PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago
items: https://peerj.com/articles/18623
items: A comparative study on leaf anatomy and photosynthetic characteristics of different growth stages of Horsfieldia hainanensis
items: N6-methyladenosine (m6A) modification in inflammation: a bibliometric analysis and literature review
items: Isolation and identification of serotonin compound from banana hump: a reproductive stimulant for tiger shrimp Penaeus monodon broodstock enhancement
items: Development of machine learning models for the prediction of the skin sensitization potential of cosmetic compounds
items: Effects of prophylactic nebulized antibiotics on the prevention of ICU-acquired pneumonia: a systematic review and meta-analysis
items: Identification of immunogenic cell death gene-related subtypes and risk model predicts prognosis and response to immunotherapy in ovarian cancer
items: Efficacy of different dietary therapy strategies in active pediatric Crohn’s disease: a systematic review and network meta-analysis
items: Adiposity and body fat distribution based on skinfold thicknesses and body circumferences in Czech preschool children, secular changes

Computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago
type: item
type: AcademicArticle
description: Background Modern workplace requirements in the banking sector require bankers to work on screens for more than 6 h a day, putting much stress and strain on their eyes, which leads to computer vision syndrome. Therefore, this study aimed to assess the prevalence of computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago. Methods and materials A cross-sectional design was applied to collect data from 399 bankers between April and June 2023. The collected data was entered into Excel worksheets and later uploaded to SPSS for further analysis. A variable with a P-value of 0.25 in binary logistic regression is a candidate for multi-variable logistic regression analysis. Finally, a variable with a P-value of 0.05 was used to declare statistical significance. Results A total of 371 participants were enrolled in this study, leading to a response rate of 92.9%. Of the total participants, 277 (74.7%) had computer vision syndrome. Working in rural areas (AOR = 2.69; 95% CI [1.41–5.13]) and using eyesight glasses (AOR = 0.57; 95% CI [0.33–0.97]) was associated with computer vision syndrome. Conclusion Despite being easily preventable, computer vision syndrome is substantially prevalent among bankers in Trinidad. The use of eye-sight glasses and the working area are significantly associated with computer vision syndrome. Therefore, it is necessary to improve workplace practices by encouraging the use of anti-glare screens and glasses for employees who work long hours on the computer.
format: application/pdf
format: text/html
creator: Kingsley Ekemiri
creator: Devonte McKnight
creator: Chioma Ekemiri
creator: Ngozika Ezinne
creator: Henrietta Ashang
creator: Virginia Victor
creator: Osaze Okonedo
creator: Ayishetu Oshoke Shuaibu
creator: Robin Seemongal-Dass
subject: Ophthalmology
subject: Public Health
subject: Environmental Health
description: doi:10.7717/peerj.18584
publisher: PeerJ Inc.
rights: © 2024 Ekemiri et al.
abstract: Background Modern workplace requirements in the banking sector require bankers to work on screens for more than 6 h a day, putting much stress and strain on their eyes, which leads to computer vision syndrome. Therefore, this study aimed to assess the prevalence of computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago. Methods and materials A cross-sectional design was applied to collect data from 399 bankers between April and June 2023. The collected data was entered into Excel worksheets and later uploaded to SPSS for further analysis. A variable with a P-value of 0.25 in binary logistic regression is a candidate for multi-variable logistic regression analysis. Finally, a variable with a P-value of 0.05 was used to declare statistical significance. Results A total of 371 participants were enrolled in this study, leading to a response rate of 92.9%. Of the total participants, 277 (74.7%) had computer vision syndrome. Working in rural areas (AOR = 2.69; 95% CI [1.41–5.13]) and using eyesight glasses (AOR = 0.57; 95% CI [0.33–0.97]) was associated with computer vision syndrome. Conclusion Despite being easily preventable, computer vision syndrome is substantially prevalent among bankers in Trinidad. The use of eye-sight glasses and the working area are significantly associated with computer vision syndrome. Therefore, it is necessary to improve workplace practices by encouraging the use of anti-glare screens and glasses for employees who work long hours on the computer.
bibliographic citation: Ekemiri et al. (2024) Computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago. PeerJ 12:e18584 https://doi.org/10.7717/peerj.18584
date submitted: 2024-03-25
date accepted: 2024-11-04
issued: 2024-12-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ekemiri
  given name: Kingsley
author list: Agent
  family name: McKnight
  given name: Devonte
author list: Agent
  family name: Ekemiri
  given name: Chioma
author list: Agent
  family name: Ezinne
  given name: Ngozika
author list: Agent
  family name: Ashang
  given name: Henrietta
author list: Agent
  family name: Victor
  given name: Virginia
author list: Agent
  family name: Okonedo
  given name: Osaze
author list: Agent
  family name: Shuaibu
  given name: Ayishetu Oshoke
author list: Agent
  family name: Seemongal-Dass
  given name: Robin
doi: 10.7717/peerj.18584
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-13
copyright: © 2024 Ekemiri et al.
attribution name: Ekemiri et al.

