland cells, and an exoskeleton comprising chitin and structural proteins, with notable differences from other anthoathecate hydroids. These results have significant implications for the taxonomy and evolutionary relationships of Clathrozoellidae and Hydroidolina, as they highlight the importance of detailed histological data in understanding the unique exoskeletal architecture of C. medeae, termed “exoskeleton tube”, which distinguishes it from other hydroids, and provide critical insights into the homology and phylogenetic position of Clathrozoellidae.
format: application/pdf
format: text/html
creator: María A. Mendoza-Becerril
creator: Antonio C. Marques
subject: Marine Biology
subject: Taxonomy
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.18407
publisher: PeerJ Inc.
rights: © 2025 Mendoza-Becerril and Marques
abstract: The taxonomic complexity of the families Clathrozoidae and Clathrozoellidae, rooted in early 20th-century hydroid descriptions, highlights the need for comprehensive and detailed morphological analyses. This study aimed to elucidate the histology of the polypoid stage of Clathrozoella medeae Peña Cantero, Vervoort & Watson, 2003, with a particular emphasis on its exoskeletal structure. Specimens from the National Museum of Natural History were examined histologically using different staining techniques. The results revealed a three-layered mesoglea, diverse gland cells, and an exoskeleton comprising chitin and structural proteins, with notable differences from other anthoathecate hydroids. These results have significant implications for the taxonomy and evolutionary relationships of Clathrozoellidae and Hydroidolina, as they highlight the importance of detailed histological data in understanding the unique exoskeletal architecture of C. medeae, termed “exoskeleton tube”, which distinguishes it from other hydroids, and provide critical insights into the homology and phylogenetic position of Clathrozoellidae.
bibliographic citation: Mendoza-Becerril et al. (2025) A morpho-histological analysis of the exoskeleton of Clathrozoella medeae (Cnidaria, Hydrozoa) reveals insights into the taxonomy of Clathrozoellidae and Hydroidolina. PeerJ 13:e18407 https://doi.org/10.7717/peerj.18407
date submitted: 2024-08-30
date accepted: 2024-10-05
issued: 2025-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mendoza-Becerril
  given name: María A.
author list: Agent
  family name: Marques
  given name: Antonio C.
doi: 10.7717/peerj.18407
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-09
copyright: ©2025 Mendoza-Becerril and Marques
attribution name: Mendoza-Becerril and Marques

The feasibility of virtual reality therapy for upper extremity mobilization during and after intensive care unit admission
type: item
type: AcademicArticle
description: Introduction Early mobilization reduces long-term muscle weakness after intensive care unit (ICU) admission, but barriers (e.g., anxiety, lack of motivation) may complicate patients’ adherence to exercise. Virtual reality (VR) presents immersive stimuli, which may increase motivation and adherence. This study aimed to examine the feasibility of VR-therapy using a VR-headset during ICU- and subsequent general ward admission. Furthermore, physical parameters before and after training were explored. Materials & Methods Ten adult ICU-patients with a median age of 71 [63–79], 70% of male registered birth sex, mechanically ventilated for ≥48 h, and willing to participate, were included. VR-therapy was offered three times a week for 20 minutes in addition to standard care. To train upper extremity functionality, patients were instructed to complete puzzles with increasing level of difficulty. Feasibility was based on patient satisfaction, session efficiency, and adherence levels during the training. Fatigue was measured after each session using the Borg Rating of Perceived Exertion Scale. Patients’ hand-grip strength and Morton Mobility Index (MMI) were evaluated at the start of VR-therapy and after four weeks of training or at hospital discharge. Results On average, patients followed three VR-therapy sessions of 20 min per week with 13 min of actual training time, over the course of 1 to 3 weeks depending on their length of stay. Session efficiency ranged from 25% to 93%. In total, patients adhered to 60% of the VR-therapy sessions. MMI scores increased significantly from the start (26 [24–44]) to the end of the VR-therapy training period (57 [41–85], p = 0.005), indicating improved balance and mobility. Conclusion VR-therapy for upper extremity rehabilitation in ICU-patients is feasible during stay in the ICU and general ward.
