PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Caragana korshinskii Kom. plantation reduced soil aggregate stability and aggregate-associated organic carbon on desert steppe
items: Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets
items: Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs
items: Interrogating COVID-19 vaccine intent in the Philippines with a nationwide open-access online survey
items: Effect of interaction between occupational stress and polymorphisms of MTHFR gene and SELE gene on hypertension
items: Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China
items: New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea)
items: The impact of COVID-19 and control measures on public health in Thailand, 2020
items: In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury
items: A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)

Caragana korshinskii Kom. plantation reduced soil aggregate stability and aggregate-associated organic carbon on desert steppe
type: item
type: AcademicArticle
description: Background After implementing of the “Grain-for-Green” project, Caragana korshinskii Kom. has been widely planted in China’s arid regions. Although natural restoration grassland and artificial Caragana plantations measures have long been focuses in carbon research, the combined influence of natural restoration grassland and artificial Caragana plantation measures on aggregate stability and the aggregate-associated organic carbon (OC) remains unclear. Method We selected natural grassland (NG) and three different densities of Caragana plantations (high planting density, HG; middle planting density, MD; low planting density, LD) on desert steppe. The soil aggregate distribution and stability index such as fractal dimension (D), mean weight diameter (MWD), geometric mean diameter (GMD), percentage of aggregation destruction (PAD), as well as aggregate-associated OC concentration and stock were measured. Results Results shows that the soil aggregates were primarily macroaggregates (>2 mm) and mesoaggregates (0.25–2 mm) under dry sieving while microaggregates (<0.25 mm) were preponderant under wet sieving (more than 57%). Overall, compared with Caragana plantations, the MWD (4.43 and 4.51 mm) and GMD (1.72 and 1.83 mm) were both highest in two soil layers under the NG and the D (2.77 and 2.71) was lowest. Compared with the NG, the aggregate-associated OC stocks in the 0–40 cm depths in the LD, MD, and HD decreased by 41.54%, 46.93%, and 42.03%, respectively. SOC stock was mainly concentrated in the soil aggregate with sizes of >2 mm and <0.25 mm. These results suggested that natural grassland restoration measures could improve the soil aggregate stability and aggregate-associated OC concentration better than Caragana plantation restoration measures, which NG may be optimal for increasing carbon sequestration and stabilizing soil aggregates on desert steppe.
format: application/pdf
format: text/html
creator: Qi Lu
creator: Hongbin Ma
creator: Yao Zhou
creator: Roberto Calvelo-Pereira
creator: Yan Shen
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Natural Resource Management
subject: Biogeochemistry
description: doi:10.7717/peerj.12507
publisher: PeerJ Inc.
rights: © 2022 Lu et al.
abstract: Background After implementing of the “Grain-for-Green” project, Caragana korshinskii Kom. has been widely planted in China’s arid regions. Although natural restoration grassland and artificial Caragana plantations measures have long been focuses in carbon research, the combined influence of natural restoration grassland and artificial Caragana plantation measures on aggregate stability and the aggregate-associated organic carbon (OC) remains unclear. Method We selected natural grassland (NG) and three different densities of Caragana plantations (high planting density, HG; middle planting density, MD; low planting density, LD) on desert steppe. The soil aggregate distribution and stability index such as fractal dimension (D), mean weight diameter (MWD), geometric mean diameter (GMD), percentage of aggregation destruction (PAD), as well as aggregate-associated OC concentration and stock were measured. Results Results shows that the soil aggregates were primarily macroaggregates (>2 mm) and mesoaggregates (0.25–2 mm) under dry sieving while microaggregates (<0.25 mm) were preponderant under wet sieving (more than 57%). Overall, compared with Caragana plantations, the MWD (4.43 and 4.51 mm) and GMD (1.72 and 1.83 mm) were both highest in two soil layers under the NG and the D (2.77 and 2.71) was lowest. Compared with the NG, the aggregate-associated OC stocks in the 0–40 cm depths in the LD, MD, and HD decreased by 41.54%, 46.93%, and 42.03%, respectively. SOC stock was mainly concentrated in the soil aggregate with sizes of >2 mm and <0.25 mm. These results suggested that natural grassland restoration measures could improve the soil aggregate stability and aggregate-associated OC concentration better than Caragana plantation restoration measures, which NG may be optimal for increasing carbon sequestration and stabilizing soil aggregates on desert steppe.
bibliographic citation: Lu et al. (2022) Caragana korshinskii Kom. plantation reduced soil aggregate stability and aggregate-associated organic carbon on desert steppe. PeerJ 10:e12507 https://doi.org/10.7717/peerj.12507
date submitted: 2021-06-11
date accepted: 2021-10-26
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Qi
author list: Agent
  family name: Ma
  given name: Hongbin
author list: Agent
  family name: Zhou
  given name: Yao
author list: Agent
  family name: Calvelo-Pereira
  given name: Roberto
author list: Agent
  family name: Shen
  given name: Yan
doi: 10.7717/peerj.12507
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: © 2022 Lu et al.
attribution name: Lu et al.

Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets
type: item
type: AcademicArticle
description: Background Within the pathogenic bacterial species Corynebacterium genus, six species that can produce diphtheria toxin (C. belfantii, C. diphtheriae, C. pseudotuberculosis, C. rouxii, C. silvaticum and C. ulcerans) form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets. Methods Forty genomes were sampled to represent species, subspecies or biovars of Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets. Results Nineteen genes were detected in the species C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria.
format: application/pdf
format: text/html
creator: Marcus Vinicius Canário Viana
creator: Rodrigo Profeta
creator: Janaína Canário Cerqueira
creator: Alice Rebecca Wattam
creator: Debmalya Barh
creator: Artur Silva
creator: Vasco Azevedo
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.12662
publisher: PeerJ Inc.
rights: © 2022 Canário Viana et al.
abstract: Background Within the pathogenic bacterial species Corynebacterium genus, six species that can produce diphtheria toxin (C. belfantii, C. diphtheriae, C. pseudotuberculosis, C. rouxii, C. silvaticum and C. ulcerans) form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets. Methods Forty genomes were sampled to represent species, subspecies or biovars of Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets. Results Nineteen genes were detected in the species C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria.
bibliographic citation: Canário Viana et al. (2022) Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets. PeerJ 10:e12662 https://doi.org/10.7717/peerj.12662
date submitted: 2021-07-22
date accepted: 2021-11-30
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Canário Viana
  given name: Marcus Vinicius
author list: Agent
  family name: Profeta
  given name: Rodrigo
author list: Agent
  family name: Cerqueira
  given name: Janaína Canário
author list: Agent
  family name: Wattam
  given name: Alice Rebecca
author list: Agent
  family name: Barh
  given name: Debmalya
author list: Agent
  family name: Silva
  given name: Artur
author list: Agent
  family name: Azevedo
  given name: Vasco
doi: 10.7717/peerj.12662
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: © 2022 Canário Viana et al.
attribution name: Canário Viana et al.

Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs
type: item
type: AcademicArticle
description: Obesity is a multifactorial nutritional disorder highly prevalent in dogs, observed in developed and developing countries. It is estimated that over 40% of the canine population suffers from obesity, which manifests in an increased risk of chronic osteoarticular, metabolic, and cardiovascular diseases. The intestinal microbiome of obese animals shows increases in the abundance of certain members capable of extracting energy from complex polysaccharides. The objective of this study was to compare the composition and predicted function of the intestinal microbiome of Chilean obese and normal weight adult dogs. Twenty clinically healthy dogs were classified according to their body condition score (BCS) as obese (n = 10) or normal weight (n = 10). DNA was extracted from stool samples, followed by next-generation sequencing of the 16S rRNA V3–V4 region and bioinformatics analysis targeting microbiome composition and function. Significant differences were observed between these groups at the phylum level, with anincrease in Firmicutes and a decrease in Bacteroidetes in obese dogs. Microbiome compositions of these animals correlated with their BCS, and obese dogs showed enrichment in pathways related to transport, chemotaxis, and flagellar assembly. These results highlight the differences in the gut microbiome between normal weight and obese dogs and prompt further research to improve animal health by modulating the gut microbiome.
format: application/pdf
format: text/html
creator: Pamela Thomson
creator: Rodrigo Santibáñez
creator: Camila Rodríguez-Salas
creator: Carla Flores-Yañez
creator: Daniel Garrido
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.12695
publisher: PeerJ Inc.
rights: © 2022 Thomson et al.
abstract: Obesity is a multifactorial nutritional disorder highly prevalent in dogs, observed in developed and developing countries. It is estimated that over 40% of the canine population suffers from obesity, which manifests in an increased risk of chronic osteoarticular, metabolic, and cardiovascular diseases. The intestinal microbiome of obese animals shows increases in the abundance of certain members capable of extracting energy from complex polysaccharides. The objective of this study was to compare the composition and predicted function of the intestinal microbiome of Chilean obese and normal weight adult dogs. Twenty clinically healthy dogs were classified according to their body condition score (BCS) as obese (n = 10) or normal weight (n = 10). DNA was extracted from stool samples, followed by next-generation sequencing of the 16S rRNA V3–V4 region and bioinformatics analysis targeting microbiome composition and function. Significant differences were observed between these groups at the phylum level, with anincrease in Firmicutes and a decrease in Bacteroidetes in obese dogs. Microbiome compositions of these animals correlated with their BCS, and obese dogs showed enrichment in pathways related to transport, chemotaxis, and flagellar assembly. These results highlight the differences in the gut microbiome between normal weight and obese dogs and prompt further research to improve animal health by modulating the gut microbiome.
