PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Associations of anthropometric indices with body adiposity for assessing cardiovascular risk in people living with HIV: a cross-sectional study
items: Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool
items: Accelerating silage maize breeding: forage yield and nutritive quality of doubled haploid-derived hybrids
items: Effects of exercise intervention on falls and balance function in older adults: a systematic review and meta-analysis
items: Prevalence and risk factors of sarcopenia and effect of sarcopenia on functional status and falls incidents among the elderly in Selangor
items: Remarkable dominance of myctophid otoliths in Upper Miocene Chagres Formation, Caribbean Panama
items: Role of initial facial attractiveness in the perceived aesthetic outcome of convex profile treatment
items: Morphological variations of the femoral head-neck junction in historical skeletal material
items: Finite element analysis of root canal filling materials in retained primary molars with congenital tooth agenesis
items: Microbiological and clinical characteristics of hypervirulent Klebsiella pneumoniae isolated from patients in tertiary centers: a retrospective study

Associations of anthropometric indices with body adiposity for assessing cardiovascular risk in people living with HIV: a cross-sectional study
type: item
type: AcademicArticle
description: Background The presence of HIV infection is associated with an elevated risk of developing cardiovascular disease (CVD), which can be attributed to a range of factors, related to the virus itself. These include increased levels of inflammation and immune activation. Following the introduction of antiretroviral therapy, people living with HIV (PLHIV) began to exhibit an increase in body weight. However, this was also associated with an elevated risk of developing metabolic disorders. The aim of this study was to examine the association between anthropometric indices of cardiovascular risk—waist-to-hip ratio (WHR), waist-to-height ratio (WHtR) and conicity index (CI)—with body composition and time of infection in PLHIV. Methods An analytical cross-sectional study consisting of 17 PLHIV of both sexes is conducted. The following anthropometric indices were measured: body weight, height, body mass index (BMI), waist and hip circumference, body fat (BF), WHR, WHtR and CI. For the purposes of statistical analysis, the agreement between the methods used for the diagnosis of cardiovascular risk was verified using the Kappa coefficient. The associations were then verified using the Pearson’s “r” coefficient. The level of significance was set at p < 0.05. Results The results of the association analyzes between the anthropometric indices WHR, WHtR and CI indicated that WHR and CI were inversely correlated with total BF (kg). Consequently, there was consensus regarding CVD risk between WHR and CI, as well as between the three indices collectively. However, no significant association was observed between the anthropometric indices WHR, WHtR and CI and the duration of HIV infection. Conclusion Therefore, it can be concluded that when evaluating the risk of CVD in PLHIV, it is more reliable to associate WHR, WHtR and CI together than to use these indices separately, and total BF can be associated with CI or WHR for a risk assessment.
format: application/pdf
format: text/html
creator: Elaine Alana Duarte Fernandes
creator: Suerda Teixeira
creator: Phelipe Wilde De Alcântara Varela
creator: Júlio César Medeiros Alves
creator: Paulo Francisco de Almeida-Neto
creator: Carlos Gomes
creator: Breno Guilherme de Araújo Tinôco Cabral
creator: Paulo Moreira Silva Dantas
subject: Cardiology
subject: Global Health
subject: HIV
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.18833
publisher: PeerJ Inc.
rights: © 2025 Duarte Fernandes et al.
abstract: Background The presence of HIV infection is associated with an elevated risk of developing cardiovascular disease (CVD), which can be attributed to a range of factors, related to the virus itself. These include increased levels of inflammation and immune activation. Following the introduction of antiretroviral therapy, people living with HIV (PLHIV) began to exhibit an increase in body weight. However, this was also associated with an elevated risk of developing metabolic disorders. The aim of this study was to examine the association between anthropometric indices of cardiovascular risk—waist-to-hip ratio (WHR), waist-to-height ratio (WHtR) and conicity index (CI)—with body composition and time of infection in PLHIV. Methods An analytical cross-sectional study consisting of 17 PLHIV of both sexes is conducted. The following anthropometric indices were measured: body weight, height, body mass index (BMI), waist and hip circumference, body fat (BF), WHR, WHtR and CI. For the purposes of statistical analysis, the agreement between the methods used for the diagnosis of cardiovascular risk was verified using the Kappa coefficient. The associations were then verified using the Pearson’s “r” coefficient. The level of significance was set at p < 0.05. Results The results of the association analyzes between the anthropometric indices WHR, WHtR and CI indicated that WHR and CI were inversely correlated with total BF (kg). Consequently, there was consensus regarding CVD risk between WHR and CI, as well as between the three indices collectively. However, no significant association was observed between the anthropometric indices WHR, WHtR and CI and the duration of HIV infection. Conclusion Therefore, it can be concluded that when evaluating the risk of CVD in PLHIV, it is more reliable to associate WHR, WHtR and CI together than to use these indices separately, and total BF can be associated with CI or WHR for a risk assessment.
bibliographic citation: Duarte Fernandes et al. (2025) Associations of anthropometric indices with body adiposity for assessing cardiovascular risk in people living with HIV: a cross-sectional study. PeerJ 13:e18833 https://doi.org/10.7717/peerj.18833
date submitted: 2024-08-13
date accepted: 2024-12-17
issued: 2025-10-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duarte Fernandes
  given name: Elaine Alana
author list: Agent
  family name: Teixeira
  given name: Suerda
author list: Agent
  family name: Varela
  given name: Phelipe Wilde De Alcântara
author list: Agent
  family name: Alves
  given name: Júlio César Medeiros
author list: Agent
  family name: Almeida-Neto
  given name: Paulo Francisco de
author list: Agent
  family name: Gomes
  given name: Carlos
author list: Agent
  family name: Cabral
  given name: Breno Guilherme de Araújo Tinôco
author list: Agent
  family name: Dantas
  given name: Paulo Moreira Silva
doi: 10.7717/peerj.18833
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-20
copyright: ©2025 Duarte Fernandes et al.
attribution name: Duarte Fernandes et al.

Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool
type: item
type: AcademicArticle
description: Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecological and biomedical significance of spore-forming Bacilli and Clostridia, most taxa remain uncultivated, limiting phenotypic characterization of their sporulation capacity. To bridge this knowledge gap, we developed SpoMAG, an ensemble machine learning framework that predicts sporulation potential of metagenome-assembled genomes (MAGs) through supervised classification models trained on the presence/absence of 160 sporulation-associated genes. This R-based tool integrates Random Forest and support vector machine algorithms, achieving probabilistic predictions with high performance (AUC = 92.2%, F1-score = 88.2%). Application to fecal metagenomes from humans, cattle, poultry, and swine identified 63 putatively spore-forming MAGs exhibiting distinct host- and order-specific patterns. Bacilli MAGs from Bacillales and Paenibacillales orders showed high sporulation probabilities and gene richness, while Clostridia MAGs exhibited more heterogeneous profiles. Predictions included undercharacterized families in the spore-forming perspective, such as Acetivibrionaceae, Christensenellaceae, and UBA1381, expanding the known phylogenetic breadth of sporulation capacity. Nine genes were consistently present across all predicted spore-formers (namely pth, yaaT, spoIIAB, spoIIIAE, spoIIIAD, ctpB, ftsW, spoVD, and lgt), suggesting conserved genetic elements across uncultivated Firmicutes for future research. Average nucleotide identity (ANI) analysis revealed seven cases of species-level sharing (ANI value > 95%) among hosts, including a putative novel Acetivibrionaceae species, suggesting possible cross-host transmission facilitated by sporulation. In all 63 genomes predicted to sporulate, we identified nine genes across sporulation steps. In ad…
format: application/pdf
format: text/html
creator: Douglas Terra Machado
creator: Otávio José Bernardes Brustolini
creator: Ellen dos Santos Corrêa
creator: Ana Tereza Ribeiro Vasconcelos
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.20232
publisher: PeerJ Inc.
rights: © 2025 Terra Machado et al.
abstract: Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecological and biomedical significance of spore-forming Bacilli and Clostridia, most taxa remain uncultivated, limiting phenotypic characterization of their sporulation capacity. To bridge this knowledge gap, we developed SpoMAG, an ensemble machine learning framework that predicts sporulation potential of metagenome-assembled genomes (MAGs) through supervised classification models trained on the presence/absence of 160 sporulation-associated genes. This R-based tool integrates Random Forest and support vector machine algorithms, achieving probabilistic predictions with high performance (AUC = 92.2%, F1-score = 88.2%). Application to fecal metagenomes from humans, cattle, poultry, and swine identified 63 putatively spore-forming MAGs exhibiting distinct host- and order-specific patterns. Bacilli MAGs from Bacillales and Paenibacillales orders showed high sporulation probabilities and gene richness, while Clostridia MAGs exhibited more heterogeneous profiles. Predictions included undercharacterized families in the spore-forming perspective, such as Acetivibrionaceae, Christensenellaceae, and UBA1381, expanding the known phylogenetic breadth of sporulation capacity. Nine genes were consistently present across all predicted spore-formers (namely pth, yaaT, spoIIAB, spoIIIAE, spoIIIAD, ctpB, ftsW, spoVD, and lgt), suggesting conserved genetic elements across uncultivated Firmicutes for future research. Average nucleotide identity (ANI) analysis revealed seven cases of species-level sharing (ANI value > 95%) among hosts, including a putative novel Acetivibrionaceae species, suggesting possible cross-host transmission facilitated by sporulation. In all 63 genomes predicted to sporulate, we identified nine genes across sporulation steps. In ad…
bibliographic citation: Terra Machado et al. (2025) Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool. PeerJ 13:e20232 https://doi.org/10.7717/peerj.20232
date submitted: 2025-07-11
date accepted: 2025-09-23
issued: 2025-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Terra Machado
  given name: Douglas
author list: Agent
  family name: Bernardes Brustolini
  given name: Otávio José
author list: Agent
  family name: dos Santos Corrêa
  given name: Ellen
author list: Agent
  family name: Ribeiro Vasconcelos
  given name: Ana Tereza
doi: 10.7717/peerj.20232
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-17
copyright: ©2025 Terra Machado et al.
attribution name: Terra Machado et al.

Accelerating silage maize breeding: forage yield and nutritive quality of doubled haploid-derived hybrids
type: item
type: AcademicArticle
description: Background Maize (Zea mays L.) is a widely cultivated cereal crop for silage production due to its high biomass yield and nutritional value. Developing high-yielding and nutritionally superior hybrids is increasingly vital in the face of climate change and rising global forage demand. Doubled haploid (DH) technology accelerates hybrid development by enabling the rapid production of fully homozygous pure lines. This study aimed to evaluate silage maize hybrids derived from DH inbred lines for the effects of yield and nutritional quality. Methods Eight recently developed hybrids (derived from doubled haploid inbred lines: S1, S2, S6, S9, and S11; derived from conventional inbred lines: S7, S8, and S10) and four commercial silage checks (S3, S4, S5, and S12) were used in this study. The experiments were arranged in a randomized complete block design with three replications. In this study, agronomic traits including plant height, ear ratio, stem ratio, and forage yield were evaluated, along with forage quality parameters such as dry matter, crude protein, neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), and relative feed value. Results Genotypes S6 and S9 provided higher forage yield, plant height, ear ratio, and a lower stem ratio. All genotypes of dry matter, crude protein, NDF, and ADF values were within the desired range. DH-derived hybrids outperformed checks and those derived from conventional inbred lines regarding forage yield and the investigated agronomic traits. The DH technology has great potential in developing high-yielding hybrids in a short time in silage maize breeding.
