PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Wearable accelerometers reveal objective assessment of walking symmetry and regularity in idiopathic scoliosis patients
items: Production of recombinant human epidermal growth factor fused with HaloTag protein and characterisation of its biological functions
items: Aspergillus niger as an efficient biological agent for separator sludge remediation: two-level factorial design for optimal fermentation
items: Evaluation of the association of physical activity levels with self-perceived health, depression, and anxiety in Spanish individuals with high cholesterol levels: a retrospective cross-sectional study
items: The skull of the Turks and Caicos rock iguana, Cyclura carinata (Squamata: Iguanidae)
items: Effects of five types of exercise on vascular function in postmenopausal women: a network meta-analysis and systematic review of 32 randomized controlled trials
items: Comparison of radiomics-based machine-learning classifiers for the pretreatment prediction of pathologic complete response to neoadjuvant therapy in breast cancer
items: Bridging the gap in medical education: comparing analysis of light microscopy and virtual microscopy in histology
items: Genetic variability and population structure of two sympatric cownose rays Rhinoptera (Myliobatiformes, Rhinopteridae) in the Western Atlantic Ocean
items: Evaluation of dentin features in teeth after caries removal by three techniques (chemomechanical, mechanical with a smart bur, and air-abrasion): an in vitro study

Wearable accelerometers reveal objective assessment of walking symmetry and regularity in idiopathic scoliosis patients
type: item
type: AcademicArticle
description: Background Scoliosis is a multifaceted three-dimensional deformity that significantly affects patients’ balance function and walking process. While existing research primarily focuses on spatial and temporal parameters of walking and trunk/pelvic kinematics asymmetry, there remains controversy regarding the symmetry and regularity of bilateral lower limb gait. This study aims to investigate the symmetry and regularity of bilateral lower limb gait and examine the balance control strategy of the head during walking in patients with idiopathic scoliosis. Methods The study involved 17 patients with idiopathic scoliosis of Lenke 1 and Lenke 5 classifications, along with 17 healthy subjects for comparison. Three-dimensional accelerometers were attached to the head and L5 spinous process of each participant, and three-dimensional motion acceleration signals were collected during a 10-meter walking test. Analysis of the collected acceleration signals involved calculating five variables related to the symmetry and regularity of walking: root mean square (RMS) of the acceleration signal, harmonic ratio (HR), step regularity, stride regularity, and gait symmetry. Results Our analysis reveals that, during the walking process, the three-dimensional motion acceleration signals acquired from the lumbar region of patients diagnosed with idiopathic scoliosis exhibit noteworthy disparities in the RMS of the vertical axis (RMS-VT) and the HR of the vertical axis (HR-VT) when compared to the corresponding values in the healthy control (RMS-VT: 1.6 ± 0.41 vs. 3 ± 0.47, P < 0.05; HR-VT: 3 ± 0.72 vs. 3.9 ± 0.71, P < 0.05). Additionally, the motion acceleration signals of the head in three-dimensional space, including the RMS in the anterior-posterior and vertical axis, the HR-VT, and the values of step regularity in both anterior-posterior and vertical axis, as well as the values of stride regularity in all three axes, are all significantly lower than those in the healthy control group (P…
format: application/pdf
format: text/html
creator: Xiaopeng Gan
creator: Xin Liu
creator: Danxian Cai
creator: Rongbin Zhang
creator: Fanqiang Li
creator: Haohuang Fang
creator: Jingrou Huang
creator: Chenguang Qiu
creator: Hongrui Zhan
subject: Kinesiology
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.17739
publisher: PeerJ Inc.
rights: © 2024 Gan et al.
abstract: Background Scoliosis is a multifaceted three-dimensional deformity that significantly affects patients’ balance function and walking process. While existing research primarily focuses on spatial and temporal parameters of walking and trunk/pelvic kinematics asymmetry, there remains controversy regarding the symmetry and regularity of bilateral lower limb gait. This study aims to investigate the symmetry and regularity of bilateral lower limb gait and examine the balance control strategy of the head during walking in patients with idiopathic scoliosis. Methods The study involved 17 patients with idiopathic scoliosis of Lenke 1 and Lenke 5 classifications, along with 17 healthy subjects for comparison. Three-dimensional accelerometers were attached to the head and L5 spinous process of each participant, and three-dimensional motion acceleration signals were collected during a 10-meter walking test. Analysis of the collected acceleration signals involved calculating five variables related to the symmetry and regularity of walking: root mean square (RMS) of the acceleration signal, harmonic ratio (HR), step regularity, stride regularity, and gait symmetry. Results Our analysis reveals that, during the walking process, the three-dimensional motion acceleration signals acquired from the lumbar region of patients diagnosed with idiopathic scoliosis exhibit noteworthy disparities in the RMS of the vertical axis (RMS-VT) and the HR of the vertical axis (HR-VT) when compared to the corresponding values in the healthy control (RMS-VT: 1.6 ± 0.41 vs. 3 ± 0.47, P < 0.05; HR-VT: 3 ± 0.72 vs. 3.9 ± 0.71, P < 0.05). Additionally, the motion acceleration signals of the head in three-dimensional space, including the RMS in the anterior-posterior and vertical axis, the HR-VT, and the values of step regularity in both anterior-posterior and vertical axis, as well as the values of stride regularity in all three axes, are all significantly lower than those in the healthy control group (P…
bibliographic citation: Gan et al. (2024) Wearable accelerometers reveal objective assessment of walking symmetry and regularity in idiopathic scoliosis patients. PeerJ 12:e17739 https://doi.org/10.7717/peerj.17739
date submitted: 2024-04-12
date accepted: 2024-06-23
issued: 2024-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gan
  given name: Xiaopeng
author list: Agent
  family name: Liu
  given name: Xin
author list: Agent
  family name: Cai
  given name: Danxian
author list: Agent
  family name: Zhang
  given name: Rongbin
author list: Agent
  family name: Li
  given name: Fanqiang
author list: Agent
  family name: Fang
  given name: Haohuang
author list: Agent
  family name: Huang
  given name: Jingrou
author list: Agent
  family name: Qiu
  given name: Chenguang
author list: Agent
  family name: Zhan
  given name: Hongrui
doi: 10.7717/peerj.17739
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-16
copyright: ©2024 Gan et al.