https://peerj.com/articles/18623
type: item
type: AcademicArticle
title: Companion animal foster caregiving: a scoping review exploring animal and caregiver welfare, barriers to caregiver recruitment and retention, and best practices for foster care programs in animal shelters
description: Each year, millions of animals enter animal shelters across the United States and are met with a variety of potential stressors that can negatively impact their experience, including noise, confinement, and social isolation. Foster care, a unique form of human–animal interaction, is increasingly understood to be an effective tool for improving welfare by allowing animals to escape the stressors of the shelter, providing an environment that allows for greater social interaction, and offering opportunities for improved health and behavior. This review includes 42 published articles, reports, master’s theses, and doctoral dissertations that have previously evaluated companion animal foster care programs. While scientific literature in this area has increased over the last decade, no review of the research exploring companion animal fostering has been published. Here, we examine foster care programs and their effects on human and animal welfare, evaluate the successes and challenges of supporting shelter foster care programs, recommend best practices for programmatic success, illuminate discrepancies in equity and diversity of caregiver engagement, and offer directions for future research in animal foster caregiving. The examinations in this review conclude that fostering provides both proximate (i.e., physiological and behavioral) and distal (i.e., length of stay and adoption outcomes) welfare benefits for shelter animals as well as their caregivers. Companion animal foster care programs may be further improved by providing greater caregiver support and increasing the diversity and extent of community engagement. Meanwhile, scientific investigations should explore lesser-researched components of foster care programs that are not yet well understood.
format: application/pdf
format: text/html
creator: Grace E. Phillips
creator: Lisa M. Gunter
subject: Animal Behavior
description: doi:10.7717/peerj.18623
publisher: PeerJ Inc.
rights: © 2024 Phillips and Gunter
abstract: Each year, millions of animals enter animal shelters across the United States and are met with a variety of potential stressors that can negatively impact their experience, including noise, confinement, and social isolation. Foster care, a unique form of human–animal interaction, is increasingly understood to be an effective tool for improving welfare by allowing animals to escape the stressors of the shelter, providing an environment that allows for greater social interaction, and offering opportunities for improved health and behavior. This review includes 42 published articles, reports, master’s theses, and doctoral dissertations that have previously evaluated companion animal foster care programs. While scientific literature in this area has increased over the last decade, no review of the research exploring companion animal fostering has been published. Here, we examine foster care programs and their effects on human and animal welfare, evaluate the successes and challenges of supporting shelter foster care programs, recommend best practices for programmatic success, illuminate discrepancies in equity and diversity of caregiver engagement, and offer directions for future research in animal foster caregiving. The examinations in this review conclude that fostering provides both proximate (i.e., physiological and behavioral) and distal (i.e., length of stay and adoption outcomes) welfare benefits for shelter animals as well as their caregivers. Companion animal foster care programs may be further improved by providing greater caregiver support and increasing the diversity and extent of community engagement. Meanwhile, scientific investigations should explore lesser-researched components of foster care programs that are not yet well understood.
bibliographic citation: Phillips et al. (2024) Companion animal foster caregiving: a scoping review exploring animal and caregiver welfare, barriers to caregiver recruitment and retention, and best practices for foster care programs in animal shelters. PeerJ 12:e18623 https://doi.org/10.7717/peerj.18623
date submitted: 2024-08-23
date accepted: 2024-11-11
issued: 2024-12-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Phillips
  given name: Grace E.
author list: Agent
  family name: Gunter
  given name: Lisa M.
doi: 10.7717/peerj.18623
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-13
copyright: © 2024 Phillips and Gunter
attribution name: Phillips and Gunter

A comparative study on leaf anatomy and photosynthetic characteristics of different growth stages of Horsfieldia hainanensis
type: item
type: AcademicArticle
description: The rare and endangered wild plant, Horsfieldia hainanensis, has been listed as a second-level key protected plant in China. Currently, its habitat is severely damaged, and the population has dramatically declined, necessitating urgent intervention for protection. In this study, the aim was to explore the correlations and differences from the perspectives of photosynthetic characteristics and leaf structure, providing scientific references for in-situ conservation and ex-situ cultivation. The results revealed the following: (1) The maximum net photosynthetic rate (Pmax) and light saturation point (LSP) of mature trees were significantly higher than those of seedlings, while the light compensation point (LCP), CO2 compensation point (CCP), and CO2 saturation point (CSP) were significantly lower in seedlings. (2) The average daily net photosynthetic rate of mature trees was significantly higher than that of seedlings. When both mature trees and seedlings exhibited a “midday depression” phenomenon, accompanied by an increase in intercellular CO2 concentration (Ci), it indicated that the “midday depression” was caused by non-stomatal limiting factors. (4) Both mature trees and seedlings showed peak values of water use efficiency (WUE) under low light conditions. Mature trees had smaller upper and lower epidermis thickness but larger leaf thickness, and their leaf structure, characterized by well-developed palisade and spongy tissues, conformed to the cellular structure adaptations for low light. Therefore, both were more adapted to low light conditions. (5) The stomatal density (SD) and individual stomatal area (SA) of seedlings were significantly higher than those of mature trees. (6) The total chlorophyll content of mature trees was significantly higher than that of seedlings, while the chlorophyll a/chlorophyll b ratio was significantly lower in mature trees and remained below three in both cases. In summary, the photosynthetic capacity and light adaptability of matu…
format: application/pdf
format: text/html
creator: Jianwang Xu
creator: Jianmin Tang
creator: Haolong Jiang
creator: Rong Zou
creator: Xiao Wei
subject: Conservation Biology
subject: Plant Science
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.18640
publisher: PeerJ Inc.
rights: © 2024 Xu et al.
