PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Association analysis of Suboptimal health Status: a cross-sectional study in China
items: Detection and estimating the blood accumulation volume of brain hemorrhage in a human anatomical skull using a RF single coil
items: Multi-year pair-bonding in Murray cod (Maccullochella peelii)
items: Determinants of behavioural and biological risk factors for cardiovascular diseases from state level STEPS survey (2017–19) in Madhya Pradesh
items: miR-21 is upregulated, promoting fibrosis and blocking G2/M in irradiated rat cardiac fibroblasts
items: Identification of biomarkers associated with clinical severity of chronic obstructive pulmonary disease
items: Deep-sea water displacement from a turbidity current induced by the Super Typhoon Hagibis
items: Effect of dietary oil from Camelina sativa on the growth performance, fillet fatty acid profile and gut microbiome of gilthead Sea bream (Sparus aurata)
items: Measuring stress in podiatric students in Spain: psychometric validation and adaptation of the KEZKAK questionnaire
items: Experimental lung injury induces cerebral cytokine mRNA production in pigs

Association analysis of Suboptimal health Status: a cross-sectional study in China
type: item
type: AcademicArticle
description: Background Suboptimal health status (SHS) among urban residents is commonplace in China. However, factors influencing SHS have not been thoroughly explored, especially with regard to the effects of internal factors (e.g., personality and health awareness) on SHS. Methods A cross-sectional study was conducted with a nationally representative sample of 5460 Chinese urban residents..SHS was measured using the Suboptimal Health Mesurement Scale Version 1.0. Demographic information, and information pertaining to lifestyle behaviors, environmental factors, and internal factors were abtained through a questionnaire. The associations between demographic information, lifestyle behaviors, environmental factors, internal factors and SHS were assessed using logistic regression. Results Of the 5460 participants (with a mean age of 41.56 ± 16.14 years), 2640 (48.4 %) were men. Out of 36 variables, 23 were significantly associated with SHS: age (odds ratio [OR]: 1.014), an education level of high school/junior college (OR: 1.443) , marital status (OR: 1.899), area of registered permanent residence (OR: 0.767), monthly household income (p < 0.001) , exposure to second-hand smoke (p = 0.001), alcohol drinking (OR: 1.284), bad eating habits (OR: 1.717), not sleeping before 11 p.m. every day (p = 0.002), spending time online more than five hours a day (OR: 1.526), having a good relationship with parents during one’s growth period (OR: 0.602), living with good quality air (OR:0.817), living in not crowded conditions (OR:0.636), having a harmonious neighborhood (OR:0.775), having adequate fitness facilities (OR:0.783), one’s health being affected by two-child policy (OR: 1.468) and medical policies (OR: 1.265) , high adverse quotient (OR: 0.488), many (≥3 kinds) interests and hobbies (OR: 0.617), mature and steady personality traits (OR: 0.469) , a high attention to one’s health (OR: 0.833), and effective health promotion induced by leading a leisurely lifestyle (OR: 0.466) were signifi…
format: application/pdf
format: text/html
creator: Yunlian Xue
creator: Zhuomin Huang
creator: Guihao Liu
creator: Yefang Feng
creator: Mengyao Xu
creator: Lijie Jiang
creator: Jun Xu
subject: Epidemiology
subject: Health Policy
subject: Public Health
description: doi:10.7717/peerj.10508
publisher: PeerJ Inc.
rights: © 2020 Xue et al.
abstract: Background Suboptimal health status (SHS) among urban residents is commonplace in China. However, factors influencing SHS have not been thoroughly explored, especially with regard to the effects of internal factors (e.g., personality and health awareness) on SHS. Methods A cross-sectional study was conducted with a nationally representative sample of 5460 Chinese urban residents..SHS was measured using the Suboptimal Health Mesurement Scale Version 1.0. Demographic information, and information pertaining to lifestyle behaviors, environmental factors, and internal factors were abtained through a questionnaire. The associations between demographic information, lifestyle behaviors, environmental factors, internal factors and SHS were assessed using logistic regression. Results Of the 5460 participants (with a mean age of 41.56 ± 16.14 years), 2640 (48.4 %) were men. Out of 36 variables, 23 were significantly associated with SHS: age (odds ratio [OR]: 1.014), an education level of high school/junior college (OR: 1.443) , marital status (OR: 1.899), area of registered permanent residence (OR: 0.767), monthly household income (p < 0.001) , exposure to second-hand smoke (p = 0.001), alcohol drinking (OR: 1.284), bad eating habits (OR: 1.717), not sleeping before 11 p.m. every day (p = 0.002), spending time online more than five hours a day (OR: 1.526), having a good relationship with parents during one’s growth period (OR: 0.602), living with good quality air (OR:0.817), living in not crowded conditions (OR:0.636), having a harmonious neighborhood (OR:0.775), having adequate fitness facilities (OR:0.783), one’s health being affected by two-child policy (OR: 1.468) and medical policies (OR: 1.265) , high adverse quotient (OR: 0.488), many (≥3 kinds) interests and hobbies (OR: 0.617), mature and steady personality traits (OR: 0.469) , a high attention to one’s health (OR: 0.833), and effective health promotion induced by leading a leisurely lifestyle (OR: 0.466) were signifi…
bibliographic citation: Xue et al. (2020) Association analysis of Suboptimal health Status: a cross-sectional study in China. PeerJ 8:e10508 https://doi.org/10.7717/peerj.10508
date submitted: 2020-07-27
date accepted: 2020-11-16
issued: 2020-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xue
  given name: Yunlian
author list: Agent
  family name: Huang
  given name: Zhuomin
author list: Agent
  family name: Liu
  given name: Guihao
author list: Agent
  family name: Feng
  given name: Yefang
author list: Agent
  family name: Xu
  given name: Mengyao
author list: Agent
  family name: Jiang
  given name: Lijie
author list: Agent
  family name: Xu
  given name: Jun
doi: 10.7717/peerj.10508
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-11
copyright: ©2020 Xue et al.
attribution name: Xue et al.

