PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: An efficient sorghum protoplast assay for transient gene expression and gene editing by CRISPR/Cas9
items: Integrating multiple microarray dataset analysis and machine learning methods to reveal the key genes and regulatory mechanisms underlying human intervertebral disc degeneration
items: Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study
items: Soil carbon, nitrogen and phosphorus ecological stoichiometry shifts with tree species in subalpine plantations
items: Genetic characterization of feline panleukopenia virus from dogs in Vietnam reveals a unique Thr101 mutation in VP2
items: Physiological aspects and energetic contribution in 20s:10s high-intensity interval exercise at different intensities
items: Genomic signatures of globally enhanced gene duplicate accumulation in the megadiverse higher Diptera fueling intralocus sexual conflict resolution
items: Instrumental validity and intra/inter-rater reliability of a novel low-cost digital pressure algometer
items: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load
items: Convolutional neural network in upper limb functional motion analysis after stroke

An efficient sorghum protoplast assay for transient gene expression and gene editing by CRISPR/Cas9
type: item
type: AcademicArticle
description: Protoplasts are commonly used in genetic and breeding research. In this study, the isolation of sorghum protoplasts was optimized and applied to transient gene expression and editing by CRISPR/Cas9. The protoplast was most viable in 0.5 M mannitol, which was the highest of three concentrations after 48- and 72-hours treatments. Using this method we can derive an average of 1.6×106 cells which vary from 5 to 22 nm in size. The average transfection of the protoplasts was 68.5% using the PEG-mediated method. The subcellular assays located Sobic.002G279100-GFP and GFP proteins in the cell compartments as predicted bioinformatically. Two CRISPR/Cas9 plasmids were transfected into sorghum protoplasts to screen for an appropriate sgRNA for gene editing. One plasmid can correctly edit the target region using a single protoplast cell as template DNA. Our results indicated that the protoplast assays as optimized are suitable for transient gene expression and sgRNA screening in CRISPR/Cas9 gene editing procedures.
format: application/pdf
format: text/html
creator: Ruirui Meng
creator: Chenchen Wang
creator: Lihua Wang
creator: Yanlong Liu
creator: Qiuwen Zhan
creator: Jiacheng Zheng
creator: Jieqin Li
subject: Plant Science
description: doi:10.7717/peerj.10077
publisher: PeerJ Inc.
rights: © 2020 Meng et al.
abstract: Protoplasts are commonly used in genetic and breeding research. In this study, the isolation of sorghum protoplasts was optimized and applied to transient gene expression and editing by CRISPR/Cas9. The protoplast was most viable in 0.5 M mannitol, which was the highest of three concentrations after 48- and 72-hours treatments. Using this method we can derive an average of 1.6×106 cells which vary from 5 to 22 nm in size. The average transfection of the protoplasts was 68.5% using the PEG-mediated method. The subcellular assays located Sobic.002G279100-GFP and GFP proteins in the cell compartments as predicted bioinformatically. Two CRISPR/Cas9 plasmids were transfected into sorghum protoplasts to screen for an appropriate sgRNA for gene editing. One plasmid can correctly edit the target region using a single protoplast cell as template DNA. Our results indicated that the protoplast assays as optimized are suitable for transient gene expression and sgRNA screening in CRISPR/Cas9 gene editing procedures.
bibliographic citation: Meng et al. (2020) An efficient sorghum protoplast assay for transient gene expression and gene editing by CRISPR/Cas9. PeerJ 8:e10077 https://doi.org/10.7717/peerj.10077
date submitted: 2019-02-07
date accepted: 2020-09-10
issued: 2020-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Ruirui
author list: Agent
  family name: Wang
  given name: Chenchen
author list: Agent
  family name: Wang
  given name: Lihua
author list: Agent
  family name: Liu
  given name: Yanlong
author list: Agent
  family name: Zhan
  given name: Qiuwen
author list: Agent
  family name: Zheng
  given name: Jiacheng
author list: Agent
  family name: Li
  given name: Jieqin
doi: 10.7717/peerj.10077
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-13
copyright: ©2020 Meng et al.
attribution name: Meng et al.

