PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Whole mitochondrial genome sequencing of Malaysian patients with cardiomyopathy
items: Pre-competition mental energy and performance relationships among physically disabled table tennis players
items: First DNA barcode library for the ichthyofauna of the Jos Plateau (Nigeria) with comments on potential undescribed fish species
items: Determination of exercise intensity domains during upright versus supine cycling: a methodological study
items: Effects of nitrogen and phosphorus addition on growth and leaf nitrogen metabolism of alfalfa in alkaline soil in Yinchuan Plain of Hetao Basin
items: Identifying and characterizing Stagonosporopsis cucurbitacearum causing spot blight on Pinellia ternata in China
items: PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification
items: Sleep health of Australian community tennis players during the COVID-19 lockdown
items: Maternal self-efficacy and emotional well-being in Chilean adolescent mothers: the relationship with their children’s social-emotional development
items: Diurnal pattern of salivary alpha-amylase and cortisol under citric acid stimulation in young adults

Whole mitochondrial genome sequencing of Malaysian patients with cardiomyopathy
type: item
type: AcademicArticle
description: Cardiomyopathy (CMP) constitutes a diverse group of myocardium diseases affecting the pumping ability of the heart. Genetic predisposition is among the major factors affecting the development of CMP. Globally, there are over 100 genes in autosomal and mitochondrial DNA (mtDNA) that have been reported to be associated with the pathogenesis of CMP. However, most of the genetic studies have been conducted in Western countries, with limited data being available for the Asian population. Therefore, this study aims to investigate the mutation spectrum in the mitochondrial genome of 145 CMP patients in Malaysia. Long-range PCR was employed to amplify the entire mtDNA, and whole mitochondrial genome sequencing was conducted on the MiSeq platform. Raw data was quality checked, mapped, and aligned to the revised Cambridge Reference Sequence (rCRS). Variants were named, annotated, and filtered. The sequencing revealed 1,077 variants, including 18 novel and 17 CMP and/or mitochondrial disease-associated variants after filtering. In-silico predictions suggested that three of the novel variants (m.8573G>C, m.11916T>A and m.11918T>G) in this study are potentially pathogenic. Two confirmed pathogenic variants (m.1555A>G and m.11778G>A) were also found in the CMP patients. The findings of this study shed light on the distribution of mitochondrial mutations in Malaysian CMP patients. Further functional studies are required to elucidate the role of these variants in the development of CMP.
format: application/pdf
format: text/html
creator: Sheh Wen Kuan
creator: Kek Heng Chua
creator: E-Wei Tan
creator: Lay Koon Tan
creator: Alexander Loch
creator: Boon Pin Kee
subject: Genomics
subject: Cardiology
subject: Medical Genetics
description: doi:10.7717/peerj.13265
publisher: PeerJ Inc.
rights: © 2022 Kuan et al.
abstract: Cardiomyopathy (CMP) constitutes a diverse group of myocardium diseases affecting the pumping ability of the heart. Genetic predisposition is among the major factors affecting the development of CMP. Globally, there are over 100 genes in autosomal and mitochondrial DNA (mtDNA) that have been reported to be associated with the pathogenesis of CMP. However, most of the genetic studies have been conducted in Western countries, with limited data being available for the Asian population. Therefore, this study aims to investigate the mutation spectrum in the mitochondrial genome of 145 CMP patients in Malaysia. Long-range PCR was employed to amplify the entire mtDNA, and whole mitochondrial genome sequencing was conducted on the MiSeq platform. Raw data was quality checked, mapped, and aligned to the revised Cambridge Reference Sequence (rCRS). Variants were named, annotated, and filtered. The sequencing revealed 1,077 variants, including 18 novel and 17 CMP and/or mitochondrial disease-associated variants after filtering. In-silico predictions suggested that three of the novel variants (m.8573G>C, m.11916T>A and m.11918T>G) in this study are potentially pathogenic. Two confirmed pathogenic variants (m.1555A>G and m.11778G>A) were also found in the CMP patients. The findings of this study shed light on the distribution of mitochondrial mutations in Malaysian CMP patients. Further functional studies are required to elucidate the role of these variants in the development of CMP.
bibliographic citation: Kuan et al. (2022) Whole mitochondrial genome sequencing of Malaysian patients with cardiomyopathy. PeerJ 10:e13265 https://doi.org/10.7717/peerj.13265
date submitted: 2021-11-09
date accepted: 2022-03-23
issued: 2022-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuan
  given name: Sheh Wen
author list: Agent
  family name: Chua
  given name: Kek Heng
author list: Agent
  family name: Tan
  given name: E-Wei
author list: Agent
  family name: Tan
  given name: Lay Koon
author list: Agent
  family name: Loch
  given name: Alexander
author list: Agent
  family name: Kee
  given name: Boon Pin
doi: 10.7717/peerj.13265
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-14
copyright: © 2022 Kuan et al.
attribution name: Kuan et al.

