PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats
items: Loading history changes the morphology and compressive force-induced expression of receptor activator of nuclear factor kappa B ligand/osteoprotegerin in MLO-Y4 osteocytes
items: MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
items: Effects of substrate and water depth of a eutrophic pond on the physiological status of a submerged plant, Vallisneria natans
items: The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species
items: Foraging efficiency, social status and body condition in group-living horses and ponies
items: COVID-19 infection: Disease detection and mobile technology
items: De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis
items: Dependence structure analysis of multisite river inflow data using vine copula-CEEMDAN based hybrid model
items: No conclusive evidence that difficult general knowledge questions cause a “Google Stroop effect”. A replication study

Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats
type: item
type: AcademicArticle
description: Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database.
format: application/pdf
format: text/html
creator: Xuefeng Fu
creator: Bingru Zhao
creator: Kechuan Tian
creator: Yujiang Wu
creator: Langda Suo
creator: Gui Ba
creator: Deji Ciren
creator: Ji De
creator: Cuoji Awang
creator: Shuangbao Gun
creator: Bohui Yang
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10217
publisher: PeerJ Inc.
rights: © 2020 Fu et al.
abstract: Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database.
bibliographic citation: Fu et al. (2020) Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats. PeerJ 8:e10217 https://doi.org/10.7717/peerj.10217
date submitted: 2020-07-16
date accepted: 2020-09-29
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Fu
  given name: Xuefeng
author list: Agent
  family name: Zhao
  given name: Bingru
author list: Agent
  family name: Tian
  given name: Kechuan
author list: Agent
  family name: Wu
  given name: Yujiang
author list: Agent
  family name: Suo
  given name: Langda
author list: Agent
  family name: Ba
  given name: Gui
author list: Agent
  family name: Ciren
  given name: Deji
author list: Agent
  family name: De
  given name: Ji
author list: Agent
  family name: Awang
  given name: Cuoji
author list: Agent
  family name: Gun
  given name: Shuangbao
author list: Agent
  family name: Yang
  given name: Bohui
doi: 10.7717/peerj.10217
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: ©2020 Fu et al.
attribution name: Fu et al.

Loading history changes the morphology and compressive force-induced expression of receptor activator of nuclear factor kappa B ligand/osteoprotegerin in MLO-Y4 osteocytes
type: item
type: AcademicArticle
description: Background In this study, we investigated the effect of the mechanical loading history on the expression of receptor activator of nuclear factor kappa B ligand (RANKL) and osteoprotegerin (OPG) in MLO-Y4 osteocyte-like cells. Methods Three hours after MLO-Y4 osteocytes were seeded, a continuous compressive force (CCF) of 31 dynes/cm2 with or without additional CCF (32 dynes/cm2) was loaded onto the osteocytes. After 36 h, the additional CCF (loading history) was removed for a recovery period of 10 h. The expression of RANKL, OPG, RANKL/OPG ratio, cell numbers, viability and morphology were time-dependently examined at 0, 3, 6 and 10 h. Then, the same additional CCF was applied again for 1 h to all osteocytes with or without the gap junction inhibitor to examine the expression of RANKL, OPG, the RANKL/OPG ratio and other genes that essential to characterize the phenotype of MLO-Y4 cells. Fluorescence recovery after photobleaching technique was also applied to test the differences of gap-junctional intercellular communications (GJIC) among MLO-Y4 cells. Results The expression of RANKL and OPG by MLO-Y4 osteocytes without a loading history was dramatically decreased and increased, respectively, in response to the 1-h loading of additional weight. However, the expression of RANKL, OPG and the RANKL/OPG ratio were maintained at the same level as in the control group in the MLO-Y4 osteocytes with a loading history but without gap junction inhibitor treatment. Treatment of loading history significantly changed the capacity of GJIC and protein expression of connexin 43 (Cx43) but not the mRNA expression of Cx43. No significant difference was observed in the cell number or viability between the MLO-Y4 osteocyte-like cells with and without a loading history or among different time checkpoints during the recovery period. The cell morphology showed significant changes and was correlated with the expression of OPG, Gja1 and Dmp1 during the recovery period. Conclusion Our finding…
format: application/pdf
format: text/html
creator: Ziyi Wang
creator: Yao Weng
creator: Yoshihito Ishihara
creator: Naoya Odagaki
creator: Ei Ei Hsu Hlaing
creator: Takashi Izawa
creator: Hirohiko Okamura
creator: Hiroshi Kamioka
subject: Biophysics
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.10244