Detection and estimating the blood accumulation volume of brain hemorrhage in a human anatomical skull using a RF single coil
type: item
type: AcademicArticle
description: Objective An experimental study for testing a simple robust algorithm on data derived from an electromagnetic radiation device that can detect small changes in the tissue/fluid ratio in a realistic head configuration. Methods Changes in the scattering parameters (S21) of an inductive coil resulting from injections of chicken blood in the 0–18 ml range into calf brain tissue in a human anatomical skull were measured over a 100–1,000 MHz frequency range. Results An algorithm that combines amplitude and phase results was found to detect changes in the tissue/fluid ratio with 90% accuracy. An algorithm that estimated the injected blood volume was found to have a 1–4 ml average error. This demonstrates the possibility of the inductive coil-based device to possess a practical ability to detect a change in the tissue/fluid ratio in the head. Significance This study is an important step towards the goal of building an inexpensive and safe device that can detect an early brain hemorrhagic stroke.
format: application/pdf
format: text/html
creator: Moshe Oziel
creator: Boris Rubinsky
creator: Rafi Korenstein
subject: Biophysics
subject: Neuroscience
subject: Drugs and Devices
subject: Neurology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.10416
publisher: PeerJ Inc.
rights: © 2020 Oziel et al.
abstract: Objective An experimental study for testing a simple robust algorithm on data derived from an electromagnetic radiation device that can detect small changes in the tissue/fluid ratio in a realistic head configuration. Methods Changes in the scattering parameters (S21) of an inductive coil resulting from injections of chicken blood in the 0–18 ml range into calf brain tissue in a human anatomical skull were measured over a 100–1,000 MHz frequency range. Results An algorithm that combines amplitude and phase results was found to detect changes in the tissue/fluid ratio with 90% accuracy. An algorithm that estimated the injected blood volume was found to have a 1–4 ml average error. This demonstrates the possibility of the inductive coil-based device to possess a practical ability to detect a change in the tissue/fluid ratio in the head. Significance This study is an important step towards the goal of building an inexpensive and safe device that can detect an early brain hemorrhagic stroke.
bibliographic citation: Oziel et al. (2020) Detection and estimating the blood accumulation volume of brain hemorrhage in a human anatomical skull using a RF single coil. PeerJ 8:e10416 https://doi.org/10.7717/peerj.10416
date submitted: 2020-07-24
date accepted: 2020-11-02
issued: 2020-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oziel
  given name: Moshe
author list: Agent
  family name: Rubinsky
  given name: Boris
author list: Agent
  family name: Korenstein
  given name: Rafi
doi: 10.7717/peerj.10416
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-10
copyright: © 2020 Oziel et al.
attribution name: Oziel et al.

Multi-year pair-bonding in Murray cod (Maccullochella peelii)
type: item
type: AcademicArticle
description: Mating strategies in fishes are known to include polygyny, polyandry and monogamy and provide valuable insights regarding powerful evolutionary forces such as sexual selection. Monogamy is a complex of mating systems that has been relatively neglected. Previous work on mating strategies in fishes has often been based on observation and focused on marine species rather than freshwater fishes. SNPs are increasingly being used as a molecular ecology tool in non-model organisms, and methods of probabilistic genetic analysis of such datasets are becoming available for use in the absence of parental genotypes. This approach can be used to infer mating strategies. The long-term pair bonding seen in mammals, reptiles and birds has not been recorded in freshwater fishes—in every other respect an extremely diverse group. This study shows that multi-year pair bonding occurs in an Australian Percichthyid fish that exhibits paternal care of eggs and larvae. Using SNPs, full sibling pairs of larvae were found over multiple years in a three-year study. Stable isotope signatures of the larvae support the genetic inference that full sibling pairs shared a common mother, the ultimate source of that isotopic signature during oogenesis. Spatial and temporal clustering also suggests that the full sibling larvae are unlikely to be false positive identifications of the probabilistic identification of siblings. For the first time, we show multi-year pair bonding in a wild freshwater fish. This will have important conservation and management implications for the species. This approach could provide insights into many behavioural, ecological and evolutionary questions, particularly if this is not a unique case. Our findings are likely to initiate interest in seeking more examples of monogamy and alternative mating strategies in freshwater fishes, particularly if others improve methods of analysis of SNP data for identification of siblings in the absence of parental genotypes.
format: application/pdf
format: text/html
creator: Alan J. Couch
creator: Fiona Dyer
creator: Mark Lintermans
subject: Animal Behavior
subject: Ecology
subject: Ecosystem Science
subject: Genomics
subject: Freshwater Biology
description: doi:10.7717/peerj.10460
publisher: PeerJ Inc.
rights: © 2020 Couch et al.
abstract: Mating strategies in fishes are known to include polygyny, polyandry and monogamy and provide valuable insights regarding powerful evolutionary forces such as sexual selection. Monogamy is a complex of mating systems that has been relatively neglected. Previous work on mating strategies in fishes has often been based on observation and focused on marine species rather than freshwater fishes. SNPs are increasingly being used as a molecular ecology tool in non-model organisms, and methods of probabilistic genetic analysis of such datasets are becoming available for use in the absence of parental genotypes. This approach can be used to infer mating strategies. The long-term pair bonding seen in mammals, reptiles and birds has not been recorded in freshwater fishes—in every other respect an extremely diverse group. This study shows that multi-year pair bonding occurs in an Australian Percichthyid fish that exhibits paternal care of eggs and larvae. Using SNPs, full sibling pairs of larvae were found over multiple years in a three-year study. Stable isotope signatures of the larvae support the genetic inference that full sibling pairs shared a common mother, the ultimate source of that isotopic signature during oogenesis. Spatial and temporal clustering also suggests that the full sibling larvae are unlikely to be false positive identifications of the probabilistic identification of siblings. For the first time, we show multi-year pair bonding in a wild freshwater fish. This will have important conservation and management implications for the species. This approach could provide insights into many behavioural, ecological and evolutionary questions, particularly if this is not a unique case. Our findings are likely to initiate interest in seeking more examples of monogamy and alternative mating strategies in freshwater fishes, particularly if others improve methods of analysis of SNP data for identification of siblings in the absence of parental genotypes.
