PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Evaluation of the diagnostic and prognostic values of serum HSP90α in sepsis patients: a retrospective study
items: Effect of magnification factor by Galilean loupes on working posture of dental students in simulated clinical procedures: associations between direct and observational measurements
items: Functional analysis of ARF1 from Cymbidium goeringii in IAA response during leaf development
items: Effect of precipitation change on the photosynthetic performance of Phragmites australis under elevated temperature conditions
items: Feature screening for survival trait with application to TCGA high-dimensional genomic data
items: The association between non-suicidal self-injury and negative life events in children and adolescents in underdeveloped regions of south-western China
items: Three new species of Microlaimus (Nematoda: Microlaimidae) from the South Atlantic
items: Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii
items: Analysis of the role and mechanism of EGCG in septic cardiomyopathy based on network pharmacology
items: Optimizing seawater temperature conditions to increase the productivity of ex situ coral nurseries

Evaluation of the diagnostic and prognostic values of serum HSP90α in sepsis patients: a retrospective study
type: item
type: AcademicArticle
description: Background Sepsis is a serious syndrome that is caused by immune responses dysfunction and leads to high mortality. The abilities of heat shock protein 90α (HSP90α) in assessing the diagnosis and prognosis in patients with sepsis remain ill-defined to date. We conducted a study to reveal the possible clinical applications of HSP90α as biomarker for the diagnosis and prognosis in patients with sepsis. Methods In total, 150 patients of sepsis, 110 patients without sepsis admitted to ICU and 110 healthy subjects were involved in this study. The serum HSP90α contents, sequential organ failure assessment (SOFA) scores, procalcitonin (PCT), and short-term survival status of the participants were measured and compared. Logistic and linear regression models adjusting for potential confounders were used to examine the association of HSP90α with sepsis survival. Moreover, serum IL-1β, IL-18, MIP-3α, and ENA-78 were also determined. Finally, Spearman correlation analysis was employed to reveal a possible mechanism that HSP90α contributed to the short-term deaths. Results Serum HSP90α levels in sepsis patients were higher than those in ICU controls and healthy controls (P < 0.001), and even increased in patients who died within 28 days (P < 0.001). Logistic and linear regression models identified HSP90α was an independent risk factors for sepsis mortality. Receiver operating characteristic (ROC) analysis displayed that HSP90α had a considerable predictive performance for sepsis outcome, with an area under curve (AUC) value up to 0.79. Survival analysis demonstrated that the mortality of sepsis individuals at 28 days was positively associated with HSP90α levels, especially the levels of HSP90α were greater than 120 ng/mL (P < 0.001). Moreover, among sepsis patients, those who died had notably elevated cytokines, IL-1β, IL-18, and chemokines, MIP-3α, ENA-78, relative to survivors. Further correlation analysis demonstrated that there was a nominally positive correlation between HS…
format: application/pdf
format: text/html
creator: Fuxing Li
creator: Yulin Zhang
creator: Bocheng Yu
creator: Zihua Zhang
creator: Yujuan Fan
creator: Li Wang
creator: Mingjing Cheng
creator: Ping Yan
creator: Weidong Zhao
subject: Emergency and Critical Care
subject: Hematology
subject: Infectious Diseases
subject: Translational Medicine
description: doi:10.7717/peerj.12997
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background Sepsis is a serious syndrome that is caused by immune responses dysfunction and leads to high mortality. The abilities of heat shock protein 90α (HSP90α) in assessing the diagnosis and prognosis in patients with sepsis remain ill-defined to date. We conducted a study to reveal the possible clinical applications of HSP90α as biomarker for the diagnosis and prognosis in patients with sepsis. Methods In total, 150 patients of sepsis, 110 patients without sepsis admitted to ICU and 110 healthy subjects were involved in this study. The serum HSP90α contents, sequential organ failure assessment (SOFA) scores, procalcitonin (PCT), and short-term survival status of the participants were measured and compared. Logistic and linear regression models adjusting for potential confounders were used to examine the association of HSP90α with sepsis survival. Moreover, serum IL-1β, IL-18, MIP-3α, and ENA-78 were also determined. Finally, Spearman correlation analysis was employed to reveal a possible mechanism that HSP90α contributed to the short-term deaths. Results Serum HSP90α levels in sepsis patients were higher than those in ICU controls and healthy controls (P < 0.001), and even increased in patients who died within 28 days (P < 0.001). Logistic and linear regression models identified HSP90α was an independent risk factors for sepsis mortality. Receiver operating characteristic (ROC) analysis displayed that HSP90α had a considerable predictive performance for sepsis outcome, with an area under curve (AUC) value up to 0.79. Survival analysis demonstrated that the mortality of sepsis individuals at 28 days was positively associated with HSP90α levels, especially the levels of HSP90α were greater than 120 ng/mL (P < 0.001). Moreover, among sepsis patients, those who died had notably elevated cytokines, IL-1β, IL-18, and chemokines, MIP-3α, ENA-78, relative to survivors. Further correlation analysis demonstrated that there was a nominally positive correlation between HS…
bibliographic citation: Li et al. (2022) Evaluation of the diagnostic and prognostic values of serum HSP90α in sepsis patients: a retrospective study. PeerJ 10:e12997 https://doi.org/10.7717/peerj.12997
date submitted: 2021-10-26
date accepted: 2022-02-02
issued: 2022-03-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Fuxing
author list: Agent
  family name: Zhang
  given name: Yulin
author list: Agent
  family name: Yu
  given name: Bocheng
author list: Agent
  family name: Zhang
  given name: Zihua
author list: Agent
  family name: Fan
  given name: Yujuan
author list: Agent
  family name: Wang
  given name: Li
author list: Agent
  family name: Cheng
  given name: Mingjing
author list: Agent
  family name: Yan
  given name: Ping
author list: Agent
  family name: Zhao
  given name: Weidong
doi: 10.7717/peerj.12997
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-10
copyright: © 2022 Li et al.
