PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The status quo and influencing factors of breastfeeding social support in China based on LASSO regression model
items: Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers
items: Knowledge, attitudes, practices, and vaccination coverage of medical students toward hepatitis B virus in North Sudan, 2023
items: Constructing age-structured matrix population models for all fishes
items: Mapping species of greatest conservation need and solar energy potential in the arid Southwest for future sustainable development
items: A giant specimen of Rhamphorhynchus muensteri and comments on the ontogeny of rhamphorhynchines
items: The application of deep learning in early enamel demineralization detection
items: The inter-trial and inter-session reliability of Theia3D-derived markerless gait analysis in tight versus loose clothing
items: How many reptile and amphibian species are in Uganda, and why it matters for global biodiversity conservation
items: Basis of single-seed formation in chestnut: cytomorphological observations reveal ovule developmental patterns of Castanea henryi

The status quo and influencing factors of breastfeeding social support in China based on LASSO regression model
type: item
type: AcademicArticle
description: Background In China, the rate of exclusive breastfeeding at 6 months is only 29.2%, well below the global breastfeeding collective target of at least 50% by 2025. This study explores the status quo of breastfeeding social support among puerpera and analyses its influencing factors, in order to provide a basis for improving breastfeeding rate in China. Methods A total of 251 puerpera were selected to fill in the general information questionnaire and the Breastfeeding Social Support Scale from three community health service centers in the city of Chengde, Hebei province, China, from September to November 2023 by completed random cluster sampling method. And the LASSO regression was used to screen and order the influencing factors of breastfeeding social support. Results The total score of the Breastfeeding Social Support Scale was (48.95 ± 7.93). The results of LASSO regression showed that when the lambda (λ) value was 0.7428, the error was the smallest, and the corresponding number of influencing factors was four, and the top four independent variables in importance ranking were whether or not breastfeeding at night, employment status, the feeding mode of the youngest baby, partner attended school/lecture for pregnant women. Conclusion The level of breastfeeding social support remains to be improved; health care providers were suggested to develop targeted intervention according to the influencing factors.
format: application/pdf
format: text/html
creator: Tian Sun
creator: Chanzhi Duan
creator: Yan Wang
creator: Qing Li
subject: Global Health
subject: Gynecology and Obstetrics
subject: Health Policy
subject: Nursing
subject: Healthcare Services
description: doi:10.7717/peerj.18779
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Background In China, the rate of exclusive breastfeeding at 6 months is only 29.2%, well below the global breastfeeding collective target of at least 50% by 2025. This study explores the status quo of breastfeeding social support among puerpera and analyses its influencing factors, in order to provide a basis for improving breastfeeding rate in China. Methods A total of 251 puerpera were selected to fill in the general information questionnaire and the Breastfeeding Social Support Scale from three community health service centers in the city of Chengde, Hebei province, China, from September to November 2023 by completed random cluster sampling method. And the LASSO regression was used to screen and order the influencing factors of breastfeeding social support. Results The total score of the Breastfeeding Social Support Scale was (48.95 ± 7.93). The results of LASSO regression showed that when the lambda (λ) value was 0.7428, the error was the smallest, and the corresponding number of influencing factors was four, and the top four independent variables in importance ranking were whether or not breastfeeding at night, employment status, the feeding mode of the youngest baby, partner attended school/lecture for pregnant women. Conclusion The level of breastfeeding social support remains to be improved; health care providers were suggested to develop targeted intervention according to the influencing factors.
bibliographic citation: Sun et al. (2025) The status quo and influencing factors of breastfeeding social support in China based on LASSO regression model. PeerJ 13:e18779 https://doi.org/10.7717/peerj.18779
date submitted: 2024-07-23
date accepted: 2024-12-09
issued: 2025-01-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Sun
  given name: Tian
author list: Agent
  family name: Duan
  given name: Chanzhi
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Li
  given name: Qing
doi: 10.7717/peerj.18779
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-03
copyright: ©2025 Sun et al.
attribution name: Sun et al.

Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers
type: item
type: AcademicArticle
description: Background Understanding the diversity and distribution of fungal communities at a regional scale is important since fungi play a crucial role in ecosystem functioning. Our study used environmental metagenomics to determine fungal communities in mountainous forest soils in the central highlands of Mexico. Methods We used four different bioinformatic workflows to profile fungal assemblages, i.e., Geneious+UNITE, single- and paired-end microbial community profiling (MiCoP), and Kraken2. Results The workflows yielded different results; one detected a higher abundance of ectomycorrhizal (EcM) and saprophytic fungi, while the other identified more saprophytic and pathogenic fungi. Environmental, vegetation, and geographical factors determined the spatial distribution of soil fungi at a regional scale. Potential hydrogen (pH), calcium (Ca), magnesium (Mg), and silt content were detected as common drivers of fungal communities across different datasets enriched towards a functional guild. Vegetation traits were found to be more influential in shaping symbiotrophic fungi composition than saprotrophic and pathogenic fungi. This highlights the importance of considering vegetation traits when studying fungal community diversity and distribution. Clustering patterns of sampling points near the volcanoes indicated shared environmental and vegetation characteristics. A weak but significant distance decay in taxonomic similarity revealed that dispersal limitation contributed to fungal community composition, although it was not the primary factor in this study. Overall, this study provides important insights into the challenges and opportunities of studying fungal communities at a regional scale using metagenomic data.
format: application/pdf
format: text/html
creator: Stephanie Hereira-Pacheco
creator: Itzel Arias-Del Razo
creator: Alejandra Miranda-Carrazco
creator: Luc Dendooven
creator: Arturo Estrada-Torres
creator: Yendi E. Navarro-Noya
subject: Bioinformatics
subject: Ecology
subject: Ecosystem Science
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.18323
publisher: PeerJ Inc.
rights: © 2025 Hereira-Pacheco et al.
abstract: Background Understanding the diversity and distribution of fungal communities at a regional scale is important since fungi play a crucial role in ecosystem functioning. Our study used environmental metagenomics to determine fungal communities in mountainous forest soils in the central highlands of Mexico. Methods We used four different bioinformatic workflows to profile fungal assemblages, i.e., Geneious+UNITE, single- and paired-end microbial community profiling (MiCoP), and Kraken2. Results The workflows yielded different results; one detected a higher abundance of ectomycorrhizal (EcM) and saprophytic fungi, while the other identified more saprophytic and pathogenic fungi. Environmental, vegetation, and geographical factors determined the spatial distribution of soil fungi at a regional scale. Potential hydrogen (pH), calcium (Ca), magnesium (Mg), and silt content were detected as common drivers of fungal communities across different datasets enriched towards a functional guild. Vegetation traits were found to be more influential in shaping symbiotrophic fungi composition than saprotrophic and pathogenic fungi. This highlights the importance of considering vegetation traits when studying fungal community diversity and distribution. Clustering patterns of sampling points near the volcanoes indicated shared environmental and vegetation characteristics. A weak but significant distance decay in taxonomic similarity revealed that dispersal limitation contributed to fungal community composition, although it was not the primary factor in this study. Overall, this study provides important insights into the challenges and opportunities of studying fungal communities at a regional scale using metagenomic data.
bibliographic citation: Hereira-Pacheco et al. (2025) Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers. PeerJ 13:e18323 https://doi.org/10.7717/peerj.18323
date submitted: 2024-05-30
date accepted: 2024-09-25
issued: 2025-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hereira-Pacheco
  given name: Stephanie
author list: Agent
  family name: Arias-Del Razo
  given name: Itzel
author list: Agent
  family name: Miranda-Carrazco
  given name: Alejandra
author list: Agent
  family name: Dendooven
  given name: Luc
author list: Agent
  family name: Estrada-Torres
  given name: Arturo
author list: Agent
  family name: Navarro-Noya
  given name: Yendi E.
doi: 10.7717/peerj.18323
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-02
copyright: © 2025 Hereira-Pacheco et al.
attribution name: Hereira-Pacheco et al.

Knowledge, attitudes, practices, and vaccination coverage of medical students toward hepatitis B virus in North Sudan, 2023
type: item
type: AcademicArticle
description: Background Hepatitis B virus (HBV) is a global health issue, particularly among healthcare personnel, including students because of its occupational exposure pattern. Healthcare Workers and medical students are recommended to have better knowledge, attitudes and good practices and vaccination toward infection control in general and HBV in particular. This study aimed to assess the knowledge, attitudes, and practices of medical students from North Sudan regarding HBV and its vaccination coverage. Methods A cross-sectional study was conducted from January to June 2023 among medical students in North Sudan. Data were collected using a structured scale using online Google Forms. Descriptive and comparative analyses were performed using SPSS version 26. Statistical significance was set at p ≤ 0.05. Results A total of 426 medical students were included in the study. The majority had good knowledge about HBV (86%) and its transmission methods (77%). The majority showed a favorable attitude (77%). The practice score was however very low (15.5%). Older age and advanced academic level were significantly associated with good knowledge (aOR: 3.9; CI 95% [3.69–12.92]; p = 0.016, and aOR: 2.6; CI 95% [1.16–6.15]; p = 0.020, respectively). Only a third of the students were vaccinated (33.0%), with only a few of them received complete doses (18.6%). Conclusion Students from medical colleges in North Sudan had good knowledge and favorable attitudes toward HBV. However, good practice was low. Older age and advanced academic level were significantly associated with knowledge level. Vaccination coverage was also low among the students in this study.