format: application/pdf
format: text/html
creator: Mirthe de Vries
creator: Lise F.E. Beumeler
creator: Johan van der Meulen
creator: Carina Bethlehem
creator: Rob den Otter
creator: E. Christiaan Boerma
subject: Drugs and Devices
subject: Emergency and Critical Care
subject: Healthcare Services
subject: Rehabilitation
description: doi:10.7717/peerj.18461
publisher: PeerJ Inc.
rights: © 2025 de Vries et al.
abstract: Introduction Early mobilization reduces long-term muscle weakness after intensive care unit (ICU) admission, but barriers (e.g., anxiety, lack of motivation) may complicate patients’ adherence to exercise. Virtual reality (VR) presents immersive stimuli, which may increase motivation and adherence. This study aimed to examine the feasibility of VR-therapy using a VR-headset during ICU- and subsequent general ward admission. Furthermore, physical parameters before and after training were explored. Materials & Methods Ten adult ICU-patients with a median age of 71 [63–79], 70% of male registered birth sex, mechanically ventilated for ≥48 h, and willing to participate, were included. VR-therapy was offered three times a week for 20 minutes in addition to standard care. To train upper extremity functionality, patients were instructed to complete puzzles with increasing level of difficulty. Feasibility was based on patient satisfaction, session efficiency, and adherence levels during the training. Fatigue was measured after each session using the Borg Rating of Perceived Exertion Scale. Patients’ hand-grip strength and Morton Mobility Index (MMI) were evaluated at the start of VR-therapy and after four weeks of training or at hospital discharge. Results On average, patients followed three VR-therapy sessions of 20 min per week with 13 min of actual training time, over the course of 1 to 3 weeks depending on their length of stay. Session efficiency ranged from 25% to 93%. In total, patients adhered to 60% of the VR-therapy sessions. MMI scores increased significantly from the start (26 [24–44]) to the end of the VR-therapy training period (57 [41–85], p = 0.005), indicating improved balance and mobility. Conclusion VR-therapy for upper extremity rehabilitation in ICU-patients is feasible during stay in the ICU and general ward.
bibliographic citation: de Vries et al. (2025) The feasibility of virtual reality therapy for upper extremity mobilization during and after intensive care unit admission. PeerJ 13:e18461 https://doi.org/10.7717/peerj.18461
date submitted: 2024-05-23
date accepted: 2024-10-14
issued: 2025-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Vries
  given name: Mirthe
author list: Agent
  family name: Beumeler
  given name: Lise F.E.
author list: Agent
  family name: van der Meulen
  given name: Johan
author list: Agent
  family name: Bethlehem
  given name: Carina
author list: Agent
  family name: den Otter
  given name: Rob
author list: Agent
  family name: Boerma
  given name: E. Christiaan
doi: 10.7717/peerj.18461
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-09
copyright: ©2025 de Vries et al.
attribution name: de Vries et al.

Identification of crucial extracellular genes as potential biomarkers in newly diagnosed Type 1 diabetes via integrated bioinformatics analysis
type: item
type: AcademicArticle
description: Purpose In this study, we aimed to study the role of extracellular proteins as biomarkers associated with newly diagnosed Type 1 diabetes (NT1D) diagnosis and prognosis. Patients and Methods We retrieved and analyzed the GSE55098 microarray dataset from the Gene Expression Omnibus (GEO) database. Using R software, we screened out the extracellular protein-differentially expressed genes (EP-DEGs) through several protein-related databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied to describe the role and function of these EP-DEGs. We used the STRING database to construct the interaction of proteins, Cytoscape software to visualize the protein-protein interaction (PPI) networks, and its plugin CytoHubba to identify the crucial genes between PPI networks. Finally, we used the comparative toxicogenomics database (CTD) to evaluate the connection between NT1D with the potential crucial genes and we validated our conclusions with another dataset (GSE33440) and some clinical samples. Results We identified 422 DEGs and 122 EP-DEGs from a dataset that includes (12) NT1D patients compared with (10) healthy people. Protein digestion and absorption, toll-like receptor signaling, and T cell receptor signaling were the most meaningful pathways defined by KEGG enrichment analyses. We recognized nine important extracellular genes: GZMB, CCL4, TNF, MMP9, CCL5, IFNG, CXCL1, GNLY, and LCN2. CTD analyses showed that LCN2, IFNG, and TNF had higher levels in NT1D and hypoglycemia; while TNF, IFNG and MMP9 increased in hyperglycemia. Further verification showed that LCN2, MMP9, TNF and IFNG were elevated in NT1D patients. Conclusion The nine identified key extracellular genes, particularly LCN2, IFNG, TNF, and MMP9, may be potential diagnostic biomarkers for NT1D. Our findings provide new insights into the molecular mechanisms and novel therapeutic targets of NT1D.