Integrating multiple microarray dataset analysis and machine learning methods to reveal the key genes and regulatory mechanisms underlying human intervertebral disc degeneration
type: item
type: AcademicArticle
description: Intervertebral disc degeneration (IDD), a major cause of lower back pain, has multiple contributing factors including genetics, environment, age, and loading history. Bioinformatics analysis has been extensively used to identify diagnostic biomarkers and therapeutic targets for IDD diagnosis and treatment. However, multiple microarray dataset analysis and machine learning methods have not been integrated. In this study, we downloaded the mRNA, microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA) expression profiles (GSE34095, GSE15227, GSE63492 GSE116726, GSE56081 and GSE67566) associated with IDD from the GEO database. Using differential expression analysis and recursive feature elimination, we extracted four optimal feature genes. We then used the support vector machine (SVM) to make a classification model with the four optimal feature genes. The ROC curve was used to evaluate the model’s performance, and the expression profiles (GSE63492, GSE116726, GSE56081, and GSE67566) were used to construct a competitive endogenous RNA (ceRNA) regulatory network and explore the underlying mechanisms of the feature genes. We found that three miRNAs (hsa-miR-4728-5p, hsa-miR-5196-5p, and hsa-miR-185-5p) and three circRNAs (hsa_circRNA_100723, hsa_circRNA_104471, and hsa_circRNA_100750) were important regulators with more interactions than the other RNAs across the whole network. The expression level analysis of the three datasets revealed that BCAS4 and SCRG1 were key genes involved in IDD development. Ultimately, our study proposes a novel approach to determining reliable and effective targets in IDD diagnosis and treatment.
format: application/pdf
format: text/html
creator: Hongze Chang
creator: Xiaolong Yang
creator: Kemin You
creator: Mingwei Jiang
creator: Feng Cai
creator: Yan Zhang
creator: Liang Liu
creator: Hui Liu
creator: Xiaodong Liu
subject: Bioinformatics
subject: Genomics
subject: Orthopedics
subject: Medical Genetics
description: doi:10.7717/peerj.10120
publisher: PeerJ Inc.
rights: © 2020 Chang et al.
abstract: Intervertebral disc degeneration (IDD), a major cause of lower back pain, has multiple contributing factors including genetics, environment, age, and loading history. Bioinformatics analysis has been extensively used to identify diagnostic biomarkers and therapeutic targets for IDD diagnosis and treatment. However, multiple microarray dataset analysis and machine learning methods have not been integrated. In this study, we downloaded the mRNA, microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA) expression profiles (GSE34095, GSE15227, GSE63492 GSE116726, GSE56081 and GSE67566) associated with IDD from the GEO database. Using differential expression analysis and recursive feature elimination, we extracted four optimal feature genes. We then used the support vector machine (SVM) to make a classification model with the four optimal feature genes. The ROC curve was used to evaluate the model’s performance, and the expression profiles (GSE63492, GSE116726, GSE56081, and GSE67566) were used to construct a competitive endogenous RNA (ceRNA) regulatory network and explore the underlying mechanisms of the feature genes. We found that three miRNAs (hsa-miR-4728-5p, hsa-miR-5196-5p, and hsa-miR-185-5p) and three circRNAs (hsa_circRNA_100723, hsa_circRNA_104471, and hsa_circRNA_100750) were important regulators with more interactions than the other RNAs across the whole network. The expression level analysis of the three datasets revealed that BCAS4 and SCRG1 were key genes involved in IDD development. Ultimately, our study proposes a novel approach to determining reliable and effective targets in IDD diagnosis and treatment.
bibliographic citation: Chang et al. (2020) Integrating multiple microarray dataset analysis and machine learning methods to reveal the key genes and regulatory mechanisms underlying human intervertebral disc degeneration. PeerJ 8:e10120 https://doi.org/10.7717/peerj.10120
date submitted: 2020-05-13
date accepted: 2020-09-16
issued: 2020-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Hongze
author list: Agent
  family name: Yang
  given name: Xiaolong
author list: Agent
  family name: You
  given name: Kemin
author list: Agent
  family name: Jiang
  given name: Mingwei
author list: Agent
  family name: Cai
  given name: Feng
author list: Agent
  family name: Zhang
  given name: Yan
author list: Agent
  family name: Liu
  given name: Liang
author list: Agent
  family name: Liu
  given name: Hui
author list: Agent
  family name: Liu
  given name: Xiaodong
doi: 10.7717/peerj.10120
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-13
copyright: ©2020 Chang et al.
attribution name: Chang et al.

Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study
type: item
type: AcademicArticle
description: As the world’s economies come out of the lockdown imposed by the COVID-19 pandemic, there is an urgent need for technologies to mitigate COVID-19 transmission in confined spaces such as buildings. This feasibility study looks at one such technology, upper-room ultraviolet (UV) air disinfection, that can be safely used while humans are present in the room space, and which has already proven its efficacy as an intervention to inhibit the transmission of airborne diseases such as measles and tuberculosis. Using published data from various sources, it is shown that the SARS-CoV-2 virus, the causative agent of COVID-19, is highly likely to be susceptible to UV-C damage when suspended in air, with a UV susceptibility constant likely to be in the region 0.377–0.590 m2/J, similar to that for other aerosolised coronaviruses. As such, the UV-C flux required to disinfect the virus is expected to be acceptable and safe for upper-room applications. Through analysis of expected and worst-case scenarios, the efficacy of the upper-room UV-C approach for reducing COVID-19 transmission in confined spaces (with moderate but sufficient ceiling height) is demonstrated. Furthermore, it is shown that with SARS-CoV-2, it should be possible to achieve high equivalent air change rates using upper-room UV air disinfection, suggesting that the technology might be particularly applicable to poorly ventilated spaces.
format: application/pdf
format: text/html
creator: Clive B. Beggs
creator: Eldad J. Avital
subject: Microbiology
subject: Virology
subject: Infectious Diseases
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.10196
publisher: PeerJ Inc.
rights: © 2020 Beggs and Avital
abstract: As the world’s economies come out of the lockdown imposed by the COVID-19 pandemic, there is an urgent need for technologies to mitigate COVID-19 transmission in confined spaces such as buildings. This feasibility study looks at one such technology, upper-room ultraviolet (UV) air disinfection, that can be safely used while humans are present in the room space, and which has already proven its efficacy as an intervention to inhibit the transmission of airborne diseases such as measles and tuberculosis. Using published data from various sources, it is shown that the SARS-CoV-2 virus, the causative agent of COVID-19, is highly likely to be susceptible to UV-C damage when suspended in air, with a UV susceptibility constant likely to be in the region 0.377–0.590 m2/J, similar to that for other aerosolised coronaviruses. As such, the UV-C flux required to disinfect the virus is expected to be acceptable and safe for upper-room applications. Through analysis of expected and worst-case scenarios, the efficacy of the upper-room UV-C approach for reducing COVID-19 transmission in confined spaces (with moderate but sufficient ceiling height) is demonstrated. Furthermore, it is shown that with SARS-CoV-2, it should be possible to achieve high equivalent air change rates using upper-room UV air disinfection, suggesting that the technology might be particularly applicable to poorly ventilated spaces.
bibliographic citation: Beggs et al. (2020) Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study. PeerJ 8:e10196 https://doi.org/10.7717/peerj.10196
date submitted: 2020-07-15
date accepted: 2020-09-25
issued: 2020-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beggs
  given name: Clive B.
author list: Agent
  family name: Avital
  given name: Eldad J.
doi: 10.7717/peerj.10196
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-13
copyright: © 2020 Beggs and Avital
attribution name: Beggs and Avital

Soil carbon, nitrogen and phosphorus ecological stoichiometry shifts with tree species in subalpine plantations
type: item
type: AcademicArticle
description: Understanding ecological stoichiometric characteristics of soil nutrient elements, such as carbon (C), nitrogen (N) and phosphorus (P) is crucial to guide ecological restoration of plantations in ecologically vulnerable areas, such as alpine and subalpine regions. However, there has been only a few related studies, and thus whether and how different tree species would affect soil C:N:P ecological stoichiometry remains unclear. We compared soil C:N:P ecological stoichiometry of Pinus tabulaeformis, Larix kaempferi and Cercidiphyllum japonicum to primary shrubland in a subalpine region. We observed strong tree-specific and depth-dependent effects on soil C:N:P stoichiometry in subalpine plantations. In general, the C:N, C:P and N:P of topsoil (0–10 cm) are higher than subsoil (>10 cm) layer at 0–30 cm depth profiles. The differences in C:N, N:P and C:P at the topsoil across target tree species were significantly linked to standing litter stock, tree biomass/total aboveground biomass and Margalef’s index of plant community, respectively, whereas the observed variations of C:N, N:P and C:P ratio among soil profiles are closely related to differences in soil bulk density, soil moisture, the quantity and quality of aboveground litter inputs as well as underground fine root across plantations examined. Our results highlight that soil nutrients in plantation depend on litter quantity and quality of selected tree species as well as soil physical attributes. Therefore, matching site with trees is crucial to enhance ecological functioning in degraded regions resulting from human activity.
format: application/pdf
format: text/html
creator: Kaibin Qi
creator: Xueyong Pang
creator: Bing Yang
creator: Weikai Bao
subject: Ecology
subject: Plant Science
subject: Climate Change Biology
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.9702
publisher: PeerJ Inc.
rights: © 2020 Qi et al.
