PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Importance of feature selection stability in the classifier evaluation on high-dimensional genetic data
items: Comparison of iRoot BP Plus and mineral trioxide aggregate for pulpotomy in primary molars under general anesthesia: a 3-year retrospective study
items: Physical development of infants born to patients with COVID-19 during pregnancy: 2 years of age
items: Impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of Maize (Zea mays L.)
items: Examining the interplay between mental health indicators and quality of life measures among first-year law students: a cross-sectional study
items: Protein profile changes during priming explants to embryogenic response in Coffea canephora: identification of the RPN12 proteasome subunit involved in the protein degradation
items: Potential of epicatechin as antioxidant and antiaging in UV-induced BJ cells by regulating COL1A1, FGF-2, GPX-1, and MMP-1 gene, protein levels, and apoptosis
items: Seroprevalence and silent infection rate during SARS-CoV-2 pandemic among children and adolescents in Western Pomerania: a multicenter, cross-sectional study—the COVIDKID study
items: Examination of optical coherence tomography findings in patients with pregabalin use disorder
items: Transperineal prostate biopsy guided by which ultrasound transducer: transrectal or transperineal: a retrospective study

Importance of feature selection stability in the classifier evaluation on high-dimensional genetic data
type: item
type: AcademicArticle
description: Classifiers trained on high-dimensional data, such as genetic datasets, often encounter situations where the number of features exceeds the number of objects. In these cases, classifiers typically rely on a small subset of features. For a robust algorithm, this subset should remain relatively stable with minor changes in the training data, such as the replacement of a few samples. While the stability of feature selection is a common focus in studies of feature selection algorithms, it is less emphasized in classifier evaluation, where only metrics such as accuracy are commonly used. We investigate the importance of feature selection stability through an empirical study of four classifiers (logistic regression, support vector machine, convex and piecewise Linear, and Random Forest) on seven high dimensional, publicly available, gene datasets. We measure the stability of feature selection using Lustgarten, Nogueira and Jaccard Index measures. We employed our own cross-validation procedure that guarantees a difference of exactly p objects between any two training sets which allows us to control the level of disturbance in the data. Our results show the existence of a drop in feature selection stability when we increase disturbance in the data in all 28 experiment configurations (seven datasets and four classifiers). The relationship is not linear, but resembles more of a hyperbolic pattern. In the evaluation of the tested classifiers, logistic regression demonstrated the highest stability. It was followed in order by support vector machine, convex and piecewise linear, with Random Forest exhibiting the lowest stability among them. This work provides evidence that all tested classifiers are very sensitive to even small changes in learning data in terms of features used by the model, while showing almost no sensitivity in terms of accuracy. The data and codes to reproduce the results in the article are available publicly on GitHub: https://github.com/tlukaszuk/feature-se…
format: application/pdf
format: text/html
creator: Tomasz Łukaszuk
creator: Jerzy Krawczuk
subject: Genomics
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.18405
publisher: PeerJ Inc.
rights: © 2024 Łukaszuk and Krawczuk
abstract: Classifiers trained on high-dimensional data, such as genetic datasets, often encounter situations where the number of features exceeds the number of objects. In these cases, classifiers typically rely on a small subset of features. For a robust algorithm, this subset should remain relatively stable with minor changes in the training data, such as the replacement of a few samples. While the stability of feature selection is a common focus in studies of feature selection algorithms, it is less emphasized in classifier evaluation, where only metrics such as accuracy are commonly used. We investigate the importance of feature selection stability through an empirical study of four classifiers (logistic regression, support vector machine, convex and piecewise Linear, and Random Forest) on seven high dimensional, publicly available, gene datasets. We measure the stability of feature selection using Lustgarten, Nogueira and Jaccard Index measures. We employed our own cross-validation procedure that guarantees a difference of exactly p objects between any two training sets which allows us to control the level of disturbance in the data. Our results show the existence of a drop in feature selection stability when we increase disturbance in the data in all 28 experiment configurations (seven datasets and four classifiers). The relationship is not linear, but resembles more of a hyperbolic pattern. In the evaluation of the tested classifiers, logistic regression demonstrated the highest stability. It was followed in order by support vector machine, convex and piecewise linear, with Random Forest exhibiting the lowest stability among them. This work provides evidence that all tested classifiers are very sensitive to even small changes in learning data in terms of features used by the model, while showing almost no sensitivity in terms of accuracy. The data and codes to reproduce the results in the article are available publicly on GitHub: https://github.com/tlukaszuk/feature-se…
bibliographic citation: Łukaszuk et al. (2024) Importance of feature selection stability in the classifier evaluation on high-dimensional genetic data. PeerJ 12:e18405 https://doi.org/10.7717/peerj.18405
date submitted: 2024-06-28
date accepted: 2024-10-05
issued: 2024-11-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Łukaszuk
  given name: Tomasz
author list: Agent
  family name: Krawczuk
  given name: Jerzy
doi: 10.7717/peerj.18405
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-12
copyright: ©2024 Łukaszuk and Krawczuk
attribution name: Łukaszuk and Krawczuk

Comparison of iRoot BP Plus and mineral trioxide aggregate for pulpotomy in primary molars under general anesthesia: a 3-year retrospective study
type: item
type: AcademicArticle
description: Background Pulpotomy is a widely recommended treatment for deep caries and reversible pulpitis in primary teeth. However, there is a significant lack of large-scale clinical studies evaluating the long-term efficacy of pulpotomy in primary molars, especially in studies with follow-up periods extending beyond a two years. Aim This study aimed to evaluate the long-term efficacy of mineral trioxide aggregate (MTA) and iRoot BP Plus for pulpotomy in primary molars performed under general anesthesia and to investigate factors influencing the success rate. Methods In this retrospective study, a total of 942 primary molars from 422 children who met the inclusion criteria underwent pulpotomy. Propensity score matching method (PSM) was used to match the MTA and iRoot BP Plus groups in a 1:1 ratio based on covariates. Efficacy was assessed using the Zurn & Seale criteria. Kaplan-Meier survival analysis and Cox proportional hazards model were performed to analyze the outcomes. Results PSM resulted in 266 pairs of matched teeth from 532 teeth of 291 children (mean age: 4.64 ± 1.07 years, ranging from 2 to 8 years). Long-term clinical and radiographic evaluations revealed higher success rates for iRoot BP Plus (24-month: 99.54%/97.25%; 36-month: 97.22%/95.83%) compared to MTA (24-month: 94.76%/95.29%; 36-month: 92.50%/91.25%). Survival analysis indicated a statistically significant difference between two groups (P = 0.0042). Age, gender, tooth position, and decayed tooth surface showed no significant impact on pulpotomy success, whereas the choice of pulp capping materials significantly influenced the outcome (HR [95% CI]=0.3745[0.1857-0.7552], P = 0.006). Conclusion Clinical and radiographic evaluations support the use of iRoot BP Plus for pulpotomy in primary molars.
