PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Lifestyle choices of Brazilian college students
items: Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)
items: Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages
items: SlMYB102 expression enhances low-temperature stress resistance in tomato plants
items: Factors influencing unmet need for contraception amongst adolescent girls and women in Cambodia
items: Lactobacillus johnsonii BS15 improves intestinal environment against fluoride-induced memory impairment in mice—a study based on the gut–brain axis hypothesis
items: CKS2 and RMI2 are two prognostic biomarkers of lung adenocarcinoma
items: A digital mapping application for quantifying and displaying air temperatures at high spatiotemporal resolutions in near real-time across Australia
items: COVID-19: molecular and serological detection methods
items: The highly rearranged mitochondrial genomes of three economically important scale insects and the mitochondrial phylogeny of Coccoidea (Hemiptera: Sternorrhyncha)

Lifestyle choices of Brazilian college students
type: item
type: AcademicArticle
description: Background Lifestyle choices reflect the beliefs that individuals attribute to aspects of life. This construct can be assessed with the Individual Lifestyle Profile (PEVI) questionnaire, which measures elements of Nutrition, Physical Activity, Preventive Behaviors, Social Relationships and Stress Management. Objective The objective of this study was to estimate the psychometric properties of the PEVI applied to a sample of Brazilian university students, identifying the prevalence of each lifestyle component according to participants’ age, sex, weight status, course area/field and economic stratum and to estimate the contribution of these characteristics on physical and psychological lifestyle. Methods The PEVI data was analyzed by confirmatory factor analysis, using the indexes chi-square per degrees of freedom ratio (χ2/df), Comparative Fit Index (CFI), Tucker-Lewis Index (TLI) and Root Mean Square Error of Approximation (RMSEA). First-order and second-order models (physical and psychological lifestyle) were tested. Prevalences of lifestyle components were calculated and compared by participants’ age, sex, weight status, course area/field and economic stratum. A hypothetical causal structural model was elaborated to investigate the impact of sample characteristics on physical and psychological lifestyles. This model was evaluated considering the global fit to the data (χ2/df, CFI, TLI and RMSEA) and the hypothetical causal trajectories (β) (α = 5%). Results A sample of 1,303 students was used. The mean age was 20.9 (standard deviation = 2.8) years, 66.8% of participants were females, 63.4% had weights in the normal range and 73.7% were students of the social and exact sciences. The PEVI data showed an adequate fit for both the first- (χ2/df = 2.03, CFI = 0.98; TLI = 0.97; RMSEA = 0.04) and second-order (χ2/df = 2.25; CFI = 0.97; TLI = 0.97; RMSEA = 0.04) models. There was a higher prevalence of unfavorable physical and psychological lifestyle choices among females,…
format: application/pdf
format: text/html
creator: Bianca G. Martins
creator: João Marôco
creator: Mauro V.G. Barros
creator: Juliana A.D.B. Campos
subject: Epidemiology
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.9830
publisher: PeerJ Inc.
rights: © 2020 Martins et al.
abstract: Background Lifestyle choices reflect the beliefs that individuals attribute to aspects of life. This construct can be assessed with the Individual Lifestyle Profile (PEVI) questionnaire, which measures elements of Nutrition, Physical Activity, Preventive Behaviors, Social Relationships and Stress Management. Objective The objective of this study was to estimate the psychometric properties of the PEVI applied to a sample of Brazilian university students, identifying the prevalence of each lifestyle component according to participants’ age, sex, weight status, course area/field and economic stratum and to estimate the contribution of these characteristics on physical and psychological lifestyle. Methods The PEVI data was analyzed by confirmatory factor analysis, using the indexes chi-square per degrees of freedom ratio (χ2/df), Comparative Fit Index (CFI), Tucker-Lewis Index (TLI) and Root Mean Square Error of Approximation (RMSEA). First-order and second-order models (physical and psychological lifestyle) were tested. Prevalences of lifestyle components were calculated and compared by participants’ age, sex, weight status, course area/field and economic stratum. A hypothetical causal structural model was elaborated to investigate the impact of sample characteristics on physical and psychological lifestyles. This model was evaluated considering the global fit to the data (χ2/df, CFI, TLI and RMSEA) and the hypothetical causal trajectories (β) (α = 5%). Results A sample of 1,303 students was used. The mean age was 20.9 (standard deviation = 2.8) years, 66.8% of participants were females, 63.4% had weights in the normal range and 73.7% were students of the social and exact sciences. The PEVI data showed an adequate fit for both the first- (χ2/df = 2.03, CFI = 0.98; TLI = 0.97; RMSEA = 0.04) and second-order (χ2/df = 2.25; CFI = 0.97; TLI = 0.97; RMSEA = 0.04) models. There was a higher prevalence of unfavorable physical and psychological lifestyle choices among females,…
bibliographic citation: Martins et al. (2020) Lifestyle choices of Brazilian college students. PeerJ 8:e9830 https://doi.org/10.7717/peerj.9830
date submitted: 2019-11-20
date accepted: 2020-08-06
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martins
  given name: Bianca G.
author list: Agent
  family name: Marôco
  given name: João
author list: Agent
  family name: Barros
  given name: Mauro V.G.
author list: Agent
  family name: Campos
  given name: Juliana A.D.B.
doi: 10.7717/peerj.9830
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: © 2020 Martins et al.
attribution name: Martins et al.

Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)
type: item
type: AcademicArticle
description: Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, “saddle-shape” deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known “biological” signals and subjected to uniform shear, deformation was typically the main source of variance but accurate “biological” information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed Diictodon specimens exhibit significant dispersion around the “true” position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specim…
format: application/pdf
format: text/html
creator: Christian F. Kammerer
creator: Michol Deutsch
creator: Jacqueline K. Lungmus
creator: Kenneth D. Angielczyk
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.9925
publisher: PeerJ Inc.
rights: © 2020 Kammerer et al.
abstract: Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, “saddle-shape” deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known “biological” signals and subjected to uniform shear, deformation was typically the main source of variance but accurate “biological” information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed Diictodon specimens exhibit significant dispersion around the “true” position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specim…
bibliographic citation: Kammerer et al. (2020) Effects of taphonomic deformation on geometric morphometric analysis of fossils: a study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia). PeerJ 8:e9925 https://doi.org/10.7717/peerj.9925
date submitted: 2020-04-27
date accepted: 2020-08-21
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kammerer
  given name: Christian F.
author list: Agent
  family name: Deutsch
  given name: Michol
author list: Agent
  family name: Lungmus
  given name: Jacqueline K.
author list: Agent
  family name: Angielczyk
  given name: Kenneth D.
doi: 10.7717/peerj.9925
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: © 2020 Kammerer et al.
attribution name: Kammerer et al.

Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages
type: item
type: AcademicArticle
description: Background The submandibular glands, as major salivary glands, participate in rumen digestion in goats. Sialic acid, lysozyme, immunoglobulin A (IgA), lactoferrin and other biologically active substances secreted in the submandibular glands were reported in succession, which suggests that the submandibular gland may have immune functions in addition to participating in digestion. The aim of this study was to map the expression profile of differentially expressed genes (DEGs) at three different stages by transcriptome sequencing, screen immune-related genes and pathways by bioinformatics methods, and predict the immune function of submandibular glands at different developmental stages. Methods Nine submandibular gland tissue samples were collected from groups of 1-month-old kids, 12-month-old adolescent goats and 24-month-old adult goats (3 samples from each group), and high-throughput transcriptome sequencing was conducted on these samples. The DEGs among the three stages were screened and analysed. Key genes and signalling pathways were selected via protein-protein interaction (PPI) network analysis. Results The results revealed 2,706, 2,525 and 52 DEGs between 1-month-old and 12-month-old goats, between 1-month-old and 24-month-old goats, and between 12-month-old and 24-month-old goats, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that most of the DEGs were enriched in immune- related GO terms and pathways. Based on functional enrichment analysis and network analysis, 10 genes (PTPRC, CD28, SELL, LCP2, MYC, LCK, ZAP70, ITGB2, SYK and CCR7), two signalling pathways (the T cell receptor signalling pathway and the NF-κβ signalling pathway) and eight GO terms (T cell receptor signalling pathway, neutrophil mediated immunity, B cell mediated immunity, regulation of alpha-beta T cell activation, positive regulation of T cell proliferation, regulation of leukocyte differentiation, positive regulation of antigen re…
format: application/pdf
format: text/html
creator: Aili Wang
creator: Tianle Chao
creator: Zhibin Ji
creator: Rong Xuan
creator: Shuang Liu
creator: Maosen Guo
creator: Guizhi Wang
creator: Jianmin Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.9947
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background The submandibular glands, as major salivary glands, participate in rumen digestion in goats. Sialic acid, lysozyme, immunoglobulin A (IgA), lactoferrin and other biologically active substances secreted in the submandibular glands were reported in succession, which suggests that the submandibular gland may have immune functions in addition to participating in digestion. The aim of this study was to map the expression profile of differentially expressed genes (DEGs) at three different stages by transcriptome sequencing, screen immune-related genes and pathways by bioinformatics methods, and predict the immune function of submandibular glands at different developmental stages. Methods Nine submandibular gland tissue samples were collected from groups of 1-month-old kids, 12-month-old adolescent goats and 24-month-old adult goats (3 samples from each group), and high-throughput transcriptome sequencing was conducted on these samples. The DEGs among the three stages were screened and analysed. Key genes and signalling pathways were selected via protein-protein interaction (PPI) network analysis. Results The results revealed 2,706, 2,525 and 52 DEGs between 1-month-old and 12-month-old goats, between 1-month-old and 24-month-old goats, and between 12-month-old and 24-month-old goats, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that most of the DEGs were enriched in immune- related GO terms and pathways. Based on functional enrichment analysis and network analysis, 10 genes (PTPRC, CD28, SELL, LCP2, MYC, LCK, ZAP70, ITGB2, SYK and CCR7), two signalling pathways (the T cell receptor signalling pathway and the NF-κβ signalling pathway) and eight GO terms (T cell receptor signalling pathway, neutrophil mediated immunity, B cell mediated immunity, regulation of alpha-beta T cell activation, positive regulation of T cell proliferation, regulation of leukocyte differentiation, positive regulation of antigen re…
bibliographic citation: Wang et al. (2020) Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages. PeerJ 8:e9947 https://doi.org/10.7717/peerj.9947
date submitted: 2020-02-04
date accepted: 2020-08-25
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Aili
author list: Agent
  family name: Chao
  given name: Tianle
author list: Agent
  family name: Ji
  given name: Zhibin
author list: Agent
  family name: Xuan
  given name: Rong
author list: Agent
  family name: Liu
  given name: Shuang
author list: Agent
  family name: Guo
  given name: Maosen
author list: Agent
  family name: Wang
  given name: Guizhi
author list: Agent
  family name: Wang
  given name: Jianmin
doi: 10.7717/peerj.9947
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: ©2020 Wang et al.