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background In this study, we investigated the effect of the mechanical loading history on the expression of receptor activator of nuclear factor kappa B ligand (RANKL) and osteoprotegerin (OPG) in MLO-Y4 osteocyte-like cells. Methods Three hours after MLO-Y4 osteocytes were seeded, a continuous compressive force (CCF) of 31 dynes/cm2 with or without additional CCF (32 dynes/cm2) was loaded onto the osteocytes. After 36 h, the additional CCF (loading history) was removed for a recovery period of 10 h. The expression of RANKL, OPG, RANKL/OPG ratio, cell numbers, viability and morphology were time-dependently examined at 0, 3, 6 and 10 h. Then, the same additional CCF was applied again for 1 h to all osteocytes with or without the gap junction inhibitor to examine the expression of RANKL, OPG, the RANKL/OPG ratio and other genes that essential to characterize the phenotype of MLO-Y4 cells. Fluorescence recovery after photobleaching technique was also applied to test the differences of gap-junctional intercellular communications (GJIC) among MLO-Y4 cells. Results The expression of RANKL and OPG by MLO-Y4 osteocytes without a loading history was dramatically decreased and increased, respectively, in response to the 1-h loading of additional weight. However, the expression of RANKL, OPG and the RANKL/OPG ratio were maintained at the same level as in the control group in the MLO-Y4 osteocytes with a loading history but without gap junction inhibitor treatment. Treatment of loading history significantly changed the capacity of GJIC and protein expression of connexin 43 (Cx43) but not the mRNA expression of Cx43. No significant difference was observed in the cell number or viability between the MLO-Y4 osteocyte-like cells with and without a loading history or among different time checkpoints during the recovery period. The cell morphology showed significant changes and was correlated with the expression of OPG, Gja1 and Dmp1 during the recovery period. Conclusion Our finding…
bibliographic citation: Wang et al. (2020) Loading history changes the morphology and compressive force-induced expression of receptor activator of nuclear factor kappa B ligand/osteoprotegerin in MLO-Y4 osteocytes. PeerJ 8:e10244 https://doi.org/10.7717/peerj.10244
date submitted: 2020-05-12
date accepted: 2020-10-05
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Ziyi
author list: Agent
  family name: Weng
  given name: Yao
author list: Agent
  family name: Ishihara
  given name: Yoshihito
author list: Agent
  family name: Odagaki
  given name: Naoya
author list: Agent
  family name: Ei Hsu Hlaing
  given name: Ei
author list: Agent
  family name: Izawa
  given name: Takashi
author list: Agent
  family name: Okamura
  given name: Hirohiko
author list: Agent
  family name: Kamioka
  given name: Hiroshi
doi: 10.7717/peerj.10244
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: © 2020 Wang et al.
attribution name: Wang et al.

MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
type: item
type: AcademicArticle
description: The rapid assignment of genotypes to phenotypes has been a historically challenging process. The discovery of genes encoding biosynthetic pathway enzymes for defined plant specialized metabolites has been informed and accelerated by the detection of gene clusters. Unfortunately, biosynthetic pathway genes are commonly dispersed across chromosomes or reside in genes clusters that provide little predictive value. More reliably, transcript abundance of genes underlying biochemical pathways for plant specialized metabolites display significant coregulation. By rapidly identifying highly coexpressed transcripts, it is possible to efficiently narrow candidate genes encoding pathway enzymes and more easily predict both functions and functional associations. Mutual Rank (MR)-based coexpression analyses in plants accurately demonstrate functional associations for many specialized metabolic pathways; however, despite the clear predictive value of MR analyses, the application is uncommonly used to drive new pathway discoveries. Moreover, many coexpression databases aid in the prediction of both functional associations and gene functions, but lack customizability for refined hypothesis testing. To facilitate and speed flexible MR-based hypothesis testing, we developed MutRank, an R Shiny web-application for coexpression analyses. MutRank provides an intuitive graphical user interface with multiple customizable features that integrates user-provided data and supporting information suitable for personal computers. Tabular and graphical outputs facilitate the rapid analyses of both unbiased and user-defined coexpression results that accelerate gene function predictions. We highlight the recent utility of MR analyses for functional predictions and discoveries in defining two maize terpenoid antibiotic pathways. Beyond applications in biosynthetic pathway discovery, MutRank provides a simple, customizable and user-friendly interface to enable coexpression analyses relating to a brea…
format: application/pdf
format: text/html
creator: Elly Poretsky
creator: Alisa Huffaker
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10264
publisher: PeerJ Inc.