format: application/pdf
format: text/html
creator: Sinem Zere Taşkın
creator: Ahmet Duman
creator: Uğur Bilgili
subject: Agricultural Science
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.20197
publisher: PeerJ Inc.
rights: © 2025 Zere Taşkın et al.
abstract: Background Maize (Zea mays L.) is a widely cultivated cereal crop for silage production due to its high biomass yield and nutritional value. Developing high-yielding and nutritionally superior hybrids is increasingly vital in the face of climate change and rising global forage demand. Doubled haploid (DH) technology accelerates hybrid development by enabling the rapid production of fully homozygous pure lines. This study aimed to evaluate silage maize hybrids derived from DH inbred lines for the effects of yield and nutritional quality. Methods Eight recently developed hybrids (derived from doubled haploid inbred lines: S1, S2, S6, S9, and S11; derived from conventional inbred lines: S7, S8, and S10) and four commercial silage checks (S3, S4, S5, and S12) were used in this study. The experiments were arranged in a randomized complete block design with three replications. In this study, agronomic traits including plant height, ear ratio, stem ratio, and forage yield were evaluated, along with forage quality parameters such as dry matter, crude protein, neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), and relative feed value. Results Genotypes S6 and S9 provided higher forage yield, plant height, ear ratio, and a lower stem ratio. All genotypes of dry matter, crude protein, NDF, and ADF values were within the desired range. DH-derived hybrids outperformed checks and those derived from conventional inbred lines regarding forage yield and the investigated agronomic traits. The DH technology has great potential in developing high-yielding hybrids in a short time in silage maize breeding.
bibliographic citation: Zere Taşkın et al. (2025) Accelerating silage maize breeding: forage yield and nutritive quality of doubled haploid-derived hybrids. PeerJ 13:e20197 https://doi.org/10.7717/peerj.20197
date submitted: 2025-07-11
date accepted: 2025-09-16
issued: 2025-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zere Taşkın
  given name: Sinem
author list: Agent
  family name: Duman
  given name: Ahmet
author list: Agent
  family name: Bilgili
  given name: Uğur
doi: 10.7717/peerj.20197
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-17
copyright: © 2025 Zere Taşkın et al.
attribution name: Zere Taşkın et al.

Effects of exercise intervention on falls and balance function in older adults: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective To systematically review the effects of an exercise intervention on falls and balance function in older adults (aged > 60 years) without diagnosed diseases. Methods PubMed, Web of Science, Embase, Cochrane Library, and CNKI databases were searched for randomized controlled trials about exercise intervention on falls and balance function in older adults. Use Review Manager 5.4 to test the risk bias in the included literature, and use Stata17 for publication bias test, sensitivity analysis, combining effect sizes, forest plots, and subgroup analysis. Results A total of 37 randomized controlled trials were included, and meta-analysis showed that after the exercise intervention in the intervention group, there was a significant increase in the Modified Fall Efficacy Scale (MFES) score (g = 1.01, 95% confidence interval (CI) [0.63–1.40], P = 0.00), the number of falls (odds ratio (OR) = 0.32, 95% CI [0.20–0.51], P = 0.00), the Berg Balance Scale (BBS) score (g = 0.92, 95% CI [0.63–1.21], P = 0.00) and Timed Up and Go Test (g = −0.62, 95% CI [−0.80, −0.45], P = 0.00) indices improved better than the control group. Subgroup analysis showed that single exercise time > 30 min, 3 times per week for 12–23 weeks was the better intervention for fall efficacy in older adults, and single exercise time ≤ 30 min, 3 times per week for ≥ 24 weeks was the better intervention for balance function in older adults. Conclusion Exercise intervention can enhance fall efficacy, reduce the number of falls, and improve balance function in older adults, and have a certain preventive effect on falls. Single exercise time, exercise frequency and exercise cycle are important factors affecting the effectiveness of exercise intervention. Systematic review registration: https://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42024590937.
format: application/pdf
format: text/html
creator: Haoran Yu
creator: Jianwei Zhong
creator: Min Li
creator: Shuainan Chen
subject: Global Health
subject: Kinesiology
subject: Public Health
description: doi:10.7717/peerj.20190
publisher: PeerJ Inc.
rights: © 2025 Yu et al.