attribution name: Gan et al.

Production of recombinant human epidermal growth factor fused with HaloTag protein and characterisation of its biological functions
type: item
type: AcademicArticle
description: Epidermal growth factor (EGF) protein is a crucial biomolecule involved in regulating cell growth, proliferation, migration and differentiation, which is used in various therapeutic applications, such as wound healing and tissue regeneration. The production of recombinant EGF is essential for studying its biological function and for its clinical translation. However, EGF protein expressed in prokaryotic cells often occurs in inclusion bodies, and co-expression with soluble tag protein is an effective method to prepare recombinant EGF. In this study, we expressed recombinant human EGF (rhEGF) fused to a HaloTag (Halo-rhEGF) and a large portion of Halo-rhEGF was found in the soluble fraction. Cell growth assay showed that the purified Halo-rhEGF protein could promote the proliferation of fibroblasts (NIH 3T3) and epithelial cells (HaCaT), and significantly increased their viability. Phosphorylation of the intracellular signaling proteins, ERK1/2 and c-Jun, was stimulated by treatment with Halo-rhEGF and the expression levels of proteins regulating cell proliferation were significantly increased. RNA sequencing analysis revealed that rhEGF could increase the transcription of genes enriched in ribosome generation and cell proliferation. Moreover, Halo-rhEGF can be labelled by HaloTag ligand for fluorescence imaging and can be slowly released in tissue repair by binding to anion biomaterials. In conclusion, HaloTag is an efficient fusion tag for rhEGF protein expression, purification and controlled release, and Halo-rhEGF can promote the proliferation and viability of epithelial and fibroblast cells.
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format: text/html
creator: Mengru Bai
creator: Yezhuo Liu
creator: Hongyin Liu
creator: Yangyang Jia
creator: Xiangqin Tian
creator: Changye Sun
subject: Biochemistry
subject: Biotechnology
subject: Cell Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.17806
publisher: PeerJ Inc.
rights: © 2024 Bai et al.
abstract: Epidermal growth factor (EGF) protein is a crucial biomolecule involved in regulating cell growth, proliferation, migration and differentiation, which is used in various therapeutic applications, such as wound healing and tissue regeneration. The production of recombinant EGF is essential for studying its biological function and for its clinical translation. However, EGF protein expressed in prokaryotic cells often occurs in inclusion bodies, and co-expression with soluble tag protein is an effective method to prepare recombinant EGF. In this study, we expressed recombinant human EGF (rhEGF) fused to a HaloTag (Halo-rhEGF) and a large portion of Halo-rhEGF was found in the soluble fraction. Cell growth assay showed that the purified Halo-rhEGF protein could promote the proliferation of fibroblasts (NIH 3T3) and epithelial cells (HaCaT), and significantly increased their viability. Phosphorylation of the intracellular signaling proteins, ERK1/2 and c-Jun, was stimulated by treatment with Halo-rhEGF and the expression levels of proteins regulating cell proliferation were significantly increased. RNA sequencing analysis revealed that rhEGF could increase the transcription of genes enriched in ribosome generation and cell proliferation. Moreover, Halo-rhEGF can be labelled by HaloTag ligand for fluorescence imaging and can be slowly released in tissue repair by binding to anion biomaterials. In conclusion, HaloTag is an efficient fusion tag for rhEGF protein expression, purification and controlled release, and Halo-rhEGF can promote the proliferation and viability of epithelial and fibroblast cells.
bibliographic citation: Bai et al. (2024) Production of recombinant human epidermal growth factor fused with HaloTag protein and characterisation of its biological functions. PeerJ 12:e17806 https://doi.org/10.7717/peerj.17806
date submitted: 2024-03-13
date accepted: 2024-07-03
issued: 2024-07-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Mengru
author list: Agent
  family name: Liu
  given name: Yezhuo
author list: Agent
  family name: Liu
  given name: Hongyin
author list: Agent
  family name: Jia
  given name: Yangyang
author list: Agent
  family name: Tian
  given name: Xiangqin
author list: Agent
  family name: Sun
  given name: Changye
doi: 10.7717/peerj.17806
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-16
copyright: © 2024 Bai et al.
attribution name: Bai et al.