rights: © 2020 Poretsky and Huffaker
abstract: The rapid assignment of genotypes to phenotypes has been a historically challenging process. The discovery of genes encoding biosynthetic pathway enzymes for defined plant specialized metabolites has been informed and accelerated by the detection of gene clusters. Unfortunately, biosynthetic pathway genes are commonly dispersed across chromosomes or reside in genes clusters that provide little predictive value. More reliably, transcript abundance of genes underlying biochemical pathways for plant specialized metabolites display significant coregulation. By rapidly identifying highly coexpressed transcripts, it is possible to efficiently narrow candidate genes encoding pathway enzymes and more easily predict both functions and functional associations. Mutual Rank (MR)-based coexpression analyses in plants accurately demonstrate functional associations for many specialized metabolic pathways; however, despite the clear predictive value of MR analyses, the application is uncommonly used to drive new pathway discoveries. Moreover, many coexpression databases aid in the prediction of both functional associations and gene functions, but lack customizability for refined hypothesis testing. To facilitate and speed flexible MR-based hypothesis testing, we developed MutRank, an R Shiny web-application for coexpression analyses. MutRank provides an intuitive graphical user interface with multiple customizable features that integrates user-provided data and supporting information suitable for personal computers. Tabular and graphical outputs facilitate the rapid analyses of both unbiased and user-defined coexpression results that accelerate gene function predictions. We highlight the recent utility of MR analyses for functional predictions and discoveries in defining two maize terpenoid antibiotic pathways. Beyond applications in biosynthetic pathway discovery, MutRank provides a simple, customizable and user-friendly interface to enable coexpression analyses relating to a brea…
bibliographic citation: Poretsky et al. (2020) MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information. PeerJ 8:e10264 https://doi.org/10.7717/peerj.10264
date submitted: 2020-08-25
date accepted: 2020-10-07
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Poretsky
  given name: Elly
author list: Agent
  family name: Huffaker
  given name: Alisa
doi: 10.7717/peerj.10264
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: © 2020 Poretsky and Huffaker
attribution name: Poretsky and Huffaker

Effects of substrate and water depth of a eutrophic pond on the physiological status of a submerged plant, Vallisneria natans
type: item
type: AcademicArticle
description: Effects of substrate and water depth on the physiological status of a submerged macrophyte, Vallisneria natans (Lour.) H. Hara, were determined by measuring biomarkers in leaves and roots, to understand factors limiting the re-establishment of V. natans in urban eutrophic ponds. Ramets of V. natans were grown in the laboratory using aquaria containing water and bottom mud from a eutrophic pond and maintained under sufficient light in an incubator. The growth and chlorophyll-a (Chl-a) content of leaves were greater in aquaria with mud than in those with sand, which was used as the reference substrate. The contents of a peroxidation product (malondialdehyde (MDA)) and three antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD)) in leaves and roots, used as stress biomarkers, changed during the experiment, although differences in these contents between mud and sand were not consistent across the experimental days. To control water depth in the field, ramets of V. natans were grown in cages with different substrates (mud and sand) installed at different depths (0.5, 1.2, and 2.0 m) in the pond. The mean light quantum during the experiment decreased with increasing depth, from 79.3 μmol/m2 s at 0.5 m to 7.9 μmol/m2 s at 2.0 m. The Chl-a content in leaves decreased, whereas the MDA content in both leaves and roots increased with increasing water depth. All enzyme activities increased at the beginning and then decreased to the end of the experiment at 2.0 m depth, suggesting deterioration of enzyme activities due to depth-related stress. The MDA content and CAT activity were higher for sand than for mud, whereas the difference in the growth and the leaf Chl-a content between substrates remained unclear in the pond. On comparing the laboratory and field experiments, the leaf Chl-a content was found to be lower and the MDA content and enzyme activities exhibited sharp increase for ramets grown in the pond, even at 0.5 m depth, when compared wi…
format: application/pdf
format: text/html
creator: Aimin Hao
creator: Sohei Kobayashi
creator: Huilin Huang
creator: Qi Mi
creator: Yasushi Iseri
subject: Ecosystem Science
subject: Plant Science
subject: Freshwater Biology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.10273
publisher: PeerJ Inc.
