PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Enhanced biomass and thermotolerance of Arabidopsis by SiERECTA isolated from Setaria italica L
items: A systematic review of effects of daytime napping strategies on sports performance in physically active individuals with and without partial-sleep deprivation
items: Humans read emotional arousal in monkey vocalizations: evidence for evolutionary continuities in communication
items: Differential responses of the seed germination of three functional groups to low temperature and darkness in a typical steppe, Northern China
items: Screening of high-risk deleterious missense variations in the CYP1B1 gene implicated in the pathogenesis of primary congenital glaucoma: A comprehensive in silico approach
items: PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2
items: Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand
items: Occurrence of Nosemosis in honey bee, Apis mellifera L. at the apiaries of East Kazakhstan
items: Hybrid purity identification using EST-SSR markers and heterosis analysis of quantitative traits of Russian wildrye
items: Adult intussusception: a challenge to laparoscopic surgery?

Enhanced biomass and thermotolerance of Arabidopsis by SiERECTA isolated from Setaria italica L
type: item
type: AcademicArticle
description: Foxtail millet is commonly used as a food and forage grass. ERECTA (ER) is a receptor-like kinase that can improve plant biomass and stress resistance. The sorghum SbER10_X1 gene was used as a probe to identify ER family genes on the Setaria italica genomes (SiERs), and determine the characteristics of the SiERs family. Herein, the structural features, expression patterns, and thermotolerance of SiERs function were identified by bioinformatics analysis, real-time PCR and transgenesis estimation. Results showed that SiERs had four members: two members were located on chromosome 1 with a total of six copies (SiER1_X1, SiER1_X2, SiER1_X3, SiER1_X4, SiER1_X5, and SiER1_X6), and two were on chromosome 4, namely, SiER4 (SiER4_X1 and SiER4_X2) and SiERL1. Among them, SiER1_X4 and SiER4_X1 were expressed highest in above-ground organs of foxtail millet, and actively responded to treatments with abscisic acid, brassinolide, gibberellin, and indole acetic acid. After overexpression of SiER1_X4 and SiER4_X1 in Arabidopsis, the plant height and biomass of the transgenic Arabidopsis significantly increased. Following high-temperature treatment, transgenic seedlings survived better compared to wild type. Transgenic lines showed higher SOD and POD activities, and expression level of AtHSF1 and AtBl1 genes significantly increased. These results indicated that SiER1_X4 and SiER4_X1 played important regulatory roles in plant growth and thermotolerance. The two genes provide potential targets for conventional breeding or biotechnological intervention to improve the biomass of forage grass and thermotolerance of field crops.
format: application/pdf
format: text/html
creator: Jiacheng Zheng
creator: Xiaoyi Huang
creator: Jieqin Li
creator: Qingyuan He
creator: Wan Zhao
creator: Chaowu Zeng
creator: Haizhou Chen
creator: Qiuwen Zhan
creator: Zhaoshi Xu
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14452
publisher: PeerJ Inc.
rights: © 2022 Zheng et al.
abstract: Foxtail millet is commonly used as a food and forage grass. ERECTA (ER) is a receptor-like kinase that can improve plant biomass and stress resistance. The sorghum SbER10_X1 gene was used as a probe to identify ER family genes on the Setaria italica genomes (SiERs), and determine the characteristics of the SiERs family. Herein, the structural features, expression patterns, and thermotolerance of SiERs function were identified by bioinformatics analysis, real-time PCR and transgenesis estimation. Results showed that SiERs had four members: two members were located on chromosome 1 with a total of six copies (SiER1_X1, SiER1_X2, SiER1_X3, SiER1_X4, SiER1_X5, and SiER1_X6), and two were on chromosome 4, namely, SiER4 (SiER4_X1 and SiER4_X2) and SiERL1. Among them, SiER1_X4 and SiER4_X1 were expressed highest in above-ground organs of foxtail millet, and actively responded to treatments with abscisic acid, brassinolide, gibberellin, and indole acetic acid. After overexpression of SiER1_X4 and SiER4_X1 in Arabidopsis, the plant height and biomass of the transgenic Arabidopsis significantly increased. Following high-temperature treatment, transgenic seedlings survived better compared to wild type. Transgenic lines showed higher SOD and POD activities, and expression level of AtHSF1 and AtBl1 genes significantly increased. These results indicated that SiER1_X4 and SiER4_X1 played important regulatory roles in plant growth and thermotolerance. The two genes provide potential targets for conventional breeding or biotechnological intervention to improve the biomass of forage grass and thermotolerance of field crops.
bibliographic citation: Zheng et al. (2022) Enhanced biomass and thermotolerance of Arabidopsis by SiERECTA isolated from Setaria italica L. PeerJ 10:e14452 https://doi.org/10.7717/peerj.14452
date submitted: 2022-04-04
date accepted: 2022-11-01
issued: 2022-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Jiacheng
author list: Agent
  family name: Huang
  given name: Xiaoyi
author list: Agent
  family name: Li
  given name: Jieqin
author list: Agent
  family name: He
  given name: Qingyuan
author list: Agent
  family name: Zhao
  given name: Wan
author list: Agent
  family name: Zeng
  given name: Chaowu
author list: Agent
  family name: Chen
  given name: Haizhou
author list: Agent
  family name: Zhan
  given name: Qiuwen
author list: Agent
  family name: Xu
  given name: Zhaoshi
doi: 10.7717/peerj.14452
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-01
copyright: ©2022 Zheng et al.
attribution name: Zheng et al.