bibliographic citation: Thomson et al. (2022) Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs. PeerJ 10:e12695 https://doi.org/10.7717/peerj.12695
date submitted: 2021-05-17
date accepted: 2021-12-06
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thomson
  given name: Pamela
author list: Agent
  family name: Santibáñez
  given name: Rodrigo
author list: Agent
  family name: Rodríguez-Salas
  given name: Camila
author list: Agent
  family name: Flores-Yañez
  given name: Carla
author list: Agent
  family name: Garrido
  given name: Daniel
doi: 10.7717/peerj.12695
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Thomson et al.
attribution name: Thomson et al.

Interrogating COVID-19 vaccine intent in the Philippines with a nationwide open-access online survey
type: item
type: AcademicArticle
description: To mitigate the unprecedented health, social, and economic damage of COVID-19, the Philippines is undertaking a nationwide vaccination program to mitigate the effects of the global pandemic. In this study, we interrogated COVID-19 vaccine intent in the country by deploying a nationwide open-access online survey, two months before the rollout of the national vaccination program. The Health Belief Model (HBM) posits that people are likely to adopt disease prevention behaviors and to accept medical interventions like vaccines if there is sufficient motivation and cues to action. A majority of our 7,193 respondents (62.5%) indicated that they were willing to be vaccinated against COVID-19. Moreover, multivariable analysis revealed that HBM constructs were associated with vaccination intention in the Philippines. Perceptions of high susceptibility, high severity, and significant benefits were all good predictors for vaccination intent. We also found that external cues to action were important. Large majorities of our respondents would only receive the COVID-19 vaccines after many others had received it (72.8%) or after politicians had received it (68.2%). Finally, our study revealed that most (21%) were willing to pay an amount of PHP 1,000 (USD20) for the COVID-19 vaccines with an average willing-to-pay amount of PHP1,892 (USD38).
format: application/pdf
format: text/html
creator: Alexandria Caple
creator: Arnie Dimaano
creator: Marc Martin Sagolili
creator: April Anne Uy
creator: Panjee Mariel Aguirre
creator: Dean Lotus Alano
creator: Giselle Sophia Camaya
creator: Brent John Ciriaco
creator: Princess Jerah Mae Clavo
creator: Dominic Cuyugan
creator: Cleinne Florence Geeseler Fermo
creator: Paul Jeremy Lanete
creator: Ardwayne Jurel La Torre
creator: Thomas Loteyro
creator: Raisa Mikaela Lua
creator: Nicole Gayle Manansala
creator: Raphael Willard Mosquito
creator: Alexa Octaviano
creator: Alexandra Erika Orfanel
creator: Gheyanna Merly Pascual
creator: Aubrey Joy Sale
creator: Sophia Lorraine Tendenilla
creator: Maria Sofia Lauren Trinidad
creator: Nicole Jan Trinidad
creator: Daphne Louise Verano
creator: Nicanor Austriaco
subject: Global Health
subject: Immunology
subject: Psychiatry and Psychology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.12887
publisher: PeerJ Inc.
rights: © 2022 Caple et al.
abstract: To mitigate the unprecedented health, social, and economic damage of COVID-19, the Philippines is undertaking a nationwide vaccination program to mitigate the effects of the global pandemic. In this study, we interrogated COVID-19 vaccine intent in the country by deploying a nationwide open-access online survey, two months before the rollout of the national vaccination program. The Health Belief Model (HBM) posits that people are likely to adopt disease prevention behaviors and to accept medical interventions like vaccines if there is sufficient motivation and cues to action. A majority of our 7,193 respondents (62.5%) indicated that they were willing to be vaccinated against COVID-19. Moreover, multivariable analysis revealed that HBM constructs were associated with vaccination intention in the Philippines. Perceptions of high susceptibility, high severity, and significant benefits were all good predictors for vaccination intent. We also found that external cues to action were important. Large majorities of our respondents would only receive the COVID-19 vaccines after many others had received it (72.8%) or after politicians had received it (68.2%). Finally, our study revealed that most (21%) were willing to pay an amount of PHP 1,000 (USD20) for the COVID-19 vaccines with an average willing-to-pay amount of PHP1,892 (USD38).