rights: © 2020 Hao et al.
abstract: Effects of substrate and water depth on the physiological status of a submerged macrophyte, Vallisneria natans (Lour.) H. Hara, were determined by measuring biomarkers in leaves and roots, to understand factors limiting the re-establishment of V. natans in urban eutrophic ponds. Ramets of V. natans were grown in the laboratory using aquaria containing water and bottom mud from a eutrophic pond and maintained under sufficient light in an incubator. The growth and chlorophyll-a (Chl-a) content of leaves were greater in aquaria with mud than in those with sand, which was used as the reference substrate. The contents of a peroxidation product (malondialdehyde (MDA)) and three antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD)) in leaves and roots, used as stress biomarkers, changed during the experiment, although differences in these contents between mud and sand were not consistent across the experimental days. To control water depth in the field, ramets of V. natans were grown in cages with different substrates (mud and sand) installed at different depths (0.5, 1.2, and 2.0 m) in the pond. The mean light quantum during the experiment decreased with increasing depth, from 79.3 μmol/m2 s at 0.5 m to 7.9 μmol/m2 s at 2.0 m. The Chl-a content in leaves decreased, whereas the MDA content in both leaves and roots increased with increasing water depth. All enzyme activities increased at the beginning and then decreased to the end of the experiment at 2.0 m depth, suggesting deterioration of enzyme activities due to depth-related stress. The MDA content and CAT activity were higher for sand than for mud, whereas the difference in the growth and the leaf Chl-a content between substrates remained unclear in the pond. On comparing the laboratory and field experiments, the leaf Chl-a content was found to be lower and the MDA content and enzyme activities exhibited sharp increase for ramets grown in the pond, even at 0.5 m depth, when compared wi…
bibliographic citation: Hao et al. (2020) Effects of substrate and water depth of a eutrophic pond on the physiological status of a submerged plant, Vallisneria natans. PeerJ 8:e10273 https://doi.org/10.7717/peerj.10273
date submitted: 2020-05-06
date accepted: 2020-10-08
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Aimin
author list: Agent
  family name: Kobayashi
  given name: Sohei
author list: Agent
  family name: Huang
  given name: Huilin
author list: Agent
  family name: Mi
  given name: Qi
author list: Agent
  family name: Iseri
  given name: Yasushi
doi: 10.7717/peerj.10273
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: © 2020 Hao et al.
attribution name: Hao et al.

The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species
type: item
type: AcademicArticle
description: Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.
format: application/pdf
format: text/html
creator: Mirella Pupo Santos
creator: João V.S. Rabelo Araujo
creator: Arthur V. Sant’anna Lopes
creator: Julio Cesar Fiorio Vettorazzi
creator: Marcela Santana Bastos Boechat
creator: Fernanda AbreuSantana Arêdes
creator: Naiara Viana Campos
creator: Emiliano Nicolas Calderon
creator: Fernando M. Gomes Santos
creator: Tais Nogueira Fernandes
creator: Rodrigo Nunes da Fonseca
creator: Messias Gonzaga Pereira
creator: Guilherme Oliveira
creator: Daniel Basilio Zandonadi
creator: RodrigoLemes Martins
creator: Francisco de Assis Esteves
subject: Conservation Biology
subject: Genetics
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.10274
publisher: PeerJ Inc.
rights: © 2020 Santos et al.
abstract: Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.
bibliographic citation: Santos et al. (2020) The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species. PeerJ 8:e10274 https://doi.org/10.7717/peerj.10274
date submitted: 2020-05-13
date accepted: 2020-10-08
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos
  given name: Mirella Pupo
author list: Agent
  family name: Araujo
  given name: João V.S. Rabelo
author list: Agent
  family name: Lopes
  given name: Arthur V. Sant’anna
author list: Agent
  family name: Vettorazzi
  given name: Julio Cesar Fiorio
author list: Agent
  family name: Boechat
  given name: Marcela Santana Bastos
author list: Agent
  family name: Arêdes
  given name: Fernanda AbreuSantana
author list: Agent
  family name: Campos
  given name: Naiara Viana
author list: Agent
  family name: Calderon
  given name: Emiliano Nicolas
author list: Agent
  family name: Santos
  given name: Fernando M. Gomes
author list: Agent
  family name: Fernandes
  given name: Tais Nogueira
author list: Agent
  family name: da Fonseca
  given name: Rodrigo Nunes
author list: Agent
  family name: Pereira
  given name: Messias Gonzaga
author list: Agent
  family name: Oliveira
  given name: Guilherme
author list: Agent
  family name: Zandonadi
  given name: Daniel Basilio
author list: Agent
  family name: Martins
  given name: RodrigoLemes
author list: Agent
  family name: Esteves
  given name: Francisco de Assis
doi: 10.7717/peerj.10274
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: ©2020 Santos et al.