A systematic review of effects of daytime napping strategies on sports performance in physically active individuals with and without partial-sleep deprivation
type: item
type: AcademicArticle
description: Background Sleep is the body’s natural recovery process, restoring routine metabolic and regulatory functions. Various sleep interventions have been developed to facilitate recovery, and athletic performance, and daytime napping are among them. However, due to inconsistencies in studies, it remains unclear whether daytime napping affects sports performance. This article aims to review the effects of daytime napping on various variables of sports performance in physically active individuals with and without partial-sleep deprivation. Methods A systematic search in three clinical databases, namely Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, and Web of Science, was conducted. To be included in the current review, the study should be a randomized controlled trial that evaluated the influence of daytime napping on one or more components of sports performance in healthy adults, 18 years old or older. Results In the accessible data available until December 2021, 1,094 records were found, of which 12 relevant randomized controlled trials were selected for qualitative synthesis. The majority of studies reported favourable effects of daytime napping on sports performance. However, only one study reported no significant impact, possibly due to a different methodological approach and a shorter nap duration. Conclusion Napping strategies optimize sports performance in physically active, athletic populations, benefitting partially sleep-deprived and well-slept individuals, with longer nap durations (~90 min) having more significant advantages. Daytime naps can be considered as cost-efficient, self-administered methods promoting recovery of body functions.
format: application/pdf
format: text/html
creator: Priya Sirohi
creator: Moazzam Hussain Khan
creator: Saurabh Sharma
creator: Shibili Nuhmani
creator: Wafa Hashem Al Muslem
creator: Turki Abualait
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.14460
publisher: PeerJ Inc.
rights: © 2022 Sirohi et al.
abstract: Background Sleep is the body’s natural recovery process, restoring routine metabolic and regulatory functions. Various sleep interventions have been developed to facilitate recovery, and athletic performance, and daytime napping are among them. However, due to inconsistencies in studies, it remains unclear whether daytime napping affects sports performance. This article aims to review the effects of daytime napping on various variables of sports performance in physically active individuals with and without partial-sleep deprivation. Methods A systematic search in three clinical databases, namely Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, and Web of Science, was conducted. To be included in the current review, the study should be a randomized controlled trial that evaluated the influence of daytime napping on one or more components of sports performance in healthy adults, 18 years old or older. Results In the accessible data available until December 2021, 1,094 records were found, of which 12 relevant randomized controlled trials were selected for qualitative synthesis. The majority of studies reported favourable effects of daytime napping on sports performance. However, only one study reported no significant impact, possibly due to a different methodological approach and a shorter nap duration. Conclusion Napping strategies optimize sports performance in physically active, athletic populations, benefitting partially sleep-deprived and well-slept individuals, with longer nap durations (~90 min) having more significant advantages. Daytime naps can be considered as cost-efficient, self-administered methods promoting recovery of body functions.
bibliographic citation: Sirohi et al. (2022) A systematic review of effects of daytime napping strategies on sports performance in physically active individuals with and without partial-sleep deprivation. PeerJ 10:e14460 https://doi.org/10.7717/peerj.14460
date submitted: 2022-05-19
date accepted: 2022-11-03
issued: 2022-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sirohi
  given name: Priya
author list: Agent
  family name: Khan
  given name: Moazzam Hussain
author list: Agent
  family name: Sharma
  given name: Saurabh
author list: Agent
  family name: Nuhmani
  given name: Shibili
author list: Agent
  family name: Al Muslem
  given name: Wafa Hashem
author list: Agent
  family name: Abualait
  given name: Turki
doi: 10.7717/peerj.14460
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-01
copyright: © 2022 Sirohi et al.
attribution name: Sirohi et al.

Humans read emotional arousal in monkey vocalizations: evidence for evolutionary continuities in communication
type: item
type: AcademicArticle
description: Humans and other mammalian species communicate emotions in ways that reflect evolutionary conservation and continuity, an observation first made by Darwin. One approach to testing this hypothesis has been to assess the capacity to perceive the emotional content of the vocalizations of other species. Using a binary forced choice task, we tested perception of the emotional intensity represented in coos and screams of infant and juvenile female rhesus macaques (Macaca mulatta) by 113 human listeners without, and 12 listeners with, experience (as researchers or care technicians) with this species. Each stimulus pair contained one high- and one low-arousal vocalization, as measured at the time of recording by stress hormone levels for coos and the degree of intensity of aggression for screams. For coos as well as screams, both inexperienced and experienced participants accurately identified the high-arousal vocalization at significantly above-chance rates. Experience was associated with significantly greater accuracy with scream stimuli but not coo stimuli, and with a tendency to indicate screams as reflecting greater emotional intensity than coos. Neither measures of empathy, human emotion recognition, nor attitudes toward animal welfare showed any relationship with responses. Participants were sensitive to the fundamental frequency, noisiness, and duration of vocalizations; some of these tendencies likely facilitated accurate perceptions, perhaps due to evolutionary homologies in the physiology of arousal and vocal production between humans and macaques. Overall, our findings support a view of evolutionary continuity in emotional vocal communication. We discuss hypotheses about how distinctive dimensions of human nonverbal communication, like the expansion of scream usage across a range of contexts, might influence perceptions of other species’ vocalizations.
format: application/pdf
format: text/html
creator: Jay W. Schwartz
creator: Harold Gouzoules
subject: Animal Behavior
subject: Anthropology
subject: Evolutionary Studies
subject: Zoology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.14471
publisher: PeerJ Inc.