abstract: Understanding ecological stoichiometric characteristics of soil nutrient elements, such as carbon (C), nitrogen (N) and phosphorus (P) is crucial to guide ecological restoration of plantations in ecologically vulnerable areas, such as alpine and subalpine regions. However, there has been only a few related studies, and thus whether and how different tree species would affect soil C:N:P ecological stoichiometry remains unclear. We compared soil C:N:P ecological stoichiometry of Pinus tabulaeformis, Larix kaempferi and Cercidiphyllum japonicum to primary shrubland in a subalpine region. We observed strong tree-specific and depth-dependent effects on soil C:N:P stoichiometry in subalpine plantations. In general, the C:N, C:P and N:P of topsoil (0–10 cm) are higher than subsoil (>10 cm) layer at 0–30 cm depth profiles. The differences in C:N, N:P and C:P at the topsoil across target tree species were significantly linked to standing litter stock, tree biomass/total aboveground biomass and Margalef’s index of plant community, respectively, whereas the observed variations of C:N, N:P and C:P ratio among soil profiles are closely related to differences in soil bulk density, soil moisture, the quantity and quality of aboveground litter inputs as well as underground fine root across plantations examined. Our results highlight that soil nutrients in plantation depend on litter quantity and quality of selected tree species as well as soil physical attributes. Therefore, matching site with trees is crucial to enhance ecological functioning in degraded regions resulting from human activity.
bibliographic citation: Qi et al. (2020) Soil carbon, nitrogen and phosphorus ecological stoichiometry shifts with tree species in subalpine plantations. PeerJ 8:e9702 https://doi.org/10.7717/peerj.9702
date submitted: 2019-12-23
date accepted: 2020-07-21
issued: 2020-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Kaibin
author list: Agent
  family name: Pang
  given name: Xueyong
author list: Agent
  family name: Yang
  given name: Bing
author list: Agent
  family name: Bao
  given name: Weikai
doi: 10.7717/peerj.9702
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-12
copyright: ©2020 Qi et al.
attribution name: Qi et al.

Genetic characterization of feline panleukopenia virus from dogs in Vietnam reveals a unique Thr101 mutation in VP2
type: item
type: AcademicArticle
description: Background Canine parvovirus type 2 (CPV-2) and feline parvovirus (FPV) are known as the main causes of several serious diseases and have a severe impact on puppies and kittens, respectively. FPV and new CPV-2 variants are all able to infect cats, causing diseases indistinguishable from feline panleukopenia. However, FPV only replicates efficiently in feline cells in vitro and replicates in dogs in the thymus and bone marrow without being shed in feces. In our previous study, the genotypes of six parvoviral isolates were unable to be identified using a SimpleProbe® real-time PCR assay. Methods In the present study, we characterized previously unidentified FPV-like viruses isolated from dogs in Vietnam. The six isolates were utilized to complete VP2 gene sequencing and to conduct phylogenetic analyses. Results Sequence analysis of the six parvoviral strains identified the species as being similar to FPV. Phylogenetic analysis demonstrated that the complete VP2 genes of the strains are similar to those of FPV. The FPV-like strains contain a Thr101 mutation in the VP2 protein, which is different from prototype FPV strains. Discussion Our data provide evidence for the existence of changes in the charge, protein contact potential and molecular surface of the core of the receptor-binding size with an Ile101 to Thr101 mutation. This is also the first study to provide reliable evidence that FPV may be a threat to the Vietnamese dog population.
format: application/pdf
format: text/html
creator: Minh Hoang
creator: Cheng-Nan Wu
creator: Chuen-Fu Lin
creator: Huong Thanh Thi Nguyen
creator: Van Phan Le
creator: Ming-Tang Chiou
creator: Chao-Nan Lin
subject: Microbiology
subject: Veterinary Medicine
subject: Virology
description: doi:10.7717/peerj.9752
publisher: PeerJ Inc.
rights: © 2020 Hoang et al.
abstract: Background Canine parvovirus type 2 (CPV-2) and feline parvovirus (FPV) are known as the main causes of several serious diseases and have a severe impact on puppies and kittens, respectively. FPV and new CPV-2 variants are all able to infect cats, causing diseases indistinguishable from feline panleukopenia. However, FPV only replicates efficiently in feline cells in vitro and replicates in dogs in the thymus and bone marrow without being shed in feces. In our previous study, the genotypes of six parvoviral isolates were unable to be identified using a SimpleProbe® real-time PCR assay. Methods In the present study, we characterized previously unidentified FPV-like viruses isolated from dogs in Vietnam. The six isolates were utilized to complete VP2 gene sequencing and to conduct phylogenetic analyses. Results Sequence analysis of the six parvoviral strains identified the species as being similar to FPV. Phylogenetic analysis demonstrated that the complete VP2 genes of the strains are similar to those of FPV. The FPV-like strains contain a Thr101 mutation in the VP2 protein, which is different from prototype FPV strains. Discussion Our data provide evidence for the existence of changes in the charge, protein contact potential and molecular surface of the core of the receptor-binding size with an Ile101 to Thr101 mutation. This is also the first study to provide reliable evidence that FPV may be a threat to the Vietnamese dog population.