bibliographic citation: Couch et al. (2020) Multi-year pair-bonding in Murray cod (Maccullochella peelii). PeerJ 8:e10460 https://doi.org/10.7717/peerj.10460
date submitted: 2018-07-11
date accepted: 2020-11-10
issued: 2020-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Couch
  given name: Alan J.
author list: Agent
  family name: Dyer
  given name: Fiona
author list: Agent
  family name: Lintermans
  given name: Mark
doi: 10.7717/peerj.10460
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-10
copyright: ©2020 Couch et al.
attribution name: Couch et al.

Determinants of behavioural and biological risk factors for cardiovascular diseases from state level STEPS survey (2017–19) in Madhya Pradesh
type: item
type: AcademicArticle
description: Background National and statewide assessment of cardiovascular risk factors needs to be conducted periodically in order to inform public health policy and prioritise allocation of funds, especially in LMICs. Although there have been studies from India which have explored the determinants of cardiovascular risk factors, they have mostly been from high epidemiological transition states. The present study assessed the determinants of cardiovascular (CVD) risk factors in a low epidemiological transition state (Madhya Pradesh) using the WHO STEPwise approach to surveillance (STEPS). Methods A total of 5,680 persons aged 18–69 years were selected from the state of Madhya Pradesh through multi-stage cluster random sampling. Key CVD risk factors we sought to evaluate were from behavioural (tobacco, alcohol, physical activity, diet) and biological domains (overweight or obese, Hypertension, Diabetes, and Raised serum cholesterol). Key socio-demographic factors of interest were the caste and tribe groups, and rural vs urban location, in addition to known influencers of CVD risk such as age, gender and education level Results Those belonging to the scheduled tribes were more at risk of consuming tobacco (OR 2.13 (95% CI [1.52–2.98]), and a diet with less than five servings of fruits and vegetables (OR 2.78 (95% CI [1.06–7.24]), but had had the least risk of physical inactivity (OR 0.31 (95% CI [0.02–0.54]). Residence in a rural area also reduced the odds of physical inactivity (OR 0.65 (95% CI [0.46–0.92])). Lack of formal education was a risk factor for both tobacco consumption and alcohol intake (OR 1.40 (95% CI [1.08–1.82]) for tobacco use; 1.68 (95% CI [1.14–2.49]) for alcohol intake). Those belonging to schedules tribes had much lower risk of being obese (OR 0.25; 95% CI [0.17–0.37]), but were at similar risk of all other clinical CVD risk factors as compared to other caste groups. Conclusion In the current study we explored socio-demographic determinants of behavioural a…
format: application/pdf
format: text/html
creator: Arun M. Kokane
creator: Rajnish Joshi
creator: Ashwin Kotnis
creator: Anirban Chatterjee
creator: Kriti Yadav
creator: G Revadi
creator: Ankur Joshi
creator: Abhijit P. Pakhare
subject: Cardiology
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Global Health
subject: Public Health
description: doi:10.7717/peerj.10476
publisher: PeerJ Inc.
rights: © 2020 Kokane et al.
abstract: Background National and statewide assessment of cardiovascular risk factors needs to be conducted periodically in order to inform public health policy and prioritise allocation of funds, especially in LMICs. Although there have been studies from India which have explored the determinants of cardiovascular risk factors, they have mostly been from high epidemiological transition states. The present study assessed the determinants of cardiovascular (CVD) risk factors in a low epidemiological transition state (Madhya Pradesh) using the WHO STEPwise approach to surveillance (STEPS). Methods A total of 5,680 persons aged 18–69 years were selected from the state of Madhya Pradesh through multi-stage cluster random sampling. Key CVD risk factors we sought to evaluate were from behavioural (tobacco, alcohol, physical activity, diet) and biological domains (overweight or obese, Hypertension, Diabetes, and Raised serum cholesterol). Key socio-demographic factors of interest were the caste and tribe groups, and rural vs urban location, in addition to known influencers of CVD risk such as age, gender and education level Results Those belonging to the scheduled tribes were more at risk of consuming tobacco (OR 2.13 (95% CI [1.52–2.98]), and a diet with less than five servings of fruits and vegetables (OR 2.78 (95% CI [1.06–7.24]), but had had the least risk of physical inactivity (OR 0.31 (95% CI [0.02–0.54]). Residence in a rural area also reduced the odds of physical inactivity (OR 0.65 (95% CI [0.46–0.92])). Lack of formal education was a risk factor for both tobacco consumption and alcohol intake (OR 1.40 (95% CI [1.08–1.82]) for tobacco use; 1.68 (95% CI [1.14–2.49]) for alcohol intake). Those belonging to schedules tribes had much lower risk of being obese (OR 0.25; 95% CI [0.17–0.37]), but were at similar risk of all other clinical CVD risk factors as compared to other caste groups. Conclusion In the current study we explored socio-demographic determinants of behavioural a…
bibliographic citation: Kokane et al. (2020) Determinants of behavioural and biological risk factors for cardiovascular diseases from state level STEPS survey (2017–19) in Madhya Pradesh. PeerJ 8:e10476 https://doi.org/10.7717/peerj.10476
date submitted: 2020-09-04
date accepted: 2020-11-11
issued: 2020-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kokane
  given name: Arun M.
author list: Agent
  family name: Joshi
  given name: Rajnish
author list: Agent
  family name: Kotnis
  given name: Ashwin
author list: Agent
  family name: Chatterjee
  given name: Anirban
author list: Agent
  family name: Yadav
  given name: Kriti
author list: Agent
  family name: Revadi
  given name: G
author list: Agent
  family name: Joshi
  given name: Ankur
author list: Agent
  family name: Pakhare
  given name: Abhijit P.
doi: 10.7717/peerj.10476
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-10
copyright: ©2020 Kokane et al.
attribution name: Kokane et al.