Pre-competition mental energy and performance relationships among physically disabled table tennis players
type: item
type: AcademicArticle
description: Energy is essential to human daily functioning and performance. However, the association of mental energy with athletes’ performance has rarely been examined. We attempted to examine the pre-competition mental energy–performance relationships by two studies. Study 1 administered Athletic Mental Energy Scale (AMES, Lu et al., 2018) to nine elite physically-disabled table tennis players one day before competition in 5 international tournaments. Then, we collected their subjective performance after each competition. In Study 2, we sampled 77 National-level physically-disabled table tennis players and examined the pre-competition mental energy-performance relationship as the procedure in Study 1. Results from Study 1 provided initial findings of how pre-competition mental energy is associated with performance and portrayed in elite physically-disabled table tennis players. Results from Study 2 further confirmed the pre-competition mental energy- performance relationships. We suggested future studies to examine the mental energy–performance relationships in physically-disabled and abled athletes and different sports.
format: application/pdf
format: text/html
creator: Wen-Chuan Chuang
creator: Frank J.H. Lu
creator: Diane L. Gill
creator: Bin-Bin Fang
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13294
publisher: PeerJ Inc.
rights: © 2022 Chuang et al.
abstract: Energy is essential to human daily functioning and performance. However, the association of mental energy with athletes’ performance has rarely been examined. We attempted to examine the pre-competition mental energy–performance relationships by two studies. Study 1 administered Athletic Mental Energy Scale (AMES, Lu et al., 2018) to nine elite physically-disabled table tennis players one day before competition in 5 international tournaments. Then, we collected their subjective performance after each competition. In Study 2, we sampled 77 National-level physically-disabled table tennis players and examined the pre-competition mental energy-performance relationship as the procedure in Study 1. Results from Study 1 provided initial findings of how pre-competition mental energy is associated with performance and portrayed in elite physically-disabled table tennis players. Results from Study 2 further confirmed the pre-competition mental energy- performance relationships. We suggested future studies to examine the mental energy–performance relationships in physically-disabled and abled athletes and different sports.
bibliographic citation: Chuang et al. (2022) Pre-competition mental energy and performance relationships among physically disabled table tennis players. PeerJ 10:e13294 https://doi.org/10.7717/peerj.13294
date submitted: 2021-12-23
date accepted: 2022-03-28
issued: 2022-04-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chuang
  given name: Wen-Chuan
author list: Agent
  family name: Lu
  given name: Frank J.H.
author list: Agent
  family name: Gill
  given name: Diane L.
author list: Agent
  family name: Fang
  given name: Bin-Bin
doi: 10.7717/peerj.13294
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-14
copyright: ©2022 Chuang et al.
attribution name: Chuang et al.

First DNA barcode library for the ichthyofauna of the Jos Plateau (Nigeria) with comments on potential undescribed fish species
type: item
type: AcademicArticle
description: Located in the central region of northern Nigeria, the Jos Plateau covers approximately 9,400 km² with an average altitude of 1,280 m and constitutes a unique terrestrial ecoregion known as the Jos Plateau forest-grassland mosaic. The biota of the Jos Plateau include endemic elements, but very limited information is available on its ichthyofauna. This is despite the fact that the ancient plateau contributes to several large rivers spanning multiple major drainage systems including the Niger and Benue Rivers, and Lake Chad. This study provides the first species list for the fishes of the Jos Plateau based mainly on 175 DNA barcoded museum voucher specimens representing 20 species, and another three species without a DNA barcode. In total, 23 species from eight families and 17 genera were collected from the Jos Plateau including five putatively new species, four in the family Cyprinidae and one in the Clariidae. With ten species, the Cyprinidae is the most diverse fish family on the Jos Plateau, followed by Clariidae and Cichlidae, each with three species. The study also provides data on species distribution and habitat parameters including information on water chemistry that strongly suggests that selected water bodies are heavily impacted by anthropogenic activities. Urgent management steps are required to preserve the unique and diverse fish communities of the Jos Plateau and their habitats.
format: application/pdf
format: text/html
creator: Michael Olaoluwa Popoola
creator: Frédéric Dieter Benedikt Schedel
creator: Paul DN Hebert
creator: Ulrich Kurt Schliewen
subject: Biodiversity
subject: Bioinformatics
subject: Genetics
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13049
publisher: PeerJ Inc.
rights: © 2022 Popoola et al.
abstract: Located in the central region of northern Nigeria, the Jos Plateau covers approximately 9,400 km² with an average altitude of 1,280 m and constitutes a unique terrestrial ecoregion known as the Jos Plateau forest-grassland mosaic. The biota of the Jos Plateau include endemic elements, but very limited information is available on its ichthyofauna. This is despite the fact that the ancient plateau contributes to several large rivers spanning multiple major drainage systems including the Niger and Benue Rivers, and Lake Chad. This study provides the first species list for the fishes of the Jos Plateau based mainly on 175 DNA barcoded museum voucher specimens representing 20 species, and another three species without a DNA barcode. In total, 23 species from eight families and 17 genera were collected from the Jos Plateau including five putatively new species, four in the family Cyprinidae and one in the Clariidae. With ten species, the Cyprinidae is the most diverse fish family on the Jos Plateau, followed by Clariidae and Cichlidae, each with three species. The study also provides data on species distribution and habitat parameters including information on water chemistry that strongly suggests that selected water bodies are heavily impacted by anthropogenic activities. Urgent management steps are required to preserve the unique and diverse fish communities of the Jos Plateau and their habitats.