attribution name: Li et al.

Effect of magnification factor by Galilean loupes on working posture of dental students in simulated clinical procedures: associations between direct and observational measurements
type: item
type: AcademicArticle
description: Objectives To determine the effect of different levels of Galilean loupe magnification on working posture as measured by compliance with ergonomic posture positions, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back region during simulated clinical conditions. Methods An experimental laboratory study was performed in which the dependent variables were compliance with ergonomic posture requirements while performing simulated restorative procedures in Restorative Dentistry, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back. The independent variable was the level of Galilean loupe magnification, which was tested at four levels (naked eye, 2.5× magnification, 3.0× magnification, and 3.5× magnification). The cavity preparations and Class I composite resin restorations were performed on artificial first molars on a mannequin in a dental chair. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) was used for the postural analysis; as was an analysis of the angular deviation from the neutral position of the neck and surface electromyography. Working posture was recorded on video over the course of the procedure. Participants were filmed from three different angles. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) assessed compliance with ergonomic posture requirements. A locally produced posture assessment software analyzed angular deviation. Surface electromyography bilaterally assessed activation of the sternocleidomastoid, descending trapezius and ascending trapezius muscles. Two-factor analysis of variance (ANOVA) and either Tukey’s post-hoc test or the Games-Howell post-hoc test were performed (α = 0.05). Results During the cavity preparations and restorations, the use of Galilean loupes at all magnifications positively influenced working posture as measured by participants’ compliance with ergonomic posture po…
format: application/pdf
format: text/html
creator: Júlia Margato Pazos
creator: Simone Cecilio Hallak Regalo
creator: Paulo de Vasconcelos
creator: Juliana Alvares Duarte Bonini Campos
creator: Patricia Petromilli Nordi Sasso Garcia
subject: Dentistry
subject: Science and Medical Education
description: doi:10.7717/peerj.13021
publisher: PeerJ Inc.
rights: © 2022 Pazos et al.
abstract: Objectives To determine the effect of different levels of Galilean loupe magnification on working posture as measured by compliance with ergonomic posture positions, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back region during simulated clinical conditions. Methods An experimental laboratory study was performed in which the dependent variables were compliance with ergonomic posture requirements while performing simulated restorative procedures in Restorative Dentistry, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back. The independent variable was the level of Galilean loupe magnification, which was tested at four levels (naked eye, 2.5× magnification, 3.0× magnification, and 3.5× magnification). The cavity preparations and Class I composite resin restorations were performed on artificial first molars on a mannequin in a dental chair. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) was used for the postural analysis; as was an analysis of the angular deviation from the neutral position of the neck and surface electromyography. Working posture was recorded on video over the course of the procedure. Participants were filmed from three different angles. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) assessed compliance with ergonomic posture requirements. A locally produced posture assessment software analyzed angular deviation. Surface electromyography bilaterally assessed activation of the sternocleidomastoid, descending trapezius and ascending trapezius muscles. Two-factor analysis of variance (ANOVA) and either Tukey’s post-hoc test or the Games-Howell post-hoc test were performed (α = 0.05). Results During the cavity preparations and restorations, the use of Galilean loupes at all magnifications positively influenced working posture as measured by participants’ compliance with ergonomic posture po…
bibliographic citation: Pazos et al. (2022) Effect of magnification factor by Galilean loupes on working posture of dental students in simulated clinical procedures: associations between direct and observational measurements. PeerJ 10:e13021 https://doi.org/10.7717/peerj.13021
date submitted: 2021-08-02
date accepted: 2022-02-07
issued: 2022-03-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pazos
  given name: Júlia Margato
author list: Agent
  family name: Regalo
  given name: Simone Cecilio Hallak
author list: Agent
  family name: de Vasconcelos
  given name: Paulo
author list: Agent
  family name: Campos
  given name: Juliana Alvares Duarte Bonini
author list: Agent
  family name: Garcia
  given name: Patricia Petromilli Nordi Sasso
doi: 10.7717/peerj.13021
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-10
copyright: © 2022 Pazos et al.
attribution name: Pazos et al.