miR-21 is upregulated, promoting fibrosis and blocking G2/M in irradiated rat cardiac fibroblasts
type: item
type: AcademicArticle
description: Background Radiation exposure of the thorax is associated with a greatly increased risk of cardiac morbidity and mortality even after several decades of advancement in the field. Although many studies have demonstrated the damaging influence of ionizing radiation on cardiac fibroblast (CF) structure and function, myocardial fibrosis, the molecular mechanism behind this damage is not well understood. miR-21, a small microRNA, promotes the activation of CFs, leading to cardiac fibrosis. miR-21 is overexpressed after irradiation; however, the relationship between increased miR-21 and myocardial fibrosis after irradiation is unclear. This study was conducted to investigate gene expression after radiation-induced CF damage and the role of miR-21 in this process in rats. Methods We sequenced irradiated rat CFs and performed weighted correlation network analysis (WGCNA) combined with differentially expressed gene (DEG) analysis to observe the effect on the expression profile of CF genes after radiation. Results DEG analysis showed that the degree of gene changes increased with the radiation dose. WGCNA revealed three module eigengenes (MEs) associated with 8.5-Gy-radiation—the Yellow, Brown, Blue modules. The three module eigengenes were related to apoptosis, G2/M phase, and cell death and S phase, respectively. By blocking with the cardiac fibrosis miRNA miR-21, we found that miR-21 was associated with G2/M blockade in the cell cycle and was mainly involved in regulating extracellular matrix-related genes, including Grem1, Clu, Gdf15, Ccl7, and Cxcl1. Stem-loop quantitative real-time PCR was performed to verify the expression of these genes. Five genes showed higher expression after 8.5 Gy-radiation in CFs. The target genes of miR-21 predicted online were Gdf15 and Rsad2, which showed much higher expression after treatment with antagomir-miR-21 in 8.5-Gy-irradiated CFs. Thus, miR-21 may play the role of fibrosis and G2/M blockade in regulating Grem1, Clu, Gdf15, Ccl7, Cxc…
format: application/pdf
format: text/html
creator: Huan Guo
creator: Xinke Zhao
creator: Haixiang Su
creator: Chengxu Ma
creator: Kai Liu
creator: Shanshan Kong
creator: Kedan Liu
creator: Haining Li
creator: Juan Chang
creator: Tao Wang
creator: Hongyun Guo
creator: Huiping Wei
creator: Zhaoyuan Fu
creator: Xinfang Lv
creator: Yingdong Li
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Cardiology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.10502
publisher: PeerJ Inc.
rights: © 2020 Guo et al.
abstract: Background Radiation exposure of the thorax is associated with a greatly increased risk of cardiac morbidity and mortality even after several decades of advancement in the field. Although many studies have demonstrated the damaging influence of ionizing radiation on cardiac fibroblast (CF) structure and function, myocardial fibrosis, the molecular mechanism behind this damage is not well understood. miR-21, a small microRNA, promotes the activation of CFs, leading to cardiac fibrosis. miR-21 is overexpressed after irradiation; however, the relationship between increased miR-21 and myocardial fibrosis after irradiation is unclear. This study was conducted to investigate gene expression after radiation-induced CF damage and the role of miR-21 in this process in rats. Methods We sequenced irradiated rat CFs and performed weighted correlation network analysis (WGCNA) combined with differentially expressed gene (DEG) analysis to observe the effect on the expression profile of CF genes after radiation. Results DEG analysis showed that the degree of gene changes increased with the radiation dose. WGCNA revealed three module eigengenes (MEs) associated with 8.5-Gy-radiation—the Yellow, Brown, Blue modules. The three module eigengenes were related to apoptosis, G2/M phase, and cell death and S phase, respectively. By blocking with the cardiac fibrosis miRNA miR-21, we found that miR-21 was associated with G2/M blockade in the cell cycle and was mainly involved in regulating extracellular matrix-related genes, including Grem1, Clu, Gdf15, Ccl7, and Cxcl1. Stem-loop quantitative real-time PCR was performed to verify the expression of these genes. Five genes showed higher expression after 8.5 Gy-radiation in CFs. The target genes of miR-21 predicted online were Gdf15 and Rsad2, which showed much higher expression after treatment with antagomir-miR-21 in 8.5-Gy-irradiated CFs. Thus, miR-21 may play the role of fibrosis and G2/M blockade in regulating Grem1, Clu, Gdf15, Ccl7, Cxc…
bibliographic citation: Guo et al. (2020) miR-21 is upregulated, promoting fibrosis and blocking G2/M in irradiated rat cardiac fibroblasts. PeerJ 8:e10502 https://doi.org/10.7717/peerj.10502
date submitted: 2020-07-06
date accepted: 2020-11-15
issued: 2020-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Huan
author list: Agent
  family name: Zhao
  given name: Xinke
author list: Agent
  family name: Su
  given name: Haixiang
author list: Agent
  family name: Ma
  given name: Chengxu
author list: Agent
  family name: Liu
  given name: Kai
author list: Agent
  family name: Kong
  given name: Shanshan
author list: Agent
  family name: Liu
  given name: Kedan
author list: Agent
  family name: Li
  given name: Haining
author list: Agent
  family name: Chang
  given name: Juan
author list: Agent
  family name: Wang
  given name: Tao
author list: Agent
  family name: Guo
  given name: Hongyun
author list: Agent
  family name: Wei
  given name: Huiping
author list: Agent
  family name: Fu
  given name: Zhaoyuan
author list: Agent
  family name: Lv
  given name: Xinfang
author list: Agent
  family name: Li
  given name: Yingdong
doi: 10.7717/peerj.10502
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-10
copyright: ©2020 Guo et al.
attribution name: Guo et al.