abstract: The rare and endangered wild plant, Horsfieldia hainanensis, has been listed as a second-level key protected plant in China. Currently, its habitat is severely damaged, and the population has dramatically declined, necessitating urgent intervention for protection. In this study, the aim was to explore the correlations and differences from the perspectives of photosynthetic characteristics and leaf structure, providing scientific references for in-situ conservation and ex-situ cultivation. The results revealed the following: (1) The maximum net photosynthetic rate (Pmax) and light saturation point (LSP) of mature trees were significantly higher than those of seedlings, while the light compensation point (LCP), CO2 compensation point (CCP), and CO2 saturation point (CSP) were significantly lower in seedlings. (2) The average daily net photosynthetic rate of mature trees was significantly higher than that of seedlings. When both mature trees and seedlings exhibited a “midday depression” phenomenon, accompanied by an increase in intercellular CO2 concentration (Ci), it indicated that the “midday depression” was caused by non-stomatal limiting factors. (4) Both mature trees and seedlings showed peak values of water use efficiency (WUE) under low light conditions. Mature trees had smaller upper and lower epidermis thickness but larger leaf thickness, and their leaf structure, characterized by well-developed palisade and spongy tissues, conformed to the cellular structure adaptations for low light. Therefore, both were more adapted to low light conditions. (5) The stomatal density (SD) and individual stomatal area (SA) of seedlings were significantly higher than those of mature trees. (6) The total chlorophyll content of mature trees was significantly higher than that of seedlings, while the chlorophyll a/chlorophyll b ratio was significantly lower in mature trees and remained below three in both cases. In summary, the photosynthetic capacity and light adaptability of matu…
bibliographic citation: Xu et al. (2024) A comparative study on leaf anatomy and photosynthetic characteristics of different growth stages of Horsfieldia hainanensis. PeerJ 12:e18640 https://doi.org/10.7717/peerj.18640
date submitted: 2024-08-07
date accepted: 2024-11-13
issued: 2024-12-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Xu
  given name: Jianwang
author list: Agent
  family name: Tang
  given name: Jianmin
author list: Agent
  family name: Jiang
  given name: Haolong
author list: Agent
  family name: Zou
  given name: Rong
author list: Agent
  family name: Wei
  given name: Xiao
doi: 10.7717/peerj.18640
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-13
copyright: © 2024 Xu et al.
attribution name: Xu et al.

N6-methyladenosine (m6A) modification in inflammation: a bibliometric analysis and literature review
type: item
type: AcademicArticle
description: N6-methyladenosine (m6A) is the most abundant internal messenger RNA modification in eukaryotes, influencing various physiological and pathological processes by regulating RNA metabolism. Numerous studies have investigated the role of m6A in inflammatory responses and inflammatory diseases. In this study, VOSviewer and Citespace were used to perform bibliometric analysis to systematically evaluating the current landscape of research on the association between m6A and inflammation. The literature was sourced from the Web of Science Core Collection, with characteristics including year, country/region, institution, author, journal, citation, and keywords. According to the bibliometric analysis results of keywords, we present a narrative summary of the potential mechanisms by which m6A regulates inflammation. The results showed that the key mechanisms by which m6A modulates inflammation include apoptosis, autophagy, oxidative stress, immune cell dysfunction, and dysregulation of signaling pathways.
format: application/pdf
format: text/html
creator: Zewen Li
creator: Yongfeng Lao
creator: Rui Yan
creator: Xin Guan
creator: Yanan Bai
creator: Fuhan Li
creator: Zhilong Dong
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
subject: Immunology
description: doi:10.7717/peerj.18645
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: N6-methyladenosine (m6A) is the most abundant internal messenger RNA modification in eukaryotes, influencing various physiological and pathological processes by regulating RNA metabolism. Numerous studies have investigated the role of m6A in inflammatory responses and inflammatory diseases. In this study, VOSviewer and Citespace were used to perform bibliometric analysis to systematically evaluating the current landscape of research on the association between m6A and inflammation. The literature was sourced from the Web of Science Core Collection, with characteristics including year, country/region, institution, author, journal, citation, and keywords. According to the bibliometric analysis results of keywords, we present a narrative summary of the potential mechanisms by which m6A regulates inflammation. The results showed that the key mechanisms by which m6A modulates inflammation include apoptosis, autophagy, oxidative stress, immune cell dysfunction, and dysregulation of signaling pathways.
bibliographic citation: Li et al. (2024) N6-methyladenosine (m6A) modification in inflammation: a bibliometric analysis and literature review. PeerJ 12:e18645 https://doi.org/10.7717/peerj.18645
date submitted: 2024-07-18
date accepted: 2024-11-14
issued: 2024-12-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zewen
author list: Agent
  family name: Lao
  given name: Yongfeng
author list: Agent
  family name: Yan
  given name: Rui
author list: Agent
  family name: Guan
  given name: Xin
author list: Agent
  family name: Bai
  given name: Yanan
author list: Agent
  family name: Li
  given name: Fuhan
author list: Agent
  family name: Dong
  given name: Zhilong
doi: 10.7717/peerj.18645
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-13
copyright: © 2024 Li et al.
attribution name: Li et al.