Aspergillus niger as an efficient biological agent for separator sludge remediation: two-level factorial design for optimal fermentation
type: item
type: AcademicArticle
description: Background The booming palm oil industry is in line with the growing population worldwide and surge in demand. This leads to a massive generation of palm oil mill effluent (POME). POME is composed of sterilizer condensate (SC), separator sludge (SS), and hydro-cyclone wastewater (HCW). Comparatively, SS exhibits the highest organic content, resulting in various environmental impacts. However, past studies mainly focused on treating the final effluent. Therefore, this pioneering research investigated the optimization of pollutant removal in SS via different aspects of bioremediation, including experimental conditions, treatment efficiencies, mechanisms, and degradation pathways. Methods A two-level factorial design was employed to optimize the removal of chemical oxygen demand (COD) and turbidity using Aspergillus niger. Bioremediation of SS was performed through submerged fermentation (SmF) under several independent variables, including temperature (20–40 °C), agitation speed (100–200 RPM), fermentation duration (72–240 h), and initial sample concentration (20–100%). The characteristics of the treated SS were then compared to that of raw sludge. Results Optimal COD and turbidity removal were achieved at 37 °C 100 RPM, 156 h, and 100% sludge. The analysis of variance (ANOVA) revealed a significant effect of selective individual and interacting variables (p < 0.05). The highest COD and turbidity removal were 97.43% and 95.11%, respectively, with less than 5% error from the predicted values. Remarkably, the selected optimized conditions also reduced other polluting attributes, namely, biological oxygen demand (BOD), oil and grease (OG), color, and carbon content. In short, this study demonstrated the effectiveness of A. niger in treating SS through the application of a two-level factorial design.
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creator: Paveethra Thegarathah
creator: Jegalakshimi Jewaratnam
creator: Khanom Simarani
creator: Amal A.M. Elgharbawy
subject: Bioengineering
subject: Biotechnology
subject: Mycology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.17151
publisher: PeerJ Inc.
rights: © 2024 Thegarathah et al.
abstract: Background The booming palm oil industry is in line with the growing population worldwide and surge in demand. This leads to a massive generation of palm oil mill effluent (POME). POME is composed of sterilizer condensate (SC), separator sludge (SS), and hydro-cyclone wastewater (HCW). Comparatively, SS exhibits the highest organic content, resulting in various environmental impacts. However, past studies mainly focused on treating the final effluent. Therefore, this pioneering research investigated the optimization of pollutant removal in SS via different aspects of bioremediation, including experimental conditions, treatment efficiencies, mechanisms, and degradation pathways. Methods A two-level factorial design was employed to optimize the removal of chemical oxygen demand (COD) and turbidity using Aspergillus niger. Bioremediation of SS was performed through submerged fermentation (SmF) under several independent variables, including temperature (20–40 °C), agitation speed (100–200 RPM), fermentation duration (72–240 h), and initial sample concentration (20–100%). The characteristics of the treated SS were then compared to that of raw sludge. Results Optimal COD and turbidity removal were achieved at 37 °C 100 RPM, 156 h, and 100% sludge. The analysis of variance (ANOVA) revealed a significant effect of selective individual and interacting variables (p < 0.05). The highest COD and turbidity removal were 97.43% and 95.11%, respectively, with less than 5% error from the predicted values. Remarkably, the selected optimized conditions also reduced other polluting attributes, namely, biological oxygen demand (BOD), oil and grease (OG), color, and carbon content. In short, this study demonstrated the effectiveness of A. niger in treating SS through the application of a two-level factorial design.
bibliographic citation: Thegarathah et al. (2024) Aspergillus niger as an efficient biological agent for separator sludge remediation: two-level factorial design for optimal fermentation. PeerJ 12:e17151 https://doi.org/10.7717/peerj.17151
date submitted: 2023-08-08
date accepted: 2024-03-03
issued: 2024-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thegarathah
  given name: Paveethra
author list: Agent
  family name: Jewaratnam
  given name: Jegalakshimi
author list: Agent
  family name: Simarani
  given name: Khanom
author list: Agent
  family name: Elgharbawy
  given name: Amal A.M.
doi: 10.7717/peerj.17151
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-15
copyright: ©2024 Thegarathah et al.
attribution name: Thegarathah et al.

Evaluation of the association of physical activity levels with self-perceived health, depression, and anxiety in Spanish individuals with high cholesterol levels: a retrospective cross-sectional study
type: item
type: AcademicArticle
description: Background Hypercholesterolemia is the most common form of dyslipidaemia in the world leading to negative health effects, both physical and mental. Physical activity (PA) can reduce total cholesterol and has positive effects on mental health. This retrospective cross-sectional study analyses the relationships between physical activity level (PAL), self-perceived health (SPH) and mental health. Methods This study was based on data from the Spanish National Health Survey 2017 (SNHS 2017), with 3,176 Spanish adults with high cholesterol as participants. Non-parametric tests were used as the data did not follow normality. Results Dependent relationships were found between PAL and SPH, depression and anxiety. Women had higher depression and anxiety prevalences than men, while men were more likely to report being very active, although the proportion of walkers was higher in women. The physically inactive population presented higher negative SPH, depression and anxiety proportions and psychological distress than physically active people. Conclusion The physically inactive people had a higher risk of negative SPH, depression and anxiety. Regular PA may improve SPH and mental health in people with high cholesterol, but more studies are needed to establish causal relationships, mechanisms, and optimal doses.