Identification of biomarkers associated with clinical severity of chronic obstructive pulmonary disease
type: item
type: AcademicArticle
description: We sought to identify the biomarkers related to the clinical severity of stage I to stage IV chronic obstructive pulmonary disease (COPD). Gene expression profiles from the blood samples of COPD patients at each of the four stages were acquired from the Gene Expression Omnibus Database (GEO, accession number: GSE54837). Genes showing expression changes among the different stages were sorted by soft clustering. We performed functional enrichment, protein–protein interaction (PPI), and miRNA regulatory network analyses for the differentially expressed genes. The biomarkers associated with the clinical classification of COPD were selected from logistic regression models and the relationships between TLR2 and inflammatory factors were verified in clinical blood samples by qPCR and ELISA. Gene clusters demonstrating continuously rising or falling changes in expression (clusters 1, 2, and 7 and clusters 5, 6, and 8, respectively) from stage I to IV were defined as upregulated and downregulated genes, respectively, and further analyzed. The upregulated genes were enriched in functions associated with defense, inflammatory, or immune responses. The downregulated genes were associated with lymphocyte activation and cell activation. TLR2, HMOX1, and CD79A were hub proteins in the integrated network of PPI and miRNA regulatory networks. TLR2 and CD79A were significantly correlated with clinical classifications. TLR2 was closely associated with inflammatory responses during COPD progression. Functions associated with inflammatory and immune responses as well as lymphocyte activation may play important roles in the progression of COPD from stage I to IV. TLR2 and CD79A may serve as potential biomarkers for the clinical severity of COPD. TLR2 and CD79A may also serve as independent biomarkers in the clinical classification in COPD. TLR2 may play an important role in the inflammatory responses of COPD.
format: application/pdf
format: text/html
creator: Jie Zhang
creator: Changli Zhu
creator: Hong Gao
creator: Xun Liang
creator: Xiaoqian Fan
creator: Yulong Zheng
creator: Song Chen
creator: Yufeng Wan
subject: Bioinformatics
subject: Respiratory Medicine
description: doi:10.7717/peerj.10513
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: We sought to identify the biomarkers related to the clinical severity of stage I to stage IV chronic obstructive pulmonary disease (COPD). Gene expression profiles from the blood samples of COPD patients at each of the four stages were acquired from the Gene Expression Omnibus Database (GEO, accession number: GSE54837). Genes showing expression changes among the different stages were sorted by soft clustering. We performed functional enrichment, protein–protein interaction (PPI), and miRNA regulatory network analyses for the differentially expressed genes. The biomarkers associated with the clinical classification of COPD were selected from logistic regression models and the relationships between TLR2 and inflammatory factors were verified in clinical blood samples by qPCR and ELISA. Gene clusters demonstrating continuously rising or falling changes in expression (clusters 1, 2, and 7 and clusters 5, 6, and 8, respectively) from stage I to IV were defined as upregulated and downregulated genes, respectively, and further analyzed. The upregulated genes were enriched in functions associated with defense, inflammatory, or immune responses. The downregulated genes were associated with lymphocyte activation and cell activation. TLR2, HMOX1, and CD79A were hub proteins in the integrated network of PPI and miRNA regulatory networks. TLR2 and CD79A were significantly correlated with clinical classifications. TLR2 was closely associated with inflammatory responses during COPD progression. Functions associated with inflammatory and immune responses as well as lymphocyte activation may play important roles in the progression of COPD from stage I to IV. TLR2 and CD79A may serve as potential biomarkers for the clinical severity of COPD. TLR2 and CD79A may also serve as independent biomarkers in the clinical classification in COPD. TLR2 may play an important role in the inflammatory responses of COPD.
bibliographic citation: Zhang et al. (2020) Identification of biomarkers associated with clinical severity of chronic obstructive pulmonary disease. PeerJ 8:e10513 https://doi.org/10.7717/peerj.10513
date submitted: 2019-12-19
date accepted: 2020-11-17
issued: 2020-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Jie
author list: Agent
  family name: Zhu
  given name: Changli
author list: Agent
  family name: Gao
  given name: Hong
author list: Agent
  family name: Liang
  given name: Xun
author list: Agent
  family name: Fan
  given name: Xiaoqian
author list: Agent
  family name: Zheng
  given name: Yulong
author list: Agent
  family name: Chen
  given name: Song
author list: Agent
  family name: Wan
  given name: Yufeng
doi: 10.7717/peerj.10513
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-10
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

Deep-sea water displacement from a turbidity current induced by the Super Typhoon Hagibis
type: item
type: AcademicArticle
description: Turbidity currents are the main drivers behind the transportation of terrestrial sediments to the deep sea, and turbidite deposits from such currents have been widely used in geological studies. Nevertheless, the contribution of turbidity currents to vertical displacement of seawater has rarely been discussed. This is partly because until recently, deep-sea turbidity currents have rarely been observed due to their unpredictable nature, being usually triggered by meteorological or geological events such as typhoons and earthquakes. Here, we report a direct observation of a deep-sea turbidity current using the recently developed Edokko Mark 1 monitoring system deployed in 2019 at a depth of 1,370 m in Suruga Bay, central Japan. A turbidity current occurred two days after its probable cause, the Super Typhoon Hagibis (2019), passed through Suruga Bay causing devastating damage. Over aperiod of 40 hours, we observed increased turbidity with turbulent conditions confirmed by a video camera. The turbidity exhibited two sharp peaks around 3:00 and 11:00 on October 14 (Japan Standard Time). The temperature and salinity characteristics during these high turbidity events agreed with independent measurements for shallow water layers in Suruga Bay at the same time, strongly suggesting that the turbidity current caused vertical displacement in the bay’s water column by transporting warmer and shallower waters downslope of the canyon. Our results add to the previous few examples that show meteorological and geological events may have significant contributions in the transportation of shallower seawater to the deep sea. Recent technological developments pertaining to the Edokko Mark 1 and similar devices enable straightforward, long-term monitoring of the deep-seafloor and will contribute to the understanding of similar spontaneous events in the deep ocean.