attribution name: Wang et al.

SlMYB102 expression enhances low-temperature stress resistance in tomato plants
type: item
type: AcademicArticle
description: Herein, we identified the tomato SlMYB102 gene as a MYB family transcription factor of the R2R3-MYB subfamily. We additionally determined that the SlMYB102 promoter region contains photoresponsive, abiotic stress-responsive, and hormone-responsive regulatory elements, and we detected higher SlMYB102 expression in the reproductive organs of tomato than that in vegetative organs, with the expression being highest in ripe fruits and in roots. SlMYB102 expression was also shown to be cold-inducible. The protein encoded by SlMYB102 localized to the nucleus wherein it was found to mediate the transcriptional activation of target genes through its C-terminal domain. Overexpression of SlMYB102 in tomato plants conferred enhanced tolerance to cold stress. Under such cold stress conditions, we found that proline levels in the leaves of SlMYB102 overexpressing transgenic plants were higher than those in WT plants. In addition, S1MYB102 overexpression was associated with the enhanced expression of cold response genes including SlCBF1, SlCBF3, SlDREB1, SlDEB2, and SlICE1. We also found that the overexpression of SlMYB102 further enhanced the cold-induced upregulation of SlP5CS and SlAPX2. Taken together, these results suggest that SlMYB102 may be involved in the C-repeat binding transcription factor (CBF) and proline synthesis pathways, thereby improving tomato plant cold resistance.
format: application/pdf
format: text/html
creator: Meiling Wang
creator: Juan Hao
creator: Xiuhua Chen
creator: Xichun Zhang
subject: Biochemistry
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10059
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Herein, we identified the tomato SlMYB102 gene as a MYB family transcription factor of the R2R3-MYB subfamily. We additionally determined that the SlMYB102 promoter region contains photoresponsive, abiotic stress-responsive, and hormone-responsive regulatory elements, and we detected higher SlMYB102 expression in the reproductive organs of tomato than that in vegetative organs, with the expression being highest in ripe fruits and in roots. SlMYB102 expression was also shown to be cold-inducible. The protein encoded by SlMYB102 localized to the nucleus wherein it was found to mediate the transcriptional activation of target genes through its C-terminal domain. Overexpression of SlMYB102 in tomato plants conferred enhanced tolerance to cold stress. Under such cold stress conditions, we found that proline levels in the leaves of SlMYB102 overexpressing transgenic plants were higher than those in WT plants. In addition, S1MYB102 overexpression was associated with the enhanced expression of cold response genes including SlCBF1, SlCBF3, SlDREB1, SlDEB2, and SlICE1. We also found that the overexpression of SlMYB102 further enhanced the cold-induced upregulation of SlP5CS and SlAPX2. Taken together, these results suggest that SlMYB102 may be involved in the C-repeat binding transcription factor (CBF) and proline synthesis pathways, thereby improving tomato plant cold resistance.