Functional analysis of ARF1 from Cymbidium goeringii in IAA response during leaf development
type: item
type: AcademicArticle
description: Background Cymbidium is an economically important genus of flowering orchids cultivated in China because of showing graceful leaf shapes and elegant flower coloration. However, the deterioration of the ecological environment and the difficulty of conservation management have become increasing challenges for maintaining its germplasm resources. ARFs are critical transcription factors in the auxin signaling pathway and have been found to play pivotal roles in leaf growth and development in previous studies. However, their functions and mechanisms in Cymbidium goeringii remain to be clarified. Methods The sequence of the CgARF1 gene was analyzed by bioinformatics. The expression of this gene in different tissues and under IAA treatment was detected by quantitative real-time PCR analysis. The CgARF1 gene was overexpressed in wild-type Arabidopsis and Nicotiana benthamiana via the Agrobacterium infection method. Acetone-ethanol solvent extraction was applied for the determination of chlorophyll contents, and the contents of endogenous hormones were determined using the enzyme-linked immunosorbent assay technique. Results CgARF1 cloned from C. goeringii ‘Songmei’ was 2,049 bp in length and encoded 682 amino acids containing three typical domains: a B3 DNA binding domain, an Aux_resp domain and an AUX/IXX family domain. The expression pattern of CgARF1 in different tissues of C. goeringii showed that its expression was highest in the leaves and changed greatly under IAA treatment. Subcellular localization studies showed that the protein was mainly localized in the cell nucleus. CgARF1-overexpressing lines exhibited leaf senescence and a decreased chlorophyll content. Under IAA treatment, CgARF1 regulates the rooting length, rooting number and rooting rate from detached leaves. The levels of endogenous hormones in transgenic leaves were also significantly changed. Conclusion These results indicated that CgARF1 overexpression is responsive to IAA treatment during leaf develo…
format: application/pdf
format: text/html
creator: Zihan Xu
creator: Fangle Li
creator: Meng Li
creator: Yuanhao He
creator: Yue Chen
creator: Fengrong Hu
subject: Developmental Biology
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13077
publisher: PeerJ Inc.
rights: © 2022 Xu et al.
abstract: Background Cymbidium is an economically important genus of flowering orchids cultivated in China because of showing graceful leaf shapes and elegant flower coloration. However, the deterioration of the ecological environment and the difficulty of conservation management have become increasing challenges for maintaining its germplasm resources. ARFs are critical transcription factors in the auxin signaling pathway and have been found to play pivotal roles in leaf growth and development in previous studies. However, their functions and mechanisms in Cymbidium goeringii remain to be clarified. Methods The sequence of the CgARF1 gene was analyzed by bioinformatics. The expression of this gene in different tissues and under IAA treatment was detected by quantitative real-time PCR analysis. The CgARF1 gene was overexpressed in wild-type Arabidopsis and Nicotiana benthamiana via the Agrobacterium infection method. Acetone-ethanol solvent extraction was applied for the determination of chlorophyll contents, and the contents of endogenous hormones were determined using the enzyme-linked immunosorbent assay technique. Results CgARF1 cloned from C. goeringii ‘Songmei’ was 2,049 bp in length and encoded 682 amino acids containing three typical domains: a B3 DNA binding domain, an Aux_resp domain and an AUX/IXX family domain. The expression pattern of CgARF1 in different tissues of C. goeringii showed that its expression was highest in the leaves and changed greatly under IAA treatment. Subcellular localization studies showed that the protein was mainly localized in the cell nucleus. CgARF1-overexpressing lines exhibited leaf senescence and a decreased chlorophyll content. Under IAA treatment, CgARF1 regulates the rooting length, rooting number and rooting rate from detached leaves. The levels of endogenous hormones in transgenic leaves were also significantly changed. Conclusion These results indicated that CgARF1 overexpression is responsive to IAA treatment during leaf develo…
bibliographic citation: Xu et al. (2022) Functional analysis of ARF1 from Cymbidium goeringii in IAA response during leaf development. PeerJ 10:e13077 https://doi.org/10.7717/peerj.13077
date submitted: 2021-11-18
date accepted: 2022-02-16
issued: 2022-03-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Zihan
author list: Agent
  family name: Li
  given name: Fangle
author list: Agent
  family name: Li
  given name: Meng
author list: Agent
  family name: He
  given name: Yuanhao
author list: Agent
  family name: Chen
  given name: Yue
author list: Agent
  family name: Hu
  given name: Fengrong
doi: 10.7717/peerj.13077
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-10
copyright: © 2022 Xu et al.
attribution name: Xu et al.