format: application/pdf
format: text/html
creator: Shinsuke Kawagucci
creator: Tetsuya Miwa
creator: Dhugal J. Lindsay
creator: Eri Ogura
creator: Hiroyuki Yamamoto
creator: Kenichiro Nishibayashi
creator: Hiroyuki Yokooka
creator: Shotaro Nishi
creator: Ayu Takahashi
creator: Sangkyun Lee
subject: Aquatic and Marine Chemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.10429
publisher: PeerJ Inc.
rights: © 2020 Kawagucci et al.
abstract: Turbidity currents are the main drivers behind the transportation of terrestrial sediments to the deep sea, and turbidite deposits from such currents have been widely used in geological studies. Nevertheless, the contribution of turbidity currents to vertical displacement of seawater has rarely been discussed. This is partly because until recently, deep-sea turbidity currents have rarely been observed due to their unpredictable nature, being usually triggered by meteorological or geological events such as typhoons and earthquakes. Here, we report a direct observation of a deep-sea turbidity current using the recently developed Edokko Mark 1 monitoring system deployed in 2019 at a depth of 1,370 m in Suruga Bay, central Japan. A turbidity current occurred two days after its probable cause, the Super Typhoon Hagibis (2019), passed through Suruga Bay causing devastating damage. Over aperiod of 40 hours, we observed increased turbidity with turbulent conditions confirmed by a video camera. The turbidity exhibited two sharp peaks around 3:00 and 11:00 on October 14 (Japan Standard Time). The temperature and salinity characteristics during these high turbidity events agreed with independent measurements for shallow water layers in Suruga Bay at the same time, strongly suggesting that the turbidity current caused vertical displacement in the bay’s water column by transporting warmer and shallower waters downslope of the canyon. Our results add to the previous few examples that show meteorological and geological events may have significant contributions in the transportation of shallower seawater to the deep sea. Recent technological developments pertaining to the Edokko Mark 1 and similar devices enable straightforward, long-term monitoring of the deep-seafloor and will contribute to the understanding of similar spontaneous events in the deep ocean.
bibliographic citation: Kawagucci et al. (2020) Deep-sea water displacement from a turbidity current induced by the Super Typhoon Hagibis. PeerJ 8:e10429 https://doi.org/10.7717/peerj.10429
date submitted: 2020-07-16
date accepted: 2020-11-03
issued: 2020-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kawagucci
  given name: Shinsuke
author list: Agent
  family name: Miwa
  given name: Tetsuya
author list: Agent
  family name: Lindsay
  given name: Dhugal J.
author list: Agent
  family name: Ogura
  given name: Eri
author list: Agent
  family name: Yamamoto
  given name: Hiroyuki
author list: Agent
  family name: Nishibayashi
  given name: Kenichiro
author list: Agent
  family name: Yokooka
  given name: Hiroyuki
author list: Agent
  family name: Nishi
  given name: Shotaro
author list: Agent
  family name: Takahashi
  given name: Ayu
author list: Agent
  family name: Lee
  given name: Sangkyun
doi: 10.7717/peerj.10429
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-09
copyright: ©2020 Kawagucci et al.
attribution name: Kawagucci et al.

Effect of dietary oil from Camelina sativa on the growth performance, fillet fatty acid profile and gut microbiome of gilthead Sea bream (Sparus aurata)
type: item
type: AcademicArticle
description: Background In the last two decades, research has focused on testing cheaper and sustainable alternatives to fish oil (FO), such as vegetable oils (VO), in aquafeeds. However, FO cannot be entirely replaced by VOs due to their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), particularly eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic (DHA; 22:6n-3) acids. The oilseed plant, Camelina sativa, may have a higher potential to replace FO since it can contains up to 40% of the omega-3 precursors α-linolenic acid (ALA; 18:3n-3) and linoleic acid (LA; 18:2n-6). Methods A 90-day feeding trial was conducted with 600 gilthead sea bream (Sparus aurata) of 32.92 ± 0.31 g mean initial weight fed three diets that replaced 20%, 40% and 60% of FO with CO and a control diet of FO. Fish were distributed into triplicate tanks per diet and with 50 fish each in a flow-through open marine system. Growth performance and fatty acid profiles of the fillet were analysed. The Illumina MiSeq platform for sequencing of 16S rRNA gene and Mothur pipeline were used to identify bacteria in the faeces, gut mucosa and diets in addition to metagenomic analysis by PICRUSt. Results and Conclusions The feed conversion rate and specific growth rate were not affected by diet, although final weight was significantly lower for fish fed the 60% CO diet. Reduced final weight was attributed to lower levels of EPA and DHA in the CO ingredient. The lipid profile of fillets were similar between the dietary groups in regards to total saturated, monounsaturated, PUFA (n-3 and n-6), and the ratio of n-3/n-6. Levels of EPA and DHA in the fillet reflected the progressive replacement of FO by CO in the diet and the EPA was significantly lower in fish fed the 60% CO diet, while ALA was increased. Alpha and beta-diversities of gut bacteria in both the faeces and mucosa were not affected by any dietary treatment, although a few indicator bacteria, such as Corynebacterium and Rhodospirillales, were …
format: application/pdf
format: text/html
creator: David Huyben
creator: Simona Rimoldi
creator: Chiara Ceccotti
creator: Daniel Montero
creator: Monica Betancor
creator: Federica Iannini
creator: Genciana Terova
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.10430
publisher: PeerJ Inc.