bibliographic citation: Wang et al. (2020) SlMYB102 expression enhances low-temperature stress resistance in tomato plants. PeerJ 8:e10059 https://doi.org/10.7717/peerj.10059
date submitted: 2019-12-30
date accepted: 2020-09-07
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wang
  given name: Meiling
author list: Agent
  family name: Hao
  given name: Juan
author list: Agent
  family name: Chen
  given name: Xiuhua
author list: Agent
  family name: Zhang
  given name: Xichun
doi: 10.7717/peerj.10059
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Factors influencing unmet need for contraception amongst adolescent girls and women in Cambodia
type: item
type: AcademicArticle
description: Background Unmet need is the gap between women’s need and their practice of using contraception. Unmet need for contraception in female adolescents and women in Cambodia is a public health concern which may lead to unintended pregnancies or abortions that can contribute to maternal morbidity and mortality. Methods Bronfenbrenner’s Social Ecological Model was used as a theoretical framework to analyze data from the 2014 Cambodian Demographic and Health Survey to ascertain demographic and social factors potentially associated with unmet need for contraception. Bivariate and weighted multiple logistic regression analyses with adjusted odds ratios (AOR) were conducted for 4,823 Cambodian, sexually active females aged 15–29 years. Results The percentage of unmet need for contraception was 11.7%. At the individual level of the Social Ecological Model, there was an increased likelihood of unmet need in adolescent girls 15–19 years and women 20–24 years. Unmet need was decreased in currently employed women. At the microenvironment level, there was an increased likelihood of unmet need with the husband’s desire for more children and when the decision for a woman’s access to healthcare was made by someone else in the household. At the macroenvironment level, unmet need was decreased in women who could access a health facility near their residence to obtain medical care. There were no urban rural differences found in the Cambodian sample population. Conclusion Unmet need for contraception in Cambodian females adolescents and women is associated with younger age, unemployment and low personal autonomy for accessing healthcare but not with education or wealth status. There is a need to implement culturally appropriate reproductive and sexual health literacy programs to increase access to modern contraception and to raise women’s autonomy.
format: application/pdf
format: text/html
creator: Farwa Rizvi
creator: Joanne Williams
creator: Steven Bowe
creator: Elizabeth Hoban
subject: Epidemiology
subject: Gynecology and Obstetrics
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.10065
publisher: PeerJ Inc.
rights: © 2020 Rizvi et al.
abstract: Background Unmet need is the gap between women’s need and their practice of using contraception. Unmet need for contraception in female adolescents and women in Cambodia is a public health concern which may lead to unintended pregnancies or abortions that can contribute to maternal morbidity and mortality. Methods Bronfenbrenner’s Social Ecological Model was used as a theoretical framework to analyze data from the 2014 Cambodian Demographic and Health Survey to ascertain demographic and social factors potentially associated with unmet need for contraception. Bivariate and weighted multiple logistic regression analyses with adjusted odds ratios (AOR) were conducted for 4,823 Cambodian, sexually active females aged 15–29 years. Results The percentage of unmet need for contraception was 11.7%. At the individual level of the Social Ecological Model, there was an increased likelihood of unmet need in adolescent girls 15–19 years and women 20–24 years. Unmet need was decreased in currently employed women. At the microenvironment level, there was an increased likelihood of unmet need with the husband’s desire for more children and when the decision for a woman’s access to healthcare was made by someone else in the household. At the macroenvironment level, unmet need was decreased in women who could access a health facility near their residence to obtain medical care. There were no urban rural differences found in the Cambodian sample population. Conclusion Unmet need for contraception in Cambodian females adolescents and women is associated with younger age, unemployment and low personal autonomy for accessing healthcare but not with education or wealth status. There is a need to implement culturally appropriate reproductive and sexual health literacy programs to increase access to modern contraception and to raise women’s autonomy.
bibliographic citation: Rizvi et al. (2020) Factors influencing unmet need for contraception amongst adolescent girls and women in Cambodia. PeerJ 8:e10065 https://doi.org/10.7717/peerj.10065
date submitted: 2020-05-18
date accepted: 2020-09-08
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rizvi
  given name: Farwa
author list: Agent
  family name: Williams
  given name: Joanne
author list: Agent
  family name: Bowe
  given name: Steven
author list: Agent
  family name: Hoban
  given name: Elizabeth
doi: 10.7717/peerj.10065
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: ©2020 Rizvi et al.
attribution name: Rizvi et al.