Isolation and identification of serotonin compound from banana hump: a reproductive stimulant for tiger shrimp Penaeus monodon broodstock enhancement
type: item
type: AcademicArticle
description: Background The banana plant is claimed to contain a serotonin compound that has the potential to stimulate and improve the reproductive performance of crustacean species. This study aimed to isolate and characterize the serotonin compound from the banana hump and its application to enhance the reproductive performance of tiger shrimp broodstock. Methods Banana hump as a part of the plant was extracted by using the maceration technique. The chemical structure of the serotonin compound was identified and characterized based on spectroscopic data, including high-performance liquid chromatography (HPLC), ultraviolet-visible (UV-Vis) spectroscopy, and infrared (IR) spectroscopy, and a comparison was made with the standard compound and the literature. The extract herb in a dose of 50 µg/g body weight was injected into the tiger shrimp broodstock in four-time administrations. During 2 months of broodstock gonadal maturation, the parameters of molting, reproduction, and gene expression related to reproduction were observed. Results Based on the chemical structure analysis, the stimulant component of the banana hump was identified as a serotonin compound (5-hydroxytryptamine) at a concentration of 0.7% of dry weight. The number of spawned broodstock was higher in the serotonin extract treatment (60%) than in the control treatment (40%), and the broodstock injected serotonin spawned up to the second re-maturation. In contrast, no re-maturation was obtained in the control treatment. The egg number was significantly higher using the serotonin extract (286,550 ± 46,402 eggs) than the control shrimp (148,585 ± 23,647 eggs), in which the serotonin extract treatment showed a comparatively larger egg diameter number. The higher expression of the genes related to female and male reproduction was observed in the tiger shrimp injected with serotonin extract than in the control treatment.
format: application/pdf
format: text/html
creator: Andi Parenrengi
creator: Emma Suryati
creator: Rachman Syah
creator: Andi Tenriulo
creator: Samuel Lante
creator: Elmi Nurhaidah Zainuddin
creator: Ratu Siti Aliah
creator: Nuril Farizah
creator: Agus Nawang
creator: Sulaeman Sulaeman
creator: Makmur Makmur
creator: Rosmiati Rosmiati
creator: Gunarto Gunarto
creator: Herlinah Herlinah
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Veterinary Medicine
description: doi:10.7717/peerj.18670
publisher: PeerJ Inc.
rights: © 2024 Parenrengi et al.
abstract: Background The banana plant is claimed to contain a serotonin compound that has the potential to stimulate and improve the reproductive performance of crustacean species. This study aimed to isolate and characterize the serotonin compound from the banana hump and its application to enhance the reproductive performance of tiger shrimp broodstock. Methods Banana hump as a part of the plant was extracted by using the maceration technique. The chemical structure of the serotonin compound was identified and characterized based on spectroscopic data, including high-performance liquid chromatography (HPLC), ultraviolet-visible (UV-Vis) spectroscopy, and infrared (IR) spectroscopy, and a comparison was made with the standard compound and the literature. The extract herb in a dose of 50 µg/g body weight was injected into the tiger shrimp broodstock in four-time administrations. During 2 months of broodstock gonadal maturation, the parameters of molting, reproduction, and gene expression related to reproduction were observed. Results Based on the chemical structure analysis, the stimulant component of the banana hump was identified as a serotonin compound (5-hydroxytryptamine) at a concentration of 0.7% of dry weight. The number of spawned broodstock was higher in the serotonin extract treatment (60%) than in the control treatment (40%), and the broodstock injected serotonin spawned up to the second re-maturation. In contrast, no re-maturation was obtained in the control treatment. The egg number was significantly higher using the serotonin extract (286,550 ± 46,402 eggs) than the control shrimp (148,585 ± 23,647 eggs), in which the serotonin extract treatment showed a comparatively larger egg diameter number. The higher expression of the genes related to female and male reproduction was observed in the tiger shrimp injected with serotonin extract than in the control treatment.
bibliographic citation: Parenrengi et al. (2024) Isolation and identification of serotonin compound from banana hump: a reproductive stimulant for tiger shrimp Penaeus monodon broodstock enhancement. PeerJ 12:e18670 https://doi.org/10.7717/peerj.18670
date submitted: 2024-09-04
date accepted: 2024-11-19
issued: 2024-12-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parenrengi
  given name: Andi
author list: Agent
  family name: Suryati
  given name: Emma
author list: Agent
  family name: Syah
  given name: Rachman
author list: Agent
  family name: Tenriulo
  given name: Andi
author list: Agent
  family name: Lante
  given name: Samuel
author list: Agent
  family name: Zainuddin
  given name: Elmi Nurhaidah
author list: Agent
  family name: Aliah
  given name: Ratu Siti
author list: Agent
  family name: Farizah
  given name: Nuril
author list: Agent
  family name: Nawang
  given name: Agus
author list: Agent
  family name: Sulaeman
  given name: Sulaeman
author list: Agent
  family name: Makmur
  given name: Makmur
author list: Agent
  family name: Rosmiati
  given name: Rosmiati
author list: Agent
  family name: Gunarto
  given name: Gunarto
author list: Agent
  family name: Herlinah
  given name: Herlinah
doi: 10.7717/peerj.18670
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-13
copyright: © 2024 Parenrengi et al.
attribution name: Parenrengi et al.

Development of machine learning models for the prediction of the skin sensitization potential of cosmetic compounds
type: item
type: AcademicArticle
description: Background To enhance the accuracy of allergen detection in cosmetic compounds, we developed a co-culture system that combines HaCaT keratinocytes (transfected with a luciferase plasmid driven by the AKR1C2 promoter) and THP-1 cells for machine learning applications. Methods Following chemical exposure, cell cytotoxicity was assessed using CCK-8 to determine appropriate stimulation concentrations. RNA-Seq was subsequently employed to analyze THP-1 cells, followed by differential expression gene (DEG) analysis and weighted gene co-expression net-work analysis (WGCNA). Using two data preprocessing methods and three feature extraction techniques, we constructed and validated models with eight machine learning algorithms. Results Our results demonstrated the effectiveness of this integrated approach. The best performing models were random forest (RF) and voom-based diagonal quadratic discriminant analysis (voomDQDA), both achieving 100% accuracy. Support vector machine (SVM) and voom based nearest shrunken centroids (voomNSC) showed excellent performance with 96.7% test accuracy, followed by voom-based diagonal linear discriminant analysis (voomDLDA) at 95.2%. Nearest shrunken centroids (NSC), Poisson linear discriminant analysis (PLDA) and negative binomial linear discriminant analysis (NBLDA) achieved 90.5% and 90.2% accuracy, respectively. K-nearest neighbors (KNN) showed the lowest accuracy at 85.7%. Conclusion This study highlights the potential of integrating co-culture systems, RNA-Seq, and machine learning to develop more accurate and comprehensive in vitro methods for skin sensitization testing. Our findings contribute to the advancement of cosmetic safety assessments, potentially reducing the reliance on animal testing.