rights: © 2022 Schwartz and Gouzoules
abstract: Humans and other mammalian species communicate emotions in ways that reflect evolutionary conservation and continuity, an observation first made by Darwin. One approach to testing this hypothesis has been to assess the capacity to perceive the emotional content of the vocalizations of other species. Using a binary forced choice task, we tested perception of the emotional intensity represented in coos and screams of infant and juvenile female rhesus macaques (Macaca mulatta) by 113 human listeners without, and 12 listeners with, experience (as researchers or care technicians) with this species. Each stimulus pair contained one high- and one low-arousal vocalization, as measured at the time of recording by stress hormone levels for coos and the degree of intensity of aggression for screams. For coos as well as screams, both inexperienced and experienced participants accurately identified the high-arousal vocalization at significantly above-chance rates. Experience was associated with significantly greater accuracy with scream stimuli but not coo stimuli, and with a tendency to indicate screams as reflecting greater emotional intensity than coos. Neither measures of empathy, human emotion recognition, nor attitudes toward animal welfare showed any relationship with responses. Participants were sensitive to the fundamental frequency, noisiness, and duration of vocalizations; some of these tendencies likely facilitated accurate perceptions, perhaps due to evolutionary homologies in the physiology of arousal and vocal production between humans and macaques. Overall, our findings support a view of evolutionary continuity in emotional vocal communication. We discuss hypotheses about how distinctive dimensions of human nonverbal communication, like the expansion of scream usage across a range of contexts, might influence perceptions of other species’ vocalizations.
bibliographic citation: Schwartz et al. (2022) Humans read emotional arousal in monkey vocalizations: evidence for evolutionary continuities in communication. PeerJ 10:e14471 https://doi.org/10.7717/peerj.14471
date submitted: 2022-09-13
date accepted: 2022-11-06
issued: 2022-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schwartz
  given name: Jay W.
author list: Agent
  family name: Gouzoules
  given name: Harold
doi: 10.7717/peerj.14471
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-01
copyright: © 2022 Schwartz and Gouzoules
attribution name: Schwartz and Gouzoules

Differential responses of the seed germination of three functional groups to low temperature and darkness in a typical steppe, Northern China
type: item
type: AcademicArticle
description: Seed germination is a key stage in the life history of plants, which has a crucial effect on plant community structure. Climate change has substantially altered the surface soil temperature and light availability, which can affect seed germination. However, whether the seed germination of different functional groups is affected by the interactions of light and temperature remains unclear. Under laboratory conditions, we examined the effects of low temperature and darkness, as well as their interaction, on the seed germination of 16 species belonging to three plant functional groups (annual and biennials, perennial grasses, and perennial forbs) in a typical steppe, Northern China. We found that low temperature had a significant negative effect on seed germination of all species. Low temperature significantly decreased the final germination percentage and germinative force of the three plant functional groups, and the germination duration of perennial grasses. Darkness significantly decreased the germinative force of perennial forbs and total seeds, and the germination duration of perennial grasses. The interactive effects of light and temperature on the seed final germination percentage and germinative force of perennial grass indicated that darkness strengthened the inhibitory effect of low temperature on the seed germination of the grass functional group. Our study indicate that the seed germination of different plant functional groups varied greatly in response to changing environmental conditions. Our results suggest that future climate change could alter the regeneration and species composition of plant communities through changing seed germination.
format: application/pdf
format: text/html
creator: Mengzhou Liu
creator: Ning Qiao
creator: Bing Zhang
creator: Fengying Liu
creator: Yuan Miao
creator: Ji Chen
creator: Yanfeng Sun
creator: Peng Wang
creator: Dong Wang
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.14485
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Seed germination is a key stage in the life history of plants, which has a crucial effect on plant community structure. Climate change has substantially altered the surface soil temperature and light availability, which can affect seed germination. However, whether the seed germination of different functional groups is affected by the interactions of light and temperature remains unclear. Under laboratory conditions, we examined the effects of low temperature and darkness, as well as their interaction, on the seed germination of 16 species belonging to three plant functional groups (annual and biennials, perennial grasses, and perennial forbs) in a typical steppe, Northern China. We found that low temperature had a significant negative effect on seed germination of all species. Low temperature significantly decreased the final germination percentage and germinative force of the three plant functional groups, and the germination duration of perennial grasses. Darkness significantly decreased the germinative force of perennial forbs and total seeds, and the germination duration of perennial grasses. The interactive effects of light and temperature on the seed final germination percentage and germinative force of perennial grass indicated that darkness strengthened the inhibitory effect of low temperature on the seed germination of the grass functional group. Our study indicate that the seed germination of different plant functional groups varied greatly in response to changing environmental conditions. Our results suggest that future climate change could alter the regeneration and species composition of plant communities through changing seed germination.
bibliographic citation: Liu et al. (2022) Differential responses of the seed germination of three functional groups to low temperature and darkness in a typical steppe, Northern China. PeerJ 10:e14485 https://doi.org/10.7717/peerj.14485
date submitted: 2022-05-30
date accepted: 2022-11-08
issued: 2022-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Mengzhou
author list: Agent
  family name: Qiao
  given name: Ning
author list: Agent
  family name: Zhang
  given name: Bing
author list: Agent
  family name: Liu
  given name: Fengying
author list: Agent
  family name: Miao
  given name: Yuan
author list: Agent
  family name: Chen
  given name: Ji
author list: Agent
  family name: Sun
  given name: Yanfeng
author list: Agent
  family name: Wang
  given name: Peng
author list: Agent
  family name: Wang
  given name: Dong
doi: 10.7717/peerj.14485
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-01
copyright: © 2022 Liu et al.
attribution name: Liu et al.