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creator: Ángel Denche-Zamorano
creator: Jofre Pisà-Canyelles
creator: Sabina Barrios-Fernández
creator: Antonio Castillo-Paredes
creator: Raquel Pastor-Cisneros
creator: Maria Mendoza-Muñoz
creator: Diana Salas Gómez
creator: Cristina Mendoza Holgado
subject: Global Health
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.17169
publisher: PeerJ Inc.
rights: © 2024 Denche-Zamorano et al.
abstract: Background Hypercholesterolemia is the most common form of dyslipidaemia in the world leading to negative health effects, both physical and mental. Physical activity (PA) can reduce total cholesterol and has positive effects on mental health. This retrospective cross-sectional study analyses the relationships between physical activity level (PAL), self-perceived health (SPH) and mental health. Methods This study was based on data from the Spanish National Health Survey 2017 (SNHS 2017), with 3,176 Spanish adults with high cholesterol as participants. Non-parametric tests were used as the data did not follow normality. Results Dependent relationships were found between PAL and SPH, depression and anxiety. Women had higher depression and anxiety prevalences than men, while men were more likely to report being very active, although the proportion of walkers was higher in women. The physically inactive population presented higher negative SPH, depression and anxiety proportions and psychological distress than physically active people. Conclusion The physically inactive people had a higher risk of negative SPH, depression and anxiety. Regular PA may improve SPH and mental health in people with high cholesterol, but more studies are needed to establish causal relationships, mechanisms, and optimal doses.
bibliographic citation: Denche-Zamorano et al. (2024) Evaluation of the association of physical activity levels with self-perceived health, depression, and anxiety in Spanish individuals with high cholesterol levels: a retrospective cross-sectional study. PeerJ 12:e17169 https://doi.org/10.7717/peerj.17169
date submitted: 2023-11-22
date accepted: 2024-03-06
issued: 2024-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Denche-Zamorano
  given name: Ángel
author list: Agent
  family name: Pisà-Canyelles
  given name: Jofre
author list: Agent
  family name: Barrios-Fernández
  given name: Sabina
author list: Agent
  family name: Castillo-Paredes
  given name: Antonio
author list: Agent
  family name: Pastor-Cisneros
  given name: Raquel
author list: Agent
  family name: Mendoza-Muñoz
  given name: Maria
author list: Agent
  family name: Salas Gómez
  given name: Diana
author list: Agent
  family name: Mendoza Holgado
  given name: Cristina
doi: 10.7717/peerj.17169
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-15
copyright: ©2024 Denche-Zamorano et al.
attribution name: Denche-Zamorano et al.

The skull of the Turks and Caicos rock iguana, Cyclura carinata (Squamata: Iguanidae)
type: item
type: AcademicArticle
description: We provide a detailed and first description of the skull, hyoid apparatus, and trachea of the Turks and Caicos rock iguana, Cyclura carinata (Squamata: Iguanidae). Cyclura is a radiation of iguanas restricted to islands of the Caribbean Sea. Species of Cyclura have high rates of endemism, and all species are severely threatened with extinction. Our anatomical description of this threatened iguana is based on high-resolution computed tomography scans of one adult, one putative adult or near adult, and one juvenile specimen, and includes three-dimensional segmented renderings and visualizations. We discuss some observations of intraspecific and ontogenetic variation, and provide a brief comparison with specimens of another species of Cyclura and published descriptions of other iguanas. Our study provides a cranial osteological framework for Cyclura and augments the body of knowledge on iguana anatomy generally. Finally, we posit that our description and future studies may facilitate identification of fossil Cyclura, which could help understand the paleobiogeography of the genus.
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format: text/html
creator: Chloe Lai
creator: Simon G. Scarpetta
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.17595
publisher: PeerJ Inc.
rights: © 2024 Lai and Scarpetta
abstract: We provide a detailed and first description of the skull, hyoid apparatus, and trachea of the Turks and Caicos rock iguana, Cyclura carinata (Squamata: Iguanidae). Cyclura is a radiation of iguanas restricted to islands of the Caribbean Sea. Species of Cyclura have high rates of endemism, and all species are severely threatened with extinction. Our anatomical description of this threatened iguana is based on high-resolution computed tomography scans of one adult, one putative adult or near adult, and one juvenile specimen, and includes three-dimensional segmented renderings and visualizations. We discuss some observations of intraspecific and ontogenetic variation, and provide a brief comparison with specimens of another species of Cyclura and published descriptions of other iguanas. Our study provides a cranial osteological framework for Cyclura and augments the body of knowledge on iguana anatomy generally. Finally, we posit that our description and future studies may facilitate identification of fossil Cyclura, which could help understand the paleobiogeography of the genus.