Effect of precipitation change on the photosynthetic performance of Phragmites australis under elevated temperature conditions
type: item
type: AcademicArticle
description: Background As a fundamental metabolism, leaf photosynthesis not only provides necessary energy for plant survival and growth but also plays an important role in global carbon fixation. However, photosynthesis is highly susceptible to environmental stresses and can be significantly influenced by future climate change. Methods In this study, we examined the photosynthetic responses of Phragmites australis (P. australis) to three precipitation treatments (control, decreased 30%, and increased 30%) under two thermal regimes (ambient temperature and +4 °C) in environment-controlled chambers. Results Our results showed that the net CO2 assimilation rate (Pn), maximal rate of Rubisco (Vcmax), maximal rate of ribulose-bisphosphate (RuBP) regeneration (Jmax) and chlorophyll (Chl) content were enhanced under increased precipitation condition, but were declined drastically under the condition of water deficit. The increased precipitation had no significant effect on malondialdehyde (MDA) content (p > 0.05), but water deficit drastically enhanced the MDA content by 10.1%. Meanwhile, a high temperature inhibited the positive effects of increased precipitation, aggravated the adverse effects of drought. The combination of high temperature and water deficit had more detrimental effect on P. australis than a single factor. Moreover, non-stomatal limitation caused by precipitation change played a major role in determining carbon assimilation rate. Under ambient temperature, Chl content had close relationship with Pn (R2 = 0.86, p < 0.01). Under high temperature, Pn was ralated to MDA content (R2 = 0.81, p < 0.01). High temperature disrupted the balance between Vcmax and Jmax (the ratio of Jmax to Vcmax decreased from 1.88 to 1.12) which resulted in a negative effect on the photosynthesis of P. australis. Furthermore, by the analysis of Chl fluorescence, we found that the xanthophyll cycle-mediated thermal dissipation played a major role in PSII photoprotection, resulting in no signi…
format: application/pdf
format: text/html
creator: Linhong Teng
creator: Hanyu Liu
creator: Xiaonan Chu
creator: Xiliang Song
creator: Lianhui Shi
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.13087
publisher: PeerJ Inc.
rights: © 2022 Teng et al.
abstract: Background As a fundamental metabolism, leaf photosynthesis not only provides necessary energy for plant survival and growth but also plays an important role in global carbon fixation. However, photosynthesis is highly susceptible to environmental stresses and can be significantly influenced by future climate change. Methods In this study, we examined the photosynthetic responses of Phragmites australis (P. australis) to three precipitation treatments (control, decreased 30%, and increased 30%) under two thermal regimes (ambient temperature and +4 °C) in environment-controlled chambers. Results Our results showed that the net CO2 assimilation rate (Pn), maximal rate of Rubisco (Vcmax), maximal rate of ribulose-bisphosphate (RuBP) regeneration (Jmax) and chlorophyll (Chl) content were enhanced under increased precipitation condition, but were declined drastically under the condition of water deficit. The increased precipitation had no significant effect on malondialdehyde (MDA) content (p > 0.05), but water deficit drastically enhanced the MDA content by 10.1%. Meanwhile, a high temperature inhibited the positive effects of increased precipitation, aggravated the adverse effects of drought. The combination of high temperature and water deficit had more detrimental effect on P. australis than a single factor. Moreover, non-stomatal limitation caused by precipitation change played a major role in determining carbon assimilation rate. Under ambient temperature, Chl content had close relationship with Pn (R2 = 0.86, p < 0.01). Under high temperature, Pn was ralated to MDA content (R2 = 0.81, p < 0.01). High temperature disrupted the balance between Vcmax and Jmax (the ratio of Jmax to Vcmax decreased from 1.88 to 1.12) which resulted in a negative effect on the photosynthesis of P. australis. Furthermore, by the analysis of Chl fluorescence, we found that the xanthophyll cycle-mediated thermal dissipation played a major role in PSII photoprotection, resulting in no signi…
bibliographic citation: Teng et al. (2022) Effect of precipitation change on the photosynthetic performance of Phragmites australis under elevated temperature conditions. PeerJ 10:e13087 https://doi.org/10.7717/peerj.13087
date submitted: 2021-10-26
date accepted: 2022-02-17
issued: 2022-03-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Teng
  given name: Linhong
author list: Agent
  family name: Liu
  given name: Hanyu
author list: Agent
  family name: Chu
  given name: Xiaonan
author list: Agent
  family name: Song
  given name: Xiliang
author list: Agent
  family name: Shi
  given name: Lianhui
doi: 10.7717/peerj.13087
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-10
copyright: © 2022 Teng et al.
attribution name: Teng et al.

Feature screening for survival trait with application to TCGA high-dimensional genomic data
type: item
type: AcademicArticle
description: Background In high-dimensional survival genomic data, identifying cancer-related genes is a challenging and important subject in the field of bioinformatics. In recent years, many feature screening approaches for survival outcomes with high-dimensional survival genomic data have been developed; however, few studies have systematically compared these methods. The primary purpose of this article is to conduct a series of simulation studies for systematic comparison; the second purpose of this article is to use these feature screening methods to further establish a more accurate prediction model for patient survival based on the survival genomic datasets of The Cancer Genome Atlas (TCGA). Results Simulation studies prove that network-adjusted feature screening measurement performs well and outperforms existing popular univariate independent feature screening methods. In the application of real data, we show that the proposed network-adjusted feature screening approach leads to more accurate survival prediction than alternative methods that do not account for gene-gene dependency information. We also use TCGA clinical survival genetic data to identify biomarkers associated with clinical survival outcomes in patients with various cancers including esophageal, pancreatic, head and neck squamous cell, lung, and breast invasive carcinomas. Conclusions These applications reveal advantages of the new proposed network-adjusted feature selection method over alternative methods that do not consider gene-gene dependency information. We also identify cancer-related genes that are almost detected in the literature. As a result, the network-based screening method is reliable and credible.