Lactobacillus johnsonii BS15 improves intestinal environment against fluoride-induced memory impairment in mice—a study based on the gut–brain axis hypothesis
type: item
type: AcademicArticle
description: Background Excessive fluoride can lead to chronic neurodegeneration characterized by neuron and myelin loss and memory dysfunction. The gut–brain axis hypothesis suggests that gut microbiota plays a crucial role in regulating brain function. Thus, using probiotics to adjust the gut microenvironment may be a potential therapy for mental diseases. Methods Mice in the prob group were administrated with Lactobacillus johnsonii BS15 for 28 days prior to and throughout a 70-day exposure to sodium fluoride. The drinking water of all groups (F and prob groups) except the control group were replaced by high-fluoride water (100 mg NaF/L) on day 28. Animals in each group were divided into two subsets: one underwent behavioral test, and the other was sacrificed for sampling. The mRNA expression level and protein content related to inflammatory reaction in the ileum and hippocampus were respectively detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA). The mRNA expression levels of proteins related to myelin structure, apoptosis, and memory in the hippocampus and tight junction proteins in the ileum were determined by RT-qPCR and/or immunohistochemistry. Gut permeability markers (D-lactate and diamine oxidase (DAO)) in the serum were also examined by ELISA. Results The results showed that fluoride exposure induced a lower spontaneous exploration (P < 0.05) in T-maze test, which indicated an impairment of memory. Spontaneous exploration of BS15-treated mice was significantly higher (P < 0.05) than that in F group. Fluoride reduced (P < 0.05) levels of myelin structural protein (proteolipid protein) and neurogenesis-associated proteins (brain-derived neurotrophic factor and cAMP/Ca2+ responsive element-binding protein), induced disordered inflammatory cytokines (TNF-α, IFN-γ, and IL-6; P < 0.05), increased pro-apoptotic genes (caspase-3; P < 0.05), and decreased anti-apoptotic genes (Bcl-2; P < 0.05) in th…
format: application/pdf
format: text/html
creator: Jinge Xin
creator: Dong Zeng
creator: Hesong Wang
creator: Ning Sun
creator: Abdul Khalique
creator: Ying Zhao
creator: Liqian Wu
creator: Kangcheng Pan
creator: Bo Jing
creator: Xueqin Ni
subject: Animal Behavior
subject: Microbiology
subject: Cognitive Disorders
description: doi:10.7717/peerj.10125
publisher: PeerJ Inc.
rights: © 2020 Xin et al.
abstract: Background Excessive fluoride can lead to chronic neurodegeneration characterized by neuron and myelin loss and memory dysfunction. The gut–brain axis hypothesis suggests that gut microbiota plays a crucial role in regulating brain function. Thus, using probiotics to adjust the gut microenvironment may be a potential therapy for mental diseases. Methods Mice in the prob group were administrated with Lactobacillus johnsonii BS15 for 28 days prior to and throughout a 70-day exposure to sodium fluoride. The drinking water of all groups (F and prob groups) except the control group were replaced by high-fluoride water (100 mg NaF/L) on day 28. Animals in each group were divided into two subsets: one underwent behavioral test, and the other was sacrificed for sampling. The mRNA expression level and protein content related to inflammatory reaction in the ileum and hippocampus were respectively detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA). The mRNA expression levels of proteins related to myelin structure, apoptosis, and memory in the hippocampus and tight junction proteins in the ileum were determined by RT-qPCR and/or immunohistochemistry. Gut permeability markers (D-lactate and diamine oxidase (DAO)) in the serum were also examined by ELISA. Results The results showed that fluoride exposure induced a lower spontaneous exploration (P < 0.05) in T-maze test, which indicated an impairment of memory. Spontaneous exploration of BS15-treated mice was significantly higher (P < 0.05) than that in F group. Fluoride reduced (P < 0.05) levels of myelin structural protein (proteolipid protein) and neurogenesis-associated proteins (brain-derived neurotrophic factor and cAMP/Ca2+ responsive element-binding protein), induced disordered inflammatory cytokines (TNF-α, IFN-γ, and IL-6; P < 0.05), increased pro-apoptotic genes (caspase-3; P < 0.05), and decreased anti-apoptotic genes (Bcl-2; P < 0.05) in th…
bibliographic citation: Xin et al. (2020) Lactobacillus johnsonii BS15 improves intestinal environment against fluoride-induced memory impairment in mice—a study based on the gut–brain axis hypothesis. PeerJ 8:e10125 https://doi.org/10.7717/peerj.10125
date submitted: 2020-03-11
date accepted: 2020-09-17
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xin
  given name: Jinge
author list: Agent
  family name: Zeng
  given name: Dong
author list: Agent
  family name: Wang
  given name: Hesong
author list: Agent
  family name: Sun
  given name: Ning
author list: Agent
  family name: Khalique
  given name: Abdul
author list: Agent
  family name: Zhao
  given name: Ying
author list: Agent
  family name: Wu
  given name: Liqian
author list: Agent
  family name: Pan
  given name: Kangcheng
author list: Agent
  family name: Jing
  given name: Bo
author list: Agent
  family name: Ni
  given name: Xueqin
doi: 10.7717/peerj.10125
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: © 2020 Xin et al.
attribution name: Xin et al.