bibliographic citation: Popoola et al. (2022) First DNA barcode library for the ichthyofauna of the Jos Plateau (Nigeria) with comments on potential undescribed fish species. PeerJ 10:e13049 https://doi.org/10.7717/peerj.13049
date submitted: 2021-07-01
date accepted: 2022-02-11
issued: 2022-04-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Popoola
  given name: Michael Olaoluwa
author list: Agent
  family name: Schedel
  given name: Frédéric Dieter Benedikt
author list: Agent
  family name: Hebert
  given name: Paul DN
author list: Agent
  family name: Schliewen
  given name: Ulrich Kurt
doi: 10.7717/peerj.13049
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-13
copyright: © 2022 Popoola et al.
attribution name: Popoola et al.

Determination of exercise intensity domains during upright versus supine cycling: a methodological study
type: item
type: AcademicArticle
description: Background There is a growing interest among the research community and clinical practitioners to investigate cardiopulmonary exercise test (CPET) procedures and protocols utilized in supine cycling. Materials and Methods The current study investigated the effects of posture on indicators of exercise intensity including gas exchange threshold (GET), respiratory compensation point (RCP), and the rate of peak oxygen uptake (V̇O2 peak), as well as the role of V̇O2 mean response time (MRT) in determining exercise intensity domains in nineteen healthy men (age: 22 ± 3 years). Two moderate-intensity step-transitions from 20 to 100 Watt (W) were completed, followed by a maximal CPET. After completing the ramp test, participants performed a constant-load at 90% of their attained peak power output (PPO). Results No differences were observed in the V̇O2 MRT between the two positions, although the phase II-time constant (τV̇O2p) was 7 s slower in supine position compared to upright (p = 0.001). The rate of O2 uptake in the supine position at GET and RCP were lower compared to the upright position (208 ± 200 mL·min−1 (p = 0.007) and 265 ± 235 mL·min−1 (p = 0.012) respectively). Besides, V̇O2 peak was significantly decreased (by 6%, p = 0.002) during supine position. These findings were confirmed by the wide limits of agreement between the measures of V̇O2 in different postures (V̇O2 peak: −341 to 859; constant-load test: −528 to 783; GET: −375 to 789; RCP: −520 to 1021 all in mL·min−1). Conclusion Since an accurate identification of an appropriate power output (PO) from a single-visit CPET remains a matter of debate, especially for supine cycling, we propose that moderate-intensity step-transitions preceding a ramp CPET could be a viable addition to ensure appropriate exercise-intensity domain determination, in particular upon GET-based prescription.
format: application/pdf
format: text/html
creator: Damir Zubac
creator: Vladimir Ivančev
creator: Vincent Martin
creator: Antonio Dello Iacono
creator: Cécil J.W. Meulenberg
creator: Adam C. McDonnell
subject: Public Health
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.13199
publisher: PeerJ Inc.
rights: © 2022 Zubac et al.
abstract: Background There is a growing interest among the research community and clinical practitioners to investigate cardiopulmonary exercise test (CPET) procedures and protocols utilized in supine cycling. Materials and Methods The current study investigated the effects of posture on indicators of exercise intensity including gas exchange threshold (GET), respiratory compensation point (RCP), and the rate of peak oxygen uptake (V̇O2 peak), as well as the role of V̇O2 mean response time (MRT) in determining exercise intensity domains in nineteen healthy men (age: 22 ± 3 years). Two moderate-intensity step-transitions from 20 to 100 Watt (W) were completed, followed by a maximal CPET. After completing the ramp test, participants performed a constant-load at 90% of their attained peak power output (PPO). Results No differences were observed in the V̇O2 MRT between the two positions, although the phase II-time constant (τV̇O2p) was 7 s slower in supine position compared to upright (p = 0.001). The rate of O2 uptake in the supine position at GET and RCP were lower compared to the upright position (208 ± 200 mL·min−1 (p = 0.007) and 265 ± 235 mL·min−1 (p = 0.012) respectively). Besides, V̇O2 peak was significantly decreased (by 6%, p = 0.002) during supine position. These findings were confirmed by the wide limits of agreement between the measures of V̇O2 in different postures (V̇O2 peak: −341 to 859; constant-load test: −528 to 783; GET: −375 to 789; RCP: −520 to 1021 all in mL·min−1). Conclusion Since an accurate identification of an appropriate power output (PO) from a single-visit CPET remains a matter of debate, especially for supine cycling, we propose that moderate-intensity step-transitions preceding a ramp CPET could be a viable addition to ensure appropriate exercise-intensity domain determination, in particular upon GET-based prescription.
bibliographic citation: Zubac et al. (2022) Determination of exercise intensity domains during upright versus supine cycling: a methodological study. PeerJ 10:e13199 https://doi.org/10.7717/peerj.13199
date submitted: 2022-01-21
date accepted: 2022-03-09
issued: 2022-04-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zubac
  given name: Damir
author list: Agent
  family name: Ivančev
  given name: Vladimir
author list: Agent
  family name: Martin
  given name: Vincent
author list: Agent
  family name: Dello Iacono
  given name: Antonio
author list: Agent
  family name: Meulenberg
  given name: Cécil J.W.
author list: Agent
  family name: McDonnell
  given name: Adam C.
doi: 10.7717/peerj.13199
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-13
copyright: © 2022 Zubac et al.
attribution name: Zubac et al.