attribution name: Santos et al.

Foraging efficiency, social status and body condition in group-living horses and ponies
type: item
type: AcademicArticle
description: Individual animals experience different costs and benefits associated with group living, which may impact on their foraging efficiency in ways not yet well specified. This study investigated associations between social dominance, body condition and interruptions to foraging behaviour in a cross-sectional study of 116 domestic horses and ponies, kept in 20 discrete herds. Social dominance was measured for each individual alongside observations of winter foraging behaviour. During bouts of foraging, the duration, frequency and category (vigilance, movement, social displacements given and received, scratching and startle responses) of interruptions were recorded, with total interruption time taken as a proxy measure of foraging efficiency. Total foraging time was not influenced by body condition or social dominance. Body condition was associated with social dominance, but more strongly associated with foraging efficiency. Specifically, lower body condition was associated with greater vigilance. This demonstrates that factors other than social dominance can result in stable differences in winter body condition.
format: application/pdf
format: text/html
creator: Sarah L. Giles
creator: Pat Harris
creator: Sean A. Rands
creator: Christine J. Nicol
subject: Animal Behavior
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.10305
publisher: PeerJ Inc.
rights: © 2020 Giles et al.
abstract: Individual animals experience different costs and benefits associated with group living, which may impact on their foraging efficiency in ways not yet well specified. This study investigated associations between social dominance, body condition and interruptions to foraging behaviour in a cross-sectional study of 116 domestic horses and ponies, kept in 20 discrete herds. Social dominance was measured for each individual alongside observations of winter foraging behaviour. During bouts of foraging, the duration, frequency and category (vigilance, movement, social displacements given and received, scratching and startle responses) of interruptions were recorded, with total interruption time taken as a proxy measure of foraging efficiency. Total foraging time was not influenced by body condition or social dominance. Body condition was associated with social dominance, but more strongly associated with foraging efficiency. Specifically, lower body condition was associated with greater vigilance. This demonstrates that factors other than social dominance can result in stable differences in winter body condition.
bibliographic citation: Giles et al. (2020) Foraging efficiency, social status and body condition in group-living horses and ponies. PeerJ 8:e10305 https://doi.org/10.7717/peerj.10305
date submitted: 2020-02-25
date accepted: 2020-10-15
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giles
  given name: Sarah L.
author list: Agent
  family name: Harris
  given name: Pat
author list: Agent
  family name: Rands
  given name: Sean A.
author list: Agent
  family name: Nicol
  given name: Christine J.
doi: 10.7717/peerj.10305
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: © 2020 Giles et al.
attribution name: Giles et al.

COVID-19 infection: Disease detection and mobile technology
type: item
type: AcademicArticle
description: Background A pneumonia outbreak of unknown etiology took place in Wuhan, Hubei province, China and spread quickly worldwide in December 2019. Chinese Center for Disease Control and Prevention identified a novel beta-coronavirus called 2019-nCoV, now officially known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) that is responsible for the pandemic. The coronavirus COVID-19 affected 215 countries and territories around the world and more than 99 hundred thousand people at present (Nature Nanotechnology, 2020). At present, there are no specific vaccines or treatments available for COVID-19. However, there are many ongoing clinical trials evaluating potential treatments. At this time the experts recommend precautions such as social distancing, hand washing, and wearing face masks to reduce disease transmission. This review article aims to improve the readers’ awareness towards the important role of mobile technology for SARS-CoV-2. Methodology To achieve this objective, we performed a COVID-19 literature review from various sources that include data from the published articles as well as World Health Organization reports on coronavirus disease and how mobile technology is useful to fight against this disease. Results Mobile technology can be helpful in mapping disease spread and provides an easy way to provide awareness that promotes safety and adoption of necessary precautions to mitigate and stop community transmission. Conclusion The spread rate of COVID-19 is very high and until now no vaccines are available to control this disease. To this end we should leverage other avenues such as digital technologies to protect ourselves from this disease. Mobile technology such as smartphones are playing an important role in this pandemic, by launching apps to track coronavirus infected people. These apps are very easy to use and provide self-isolation guidelines as well as other safety tips.