format: application/pdf
format: text/html
creator: Ming Gao
creator: Qing Liu
creator: Lingyu Zhang
creator: Fatema Tabak
creator: Yifei Hua
creator: Wei Shao
creator: Yangyang Li
creator: Li Qian
creator: Yu Liu
subject: Genomics
subject: Diabetes and Endocrinology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.18660
publisher: PeerJ Inc.
rights: © 2025 Gao et al.
abstract: Purpose In this study, we aimed to study the role of extracellular proteins as biomarkers associated with newly diagnosed Type 1 diabetes (NT1D) diagnosis and prognosis. Patients and Methods We retrieved and analyzed the GSE55098 microarray dataset from the Gene Expression Omnibus (GEO) database. Using R software, we screened out the extracellular protein-differentially expressed genes (EP-DEGs) through several protein-related databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied to describe the role and function of these EP-DEGs. We used the STRING database to construct the interaction of proteins, Cytoscape software to visualize the protein-protein interaction (PPI) networks, and its plugin CytoHubba to identify the crucial genes between PPI networks. Finally, we used the comparative toxicogenomics database (CTD) to evaluate the connection between NT1D with the potential crucial genes and we validated our conclusions with another dataset (GSE33440) and some clinical samples. Results We identified 422 DEGs and 122 EP-DEGs from a dataset that includes (12) NT1D patients compared with (10) healthy people. Protein digestion and absorption, toll-like receptor signaling, and T cell receptor signaling were the most meaningful pathways defined by KEGG enrichment analyses. We recognized nine important extracellular genes: GZMB, CCL4, TNF, MMP9, CCL5, IFNG, CXCL1, GNLY, and LCN2. CTD analyses showed that LCN2, IFNG, and TNF had higher levels in NT1D and hypoglycemia; while TNF, IFNG and MMP9 increased in hyperglycemia. Further verification showed that LCN2, MMP9, TNF and IFNG were elevated in NT1D patients. Conclusion The nine identified key extracellular genes, particularly LCN2, IFNG, TNF, and MMP9, may be potential diagnostic biomarkers for NT1D. Our findings provide new insights into the molecular mechanisms and novel therapeutic targets of NT1D.
bibliographic citation: Gao et al. (2025) Identification of crucial extracellular genes as potential biomarkers in newly diagnosed Type 1 diabetes via integrated bioinformatics analysis. PeerJ 13:e18660 https://doi.org/10.7717/peerj.18660
date submitted: 2024-07-30
date accepted: 2024-11-17
issued: 2025-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Gao
  given name: Ming
author list: Agent
  family name: Liu
  given name: Qing
author list: Agent
  family name: Zhang
  given name: Lingyu
author list: Agent
  family name: Tabak
  given name: Fatema
author list: Agent
  family name: Hua
  given name: Yifei
author list: Agent
  family name: Shao
  given name: Wei
author list: Agent
  family name: Li
  given name: Yangyang
author list: Agent
  family name: Qian
  given name: Li
author list: Agent
  family name: Liu
  given name: Yu
doi: 10.7717/peerj.18660
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-09
copyright: © 2025 Gao et al.
attribution name: Gao et al.