Effects of nitrogen and phosphorus addition on growth and leaf nitrogen metabolism of alfalfa in alkaline soil in Yinchuan Plain of Hetao Basin
type: item
type: AcademicArticle
description: Alkaline soil is widely distributed in China. Its rational utilization is an effective measure to solve land shortage and improve the environment. Alfalfa is characterized by strong salt and alkali tolerance and high yield and protein content. Nitrogen (N) and phosphorus (P) are the main nutrients for plant growth, and N metabolism is one of the primary forms of plant metabolism, which plays a vital role in quality and yield formation. The exploration of the effect of N and P on N metabolism and alfalfa growth will provide a theoretical basis for scientific fertilization for alfalfa in the alkaline soil of the Yinchuan Plain of the Hetao Basin. Therefore, a 2-year experiment of N and P addition was conducted. Six treatments were set up with a randomized block design, including without N (WN), medium N (MN), high N (HN), without P (WP), medium P (MP), and high P (HP). It was found that the MN and MP treatments increased plant height, stem diameter, stem/leaf, dry/fresh, and dry matter of alfalfa. The HN and HP treatments inhibited alfalfa biomass formation. The MN and MP treatments increased key products and enzymes of leaf N metabolism of alfalfa and promoted activities of leaf nitrate reductase (NR), glutamine synthase (GS), glutamate synthase (GOGAT), glutamic-oxalacetic transaminase (GOT), and glutamic-pyruvate transaminase (GPT), and inhibited activities of leaf protease of alfalfa. The MN and MP treatments increased contents of leaf N, P, ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3−-N), total chlorophyll, and protein and reduced leaf chlorophyll a/b and amino acid, results after HN and HP treatments were opposite. The correlation among leaf P, N, NO3−-N, amino acid, and protein reached significant levels (P < 0.01). It is suggested that MN and MP treatments can improve the yield and quality of alfalfa by increasing key products and enzymes of N metabolism and can be adopted to promote alfalfa production in the alkaline soil of the Yinchuan Plain of the He…
format: application/pdf
format: text/html
creator: Gu Xudong
creator: Zhang Fengju
creator: Wang Teng
creator: Xie Xiaowei
creator: Jia Xiaohui
creator: Xu Xing
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.13261
publisher: PeerJ Inc.
rights: © 2022 Xudong et al.
abstract: Alkaline soil is widely distributed in China. Its rational utilization is an effective measure to solve land shortage and improve the environment. Alfalfa is characterized by strong salt and alkali tolerance and high yield and protein content. Nitrogen (N) and phosphorus (P) are the main nutrients for plant growth, and N metabolism is one of the primary forms of plant metabolism, which plays a vital role in quality and yield formation. The exploration of the effect of N and P on N metabolism and alfalfa growth will provide a theoretical basis for scientific fertilization for alfalfa in the alkaline soil of the Yinchuan Plain of the Hetao Basin. Therefore, a 2-year experiment of N and P addition was conducted. Six treatments were set up with a randomized block design, including without N (WN), medium N (MN), high N (HN), without P (WP), medium P (MP), and high P (HP). It was found that the MN and MP treatments increased plant height, stem diameter, stem/leaf, dry/fresh, and dry matter of alfalfa. The HN and HP treatments inhibited alfalfa biomass formation. The MN and MP treatments increased key products and enzymes of leaf N metabolism of alfalfa and promoted activities of leaf nitrate reductase (NR), glutamine synthase (GS), glutamate synthase (GOGAT), glutamic-oxalacetic transaminase (GOT), and glutamic-pyruvate transaminase (GPT), and inhibited activities of leaf protease of alfalfa. The MN and MP treatments increased contents of leaf N, P, ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3−-N), total chlorophyll, and protein and reduced leaf chlorophyll a/b and amino acid, results after HN and HP treatments were opposite. The correlation among leaf P, N, NO3−-N, amino acid, and protein reached significant levels (P < 0.01). It is suggested that MN and MP treatments can improve the yield and quality of alfalfa by increasing key products and enzymes of N metabolism and can be adopted to promote alfalfa production in the alkaline soil of the Yinchuan Plain of the He…
bibliographic citation: Xudong et al. (2022) Effects of nitrogen and phosphorus addition on growth and leaf nitrogen metabolism of alfalfa in alkaline soil in Yinchuan Plain of Hetao Basin. PeerJ 10:e13261 https://doi.org/10.7717/peerj.13261
date submitted: 2021-11-22
date accepted: 2022-03-22
issued: 2022-04-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xudong
  given name: Gu
author list: Agent
  family name: Fengju
  given name: Zhang
author list: Agent
  family name: Teng
  given name: Wang
author list: Agent
  family name: Xiaowei
  given name: Xie
author list: Agent
  family name: Xiaohui
  given name: Jia
author list: Agent
  family name: Xing
  given name: Xu
doi: 10.7717/peerj.13261
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-13
copyright: © 2022 Xudong et al.
attribution name: Xudong et al.