bibliographic citation: Hoang et al. (2020) Genetic characterization of feline panleukopenia virus from dogs in Vietnam reveals a unique Thr101 mutation in VP2. PeerJ 8:e9752 https://doi.org/10.7717/peerj.9752
date submitted: 2020-03-10
date accepted: 2020-07-28
issued: 2020-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoang
  given name: Minh
author list: Agent
  family name: Wu
  given name: Cheng-Nan
author list: Agent
  family name: Lin
  given name: Chuen-Fu
author list: Agent
  family name: Nguyen
  given name: Huong Thanh Thi
author list: Agent
  family name: Le
  given name: Van Phan
author list: Agent
  family name: Chiou
  given name: Ming-Tang
author list: Agent
  family name: Lin
  given name: Chao-Nan
doi: 10.7717/peerj.9752
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-12
copyright: ©2020 Hoang et al.
attribution name: Hoang et al.

Physiological aspects and energetic contribution in 20s:10s high-intensity interval exercise at different intensities
type: item
type: AcademicArticle
description: Background One of the most popular high-intensity interval exercises is the called “Tabata Protocol”. However, most investigations have limitations in describing the work intensity, and this fact appears to be due to the protocol unfeasibility. Furthermore, the physiological demands and energetic contribution during this kind of exercise remain unclear. Methods Eight physically active students (21.8 ± 3.7 years) and eight well-trained cycling athletes (27.8 ± 6.4 years) were enrolled. In the first visit, we collected descriptive data and the peak power output (PPO). On the next three visits, in random order, participants performed interval training with the same time structure (effort:rest 20s:10s) but using different intensities (115%, 130%, and 170% of PPO). We collected the number of sprints, power output, oxygen consumption, blood lactate, and heart rate. Results The analysis of variance for multivariate test (number of sprints, power output, blood lactate, peak heart rate and percentage of maximal heart rate) showed significant differences between groups (F = 9.62; p = 0.001) and intensities (F = 384.05; p < 0.001), with no interactions (F = 0.94; p = 0.57). All three energetic contributions and intensities were different between protocols. The higher contribution was aerobic, followed by alactic and lactic. The aerobic contribution was higher at 115%PPO, while the alactic system showed higher contribution at 130%PPO. In conclusion, the aerobic system was predominant in the three exercise protocols, and we observed a higher contribution at lower intensities.
format: application/pdf
format: text/html
creator: Gabriel V. Protzen
creator: Charles Bartel
creator: Victor S. Coswig
creator: Paulo Gentil
creator: Fabricio B. Del Vecchio
subject: Biochemistry
subject: Anatomy and Physiology
subject: Metabolic Sciences
description: doi:10.7717/peerj.9791
publisher: PeerJ Inc.
rights: © 2020 Protzen et al.
abstract: Background One of the most popular high-intensity interval exercises is the called “Tabata Protocol”. However, most investigations have limitations in describing the work intensity, and this fact appears to be due to the protocol unfeasibility. Furthermore, the physiological demands and energetic contribution during this kind of exercise remain unclear. Methods Eight physically active students (21.8 ± 3.7 years) and eight well-trained cycling athletes (27.8 ± 6.4 years) were enrolled. In the first visit, we collected descriptive data and the peak power output (PPO). On the next three visits, in random order, participants performed interval training with the same time structure (effort:rest 20s:10s) but using different intensities (115%, 130%, and 170% of PPO). We collected the number of sprints, power output, oxygen consumption, blood lactate, and heart rate. Results The analysis of variance for multivariate test (number of sprints, power output, blood lactate, peak heart rate and percentage of maximal heart rate) showed significant differences between groups (F = 9.62; p = 0.001) and intensities (F = 384.05; p < 0.001), with no interactions (F = 0.94; p = 0.57). All three energetic contributions and intensities were different between protocols. The higher contribution was aerobic, followed by alactic and lactic. The aerobic contribution was higher at 115%PPO, while the alactic system showed higher contribution at 130%PPO. In conclusion, the aerobic system was predominant in the three exercise protocols, and we observed a higher contribution at lower intensities.