format: application/pdf
format: text/html
creator: Jaya Verma
creator: Amar Shankar Mishra
subject: Global Health
subject: Infectious Diseases
subject: Public Health
subject: Respiratory Medicine
subject: Science and Medical Education
description: doi:10.7717/peerj.10345
publisher: PeerJ Inc.
rights: © 2020 Verma and Mishra
abstract: Background A pneumonia outbreak of unknown etiology took place in Wuhan, Hubei province, China and spread quickly worldwide in December 2019. Chinese Center for Disease Control and Prevention identified a novel beta-coronavirus called 2019-nCoV, now officially known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) that is responsible for the pandemic. The coronavirus COVID-19 affected 215 countries and territories around the world and more than 99 hundred thousand people at present (Nature Nanotechnology, 2020). At present, there are no specific vaccines or treatments available for COVID-19. However, there are many ongoing clinical trials evaluating potential treatments. At this time the experts recommend precautions such as social distancing, hand washing, and wearing face masks to reduce disease transmission. This review article aims to improve the readers’ awareness towards the important role of mobile technology for SARS-CoV-2. Methodology To achieve this objective, we performed a COVID-19 literature review from various sources that include data from the published articles as well as World Health Organization reports on coronavirus disease and how mobile technology is useful to fight against this disease. Results Mobile technology can be helpful in mapping disease spread and provides an easy way to provide awareness that promotes safety and adoption of necessary precautions to mitigate and stop community transmission. Conclusion The spread rate of COVID-19 is very high and until now no vaccines are available to control this disease. To this end we should leverage other avenues such as digital technologies to protect ourselves from this disease. Mobile technology such as smartphones are playing an important role in this pandemic, by launching apps to track coronavirus infected people. These apps are very easy to use and provide self-isolation guidelines as well as other safety tips.
bibliographic citation: Verma et al. (2020) COVID-19 infection: Disease detection and mobile technology. PeerJ 8:e10345 https://doi.org/10.7717/peerj.10345
date submitted: 2020-05-25
date accepted: 2020-10-20
issued: 2020-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Verma
  given name: Jaya
author list: Agent
  family name: Mishra
  given name: Amar Shankar
doi: 10.7717/peerj.10345
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-09
copyright: © 2020 Verma and Mishra
attribution name: Verma and Mishra

De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis
type: item
type: AcademicArticle
description: Cnidium monnieri (L.) Cuss (C. monnieri) is one of the most widely used traditional herbal medicines, exhibiting a wide range of pharmacological functions for treating asynodia, trichomonas vaginitis, and osphyalgia. Its important medicinal value comes from its abundance of coumarins. To identify genes involved in coumarin biosynthesis and accumulation, we analyzed transcriptome data from flower, leaf, root and stem tissues of C. monnieri. A total of 173,938 unigenes with a mean length of 1,272 bp, GC content of 38.79%, and N50 length of 2,121 bp were assembled using the Trinity program. Of these, 119,177 unigenes were annotated in public databases. We identified differentially expressed genes (DEGs) based on expression profile analysis. These DEGs exhibited higher expression levels in flower tissue than in leaf, stem or root tissues. We identified and analyzed numerous genes encoding enzymes involved in coumarin biosynthesis, and verified genes encoding key enzymes using quantitative real-time PCR. Our transcriptome data will make great contributions to research on C. monnieri and provide clues for identifying candidate genes involved in coumarin metabolic pathways.
format: application/pdf
format: text/html
creator: Yuanyuan Shi
creator: Shengxiang Zhang
creator: Daiyin Peng
creator: Chunmiao Shan
creator: Liqiang Zhao
creator: Bin Wang
creator: Jiawen Wu
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10157
publisher: PeerJ Inc.
rights: © 2020 Shi et al.