bibliographic citation: Lai et al. (2024) The skull of the Turks and Caicos rock iguana, Cyclura carinata (Squamata: Iguanidae). PeerJ 12:e17595 https://doi.org/10.7717/peerj.17595
date submitted: 2024-01-19
date accepted: 2024-05-28
issued: 2024-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lai
  given name: Chloe
author list: Agent
  family name: Scarpetta
  given name: Simon G.
doi: 10.7717/peerj.17595
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-15
copyright: ©2024 Lai and Scarpetta
attribution name: Lai and Scarpetta

Effects of five types of exercise on vascular function in postmenopausal women: a network meta-analysis and systematic review of 32 randomized controlled trials
type: item
type: AcademicArticle
description: Background As women age, especially after menopause, cardiovascular disease (CVD) prevalence rises, posing a significant global health concern. Regular exercise can mitigate CVD risks by improving blood pressure and lipid levels in postmenopausal women. Yet, the optimal exercise modality for enhancing vascular structure and function in this demographic remains uncertain. This study aims to compare five exercise forms to discern the most effective interventions for reducing cardiovascular risk in postmenopausal women. Methods The study searched PubMed, Web of Science, Cochrane, EBSCO, and Embase databases. It conducted a network meta-analysis (NMA) of randomized controlled trials (RCTs) on five exercise interventions: continuous endurance training (CET), interval training (INT), resistance training (RT), aerobic combined with resistance training (CT), and hybrid-type training (HYB). Outcome measures included carotid artery intima-media thickness (IMT), nitric oxide (NO), augmentation index (AIx), pulse wave velocity (PWV), and flow-mediated dilatation (FMD) of the brachial artery. Eligible studies were assessed for bias using the Cochrane tool. A frequentist random-effects NMA was employed to rank exercise effects, calculating standardized mean differences (SMDs) with 95% confidence intervals (CIs). Results The analysis of 32 studies (n = 1,427) indicates significant increases in FMD with CET, INT, RT, and HYB in postmenopausal women. Reductions in PWV were significant with CET, INT, RT, CT, and HYB. AIx decreased significantly with INT and HYB. CET, INT, and CT significantly increased NO levels. However, no significant reduction in IMT was observed. SUCRA probabilities show INT as most effective for increasing FMD, CT for reducing PWV, INT for decreasing AIx, CT for lowering IMT, and INT for increasing NO in postmenopausal women. Conclusion The study demonstrates that CET, INT, RT, and HYB have a significant positive impact on FMD in postmenopausal women. Furthermor…
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creator: Weihao Sun
creator: Yanli Han
creator: Song Gu
subject: Cardiology
subject: Women’s Health
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.17621
publisher: PeerJ Inc.
rights: © 2024 Sun et al.
abstract: Background As women age, especially after menopause, cardiovascular disease (CVD) prevalence rises, posing a significant global health concern. Regular exercise can mitigate CVD risks by improving blood pressure and lipid levels in postmenopausal women. Yet, the optimal exercise modality for enhancing vascular structure and function in this demographic remains uncertain. This study aims to compare five exercise forms to discern the most effective interventions for reducing cardiovascular risk in postmenopausal women. Methods The study searched PubMed, Web of Science, Cochrane, EBSCO, and Embase databases. It conducted a network meta-analysis (NMA) of randomized controlled trials (RCTs) on five exercise interventions: continuous endurance training (CET), interval training (INT), resistance training (RT), aerobic combined with resistance training (CT), and hybrid-type training (HYB). Outcome measures included carotid artery intima-media thickness (IMT), nitric oxide (NO), augmentation index (AIx), pulse wave velocity (PWV), and flow-mediated dilatation (FMD) of the brachial artery. Eligible studies were assessed for bias using the Cochrane tool. A frequentist random-effects NMA was employed to rank exercise effects, calculating standardized mean differences (SMDs) with 95% confidence intervals (CIs). Results The analysis of 32 studies (n = 1,427) indicates significant increases in FMD with CET, INT, RT, and HYB in postmenopausal women. Reductions in PWV were significant with CET, INT, RT, CT, and HYB. AIx decreased significantly with INT and HYB. CET, INT, and CT significantly increased NO levels. However, no significant reduction in IMT was observed. SUCRA probabilities show INT as most effective for increasing FMD, CT for reducing PWV, INT for decreasing AIx, CT for lowering IMT, and INT for increasing NO in postmenopausal women. Conclusion The study demonstrates that CET, INT, RT, and HYB have a significant positive impact on FMD in postmenopausal women. Furthermor…
bibliographic citation: Sun et al. (2024) Effects of five types of exercise on vascular function in postmenopausal women: a network meta-analysis and systematic review of 32 randomized controlled trials. PeerJ 12:e17621 https://doi.org/10.7717/peerj.17621
date submitted: 2024-04-12
date accepted: 2024-06-01
issued: 2024-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Weihao
author list: Agent
  family name: Han
  given name: Yanli
author list: Agent
  family name: Gu
  given name: Song
doi: 10.7717/peerj.17621
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-15
copyright: © 2024 Sun et al.
attribution name: Sun et al.