CKS2 and RMI2 are two prognostic biomarkers of lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Lung adenocarcinoma (ACA) is the most common subtype of non-small-cell lung cancer. About 70%–80% patients are diagnosed at an advanced stage; therefore, the survival rate is poor. It is urgent to discover accurate markers that can differentiate the late stages of lung ACA from the early stages. With the development of biochips, researchers are able to efficiently screen large amounts of biological analytes for multiple purposes. Methods Our team downloaded GSE75037 and GSE32863 from the Gene Expression Omnibus (GEO) database. Next, we utilized GEO’s online tool, GEO2R, to analyze the differentially expressed genes (DEGs) between stage I and stage II–IV lung ACA. The using the Cytoscape software was used to analyze the DEGs and the protein-protein interaction (PPI) network was further constructed. The function of the DEGs were further analyzed by cBioPortal and Gene Expression Profiling Interactive Analysis (GEPIA) online tools. We validated these results in 72 pairs human samples. Results We identified 109 co-DEGs, most of which were involved in either proliferation, S phase of mitotic cell cycle, regulation of exit from mitosis, DNA replication initiation, DNA replication, and chromosome segregation. Utilizing cBioPortal and University of California Santa Cruz databases, we further confirmed 35 hub genes. Two of these genes, encoding CDC28 protein kinase regulatory subunit 2 (CKS2) and RecQ-mediated genome instability 2 (RMI2), were upregulated in lung ACA compared with adjacent normal tissues. The Kaplan–Meier curves revealed upregulation of CKS2 and RMI2 are associated with worse survival. Using CMap analysis, we discovered 10 small molecular compounds that reversed the altered DEGs, the top five are phenoxybenzamine, adiphenine, resveratrol, and trifluoperazine. We also evaluated 72 pairs resected samples, results revealed that upregulation of CKS2 and RMI2 in lung ACA were associated with larger tumor size. Our results allow the deeper recognizing o…
format: application/pdf
format: text/html
creator: Dayong Xiao
creator: Siyuan Dong
creator: Shize Yang
creator: Zhenghua Liu
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Translational Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.10126
publisher: PeerJ Inc.
rights: © 2020 Xiao et al.
abstract: Background Lung adenocarcinoma (ACA) is the most common subtype of non-small-cell lung cancer. About 70%–80% patients are diagnosed at an advanced stage; therefore, the survival rate is poor. It is urgent to discover accurate markers that can differentiate the late stages of lung ACA from the early stages. With the development of biochips, researchers are able to efficiently screen large amounts of biological analytes for multiple purposes. Methods Our team downloaded GSE75037 and GSE32863 from the Gene Expression Omnibus (GEO) database. Next, we utilized GEO’s online tool, GEO2R, to analyze the differentially expressed genes (DEGs) between stage I and stage II–IV lung ACA. The using the Cytoscape software was used to analyze the DEGs and the protein-protein interaction (PPI) network was further constructed. The function of the DEGs were further analyzed by cBioPortal and Gene Expression Profiling Interactive Analysis (GEPIA) online tools. We validated these results in 72 pairs human samples. Results We identified 109 co-DEGs, most of which were involved in either proliferation, S phase of mitotic cell cycle, regulation of exit from mitosis, DNA replication initiation, DNA replication, and chromosome segregation. Utilizing cBioPortal and University of California Santa Cruz databases, we further confirmed 35 hub genes. Two of these genes, encoding CDC28 protein kinase regulatory subunit 2 (CKS2) and RecQ-mediated genome instability 2 (RMI2), were upregulated in lung ACA compared with adjacent normal tissues. The Kaplan–Meier curves revealed upregulation of CKS2 and RMI2 are associated with worse survival. Using CMap analysis, we discovered 10 small molecular compounds that reversed the altered DEGs, the top five are phenoxybenzamine, adiphenine, resveratrol, and trifluoperazine. We also evaluated 72 pairs resected samples, results revealed that upregulation of CKS2 and RMI2 in lung ACA were associated with larger tumor size. Our results allow the deeper recognizing o…
bibliographic citation: Xiao et al. (2020) CKS2 and RMI2 are two prognostic biomarkers of lung adenocarcinoma. PeerJ 8:e10126 https://doi.org/10.7717/peerj.10126
date submitted: 2020-05-21
date accepted: 2020-09-17
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Dayong
author list: Agent
  family name: Dong
  given name: Siyuan
author list: Agent
  family name: Yang
  given name: Shize
author list: Agent
  family name: Liu
  given name: Zhenghua
doi: 10.7717/peerj.10126
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: ©2020 Xiao et al.
attribution name: Xiao et al.

A digital mapping application for quantifying and displaying air temperatures at high spatiotemporal resolutions in near real-time across Australia
type: item
type: AcademicArticle
description: Surface air temperature (Ta) required for real-time environmental modelling applications should be spatially quantified to capture the nuances of local-scale climates. This study created near real-time air temperature maps at a high spatial resolution across Australia. This mapping is achieved using the thin plate spline interpolation in concert with a digital elevation model and ‘live’ recordings garnered from 534 telemetered Australian Bureau of Meteorology automatic weather station (AWS) sites. The interpolation was assessed using cross-validation analysis in a 1-year period using 30-min interval observation. This was then applied to a fully automated mapping system—based in the R programming language—to produce near real-time maps at sub-hourly intervals. The cross-validation analysis revealed broad similarities across the seasons with mean-absolute error ranging from 1.2 °C (autumn and summer) to 1.3 °C (winter and spring), and corresponding root-mean-square error in the range 1.6 °C to 1.7 °C. The R2 and concordance correlation coefficient (Pc ) values were also above 0.8 in each season indicating predictions were strongly correlated to the validation data. On an hourly basis, errors tended to be highest during the late afternoons in spring and summer from 3 pm to 6 pm, particularly for the coastal areas of Western Australia. The mapping system was trialled over a 21-day period from 1 June 2020 to 21 June 2020 with majority of maps completed within 28-min of AWS site observations being recorded. All outputs were displayed in a web mapping application to exemplify a real-time application of the outputs. This study found that the methods employed would be highly suited for similar applications requiring real-time processing and delivery of climate data at high spatiotemporal resolutions across a considerably large land mass.