abstract: Objective To systematically review the effects of an exercise intervention on falls and balance function in older adults (aged > 60 years) without diagnosed diseases. Methods PubMed, Web of Science, Embase, Cochrane Library, and CNKI databases were searched for randomized controlled trials about exercise intervention on falls and balance function in older adults. Use Review Manager 5.4 to test the risk bias in the included literature, and use Stata17 for publication bias test, sensitivity analysis, combining effect sizes, forest plots, and subgroup analysis. Results A total of 37 randomized controlled trials were included, and meta-analysis showed that after the exercise intervention in the intervention group, there was a significant increase in the Modified Fall Efficacy Scale (MFES) score (g = 1.01, 95% confidence interval (CI) [0.63–1.40], P = 0.00), the number of falls (odds ratio (OR) = 0.32, 95% CI [0.20–0.51], P = 0.00), the Berg Balance Scale (BBS) score (g = 0.92, 95% CI [0.63–1.21], P = 0.00) and Timed Up and Go Test (g = −0.62, 95% CI [−0.80, −0.45], P = 0.00) indices improved better than the control group. Subgroup analysis showed that single exercise time > 30 min, 3 times per week for 12–23 weeks was the better intervention for fall efficacy in older adults, and single exercise time ≤ 30 min, 3 times per week for ≥ 24 weeks was the better intervention for balance function in older adults. Conclusion Exercise intervention can enhance fall efficacy, reduce the number of falls, and improve balance function in older adults, and have a certain preventive effect on falls. Single exercise time, exercise frequency and exercise cycle are important factors affecting the effectiveness of exercise intervention. Systematic review registration: https://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42024590937.
bibliographic citation: Yu et al. (2025) Effects of exercise intervention on falls and balance function in older adults: a systematic review and meta-analysis. PeerJ 13:e20190 https://doi.org/10.7717/peerj.20190
date submitted: 2024-12-06
date accepted: 2025-09-15
issued: 2025-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Haoran
author list: Agent
  family name: Zhong
  given name: Jianwei
author list: Agent
  family name: Li
  given name: Min
author list: Agent
  family name: Chen
  given name: Shuainan
doi: 10.7717/peerj.20190
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-17
copyright: ©2025 Yu et al.
attribution name: Yu et al.

Prevalence and risk factors of sarcopenia and effect of sarcopenia on functional status and falls incidents among the elderly in Selangor
type: item
type: AcademicArticle
description: Background The burden of sarcopenia is increasing but studies on sarcopenia at the population level are limited in Malaysia. This study was conducted to identify the prevalence, risk factors and effect of sarcopenia on functional status and falls among the elderly in Selangor state. Methods Anthropometry, body composition measurements and face-to-face interview using questionnaires on functional status and falls were conducted on 469 respondents. Prior to the interview, written informed consent was obtained from the respondents. The inclusion criteria for this study is being 60-years old and above, able to understand, read and speak Bahasa Malaysia or English language and voluntarily consents to participates in the study. Multifrequency bioelectrical impedance analysis (BIA) was used to measure the body composition. Sarcopenia assessment was done using the guideline from Asian Working Group for Sarcopenia (AWGS) 2019. Results The prevalence of possible sarcopenia, confirmed sarcopenia and severe sarcopenia were 38.4%, 10.0% and 24.5%, respectively. Prevalence of activities of daily living (ADL) and instrumental activities of daily living (IADL) dependence were 26.0% and 25.4%, respectively and 42.2% of the respondents experienced falls in the last 12 months. Multinomial logistic regression model showed that locality (AOR = 2.90; p < 0.001), type-2 diabetes mellitus (adjusted odds ratio (AOR) = 1.87; p = 0.031) and female gender (AOR = 2.58; p < 0.001) were significantly associated with possible sarcopenia. Female gender (AOR = 3.04; p = 0.005) and depression (AOR = 3.27; p = 0.048) were significantly associated with confirmed sarcopenia, where else hypertension (AOR = 0.45; p = 0.039) were found to be a protective factor for confirmed sarcopenia. Age (AOR = 4.52; p < 0.001), female gender (AOR = 1.84; p = 0.045), race (AOR = 3.82; p = 0.001), locality (AOR = 3.82; p < 0.001), level of education (AOR = 5.32; p = 0.010) and physical activity (AOR = 2.28; p = 0.029) we…
format: application/pdf
format: text/html
creator: Thinakaran Kandayah
creator: Nazarudin Safian
creator: Shamsul Azhar Shah
subject: Epidemiology
subject: Geriatrics
subject: Public Health
subject: Rehabilitation
description: doi:10.7717/peerj.20175
publisher: PeerJ Inc.
rights: © 2025
abstract: Background The burden of sarcopenia is increasing but studies on sarcopenia at the population level are limited in Malaysia. This study was conducted to identify the prevalence, risk factors and effect of sarcopenia on functional status and falls among the elderly in Selangor state. Methods Anthropometry, body composition measurements and face-to-face interview using questionnaires on functional status and falls were conducted on 469 respondents. Prior to the interview, written informed consent was obtained from the respondents. The inclusion criteria for this study is being 60-years old and above, able to understand, read and speak Bahasa Malaysia or English language and voluntarily consents to participates in the study. Multifrequency bioelectrical impedance analysis (BIA) was used to measure the body composition. Sarcopenia assessment was done using the guideline from Asian Working Group for Sarcopenia (AWGS) 2019. Results The prevalence of possible sarcopenia, confirmed sarcopenia and severe sarcopenia were 38.4%, 10.0% and 24.5%, respectively. Prevalence of activities of daily living (ADL) and instrumental activities of daily living (IADL) dependence were 26.0% and 25.4%, respectively and 42.2% of the respondents experienced falls in the last 12 months. Multinomial logistic regression model showed that locality (AOR = 2.90; p < 0.001), type-2 diabetes mellitus (adjusted odds ratio (AOR) = 1.87; p = 0.031) and female gender (AOR = 2.58; p < 0.001) were significantly associated with possible sarcopenia. Female gender (AOR = 3.04; p = 0.005) and depression (AOR = 3.27; p = 0.048) were significantly associated with confirmed sarcopenia, where else hypertension (AOR = 0.45; p = 0.039) were found to be a protective factor for confirmed sarcopenia. Age (AOR = 4.52; p < 0.001), female gender (AOR = 1.84; p = 0.045), race (AOR = 3.82; p = 0.001), locality (AOR = 3.82; p < 0.001), level of education (AOR = 5.32; p = 0.010) and physical activity (AOR = 2.28; p = 0.029) we…