Identifying and characterizing Stagonosporopsis cucurbitacearum causing spot blight on Pinellia ternata in China
type: item
type: AcademicArticle
description: Background Pinellia ternata (Thunb.), a perennial herbal plant in the Araceae family, has great medicinal value and market demand. In August 2020, an outbreak of severe leaf spot blight disease resulted in a huge yield loss of P. ternata. It is necessary to isolate and identify the pathogens that cause spot blight on P. ternata. Methods In this study, we isolated and identified the pathogens by fulfilling Koch’s postulates. Disease samples with typical spot blight symptoms were collected and pathogens were isolated from the diseased tissues. The pathogen was identified based on its biological characteristics and molecular analysis of internal transcribed (rDNA-ITS) and large subunit (LSU) sequences. Phylogenetic tree were constructed using MEGA7 software and pathogenicity tests were performed using in vivo inoculation. Finally, the pathogen was recovered and identified from the inoculated plants. Results Based on Koch’s postulates, we identified the pathogen causing spot blight on P. ternata as Stagonosporopsis cucurbitacearum. To our knowledge, this is the first study to explore spot blight on P. ternata caused by S. cucurbitacearum in China.
format: application/pdf
format: text/html
creator: Jia Zhou
creator: Jiawei Xu
creator: Rong Xu
creator: Qiaohuan Chen
creator: Yunhan Wang
creator: Bisheng Huang
creator: Dahui Liu
creator: Yuhuan Miao
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.13278
publisher: PeerJ Inc.
rights: © 2022 Zhou et al.
abstract: Background Pinellia ternata (Thunb.), a perennial herbal plant in the Araceae family, has great medicinal value and market demand. In August 2020, an outbreak of severe leaf spot blight disease resulted in a huge yield loss of P. ternata. It is necessary to isolate and identify the pathogens that cause spot blight on P. ternata. Methods In this study, we isolated and identified the pathogens by fulfilling Koch’s postulates. Disease samples with typical spot blight symptoms were collected and pathogens were isolated from the diseased tissues. The pathogen was identified based on its biological characteristics and molecular analysis of internal transcribed (rDNA-ITS) and large subunit (LSU) sequences. Phylogenetic tree were constructed using MEGA7 software and pathogenicity tests were performed using in vivo inoculation. Finally, the pathogen was recovered and identified from the inoculated plants. Results Based on Koch’s postulates, we identified the pathogen causing spot blight on P. ternata as Stagonosporopsis cucurbitacearum. To our knowledge, this is the first study to explore spot blight on P. ternata caused by S. cucurbitacearum in China.
bibliographic citation: Zhou et al. (2022) Identifying and characterizing Stagonosporopsis cucurbitacearum causing spot blight on Pinellia ternata in China. PeerJ 10:e13278 https://doi.org/10.7717/peerj.13278
date submitted: 2022-01-13
date accepted: 2022-03-24
issued: 2022-04-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Jia
author list: Agent
  family name: Xu
  given name: Jiawei
author list: Agent
  family name: Xu
  given name: Rong
author list: Agent
  family name: Chen
  given name: Qiaohuan
author list: Agent
  family name: Wang
  given name: Yunhan
author list: Agent
  family name: Huang
  given name: Bisheng
author list: Agent
  family name: Liu
  given name: Dahui
author list: Agent
  family name: Miao
  given name: Yuhuan
doi: 10.7717/peerj.13278
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-13
copyright: © 2022 Zhou et al.
attribution name: Zhou et al.

PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification
type: item
type: AcademicArticle
description: Motivation Since the identification of the novel coronavirus (SARS-CoV-2), the scientific community has made a huge effort to understand the virus biology and to develop vaccines. Next-generation sequencing strategies have been successful in understanding the evolution of infectious diseases as well as facilitating the development of molecular diagnostics and treatments. Thousands of genomes are being generated weekly to understand the genetic characteristics of this virus. Efficient pipelines are needed to analyze the vast amount of data generated. Here we present a new pipeline designed for genomic analysis and variant identification of the SARS-CoV-2 virus. Results PipeCoV shows better performance when compared to well-established SARS-CoV-2 pipelines, with a lower content of Ns and higher genome coverage when compared to the Wuhan reference. It also provides a variant report not offered by other tested pipelines. Availability https://github.com/alvesrco/pipecov.
format: application/pdf
format: text/html
creator: Renato R. M. Oliveira
creator: Tatianne Costa Negri
creator: Gisele Nunes
creator: Inácio Medeiros
creator: Guilherme Araújo
creator: Fabricio de Oliveira Silva
creator: Jorge Estefano Santana de Souza
creator: Ronnie Alves
creator: Guilherme Oliveira
subject: Bioinformatics
subject: Genomics
subject: Virology
subject: COVID-19
description: doi:10.7717/peerj.13300
publisher: PeerJ Inc.