format: application/pdf
format: text/html
creator: Mathew Webb
creator: Budiman Minasny
subject: Computational Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10106
publisher: PeerJ Inc.
rights: © 2020 Webb and Minasny
abstract: Surface air temperature (Ta) required for real-time environmental modelling applications should be spatially quantified to capture the nuances of local-scale climates. This study created near real-time air temperature maps at a high spatial resolution across Australia. This mapping is achieved using the thin plate spline interpolation in concert with a digital elevation model and ‘live’ recordings garnered from 534 telemetered Australian Bureau of Meteorology automatic weather station (AWS) sites. The interpolation was assessed using cross-validation analysis in a 1-year period using 30-min interval observation. This was then applied to a fully automated mapping system—based in the R programming language—to produce near real-time maps at sub-hourly intervals. The cross-validation analysis revealed broad similarities across the seasons with mean-absolute error ranging from 1.2 °C (autumn and summer) to 1.3 °C (winter and spring), and corresponding root-mean-square error in the range 1.6 °C to 1.7 °C. The R2 and concordance correlation coefficient (Pc ) values were also above 0.8 in each season indicating predictions were strongly correlated to the validation data. On an hourly basis, errors tended to be highest during the late afternoons in spring and summer from 3 pm to 6 pm, particularly for the coastal areas of Western Australia. The mapping system was trialled over a 21-day period from 1 June 2020 to 21 June 2020 with majority of maps completed within 28-min of AWS site observations being recorded. All outputs were displayed in a web mapping application to exemplify a real-time application of the outputs. This study found that the methods employed would be highly suited for similar applications requiring real-time processing and delivery of climate data at high spatiotemporal resolutions across a considerably large land mass.
bibliographic citation: Webb et al. (2020) A digital mapping application for quantifying and displaying air temperatures at high spatiotemporal resolutions in near real-time across Australia. PeerJ 8:e10106 https://doi.org/10.7717/peerj.10106
date submitted: 2020-07-06
date accepted: 2020-09-15
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Webb
  given name: Mathew
author list: Agent
  family name: Minasny
  given name: Budiman
doi: 10.7717/peerj.10106
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: © 2020 Webb and Minasny
attribution name: Webb and Minasny

COVID-19: molecular and serological detection methods
type: item
type: AcademicArticle
description: Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. SARS-CoV-2 is a positive-sense single RNA (+ssRNA) coronavirus and mainly spreads through droplets, respiratory secretions, and direct contact. The early detection of the virus plays a central role in lowering COVID19 incidents and mortality rates. Thus, finding a simple, accurate, cheap and quick detection approach for SARS-CoV-2 at early stage of the viral infection is urgent and at high demand all around the world. The Food and Drug Administration and other health agencies have declared Emergency Use Authorization to develop diagnostic methods for COVID-19 and fulfill the demand. However, not all developed methods are appropriate and selecting a suitable method is challenging. Among all detection methods, rRT-PCR is the gold standard method. Unlike molecular methods, serological methods lack the ability of early detection with low accuracy. In this review, we summarized the current knowledge about COVID-19 detection methods aiming to highlight the advantages and disadvantages of molecular and serological methods.
format: application/pdf
format: text/html
creator: Ahmed E. Dhamad
creator: Muna A. Abdal Rhida
subject: Microbiology
subject: Virology
subject: Epidemiology
subject: Infectious Diseases
subject: Pathology
description: doi:10.7717/peerj.10180
publisher: PeerJ Inc.
rights: © 2020 Dhamad and Abdal Rhida
abstract: Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. SARS-CoV-2 is a positive-sense single RNA (+ssRNA) coronavirus and mainly spreads through droplets, respiratory secretions, and direct contact. The early detection of the virus plays a central role in lowering COVID19 incidents and mortality rates. Thus, finding a simple, accurate, cheap and quick detection approach for SARS-CoV-2 at early stage of the viral infection is urgent and at high demand all around the world. The Food and Drug Administration and other health agencies have declared Emergency Use Authorization to develop diagnostic methods for COVID-19 and fulfill the demand. However, not all developed methods are appropriate and selecting a suitable method is challenging. Among all detection methods, rRT-PCR is the gold standard method. Unlike molecular methods, serological methods lack the ability of early detection with low accuracy. In this review, we summarized the current knowledge about COVID-19 detection methods aiming to highlight the advantages and disadvantages of molecular and serological methods.