format: application/pdf
format: text/html
creator: Yiming Zhao
creator: Yuyan Tao
creator: Yan Wang
creator: Jing Zou
creator: Qiong Zhang
subject: Dentistry
subject: Pediatrics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.18453
publisher: PeerJ Inc.
rights: © 2024 Zhao et al.
abstract: Background Pulpotomy is a widely recommended treatment for deep caries and reversible pulpitis in primary teeth. However, there is a significant lack of large-scale clinical studies evaluating the long-term efficacy of pulpotomy in primary molars, especially in studies with follow-up periods extending beyond a two years. Aim This study aimed to evaluate the long-term efficacy of mineral trioxide aggregate (MTA) and iRoot BP Plus for pulpotomy in primary molars performed under general anesthesia and to investigate factors influencing the success rate. Methods In this retrospective study, a total of 942 primary molars from 422 children who met the inclusion criteria underwent pulpotomy. Propensity score matching method (PSM) was used to match the MTA and iRoot BP Plus groups in a 1:1 ratio based on covariates. Efficacy was assessed using the Zurn & Seale criteria. Kaplan-Meier survival analysis and Cox proportional hazards model were performed to analyze the outcomes. Results PSM resulted in 266 pairs of matched teeth from 532 teeth of 291 children (mean age: 4.64 ± 1.07 years, ranging from 2 to 8 years). Long-term clinical and radiographic evaluations revealed higher success rates for iRoot BP Plus (24-month: 99.54%/97.25%; 36-month: 97.22%/95.83%) compared to MTA (24-month: 94.76%/95.29%; 36-month: 92.50%/91.25%). Survival analysis indicated a statistically significant difference between two groups (P = 0.0042). Age, gender, tooth position, and decayed tooth surface showed no significant impact on pulpotomy success, whereas the choice of pulp capping materials significantly influenced the outcome (HR [95% CI]=0.3745[0.1857-0.7552], P = 0.006). Conclusion Clinical and radiographic evaluations support the use of iRoot BP Plus for pulpotomy in primary molars.
bibliographic citation: Zhao et al. (2024) Comparison of iRoot BP Plus and mineral trioxide aggregate for pulpotomy in primary molars under general anesthesia: a 3-year retrospective study. PeerJ 12:e18453 https://doi.org/10.7717/peerj.18453
date submitted: 2024-06-11
date accepted: 2024-10-14
issued: 2024-11-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yiming
author list: Agent
  family name: Tao
  given name: Yuyan
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Zou
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Qiong
doi: 10.7717/peerj.18453
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-12
copyright: ©2024 Zhao et al.
attribution name: Zhao et al.

Physical development of infants born to patients with COVID-19 during pregnancy: 2 years of age
type: item
type: AcademicArticle
description: Background SARS-CoV-2 infection during pregnancy and pandemic circumstances could negatively impact infant development. This study aimed to investigate the physical development, common pediatric illness incidence, and healthcare utilization over the first 2 years of life of infants born to COVID+ and COVID- patients. Comparisons were also made with infants born pre-pandemic. Methods This is a retrospective observational study at a major academic health system in New York City. Participants include all infants born to birthing persons with SARS-CoV-2 infection during pregnancy (N = 758) and without (N = 9,345) from 03/01/2020 to 08/17/2022, infants born pre-pandemic (N = 3,221) from 03/01/2017 to 08/17/2019, and birthing persons of all infants. Results There were no differences in weight, length, or head circumference curves between pandemic infants born to COVID+ and COVID- patients over the first 2 years of life (p > 0.05, repeated ANOVA). Annualized incidence of illness occurrence and healthcare utilization were similar between groups. Compared to pre-pandemic infants, the length of pandemic (COVID-) infants was lower from birth to 9 months (p < 0.0001). Pandemic infants additionally had more adverse perinatal outcomes including increased stillbirth (0.75% vs. 0.12%, p = 0.0001) and decreased gestational age (38.41 ± 2.71 vs. 38.68 ± 2.55 weeks, Cohen’s d = −0.10, p < 0.0001), birthweight (2,597 ± 335 vs. 3,142 ± 643 g, Cohen’s d = −1.06, p < 0.0001), and birth length (48.08 ± 4.61 vs. 49.09 ± 3.93 cm, Cohen’s d = −0.24, p < 0.0001). Conclusions Birthing persons’ SARS-CoV-2 infection status, birthing persons’ profiles, and pandemic circumstances negatively affected perinatal outcomes, newborn physical development, and healthcare utilization. These findings draw clinical attention to the need to follow infants closely and implement enrichment to ensure optimal developmental outcomes.