abstract: Cnidium monnieri (L.) Cuss (C. monnieri) is one of the most widely used traditional herbal medicines, exhibiting a wide range of pharmacological functions for treating asynodia, trichomonas vaginitis, and osphyalgia. Its important medicinal value comes from its abundance of coumarins. To identify genes involved in coumarin biosynthesis and accumulation, we analyzed transcriptome data from flower, leaf, root and stem tissues of C. monnieri. A total of 173,938 unigenes with a mean length of 1,272 bp, GC content of 38.79%, and N50 length of 2,121 bp were assembled using the Trinity program. Of these, 119,177 unigenes were annotated in public databases. We identified differentially expressed genes (DEGs) based on expression profile analysis. These DEGs exhibited higher expression levels in flower tissue than in leaf, stem or root tissues. We identified and analyzed numerous genes encoding enzymes involved in coumarin biosynthesis, and verified genes encoding key enzymes using quantitative real-time PCR. Our transcriptome data will make great contributions to research on C. monnieri and provide clues for identifying candidate genes involved in coumarin metabolic pathways.
bibliographic citation: Shi et al. (2020) De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis. PeerJ 8:e10157 https://doi.org/10.7717/peerj.10157
date submitted: 2020-01-15
date accepted: 2020-09-21
issued: 2020-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Yuanyuan
author list: Agent
  family name: Zhang
  given name: Shengxiang
author list: Agent
  family name: Peng
  given name: Daiyin
author list: Agent
  family name: Shan
  given name: Chunmiao
author list: Agent
  family name: Zhao
  given name: Liqiang
author list: Agent
  family name: Wang
  given name: Bin
author list: Agent
  family name: Wu
  given name: Jiawen
doi: 10.7717/peerj.10157
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-06
copyright: ©2020 Shi et al.
attribution name: Shi et al.

Dependence structure analysis of multisite river inflow data using vine copula-CEEMDAN based hybrid model
type: item
type: AcademicArticle
description: Several data-driven and hybrid models are univariate and not considered the dependance structure of multivariate random variables, especially the multi-site river inflow data, which requires the joint distribution of the same river basin system. In this paper, we proposed a Complete Ensemble Empirical Mode Decomposition with Adaptive Noise (CEEMDAN) Vine copula-based approach to address this issue. The proposed hybrid model comprised on two stages: In the first stage, the CEEMDAN is used to extract the high dimensional multi-scale features. Further, the multiple models are used to predict multi-scale components and residuals. In the second stage, the residuals obtained from the first stage are used to model the joint uncertainty of multi-site river inflow data by using Canonical Vine. For the application of the proposed two-step architecture, daily river inflow data of the Indus River Basin is used. The proposed two-stage methodology is compared with only the first stage proposed model, Vector Autoregressive and copula-based Autoregressive Integrated Moving Average models. The four evaluation measures, that is, Mean Absolute Relative Error (MARE), Mean Absolute Deviation (MAD), Nash-Sutcliffe Efficiency (NSE) and Mean Square Error (MSE), are used to observe the prediction performance. The results demonstrated that the proposed model outperforms significantly with minimum MARE, MAD, NSE, and MSE for two case studies having significant joint dependance. Therefore, it is concluded that the prediction can be improved by appropriately modeling the dependance structure of the multi-site river inflow data.
format: application/pdf
format: text/html
creator: Hafiza Mamona Nazir
creator: Ijaz Hussain
creator: Muhammad Faisal
creator: Alaa Mohamd Shoukry
creator: Mohammed Abdel Wahab Sharkawy
creator: Fares Fawzi Al-Deek
creator: Muhammad Ismail
subject: Statistics
subject: Computational Science
subject: Natural Resource Management
subject: Ecohydrology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10285
publisher: PeerJ Inc.
rights: © 2020 Nazir et al.
abstract: Several data-driven and hybrid models are univariate and not considered the dependance structure of multivariate random variables, especially the multi-site river inflow data, which requires the joint distribution of the same river basin system. In this paper, we proposed a Complete Ensemble Empirical Mode Decomposition with Adaptive Noise (CEEMDAN) Vine copula-based approach to address this issue. The proposed hybrid model comprised on two stages: In the first stage, the CEEMDAN is used to extract the high dimensional multi-scale features. Further, the multiple models are used to predict multi-scale components and residuals. In the second stage, the residuals obtained from the first stage are used to model the joint uncertainty of multi-site river inflow data by using Canonical Vine. For the application of the proposed two-step architecture, daily river inflow data of the Indus River Basin is used. The proposed two-stage methodology is compared with only the first stage proposed model, Vector Autoregressive and copula-based Autoregressive Integrated Moving Average models. The four evaluation measures, that is, Mean Absolute Relative Error (MARE), Mean Absolute Deviation (MAD), Nash-Sutcliffe Efficiency (NSE) and Mean Square Error (MSE), are used to observe the prediction performance. The results demonstrated that the proposed model outperforms significantly with minimum MARE, MAD, NSE, and MSE for two case studies having significant joint dependance. Therefore, it is concluded that the prediction can be improved by appropriately modeling the dependance structure of the multi-site river inflow data.