format: application/pdf
format: text/html
creator: Wu Qiao
creator: Tong Xie
creator: Jing Lu
creator: Tinghan Jia
subject: Bioinformatics
subject: Cell Biology
subject: Immunology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.18672
publisher: PeerJ Inc.
rights: © 2024 Qiao et al.
abstract: Background To enhance the accuracy of allergen detection in cosmetic compounds, we developed a co-culture system that combines HaCaT keratinocytes (transfected with a luciferase plasmid driven by the AKR1C2 promoter) and THP-1 cells for machine learning applications. Methods Following chemical exposure, cell cytotoxicity was assessed using CCK-8 to determine appropriate stimulation concentrations. RNA-Seq was subsequently employed to analyze THP-1 cells, followed by differential expression gene (DEG) analysis and weighted gene co-expression net-work analysis (WGCNA). Using two data preprocessing methods and three feature extraction techniques, we constructed and validated models with eight machine learning algorithms. Results Our results demonstrated the effectiveness of this integrated approach. The best performing models were random forest (RF) and voom-based diagonal quadratic discriminant analysis (voomDQDA), both achieving 100% accuracy. Support vector machine (SVM) and voom based nearest shrunken centroids (voomNSC) showed excellent performance with 96.7% test accuracy, followed by voom-based diagonal linear discriminant analysis (voomDLDA) at 95.2%. Nearest shrunken centroids (NSC), Poisson linear discriminant analysis (PLDA) and negative binomial linear discriminant analysis (NBLDA) achieved 90.5% and 90.2% accuracy, respectively. K-nearest neighbors (KNN) showed the lowest accuracy at 85.7%. Conclusion This study highlights the potential of integrating co-culture systems, RNA-Seq, and machine learning to develop more accurate and comprehensive in vitro methods for skin sensitization testing. Our findings contribute to the advancement of cosmetic safety assessments, potentially reducing the reliance on animal testing.
bibliographic citation: Qiao et al. (2024) Development of machine learning models for the prediction of the skin sensitization potential of cosmetic compounds. PeerJ 12:e18672 https://doi.org/10.7717/peerj.18672
date submitted: 2024-09-18
date accepted: 2024-11-19
issued: 2024-12-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qiao
  given name: Wu
author list: Agent
  family name: Xie
  given name: Tong
author list: Agent
  family name: Lu
  given name: Jing
author list: Agent
  family name: Jia
  given name: Tinghan
doi: 10.7717/peerj.18672
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-13
copyright: © 2024 Qiao et al.
attribution name: Qiao et al.

Effects of prophylactic nebulized antibiotics on the prevention of ICU-acquired pneumonia: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective To evaluate the efficacy and safety of prophylactic nebulized antibiotics in preventing intensive care unit (ICU)-acquired pneumonia through a meta-analysis. Methods Randomized controlled trials (RCTs) investigating the potential reduction in the incidence of ICU-acquired pneumonia through prophylactic nebulized antibiotics were collected by searching the PubMed, Embase, and Cochrane Library databases from their inception to January 23, 2024. The primary endpoint was the incidence of ICU-acquired pneumonia, while the secondary endpoints included mortality, length of ICU stay, mechanical ventilation days, and nebulization-related side effects. Statistical analyses were performed using RevMan 5.3 and STATA 14.0 software. Results A total of six RCTs were included in the analysis, involving 1,287 patients (636 patients in the study group received prophylactic antibiotic therapy, including Polymyxin B, Tobramycin, Ceftazidime, Colistimethate sodium, and amikacin; 651 patients in the control group primarily received saline). The results indicated that prophylactic nebulized antibiotic therapy significantly reduced the incidence of ICU-acquired pneumonia compared to that in the control group (odds ratio (OR) = 0.57, 95% confidence interval (CI) [0.43–0.74], P < 0.0001). No significant difference was observed in the mortality rate between the treatment and control groups (OR = 0.86, 95% CI [0.68–1.10], P = 0.24). Prophylactic nebulized antibiotic therapy also did not significantly reduce the length of ICU stay (MD = 0.2 days; 95% CI [−0.81 to 1.20], P = 0.70) or the number of mechanical ventilation days (MD = 0.43 days; 95% CI [−0.47 to 1.33], P = 0.35). Additionally, there was no evidence that prophylactic nebulized antibiotic therapy contributed to the development of multiple drug-resistant (MDR) bacterial pneumonia or increased the incidence of associated side effects, such as airway spasms. Conclusions This meta-analysis suggests that ICU-acquired pneumonia ca…
format: application/pdf
format: text/html
creator: Ming Gao
creator: Xiaoxu Yu
creator: Xiaoxuan Liu
creator: Yuan Xu
creator: Hua Zhou
creator: Yan Zhu
subject: Emergency and Critical Care
subject: Evidence Based Medicine
subject: Infectious Diseases
subject: Respiratory Medicine
description: doi:10.7717/peerj.18686
publisher: PeerJ Inc.