format: application/pdf
format: text/html
creator: Anna Eligulashvili
creator: Moshe Gordon
creator: Sheri Nemerofsky
creator: Tomas Havranek
creator: Peter Bernstein
creator: Judy Yee
creator: Wei Hou
creator: Tim Duong
subject: Gynecology and Obstetrics
subject: Infectious Diseases
subject: Pediatrics
subject: COVID-19
description: doi:10.7717/peerj.18481
publisher: PeerJ Inc.
rights: © 2024 Eligulashvili et al.
abstract: Background SARS-CoV-2 infection during pregnancy and pandemic circumstances could negatively impact infant development. This study aimed to investigate the physical development, common pediatric illness incidence, and healthcare utilization over the first 2 years of life of infants born to COVID+ and COVID- patients. Comparisons were also made with infants born pre-pandemic. Methods This is a retrospective observational study at a major academic health system in New York City. Participants include all infants born to birthing persons with SARS-CoV-2 infection during pregnancy (N = 758) and without (N = 9,345) from 03/01/2020 to 08/17/2022, infants born pre-pandemic (N = 3,221) from 03/01/2017 to 08/17/2019, and birthing persons of all infants. Results There were no differences in weight, length, or head circumference curves between pandemic infants born to COVID+ and COVID- patients over the first 2 years of life (p > 0.05, repeated ANOVA). Annualized incidence of illness occurrence and healthcare utilization were similar between groups. Compared to pre-pandemic infants, the length of pandemic (COVID-) infants was lower from birth to 9 months (p < 0.0001). Pandemic infants additionally had more adverse perinatal outcomes including increased stillbirth (0.75% vs. 0.12%, p = 0.0001) and decreased gestational age (38.41 ± 2.71 vs. 38.68 ± 2.55 weeks, Cohen’s d = −0.10, p < 0.0001), birthweight (2,597 ± 335 vs. 3,142 ± 643 g, Cohen’s d = −1.06, p < 0.0001), and birth length (48.08 ± 4.61 vs. 49.09 ± 3.93 cm, Cohen’s d = −0.24, p < 0.0001). Conclusions Birthing persons’ SARS-CoV-2 infection status, birthing persons’ profiles, and pandemic circumstances negatively affected perinatal outcomes, newborn physical development, and healthcare utilization. These findings draw clinical attention to the need to follow infants closely and implement enrichment to ensure optimal developmental outcomes.
bibliographic citation: Eligulashvili et al. (2024) Physical development of infants born to patients with COVID-19 during pregnancy: 2 years of age. PeerJ 12:e18481 https://doi.org/10.7717/peerj.18481
date submitted: 2024-03-08
date accepted: 2024-10-16
issued: 2024-11-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eligulashvili
  given name: Anna
author list: Agent
  family name: Gordon
  given name: Moshe
author list: Agent
  family name: Nemerofsky
  given name: Sheri
author list: Agent
  family name: Havranek
  given name: Tomas
author list: Agent
  family name: Bernstein
  given name: Peter
author list: Agent
  family name: Yee
  given name: Judy
author list: Agent
  family name: Hou
  given name: Wei
author list: Agent
  family name: Duong
  given name: Tim
doi: 10.7717/peerj.18481
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-12
copyright: © 2024 Eligulashvili et al.
attribution name: Eligulashvili et al.

Impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of Maize (Zea mays L.)
type: item
type: AcademicArticle
description: Aging induces many deteriorative changes to seeds during storage like protein degradation, enzyme inactivation and loss of membrane integrity. In this study, we investigate the impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of maize. Three genotypes African Tall, MAH 14-5 and a local landrace were selected and artificially aged for 96 and 120 h. The aging process led to a decrease in germination, vigour, and total dehydrogenase in seeds, while the electrical conductivity of seed leachates increased, indicating a decline in seed quality. Additionally, there was a variation in the microsculpture pattern of seed coats between genotypes. There was an accumulation of damage on the seed coat surface as the seeds aged and higher damage occurred in African Tall followed by MAH 14-5 and local landrace. Higher catalase, superoxide dismutase, peroxidase and polyphenol oxidase activity were reported in the seed coat of Local landrace and MAH 14-5 that resisted aging and deterioration while, lower catalase, superoxide dismutase, peroxidase and polyphenol oxidase activity was reported in African Tall seed coat that deteriorated during aging. Decrease antioxidant activity in aged seeds might be a possible cause of seed deterioration due to the accumulation of free radicals. Thus, these results clearly show the influence of seed coat structure and antioxidant activity on seed quality during aging.
format: application/pdf
format: text/html
creator: Vijayan Satya Srii
creator: Nethra Nagarajappa
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.17988
publisher: PeerJ Inc.
rights: © 2024 Satya Srii and Nagarajappa
abstract: Aging induces many deteriorative changes to seeds during storage like protein degradation, enzyme inactivation and loss of membrane integrity. In this study, we investigate the impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of maize. Three genotypes African Tall, MAH 14-5 and a local landrace were selected and artificially aged for 96 and 120 h. The aging process led to a decrease in germination, vigour, and total dehydrogenase in seeds, while the electrical conductivity of seed leachates increased, indicating a decline in seed quality. Additionally, there was a variation in the microsculpture pattern of seed coats between genotypes. There was an accumulation of damage on the seed coat surface as the seeds aged and higher damage occurred in African Tall followed by MAH 14-5 and local landrace. Higher catalase, superoxide dismutase, peroxidase and polyphenol oxidase activity were reported in the seed coat of Local landrace and MAH 14-5 that resisted aging and deterioration while, lower catalase, superoxide dismutase, peroxidase and polyphenol oxidase activity was reported in African Tall seed coat that deteriorated during aging. Decrease antioxidant activity in aged seeds might be a possible cause of seed deterioration due to the accumulation of free radicals. Thus, these results clearly show the influence of seed coat structure and antioxidant activity on seed quality during aging.