rights: © 2022 Oliveira et al.
abstract: Motivation Since the identification of the novel coronavirus (SARS-CoV-2), the scientific community has made a huge effort to understand the virus biology and to develop vaccines. Next-generation sequencing strategies have been successful in understanding the evolution of infectious diseases as well as facilitating the development of molecular diagnostics and treatments. Thousands of genomes are being generated weekly to understand the genetic characteristics of this virus. Efficient pipelines are needed to analyze the vast amount of data generated. Here we present a new pipeline designed for genomic analysis and variant identification of the SARS-CoV-2 virus. Results PipeCoV shows better performance when compared to well-established SARS-CoV-2 pipelines, with a lower content of Ns and higher genome coverage when compared to the Wuhan reference. It also provides a variant report not offered by other tested pipelines. Availability https://github.com/alvesrco/pipecov.
bibliographic citation: Oliveira et al. (2022) PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification. PeerJ 10:e13300 https://doi.org/10.7717/peerj.13300
date submitted: 2021-11-22
date accepted: 2022-03-29
issued: 2022-04-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliveira
  given name: Renato R. M.
author list: Agent
  family name: Costa Negri
  given name: Tatianne
author list: Agent
  family name: Nunes
  given name: Gisele
author list: Agent
  family name: Medeiros
  given name: Inácio
author list: Agent
  family name: Araújo
  given name: Guilherme
author list: Agent
  family name: de Oliveira Silva
  given name: Fabricio
author list: Agent
  family name: Estefano Santana de Souza
  given name: Jorge
author list: Agent
  family name: Alves
  given name: Ronnie
author list: Agent
  family name: Oliveira
  given name: Guilherme
doi: 10.7717/peerj.13300
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-13
copyright: © 2022 Oliveira et al.
attribution name: Oliveira et al.

Sleep health of Australian community tennis players during the COVID-19 lockdown
type: item
type: AcademicArticle
description: Background Poorer sleep health outcomes have been documented in the general population during the COVID-19 outbreak. However, the impact of the COVID-19 outbreak on sleep health outcomes in specific population groups, including the sporting community, has not been extensively investigated. This study evaluated sleep health outcomes and their relationship with lifestyle behaviours during the initial COVID-19 lockdown period in Australian community tennis players. Methods This cross-sectional study evaluated sleep health outcomes and lifestyle behaviours using an online survey. The survey was disseminated online between the 24th of April and the 6th of June 2020 and comprised the Sleep Health Index, Sleep Satisfaction Tool and questions regarding weekly hours of tennis play, general physical activity, training location and alcohol consumption. Two-hundred and eighty-five individuals completed the survey. Results Compared to normative data, respondents displayed positive sleep health values during the initial COVID-19 lockdown period, with median values (IQR) of 85.3 (73.4, 91.7) and 64.8 (54.4, 73.4) for the Sleep Health Index and Sleep Satisfaction Tool, respectively. Sleep health outcomes were not significantly correlated (p > 0.05) with tennis play (Tb = 0.054–0.077), physical activity (Tb = −0.008 to 0.036), training location (Tb = −0.012 to −0.005) or alcohol consumption (Tb = −0.079 to −0.018). Conclusion Positive sleep health values were observed in Australian community-level tennis players during the initial COVID-19 pandemic. Sleep health values were not associated with lifestyle behaviours. Other unexplored factors may have influenced sleep health outcomes, including personal finances and socialisation, however these factors need to be investigated in future studies.
format: application/pdf
format: text/html
creator: Philipp Beranek
creator: Travis Cruickshank
creator: Olivier Girard
creator: Kazunori Nosaka
creator: Danielle Bartlett
creator: Mitchell Turner
subject: Global Health
subject: Public Health
description: doi:10.7717/peerj.13045
publisher: PeerJ Inc.
rights: © 2022 Beranek et al.
abstract: Background Poorer sleep health outcomes have been documented in the general population during the COVID-19 outbreak. However, the impact of the COVID-19 outbreak on sleep health outcomes in specific population groups, including the sporting community, has not been extensively investigated. This study evaluated sleep health outcomes and their relationship with lifestyle behaviours during the initial COVID-19 lockdown period in Australian community tennis players. Methods This cross-sectional study evaluated sleep health outcomes and lifestyle behaviours using an online survey. The survey was disseminated online between the 24th of April and the 6th of June 2020 and comprised the Sleep Health Index, Sleep Satisfaction Tool and questions regarding weekly hours of tennis play, general physical activity, training location and alcohol consumption. Two-hundred and eighty-five individuals completed the survey. Results Compared to normative data, respondents displayed positive sleep health values during the initial COVID-19 lockdown period, with median values (IQR) of 85.3 (73.4, 91.7) and 64.8 (54.4, 73.4) for the Sleep Health Index and Sleep Satisfaction Tool, respectively. Sleep health outcomes were not significantly correlated (p > 0.05) with tennis play (Tb = 0.054–0.077), physical activity (Tb = −0.008 to 0.036), training location (Tb = −0.012 to −0.005) or alcohol consumption (Tb = −0.079 to −0.018). Conclusion Positive sleep health values were observed in Australian community-level tennis players during the initial COVID-19 pandemic. Sleep health values were not associated with lifestyle behaviours. Other unexplored factors may have influenced sleep health outcomes, including personal finances and socialisation, however these factors need to be investigated in future studies.