bibliographic citation: Dhamad et al. (2020) COVID-19: molecular and serological detection methods. PeerJ 8:e10180 https://doi.org/10.7717/peerj.10180
date submitted: 2020-07-04
date accepted: 2020-09-23
issued: 2020-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dhamad
  given name: Ahmed E.
author list: Agent
  family name: Abdal Rhida
  given name: Muna A.
doi: 10.7717/peerj.10180
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-07
copyright: © 2020 Dhamad and Abdal Rhida
attribution name: Dhamad and Abdal Rhida

The highly rearranged mitochondrial genomes of three economically important scale insects and the mitochondrial phylogeny of Coccoidea (Hemiptera: Sternorrhyncha)
type: item
type: AcademicArticle
description: The mitochondrial genomes (mitogenomes) of scale insects are less known in comparison to other insects, which hinders the phylogenetic and evolutionary studies of Coccoidea and higher taxa. Herein, the complete mitogenomes of Unaspis yanonensis, Planococcus citri and Ceroplastes rubens were sequenced for Coccoidea. The 15,220-bp long mitogenome of U. yanonensis contained the typical set of 37 genes including 13 PCGs, 22 tRNA genes and two rRNA genes; the 15,549-bp long mitogenome of P. citri lacked the tRNA gene trnV; the 15,387-bp long mitogenome of C. rubens exhibited several shortened PCGs and lacked five tRNA genes. The mitochondrial gene arrangement of the three mitogenomes was different from other scale insects and Drosophila yakuba. Most PCGs used standard ATN (ATA, ATT, ATC and ATG) start codons and complete TAN (TAA or TAG) termination codons. The ND4L had the highest evolutionary rate but COX1 and CYTB were the lowest. Most tRNA genes had cloverleaf secondary structures, whereas the reduction of dihydrouridine (DHU) arms and TψC arms were detected. Tandem repeats, stem-loop (SL) structures and poly-[TA]n stretch were found in the control regions (CRs) of the three mitogenomes. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) showed identical results, both supporting the inner relationship of Coccoidea as Coccidae + (Pseudococcidae + Diaspididae).
format: application/pdf
format: text/html
creator: Hong-Ling Liu
creator: Qing-Dong Chen
creator: Song Chen
creator: De-Qiang Pu
creator: Zhi-Teng Chen
creator: Yue-Yue Liu
creator: Xu Liu
subject: Agricultural Science
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Taxonomy
description: doi:10.7717/peerj.9932
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: The mitochondrial genomes (mitogenomes) of scale insects are less known in comparison to other insects, which hinders the phylogenetic and evolutionary studies of Coccoidea and higher taxa. Herein, the complete mitogenomes of Unaspis yanonensis, Planococcus citri and Ceroplastes rubens were sequenced for Coccoidea. The 15,220-bp long mitogenome of U. yanonensis contained the typical set of 37 genes including 13 PCGs, 22 tRNA genes and two rRNA genes; the 15,549-bp long mitogenome of P. citri lacked the tRNA gene trnV; the 15,387-bp long mitogenome of C. rubens exhibited several shortened PCGs and lacked five tRNA genes. The mitochondrial gene arrangement of the three mitogenomes was different from other scale insects and Drosophila yakuba. Most PCGs used standard ATN (ATA, ATT, ATC and ATG) start codons and complete TAN (TAA or TAG) termination codons. The ND4L had the highest evolutionary rate but COX1 and CYTB were the lowest. Most tRNA genes had cloverleaf secondary structures, whereas the reduction of dihydrouridine (DHU) arms and TψC arms were detected. Tandem repeats, stem-loop (SL) structures and poly-[TA]n stretch were found in the control regions (CRs) of the three mitogenomes. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) showed identical results, both supporting the inner relationship of Coccoidea as Coccidae + (Pseudococcidae + Diaspididae).
bibliographic citation: Liu et al. (2020) The highly rearranged mitochondrial genomes of three economically important scale insects and the mitochondrial phylogeny of Coccoidea (Hemiptera: Sternorrhyncha). PeerJ 8:e9932 https://doi.org/10.7717/peerj.9932
date submitted: 2020-07-09
date accepted: 2020-08-22
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hong-Ling
author list: Agent
  family name: Chen
  given name: Qing-Dong
author list: Agent
  family name: Chen
  given name: Song
author list: Agent
  family name: Pu
  given name: De-Qiang
author list: Agent
  family name: Chen
  given name: Zhi-Teng
author list: Agent
  family name: Liu
  given name: Yue-Yue
author list: Agent
  family name: Liu
  given name: Xu
doi: 10.7717/peerj.9932
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Liu et al.
attribution name: Liu et al.

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