Screening of high-risk deleterious missense variations in the CYP1B1 gene implicated in the pathogenesis of primary congenital glaucoma: A comprehensive in silico approach
type: item
type: AcademicArticle
description: Background Primary congenital glaucoma (PCG) is the most common subtype of glaucoma caused by defects in the cytochrome P450 1B1 (CYP1B1) gene. It is developing among infants in more than 80% of cases who exhibit impairments in the anterior chamber angle and the trabecular meshwork. Thus, a comprehensive in silico approach was performed to evaluate the effect of high-risk deleterious missense variations in the CYP1B1 gene. Material and methods All the information for CYP1B1 missense variants was retrieved from the dbSNP database. Seven different tools, namely: SIFT, PolyPhen-2, PROVEAN, SNAP2, PANTHER, PhD-SNP, and Predict-SNP, were used for functional annotation, and two packages, which were I-Mutant 2.0 and MUpro, were used to predict the effect of the variants on protein stability. A phylogenetic conservation analysis using deleterious variants was performed by the ConSurf server. The 3D structures of the wild-type and mutants were generated using the I-TASSER tool, and a 50 ns molecular dynamic simulation (MDS) was executed using the GROMACS webserver to determine the stability of mutants compared to the native protein. Co-expression, protein-protein interaction (PPI), gene ontology (GO), and pathway analyses were additionally performed for the CYP1B1 in-depth study. Results All the retrieved data from the dbSNP database was subjected to functional, structural, and phylogenetic analysis. From the conducted analyses, a total of 19 high-risk variants (P52L, G61E, G90R, P118L, E173K, D291G, Y349D, G365W, G365R, R368H, R368C, D374N, N423Y, D430E, P442A, R444Q, F445L, R469W, and C470Y) were screened out that were considered to be deleterious to the CYP1B1 gene. The phylogenetic analysis revealed that the majority of the variants occurred in highly conserved regions. The MD simulation analysis exhibited that all mutants’ average root mean square deviation (RMSD) values were higher compared to the wild-type protein, which could potentially cause CYP1B1 protein dysfunct…
format: application/pdf
format: text/html
creator: Muhammad Shahid
creator: Ahmad Azfaralariff
creator: Muhammad Tufail
creator: Nazeer Hussain Khan
creator: Ahmed Abdulkareem Najm
creator: Sabika Firasat
creator: Muhammad Zubair
creator: Shazrul Fazry
creator: Douglas Law
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Molecular Biology
subject: Ophthalmology
description: doi:10.7717/peerj.14132
publisher: PeerJ Inc.
rights: © 2022 Shahid et al.
abstract: Background Primary congenital glaucoma (PCG) is the most common subtype of glaucoma caused by defects in the cytochrome P450 1B1 (CYP1B1) gene. It is developing among infants in more than 80% of cases who exhibit impairments in the anterior chamber angle and the trabecular meshwork. Thus, a comprehensive in silico approach was performed to evaluate the effect of high-risk deleterious missense variations in the CYP1B1 gene. Material and methods All the information for CYP1B1 missense variants was retrieved from the dbSNP database. Seven different tools, namely: SIFT, PolyPhen-2, PROVEAN, SNAP2, PANTHER, PhD-SNP, and Predict-SNP, were used for functional annotation, and two packages, which were I-Mutant 2.0 and MUpro, were used to predict the effect of the variants on protein stability. A phylogenetic conservation analysis using deleterious variants was performed by the ConSurf server. The 3D structures of the wild-type and mutants were generated using the I-TASSER tool, and a 50 ns molecular dynamic simulation (MDS) was executed using the GROMACS webserver to determine the stability of mutants compared to the native protein. Co-expression, protein-protein interaction (PPI), gene ontology (GO), and pathway analyses were additionally performed for the CYP1B1 in-depth study. Results All the retrieved data from the dbSNP database was subjected to functional, structural, and phylogenetic analysis. From the conducted analyses, a total of 19 high-risk variants (P52L, G61E, G90R, P118L, E173K, D291G, Y349D, G365W, G365R, R368H, R368C, D374N, N423Y, D430E, P442A, R444Q, F445L, R469W, and C470Y) were screened out that were considered to be deleterious to the CYP1B1 gene. The phylogenetic analysis revealed that the majority of the variants occurred in highly conserved regions. The MD simulation analysis exhibited that all mutants’ average root mean square deviation (RMSD) values were higher compared to the wild-type protein, which could potentially cause CYP1B1 protein dysfunct…
bibliographic citation: Shahid et al. (2022) Screening of high-risk deleterious missense variations in the CYP1B1 gene implicated in the pathogenesis of primary congenital glaucoma: A comprehensive in silico approach. PeerJ 10:e14132 https://doi.org/10.7717/peerj.14132
date submitted: 2022-06-23
date accepted: 2022-09-06
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shahid
  given name: Muhammad
author list: Agent
  family name: Azfaralariff
  given name: Ahmad
author list: Agent
  family name: Tufail
  given name: Muhammad
author list: Agent
  family name: Hussain Khan
  given name: Nazeer
author list: Agent
  family name: Abdulkareem Najm
  given name: Ahmed
author list: Agent
  family name: Firasat
  given name: Sabika
author list: Agent
  family name: Zubair
  given name: Muhammad
author list: Agent
  family name: Fazry
  given name: Shazrul
author list: Agent
  family name: Law
  given name: Douglas
doi: 10.7717/peerj.14132
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: ©2022 Shahid et al.
attribution name: Shahid et al.

PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2
type: item
type: AcademicArticle
description: The optimization of resources for research in developing countries forces us to consider strategies in the wet lab that allow the reuse of molecular biology reagents to reduce costs. In this study, we used linear regression as a method for predictive modeling of coverage depth given the number of MinION reads sequenced to define the optimum number of reads necessary to obtain >200X coverage depth with a good lineage-clade assignment of SARS-CoV-2 genomes. The research aimed to create and implement a model based on machine learning algorithms to predict different variables (e.g., coverage depth) given the number of MinION reads produced by Nanopore sequencing to maximize the yield of high-quality SARS-CoV-2 genomes, determine the best sequencing runtime, and to be able to reuse the flow cell with the remaining nanopores available for sequencing in a new run. The best accuracy was −0.98 according to the R squared performance metric of the models. A demo version is available at https://genomicdashboard.herokuapp.com/.
format: application/pdf
format: text/html
creator: David E. Valencia-Valencia
creator: Diana Lopez-Alvarez
creator: Nelson Rivera-Franco
creator: Andres Castillo
creator: Johan S. Piña
creator: Carlos A. Pardo
creator: Beatriz Parra
subject: Bioinformatics
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Data Science
subject: COVID-19
description: doi:10.7717/peerj.14425
publisher: PeerJ Inc.
rights: © 2022 Valencia-Valencia et al.
abstract: The optimization of resources for research in developing countries forces us to consider strategies in the wet lab that allow the reuse of molecular biology reagents to reduce costs. In this study, we used linear regression as a method for predictive modeling of coverage depth given the number of MinION reads sequenced to define the optimum number of reads necessary to obtain >200X coverage depth with a good lineage-clade assignment of SARS-CoV-2 genomes. The research aimed to create and implement a model based on machine learning algorithms to predict different variables (e.g., coverage depth) given the number of MinION reads produced by Nanopore sequencing to maximize the yield of high-quality SARS-CoV-2 genomes, determine the best sequencing runtime, and to be able to reuse the flow cell with the remaining nanopores available for sequencing in a new run. The best accuracy was −0.98 according to the R squared performance metric of the models. A demo version is available at https://genomicdashboard.herokuapp.com/.
bibliographic citation: Valencia-Valencia et al. (2022) PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2. PeerJ 10:e14425 https://doi.org/10.7717/peerj.14425
date submitted: 2022-07-19
date accepted: 2022-10-30
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valencia-Valencia
  given name: David E.
author list: Agent
  family name: Lopez-Alvarez
  given name: Diana
author list: Agent
  family name: Rivera-Franco
  given name: Nelson
author list: Agent
  family name: Castillo
  given name: Andres
author list: Agent
  family name: Piña
  given name: Johan S.
author list: Agent
  family name: Pardo
  given name: Carlos A.
author list: Agent
  family name: Parra
  given name: Beatriz
doi: 10.7717/peerj.14425
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: ©2022 Valencia-Valencia et al.
attribution name: Valencia-Valencia et al.

Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand
type: item
type: AcademicArticle
description: Background Ongoing outbreaks of H5N1 highly pathogenic avian influenza (HPAI) viruses and the emergence of the genetic-related hemagglutinin (HA) gene of reassortant H5Nx viruses currently circulating in wild birds and poultries pose a great global public health concern. In this study, we comprehensively analyzed the genetic evolution of Thai H5N1 HA and neuraminidase (NA) genes between 2003 and 2010. The H5N1 Thailand virus clade 2.3.4 was also genetically compared to the currently circulating clade 2.3.4.4 of H5Nx viruses. Methods Full-length nucleotide sequences of 178 HA and 143 NA genes of H5N1 viruses circulating between 2003 and 2010 were phylogenetically analyzed using maximum likelihood (ML) phylogenetic construction. Bayesian phylogenetic trees were reconstructed using BEAST analysis with a Bayesian Markov chain Monte Carlo (MCMC) approach. The maximum clade credibility (MCC) tree was determined, and the time of the most recent common ancestor (tMRCA) was estimated. The H5N1 HA nucleotide sequences of clade 2.3.4 Thailand viruses were phylogenetically analyzed using ML phylogenetic tree construction and analyzed for nucleotide similarities with various subtypes of reassortant H5Nx HA clade 2.3.4.4. Results ML phylogenetic analysis revealed two distinct HA clades, clade 1 and clade 2.3.4, and two distinct NA groups within the corresponding H5 clade 1 viruses. Bayesian phylogenetic reconstruction for molecular clock suggested that the Thai H5N1 HA and NA emerged in 2001.87 (95% HPD: 2001.34-2002.49) and 2002.38 (95% HPD: 2001.99-2002.82), respectively, suggesting that the virus existed before it was first reported in 2004. The Thai H5N1 HA clade 2.3.4 was grouped into corresponding clades 2.3.4, 2.3.4.1, 2.3.4.2, and 2.3.4.3, and shared nucleotide similarities to reassortant H5Nx clade 2.3.4.4 ranged from 92.4-96.8%. Phylogenetic analysis revealed monophyletic H5Nx clade 2.3.4.4 evolved from H5N1 clade 2.3.4. Conclusion H5N1 viruses existed, and were presuma…
format: application/pdf
format: text/html
creator: Pirom Noisumdaeng
creator: Juthamas Phadungsombat
creator: Sasrinakarn Weerated
creator: Witthawat Wiriyarat
creator: Pilaipan Puthavathana
subject: Bioinformatics
subject: Evolutionary Studies
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.14419
publisher: PeerJ Inc.
rights: © 2022 Noisumdaeng et al.