Efficacy of root canal treatment for autotransplanted third molars: a 6-Year cohort study of 167 teeth in southern China
type: item
type: AcademicArticle
description: Background Autogenous tooth transplantation offers significant advantages and promising success rates for replacing non-retainable teeth. This study aimed to investigate the prognostic factors, especially the impact of root canal treatment (RCT), of autotransplanted teeth in an up-to-6-year follow-up cohort of 167 teeth in Southern China. Methods We enrolled adult patients from the Southern Medical University-Shenzhen Stomatology Hospital between 2017 and 2023. Patients underwent autogenous tooth transplantation to replace non-retainable molars with upper or lower third molars with Moorrees tooth development stage ≥5. All surgical procedures were performed by an experienced surgeon. The included patients were followed up for 6~72 (median 28.5) months. Success, failure, and survival rate and prognostic factors were evaluated using univariable Kaplan-Meier, multivariable generalized linear regression, and multivariable COX regression analyses. Results The overall success rate is 97.6% with four unsuccessful cases. Herein, two of them were removed, leading to an overall survival rate of 98.8%. A total of 159 cases (95%) received RCT in 3 months. Univariable log-rank analysis showed that RCT (RR 0.109, 95%CI 0.010 to 1.202, P = 0.028) and site relationship between donor and receipt sites (RR 3.359, 95% CI [1.210–9.329], P = 0.020) were two significant prognostic factors of autotransplanted teeth. Multivariable generalized linear regression revealed that RCT is the only significant factor protecting the success rate of autotransplanted teeth (HR 0.003, 95% CI [0.000–0.249], P = 0.010). However, in the Cox regression model, the effects of RCT (HR 0.009, 95% CI [0.000–2.514], P = 0.101) did not reach statistical significance. Other factors did not demonstrate a significant impact in this cohort. These results supported that autogenous tooth transplantation is a viable alternative to conventional implant treatment with strict indications. Our findings underscore the importa…
format: application/pdf
format: text/html
creator: Bangfeng Han
creator: Liu Liu
creator: Zhishen Jiang
creator: Li Ye
creator: Yubin Cao
creator: Jian Pan
subject: Dentistry
description: doi:10.7717/peerj.18824
publisher: PeerJ Inc.
rights: © 2025 Han et al.
abstract: Background Autogenous tooth transplantation offers significant advantages and promising success rates for replacing non-retainable teeth. This study aimed to investigate the prognostic factors, especially the impact of root canal treatment (RCT), of autotransplanted teeth in an up-to-6-year follow-up cohort of 167 teeth in Southern China. Methods We enrolled adult patients from the Southern Medical University-Shenzhen Stomatology Hospital between 2017 and 2023. Patients underwent autogenous tooth transplantation to replace non-retainable molars with upper or lower third molars with Moorrees tooth development stage ≥5. All surgical procedures were performed by an experienced surgeon. The included patients were followed up for 6~72 (median 28.5) months. Success, failure, and survival rate and prognostic factors were evaluated using univariable Kaplan-Meier, multivariable generalized linear regression, and multivariable COX regression analyses. Results The overall success rate is 97.6% with four unsuccessful cases. Herein, two of them were removed, leading to an overall survival rate of 98.8%. A total of 159 cases (95%) received RCT in 3 months. Univariable log-rank analysis showed that RCT (RR 0.109, 95%CI 0.010 to 1.202, P = 0.028) and site relationship between donor and receipt sites (RR 3.359, 95% CI [1.210–9.329], P = 0.020) were two significant prognostic factors of autotransplanted teeth. Multivariable generalized linear regression revealed that RCT is the only significant factor protecting the success rate of autotransplanted teeth (HR 0.003, 95% CI [0.000–0.249], P = 0.010). However, in the Cox regression model, the effects of RCT (HR 0.009, 95% CI [0.000–2.514], P = 0.101) did not reach statistical significance. Other factors did not demonstrate a significant impact in this cohort. These results supported that autogenous tooth transplantation is a viable alternative to conventional implant treatment with strict indications. Our findings underscore the importa…
bibliographic citation: Han et al. (2025) Efficacy of root canal treatment for autotransplanted third molars: a 6-Year cohort study of 167 teeth in southern China. PeerJ 13:e18824 https://doi.org/10.7717/peerj.18824
date submitted: 2024-08-21
date accepted: 2024-12-17
issued: 2025-01-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Bangfeng
author list: Agent
  family name: Liu
  given name: Liu
author list: Agent
  family name: Jiang
  given name: Zhishen
author list: Agent
  family name: Ye
  given name: Li
author list: Agent
  family name: Cao
  given name: Yubin
author list: Agent
  family name: Pan
  given name: Jian
doi: 10.7717/peerj.18824
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-09
copyright: © 2025 Han et al.
attribution name: Han et al.