format: application/pdf
format: text/html
creator: Osama M.I. Mohamed
creator: Hassan S.H. Mohammedali
creator: Shimaa N.A. Mohamed
creator: Hussein A.S. Ahmed
creator: Alaa A.M. Mohamedsalih
creator: Ola M.A. Abdalgani
creator: Tebian A.A. Mohammedosman
creator: Alaa A.A. Ali
creator: Thuiba A.H. Ali
creator: Othman N.O. Amin
creator: Mohamed A. Issak
creator: Mohamed O. Abdelaziz
subject: Virology
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Global Health
subject: Infectious Diseases
description: doi:10.7717/peerj.18339
publisher: PeerJ Inc.
rights: © 2025 Mohamed et al.
abstract: Background Hepatitis B virus (HBV) is a global health issue, particularly among healthcare personnel, including students because of its occupational exposure pattern. Healthcare Workers and medical students are recommended to have better knowledge, attitudes and good practices and vaccination toward infection control in general and HBV in particular. This study aimed to assess the knowledge, attitudes, and practices of medical students from North Sudan regarding HBV and its vaccination coverage. Methods A cross-sectional study was conducted from January to June 2023 among medical students in North Sudan. Data were collected using a structured scale using online Google Forms. Descriptive and comparative analyses were performed using SPSS version 26. Statistical significance was set at p ≤ 0.05. Results A total of 426 medical students were included in the study. The majority had good knowledge about HBV (86%) and its transmission methods (77%). The majority showed a favorable attitude (77%). The practice score was however very low (15.5%). Older age and advanced academic level were significantly associated with good knowledge (aOR: 3.9; CI 95% [3.69–12.92]; p = 0.016, and aOR: 2.6; CI 95% [1.16–6.15]; p = 0.020, respectively). Only a third of the students were vaccinated (33.0%), with only a few of them received complete doses (18.6%). Conclusion Students from medical colleges in North Sudan had good knowledge and favorable attitudes toward HBV. However, good practice was low. Older age and advanced academic level were significantly associated with knowledge level. Vaccination coverage was also low among the students in this study.
bibliographic citation: Mohamed et al. (2025) Knowledge, attitudes, practices, and vaccination coverage of medical students toward hepatitis B virus in North Sudan, 2023. PeerJ 13:e18339 https://doi.org/10.7717/peerj.18339
date submitted: 2024-06-17
date accepted: 2024-09-26
issued: 2025-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohamed
  given name: Osama M.I.
author list: Agent
  family name: Mohammedali
  given name: Hassan S.H.
author list: Agent
  family name: Mohamed
  given name: Shimaa N.A.
author list: Agent
  family name: Ahmed
  given name: Hussein A.S.
author list: Agent
  family name: Mohamedsalih
  given name: Alaa A.M.
author list: Agent
  family name: Abdalgani
  given name: Ola M.A.
author list: Agent
  family name: Mohammedosman
  given name: Tebian A.A.
author list: Agent
  family name: Ali
  given name: Alaa A.A.
author list: Agent
  family name: Ali
  given name: Thuiba A.H.
author list: Agent
  family name: Amin
  given name: Othman N.O.
author list: Agent
  family name: Issak
  given name: Mohamed A.
author list: Agent
  family name: Abdelaziz
  given name: Mohamed O.
doi: 10.7717/peerj.18339
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-02
copyright: ©2025 Mohamed et al.
attribution name: Mohamed et al.

Constructing age-structured matrix population models for all fishes
type: item
type: AcademicArticle
description: Matrix population models are essential tools in conservation biology, offering key metrics to guide species management and conservation planning. However, the development of these models is often limited by insufficient life history data, particularly for non-charismatic species. This study addresses this gap by using life history data from FishBase and the FishLife R package, complemented by size-dependent natural mortality estimates, to parameterize age-structured matrix population models applicable to most fish species. The method was applied to 30 fish species common around oil and gas platforms in the Northern Gulf of Mexico, generating seven key metrics: damping ratio, resilience, generation time, stable age distribution, reproductive value, sensitivity matrix, and elasticity matrix. The damping ratio reflects how quickly a population returns to a stable age distribution after a disturbance, while resilience indicates the speed of recovery from perturbations. Generation time captures the average age of reproduction, and the stable age distribution represents the long-term proportion of individuals in each age class. Reproductive value quantifies future reproductive potential by age class. The sensitivity matrix highlights the age-class transitions most affecting population growth, and the elasticity matrix shows the proportional influence of these factors on population growth. The results demonstrate that robust population models can be constructed with limited species-specific data and reveal notable differences in population dynamics among species. For example, species with longer generation times, like the greater barracuda (Sphyraena guachancho), have lower damping ratios, indicating prolonged transient dynamics. In contrast, species such as the round scad (Decapterus punctatus) exhibit shorter generation times and higher damping ratios, suggesting faster returns to equilibrium. These findings underscore the importance of life history variability in shapin…
format: application/pdf
format: text/html
creator: Masami Fujiwara
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Mathematical Biology
subject: Data Science
description: doi:10.7717/peerj.18387
publisher: PeerJ Inc.