Comparison of radiomics-based machine-learning classifiers for the pretreatment prediction of pathologic complete response to neoadjuvant therapy in breast cancer
type: item
type: AcademicArticle
description: Background Machine learning classifiers are increasingly used to create predictive models for pathological complete response (pCR) in breast cancer after neoadjuvant therapy (NAT). Few studies have compared the effectiveness of different ML classifiers. This study evaluated radiomics models based on pre- and post-contrast first-phase T1 weighted images (T1WI) in predicting breast cancer pCR after NAT and compared the performance of ML classifiers. Methods This retrospective study enrolled 281 patients undergoing NAT from the Duke-Breast-Cancer-MRI dataset. Radiomic features were extracted from pre- and post-contrast first-phase T1WI images. The Synthetic Minority Oversampling Technique (SMOTE) was applied, then the dataset was randomly divided into training and validation groups (7:3). The radiomics model was built using selected optimal features. Support vector machine (SVM), random forest (RF), decision tree (DT), k-nearest neighbor (KNN), extreme gradient boosting (XGBoost), and light gradient boosting machine (LightGBM) were classifiers. Receiver operating characteristic curves were used to assess predictive performance. Results LightGBM performed best in predicting pCR [area under the curve (AUC): 0.823, 95% confidence interval (CI) [0.743–0.902], accuracy 74.0%, sensitivity 85.0%, specificity 67.2%]. During subgroup analysis, RF was most effective in pCR prediction in luminal breast cancers (AUC: 0.914, 95% CI [0.847–0.981], accuracy 87.0%, sensitivity 85.2%, specificity 88.1%). In triple-negative breast cancers, LightGBM performed best (AUC: 0.836, 95% CI [0.708–0.965], accuracy 78.6%, sensitivity 68.2%, specificity 90.0%). Conclusion The LightGBM-based radiomics model performed best in predicting pCR in patients with breast cancer. RF and LightGBM showed promising results for luminal and triple-negative breast cancers, respectively.
format: application/pdf
format: text/html
creator: Xue Li
creator: Chunmei Li
creator: Hong Wang
creator: Lei Jiang
creator: Min Chen
subject: Oncology
subject: Radiology and Medical Imaging
subject: Women’s Health
subject: Computational Science
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17683
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background Machine learning classifiers are increasingly used to create predictive models for pathological complete response (pCR) in breast cancer after neoadjuvant therapy (NAT). Few studies have compared the effectiveness of different ML classifiers. This study evaluated radiomics models based on pre- and post-contrast first-phase T1 weighted images (T1WI) in predicting breast cancer pCR after NAT and compared the performance of ML classifiers. Methods This retrospective study enrolled 281 patients undergoing NAT from the Duke-Breast-Cancer-MRI dataset. Radiomic features were extracted from pre- and post-contrast first-phase T1WI images. The Synthetic Minority Oversampling Technique (SMOTE) was applied, then the dataset was randomly divided into training and validation groups (7:3). The radiomics model was built using selected optimal features. Support vector machine (SVM), random forest (RF), decision tree (DT), k-nearest neighbor (KNN), extreme gradient boosting (XGBoost), and light gradient boosting machine (LightGBM) were classifiers. Receiver operating characteristic curves were used to assess predictive performance. Results LightGBM performed best in predicting pCR [area under the curve (AUC): 0.823, 95% confidence interval (CI) [0.743–0.902], accuracy 74.0%, sensitivity 85.0%, specificity 67.2%]. During subgroup analysis, RF was most effective in pCR prediction in luminal breast cancers (AUC: 0.914, 95% CI [0.847–0.981], accuracy 87.0%, sensitivity 85.2%, specificity 88.1%). In triple-negative breast cancers, LightGBM performed best (AUC: 0.836, 95% CI [0.708–0.965], accuracy 78.6%, sensitivity 68.2%, specificity 90.0%). Conclusion The LightGBM-based radiomics model performed best in predicting pCR in patients with breast cancer. RF and LightGBM showed promising results for luminal and triple-negative breast cancers, respectively.
bibliographic citation: Li et al. (2024) Comparison of radiomics-based machine-learning classifiers for the pretreatment prediction of pathologic complete response to neoadjuvant therapy in breast cancer. PeerJ 12:e17683 https://doi.org/10.7717/peerj.17683
date submitted: 2024-02-12
date accepted: 2024-06-13
issued: 2024-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xue
author list: Agent
  family name: Li
  given name: Chunmei
author list: Agent
  family name: Wang
  given name: Hong
author list: Agent
  family name: Jiang
  given name: Lei
author list: Agent
  family name: Chen
  given name: Min
doi: 10.7717/peerj.17683
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-15
copyright: ©2024 Li et al.
attribution name: Li et al.