bibliographic citation: Protzen et al. (2020) Physiological aspects and energetic contribution in 20s:10s high-intensity interval exercise at different intensities. PeerJ 8:e9791 https://doi.org/10.7717/peerj.9791
date submitted: 2020-02-18
date accepted: 2020-07-31
issued: 2020-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Protzen
  given name: Gabriel V.
author list: Agent
  family name: Bartel
  given name: Charles
author list: Agent
  family name: Coswig
  given name: Victor S.
author list: Agent
  family name: Gentil
  given name: Paulo
author list: Agent
  family name: Del Vecchio
  given name: Fabricio B.
doi: 10.7717/peerj.9791
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-12
copyright: ©2020 Protzen et al.
attribution name: Protzen et al.

Genomic signatures of globally enhanced gene duplicate accumulation in the megadiverse higher Diptera fueling intralocus sexual conflict resolution
type: item
type: AcademicArticle
description: Gene duplication is an important source of evolutionary innovation. To explore the relative impact of gene duplication during the diversification of major insect model system lineages, we performed a comparative analysis of lineage-specific gene duplications in the fruit fly Drosophila melanogaster (Diptera: Brachycera), the mosquito Anopheles gambiae (Diptera: Culicomorpha), the red flour beetle Tribolium castaneum (Coleoptera), and the honeybee Apis mellifera (Hymenoptera). Focusing on close to 6,000 insect core gene families containing maximally six paralogs, we detected a conspicuously higher number of lineage-specific duplications in Drosophila (689) compared to Anopheles (315), Tribolium (386), and Apis (223). Based on analyses of sequence divergence, phylogenetic distribution, and gene ontology information, we present evidence that an increased background rate of gene duplicate accumulation played an exceptional role during the diversification of the higher Diptera (Brachycera), in part by providing enriched opportunities for intralocus sexual conflict resolution, which may have boosted speciation rates during the early radiation of the megadiverse brachyceran subclade Schizophora.
format: application/pdf
format: text/html
creator: Riyue Bao
creator: Markus Friedrich
subject: Biodiversity
subject: Entomology
subject: Genetics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.10012
publisher: PeerJ Inc.
rights: © 2020 Bao and Friedrich
abstract: Gene duplication is an important source of evolutionary innovation. To explore the relative impact of gene duplication during the diversification of major insect model system lineages, we performed a comparative analysis of lineage-specific gene duplications in the fruit fly Drosophila melanogaster (Diptera: Brachycera), the mosquito Anopheles gambiae (Diptera: Culicomorpha), the red flour beetle Tribolium castaneum (Coleoptera), and the honeybee Apis mellifera (Hymenoptera). Focusing on close to 6,000 insect core gene families containing maximally six paralogs, we detected a conspicuously higher number of lineage-specific duplications in Drosophila (689) compared to Anopheles (315), Tribolium (386), and Apis (223). Based on analyses of sequence divergence, phylogenetic distribution, and gene ontology information, we present evidence that an increased background rate of gene duplicate accumulation played an exceptional role during the diversification of the higher Diptera (Brachycera), in part by providing enriched opportunities for intralocus sexual conflict resolution, which may have boosted speciation rates during the early radiation of the megadiverse brachyceran subclade Schizophora.
bibliographic citation: Bao et al. (2020) Genomic signatures of globally enhanced gene duplicate accumulation in the megadiverse higher Diptera fueling intralocus sexual conflict resolution. PeerJ 8:e10012 https://doi.org/10.7717/peerj.10012
date submitted: 2020-01-15
date accepted: 2020-08-31
issued: 2020-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bao
  given name: Riyue
author list: Agent
  family name: Friedrich
  given name: Markus
doi: 10.7717/peerj.10012
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-12
copyright: © 2020 Bao and Friedrich
attribution name: Bao and Friedrich

Instrumental validity and intra/inter-rater reliability of a novel low-cost digital pressure algometer
type: item
type: AcademicArticle
description: Background Pain assessment is a key measure that accompanies treatments in a wide range of clinical settings. A low-cost valid and reliable pressure algometer would allow objective assessment of pressure pain to assist a variety of health professionals. However, the pressure algometer is often expensive, which limits its daily use in both clinical and research settings. Objectives This study aimed to assess the instrumental validity, and the intra- and inter-rater reliability of an inexpensive digital adapted pressure algometer. Methods A single rater applied 60 random compressions on a force platform. The pressure pain thresholds of 20 volunteers were collected twice (3 days apart) by two raters. The main outcome measurements were as follows: the maximal peak force (in kPa) and the pressure pain threshold (adapted pressure algometer vs. force platform). Cronbach’s α test was used to assess internal consistency. The standard error of measurement provided estimates of measurement error, and the measurement bias was estimated with the Bland–Altman method, with lower and upper limits of agreement. Results No differences were observed when comparing the compression results (P = 0.51). The validity and internal intra-rater consistencies ranged from 0.84 to 0.99, and the standard error of measurement from 0.005 to 0.04 kPa. Very strong (r = 0.73–0.74) to near-perfect (r = 0.99) correlations were found, with a low risk of bias for all measurements. The results demonstrated the validity and intra-rater reliability of the digitally adapted pressure algometer. Inter-rater reliability results were moderate (r = 0.55–0.60; Cronbach’s α = 0.71–0.75). Conclusion The adapted pressure algometer provide valid and reliable measurements of pressure pain threshold. The results support more widespread use of the pressure pain threshold method among clinicians.