bibliographic citation: Satya Srii et al. (2024) Impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of Maize (Zea mays L.). PeerJ 12:e17988 https://doi.org/10.7717/peerj.17988
date submitted: 2024-05-17
date accepted: 2024-08-07
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Satya Srii
  given name: Vijayan
author list: Agent
  family name: Nagarajappa
  given name: Nethra
doi: 10.7717/peerj.17988
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: ©2024 Satya Srii and Nagarajappa
attribution name: Satya Srii and Nagarajappa

Examining the interplay between mental health indicators and quality of life measures among first-year law students: a cross-sectional study
type: item
type: AcademicArticle
description: Introduction This research explores the intricate relationships between mental health indicators (depression, stress, and anxiety) and various dimensions of quality of life among first-year law students. The study aims to understand how affective valence, mood states, physical activity, body image perception, and social relations influence mental health outcomes. Methods Data were collected from 75 first-year law students (46 females, 29 males), a group predominantly composed of young adults with limited financial means, living in various housing situations, primarily within urban environments, and generally reporting low levels of physical activity. Standardized questionnaires were used to assess mental health and quality of life, including the Depression, Anxiety, and Stress Scale-21 Items (DASS-21), Feeling Scale (FS), Exercise-Induced Feeling Inventory (EIFI), Modified Baecke Physical Activity Questionnaire (MBPAQ), World Health Organization Quality of Life-BREF (WHOQOL-BREF), and Contour Drawing Rating Scale (CDRS). Descriptive statistics, Pearson correlation, and regression analysis were employed to analyze the data. Results The analysis revealed significant correlations between depression (mean = 5.97, SD = 4.21), stress (mean = 7.81, SD = 4.80), and anxiety (mean = 6.17, SD = 4.58) with affective valence (p < 0.05), mood states (p < 0.05), physical activity (p < 0.05), body image perception (p < 0.05), and social relations quality (p < 0.05). Additionally, mood states (mean = 20.73, SD = 10.60), physical activity (mean = 8.43, SD = 1.35), body image perception (mean = 4.21, SD = 1.91), and social relations quality (mean = 12.46, SD = 2.33) were identified as significant predictors of mental health outcomes (p < 0.05). Conclusions These findings underscore the complex interplay between mental health indicators and various dimensions of quality of life, emphasizing the necessity for a comprehensive approach to mental health care. By identifying these predictor…
format: application/pdf
format: text/html
creator: Rаul-Ioаn Muntean
creator: Valentina Stefanica
creator: Daniel Rosu
creator: Alexandru Boncu
creator: Iulian Stoian
creator: Mihaela Oravitan
subject: Psychiatry and Psychology
subject: Public Health
subject: Science and Medical Education
subject: Mental Health
description: doi:10.7717/peerj.18245
publisher: PeerJ Inc.
rights: © 2024 Muntean et al.
abstract: Introduction This research explores the intricate relationships between mental health indicators (depression, stress, and anxiety) and various dimensions of quality of life among first-year law students. The study aims to understand how affective valence, mood states, physical activity, body image perception, and social relations influence mental health outcomes. Methods Data were collected from 75 first-year law students (46 females, 29 males), a group predominantly composed of young adults with limited financial means, living in various housing situations, primarily within urban environments, and generally reporting low levels of physical activity. Standardized questionnaires were used to assess mental health and quality of life, including the Depression, Anxiety, and Stress Scale-21 Items (DASS-21), Feeling Scale (FS), Exercise-Induced Feeling Inventory (EIFI), Modified Baecke Physical Activity Questionnaire (MBPAQ), World Health Organization Quality of Life-BREF (WHOQOL-BREF), and Contour Drawing Rating Scale (CDRS). Descriptive statistics, Pearson correlation, and regression analysis were employed to analyze the data. Results The analysis revealed significant correlations between depression (mean = 5.97, SD = 4.21), stress (mean = 7.81, SD = 4.80), and anxiety (mean = 6.17, SD = 4.58) with affective valence (p < 0.05), mood states (p < 0.05), physical activity (p < 0.05), body image perception (p < 0.05), and social relations quality (p < 0.05). Additionally, mood states (mean = 20.73, SD = 10.60), physical activity (mean = 8.43, SD = 1.35), body image perception (mean = 4.21, SD = 1.91), and social relations quality (mean = 12.46, SD = 2.33) were identified as significant predictors of mental health outcomes (p < 0.05). Conclusions These findings underscore the complex interplay between mental health indicators and various dimensions of quality of life, emphasizing the necessity for a comprehensive approach to mental health care. By identifying these predictor…
bibliographic citation: Muntean et al. (2024) Examining the interplay between mental health indicators and quality of life measures among first-year law students: a cross-sectional study. PeerJ 12:e18245 https://doi.org/10.7717/peerj.18245
date submitted: 2024-07-08
date accepted: 2024-09-15
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Muntean
  given name: Rаul-Ioаn
author list: Agent
  family name: Stefanica
  given name: Valentina
author list: Agent
  family name: Rosu
  given name: Daniel
author list: Agent
  family name: Boncu
  given name: Alexandru
author list: Agent
  family name: Stoian
  given name: Iulian
author list: Agent
  family name: Oravitan
  given name: Mihaela
doi: 10.7717/peerj.18245
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: © 2024 Muntean et al.
attribution name: Muntean et al.