abstract: Background Ongoing outbreaks of H5N1 highly pathogenic avian influenza (HPAI) viruses and the emergence of the genetic-related hemagglutinin (HA) gene of reassortant H5Nx viruses currently circulating in wild birds and poultries pose a great global public health concern. In this study, we comprehensively analyzed the genetic evolution of Thai H5N1 HA and neuraminidase (NA) genes between 2003 and 2010. The H5N1 Thailand virus clade 2.3.4 was also genetically compared to the currently circulating clade 2.3.4.4 of H5Nx viruses. Methods Full-length nucleotide sequences of 178 HA and 143 NA genes of H5N1 viruses circulating between 2003 and 2010 were phylogenetically analyzed using maximum likelihood (ML) phylogenetic construction. Bayesian phylogenetic trees were reconstructed using BEAST analysis with a Bayesian Markov chain Monte Carlo (MCMC) approach. The maximum clade credibility (MCC) tree was determined, and the time of the most recent common ancestor (tMRCA) was estimated. The H5N1 HA nucleotide sequences of clade 2.3.4 Thailand viruses were phylogenetically analyzed using ML phylogenetic tree construction and analyzed for nucleotide similarities with various subtypes of reassortant H5Nx HA clade 2.3.4.4. Results ML phylogenetic analysis revealed two distinct HA clades, clade 1 and clade 2.3.4, and two distinct NA groups within the corresponding H5 clade 1 viruses. Bayesian phylogenetic reconstruction for molecular clock suggested that the Thai H5N1 HA and NA emerged in 2001.87 (95% HPD: 2001.34-2002.49) and 2002.38 (95% HPD: 2001.99-2002.82), respectively, suggesting that the virus existed before it was first reported in 2004. The Thai H5N1 HA clade 2.3.4 was grouped into corresponding clades 2.3.4, 2.3.4.1, 2.3.4.2, and 2.3.4.3, and shared nucleotide similarities to reassortant H5Nx clade 2.3.4.4 ranged from 92.4-96.8%. Phylogenetic analysis revealed monophyletic H5Nx clade 2.3.4.4 evolved from H5N1 clade 2.3.4. Conclusion H5N1 viruses existed, and were presuma…
bibliographic citation: Noisumdaeng et al. (2022) Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand. PeerJ 10:e14419 https://doi.org/10.7717/peerj.14419
date submitted: 2022-06-27
date accepted: 2022-10-28
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Noisumdaeng
  given name: Pirom
author list: Agent
  family name: Phadungsombat
  given name: Juthamas
author list: Agent
  family name: Weerated
  given name: Sasrinakarn
author list: Agent
  family name: Wiriyarat
  given name: Witthawat
author list: Agent
  family name: Puthavathana
  given name: Pilaipan
doi: 10.7717/peerj.14419
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: ©2022 Noisumdaeng et al.
attribution name: Noisumdaeng et al.

Occurrence of Nosemosis in honey bee, Apis mellifera L. at the apiaries of East Kazakhstan
type: item
type: AcademicArticle
description: Nosemosis is the most common disease in honey bee Apis mellifera L., and is a major issue related to bee health worldwide. Therefore, the purpose of this research study was to determine prevalence of microsporidia parasitic infection of the genus Nosema spp. in East Kazakhstan Region (EKR). In the years of 2018 –2021, 394 honey bee samples were collected at 30 apiaries located in four districts of East Kazakhstan Region (Katon-Karagay, Urzhar, Borodulikhinsky, and Shemonaikhinsky). In order to determine the level of infestation, firstly, the presence of Nosema spp. spores was detected using optical microscopy, and then the average amount of spores per bee was counted using a hemocytometer. The degree of nosemosis prevalence was determined in points by means of a semi-quantitative method, and as a percentage from the total of samples and of the amount of positive tests. At the outcome of the study, microsporidia of the genus Nosema spp. were detected in 23.3% of cases (92 samples). Prevalence at its low degree was found in six samples (1.5%), at an average degree in 55 samples (14%), and at a high one in 31 samples (7.9%). This research study proved that microsporidia of the genus Nosema spp. are widely spread at the apiaries of East Kazakhstan Region in different orographic and climatic conditions. Notwithstanding that it was impossible to statistically determine any significant differences between the dependence of nosemosis prevalence and the apiary location, this indicator is actually higher in the mountainous regions than in the steppe. Concurrently, a close inverse correlation was recognized between the amount of spores in one bee and the level of infestation in bee families from the duration of the vegetation season at the apiary location. This gives grounds to assert that the environmental factors have an impact on formation and development of nosemosis. The results of the research presented in the article indicate the need for further research aimed at incre…
format: application/pdf
format: text/html
creator: Abdrakhman Baigazanov
creator: Yelena Tikhomirova
creator: Natalya Valitova
creator: Maral Nurkenova
creator: Ainur Koigeldinova
creator: Elmira Abdullina
creator: Olga Zaikovskaya
creator: Nurgul Ikimbayeva
creator: Dinara Zainettinova
creator: Lyailya Bauzhanova
subject: Agricultural Science
subject: Entomology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.14430
publisher: PeerJ Inc.
rights: © 2022 Baigazanov et al.