format: application/pdf
format: text/html
creator: Daniel Jerez-Mayorga
creator: Carolina Fernanda dos Anjos
creator: Maria de Cássia Macedo
creator: Ilha Gonçalves Fernandes
creator: Esteban Aedo-Muñoz
creator: Leonardo Intelangelo
creator: Alexandre Carvalho Barbosa
subject: Anesthesiology and Pain Management
subject: Drugs and Devices
subject: Evidence Based Medicine
subject: Kinesiology
description: doi:10.7717/peerj.10162
publisher: PeerJ Inc.
rights: © 2020 Jerez-Mayorga et al.
abstract: Background Pain assessment is a key measure that accompanies treatments in a wide range of clinical settings. A low-cost valid and reliable pressure algometer would allow objective assessment of pressure pain to assist a variety of health professionals. However, the pressure algometer is often expensive, which limits its daily use in both clinical and research settings. Objectives This study aimed to assess the instrumental validity, and the intra- and inter-rater reliability of an inexpensive digital adapted pressure algometer. Methods A single rater applied 60 random compressions on a force platform. The pressure pain thresholds of 20 volunteers were collected twice (3 days apart) by two raters. The main outcome measurements were as follows: the maximal peak force (in kPa) and the pressure pain threshold (adapted pressure algometer vs. force platform). Cronbach’s α test was used to assess internal consistency. The standard error of measurement provided estimates of measurement error, and the measurement bias was estimated with the Bland–Altman method, with lower and upper limits of agreement. Results No differences were observed when comparing the compression results (P = 0.51). The validity and internal intra-rater consistencies ranged from 0.84 to 0.99, and the standard error of measurement from 0.005 to 0.04 kPa. Very strong (r = 0.73–0.74) to near-perfect (r = 0.99) correlations were found, with a low risk of bias for all measurements. The results demonstrated the validity and intra-rater reliability of the digitally adapted pressure algometer. Inter-rater reliability results were moderate (r = 0.55–0.60; Cronbach’s α = 0.71–0.75). Conclusion The adapted pressure algometer provide valid and reliable measurements of pressure pain threshold. The results support more widespread use of the pressure pain threshold method among clinicians.
bibliographic citation: Jerez-Mayorga et al. (2020) Instrumental validity and intra/inter-rater reliability of a novel low-cost digital pressure algometer. PeerJ 8:e10162 https://doi.org/10.7717/peerj.10162
date submitted: 2020-03-05
date accepted: 2020-09-21
issued: 2020-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jerez-Mayorga
  given name: Daniel
author list: Agent
  family name: dos Anjos
  given name: Carolina Fernanda
author list: Agent
  family name: Macedo
  given name: Maria de Cássia
author list: Agent
  family name: Fernandes
  given name: Ilha Gonçalves
author list: Agent
  family name: Aedo-Muñoz
  given name: Esteban
author list: Agent
  family name: Intelangelo
  given name: Leonardo
author list: Agent
  family name: Barbosa
  given name: Alexandre Carvalho
doi: 10.7717/peerj.10162
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-12
copyright: © 2020 Jerez-Mayorga et al.
attribution name: Jerez-Mayorga et al.

Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load
type: item
type: AcademicArticle
description: SARS-CoV-2 is a betacoronavirus responsible for COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic origins of the virus and the human host adaptation process. As a virus with an RNA genome that codes for its own genomic replication proteins, mutations in these proteins can significantly impact the variance rate of the genome, affecting both the survival and infection rate of the virus, and attempts at combating the disease. In this study, we analyzed the mutation densities of viral isolates carrying frequently observed mutations for four proteins in the RNA synthesis complex over time in comparison to wildtype isolates. Our observations suggest mutations in nsp14, an error-correcting exonuclease protein, have the strongest association with increased mutation load without selective pressure and across the genome, compared to nsp7, nsp8 and nsp12, which form the core polymerase complex. We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates and nsp14 mutations as potential predictors for high mutability strains.
format: application/pdf
format: text/html
creator: Doğa Eskier
creator: Aslı Suner
creator: Yavuz Oktay
creator: Gökhan Karakülah
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Virology
subject: Statistics
description: doi:10.7717/peerj.10181
publisher: PeerJ Inc.
rights: © 2020 Eskier et al.
abstract: SARS-CoV-2 is a betacoronavirus responsible for COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic origins of the virus and the human host adaptation process. As a virus with an RNA genome that codes for its own genomic replication proteins, mutations in these proteins can significantly impact the variance rate of the genome, affecting both the survival and infection rate of the virus, and attempts at combating the disease. In this study, we analyzed the mutation densities of viral isolates carrying frequently observed mutations for four proteins in the RNA synthesis complex over time in comparison to wildtype isolates. Our observations suggest mutations in nsp14, an error-correcting exonuclease protein, have the strongest association with increased mutation load without selective pressure and across the genome, compared to nsp7, nsp8 and nsp12, which form the core polymerase complex. We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates and nsp14 mutations as potential predictors for high mutability strains.
bibliographic citation: Eskier et al. (2020) Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load. PeerJ 8:e10181 https://doi.org/10.7717/peerj.10181
date submitted: 2020-08-09
date accepted: 2020-09-23
issued: 2020-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eskier
  given name: Doğa
author list: Agent
  family name: Suner
  given name: Aslı
author list: Agent
  family name: Oktay
  given name: Yavuz
author list: Agent
  family name: Karakülah
  given name: Gökhan
doi: 10.7717/peerj.10181
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-12
copyright: © 2020 Eskier et al.
attribution name: Eskier et al.

Convolutional neural network in upper limb functional motion analysis after stroke
type: item
type: AcademicArticle
description: In this work, implementation of Convolutional Neural Network (CNN) for the purpose of analysis of functional upper limb movement pattern was applied. The main aim of the study was to compare motion of selected activities of daily living of participants after stroke with the healthy ones (in similar age). The optical, marker-based motion capture system was applied for the purpose of data acquisition. There were some attempts made in order to find the existing differences in the motion pattern of the upper limb. For this purpose, the motion features of dominant and non-dominant upper limb of healthy participants were compared with motion features of paresis and non-paresis upper limbs of participants after stroke. On the basis of the newly collected data set, a new CNN application was presented to the classification of motion data in two different class label configurations. Analyzing individual segments of the upper body, it turned out that the arm was the most sensitive segment for capturing changes in the trajectory of the lifting movements of objects.
format: application/pdf
format: text/html
creator: Agnieszka Szczęsna
creator: Monika Błaszczyszyn
creator: Aleksandra Kawala-Sterniuk
subject: Neuroscience
subject: Cognitive Disorders
subject: Kinesiology
subject: Neurology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.10124
publisher: PeerJ Inc.
rights: © 2020 Szczęsna et al.
abstract: In this work, implementation of Convolutional Neural Network (CNN) for the purpose of analysis of functional upper limb movement pattern was applied. The main aim of the study was to compare motion of selected activities of daily living of participants after stroke with the healthy ones (in similar age). The optical, marker-based motion capture system was applied for the purpose of data acquisition. There were some attempts made in order to find the existing differences in the motion pattern of the upper limb. For this purpose, the motion features of dominant and non-dominant upper limb of healthy participants were compared with motion features of paresis and non-paresis upper limbs of participants after stroke. On the basis of the newly collected data set, a new CNN application was presented to the classification of motion data in two different class label configurations. Analyzing individual segments of the upper body, it turned out that the arm was the most sensitive segment for capturing changes in the trajectory of the lifting movements of objects.
bibliographic citation: Szczęsna et al. (2020) Convolutional neural network in upper limb functional motion analysis after stroke. PeerJ 8:e10124 https://doi.org/10.7717/peerj.10124
date submitted: 2020-03-13
date accepted: 2020-09-17
issued: 2020-10-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Szczęsna
  given name: Agnieszka
author list: Agent
  family name: Błaszczyszyn
  given name: Monika
author list: Agent
  family name: Kawala-Sterniuk
  given name: Aleksandra
doi: 10.7717/peerj.10124
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-09
copyright: ©2020 Szczęsna et al.
attribution name: Szczęsna et al.

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