Genetic analysis of Pinna rudis L 1758 (Mollusca, Bivalvia, Pinnidae) in the Northwest Cabo Verde Islands (Central-East Atlantic)
type: item
type: AcademicArticle
description: The rough pen shell Pinna rudis Linnaeus, 1758 (family Pinnidae) is a mollusc with an Atlantic–Mediterranean distribution, typically inhabiting coarse sandy substrates. Habitat degradation is considered the primary cause of population decline, leading to the designation ‘Vulnerable’ in certain regions. In this study, we conducted a genetic analysis of populations of P. rudis from Cabo Verde and compared them with populations from the Mediterranean and Macaronesia. We based our analysis on two mitochondrial DNA markers, cytochrome oxidase I (COI) and 16S rRNA, and one nuclear marker, 28S rRNA. The results showed a strong genetic structuring among Macaronesia populations, with each island tending to have unique or exclusive haplotypes, though some sharing occurred between islands. We found significant genetic divergence between the population from Cabo Verde and the other sampled population, suggesting that P. rudis is not monotypic, but may include several cryptic species. Bayesian and maximum-likelihood phylogenetic analysis, including all Pinnidae species, indicated that P. rudis from Gorée Island (Senegal) and Baía das Gatas (São Vicente Island) might be undergoing speciation. The high genetic structure found for P. rudis could be influenced by hydrodynamic barriers, local currents and hydrographic isolation, in association with the short larval duration (planktotrophic) reported for this species. Altogether, our findings highlight significant genetic divergence in P. rudis populations, possibly supporting speciation events in the Cabo Verde archipelago among widely distributed taxonomic groups.
format: application/pdf
format: text/html
creator: Evandro P. Lopes
creator: Sarah Santos
creator: Raquel Xavier
creator: Joana L. Santos
creator: M. Pilar Cabezas
creator: Fernando Sequeira
creator: António M. Santos
subject: Biodiversity
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.18328
publisher: PeerJ Inc.
rights: © 2025 Lopes et al.
abstract: The rough pen shell Pinna rudis Linnaeus, 1758 (family Pinnidae) is a mollusc with an Atlantic–Mediterranean distribution, typically inhabiting coarse sandy substrates. Habitat degradation is considered the primary cause of population decline, leading to the designation ‘Vulnerable’ in certain regions. In this study, we conducted a genetic analysis of populations of P. rudis from Cabo Verde and compared them with populations from the Mediterranean and Macaronesia. We based our analysis on two mitochondrial DNA markers, cytochrome oxidase I (COI) and 16S rRNA, and one nuclear marker, 28S rRNA. The results showed a strong genetic structuring among Macaronesia populations, with each island tending to have unique or exclusive haplotypes, though some sharing occurred between islands. We found significant genetic divergence between the population from Cabo Verde and the other sampled population, suggesting that P. rudis is not monotypic, but may include several cryptic species. Bayesian and maximum-likelihood phylogenetic analysis, including all Pinnidae species, indicated that P. rudis from Gorée Island (Senegal) and Baía das Gatas (São Vicente Island) might be undergoing speciation. The high genetic structure found for P. rudis could be influenced by hydrodynamic barriers, local currents and hydrographic isolation, in association with the short larval duration (planktotrophic) reported for this species. Altogether, our findings highlight significant genetic divergence in P. rudis populations, possibly supporting speciation events in the Cabo Verde archipelago among widely distributed taxonomic groups.
bibliographic citation: Lopes et al. (2025) Genetic analysis of Pinna rudis L 1758 (Mollusca, Bivalvia, Pinnidae) in the Northwest Cabo Verde Islands (Central-East Atlantic). PeerJ 13:e18328 https://doi.org/10.7717/peerj.18328
date submitted: 2024-06-27
date accepted: 2024-09-25
issued: 2025-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lopes
  given name: Evandro P.
author list: Agent
  family name: Santos
  given name: Sarah
author list: Agent
  family name: Xavier
  given name: Raquel
author list: Agent
  family name: Santos
  given name: Joana L.
author list: Agent
  family name: Cabezas
  given name: M. Pilar
author list: Agent
  family name: Sequeira
  given name: Fernando
author list: Agent
  family name: Santos
  given name: António M.
doi: 10.7717/peerj.18328
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-08
copyright: © 2025 Lopes et al.
attribution name: Lopes et al.