rights: © 2025 Fujiwara
abstract: Matrix population models are essential tools in conservation biology, offering key metrics to guide species management and conservation planning. However, the development of these models is often limited by insufficient life history data, particularly for non-charismatic species. This study addresses this gap by using life history data from FishBase and the FishLife R package, complemented by size-dependent natural mortality estimates, to parameterize age-structured matrix population models applicable to most fish species. The method was applied to 30 fish species common around oil and gas platforms in the Northern Gulf of Mexico, generating seven key metrics: damping ratio, resilience, generation time, stable age distribution, reproductive value, sensitivity matrix, and elasticity matrix. The damping ratio reflects how quickly a population returns to a stable age distribution after a disturbance, while resilience indicates the speed of recovery from perturbations. Generation time captures the average age of reproduction, and the stable age distribution represents the long-term proportion of individuals in each age class. Reproductive value quantifies future reproductive potential by age class. The sensitivity matrix highlights the age-class transitions most affecting population growth, and the elasticity matrix shows the proportional influence of these factors on population growth. The results demonstrate that robust population models can be constructed with limited species-specific data and reveal notable differences in population dynamics among species. For example, species with longer generation times, like the greater barracuda (Sphyraena guachancho), have lower damping ratios, indicating prolonged transient dynamics. In contrast, species such as the round scad (Decapterus punctatus) exhibit shorter generation times and higher damping ratios, suggesting faster returns to equilibrium. These findings underscore the importance of life history variability in shapin…
bibliographic citation: Fujiwara (2025) Constructing age-structured matrix population models for all fishes. PeerJ 13:e18387 https://doi.org/10.7717/peerj.18387
date submitted: 2024-06-20
date accepted: 2024-10-02
issued: 2025-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fujiwara
  given name: Masami
doi: 10.7717/peerj.18387
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-02
copyright: ©2025 Fujiwara
attribution name: Fujiwara

Mapping species of greatest conservation need and solar energy potential in the arid Southwest for future sustainable development
type: item
type: AcademicArticle
description: The need for renewable energy has become increasingly evident in response to the climate change crisis, presenting a paradoxical challenge to biodiversity conservation. The Southwest United States is desirable for large-scale solar energy development (SED) due to its high global horizontal irradiance (GHI) values and vast open landscapes. However, this region is also rich in unique ecological and biological diversity. Several distinct species have garnered special attention as human population growth, habitat alteration, and climate change have accelerated in recent decades (i.e., LeConte’s Thrasher (Toxostoma lecontei), Bendire’s Thrasher (Toxostoma bendirei), Sonoran Desert Tortoise (Gopherus morafkai), Mojave Desert Tortoise (Gopherus agassizii), and the Southwestern population of the Burrowing Owl (Athene cunicularia). As the United States prepares to increase its development in renewable energies, particularly solar energy, there has been a growing concern about how this development will further impact these species. In this study, we propose a novel combined approach to find areas of high habitat suitability for endangered species within areas of high SED potential. Specifically, we employed species distribution modeling (SDM) to identify areas with suitable habitats and likely species presence, and we conducted a site suitability analysis for potential SED locations within the Southwest. As a result, we found significant overlap between potential SED locations and the high-priority habitats of all target species, thus underlining the importance of prioritizing conservation efforts as more solar projects are reviewed in these Southwestern states. Our study aims to inform conservationists and developers in making sustainable decisions for the region’s future development.
format: application/pdf
format: text/html
creator: Kylee Fleckenstein
creator: Adam Stein
creator: Heather L. Bateman
creator: Fabio De Albuquerque
subject: Biogeography
subject: Ecology
subject: Zoology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.18568
publisher: PeerJ Inc.
rights: © 2025 Fleckenstein et al.