rights: © 2024 Gao et al.
abstract: Objective To evaluate the efficacy and safety of prophylactic nebulized antibiotics in preventing intensive care unit (ICU)-acquired pneumonia through a meta-analysis. Methods Randomized controlled trials (RCTs) investigating the potential reduction in the incidence of ICU-acquired pneumonia through prophylactic nebulized antibiotics were collected by searching the PubMed, Embase, and Cochrane Library databases from their inception to January 23, 2024. The primary endpoint was the incidence of ICU-acquired pneumonia, while the secondary endpoints included mortality, length of ICU stay, mechanical ventilation days, and nebulization-related side effects. Statistical analyses were performed using RevMan 5.3 and STATA 14.0 software. Results A total of six RCTs were included in the analysis, involving 1,287 patients (636 patients in the study group received prophylactic antibiotic therapy, including Polymyxin B, Tobramycin, Ceftazidime, Colistimethate sodium, and amikacin; 651 patients in the control group primarily received saline). The results indicated that prophylactic nebulized antibiotic therapy significantly reduced the incidence of ICU-acquired pneumonia compared to that in the control group (odds ratio (OR) = 0.57, 95% confidence interval (CI) [0.43–0.74], P < 0.0001). No significant difference was observed in the mortality rate between the treatment and control groups (OR = 0.86, 95% CI [0.68–1.10], P = 0.24). Prophylactic nebulized antibiotic therapy also did not significantly reduce the length of ICU stay (MD = 0.2 days; 95% CI [−0.81 to 1.20], P = 0.70) or the number of mechanical ventilation days (MD = 0.43 days; 95% CI [−0.47 to 1.33], P = 0.35). Additionally, there was no evidence that prophylactic nebulized antibiotic therapy contributed to the development of multiple drug-resistant (MDR) bacterial pneumonia or increased the incidence of associated side effects, such as airway spasms. Conclusions This meta-analysis suggests that ICU-acquired pneumonia ca…
bibliographic citation: Gao et al. (2024) Effects of prophylactic nebulized antibiotics on the prevention of ICU-acquired pneumonia: a systematic review and meta-analysis. PeerJ 12:e18686 https://doi.org/10.7717/peerj.18686
date submitted: 2024-04-29
date accepted: 2024-11-20
issued: 2024-12-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Ming
author list: Agent
  family name: Yu
  given name: Xiaoxu
author list: Agent
  family name: Liu
  given name: Xiaoxuan
author list: Agent
  family name: Xu
  given name: Yuan
author list: Agent
  family name: Zhou
  given name: Hua
author list: Agent
  family name: Zhu
  given name: Yan
doi: 10.7717/peerj.18686
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-13
copyright: © 2024 Gao et al.
attribution name: Gao et al.

Identification of immunogenic cell death gene-related subtypes and risk model predicts prognosis and response to immunotherapy in ovarian cancer
type: item
type: AcademicArticle
description: Background Immunogenic cell death (ICD) has been associated with enhanced anti-tumor immunotherapy by stimulating adaptive immune responses and remodeling the immune microenvironment in tumors. Nevertheless, the role of ICD-related genes in ovarian cancer (OC) and tumor microenvironment remains unexplored. Methods In this study, high-throughput transcriptomic data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases as training and validation sets separately were obtained and proceeded to explore ICD-related clusters, and an ICD-related risk signature was conducted based on the least absolute shrinkage and selection operator (LASSO) Cox regression model by iteration. Multiple tools including CIBERSORT, ESTIMATE, GSEA, TIDE, and immunohistochemistry were further applied to illustrate the biological roles of ICD-related genes as well as the prognostic capacity of ICD risk signature in OC. Results Two ICD-related subtypes were identified, with the ICD-high subtype showing more intense immune cell infiltration and higher activities of immune response signaling, along with a favorable prognosis. Additionally, four candidate ICD genes (IFNG, NLRP3, FOXP3, and IL1B) were determined to potentially impact OC prognosis, with an upregulated expression of NLRP3 in OC and metastatic omental tissues. A prognostic model based on these genes was established, which could predict overall survival (OS) and response to immunotherapy for OC patients, with lower-risk patients benefiting more from immunotherapy. Conclusion Our research conducted a prognostic and prediction of immunotherapy response model based on ICD genes, which could be instrumental in assessing prognosis and assigning immunotherapeutic strategies for OC patients. NLRP3 is a promising target for prognosis in OC.
format: application/pdf
format: text/html
creator: Wenjing Pan
creator: Zhaoyang Jia
creator: Xibo Zhao
creator: Kexin Chang
creator: Wei Liu
creator: Wenhua Tan
subject: Bioinformatics
subject: Molecular Biology
subject: Gynecology and Obstetrics
subject: Oncology
subject: Histology
description: doi:10.7717/peerj.18690
publisher: PeerJ Inc.
rights: © 2024 Pan et al.