bibliographic citation: Nazir et al. (2020) Dependence structure analysis of multisite river inflow data using vine copula-CEEMDAN based hybrid model. PeerJ 8:e10285 https://doi.org/10.7717/peerj.10285
date submitted: 2020-04-06
date accepted: 2020-10-10
issued: 2020-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nazir
  given name: Hafiza Mamona
author list: Agent
  family name: Hussain
  given name: Ijaz
author list: Agent
  family name: Faisal
  given name: Muhammad
author list: Agent
  family name: Mohamd Shoukry
  given name: Alaa
author list: Agent
  family name: Abdel Wahab Sharkawy
  given name: Mohammed
author list: Agent
  family name: Fawzi Al-Deek
  given name: Fares
author list: Agent
  family name: Ismail
  given name: Muhammad
doi: 10.7717/peerj.10285
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-06
copyright: © 2020 Nazir et al.
attribution name: Nazir et al.

No conclusive evidence that difficult general knowledge questions cause a “Google Stroop effect”. A replication study
type: item
type: AcademicArticle
description: Access to the digital “all-knowing cloud” has become an integral part of our daily lives. It has been suggested that the increasing offloading of information and information processing services to the cloud will alter human cognition and metacognition in the short and long term. A much-cited study published in Science in 2011 provided first behavioral evidence for such changes in human cognition. Participants had to answer difficult trivia questions, and subsequently showed longer response times in a variant of the Stroop task with internet-related words (“Google Stroop effect”). The authors of this study concluded that the concept of the Internet is automatically activated in situations where information is missing (e.g., because we might feel the urge to “google” the information). However, the “Google Stroop effect” could not be replicated in two recent replication attempts as part of a large replicability project. After the failed replication was published in 2018, the first author of the original study pointed out some problems with the design of the failed replication. In our study, we therefore aimed to replicate the “Google Stroop effect” with a research design closer to the original experiment. Our results revealed no conclusive evidence in favor of the notion that the concept of the Internet or internet access (via computers or smartphones) is automatically activated when participants are faced with hard trivia questions. We provide recommendations for follow-up research.
format: application/pdf
format: text/html
creator: Guido Hesselmann
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.10325
publisher: PeerJ Inc.
rights: © 2020 Hesselmann
abstract: Access to the digital “all-knowing cloud” has become an integral part of our daily lives. It has been suggested that the increasing offloading of information and information processing services to the cloud will alter human cognition and metacognition in the short and long term. A much-cited study published in Science in 2011 provided first behavioral evidence for such changes in human cognition. Participants had to answer difficult trivia questions, and subsequently showed longer response times in a variant of the Stroop task with internet-related words (“Google Stroop effect”). The authors of this study concluded that the concept of the Internet is automatically activated in situations where information is missing (e.g., because we might feel the urge to “google” the information). However, the “Google Stroop effect” could not be replicated in two recent replication attempts as part of a large replicability project. After the failed replication was published in 2018, the first author of the original study pointed out some problems with the design of the failed replication. In our study, we therefore aimed to replicate the “Google Stroop effect” with a research design closer to the original experiment. Our results revealed no conclusive evidence in favor of the notion that the concept of the Internet or internet access (via computers or smartphones) is automatically activated when participants are faced with hard trivia questions. We provide recommendations for follow-up research.
bibliographic citation: Hesselmann (2020) No conclusive evidence that difficult general knowledge questions cause a “Google Stroop effect”. A replication study. PeerJ 8:e10325 https://doi.org/10.7717/peerj.10325
date submitted: 2020-08-12
date accepted: 2020-10-19
issued: 2020-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hesselmann
  given name: Guido
doi: 10.7717/peerj.10325
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-06
copyright: ©2020 Hesselmann
attribution name: Hesselmann

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