abstract: The need for renewable energy has become increasingly evident in response to the climate change crisis, presenting a paradoxical challenge to biodiversity conservation. The Southwest United States is desirable for large-scale solar energy development (SED) due to its high global horizontal irradiance (GHI) values and vast open landscapes. However, this region is also rich in unique ecological and biological diversity. Several distinct species have garnered special attention as human population growth, habitat alteration, and climate change have accelerated in recent decades (i.e., LeConte’s Thrasher (Toxostoma lecontei), Bendire’s Thrasher (Toxostoma bendirei), Sonoran Desert Tortoise (Gopherus morafkai), Mojave Desert Tortoise (Gopherus agassizii), and the Southwestern population of the Burrowing Owl (Athene cunicularia). As the United States prepares to increase its development in renewable energies, particularly solar energy, there has been a growing concern about how this development will further impact these species. In this study, we propose a novel combined approach to find areas of high habitat suitability for endangered species within areas of high SED potential. Specifically, we employed species distribution modeling (SDM) to identify areas with suitable habitats and likely species presence, and we conducted a site suitability analysis for potential SED locations within the Southwest. As a result, we found significant overlap between potential SED locations and the high-priority habitats of all target species, thus underlining the importance of prioritizing conservation efforts as more solar projects are reviewed in these Southwestern states. Our study aims to inform conservationists and developers in making sustainable decisions for the region’s future development.
bibliographic citation: Fleckenstein et al. (2025) Mapping species of greatest conservation need and solar energy potential in the arid Southwest for future sustainable development. PeerJ 13:e18568 https://doi.org/10.7717/peerj.18568
date submitted: 2024-08-15
date accepted: 2024-10-31
issued: 2025-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fleckenstein
  given name: Kylee
author list: Agent
  family name: Stein
  given name: Adam
author list: Agent
  family name: Bateman
  given name: Heather L.
author list: Agent
  family name: De Albuquerque
  given name: Fabio
doi: 10.7717/peerj.18568
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-02
copyright: ©2025 Fleckenstein et al.
attribution name: Fleckenstein et al.

A giant specimen of Rhamphorhynchus muensteri and comments on the ontogeny of rhamphorhynchines
type: item
type: AcademicArticle
description: Rhamphorhynchus is one of the best-known pterosaurs, with well over 100 specimens being held in public collections. Most of these represent juvenile animals, and the adults known are typically around 1 m in wingspan. Here we describe a near complete skeleton, preserved partially in 3D, of an animal with a wingspan of around 1.8 m, that is considerably larger than other known specimens, and is among the largest known non-pterodactyloid pterosaurs. This animal shows differences in the anatomy not seen in smaller specimens, revealing details of late-stage ontogeny in this genus. The specimen exhibits a disproportionate reduction in the size of the orbit and increase in the size of the lower temporal fenestra, a reduction in the proportional mandibular symphysis, and unusually laterally flattened teeth, which may point to a changing diet as these animals grew. These features show a transition from smaller to larger specimens of Rhamphorhynchus and also appear in other large specimens of rhamphorhyhchines and point to a consistent pattern in their development.
format: application/pdf
format: text/html
creator: David W.E. Hone
creator: Skye N. McDavid
subject: Ecology
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.18587
publisher: PeerJ Inc.
rights: © 2025 Hone and McDavid
abstract: Rhamphorhynchus is one of the best-known pterosaurs, with well over 100 specimens being held in public collections. Most of these represent juvenile animals, and the adults known are typically around 1 m in wingspan. Here we describe a near complete skeleton, preserved partially in 3D, of an animal with a wingspan of around 1.8 m, that is considerably larger than other known specimens, and is among the largest known non-pterodactyloid pterosaurs. This animal shows differences in the anatomy not seen in smaller specimens, revealing details of late-stage ontogeny in this genus. The specimen exhibits a disproportionate reduction in the size of the orbit and increase in the size of the lower temporal fenestra, a reduction in the proportional mandibular symphysis, and unusually laterally flattened teeth, which may point to a changing diet as these animals grew. These features show a transition from smaller to larger specimens of Rhamphorhynchus and also appear in other large specimens of rhamphorhyhchines and point to a consistent pattern in their development.
bibliographic citation: Hone et al. (2025) A giant specimen of Rhamphorhynchus muensteri and comments on the ontogeny of rhamphorhynchines. PeerJ 13:e18587 https://doi.org/10.7717/peerj.18587
date submitted: 2024-06-19
date accepted: 2024-11-04
issued: 2025-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hone
  given name: David W.E.
author list: Agent
  family name: McDavid
  given name: Skye N.