Niche-related processes explain phylogenetic structure of acoustic bird communities in Mexico
type: item
type: AcademicArticle
description: Acoustic communities are acoustically active species aggregations within a habitat, where vocal interactions between species can interfere their communication. The acoustic adaptation hypothesis (AAH) explains how the habitat favors the transmission of acoustic signals. To understand how bird acoustic communities are structured, we tested the effect of habitat structure on the phylogenetic structure, and on the phylogenetic and vocal diversity of acoustic communities in a semi-arid zone of Mexico. From autonomous recordings in three types of vegetation (crop fields, tetecheras, and mesquiteras), which differ in terms of complexity and canopy openness, we evaluated sound attenuation, and estimated metrics of phylogenetic structure and diversity as well as acoustic diversity with the use of two indices. Mesquiteras showed greater vegetation density, more attenuation, more vocal diversity, as well as a phylogenetic structure that tended towards overdispersion, in contrast to crop fields that showed less vegetation density, less attenuation, less vocal diversity and more phylogenetic relatedness, while tetecheras showed intermediate patterns. Phylogenetic structure was explained by vegetation density and excess attenuation. The higher vocal diversity, phylogenetic structure tended towards overdispersion. These results suggest a role for environmental filters in the crop fields, where more closely related species with similar vocal characteristics coexist (supporting AAH), and probably competitive exclusion in the mesquiteras, where more distantly related species coexist, promoting vocal diversity. This study offers information about the influence of habitat on the acoustic community structure, which could inform our understanding of the distribution of species from acoustic perspective.
format: application/pdf
format: text/html
creator: Christian D. Morán-Titla
creator: Juan-Hector García-Chávez
creator: Leonel Lopez-Toledo
creator: Clementina González
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.18412
publisher: PeerJ Inc.
rights: © 2025 Morán-Titla et al.
abstract: Acoustic communities are acoustically active species aggregations within a habitat, where vocal interactions between species can interfere their communication. The acoustic adaptation hypothesis (AAH) explains how the habitat favors the transmission of acoustic signals. To understand how bird acoustic communities are structured, we tested the effect of habitat structure on the phylogenetic structure, and on the phylogenetic and vocal diversity of acoustic communities in a semi-arid zone of Mexico. From autonomous recordings in three types of vegetation (crop fields, tetecheras, and mesquiteras), which differ in terms of complexity and canopy openness, we evaluated sound attenuation, and estimated metrics of phylogenetic structure and diversity as well as acoustic diversity with the use of two indices. Mesquiteras showed greater vegetation density, more attenuation, more vocal diversity, as well as a phylogenetic structure that tended towards overdispersion, in contrast to crop fields that showed less vegetation density, less attenuation, less vocal diversity and more phylogenetic relatedness, while tetecheras showed intermediate patterns. Phylogenetic structure was explained by vegetation density and excess attenuation. The higher vocal diversity, phylogenetic structure tended towards overdispersion. These results suggest a role for environmental filters in the crop fields, where more closely related species with similar vocal characteristics coexist (supporting AAH), and probably competitive exclusion in the mesquiteras, where more distantly related species coexist, promoting vocal diversity. This study offers information about the influence of habitat on the acoustic community structure, which could inform our understanding of the distribution of species from acoustic perspective.
bibliographic citation: Morán-Titla et al. (2025) Niche-related processes explain phylogenetic structure of acoustic bird communities in Mexico. PeerJ 13:e18412 https://doi.org/10.7717/peerj.18412
date submitted: 2024-06-04
date accepted: 2024-10-07
issued: 2025-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morán-Titla
  given name: Christian D.
author list: Agent
  family name: García-Chávez
  given name: Juan-Hector
author list: Agent
  family name: Lopez-Toledo
  given name: Leonel
author list: Agent
  family name: González
  given name: Clementina
doi: 10.7717/peerj.18412
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-08
copyright: ©2025 Morán-Titla et al.
attribution name: Morán-Titla et al.