bibliographic citation: Kandayah et al. (2025) Prevalence and risk factors of sarcopenia and effect of sarcopenia on functional status and falls incidents among the elderly in Selangor. PeerJ 13:e20175 https://doi.org/10.7717/peerj.20175
date submitted: 2025-04-07
date accepted: 2025-09-12
issued: 2025-10-17
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Kandayah
  given name: Thinakaran
author list: Agent
  family name: Safian
  given name: Nazarudin
author list: Agent
  family name: Shah
  given name: Shamsul Azhar
doi: 10.7717/peerj.20175
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-17

Remarkable dominance of myctophid otoliths in Upper Miocene Chagres Formation, Caribbean Panama
type: item
type: AcademicArticle
description: Marine fossils from the Upper Miocene Chagres Formation in northern Panama offer critical insights into the paleoenvironmental conditions and ecological responses prior to the separation of the Atlantic from the Pacific by the formation of the Isthmus of Panama. Here we present a systematic study based on more than 6,200 otoliths collected from a coastal exposure near the town of Piña, Colón. This assemblage is remarkable for the extraordinary dominance of the family Myctophidae, constituting over 96% of specimens. The otolith density in the sediments is among the richest known globally (278.80 ± 135.59 otoliths/kg). The taxonomic composition is represented by 31 taxa across 12 families, including four new species: namely Chiloconger aflorens sp. nov., Dasyscopelus inopinatus sp. nov., Hoplostethus boyae sp. nov., and Malakichthys schwarzhansi sp. nov. Taphonomic evidence, combined with abundant predatory marine vertebrate fossils and extensive burrow ichnofossils, indicates a dynamic and highly productive nearshore ecosystem. The dominance of myctophids and multiple lines of evidence support the existence of a Late Miocene coastal upwelling system in the region, highlighted by efficient trophic transfer channeled from high primary production to apex predators. These findings provide a nuanced understanding of Neogene marine ecosystems prior to the final emergence of the Isthmus of Panama.
format: application/pdf
format: text/html
creator: Chien-Hsiang Lin
creator: Aaron O’Dea
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.20155
publisher: PeerJ Inc.
rights: © 2025 Lin and O’Dea
abstract: Marine fossils from the Upper Miocene Chagres Formation in northern Panama offer critical insights into the paleoenvironmental conditions and ecological responses prior to the separation of the Atlantic from the Pacific by the formation of the Isthmus of Panama. Here we present a systematic study based on more than 6,200 otoliths collected from a coastal exposure near the town of Piña, Colón. This assemblage is remarkable for the extraordinary dominance of the family Myctophidae, constituting over 96% of specimens. The otolith density in the sediments is among the richest known globally (278.80 ± 135.59 otoliths/kg). The taxonomic composition is represented by 31 taxa across 12 families, including four new species: namely Chiloconger aflorens sp. nov., Dasyscopelus inopinatus sp. nov., Hoplostethus boyae sp. nov., and Malakichthys schwarzhansi sp. nov. Taphonomic evidence, combined with abundant predatory marine vertebrate fossils and extensive burrow ichnofossils, indicates a dynamic and highly productive nearshore ecosystem. The dominance of myctophids and multiple lines of evidence support the existence of a Late Miocene coastal upwelling system in the region, highlighted by efficient trophic transfer channeled from high primary production to apex predators. These findings provide a nuanced understanding of Neogene marine ecosystems prior to the final emergence of the Isthmus of Panama.
bibliographic citation: Lin et al. (2025) Remarkable dominance of myctophid otoliths in Upper Miocene Chagres Formation, Caribbean Panama. PeerJ 13:e20155 https://doi.org/10.7717/peerj.20155
date submitted: 2025-05-21
date accepted: 2025-09-08
issued: 2025-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Chien-Hsiang
author list: Agent
  family name: O’Dea
  given name: Aaron
doi: 10.7717/peerj.20155
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-17
copyright: ©2025 Lin and O’Dea
attribution name: Lin and O’Dea

Role of initial facial attractiveness in the perceived aesthetic outcome of convex profile treatment
type: item
type: AcademicArticle
description: Background Facial attractiveness significantly influences various life outcomes, motivating individuals to seek interventions for improvement. However, the actual benefits of such interventions and patient satisfaction largely depend on the perceived changes in facial appearance. This perception may be influenced by certain mediating factors. This study aimed to investigate how pre-treatment facial attractiveness affects the perceived facial appearance changes in convex profile patients undergoing orthodontic-surgical vs. orthodontic-only treatments. Methods The sample comprised 36 non-growing Class II Division 1 patients, divided evenly between treatments, with similar demographics, overjet, and treatment durations. The treatments had distinct effects on the facial contour angle (orthodontics-only: −1.2 ± 2.1°, combined orthodontics/surgery: −6.2 ± 3.9°; p < 0.001). Pre-treatment attractiveness and perceived facial changes were evaluated using frontal and profile photographs, assessed on a 100 mm visual analog scale (VAS). Each photographic set was rated by 10 surgeons, 10 orthodontists, 10 patients, and 20 laypeople, resulting in 3,600 completed questionnaires for perceived treatment effects and an additional 3,600 for attractiveness ratings. Results The overall facial attractiveness was lower than average (mean: 36.1), with orthodontics-only patients being significantly more attractive than patients that received surgery (mean difference: 8.2%, p < 0.001) and no significant influence of patient sex or rater type. For every 1% increase in overall facial attractiveness, there was a 0.3% decrease in the perceived facial change (p = 0.002). After accounting for pre-treatment facial attractiveness, the combined orthodontic/surgical treatment led to a substantial improvement (16%) of facial appearance, as compared to the orthodontics-only group. Conclusions The study highlights the critical role of facial attractiveness in shaping perceived treatment outcomes. Pre-trea…
format: application/pdf
format: text/html
creator: Simos Psomiadis
creator: Ioannis Iatrou
creator: Iosif Sifakakis
creator: Nikolaos Gkantidis
subject: Dentistry
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.19997
publisher: PeerJ Inc.