doi: 10.7717/peerj.18587
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-02
copyright: ©2025 Hone and McDavid
attribution name: Hone and McDavid

The application of deep learning in early enamel demineralization detection
type: item
type: AcademicArticle
description: Objective The study aims to develop a diagnostic model using intraoral photographs to accurately detect and classify early detection of enamel demineralization on tooth surfaces. Methods A retrospective analysis was conducted with 208 patients aged 14 to 44. A total of 624 high-quality digital images captured under standardized conditions were used to construct a deep learning model based on the Mask region-based convolutional neural network (Mask R-CNN). The model was trained to automate the detection of enamel demineralization. Its performance was compared to two junior dentists’ diagnostic abilities. Results The model achieved an F1-score of 0.856 for detecting demineralized teeth on the validation set, a metric that reflects comprehensive diagnostic performance, demonstrating performance close to that of senior dentists. With the the model’s assistance, the junior dentists’ average F1-scores improved significantly—from 0.713 and 0.689 to 0.897 and 0.949, respectively (p < 0.05). The model accurately segmented tooth surfaces and detected demineralized areas, allowing for precise detection of demineralized areas and monitoring of lesion progression. Conclusion Deep learning can accurately segment tooth surfaces and lesion contours, enhancing the precision, accuracy, and efficiency of enamel demineralization diagnosis and area delineation.
format: application/pdf
format: text/html
creator: Ketai He
creator: Rongxiu Zhang
creator: Muchun Liang
creator: Keyue Tian
creator: Kaihui Luo
creator: Ruoshi Chen
creator: Jianpeng Ren
creator: Jiajun Wang
creator: Juan Li
subject: Dentistry
subject: Computational Science
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.18593
publisher: PeerJ Inc.
rights: © 2025 He et al.
abstract: Objective The study aims to develop a diagnostic model using intraoral photographs to accurately detect and classify early detection of enamel demineralization on tooth surfaces. Methods A retrospective analysis was conducted with 208 patients aged 14 to 44. A total of 624 high-quality digital images captured under standardized conditions were used to construct a deep learning model based on the Mask region-based convolutional neural network (Mask R-CNN). The model was trained to automate the detection of enamel demineralization. Its performance was compared to two junior dentists’ diagnostic abilities. Results The model achieved an F1-score of 0.856 for detecting demineralized teeth on the validation set, a metric that reflects comprehensive diagnostic performance, demonstrating performance close to that of senior dentists. With the the model’s assistance, the junior dentists’ average F1-scores improved significantly—from 0.713 and 0.689 to 0.897 and 0.949, respectively (p < 0.05). The model accurately segmented tooth surfaces and detected demineralized areas, allowing for precise detection of demineralized areas and monitoring of lesion progression. Conclusion Deep learning can accurately segment tooth surfaces and lesion contours, enhancing the precision, accuracy, and efficiency of enamel demineralization diagnosis and area delineation.
bibliographic citation: He et al. (2025) The application of deep learning in early enamel demineralization detection. PeerJ 13:e18593 https://doi.org/10.7717/peerj.18593
date submitted: 2024-05-10
date accepted: 2024-11-05
issued: 2025-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Ketai
author list: Agent
  family name: Zhang
  given name: Rongxiu
author list: Agent
  family name: Liang
  given name: Muchun
author list: Agent
  family name: Tian
  given name: Keyue
author list: Agent
  family name: Luo
  given name: Kaihui
author list: Agent
  family name: Chen
  given name: Ruoshi
author list: Agent
  family name: Ren
  given name: Jianpeng
author list: Agent
  family name: Wang
  given name: Jiajun
author list: Agent
  family name: Li
  given name: Juan
doi: 10.7717/peerj.18593
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-02
copyright: © 2025 He et al.
attribution name: He et al.

The inter-trial and inter-session reliability of Theia3D-derived markerless gait analysis in tight versus loose clothing
type: item
type: AcademicArticle
description: Background Gait analysis is traditionally conducted using marker-based methods yet markerless motion capture is emerging as an alternative. Initial studies have begun to evaluate the reliability of markerless motion capture yet the evaluation of different clothing conditions across sessions and complete evaluation of the lower limb and pelvis reliability have yet to be considered. The aim of this study was to evaluate the inter-trial, inter-session and inter-session-clothing variation and root mean square differences between tight- or loose-fitting clothing during walking. Method Twenty-two healthy adult participants walked along an indoor walkway whilst eight video cameras recorded their gait in either tight- or loose-fitting clothing. A commercial markerless motion capture system (Theia3D) provided gait kinematics for evaluation. Results Reliability results showed average inter-trial variation of <2°, inter-session variation of <3° and inter-session-clothing variation <3.5°. Root mean square differences (RMSD) between clothing conditions were <2°. Discussion Pelvis variations were smaller than those at the hip, knee and ankle. Our results showed smaller variation than in previous studies which may be due to updates to software. The demonstration of the reliability of markerless motion capture for gait analysis in healthy adults should prompt further evaluation in clinical conditions and reconsideration of multi-assessor marker-based gait analysis protocols, where variation is highest.