format: application/pdf
format: text/html
creator: Jie-Huei Wang
creator: Cai-Rong Li
creator: Po-Lin Hou
subject: Bioinformatics
subject: Statistics
description: doi:10.7717/peerj.13098
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background In high-dimensional survival genomic data, identifying cancer-related genes is a challenging and important subject in the field of bioinformatics. In recent years, many feature screening approaches for survival outcomes with high-dimensional survival genomic data have been developed; however, few studies have systematically compared these methods. The primary purpose of this article is to conduct a series of simulation studies for systematic comparison; the second purpose of this article is to use these feature screening methods to further establish a more accurate prediction model for patient survival based on the survival genomic datasets of The Cancer Genome Atlas (TCGA). Results Simulation studies prove that network-adjusted feature screening measurement performs well and outperforms existing popular univariate independent feature screening methods. In the application of real data, we show that the proposed network-adjusted feature screening approach leads to more accurate survival prediction than alternative methods that do not account for gene-gene dependency information. We also use TCGA clinical survival genetic data to identify biomarkers associated with clinical survival outcomes in patients with various cancers including esophageal, pancreatic, head and neck squamous cell, lung, and breast invasive carcinomas. Conclusions These applications reveal advantages of the new proposed network-adjusted feature selection method over alternative methods that do not consider gene-gene dependency information. We also identify cancer-related genes that are almost detected in the literature. As a result, the network-based screening method is reliable and credible.
bibliographic citation: Wang et al. (2022) Feature screening for survival trait with application to TCGA high-dimensional genomic data. PeerJ 10:e13098 https://doi.org/10.7717/peerj.13098
date submitted: 2021-09-29
date accepted: 2022-02-21
issued: 2022-03-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jie-Huei
author list: Agent
  family name: Li
  given name: Cai-Rong
author list: Agent
  family name: Hou
  given name: Po-Lin
doi: 10.7717/peerj.13098
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-10
copyright: © 2022 Wang et al.
attribution name: Wang et al.

The association between non-suicidal self-injury and negative life events in children and adolescents in underdeveloped regions of south-western China
type: item
type: AcademicArticle
description: Background The association between negative life events and Non-suicidal self-injury (NSSI) in children and adolescents has been extensively discussed. Nevertheless, little is known about the relationship between negative life events and repetition and severity of NSSI. This survey aims to understand the association between NSSI prevalence, severity, repetition and the negative life events in children and adolescents in underdeveloped regions in south-western China. Methods In this population-based cross-sectional study, 3,146 children and adolescents were included from underdeveloped regions of south-western China, and each of them requested to complete a self-assessment questionnaire. The Modified Version of Adolescents Self-Harm Scale (MASHS) and the Adolescent Self-rating negative Life Events Check-list were used to evaluate NSSI behaviors and negative life events, respectively. The statistical implementation of this study was carried out in the R statistical software, and the logistic regression analysis method was used to analyze the relationship between negative life events and adolescents’ non-suicidal self-injury behaviors. Results The average age of all included participants was 13.31 years old. The lifetime prevalence of NSSI was 47.0% (95% CI [36.3–58.0%]). Gender, grade level and ASLEC was positively associated with NSSI. Further analysis revealed that, for all five dimensions of ASLEC, only interpersonal relationship factor (IRF) (OR 1.77 (95% CI [1.06–2.97])), health adaptation factor (HAF) (OR 2.08 (95% CI [1.31–3.31])) showed prominent association with NSSI. Multivariate Logistic regression models revealed that, repetitive NSSI (OR 4.54 (95% CI [3.66–5.63])) and NSSI severity (OR 9.01 (95% CI [6.11–13.29])) were positively associated with ASLEC. Conclusion NSSI is very common among children and adolescents in underdeveloped regions of south-western China. Negative life event are positively associated with NSSI, repeated NSSI, and severe NSSI. Negati…
format: application/pdf
format: text/html
creator: Fan Yang
creator: Linling Jiang
creator: Jing Miao
creator: Xiufeng Xu
creator: Hailiang Ran
creator: Yusan Che
creator: Die Fang
creator: TianLan Wang
creator: Yuanyuan Xiao
creator: Jin Lu
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.12665