rights: © 2025 Psomiadis et al.
abstract: Background Facial attractiveness significantly influences various life outcomes, motivating individuals to seek interventions for improvement. However, the actual benefits of such interventions and patient satisfaction largely depend on the perceived changes in facial appearance. This perception may be influenced by certain mediating factors. This study aimed to investigate how pre-treatment facial attractiveness affects the perceived facial appearance changes in convex profile patients undergoing orthodontic-surgical vs. orthodontic-only treatments. Methods The sample comprised 36 non-growing Class II Division 1 patients, divided evenly between treatments, with similar demographics, overjet, and treatment durations. The treatments had distinct effects on the facial contour angle (orthodontics-only: −1.2 ± 2.1°, combined orthodontics/surgery: −6.2 ± 3.9°; p < 0.001). Pre-treatment attractiveness and perceived facial changes were evaluated using frontal and profile photographs, assessed on a 100 mm visual analog scale (VAS). Each photographic set was rated by 10 surgeons, 10 orthodontists, 10 patients, and 20 laypeople, resulting in 3,600 completed questionnaires for perceived treatment effects and an additional 3,600 for attractiveness ratings. Results The overall facial attractiveness was lower than average (mean: 36.1), with orthodontics-only patients being significantly more attractive than patients that received surgery (mean difference: 8.2%, p < 0.001) and no significant influence of patient sex or rater type. For every 1% increase in overall facial attractiveness, there was a 0.3% decrease in the perceived facial change (p = 0.002). After accounting for pre-treatment facial attractiveness, the combined orthodontic/surgical treatment led to a substantial improvement (16%) of facial appearance, as compared to the orthodontics-only group. Conclusions The study highlights the critical role of facial attractiveness in shaping perceived treatment outcomes. Pre-trea…
bibliographic citation: Psomiadis et al. (2025) Role of initial facial attractiveness in the perceived aesthetic outcome of convex profile treatment. PeerJ 13:e19997 https://doi.org/10.7717/peerj.19997
date submitted: 2025-02-26
date accepted: 2025-08-06
issued: 2025-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Psomiadis
  given name: Simos
author list: Agent
  family name: Iatrou
  given name: Ioannis
author list: Agent
  family name: Sifakakis
  given name: Iosif
author list: Agent
  family name: Gkantidis
  given name: Nikolaos
doi: 10.7717/peerj.19997
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-17
copyright: © 2025 Psomiadis et al.
attribution name: Psomiadis et al.

Morphological variations of the femoral head-neck junction in historical skeletal material
type: item
type: AcademicArticle
description: Background Poirier’s facet, Allen’s fossa and femoral plague are the main morphological variations of the femoral head-neck junction. The study aimed to answer questions about the association between the shape of the proximal end of the femoral bone and acetabulum in bones with head-neck junction changes and the differences in shape and size between joints with the above changes and joints without ones. Methods The analyses were performed on the computed tomography scans (CTs) of the 52 sets of bones (femur and pelvic bone) from the Polish skeletal material dated to the 14th–19th centuries. Based on CTs, three-dimensional models of the femurs and pelvic bones were created and then analysed using linear measurements and a geometric morphometric approach. Analysis of variance (ANOVA) was calculated to analyse differences in size; in turn, canonical variate analysis (CVA) was calculated to investigate changes in shape between bones with femoral-neck changes and bones without ones. Results According to the CVA, there were no significant differences in shape between bones with Allen’s fossa, femoral plaque, or Porier’s facet and hip joints without any observable changes (p > 0.05). Bones with observable Allen’s fossa, femoral plaque, Porier’s facet and hip joints without changes showed similar variations in femoral head shape. The difference was in the femoral head height between bones femoral plaque and bones with Allen’s fossa (p = 0.047, mean difference = 3.78 mm). Acetabula in the sets of bones without head-neck junction changes showed slightly lower shape variation than acetabulum in the sets of bones with changes. In joints with head-neck junction changes, a more indented antero-posterior part of the lunate surface and indented inferior edge along its entire length were observed. Conclusions Geometric morphometrics and measurements showed similarities in the shape of the joints with and without changes in head-neck junction region. This may indicate that morphologi…
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format: text/html
creator: Anna Myszka
creator: Anna Maria Kubicka
subject: Anthropology
subject: Anatomy and Physiology
subject: Orthopedics
description: doi:10.7717/peerj.20236
publisher: PeerJ Inc.