format: application/pdf
format: text/html
creator: Sylvia Augustine
creator: Richard Foster
creator: Gabor Barton
creator: Mark J. Lake
creator: Raihana Sharir
creator: Mark A. Robinson
subject: Kinesiology
subject: Biomechanics
description: doi:10.7717/peerj.18613
publisher: PeerJ Inc.
rights: © 2025 Augustine et al.
abstract: Background Gait analysis is traditionally conducted using marker-based methods yet markerless motion capture is emerging as an alternative. Initial studies have begun to evaluate the reliability of markerless motion capture yet the evaluation of different clothing conditions across sessions and complete evaluation of the lower limb and pelvis reliability have yet to be considered. The aim of this study was to evaluate the inter-trial, inter-session and inter-session-clothing variation and root mean square differences between tight- or loose-fitting clothing during walking. Method Twenty-two healthy adult participants walked along an indoor walkway whilst eight video cameras recorded their gait in either tight- or loose-fitting clothing. A commercial markerless motion capture system (Theia3D) provided gait kinematics for evaluation. Results Reliability results showed average inter-trial variation of <2°, inter-session variation of <3° and inter-session-clothing variation <3.5°. Root mean square differences (RMSD) between clothing conditions were <2°. Discussion Pelvis variations were smaller than those at the hip, knee and ankle. Our results showed smaller variation than in previous studies which may be due to updates to software. The demonstration of the reliability of markerless motion capture for gait analysis in healthy adults should prompt further evaluation in clinical conditions and reconsideration of multi-assessor marker-based gait analysis protocols, where variation is highest.
bibliographic citation: Augustine et al. (2025) The inter-trial and inter-session reliability of Theia3D-derived markerless gait analysis in tight versus loose clothing. PeerJ 13:e18613 https://doi.org/10.7717/peerj.18613
date submitted: 2024-06-24
date accepted: 2024-11-08
issued: 2025-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Augustine
  given name: Sylvia
author list: Agent
  family name: Foster
  given name: Richard
author list: Agent
  family name: Barton
  given name: Gabor
author list: Agent
  family name: Lake
  given name: Mark J.
author list: Agent
  family name: Sharir
  given name: Raihana
author list: Agent
  family name: Robinson
  given name: Mark A.
doi: 10.7717/peerj.18613
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-02
copyright: ©2025 Augustine et al.
attribution name: Augustine et al.

How many reptile and amphibian species are in Uganda, and why it matters for global biodiversity conservation
type: item
type: AcademicArticle
description: Biodiversity is unevenly distributed across the globe. Regional differences in biodiversity impact conservation through the allocation of financial resources, development of infrastructure, and public attention. Such resources are often prioritized to areas that are in more need than others. However, reasons for deciding which locations are more deserving are derived from an accurate knowledge of the number and composition of species that occur in each region. Regional differences in biodiversity, however, can reflect differences in the source of information consulted, rather than bona fide differences between areas. As a result, conservation resources may not be directed to regions in proportion to their actual need, especially if there is no consensus among sources of information. Here, we compared major sources of information on species of reptiles and amphibians that occur in Uganda, Africa. We found that none of the sources agreed on the total number, nor composition, of species in the country, with estimates for amphibians ranging more widely than those for reptiles. Notably, sources with similar species richness differed in species composition, which had an impact on the number of threatened species in the country. These results for a conspicuous group of vertebrates suggest that lesser-known groups are also likely misrepresented in sources, especially in other underexplored regions of tropical Africa. We discuss the implications for biodiversity conservation that are derived from inaccurate species lists that are commonly used by agencies, scientists, and practitioners. We argue that more critical evaluations of biodiversity resources, in addition to greater capacity building for field programs, taxonomy, and museum collections, will be essential to ensure that resources are allocated to regions that need them the most.
format: application/pdf
format: text/html
creator: Daniel F. Hughes
creator: Mathias Behangana
subject: Biodiversity
subject: Conservation Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.18704
publisher: PeerJ Inc.