The impact of a disaster medicine clinical training program on medical students’ disaster literacy
type: item
type: AcademicArticle
description: Background This study was conducted to assess how students’ disaster literacy was affected by the Disaster Medicine Clinical Training Program at the Izmir Democracy University Faculty of Medicine (IDUFM) during the academic year 2022–2023. Methods Using an experimental method involving experimental and control groups, measurements were made at different times. The sample consisted of 5th-year students at IDUFM for the experimental group, while the control group was composed of 3rd- and 4th-year students from different buildings with limited interaction with the experimental group. The clinical training program was organized to improve the clinical practice skills of students in the field of disaster medicine and provide theoretical information. Throughout their internship, the students were provided with a program including information on types of disasters, preparation, response, relief, emergency surgical procedures, hospital disaster plans, national and international organizations and institutions working in disasters, and other relevant topics. The Disaster Literacy Scale (DLS) was used to collect data. This scale is a self-report scale that was developed to evaluate knowledge levels about disasters. In this study, the scale was applied as a pretest and a posttest, and the obtained data were analyzed using independent samples and paired-sample t-tests. Result The DLS scores of the experimental group showed significant improvement after the training program compared to their pretest scores (Total Scale: p < 0.001, Damage Mitigation: p = 0.002, Preparation: p < 0.001, Response: p < 0.001, and Relief: p = 0.004). When comparing the posttest results of the experimental group with the control group, the experimental group demonstrated significantly higher scores in Total Scale (p = 0.01), Damage Mitigation (p = 0.02), Response (p = 0.03), and Relief (p < 0.001). However, no significant differences were observed between the experimental group’s pretest (T1) scores and…
format: application/pdf
format: text/html
creator: Aysel Başer
creator: Zeynep Sofuoğlu
subject: Emergency and Critical Care
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.18800
publisher: PeerJ Inc.
rights: © 2025 Başer and Sofuoğlu
abstract: Background This study was conducted to assess how students’ disaster literacy was affected by the Disaster Medicine Clinical Training Program at the Izmir Democracy University Faculty of Medicine (IDUFM) during the academic year 2022–2023. Methods Using an experimental method involving experimental and control groups, measurements were made at different times. The sample consisted of 5th-year students at IDUFM for the experimental group, while the control group was composed of 3rd- and 4th-year students from different buildings with limited interaction with the experimental group. The clinical training program was organized to improve the clinical practice skills of students in the field of disaster medicine and provide theoretical information. Throughout their internship, the students were provided with a program including information on types of disasters, preparation, response, relief, emergency surgical procedures, hospital disaster plans, national and international organizations and institutions working in disasters, and other relevant topics. The Disaster Literacy Scale (DLS) was used to collect data. This scale is a self-report scale that was developed to evaluate knowledge levels about disasters. In this study, the scale was applied as a pretest and a posttest, and the obtained data were analyzed using independent samples and paired-sample t-tests. Result The DLS scores of the experimental group showed significant improvement after the training program compared to their pretest scores (Total Scale: p < 0.001, Damage Mitigation: p = 0.002, Preparation: p < 0.001, Response: p < 0.001, and Relief: p = 0.004). When comparing the posttest results of the experimental group with the control group, the experimental group demonstrated significantly higher scores in Total Scale (p = 0.01), Damage Mitigation (p = 0.02), Response (p = 0.03), and Relief (p < 0.001). However, no significant differences were observed between the experimental group’s pretest (T1) scores and…
bibliographic citation: Başer et al. (2025) The impact of a disaster medicine clinical training program on medical students’ disaster literacy. PeerJ 13:e18800 https://doi.org/10.7717/peerj.18800
date submitted: 2024-09-12
date accepted: 2024-12-11
issued: 2025-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Başer
  given name: Aysel
author list: Agent
  family name: Sofuoğlu
  given name: Zeynep
doi: 10.7717/peerj.18800
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-08
copyright: ©2025 Başer and Sofuoğlu
attribution name: Başer and Sofuoğlu

Clinical characteristics of pathogens in children with community-acquired pneumonia were analyzed via targeted next-generation sequencing detection
type: item