rights: © 2025 Myszka and Kubicka
abstract: Background Poirier’s facet, Allen’s fossa and femoral plague are the main morphological variations of the femoral head-neck junction. The study aimed to answer questions about the association between the shape of the proximal end of the femoral bone and acetabulum in bones with head-neck junction changes and the differences in shape and size between joints with the above changes and joints without ones. Methods The analyses were performed on the computed tomography scans (CTs) of the 52 sets of bones (femur and pelvic bone) from the Polish skeletal material dated to the 14th–19th centuries. Based on CTs, three-dimensional models of the femurs and pelvic bones were created and then analysed using linear measurements and a geometric morphometric approach. Analysis of variance (ANOVA) was calculated to analyse differences in size; in turn, canonical variate analysis (CVA) was calculated to investigate changes in shape between bones with femoral-neck changes and bones without ones. Results According to the CVA, there were no significant differences in shape between bones with Allen’s fossa, femoral plaque, or Porier’s facet and hip joints without any observable changes (p > 0.05). Bones with observable Allen’s fossa, femoral plaque, Porier’s facet and hip joints without changes showed similar variations in femoral head shape. The difference was in the femoral head height between bones femoral plaque and bones with Allen’s fossa (p = 0.047, mean difference = 3.78 mm). Acetabula in the sets of bones without head-neck junction changes showed slightly lower shape variation than acetabulum in the sets of bones with changes. In joints with head-neck junction changes, a more indented antero-posterior part of the lunate surface and indented inferior edge along its entire length were observed. Conclusions Geometric morphometrics and measurements showed similarities in the shape of the joints with and without changes in head-neck junction region. This may indicate that morphologi…
bibliographic citation: Myszka et al. (2025) Morphological variations of the femoral head-neck junction in historical skeletal material. PeerJ 13:e20236 https://doi.org/10.7717/peerj.20236
date submitted: 2025-05-28
date accepted: 2025-09-23
issued: 2025-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Myszka
  given name: Anna
author list: Agent
  family name: Kubicka
  given name: Anna Maria
doi: 10.7717/peerj.20236
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-16
copyright: ©2025 Myszka and Kubicka
attribution name: Myszka and Kubicka

Finite element analysis of root canal filling materials in retained primary molars with congenital tooth agenesis
type: item
type: AcademicArticle
description: Background The selection of an appropriate filling material in root canal treatments of primary molars is crucial for long-term success. However, evaluating the biomechanical behavior of these materials under in vivo conditions remains challenging. This study aimed to investigate the effect of different root canal filling materials on the fracture resistance of the mandibular second primary molar by analyzing stress distributions and failure risk using finite element analysis (FEA) models. Methods A mandibular second primary molar extracted for orthodontic reasons was used in the study. The tooth was scanned using micro-computed tomography (micro-CT) to obtain original DICOM data, which were imported into Geomagic + SpaceClaim 2023R2 to create a solid model. A total force of 330 N was applied to three points on the occlusal surface of each model. The analysis was conducted using Ansys mesh and evaluated with Hyperview 2024. Maximum von Mises (vM) stress values were used to assess stress distribution. Results The highest vM stress in the remaining dentin was observed in the gutta-percha (GP) + AH Plus model (148.5 MPa), followed by mineral trioxide aggregate (MTA) (127.24 MPa), Biodentine (125.65 MPa), and GP + BioRoot RCS (118.37 MPa). Stress concentrations were primarily located in the pericervical region. The GP + AH Plus group showed the highest stress, while the GP + BioRoot RCS group showed the lowest. Among contemporary filling materials, GP + BioRoot RCS demonstrated the lowest dentin stress, suggesting it may offer better root fracture resistance. However, generalizing these findings is difficult due to limited data on primary teeth in the literature. Conclusion The study suggests that GP + BioRoot RCS may be a more promising filling material for enhancing root fracture resistance in primary molars. Further research is needed to validate these findings in clinical settings.
format: application/pdf
format: text/html
creator: Gizem Karagöz Doğan
creator: Yelda Polat Yavuz
creator: Büşra Karaağaç Eskibağlar
subject: Bioengineering
subject: Dentistry
subject: Computational Science
subject: Data Science
description: doi:10.7717/peerj.20206
publisher: PeerJ Inc.
rights: © 2025 Karagöz Doğan et al.
abstract: Background The selection of an appropriate filling material in root canal treatments of primary molars is crucial for long-term success. However, evaluating the biomechanical behavior of these materials under in vivo conditions remains challenging. This study aimed to investigate the effect of different root canal filling materials on the fracture resistance of the mandibular second primary molar by analyzing stress distributions and failure risk using finite element analysis (FEA) models. Methods A mandibular second primary molar extracted for orthodontic reasons was used in the study. The tooth was scanned using micro-computed tomography (micro-CT) to obtain original DICOM data, which were imported into Geomagic + SpaceClaim 2023R2 to create a solid model. A total force of 330 N was applied to three points on the occlusal surface of each model. The analysis was conducted using Ansys mesh and evaluated with Hyperview 2024. Maximum von Mises (vM) stress values were used to assess stress distribution. Results The highest vM stress in the remaining dentin was observed in the gutta-percha (GP) + AH Plus model (148.5 MPa), followed by mineral trioxide aggregate (MTA) (127.24 MPa), Biodentine (125.65 MPa), and GP + BioRoot RCS (118.37 MPa). Stress concentrations were primarily located in the pericervical region. The GP + AH Plus group showed the highest stress, while the GP + BioRoot RCS group showed the lowest. Among contemporary filling materials, GP + BioRoot RCS demonstrated the lowest dentin stress, suggesting it may offer better root fracture resistance. However, generalizing these findings is difficult due to limited data on primary teeth in the literature. Conclusion The study suggests that GP + BioRoot RCS may be a more promising filling material for enhancing root fracture resistance in primary molars. Further research is needed to validate these findings in clinical settings.
bibliographic citation: Karagöz Doğan et al. (2025) Finite element analysis of root canal filling materials in retained primary molars with congenital tooth agenesis. PeerJ 13:e20206 https://doi.org/10.7717/peerj.20206
date submitted: 2025-03-25
date accepted: 2025-09-17
issued: 2025-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karagöz Doğan
  given name: Gizem
author list: Agent
  family name: Yavuz
  given name: Yelda Polat
author list: Agent
  family name: Karaağaç Eskibağlar
  given name: Büşra
doi: 10.7717/peerj.20206
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-16
copyright: ©2025 Karagöz Doğan et al.
attribution name: Karagöz Doğan et al.