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Background The association between negative life events and Non-suicidal self-injury (NSSI) in children and adolescents has been extensively discussed. Nevertheless, little is known about the relationship between negative life events and repetition and severity of NSSI. This survey aims to understand the association between NSSI prevalence, severity, repetition and the negative life events in children and adolescents in underdeveloped regions in south-western China. Methods In this population-based cross-sectional study, 3,146 children and adolescents were included from underdeveloped regions of south-western China, and each of them requested to complete a self-assessment questionnaire. The Modified Version of Adolescents Self-Harm Scale (MASHS) and the Adolescent Self-rating negative Life Events Check-list were used to evaluate NSSI behaviors and negative life events, respectively. The statistical implementation of this study was carried out in the R statistical software, and the logistic regression analysis method was used to analyze the relationship between negative life events and adolescents’ non-suicidal self-injury behaviors. Results The average age of all included participants was 13.31 years old. The lifetime prevalence of NSSI was 47.0% (95% CI [36.3–58.0%]). Gender, grade level and ASLEC was positively associated with NSSI. Further analysis revealed that, for all five dimensions of ASLEC, only interpersonal relationship factor (IRF) (OR 1.77 (95% CI [1.06–2.97])), health adaptation factor (HAF) (OR 2.08 (95% CI [1.31–3.31])) showed prominent association with NSSI. Multivariate Logistic regression models revealed that, repetitive NSSI (OR 4.54 (95% CI [3.66–5.63])) and NSSI severity (OR 9.01 (95% CI [6.11–13.29])) were positively associated with ASLEC. Conclusion NSSI is very common among children and adolescents in underdeveloped regions of south-western China. Negative life event are positively associated with NSSI, repeated NSSI, and severe NSSI. Negati…
bibliographic citation: Yang et al. (2022) The association between non-suicidal self-injury and negative life events in children and adolescents in underdeveloped regions of south-western China. PeerJ 10:e12665 https://doi.org/10.7717/peerj.12665
date submitted: 2021-08-02
date accepted: 2021-11-30
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Fan
author list: Agent
  family name: Jiang
  given name: Linling
author list: Agent
  family name: Miao
  given name: Jing
author list: Agent
  family name: Xu
  given name: Xiufeng
author list: Agent
  family name: Ran
  given name: Hailiang
author list: Agent
  family name: Che
  given name: Yusan
author list: Agent
  family name: Fang
  given name: Die
author list: Agent
  family name: Wang
  given name: TianLan
author list: Agent
  family name: Xiao
  given name: Yuanyuan
author list: Agent
  family name: Lu
  given name: Jin
doi: 10.7717/peerj.12665
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: © 2022 Yang et al.
attribution name: Yang et al.

Three new species of Microlaimus (Nematoda: Microlaimidae) from the South Atlantic
type: item
type: AcademicArticle
description: Three new species of Microlaimus are described from the continental shelf of the Campos Basin, southwest Atlantic, Brazil. Microlaimus campiensis sp. n. differs from all other species in the presence of two anterior testes, slender spicules with enlarged proximal ends, 7–11 pre-cloacal papilliform supplements, and females with a pair of constriction structures, one on each branch of the ovary. Microlaimus alexandri sp. n. shows sexual dimorphism in the size of the amphidial fovea, which occupies 100% of the diameter of the corresponding area in the male; the buccal cavity provided with five teeth and a slightly cuticularized cuticular ring. Microlaimus vitorius sp. n. has four longitudinal-lateral rows of glands associated with small pores, one seta and three pores small pre-cloacal, and the gubernaculum has a triangular base. An amendment to the diagnosis of the genus is proposed, where the number of teeth was modified.
format: application/pdf
format: text/html
creator: Rita C. Lima
creator: Patrícia F. Neres
creator: André M. Esteves
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12734
publisher: PeerJ Inc.
rights: © 2022 Lima et al.
abstract: Three new species of Microlaimus are described from the continental shelf of the Campos Basin, southwest Atlantic, Brazil. Microlaimus campiensis sp. n. differs from all other species in the presence of two anterior testes, slender spicules with enlarged proximal ends, 7–11 pre-cloacal papilliform supplements, and females with a pair of constriction structures, one on each branch of the ovary. Microlaimus alexandri sp. n. shows sexual dimorphism in the size of the amphidial fovea, which occupies 100% of the diameter of the corresponding area in the male; the buccal cavity provided with five teeth and a slightly cuticularized cuticular ring. Microlaimus vitorius sp. n. has four longitudinal-lateral rows of glands associated with small pores, one seta and three pores small pre-cloacal, and the gubernaculum has a triangular base. An amendment to the diagnosis of the genus is proposed, where the number of teeth was modified.
bibliographic citation: Lima et al. (2022) Three new species of Microlaimus (Nematoda: Microlaimidae) from the South Atlantic. PeerJ 10:e12734 https://doi.org/10.7717/peerj.12734
date submitted: 2020-10-19
date accepted: 2021-12-12
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lima
  given name: Rita C.
author list: Agent
  family name: Neres
  given name: Patrícia F.
author list: Agent
  family name: Esteves
  given name: André M.
doi: 10.7717/peerj.12734
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: © 2022 Lima et al.
attribution name: Lima et al.

Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii
type: item
type: AcademicArticle
description: Background Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology. Methods We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species. Results The protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii. The closest species with the genome assembly is Schizochytrium aggregatum. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes. Conclusion Our findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.
format: application/pdf
format: text/html
creator: Dmitrii K. Konstantinov
creator: Aleksei Menzorov
creator: Olga Krivenko
creator: Alexey V. Doroshkov
subject: Bioinformatics
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12737
publisher: PeerJ Inc.
rights: © 2022 Konstantinov et al.
abstract: Background Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology. Methods We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species. Results The protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii. The closest species with the genome assembly is Schizochytrium aggregatum. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes. Conclusion Our findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.
bibliographic citation: Konstantinov et al. (2022) Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii. PeerJ 10:e12737 https://doi.org/10.7717/peerj.12737
date submitted: 2020-12-01
date accepted: 2021-12-13
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Konstantinov
  given name: Dmitrii K.
author list: Agent
  family name: Menzorov
  given name: Aleksei
author list: Agent
  family name: Krivenko
  given name: Olga
author list: Agent
  family name: Doroshkov
  given name: Alexey V.
doi: 10.7717/peerj.12737
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Konstantinov et al.
attribution name: Konstantinov et al.

Analysis of the role and mechanism of EGCG in septic cardiomyopathy based on network pharmacology
type: item
type: AcademicArticle
description: Background Septic cardiomyopathy (SC) is a common complication of sepsis that leads to an increase in mortality. The pathogenesis of septic cardiomyopathy is unclear, and there is currently no effective treatment. EGCG (epigallocatechin gallate) is a polyphenol that has anti-inflammatory, antiapoptotic, and antioxidative stress effects. However, the role of EGCG in septic cardiomyopathy is unknown. Methods Network pharmacology was used to predict the potential targets and molecular mechanisms of EGCG in the treatment of septic cardiomyopathy, including the construction and analysis of protein-protein interaction (PPI) network, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and molecular docking. The mouse model of septic cardiomyopathy was established after intraperitoneal injection of LPS (lipopolysaccharide). The myocardial protective effect of EGCG on septic mice is observed by cardiac ultrasound and HE staining. RT-PCR is used to verify the expression level of the EGCG target in the septic cardiomyopathy mouse model. Results A total of 128 anti-SC potential targets of EGCGareselected for analysis. The GO enrichment analysis and KEGG pathway analysis results indicated that the anti-SC targets of EGCG mainly participate in inflammatory and apoptosis processes. Molecular docking results suggest that EGCG has a high affinity for the crystal structure of six targets (IL-6 (interleukin-6), TNF (tumor necrosis factor), Caspase3, MAPK3 (Mitogen-activated protein kinase 3), AKT1, and VEGFA (vascular endothelial growth factor)), and the experimental verification result showed levated expression of these 6 hub targets in the LPS group, but there is an obvious decrease in expression in the LPS + EGCG group. The functional and morphological changes found by echocardiography and HE staining show that EGCG can effectively improve the cardiac function that is reduced by LPS. Conclusion Our results reveal that EGCG may be a potentially ef…
format: application/pdf
format: text/html
creator: Ji Wu
creator: Zhenhua Wang
creator: Shanling Xu
creator: Yang Fu
creator: Yi Gao
creator: Zuxiang Wu
creator: Yun Yu
creator: Yougen Yuan
creator: Lin Zhou
creator: Ping Li
subject: Bioinformatics
subject: Molecular Biology
subject: Cardiology
subject: Radiology and Medical Imaging
subject: Histology
description: doi:10.7717/peerj.12994
publisher: PeerJ Inc.
rights: © 2022 Wu et al.
abstract: Background Septic cardiomyopathy (SC) is a common complication of sepsis that leads to an increase in mortality. The pathogenesis of septic cardiomyopathy is unclear, and there is currently no effective treatment. EGCG (epigallocatechin gallate) is a polyphenol that has anti-inflammatory, antiapoptotic, and antioxidative stress effects. However, the role of EGCG in septic cardiomyopathy is unknown. Methods Network pharmacology was used to predict the potential targets and molecular mechanisms of EGCG in the treatment of septic cardiomyopathy, including the construction and analysis of protein-protein interaction (PPI) network, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and molecular docking. The mouse model of septic cardiomyopathy was established after intraperitoneal injection of LPS (lipopolysaccharide). The myocardial protective effect of EGCG on septic mice is observed by cardiac ultrasound and HE staining. RT-PCR is used to verify the expression level of the EGCG target in the septic cardiomyopathy mouse model. Results A total of 128 anti-SC potential targets of EGCGareselected for analysis. The GO enrichment analysis and KEGG pathway analysis results indicated that the anti-SC targets of EGCG mainly participate in inflammatory and apoptosis processes. Molecular docking results suggest that EGCG has a high affinity for the crystal structure of six targets (IL-6 (interleukin-6), TNF (tumor necrosis factor), Caspase3, MAPK3 (Mitogen-activated protein kinase 3), AKT1, and VEGFA (vascular endothelial growth factor)), and the experimental verification result showed levated expression of these 6 hub targets in the LPS group, but there is an obvious decrease in expression in the LPS + EGCG group. The functional and morphological changes found by echocardiography and HE staining show that EGCG can effectively improve the cardiac function that is reduced by LPS. Conclusion Our results reveal that EGCG may be a potentially ef…
bibliographic citation: Wu et al. (2022) Analysis of the role and mechanism of EGCG in septic cardiomyopathy based on network pharmacology. PeerJ 10:e12994 https://doi.org/10.7717/peerj.12994
date submitted: 2021-08-04
date accepted: 2022-02-02
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Ji
author list: Agent
  family name: Wang
  given name: Zhenhua
author list: Agent
  family name: Xu
  given name: Shanling
author list: Agent
  family name: Fu
  given name: Yang
author list: Agent
  family name: Gao
  given name: Yi
author list: Agent
  family name: Wu
  given name: Zuxiang
author list: Agent
  family name: Yu
  given name: Yun
author list: Agent
  family name: Yuan
  given name: Yougen
author list: Agent
  family name: Zhou
  given name: Lin
author list: Agent
  family name: Li
  given name: Ping
doi: 10.7717/peerj.12994
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: ©2022 Wu et al.