rights: © 2020 Huyben et al.
abstract: Background In the last two decades, research has focused on testing cheaper and sustainable alternatives to fish oil (FO), such as vegetable oils (VO), in aquafeeds. However, FO cannot be entirely replaced by VOs due to their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), particularly eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic (DHA; 22:6n-3) acids. The oilseed plant, Camelina sativa, may have a higher potential to replace FO since it can contains up to 40% of the omega-3 precursors α-linolenic acid (ALA; 18:3n-3) and linoleic acid (LA; 18:2n-6). Methods A 90-day feeding trial was conducted with 600 gilthead sea bream (Sparus aurata) of 32.92 ± 0.31 g mean initial weight fed three diets that replaced 20%, 40% and 60% of FO with CO and a control diet of FO. Fish were distributed into triplicate tanks per diet and with 50 fish each in a flow-through open marine system. Growth performance and fatty acid profiles of the fillet were analysed. The Illumina MiSeq platform for sequencing of 16S rRNA gene and Mothur pipeline were used to identify bacteria in the faeces, gut mucosa and diets in addition to metagenomic analysis by PICRUSt. Results and Conclusions The feed conversion rate and specific growth rate were not affected by diet, although final weight was significantly lower for fish fed the 60% CO diet. Reduced final weight was attributed to lower levels of EPA and DHA in the CO ingredient. The lipid profile of fillets were similar between the dietary groups in regards to total saturated, monounsaturated, PUFA (n-3 and n-6), and the ratio of n-3/n-6. Levels of EPA and DHA in the fillet reflected the progressive replacement of FO by CO in the diet and the EPA was significantly lower in fish fed the 60% CO diet, while ALA was increased. Alpha and beta-diversities of gut bacteria in both the faeces and mucosa were not affected by any dietary treatment, although a few indicator bacteria, such as Corynebacterium and Rhodospirillales, were …
bibliographic citation: Huyben et al. (2020) Effect of dietary oil from Camelina sativa on the growth performance, fillet fatty acid profile and gut microbiome of gilthead Sea bream (Sparus aurata). PeerJ 8:e10430 https://doi.org/10.7717/peerj.10430
date submitted: 2020-08-25
date accepted: 2020-11-03
issued: 2020-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huyben
  given name: David
author list: Agent
  family name: Rimoldi
  given name: Simona
author list: Agent
  family name: Ceccotti
  given name: Chiara
author list: Agent
  family name: Montero
  given name: Daniel
author list: Agent
  family name: Betancor
  given name: Monica
author list: Agent
  family name: Iannini
  given name: Federica
author list: Agent
  family name: Terova
  given name: Genciana
doi: 10.7717/peerj.10430
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-09
copyright: ©2020 Huyben et al.
attribution name: Huyben et al.

Measuring stress in podiatric students in Spain: psychometric validation and adaptation of the KEZKAK questionnaire
type: item
type: AcademicArticle
description: Objective The study aim was to develop a linguistic-cultural adaptation of the KEZKAK questionnaire to be completed during the practicum of podiatric medical students in Spain, to validate the questionnaire and to evaluate its psychometric properties. Methods The cross-sectional study was carried out in two stages: 1. Cross-cultural adaptation; 2. Clinimetric validation based on assessments of interobserver reliability, test-retest reliability and internal consistency. The participants were podiatric medical students at the universities of Malaga and Miguel Hernandez, Alicante (Spain) and were recruited during the period February–October 2019. The following inclusion criteria were applied: aged at least 18 years, studying the third or fourth year of a university degree in Podiatry. All gave signed informed consent and completed the State-Trait Anxiety Inventory and the Podiatry version of the KEZKAK questionnaire. No sampling was performed and thus the entire eligible population was included in the study. Results The analysis was based on 205 participants (33.5% male, 66.5% female), with a mean age of 23.05 (SD 5.37) years. Internal consistency was excellent, with a Cronbach’s alpha of 0.95. This version of the questionnaire had five factorial structures (61.18%). No floor/ceiling effect was observed in any item. The KEZKAK presented high test-retest reliability after 21 days, with an overall ICC of 0.95 (95% CI [0.93–0.98]). Conclusion For university students of podiatry in Spain, the KEZKAK Podiatry version questionnaire is a valid, reliable instrument for measuring stressors during the practicum.
format: application/pdf
format: text/html
creator: Ana Belen Ortega-Avila
creator: Pablo Cervera-Garvi
creator: Ana Maria Jimenez-Cebrian
creator: Esther Chicharro-Luna
creator: Irene Garcia-Paya
creator: Gabriel Gijon-Nogueron
subject: Global Health
subject: Nursing
subject: Psychiatry and Psychology
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.10439
publisher: PeerJ Inc.
rights: © 2020 Ortega-Avila et al.
abstract: Objective The study aim was to develop a linguistic-cultural adaptation of the KEZKAK questionnaire to be completed during the practicum of podiatric medical students in Spain, to validate the questionnaire and to evaluate its psychometric properties. Methods The cross-sectional study was carried out in two stages: 1. Cross-cultural adaptation; 2. Clinimetric validation based on assessments of interobserver reliability, test-retest reliability and internal consistency. The participants were podiatric medical students at the universities of Malaga and Miguel Hernandez, Alicante (Spain) and were recruited during the period February–October 2019. The following inclusion criteria were applied: aged at least 18 years, studying the third or fourth year of a university degree in Podiatry. All gave signed informed consent and completed the State-Trait Anxiety Inventory and the Podiatry version of the KEZKAK questionnaire. No sampling was performed and thus the entire eligible population was included in the study. Results The analysis was based on 205 participants (33.5% male, 66.5% female), with a mean age of 23.05 (SD 5.37) years. Internal consistency was excellent, with a Cronbach’s alpha of 0.95. This version of the questionnaire had five factorial structures (61.18%). No floor/ceiling effect was observed in any item. The KEZKAK presented high test-retest reliability after 21 days, with an overall ICC of 0.95 (95% CI [0.93–0.98]). Conclusion For university students of podiatry in Spain, the KEZKAK Podiatry version questionnaire is a valid, reliable instrument for measuring stressors during the practicum.