abstract: Nosemosis is the most common disease in honey bee Apis mellifera L., and is a major issue related to bee health worldwide. Therefore, the purpose of this research study was to determine prevalence of microsporidia parasitic infection of the genus Nosema spp. in East Kazakhstan Region (EKR). In the years of 2018 –2021, 394 honey bee samples were collected at 30 apiaries located in four districts of East Kazakhstan Region (Katon-Karagay, Urzhar, Borodulikhinsky, and Shemonaikhinsky). In order to determine the level of infestation, firstly, the presence of Nosema spp. spores was detected using optical microscopy, and then the average amount of spores per bee was counted using a hemocytometer. The degree of nosemosis prevalence was determined in points by means of a semi-quantitative method, and as a percentage from the total of samples and of the amount of positive tests. At the outcome of the study, microsporidia of the genus Nosema spp. were detected in 23.3% of cases (92 samples). Prevalence at its low degree was found in six samples (1.5%), at an average degree in 55 samples (14%), and at a high one in 31 samples (7.9%). This research study proved that microsporidia of the genus Nosema spp. are widely spread at the apiaries of East Kazakhstan Region in different orographic and climatic conditions. Notwithstanding that it was impossible to statistically determine any significant differences between the dependence of nosemosis prevalence and the apiary location, this indicator is actually higher in the mountainous regions than in the steppe. Concurrently, a close inverse correlation was recognized between the amount of spores in one bee and the level of infestation in bee families from the duration of the vegetation season at the apiary location. This gives grounds to assert that the environmental factors have an impact on formation and development of nosemosis. The results of the research presented in the article indicate the need for further research aimed at incre…
bibliographic citation: Baigazanov et al. (2022) Occurrence of Nosemosis in honey bee, Apis mellifera L. at the apiaries of East Kazakhstan. PeerJ 10:e14430 https://doi.org/10.7717/peerj.14430
date submitted: 2022-07-07
date accepted: 2022-10-30
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baigazanov
  given name: Abdrakhman
author list: Agent
  family name: Tikhomirova
  given name: Yelena
author list: Agent
  family name: Valitova
  given name: Natalya
author list: Agent
  family name: Nurkenova
  given name: Maral
author list: Agent
  family name: Koigeldinova
  given name: Ainur
author list: Agent
  family name: Abdullina
  given name: Elmira
author list: Agent
  family name: Zaikovskaya
  given name: Olga
author list: Agent
  family name: Ikimbayeva
  given name: Nurgul
author list: Agent
  family name: Zainettinova
  given name: Dinara
author list: Agent
  family name: Bauzhanova
  given name: Lyailya
doi: 10.7717/peerj.14430
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: ©2022 Baigazanov et al.
attribution name: Baigazanov et al.

Hybrid purity identification using EST-SSR markers and heterosis analysis of quantitative traits of Russian wildrye
type: item
type: AcademicArticle
description: Russian wildrye, Psathyrostachys junceus (Fisch.) Nevski, is widely distributed in the high latitude areas of Eurasia. It plays an important role in grassland ecosystem maintenance, as well as being a valuable palatable forage species for livestock and wildlife. Russian wildrye germplasm has rich phenotypic and genetic diversity and has potential for improvement through crossbreeding. In this study, fifteen Russian wildrye hybrid combinations were produced and one F1 population with 123 putative hybrids was obtained by crossing two individual plants with significant differences in nutritional characteristics and reproductive tiller number. Twelve phenotypic traits of the F1 population were measured for three consecutive years, and ten of the twelve traits were in line with the genetic characteristics of quantitative traits. Hybrid superiority was revealed among F1 hybrids in both nutritional and reproductive traits. One non-recurrent parent plant with the highest PCA-synthesis score was selected and used to make a backcross with the ‘BOZOISKY SELECT’ male parent, and 143 putative BC1 hybrids were obtained. Sixteen pairs of EST-SSR primers were randomly selected from polymorphic primers derived from different expressed tiller trait related genes. Three primer pairs that amplified both the paternal and maternal characteristic band were used to assess the purity of the F1 population, and three primer pairs (with one shared primer pair) were used to identify the BC1 population. The hybrid purity was 96.75% for the F1 population and 95.80% for the BC1 population, and the results were confirmed by self-fertility test through bagging isolation. The genetic similarity coefficients between the F1 progeny and the male parent ranged from 0.500 to 0.895, and those between the BC1 progeny and the male parent ranged from 0.667 to 0.939. A subset of individuals in the BC1 population had closer genetic distance to the recurrent parent, and genetic variation within the BC1 populatio…
format: application/pdf
format: text/html
creator: Zhiqi Gao
creator: Lan Yun
creator: Zhen Li
creator: Qiyu Liu
creator: Chen Zhang
creator: Yingmei Ma
creator: Fengling Shi
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.14442
publisher: PeerJ Inc.
rights: © 2022 Gao et al.