abstract: Background Immunogenic cell death (ICD) has been associated with enhanced anti-tumor immunotherapy by stimulating adaptive immune responses and remodeling the immune microenvironment in tumors. Nevertheless, the role of ICD-related genes in ovarian cancer (OC) and tumor microenvironment remains unexplored. Methods In this study, high-throughput transcriptomic data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases as training and validation sets separately were obtained and proceeded to explore ICD-related clusters, and an ICD-related risk signature was conducted based on the least absolute shrinkage and selection operator (LASSO) Cox regression model by iteration. Multiple tools including CIBERSORT, ESTIMATE, GSEA, TIDE, and immunohistochemistry were further applied to illustrate the biological roles of ICD-related genes as well as the prognostic capacity of ICD risk signature in OC. Results Two ICD-related subtypes were identified, with the ICD-high subtype showing more intense immune cell infiltration and higher activities of immune response signaling, along with a favorable prognosis. Additionally, four candidate ICD genes (IFNG, NLRP3, FOXP3, and IL1B) were determined to potentially impact OC prognosis, with an upregulated expression of NLRP3 in OC and metastatic omental tissues. A prognostic model based on these genes was established, which could predict overall survival (OS) and response to immunotherapy for OC patients, with lower-risk patients benefiting more from immunotherapy. Conclusion Our research conducted a prognostic and prediction of immunotherapy response model based on ICD genes, which could be instrumental in assessing prognosis and assigning immunotherapeutic strategies for OC patients. NLRP3 is a promising target for prognosis in OC.
bibliographic citation: Pan et al. (2024) Identification of immunogenic cell death gene-related subtypes and risk model predicts prognosis and response to immunotherapy in ovarian cancer. PeerJ 12:e18690 https://doi.org/10.7717/peerj.18690
date submitted: 2024-08-09
date accepted: 2024-11-20
issued: 2024-12-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Wenjing
author list: Agent
  family name: Jia
  given name: Zhaoyang
author list: Agent
  family name: Zhao
  given name: Xibo
author list: Agent
  family name: Chang
  given name: Kexin
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Tan
  given name: Wenhua
doi: 10.7717/peerj.18690
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-13
copyright: © 2024 Pan et al.
attribution name: Pan et al.

Efficacy of different dietary therapy strategies in active pediatric Crohn’s disease: a systematic review and network meta-analysis
type: item
type: AcademicArticle
description: Background Dietary therapy strategies play an important role in the treatment of pediatric patients with Crohn’s disease (CD), but the relative efficacy of different dietary therapy strategies for Crohn’s remission is unknown. This study aims to compare the effectiveness and tolerance of these dietary therapy strategies for active pediatric CD. Methods We searched the medical literature up to August 30, 2024 to identify randomized controlled trials (RCTs) of dietary therapy strategies for pediatric CD. The primary outcomes were clinical remission rate and tolerance, secondary outcomes included differences between pre- and post-treatment levels of albumin, C-reactive protein (CRP), and fecal calprotectin levels. A network meta-analysis (NMA) was performed by using the frequentist model. For binary outcome variables and continuous outcome variables, odds ratios (OR) and mean differences (MD) with corresponding 95% confidence intervals (CI) were utilized, respectively. The ranking of dietary therapy strategies was determined based on the surface under the cumulative ranking area (SUCRA) for each comparison analyzed. Results Overall, 14 studies involving 564 participants were included. In terms of clinical remission rate, the partial enteral nutrition (PEN) plus Crohn’s disease exclusion diet (PEN+CDED) (OR = 7.86, 95% CI [1.85–33.40]) and exclusive enteral nutrition (EEN) (OR = 3.74, 95% CI [1.30–10.76]) exhibited significant superiority over PEN alone. The tolerance of PEN+CDED was significantly higher than that of EEN (OR = 0.07, 95% CI [0.01–0.61]). According to the surface under the cumulative ranking area (SUCRA) values, the PEN+CDED intervention (90.5%) achieved the highest ranking in clinical remission rate. In terms of tolerance, PEN+CDED ranked first (88.0%), while EEN ranked last (16.3%). Conclusions In conclusion, PEN+CDED was associated with the highest clinical remission rate and tolerance among the various dietary therapy strategies evaluated. Despite lim…
format: application/pdf
format: text/html
creator: Jiaze Ma
creator: Jinchen Chong
creator: Zhengxi Qiu
creator: Yuji Wang
creator: Tuo Chen
creator: Yugen Chen
subject: Gastroenterology and Hepatology
subject: Pediatrics
description: doi:10.7717/peerj.18692
publisher: PeerJ Inc.
rights: © 2024 Ma et al.
abstract: Background Dietary therapy strategies play an important role in the treatment of pediatric patients with Crohn’s disease (CD), but the relative efficacy of different dietary therapy strategies for Crohn’s remission is unknown. This study aims to compare the effectiveness and tolerance of these dietary therapy strategies for active pediatric CD. Methods We searched the medical literature up to August 30, 2024 to identify randomized controlled trials (RCTs) of dietary therapy strategies for pediatric CD. The primary outcomes were clinical remission rate and tolerance, secondary outcomes included differences between pre- and post-treatment levels of albumin, C-reactive protein (CRP), and fecal calprotectin levels. A network meta-analysis (NMA) was performed by using the frequentist model. For binary outcome variables and continuous outcome variables, odds ratios (OR) and mean differences (MD) with corresponding 95% confidence intervals (CI) were utilized, respectively. The ranking of dietary therapy strategies was determined based on the surface under the cumulative ranking area (SUCRA) for each comparison analyzed. Results Overall, 14 studies involving 564 participants were included. In terms of clinical remission rate, the partial enteral nutrition (PEN) plus Crohn’s disease exclusion diet (PEN+CDED) (OR = 7.86, 95% CI [1.85–33.40]) and exclusive enteral nutrition (EEN) (OR = 3.74, 95% CI [1.30–10.76]) exhibited significant superiority over PEN alone. The tolerance of PEN+CDED was significantly higher than that of EEN (OR = 0.07, 95% CI [0.01–0.61]). According to the surface under the cumulative ranking area (SUCRA) values, the PEN+CDED intervention (90.5%) achieved the highest ranking in clinical remission rate. In terms of tolerance, PEN+CDED ranked first (88.0%), while EEN ranked last (16.3%). Conclusions In conclusion, PEN+CDED was associated with the highest clinical remission rate and tolerance among the various dietary therapy strategies evaluated. Despite lim…
bibliographic citation: Ma et al. (2024) Efficacy of different dietary therapy strategies in active pediatric Crohn’s disease: a systematic review and network meta-analysis. PeerJ 12:e18692 https://doi.org/10.7717/peerj.18692
date submitted: 2024-10-25
date accepted: 2024-11-20
issued: 2024-12-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Jiaze
author list: Agent
  family name: Chong
  given name: Jinchen
author list: Agent
  family name: Qiu
  given name: Zhengxi
author list: Agent
  family name: Wang
  given name: Yuji
author list: Agent
  family name: Chen
  given name: Tuo
author list: Agent
  family name: Chen
  given name: Yugen
doi: 10.7717/peerj.18692
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-13
copyright: © 2024 Ma et al.