Protein profile changes during priming explants to embryogenic response in Coffea canephora: identification of the RPN12 proteasome subunit involved in the protein degradation
type: item
type: AcademicArticle
description: Plant somatic embryogenesis encompasses somatic cells switch into embryogenic cells that can later produce somatic embryos with the ability to produce plantlets. Previously, we defined in vitro culture settings for the somatic embryogenesis process of Coffea canephora that comprise adequate plantlets with auxin plus cytokinin followed by cut-leaf explant cultivation with cytokinin, producing embryos with the ability to regenerate plantlets. Here, we confirmed that cultivating cut-leaf explants with cytokinin is sufficient to promote somatic embryos proliferation and the high yield of somatic embryos in the protocol requires adequate plantlets with auxin plus cytokinin. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels reveal auxin-plus cytokinin-dependent regulated proteins in plantlets with up and down abundance. Chitinase A class III, proteins involved in the metabolism and folding of proteins, photosynthesis, antioxidant activity, and chromatin organization were identified. The RPN12 protein, which is a subunit of the proteasome 26S, has an abundance that is not associated with transcript changes, suggesting post-translational regulation.
format: application/pdf
format: text/html
creator: Evelyn A. Carrillo-Bermejo
creator: Ligia Brito-Argáez
creator: Rosa M. Galaz-Ávalos
creator: Felipe Barredo-Pool
creator: Víctor M. Loyola-Vargas
creator: Victor Aguilar-Hernández
subject: Agricultural Science
subject: Biotechnology
subject: Developmental Biology
subject: Plant Science
description: doi:10.7717/peerj.18372
publisher: PeerJ Inc.
rights: © 2024 Carrillo-Bermejo et al.
abstract: Plant somatic embryogenesis encompasses somatic cells switch into embryogenic cells that can later produce somatic embryos with the ability to produce plantlets. Previously, we defined in vitro culture settings for the somatic embryogenesis process of Coffea canephora that comprise adequate plantlets with auxin plus cytokinin followed by cut-leaf explant cultivation with cytokinin, producing embryos with the ability to regenerate plantlets. Here, we confirmed that cultivating cut-leaf explants with cytokinin is sufficient to promote somatic embryos proliferation and the high yield of somatic embryos in the protocol requires adequate plantlets with auxin plus cytokinin. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels reveal auxin-plus cytokinin-dependent regulated proteins in plantlets with up and down abundance. Chitinase A class III, proteins involved in the metabolism and folding of proteins, photosynthesis, antioxidant activity, and chromatin organization were identified. The RPN12 protein, which is a subunit of the proteasome 26S, has an abundance that is not associated with transcript changes, suggesting post-translational regulation.
bibliographic citation: Carrillo-Bermejo et al. (2024) Protein profile changes during priming explants to embryogenic response in Coffea canephora: identification of the RPN12 proteasome subunit involved in the protein degradation. PeerJ 12:e18372 https://doi.org/10.7717/peerj.18372
date submitted: 2024-05-22
date accepted: 2024-09-30
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carrillo-Bermejo
  given name: Evelyn A.
author list: Agent
  family name: Brito-Argáez
  given name: Ligia
author list: Agent
  family name: Galaz-Ávalos
  given name: Rosa M.
author list: Agent
  family name: Barredo-Pool
  given name: Felipe
author list: Agent
  family name: Loyola-Vargas
  given name: Víctor M.
author list: Agent
  family name: Aguilar-Hernández
  given name: Victor
doi: 10.7717/peerj.18372
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: © 2024 Carrillo-Bermejo et al.
attribution name: Carrillo-Bermejo et al.

Potential of epicatechin as antioxidant and antiaging in UV-induced BJ cells by regulating COL1A1, FGF-2, GPX-1, and MMP-1 gene, protein levels, and apoptosis
type: item
type: AcademicArticle
description: Background Oxidative stress caused by exposure to ultraviolet (UV) light on the skin can damage deoxyribonucleic acid (DNA) and cause keratinocytes to undergo apoptosis. Endogenous antioxidants which play a role in trapping free radicals are also unable to overcome excess reactive oxygen species (ROS) in the body due to UV exposure, so exogenous antioxidants are needed. Polyphenolic compounds extracted from natural ingredients such as flavonoids, quercetin, and epicatechin have quite strong antioxidant activity. This is influenced by the chemical structure of these compounds which are rich in hydroxyl groups and aromatic groups. This structure allows the compound to become an electron donor so that it can neutralize free radicals. In vitro research was used to see the potential effectiveness of epicatechin as an antiaging and antioxidant. The study aims to confirm the potential of epicatechin as an antiaging by in vitro assay. Methods The viability test of epicatechin on human skin fibroblast (BJ) cells was carried out using the water-soluble tetrazolium (WST) assay. BJ cells were UV-induced as a cell model of premature aging. Epicatechin 6.25, 12.5, and 25 µg/mL were administered to UV-induced BJ cells. The gene expression of Collagen I Alpha 1 (COL1A1), matrix metalloproteinase-1 (MMP-1), fibroblast growth factor-2 (FGF-2), and glutathione peroxidase-1 (GPX-1) were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Elastin (ELN), hyaluronidase (HAase), cyclooxigenase-2 (COX-2), 8-hydroxydeoxyguanosine (8-OhdG), and melatonin (MT) protein levels were analyzed by enzyme-linked immunosorbent assay (ELISA). The apoptosis of BJ cells was analyzed using flow cytometry. Results Treatment with epicatechin increased relative gene expression including COL1A1 (5.94), FGF-2 (8.34), and GPX-1 (8.09), and also decreased MMP-1 (2.90) relative gene expression compared to the UV-induced BJ cells. Epicatechin also increased levels of ELN (107.7 ng/mg protein) a…
format: application/pdf
format: text/html
creator: Wahyu Widowati
creator: Teresa Liliana Wargasetia
creator: Fanny Rahardja
creator: Fen Tih
creator: Philips Onggowidjaja
creator: Rita Tjokropranoto
creator: Fadhilah Haifa Zahiroh
creator: Rizal Azis
creator: Didik Priyandoko
creator: Wahyu Surakusumah
creator: Dhanar Septyawan Hadiprasetyo
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
subject: Science and Medical Education
description: doi:10.7717/peerj.18382
publisher: PeerJ Inc.