type: AcademicArticle
description: Background The primary purpose of this study was to detect the pathogen species using targeted next-generation sequencing (tNGS) to investigate the characteristics of community-acquired pneumonia (CAP)-related pathogens in children in Xiantao city, Hubei province, China. Methods A total of 1,527 children with CAP were prospectively recruited from our hospital between May 2022 and February 2023. Information on age and sex was collected from the medical records. Pathogen detection was performed using standard detection methods and tNGS. Results The positive coincidence rate of standard detection methods and tNGS were 61.95% (946/1,527) and 97.05% (1,482/1,527), respectively. Among the 1,482 children with CAP, the numbers of bacteria, virus, chlamydia, and mycoplasma infection were 1,188, 975, 321, and 1, respectively. Co-existing species showed high prevalence in CAP, and the prevalence of children infected with only one pathogen was 20.31%. The numbers of children infected with two and three pathogens were the highest, accounting for 29.22% and 25.17%, respectively. Among the 44 pathogens detected using tNGS, 17 species of bacteria, 25 species of viruses, one species of chlamydia, and one species of mycoplasma were documented. Among all infectious pathogens, the top five were Haemophilus influenzae, Acinetobacter baumannii, Streptococcus pneumoniae, human herpes virus type 5 (HHV-5), and Mycoplasma pneumoniae. The results showed that pathogenic infections in children with CAP were related to age but not to gender. Conclusion The infection pathogens in children with CAP were complex and the incidence of co-existence was observed to be high. The pathogens involved in CAP were closely related to the age of the child. In addition, tNGS was shown to better identify pathogens than the standard detection method, which is crucial for improving the accuracy of early CAP diagnosis and initiating appropriate treatment in a timely manner, ultimately enhancing treatment outcomes.
format: application/pdf
format: text/html
creator: Junhua Zhao
creator: Mingfeng Xu
creator: Zheng Tian
creator: Yu Wang
subject: Microbiology
subject: Epidemiology
subject: Infectious Diseases
subject: Pediatrics
subject: Translational Medicine
description: doi:10.7717/peerj.18810
publisher: PeerJ Inc.
rights: © 2025 Zhao et al.
abstract: Background The primary purpose of this study was to detect the pathogen species using targeted next-generation sequencing (tNGS) to investigate the characteristics of community-acquired pneumonia (CAP)-related pathogens in children in Xiantao city, Hubei province, China. Methods A total of 1,527 children with CAP were prospectively recruited from our hospital between May 2022 and February 2023. Information on age and sex was collected from the medical records. Pathogen detection was performed using standard detection methods and tNGS. Results The positive coincidence rate of standard detection methods and tNGS were 61.95% (946/1,527) and 97.05% (1,482/1,527), respectively. Among the 1,482 children with CAP, the numbers of bacteria, virus, chlamydia, and mycoplasma infection were 1,188, 975, 321, and 1, respectively. Co-existing species showed high prevalence in CAP, and the prevalence of children infected with only one pathogen was 20.31%. The numbers of children infected with two and three pathogens were the highest, accounting for 29.22% and 25.17%, respectively. Among the 44 pathogens detected using tNGS, 17 species of bacteria, 25 species of viruses, one species of chlamydia, and one species of mycoplasma were documented. Among all infectious pathogens, the top five were Haemophilus influenzae, Acinetobacter baumannii, Streptococcus pneumoniae, human herpes virus type 5 (HHV-5), and Mycoplasma pneumoniae. The results showed that pathogenic infections in children with CAP were related to age but not to gender. Conclusion The infection pathogens in children with CAP were complex and the incidence of co-existence was observed to be high. The pathogens involved in CAP were closely related to the age of the child. In addition, tNGS was shown to better identify pathogens than the standard detection method, which is crucial for improving the accuracy of early CAP diagnosis and initiating appropriate treatment in a timely manner, ultimately enhancing treatment outcomes.
bibliographic citation: Zhao et al. (2025) Clinical characteristics of pathogens in children with community-acquired pneumonia were analyzed via targeted next-generation sequencing detection. PeerJ 13:e18810 https://doi.org/10.7717/peerj.18810
date submitted: 2024-09-30
date accepted: 2024-12-12
issued: 2025-01-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Junhua
author list: Agent
  family name: Xu
  given name: Mingfeng
author list: Agent
  family name: Tian
  given name: Zheng
author list: Agent
  family name: Wang
  given name: Yu
doi: 10.7717/peerj.18810
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-08
copyright: ©2025 Zhao et al.
attribution name: Zhao et al.

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