Microbiological and clinical characteristics of hypervirulent Klebsiella pneumoniae isolated from patients in tertiary centers: a retrospective study
type: item
type: AcademicArticle
description: This cross-sectional, retrospective study aimed to investigate the prevalence of hypervirulent Klebsiella pneumoniae (hvKp), its virulence-associated genes, and the clinical manifestations of hvKp infections. HvKp was defined in this study as K. pneumoniae with a positive string test and harboring the serotype K1 or K2 gene. A total of 180 isolates from various clinical specimens were collected from four main hospitals in Kelantan. All isolates were examined for the hypermucoviscous phenotype using the string test, while the presence of capsular serotypes and other virulence genes (rmpA, rmpA2, iucA, magA, and peg-344) was determined by polymerase chain reaction (PCR). Patients’ clinical data were collected and analyzed. String test-positive isolates (23.8%, n = 43) were identified as hypermucoviscous K. pneumoniae (hmKp). Capsular serotypes K1 and K2 were detected in 11.1% (n = 20) and 6.1% (n = 11) of isolates, respectively. The prevalence of hvKp was 9.4% (n = 17). All hvKp isolates were positive for rmpA, rmpA2, iucA, and peg-344 genes, while all ten hvKp-K1 serotype isolates were positive for magA, the K1 serotype-specific gene. The associations between all corresponding virulence genes and serotypes K1 and K2 were statistically significant (p < 0.05). HvKp infections were more prevalent in men and individuals with hypertension. Pneumonia was the most common clinical diagnosis in hvKp-infected patients, with a mortality rate of 12%. The presence of all biomarkers (rmpA, rmpA2, magA (for K1 serotype), iucA, and peg-344) in hmKp, in combination with clinical manifestations, may serve as a reliable approach for hvKp diagnosis and epidemiological surveillance.
format: application/pdf
format: text/html
creator: Aimi Khairuddin
creator: Nik Mohd Noor Nik Zuraina
creator: Nur Syafiqah Mohamad Nasir
creator: Wei Chuan Chua
creator: Hamimi Salihah Abdul Halim
creator: Wardah Yusof
creator: Azura Hussin
creator: Chan Yean Yean
creator: Siti Asma’ Hassan
subject: Microbiology
subject: Molecular Biology
subject: Global Health
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.20198
publisher: PeerJ Inc.
rights: © 2025 Khairuddin et al.
abstract: This cross-sectional, retrospective study aimed to investigate the prevalence of hypervirulent Klebsiella pneumoniae (hvKp), its virulence-associated genes, and the clinical manifestations of hvKp infections. HvKp was defined in this study as K. pneumoniae with a positive string test and harboring the serotype K1 or K2 gene. A total of 180 isolates from various clinical specimens were collected from four main hospitals in Kelantan. All isolates were examined for the hypermucoviscous phenotype using the string test, while the presence of capsular serotypes and other virulence genes (rmpA, rmpA2, iucA, magA, and peg-344) was determined by polymerase chain reaction (PCR). Patients’ clinical data were collected and analyzed. String test-positive isolates (23.8%, n = 43) were identified as hypermucoviscous K. pneumoniae (hmKp). Capsular serotypes K1 and K2 were detected in 11.1% (n = 20) and 6.1% (n = 11) of isolates, respectively. The prevalence of hvKp was 9.4% (n = 17). All hvKp isolates were positive for rmpA, rmpA2, iucA, and peg-344 genes, while all ten hvKp-K1 serotype isolates were positive for magA, the K1 serotype-specific gene. The associations between all corresponding virulence genes and serotypes K1 and K2 were statistically significant (p < 0.05). HvKp infections were more prevalent in men and individuals with hypertension. Pneumonia was the most common clinical diagnosis in hvKp-infected patients, with a mortality rate of 12%. The presence of all biomarkers (rmpA, rmpA2, magA (for K1 serotype), iucA, and peg-344) in hmKp, in combination with clinical manifestations, may serve as a reliable approach for hvKp diagnosis and epidemiological surveillance.
bibliographic citation: Khairuddin et al. (2025) Microbiological and clinical characteristics of hypervirulent Klebsiella pneumoniae isolated from patients in tertiary centers: a retrospective study. PeerJ 13:e20198 https://doi.org/10.7717/peerj.20198
date submitted: 2025-03-31
date accepted: 2025-09-16
issued: 2025-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khairuddin
  given name: Aimi
author list: Agent
  family name: Nik Zuraina
  given name: Nik Mohd Noor
author list: Agent
  family name: Mohamad Nasir
  given name: Nur Syafiqah
author list: Agent
  family name: Chua
  given name: Wei Chuan
author list: Agent
  family name: Abdul Halim
  given name: Hamimi Salihah
author list: Agent
  family name: Yusof
  given name: Wardah
author list: Agent
  family name: Hussin
  given name: Azura
author list: Agent
  family name: Yean Yean
  given name: Chan
author list: Agent
  family name: Hassan
  given name: Siti Asma’
doi: 10.7717/peerj.20198
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-16
copyright: ©2025 Khairuddin et al.
attribution name: Khairuddin et al.

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