rights: © 2024 Widowati et al.
abstract: Background Oxidative stress caused by exposure to ultraviolet (UV) light on the skin can damage deoxyribonucleic acid (DNA) and cause keratinocytes to undergo apoptosis. Endogenous antioxidants which play a role in trapping free radicals are also unable to overcome excess reactive oxygen species (ROS) in the body due to UV exposure, so exogenous antioxidants are needed. Polyphenolic compounds extracted from natural ingredients such as flavonoids, quercetin, and epicatechin have quite strong antioxidant activity. This is influenced by the chemical structure of these compounds which are rich in hydroxyl groups and aromatic groups. This structure allows the compound to become an electron donor so that it can neutralize free radicals. In vitro research was used to see the potential effectiveness of epicatechin as an antiaging and antioxidant. The study aims to confirm the potential of epicatechin as an antiaging by in vitro assay. Methods The viability test of epicatechin on human skin fibroblast (BJ) cells was carried out using the water-soluble tetrazolium (WST) assay. BJ cells were UV-induced as a cell model of premature aging. Epicatechin 6.25, 12.5, and 25 µg/mL were administered to UV-induced BJ cells. The gene expression of Collagen I Alpha 1 (COL1A1), matrix metalloproteinase-1 (MMP-1), fibroblast growth factor-2 (FGF-2), and glutathione peroxidase-1 (GPX-1) were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Elastin (ELN), hyaluronidase (HAase), cyclooxigenase-2 (COX-2), 8-hydroxydeoxyguanosine (8-OhdG), and melatonin (MT) protein levels were analyzed by enzyme-linked immunosorbent assay (ELISA). The apoptosis of BJ cells was analyzed using flow cytometry. Results Treatment with epicatechin increased relative gene expression including COL1A1 (5.94), FGF-2 (8.34), and GPX-1 (8.09), and also decreased MMP-1 (2.90) relative gene expression compared to the UV-induced BJ cells. Epicatechin also increased levels of ELN (107.7 ng/mg protein) a…
bibliographic citation: Widowati et al. (2024) Potential of epicatechin as antioxidant and antiaging in UV-induced BJ cells by regulating COL1A1, FGF-2, GPX-1, and MMP-1 gene, protein levels, and apoptosis. PeerJ 12:e18382 https://doi.org/10.7717/peerj.18382
date submitted: 2024-06-14
date accepted: 2024-10-01
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Widowati
  given name: Wahyu
author list: Agent
  family name: Wargasetia
  given name: Teresa Liliana
author list: Agent
  family name: Rahardja
  given name: Fanny
author list: Agent
  family name: Tih
  given name: Fen
author list: Agent
  family name: Onggowidjaja
  given name: Philips
author list: Agent
  family name: Tjokropranoto
  given name: Rita
author list: Agent
  family name: Zahiroh
  given name: Fadhilah Haifa
author list: Agent
  family name: Azis
  given name: Rizal
author list: Agent
  family name: Priyandoko
  given name: Didik
author list: Agent
  family name: Surakusumah
  given name: Wahyu
author list: Agent
  family name: Hadiprasetyo
  given name: Dhanar Septyawan
doi: 10.7717/peerj.18382
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: © 2024 Widowati et al.
attribution name: Widowati et al.

Seroprevalence and silent infection rate during SARS-CoV-2 pandemic among children and adolescents in Western Pomerania: a multicenter, cross-sectional study—the COVIDKID study
type: item
type: AcademicArticle
description: Background Limited data on SARS-CoV-2 seroprevalence in rural areas of northern Germany necessitate comprehensive cohort studies. We aimed to evaluate the seroprevalence, silent infection (SI) rates and risk factors for infections among children and adolescents in Western Pomerania from December 2020 to August 2022. Methods In this cross-sectional study, serum or plasma samples from children and adolescents (6 months to 17 years) were collected during routine blood draw. SARS-CoV-2 specific antibodies (S1 and nucleocapsid) and their neutralizing capacity were analyzed using commercially available enzyme-linked immunosorbent and neutralization assays. Socio-demographic data and information about SARS-CoV-2 infection or vaccination were obtained. Multivariable logistic regression was used to identify independent risk factors for SARS-CoV-2 infections and SI. Results A total of 1,131 blood samples were included into the study. Overall, SARS-CoV-2 seroprevalence was 25.1%, strongly influenced by the pandemic course, predominant virus variants, age and approval of vaccination. SI rate was 5.4% (95%-CI [3.7%–6.8%]) among unvaccinated and undiagnosed children over the entire study period with highest rates among adolescents. Main risk factor despite the time at risk for silent infections was an infected household member (Odds ratio = 9.88, 95%-CI [4.23–22.9], p < 0.001). Factors associated with overall infections (known and silent) also include the infection of a household member (Odds ratio = 17.8, 95%-CI [10.7–29.6], p < 0.001). Conclusions We believe that the introduction of governmental measures and systematic test strategies in schools strongly impacted on the SI rate, as we suspect that asymptomatic cases have already been identified, resulting in surprisingly low SI identified in our study.
format: application/pdf
format: text/html
creator: Marcus Vollmer
creator: Daniela Kuthning
creator: Jana Gramenz
creator: Arevik Scholz
creator: Robin Michael
creator: Nico Wittmann
creator: Udo Gesser
creator: Christian Niesytto
creator: Antje Vogler
creator: Vanda Tuxhorn
creator: Ute Lenschow
creator: Anja Lange
creator: Kristina Linnemann
creator: Holger Lode
creator: Lars Kaderali
creator: Almut Meyer-Bahlburg
subject: Epidemiology
subject: Infectious Diseases
subject: Pediatrics
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.18384
publisher: PeerJ Inc.