Bridging the gap in medical education: comparing analysis of light microscopy and virtual microscopy in histology
type: item
type: AcademicArticle
description: This study aims to investigate the impact of virtual microscopy (VM) and light microscopy (LM) on the satisfaction of second-year medical students and how they affect student performance in different educational settings. The research involved 94 second-year students from Izmir Democracy University’s School of Medicine, with criteria requiring enrollment in the 2021–2022 academic year and attendance of at least 80% in histology practical course. A paired two-tailed t-test was used for comparison, with a researcher-designed questionnaire for data collection. Cronbach’s alpha was 0.894 for the LM questionnaire, and 0.918 for the VM questionnaire, indicating high level of reliability. LM scored higher in the questionnaire (p = 0.010), but VM showed higher exam averages (p = 0.013). The study found VM more effective in exams, with students showing high satisfaction with LM. VM’s accessibility to histological preparations and its impact on learning levels and board exam success rates were noted. The study concludes that while VM is becoming essential in histology education due to its positive impact on exam performance and accessibility, LM remains highly valued by students for its hands-on experience and satisfaction levels.
format: application/pdf
format: text/html
creator: Aysel Başer
creator: Başak Büyük
subject: Science and Medical Education
subject: Histology
description: doi:10.7717/peerj.17695
publisher: PeerJ Inc.
rights: © 2024 Başer and Büyük
abstract: This study aims to investigate the impact of virtual microscopy (VM) and light microscopy (LM) on the satisfaction of second-year medical students and how they affect student performance in different educational settings. The research involved 94 second-year students from Izmir Democracy University’s School of Medicine, with criteria requiring enrollment in the 2021–2022 academic year and attendance of at least 80% in histology practical course. A paired two-tailed t-test was used for comparison, with a researcher-designed questionnaire for data collection. Cronbach’s alpha was 0.894 for the LM questionnaire, and 0.918 for the VM questionnaire, indicating high level of reliability. LM scored higher in the questionnaire (p = 0.010), but VM showed higher exam averages (p = 0.013). The study found VM more effective in exams, with students showing high satisfaction with LM. VM’s accessibility to histological preparations and its impact on learning levels and board exam success rates were noted. The study concludes that while VM is becoming essential in histology education due to its positive impact on exam performance and accessibility, LM remains highly valued by students for its hands-on experience and satisfaction levels.
bibliographic citation: Başer et al. (2024) Bridging the gap in medical education: comparing analysis of light microscopy and virtual microscopy in histology. PeerJ 12:e17695 https://doi.org/10.7717/peerj.17695
date submitted: 2024-04-01
date accepted: 2024-06-14
issued: 2024-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Başer
  given name: Aysel
author list: Agent
  family name: Büyük
  given name: Başak
doi: 10.7717/peerj.17695
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-15
copyright: © 2024 Başer and Büyük
attribution name: Başer and Büyük

Genetic variability and population structure of two sympatric cownose rays Rhinoptera (Myliobatiformes, Rhinopteridae) in the Western Atlantic Ocean
type: item
type: AcademicArticle
description: Cownose rays Rhinoptera bonasus and R. brasiliensis, are species distributed along the coastal waters from eastern United States, Gulf of Mexico to Brazil. This study represents the most extensive evaluation to date of the genetic diversity and population genetic structure of R. bonasus across its distribution, and it is the first to investigate the population genetics of R. brasiliensis. We analyzed sequences of COI and Cytb genes for Rhinoptera bonasus (COI: 230, Cytb: 108) and R. brasiliensis (COI: 181, Cytb: 105) to investigate the genetic diversity and their relationship with environmental variables, genetic structure, as well as demographic parameters. We found that benthic temperature and current velocity were the most important environmental variables in genetic diversity. The global population structure reveals the presence of significant population genetic structure in both species. Bayesian clusters in BAPS were consistent with the segregation pattern observed for haplotype networks based on COI and Cytb markers for both species, which may respond to philopatry and temperature. These results will further improve management and conservation efforts for these species of ecological and economic importance.
format: application/pdf
format: text/html
creator: Paola Palacios Barreto
creator: Verónica Mendoza-Portillo
creator: Douglas H. Adams
creator: Vanessa P. Cruz
creator: Fausto Foresti
creator: Píndaro Díaz-Jaimes
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Conservation Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.17700
publisher: PeerJ Inc.
rights: © 2024 Palacios Barreto et al.
abstract: Cownose rays Rhinoptera bonasus and R. brasiliensis, are species distributed along the coastal waters from eastern United States, Gulf of Mexico to Brazil. This study represents the most extensive evaluation to date of the genetic diversity and population genetic structure of R. bonasus across its distribution, and it is the first to investigate the population genetics of R. brasiliensis. We analyzed sequences of COI and Cytb genes for Rhinoptera bonasus (COI: 230, Cytb: 108) and R. brasiliensis (COI: 181, Cytb: 105) to investigate the genetic diversity and their relationship with environmental variables, genetic structure, as well as demographic parameters. We found that benthic temperature and current velocity were the most important environmental variables in genetic diversity. The global population structure reveals the presence of significant population genetic structure in both species. Bayesian clusters in BAPS were consistent with the segregation pattern observed for haplotype networks based on COI and Cytb markers for both species, which may respond to philopatry and temperature. These results will further improve management and conservation efforts for these species of ecological and economic importance.
bibliographic citation: Palacios Barreto et al. (2024) Genetic variability and population structure of two sympatric cownose rays Rhinoptera (Myliobatiformes, Rhinopteridae) in the Western Atlantic Ocean. PeerJ 12:e17700 https://doi.org/10.7717/peerj.17700
date submitted: 2024-03-20
date accepted: 2024-06-17
issued: 2024-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palacios Barreto
  given name: Paola
author list: Agent
  family name: Mendoza-Portillo
  given name: Verónica
author list: Agent
  family name: Adams
  given name: Douglas H.
author list: Agent
  family name: Cruz
  given name: Vanessa P.
author list: Agent
  family name: Foresti
  given name: Fausto
author list: Agent
  family name: Díaz-Jaimes
  given name: Píndaro
doi: 10.7717/peerj.17700
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-15
copyright: © 2024 Palacios Barreto et al.
attribution name: Palacios Barreto et al.