rights: © 2025 Hughes and Behangana
abstract: Biodiversity is unevenly distributed across the globe. Regional differences in biodiversity impact conservation through the allocation of financial resources, development of infrastructure, and public attention. Such resources are often prioritized to areas that are in more need than others. However, reasons for deciding which locations are more deserving are derived from an accurate knowledge of the number and composition of species that occur in each region. Regional differences in biodiversity, however, can reflect differences in the source of information consulted, rather than bona fide differences between areas. As a result, conservation resources may not be directed to regions in proportion to their actual need, especially if there is no consensus among sources of information. Here, we compared major sources of information on species of reptiles and amphibians that occur in Uganda, Africa. We found that none of the sources agreed on the total number, nor composition, of species in the country, with estimates for amphibians ranging more widely than those for reptiles. Notably, sources with similar species richness differed in species composition, which had an impact on the number of threatened species in the country. These results for a conspicuous group of vertebrates suggest that lesser-known groups are also likely misrepresented in sources, especially in other underexplored regions of tropical Africa. We discuss the implications for biodiversity conservation that are derived from inaccurate species lists that are commonly used by agencies, scientists, and practitioners. We argue that more critical evaluations of biodiversity resources, in addition to greater capacity building for field programs, taxonomy, and museum collections, will be essential to ensure that resources are allocated to regions that need them the most.
bibliographic citation: Hughes et al. (2025) How many reptile and amphibian species are in Uganda, and why it matters for global biodiversity conservation. PeerJ 13:e18704 https://doi.org/10.7717/peerj.18704
date submitted: 2024-08-27
date accepted: 2024-11-22
issued: 2025-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hughes
  given name: Daniel F.
author list: Agent
  family name: Behangana
  given name: Mathias
doi: 10.7717/peerj.18704
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-02
copyright: ©2025 Hughes and Behangana
attribution name: Hughes and Behangana

Basis of single-seed formation in chestnut: cytomorphological observations reveal ovule developmental patterns of Castanea henryi
type: item
type: AcademicArticle
description: Background Many plants, including those commonly found in the Fagaceae family, produce more flowers and ovules than mature fruits and seeds. In Castanea henryi, an ovary contains 16–24 ovules, but only one develops into a seed. The other ovules abort or otherwise fail to fully develop, but the reason for this is unknown. Such a strict reproductive screening mechanism is rare in plants. Methods In this study, controlled pollination scheme were adopted, and conventional paraffin embedding and semi-thin sectioning techniques, followed by microscopy, were used for cytological studies of ovule development in C. henryi. Results Pollination affected not only the process of ovule development, but also the proportion of ovules that formed mature embryo sacs. Approximately 53.53% of the ovules in the pollinated treatment developed normally, while only 16.55% of the ovules in the unpollinated treatment developed into mature embryo sacs with a seven-cell, eight-nucleated structure. Failure to form mature embryo sacs and the abnormal divisions of the zygote, respectively, were the reasons for the pre- and post-fertilization ovule failures. Our findings not only provide basic information on the reproductive biology and also information on seed production of C. henryi.
format: application/pdf
format: text/html
creator: Qi Qiu
creator: Xiaoming Tian
creator: Guolong Wu
creator: Juntao Wu
creator: Deyi Yuan
creator: Xiaoming Fan
subject: Cell Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.18711
publisher: PeerJ Inc.
rights: © 2025 Qiu et al.
abstract: Background Many plants, including those commonly found in the Fagaceae family, produce more flowers and ovules than mature fruits and seeds. In Castanea henryi, an ovary contains 16–24 ovules, but only one develops into a seed. The other ovules abort or otherwise fail to fully develop, but the reason for this is unknown. Such a strict reproductive screening mechanism is rare in plants. Methods In this study, controlled pollination scheme were adopted, and conventional paraffin embedding and semi-thin sectioning techniques, followed by microscopy, were used for cytological studies of ovule development in C. henryi. Results Pollination affected not only the process of ovule development, but also the proportion of ovules that formed mature embryo sacs. Approximately 53.53% of the ovules in the pollinated treatment developed normally, while only 16.55% of the ovules in the unpollinated treatment developed into mature embryo sacs with a seven-cell, eight-nucleated structure. Failure to form mature embryo sacs and the abnormal divisions of the zygote, respectively, were the reasons for the pre- and post-fertilization ovule failures. Our findings not only provide basic information on the reproductive biology and also information on seed production of C. henryi.
bibliographic citation: Qiu et al. (2025) Basis of single-seed formation in chestnut: cytomorphological observations reveal ovule developmental patterns of Castanea henryi. PeerJ 13:e18711 https://doi.org/10.7717/peerj.18711
date submitted: 2024-03-20
date accepted: 2024-11-24
issued: 2025-01-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qiu
  given name: Qi
author list: Agent
  family name: Tian
  given name: Xiaoming
author list: Agent
  family name: Wu
  given name: Guolong
author list: Agent
  family name: Wu
  given name: Juntao
author list: Agent
  family name: Yuan
  given name: Deyi
author list: Agent
  family name: Fan
  given name: Xiaoming
doi: 10.7717/peerj.18711
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-02
copyright: © 2025 Qiu et al.
attribution name: Qiu et al.

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