rights: © 2024 Vollmer et al.
abstract: Background Limited data on SARS-CoV-2 seroprevalence in rural areas of northern Germany necessitate comprehensive cohort studies. We aimed to evaluate the seroprevalence, silent infection (SI) rates and risk factors for infections among children and adolescents in Western Pomerania from December 2020 to August 2022. Methods In this cross-sectional study, serum or plasma samples from children and adolescents (6 months to 17 years) were collected during routine blood draw. SARS-CoV-2 specific antibodies (S1 and nucleocapsid) and their neutralizing capacity were analyzed using commercially available enzyme-linked immunosorbent and neutralization assays. Socio-demographic data and information about SARS-CoV-2 infection or vaccination were obtained. Multivariable logistic regression was used to identify independent risk factors for SARS-CoV-2 infections and SI. Results A total of 1,131 blood samples were included into the study. Overall, SARS-CoV-2 seroprevalence was 25.1%, strongly influenced by the pandemic course, predominant virus variants, age and approval of vaccination. SI rate was 5.4% (95%-CI [3.7%–6.8%]) among unvaccinated and undiagnosed children over the entire study period with highest rates among adolescents. Main risk factor despite the time at risk for silent infections was an infected household member (Odds ratio = 9.88, 95%-CI [4.23–22.9], p < 0.001). Factors associated with overall infections (known and silent) also include the infection of a household member (Odds ratio = 17.8, 95%-CI [10.7–29.6], p < 0.001). Conclusions We believe that the introduction of governmental measures and systematic test strategies in schools strongly impacted on the SI rate, as we suspect that asymptomatic cases have already been identified, resulting in surprisingly low SI identified in our study.
bibliographic citation: Vollmer et al. (2024) Seroprevalence and silent infection rate during SARS-CoV-2 pandemic among children and adolescents in Western Pomerania: a multicenter, cross-sectional study—the COVIDKID study. PeerJ 12:e18384 https://doi.org/10.7717/peerj.18384
date submitted: 2024-04-18
date accepted: 2024-10-01
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vollmer
  given name: Marcus
author list: Agent
  family name: Kuthning
  given name: Daniela
author list: Agent
  family name: Gramenz
  given name: Jana
author list: Agent
  family name: Scholz
  given name: Arevik
author list: Agent
  family name: Michael
  given name: Robin
author list: Agent
  family name: Wittmann
  given name: Nico
author list: Agent
  family name: Gesser
  given name: Udo
author list: Agent
  family name: Niesytto
  given name: Christian
author list: Agent
  family name: Vogler
  given name: Antje
author list: Agent
  family name: Tuxhorn
  given name: Vanda
author list: Agent
  family name: Lenschow
  given name: Ute
author list: Agent
  family name: Lange
  given name: Anja
author list: Agent
  family name: Linnemann
  given name: Kristina
author list: Agent
  family name: Lode
  given name: Holger
author list: Agent
  family name: Kaderali
  given name: Lars
author list: Agent
  family name: Meyer-Bahlburg
  given name: Almut
doi: 10.7717/peerj.18384
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: ©2024 Vollmer et al.
attribution name: Vollmer et al.

Examination of optical coherence tomography findings in patients with pregabalin use disorder
type: item
type: AcademicArticle
description: Background Pregabalin abuse is a rapidly growing health problem worldwide, and little is known about the effects of prolonged high-dose use in patients with pregabalin use disorder. Objective In this study, the effects of pregabalin abuse on retinal layers were investigated in patients with pregabalin use disorder (PGUD). Methods This study included 35 controls and 34 patients with PGUD, according to Diagnostic and Statistical Manual of Mental Disorders (DSM)-5 criteria. Optic coherence tomography (OCT) measurements including the retinal nerve fiber layer (RNFL), ganglion cell layer-inner plexiform layer (GCL-IPL) and ganglion cell complex (GCC) were performed. RNFL thickness was evaluated in four quadrants (inferior, superior, nasal, temporal). GCL-IPL and GCC thickness were evaluated in six sectors (superior, superonasal, inferonasal, inferior, inferotemporal, superotemporal). Results GCC inferonasal (p = 0.040, r = 0.354), GCC inferior (p = 0.018, r = 0.402) GCL-IPL inferior (p = 0.031, r = 0.370) and GCL-IPL inferotemporal (p = 0.029, r = 0.376) thickness were positively correlated with the duration of pregabalin use. There was no significant sector or quadrant-wise difference between groups (p > 0.05). Conclusion Our findings emphasized the drug’s potential neuroprotective effect. It should be taken into consideration that neurodegenerative changes due to substance use disorder occur with long-term. Longitudinal prospective studies investigating dose-duration relationship are needed.
format: application/pdf
format: text/html
creator: Osman Hasan Tahsin Kılıç
creator: Zehra Nur Bayram
creator: Pelin Kiyat
creator: Omer Karti
creator: Arzu Aral
creator: Nazlı Deniz Munis
creator: Berfin Gurbet Mutlu
subject: Ophthalmology
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.18395
publisher: PeerJ Inc.
rights: © 2024 Kılıç et al.