bibliographic citation: Ortega-Avila et al. (2020) Measuring stress in podiatric students in Spain: psychometric validation and adaptation of the KEZKAK questionnaire. PeerJ 8:e10439 https://doi.org/10.7717/peerj.10439
date submitted: 2020-07-08
date accepted: 2020-11-06
issued: 2020-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ortega-Avila
  given name: Ana Belen
author list: Agent
  family name: Cervera-Garvi
  given name: Pablo
author list: Agent
  family name: Jimenez-Cebrian
  given name: Ana Maria
author list: Agent
  family name: Chicharro-Luna
  given name: Esther
author list: Agent
  family name: Garcia-Paya
  given name: Irene
author list: Agent
  family name: Gijon-Nogueron
  given name: Gabriel
doi: 10.7717/peerj.10439
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-09
copyright: ©2020 Ortega-Avila et al.
attribution name: Ortega-Avila et al.

Experimental lung injury induces cerebral cytokine mRNA production in pigs
type: item
type: AcademicArticle
description: Background Acute respiratory distress syndrome (ARDS) is an important disease with a high incidence among patients admitted to intensive care units. Over the last decades, the survival of critically ill patients has improved; however, cognitive deficits are among the long-term sequelae. We hypothesize that acute lung injury leads to upregulation of cerebral cytokine synthesis. Methods After approval of the institutional and animal care committee, 20 male pigs were randomized to one of three groups: (1) Lung injury by oleic acid injection (OAI), (2) ventilation only (CTR) or (3) untreated. We compared neuronal numbers, proportion of neurons with markers for apoptosis, activation state of Iba-1 stained microglia cells and cerebral mRNA levels of different cytokines between the groups 18 hours after onset of lung injury. Results We found an increase in hippocampal TNFalpha (p < 0.05) and IL-6 (p < 0.05) messenger RNA (mRNA) in the OAI compared to untreated group as well as higher hippocampal IL-6 mRNA compared to control (p < 0.05). IL-8 and IL-1beta mRNA showed no differences between the groups. We found histologic markers for beginning apoptosis in OAI compared to untreated (p < 0.05) and more active microglia cells in OAI and CTR compared to untreated (p < 0.001 each). Conclusion Hippocampal cytokine transcription increases within 18 hours after the induction of acute lung injury with histological evidence of neuronal damage. It remains to be elucidated if increased cytokine mRNA synthesis plays a role in the cognitive decline observed in survivors of ARDS.
format: application/pdf
format: text/html
creator: Jens Kamuf
creator: Andreas Garcia Bardon
creator: Alexander Ziebart
creator: Katrin Frauenknecht
creator: Konstantin Folkert
creator: Johannes Schwab
creator: Robert Ruemmler
creator: Miriam Renz
creator: Denis Cana
creator: Serge C. Thal
creator: Erik K. Hartmann
subject: Cognitive Disorders
subject: Emergency and Critical Care
subject: Neurology
subject: Respiratory Medicine
description: doi:10.7717/peerj.10471
publisher: PeerJ Inc.
rights: © 2020 Kamuf et al.
abstract: Background Acute respiratory distress syndrome (ARDS) is an important disease with a high incidence among patients admitted to intensive care units. Over the last decades, the survival of critically ill patients has improved; however, cognitive deficits are among the long-term sequelae. We hypothesize that acute lung injury leads to upregulation of cerebral cytokine synthesis. Methods After approval of the institutional and animal care committee, 20 male pigs were randomized to one of three groups: (1) Lung injury by oleic acid injection (OAI), (2) ventilation only (CTR) or (3) untreated. We compared neuronal numbers, proportion of neurons with markers for apoptosis, activation state of Iba-1 stained microglia cells and cerebral mRNA levels of different cytokines between the groups 18 hours after onset of lung injury. Results We found an increase in hippocampal TNFalpha (p < 0.05) and IL-6 (p < 0.05) messenger RNA (mRNA) in the OAI compared to untreated group as well as higher hippocampal IL-6 mRNA compared to control (p < 0.05). IL-8 and IL-1beta mRNA showed no differences between the groups. We found histologic markers for beginning apoptosis in OAI compared to untreated (p < 0.05) and more active microglia cells in OAI and CTR compared to untreated (p < 0.001 each). Conclusion Hippocampal cytokine transcription increases within 18 hours after the induction of acute lung injury with histological evidence of neuronal damage. It remains to be elucidated if increased cytokine mRNA synthesis plays a role in the cognitive decline observed in survivors of ARDS.
bibliographic citation: Kamuf et al. (2020) Experimental lung injury induces cerebral cytokine mRNA production in pigs. PeerJ 8:e10471 https://doi.org/10.7717/peerj.10471
date submitted: 2020-04-07
date accepted: 2020-11-11
issued: 2020-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kamuf
  given name: Jens
author list: Agent
  family name: Garcia Bardon
  given name: Andreas
author list: Agent
  family name: Ziebart
  given name: Alexander
author list: Agent
  family name: Frauenknecht
  given name: Katrin
author list: Agent
  family name: Folkert
  given name: Konstantin
author list: Agent
  family name: Schwab
  given name: Johannes
author list: Agent
  family name: Ruemmler
  given name: Robert
author list: Agent
  family name: Renz
  given name: Miriam
author list: Agent
  family name: Cana
  given name: Denis
author list: Agent
  family name: Thal
  given name: Serge C.
author list: Agent
  family name: Hartmann
  given name: Erik K.
doi: 10.7717/peerj.10471
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-09
copyright: ©2020 Kamuf et al.
attribution name: Kamuf et al.

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