attribution name: Wu et al.

Optimizing seawater temperature conditions to increase the productivity of ex situ coral nurseries
type: item
type: AcademicArticle
description: Large scale ex situ propagation of coral colonies for reef restoration is a relatively new and developing field. One of the many advantages of utilizing ex situ coral nurseries is the ability to optimize water quality conditions for coral health and survival. Slight alterations in environmental parameters (light, pH, temperature etc.) can affect the health and grow-out time of cultured coral, ultimately influencing production rates. However, corals are also subjected to pests associated with culture facilities such as ciliates, cyanobacterial blooms, and infectious diseases. Therefore, adjusting environmental parameters to optimize coral growth for a shorter ex situ residency time will lead to greater survival and faster restoration. Studies indicate that some coral species demonstrate parabolic tissue growth in response to increasing sea-surface temperatures until the maximum temperature tolerance is reached, whereafter they bleach. To maximize coral growth in Mote Marine Laboratory’s ex situ system, we tested the effect of two water temperature treatments (high temperature: 29.5 ± 0.03 °C; control: 25.2 ± 0.08 °C) on two coral species commonly used in reef restoration. To quantify this, we used four replicates of three genotypes each of Montastraea cavernosa (n = 12) and Acropora palmata (n = 12). Two-dimensional tissue area was recorded monthly using ImageJ and survival rates within each treatment were documented for 7 months. Results found that M. cavernosa had greater growth rates and equal survivorship in the high temperature treatment compared to the control treatment. A. palmata grew faster and had equal survivorship in the control treatment compared with the high temperature treatment. These results suggest that temperature preferences exist among coral species within ex situ systems and restoration practitioners should consider species-specific temperature regimes to maximize ex situ coral growth rates. This information is critical for optimizing productio…
format: application/pdf
format: text/html
creator: Dakotah E. Merck
creator: Chelsea G. Petrik
creator: Alicia A. Manfroy
creator: Erinn M. Muller
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.13017
publisher: PeerJ Inc.
rights: © 2022 Merck et al.
abstract: Large scale ex situ propagation of coral colonies for reef restoration is a relatively new and developing field. One of the many advantages of utilizing ex situ coral nurseries is the ability to optimize water quality conditions for coral health and survival. Slight alterations in environmental parameters (light, pH, temperature etc.) can affect the health and grow-out time of cultured coral, ultimately influencing production rates. However, corals are also subjected to pests associated with culture facilities such as ciliates, cyanobacterial blooms, and infectious diseases. Therefore, adjusting environmental parameters to optimize coral growth for a shorter ex situ residency time will lead to greater survival and faster restoration. Studies indicate that some coral species demonstrate parabolic tissue growth in response to increasing sea-surface temperatures until the maximum temperature tolerance is reached, whereafter they bleach. To maximize coral growth in Mote Marine Laboratory’s ex situ system, we tested the effect of two water temperature treatments (high temperature: 29.5 ± 0.03 °C; control: 25.2 ± 0.08 °C) on two coral species commonly used in reef restoration. To quantify this, we used four replicates of three genotypes each of Montastraea cavernosa (n = 12) and Acropora palmata (n = 12). Two-dimensional tissue area was recorded monthly using ImageJ and survival rates within each treatment were documented for 7 months. Results found that M. cavernosa had greater growth rates and equal survivorship in the high temperature treatment compared to the control treatment. A. palmata grew faster and had equal survivorship in the control treatment compared with the high temperature treatment. These results suggest that temperature preferences exist among coral species within ex situ systems and restoration practitioners should consider species-specific temperature regimes to maximize ex situ coral growth rates. This information is critical for optimizing productio…
bibliographic citation: Merck et al. (2022) Optimizing seawater temperature conditions to increase the productivity of ex situ coral nurseries. PeerJ 10:e13017 https://doi.org/10.7717/peerj.13017
date submitted: 2021-10-04
date accepted: 2022-02-06
issued: 2022-03-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Merck
  given name: Dakotah E.
author list: Agent
  family name: Petrik
  given name: Chelsea G.
author list: Agent
  family name: Manfroy
  given name: Alicia A.
author list: Agent
  family name: Muller
  given name: Erinn M.
doi: 10.7717/peerj.13017
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-09
copyright: © 2022 Merck et al.
attribution name: Merck et al.

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