abstract: Background Pregabalin abuse is a rapidly growing health problem worldwide, and little is known about the effects of prolonged high-dose use in patients with pregabalin use disorder. Objective In this study, the effects of pregabalin abuse on retinal layers were investigated in patients with pregabalin use disorder (PGUD). Methods This study included 35 controls and 34 patients with PGUD, according to Diagnostic and Statistical Manual of Mental Disorders (DSM)-5 criteria. Optic coherence tomography (OCT) measurements including the retinal nerve fiber layer (RNFL), ganglion cell layer-inner plexiform layer (GCL-IPL) and ganglion cell complex (GCC) were performed. RNFL thickness was evaluated in four quadrants (inferior, superior, nasal, temporal). GCL-IPL and GCC thickness were evaluated in six sectors (superior, superonasal, inferonasal, inferior, inferotemporal, superotemporal). Results GCC inferonasal (p = 0.040, r = 0.354), GCC inferior (p = 0.018, r = 0.402) GCL-IPL inferior (p = 0.031, r = 0.370) and GCL-IPL inferotemporal (p = 0.029, r = 0.376) thickness were positively correlated with the duration of pregabalin use. There was no significant sector or quadrant-wise difference between groups (p > 0.05). Conclusion Our findings emphasized the drug’s potential neuroprotective effect. It should be taken into consideration that neurodegenerative changes due to substance use disorder occur with long-term. Longitudinal prospective studies investigating dose-duration relationship are needed.
bibliographic citation: Kılıç et al. (2024) Examination of optical coherence tomography findings in patients with pregabalin use disorder. PeerJ 12:e18395 https://doi.org/10.7717/peerj.18395
date submitted: 2024-04-10
date accepted: 2024-10-03
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kılıç
  given name: Osman Hasan Tahsin
author list: Agent
  family name: Bayram
  given name: Zehra Nur
author list: Agent
  family name: Kiyat
  given name: Pelin
author list: Agent
  family name: Karti
  given name: Omer
author list: Agent
  family name: Aral
  given name: Arzu
author list: Agent
  family name: Munis
  given name: Nazlı Deniz
author list: Agent
  family name: Mutlu
  given name: Berfin Gurbet
doi: 10.7717/peerj.18395
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: © 2024 Kılıç et al.
attribution name: Kılıç et al.

Transperineal prostate biopsy guided by which ultrasound transducer: transrectal or transperineal: a retrospective study
type: item
type: AcademicArticle
description: Background Prostate biopsies are primarily conducted using either the transrectal or transperineal approach, with the ultrasound probe positioned in the rectum to obtain a clear view of the prostate. Reports on the utilization of transperineal prostate biopsies with the ultrasound probe placed on the perineal skin are limited. Methods A retrospective investigation was conducted on 119 patients who underwent transperineal ultrasound guided transperineal prostate biopsy (TP-TPPB). Additionally, 85 patients who underwent transrectal ultrasound guided transperineal prostate biopsy (TR-TPPB) were included as controls. The prostate cancer detection rates (PCDRs) and postoperative complication rates were compared between the two groups, and their application values were also evaluated. Results The overall PCDRs were 35.3% (42/119) in the TP-TPPB and 32.9% (28/85) in the TR-TPPB group (χ2 = 0.122, p = 0.727). When categorized by PSA level, there was no significant difference between the two groups in PCDRs in any category (p > 0.05). However, the single-needle PCDRs in some regions (L4, L5, R2, and apex) showed significant differences (p < 0.05). There was no difference in postoperative complication rates between the groups. Conclusion The PCDRs and the postoperative complication rates of TP-TPPB and TR-TPPB are similar. However, TP-TPPB requires simpler equipment and does not require intestinal preparation, which is especially useful for patients with rectal contraindications, such as those with severe hemorrhoids and rectal/anal diseases.
format: application/pdf
format: text/html
creator: Yang Xiao
creator: Lina Han
creator: Han Wang
creator: Guorong Lyu
creator: Shilin Li
subject: Andrology
subject: Oncology
subject: Pathology
subject: Radiology and Medical Imaging
subject: Urology
description: doi:10.7717/peerj.18424
publisher: PeerJ Inc.
rights: © 2024 Xiao et al.
abstract: Background Prostate biopsies are primarily conducted using either the transrectal or transperineal approach, with the ultrasound probe positioned in the rectum to obtain a clear view of the prostate. Reports on the utilization of transperineal prostate biopsies with the ultrasound probe placed on the perineal skin are limited. Methods A retrospective investigation was conducted on 119 patients who underwent transperineal ultrasound guided transperineal prostate biopsy (TP-TPPB). Additionally, 85 patients who underwent transrectal ultrasound guided transperineal prostate biopsy (TR-TPPB) were included as controls. The prostate cancer detection rates (PCDRs) and postoperative complication rates were compared between the two groups, and their application values were also evaluated. Results The overall PCDRs were 35.3% (42/119) in the TP-TPPB and 32.9% (28/85) in the TR-TPPB group (χ2 = 0.122, p = 0.727). When categorized by PSA level, there was no significant difference between the two groups in PCDRs in any category (p > 0.05). However, the single-needle PCDRs in some regions (L4, L5, R2, and apex) showed significant differences (p < 0.05). There was no difference in postoperative complication rates between the groups. Conclusion The PCDRs and the postoperative complication rates of TP-TPPB and TR-TPPB are similar. However, TP-TPPB requires simpler equipment and does not require intestinal preparation, which is especially useful for patients with rectal contraindications, such as those with severe hemorrhoids and rectal/anal diseases.
bibliographic citation: Xiao et al. (2024) Transperineal prostate biopsy guided by which ultrasound transducer: transrectal or transperineal: a retrospective study. PeerJ 12:e18424 https://doi.org/10.7717/peerj.18424
date submitted: 2024-04-15
date accepted: 2024-10-08
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Yang
author list: Agent
  family name: Han
  given name: Lina
author list: Agent
  family name: Wang
  given name: Han
author list: Agent
  family name: Lyu
  given name: Guorong
author list: Agent
  family name: Li
  given name: Shilin
doi: 10.7717/peerj.18424
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: ©2024 Xiao et al.
attribution name: Xiao et al.

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