abstract: Russian wildrye, Psathyrostachys junceus (Fisch.) Nevski, is widely distributed in the high latitude areas of Eurasia. It plays an important role in grassland ecosystem maintenance, as well as being a valuable palatable forage species for livestock and wildlife. Russian wildrye germplasm has rich phenotypic and genetic diversity and has potential for improvement through crossbreeding. In this study, fifteen Russian wildrye hybrid combinations were produced and one F1 population with 123 putative hybrids was obtained by crossing two individual plants with significant differences in nutritional characteristics and reproductive tiller number. Twelve phenotypic traits of the F1 population were measured for three consecutive years, and ten of the twelve traits were in line with the genetic characteristics of quantitative traits. Hybrid superiority was revealed among F1 hybrids in both nutritional and reproductive traits. One non-recurrent parent plant with the highest PCA-synthesis score was selected and used to make a backcross with the ‘BOZOISKY SELECT’ male parent, and 143 putative BC1 hybrids were obtained. Sixteen pairs of EST-SSR primers were randomly selected from polymorphic primers derived from different expressed tiller trait related genes. Three primer pairs that amplified both the paternal and maternal characteristic band were used to assess the purity of the F1 population, and three primer pairs (with one shared primer pair) were used to identify the BC1 population. The hybrid purity was 96.75% for the F1 population and 95.80% for the BC1 population, and the results were confirmed by self-fertility test through bagging isolation. The genetic similarity coefficients between the F1 progeny and the male parent ranged from 0.500 to 0.895, and those between the BC1 progeny and the male parent ranged from 0.667 to 0.939. A subset of individuals in the BC1 population had closer genetic distance to the recurrent parent, and genetic variation within the BC1 populatio…
bibliographic citation: Gao et al. (2022) Hybrid purity identification using EST-SSR markers and heterosis analysis of quantitative traits of Russian wildrye. PeerJ 10:e14442 https://doi.org/10.7717/peerj.14442
date submitted: 2021-09-01
date accepted: 2022-11-01
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Zhiqi
author list: Agent
  family name: Yun
  given name: Lan
author list: Agent
  family name: Li
  given name: Zhen
author list: Agent
  family name: Liu
  given name: Qiyu
author list: Agent
  family name: Zhang
  given name: Chen
author list: Agent
  family name: Ma
  given name: Yingmei
author list: Agent
  family name: Shi
  given name: Fengling
doi: 10.7717/peerj.14442
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: © 2022 Gao et al.
attribution name: Gao et al.

Adult intussusception: a challenge to laparoscopic surgery?
type: item
type: AcademicArticle
description: Background Intussusception can occur at any age and is common in children but less common in adults. This study aimed to evaluate our experience of 51 adult intussusception and study the etiology, clinical manifestations, diagnosis, and treatment. Methods This analysis assessed the clinical manifestations, etiology, diagnosis, and treatment of adult intussusception in 51 adult patients at the Department of Gastrointestinal Surgery of China-Japan Union Hospital of Jilin University from January 2010 to December 2020. Results The mean age of the cohort was 54.43 ± 18.21 years, and 42 patients were diagnosed by abdominal ultrasonography and abdominal computed tomography (CT). Among them, 76.5% (39/51) had abdominal pain, 11.8% (6/51) had blood in stool, and 5.9% (3/51) had a palpable abdominal mass. Of these, 62.7% had tumors: malignant accounted for 39.2% (20/51) and benign accounted for 23.5% (12/51). CT is the preferred imaging method with a sensitivity of 92.2%, while colonoscopy provides a complementary diagnosis in patients involving the colon. All patients underwent surgical treatment, including 21.6% (11/51) laparoscopic surgery, 74.5% (38/51) open surgery, and 5.9% (3/51) intussusception reduction during the operation. The average operation time of the open group was 133.27 ± 43.75 min and the average hospital stay was 16.24 ± 12.55 days, while the average operation time of the laparoscopic group was 140.50 ± 46.15 mins, and the average hospital stay was 16.60 ± 16.98 days (P > 0.05). Conclusion Adult intussusception is a rare disease in clinic. Laparoscopic surgery can be useful and safe for adult intussusception.
format: application/pdf
format: text/html
creator: Mingze Sun
creator: Zhongmin Li
creator: Zhenbo Shu
creator: Qi Wu
creator: Xue Liu
subject: Gastroenterology and Hepatology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.14495
publisher: PeerJ Inc.
rights: © 2022 Sun et al.
abstract: Background Intussusception can occur at any age and is common in children but less common in adults. This study aimed to evaluate our experience of 51 adult intussusception and study the etiology, clinical manifestations, diagnosis, and treatment. Methods This analysis assessed the clinical manifestations, etiology, diagnosis, and treatment of adult intussusception in 51 adult patients at the Department of Gastrointestinal Surgery of China-Japan Union Hospital of Jilin University from January 2010 to December 2020. Results The mean age of the cohort was 54.43 ± 18.21 years, and 42 patients were diagnosed by abdominal ultrasonography and abdominal computed tomography (CT). Among them, 76.5% (39/51) had abdominal pain, 11.8% (6/51) had blood in stool, and 5.9% (3/51) had a palpable abdominal mass. Of these, 62.7% had tumors: malignant accounted for 39.2% (20/51) and benign accounted for 23.5% (12/51). CT is the preferred imaging method with a sensitivity of 92.2%, while colonoscopy provides a complementary diagnosis in patients involving the colon. All patients underwent surgical treatment, including 21.6% (11/51) laparoscopic surgery, 74.5% (38/51) open surgery, and 5.9% (3/51) intussusception reduction during the operation. The average operation time of the open group was 133.27 ± 43.75 min and the average hospital stay was 16.24 ± 12.55 days, while the average operation time of the laparoscopic group was 140.50 ± 46.15 mins, and the average hospital stay was 16.60 ± 16.98 days (P > 0.05). Conclusion Adult intussusception is a rare disease in clinic. Laparoscopic surgery can be useful and safe for adult intussusception.
bibliographic citation: Sun et al. (2022) Adult intussusception: a challenge to laparoscopic surgery?. PeerJ 10:e14495 https://doi.org/10.7717/peerj.14495
date submitted: 2022-07-28
date accepted: 2022-11-09
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Mingze
author list: Agent
  family name: Li
  given name: Zhongmin
author list: Agent
  family name: Shu
  given name: Zhenbo
author list: Agent
  family name: Wu
  given name: Qi
author list: Agent
  family name: Liu
  given name: Xue
doi: 10.7717/peerj.14495
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: © 2022 Sun et al.
attribution name: Sun et al.

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