bibliographic citation: Beranek et al. (2022) Sleep health of Australian community tennis players during the COVID-19 lockdown. PeerJ 10:e13045 https://doi.org/10.7717/peerj.13045
date submitted: 2021-08-23
date accepted: 2022-02-10
issued: 2022-04-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beranek
  given name: Philipp
author list: Agent
  family name: Cruickshank
  given name: Travis
author list: Agent
  family name: Girard
  given name: Olivier
author list: Agent
  family name: Nosaka
  given name: Kazunori
author list: Agent
  family name: Bartlett
  given name: Danielle
author list: Agent
  family name: Turner
  given name: Mitchell
doi: 10.7717/peerj.13045
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-12
copyright: © 2022 Beranek et al.
attribution name: Beranek et al.

Maternal self-efficacy and emotional well-being in Chilean adolescent mothers: the relationship with their children’s social-emotional development
type: item
type: AcademicArticle
description: Background Low maternal self-efficacy and high levels of anxiety, depression, and stress can be triggered in adolescent mothers due to an incomplete development process that makes them physically or psychologically unprepared for the responsibilities of motherhood and parenting. These factors may be linked to difficulties with their children’s social-emotional development. The present study aims to: (a) analyze the relationship between maternal self-efficacy and stress, depression, and anxiety levels in low-income adolescent mothers; (b) examine the relationship between maternal self-efficacy and well-being with children’s social-emotional development; and (c) describe the effects of maternal self-efficacy on children’s social-emotional development, mediated by maternal well-being. Methods A sample of 79 dyads comprising low-income Chilean adolescent mothers aged from 15 to 21 years old (M = 19.1, SD = 1.66) and their children aged 10 to 24 months (M = 15.5, SD = 4.2) participated in this research. A set of psychometric scales was used to measure maternal self-efficacy (Parental Evaluation Scale, EEP), the mothers’ anxiety and depression (Hospital Anxiety and Depression Scale, HADS), maternal stress (Parental Stress Scale, PSS), and the children’s social-emotional development (Ages and Stages Questionnaire Socio-emotional, ASQ-SE). Bivariate analyses and mediation models were employed to estimate and test the relevant relationships. Results A bivariate analysis showed that maternal self-efficacy was negatively related to the mother’s anxiety, depression, and stress. Moreover, there was a significant relationship between maternal self-efficacy and maternal stress, and children’s self-regulation and social-emotional development. Maternal self-efficacy, mediated by maternal anxiety, depression, and stress scores, had a significant effect on the development of children’s self-regulation. Conclusions The results confirm the importance of adolescent mothers’ emotional wel…
format: application/pdf
format: text/html
creator: Laura Léniz-Maturana
creator: Rosa Vilaseca
creator: David Leiva
subject: Global Health
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Women’s Health
description: doi:10.7717/peerj.13162
publisher: PeerJ Inc.
rights: © 2022 Léniz-Maturana et al.
abstract: Background Low maternal self-efficacy and high levels of anxiety, depression, and stress can be triggered in adolescent mothers due to an incomplete development process that makes them physically or psychologically unprepared for the responsibilities of motherhood and parenting. These factors may be linked to difficulties with their children’s social-emotional development. The present study aims to: (a) analyze the relationship between maternal self-efficacy and stress, depression, and anxiety levels in low-income adolescent mothers; (b) examine the relationship between maternal self-efficacy and well-being with children’s social-emotional development; and (c) describe the effects of maternal self-efficacy on children’s social-emotional development, mediated by maternal well-being. Methods A sample of 79 dyads comprising low-income Chilean adolescent mothers aged from 15 to 21 years old (M = 19.1, SD = 1.66) and their children aged 10 to 24 months (M = 15.5, SD = 4.2) participated in this research. A set of psychometric scales was used to measure maternal self-efficacy (Parental Evaluation Scale, EEP), the mothers’ anxiety and depression (Hospital Anxiety and Depression Scale, HADS), maternal stress (Parental Stress Scale, PSS), and the children’s social-emotional development (Ages and Stages Questionnaire Socio-emotional, ASQ-SE). Bivariate analyses and mediation models were employed to estimate and test the relevant relationships. Results A bivariate analysis showed that maternal self-efficacy was negatively related to the mother’s anxiety, depression, and stress. Moreover, there was a significant relationship between maternal self-efficacy and maternal stress, and children’s self-regulation and social-emotional development. Maternal self-efficacy, mediated by maternal anxiety, depression, and stress scores, had a significant effect on the development of children’s self-regulation. Conclusions The results confirm the importance of adolescent mothers’ emotional wel…
bibliographic citation: Léniz-Maturana et al. (2022) Maternal self-efficacy and emotional well-being in Chilean adolescent mothers: the relationship with their children’s social-emotional development. PeerJ 10:e13162 https://doi.org/10.7717/peerj.13162
date submitted: 2021-05-03
date accepted: 2022-03-03
issued: 2022-04-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Léniz-Maturana
  given name: Laura
author list: Agent
  family name: Vilaseca
  given name: Rosa
author list: Agent
  family name: Leiva
  given name: David
doi: 10.7717/peerj.13162
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-12
copyright: © 2022 Léniz-Maturana et al.
attribution name: Léniz-Maturana et al.