Evaluation of dentin features in teeth after caries removal by three techniques (chemomechanical, mechanical with a smart bur, and air-abrasion): an in vitro study
type: item
type: AcademicArticle
description: Background Different methods for removing dental carious lesions exist, including conventional rotary caries removal and new advanced technology like polymer-based burs, chemomechanical agents, air abrasion, and laser. Objectives This study shows the differences in features of dentin (smear layer, patency of dentinal tubules, surface irregularities, intertubular micro porosities, and exposed dentinal tubules) among different types of caries removal techniques. Materials and Methods An in vitro study was done on 60 primary molars with occlusal class I active caries. Teeth were divided into three groups according to a method of caries removal (G1: chemomechanical, G2: mechanical with a smart bur, and G3: air-abrasion). After complete caries excavation, the teeth were examined under a scanning electronic microscope (SEM) with the power of magnification 4,000x and 8,000x to show the morphological dentinal features with SEM microphotographs. Data obtained was analyzed using the SPSS program where Fisher exact, Kruskal–Wallis and multiple Wilcoxon sum rank tests were used. The level of significance is when the p-value is less than 0.05. Results Generally, SEM showed the highest ratio of score 1 of smear layer presence, surface irregularities, and microporosity in all groups in both magnifications. The patency of tubules showed the highest ratio of score 1 in G1, scores 2 in both G2 and G3 in magnification 4,000x, while 8,000x there was the highest ratio of its score 1 in G1 and G2 while the G3 has score 2 as the highest score. The exposed dentinal tubules showed the highest ratio in G1 in score 3, in G2 in score 2, and in G3 in score 1 in magnification 4,000x, while 8,000x there was the highest ratio of its score 2 in both G1 and G3 while the G3 has highest score 1. The study with magnification 4,000x showed a significant difference (S) among three groups in exposed dentinal tubules with a p-value (0.012), and there was S between chemomechanical and smart, chemomechanical…
format: application/pdf
format: text/html
creator: Maha Abdul-Kareem Mahmood
creator: Haraa Khairi Al-Hadithi
creator: Hashim Mueen Hussein
subject: Dentistry
subject: Histology
description: doi:10.7717/peerj.17717
publisher: PeerJ Inc.
rights: © 2024 Abdul-Kareem Mahmood et al.
abstract: Background Different methods for removing dental carious lesions exist, including conventional rotary caries removal and new advanced technology like polymer-based burs, chemomechanical agents, air abrasion, and laser. Objectives This study shows the differences in features of dentin (smear layer, patency of dentinal tubules, surface irregularities, intertubular micro porosities, and exposed dentinal tubules) among different types of caries removal techniques. Materials and Methods An in vitro study was done on 60 primary molars with occlusal class I active caries. Teeth were divided into three groups according to a method of caries removal (G1: chemomechanical, G2: mechanical with a smart bur, and G3: air-abrasion). After complete caries excavation, the teeth were examined under a scanning electronic microscope (SEM) with the power of magnification 4,000x and 8,000x to show the morphological dentinal features with SEM microphotographs. Data obtained was analyzed using the SPSS program where Fisher exact, Kruskal–Wallis and multiple Wilcoxon sum rank tests were used. The level of significance is when the p-value is less than 0.05. Results Generally, SEM showed the highest ratio of score 1 of smear layer presence, surface irregularities, and microporosity in all groups in both magnifications. The patency of tubules showed the highest ratio of score 1 in G1, scores 2 in both G2 and G3 in magnification 4,000x, while 8,000x there was the highest ratio of its score 1 in G1 and G2 while the G3 has score 2 as the highest score. The exposed dentinal tubules showed the highest ratio in G1 in score 3, in G2 in score 2, and in G3 in score 1 in magnification 4,000x, while 8,000x there was the highest ratio of its score 2 in both G1 and G3 while the G3 has highest score 1. The study with magnification 4,000x showed a significant difference (S) among three groups in exposed dentinal tubules with a p-value (0.012), and there was S between chemomechanical and smart, chemomechanical…
bibliographic citation: Abdul-Kareem Mahmood et al. (2024) Evaluation of dentin features in teeth after caries removal by three techniques (chemomechanical, mechanical with a smart bur, and air-abrasion): an in vitro study. PeerJ 12:e17717 https://doi.org/10.7717/peerj.17717
date submitted: 2024-01-15
date accepted: 2024-06-18
issued: 2024-07-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdul-Kareem Mahmood
  given name: Maha
author list: Agent
  family name: Khairi Al-Hadithi
  given name: Haraa
author list: Agent
  family name: Mueen Hussein
  given name: Hashim
doi: 10.7717/peerj.17717
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-15
copyright: ©2024 Abdul-Kareem Mahmood et al.
attribution name: Abdul-Kareem Mahmood et al.

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