attribution name: Ma et al.

Adiposity and body fat distribution based on skinfold thicknesses and body circumferences in Czech preschool children, secular changes
type: item
type: AcademicArticle
description: Background The long-standing widespread prevalence of obesity includes issues of its evaluation. Nutritional status may be assessed using various tools and methods; among others simple anthropometric measurements are well established. Widely used body mass index (BMI), presents an obstacle of needing to calculate a standard deviation score (SD) for correct use in the child population. As BMI overlooks body composition, it is necessary to evaluate fat and muscle mass with different methods. Established skinfolds and circumferences are used in many variations and equations to accomplish that goal; however, the parameters used in these methods also undergo secular changes. Furthermore, secular changes have been documented in fat mass distribution. The aim of the study is to assess secular changes of skinfolds thickness and body circumferences and evaluate their validity for use in clinical practice and population research. Methods and sample Our database consisted of a recent (2016–2022) sample with 594 participants (298 males) and a reference sample (from 1990) with 2,910 participants (1,207 males). Both cohorts comprised Czech preschool children, aged 4.00 to 6.99 years. With standard methodology, anthropometric parameters were obtained for 13 skinfolds and eight circumferences, by trained staff. The equations of Slaughter, Durnin and Deurenberg were correspondingly calculated. Statistical evaluation was conducted in the R programming language, using Welch’s test, Cohen’s d and the Bland–Altman method. Results Our study found significant increases in skinfold thickness on the abdomen, chest I. and forearm, with high clinical relevance (p ≥ 0.01; d = range from 0.20 to 0.70). Contrastingly, apart from the abdominal area, a decrease of circumferences was observed. The body fat percentage estimation equations were tested for bias in the recent sample in the context of bioimpedance analysis with the Bland–Altman method. All equations are suitable for application in clini…
format: application/pdf
format: text/html
creator: Anna Vážná
creator: Jan M. Novák
creator: Robert Daniš
creator: Petr Sedlak
subject: Anthropology
subject: Nutrition
subject: Pediatrics
subject: Public Health
subject: Obesity
description: doi:10.7717/peerj.18695
publisher: PeerJ Inc.
rights: © 2024 Vážná et al.
abstract: Background The long-standing widespread prevalence of obesity includes issues of its evaluation. Nutritional status may be assessed using various tools and methods; among others simple anthropometric measurements are well established. Widely used body mass index (BMI), presents an obstacle of needing to calculate a standard deviation score (SD) for correct use in the child population. As BMI overlooks body composition, it is necessary to evaluate fat and muscle mass with different methods. Established skinfolds and circumferences are used in many variations and equations to accomplish that goal; however, the parameters used in these methods also undergo secular changes. Furthermore, secular changes have been documented in fat mass distribution. The aim of the study is to assess secular changes of skinfolds thickness and body circumferences and evaluate their validity for use in clinical practice and population research. Methods and sample Our database consisted of a recent (2016–2022) sample with 594 participants (298 males) and a reference sample (from 1990) with 2,910 participants (1,207 males). Both cohorts comprised Czech preschool children, aged 4.00 to 6.99 years. With standard methodology, anthropometric parameters were obtained for 13 skinfolds and eight circumferences, by trained staff. The equations of Slaughter, Durnin and Deurenberg were correspondingly calculated. Statistical evaluation was conducted in the R programming language, using Welch’s test, Cohen’s d and the Bland–Altman method. Results Our study found significant increases in skinfold thickness on the abdomen, chest I. and forearm, with high clinical relevance (p ≥ 0.01; d = range from 0.20 to 0.70). Contrastingly, apart from the abdominal area, a decrease of circumferences was observed. The body fat percentage estimation equations were tested for bias in the recent sample in the context of bioimpedance analysis with the Bland–Altman method. All equations are suitable for application in clini…
bibliographic citation: Vážná et al. (2024) Adiposity and body fat distribution based on skinfold thicknesses and body circumferences in Czech preschool children, secular changes. PeerJ 12:e18695 https://doi.org/10.7717/peerj.18695
date submitted: 2024-09-17
date accepted: 2024-11-21
issued: 2024-12-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vážná
  given name: Anna
author list: Agent
  family name: Novák
  given name: Jan M.
author list: Agent
  family name: Daniš
  given name: Robert
author list: Agent
  family name: Sedlak
  given name: Petr
doi: 10.7717/peerj.18695
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-13
copyright: © 2024 Vážná et al.
attribution name: Vážná et al.

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