Diurnal pattern of salivary alpha-amylase and cortisol under citric acid stimulation in young adults
type: item
type: AcademicArticle
description: Background Saliva composition has diurnal variations. Citric acid stimulation plays a major role in the change of salivary flow rate and salivary composition. However, diurnal variations and sex differences in salivary alpha-amylase (sAA), pH, salivary flow rate (SFR), and salivary cortisol before and after citric acid stimulation remain unclear. Methods We recruited 30 healthy volunteers, including 15 women (24.7 ± 1.0 years old) and 15 men (25.3 ± 1.3 years old). At four time points (T1, 7:00; T2, 10:00; T3, 16:00; and T4, 20:00), saliva was collected from healthy volunteers before and after citric acid stimulation; and sAA, pH, SFR and salivary cortisol were measured and compared between men and women. Results There were circadian fluctuations in sAA activity, SFR, pH, and cortisol level both before and after citric acid stimulation, and the diurnal fluctuations of these indexes were not affected by citric acid stimulation. There were significant differences in salivary cortisol between men and women before and after acid stimulation in T1. Neither SFR nor pH showed sex-related differences before or after acid stimulation. The variation trend of sAA activity was contrary to that of cortisol, with a significant negative correlation. Conclusions Our data suggest that sAA and cortisol showed diurnal fluctuation, and the variation characteristics of male and female under resting state and acid stimulation were basically the same. The variation trend of salivary alpha-amylase activity was opposite to that of cortisol, with significant negative correlation. Our findings may enable the selection of the correct sampling time for research and the selection of appropriate sampling strategies in studies investigating chronic psychosocial conditions.
format: application/pdf
format: text/html
creator: Haimei Xie
creator: Xiaomei Zheng
creator: Ye Huang
creator: Weihao Li
creator: Wenkai Wang
creator: Qiao Li
creator: Jiangtao Hou
creator: Lulu Luo
creator: Xiuying Kuang
creator: Chuan-quan Lin
subject: Anatomy and Physiology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.13178
publisher: PeerJ Inc.
rights: © 2022 Xie et al.
abstract: Background Saliva composition has diurnal variations. Citric acid stimulation plays a major role in the change of salivary flow rate and salivary composition. However, diurnal variations and sex differences in salivary alpha-amylase (sAA), pH, salivary flow rate (SFR), and salivary cortisol before and after citric acid stimulation remain unclear. Methods We recruited 30 healthy volunteers, including 15 women (24.7 ± 1.0 years old) and 15 men (25.3 ± 1.3 years old). At four time points (T1, 7:00; T2, 10:00; T3, 16:00; and T4, 20:00), saliva was collected from healthy volunteers before and after citric acid stimulation; and sAA, pH, SFR and salivary cortisol were measured and compared between men and women. Results There were circadian fluctuations in sAA activity, SFR, pH, and cortisol level both before and after citric acid stimulation, and the diurnal fluctuations of these indexes were not affected by citric acid stimulation. There were significant differences in salivary cortisol between men and women before and after acid stimulation in T1. Neither SFR nor pH showed sex-related differences before or after acid stimulation. The variation trend of sAA activity was contrary to that of cortisol, with a significant negative correlation. Conclusions Our data suggest that sAA and cortisol showed diurnal fluctuation, and the variation characteristics of male and female under resting state and acid stimulation were basically the same. The variation trend of salivary alpha-amylase activity was opposite to that of cortisol, with significant negative correlation. Our findings may enable the selection of the correct sampling time for research and the selection of appropriate sampling strategies in studies investigating chronic psychosocial conditions.
bibliographic citation: Xie et al. (2022) Diurnal pattern of salivary alpha-amylase and cortisol under citric acid stimulation in young adults. PeerJ 10:e13178 https://doi.org/10.7717/peerj.13178
date submitted: 2021-10-27
date accepted: 2022-03-07
issued: 2022-04-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Haimei
author list: Agent
  family name: Zheng
  given name: Xiaomei
author list: Agent
  family name: Huang
  given name: Ye
author list: Agent
  family name: Li
  given name: Weihao
author list: Agent
  family name: Wang
  given name: Wenkai
author list: Agent
  family name: Li
  given name: Qiao
author list: Agent
  family name: Hou
  given name: Jiangtao
author list: Agent
  family name: Luo
  given name: Lulu
author list: Agent
  family name: Kuang
  given name: Xiuying
author list: Agent
  family name: Lin
  given name: Chuan-quan
doi: 10.7717/peerj.13178
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-12
copyright: ©2022 Xie et al.
attribution name: Xie et al.

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