bibliographic citation: Caple et al. (2022) Interrogating COVID-19 vaccine intent in the Philippines with a nationwide open-access online survey. PeerJ 10:e12887 https://doi.org/10.7717/peerj.12887
date submitted: 2021-09-20
date accepted: 2022-01-14
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caple
  given name: Alexandria
author list: Agent
  family name: Dimaano
  given name: Arnie
author list: Agent
  family name: Sagolili
  given name: Marc Martin
author list: Agent
  family name: Uy
  given name: April Anne
author list: Agent
  family name: Aguirre
  given name: Panjee Mariel
author list: Agent
  family name: Alano
  given name: Dean Lotus
author list: Agent
  family name: Camaya
  given name: Giselle Sophia
author list: Agent
  family name: Ciriaco
  given name: Brent John
author list: Agent
  family name: Clavo
  given name: Princess Jerah Mae
author list: Agent
  family name: Cuyugan
  given name: Dominic
author list: Agent
  family name: Fermo
  given name: Cleinne Florence Geeseler
author list: Agent
  family name: Lanete
  given name: Paul Jeremy
author list: Agent
  family name: La Torre
  given name: Ardwayne Jurel
author list: Agent
  family name: Loteyro
  given name: Thomas
author list: Agent
  family name: Lua
  given name: Raisa Mikaela
author list: Agent
  family name: Manansala
  given name: Nicole Gayle
author list: Agent
  family name: Mosquito
  given name: Raphael Willard
author list: Agent
  family name: Octaviano
  given name: Alexa
author list: Agent
  family name: Orfanel
  given name: Alexandra Erika
author list: Agent
  family name: Pascual
  given name: Gheyanna Merly
author list: Agent
  family name: Sale
  given name: Aubrey Joy
author list: Agent
  family name: Tendenilla
  given name: Sophia Lorraine
author list: Agent
  family name: Trinidad
  given name: Maria Sofia Lauren
author list: Agent
  family name: Trinidad
  given name: Nicole Jan
author list: Agent
  family name: Verano
  given name: Daphne Louise
author list: Agent
  family name: Austriaco
  given name: Nicanor
doi: 10.7717/peerj.12887
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Caple et al.
attribution name: Caple et al.

Effect of interaction between occupational stress and polymorphisms of MTHFR gene and SELE gene on hypertension
type: item
type: AcademicArticle
description: Background Gene-environment interaction is related to the prevalence of hypertension, but the impact of genetic polymorphisms on hypertension may vary due to different geography and population. Objective To explore the impact of the interaction among occupational stress and MTHFR gene and SELE gene polymorphism on the prevalence of hypertension in Xinjiang oil workers. Methods A case-control study was conducted on 310 oil workers. In an oilfield base in Karamay City, Xinjiang, 155 hypertensive patients aged 18~60 years old with more than one year of service were selected as the case group, and 155 oil workers without hypertension were selected as the control group according to the 1:1 matching principle (matching conditions: the gender and shift were the same. The age is around 2 years old). The Occupational Stress Scale was used to evaluate the degree of occupational stress, PCR technique was used to detect MTHFR and SELE gene polymorphism, Logistic regression analysis was used to analyze the effects of gene and occupational stress on hypertension, and gene-gene and gene-environment interactions were analyzed by generalized multi-factor dimension reduction method. Results The G98T polymorphism of SELE gene (χ2 = 6.776, P = 0.034), the C677T (χ2 = 7.130, P = 0.028) and A1298C (χ2 = 12.036, P = 0.002) loci of MTHFR gene and the degree of occupational stress (χ2 = 11.921, P = 0.003) were significantly different between the case group and the control group. The genotypes GT at the G98T polymorphism of the SELE gene (OR = 2.151, 95% CI [1.227–3.375]), and the dominant model (AC/CC vs AA, OR = 1.925, 95% CI [1.613–3.816]); AC and CC at the A1298C polymorphism of the MTHFR gene (ORAC = 1.917, 95% CI [1.064–3.453]; ORCC = 2.233, 95% CI [1.082–4.609]), the additive model (CC vs AA, OR = 2.497, 95% CI [1.277–4.883]) and the dominant model (AC/CC vs AA, OR = 2.012, 95% CI [1.200–3.373]); at the C677T polymorphism of the MTHFR gene CT and TT (ORCT = 1.913, 95% CI [1.085–3.375]…
format: application/pdf
format: text/html
creator: Fen Yang
creator: Ruiying Qiu
creator: Saimaitikari Abudoubari
creator: Ning Tao
creator: Hengqing An
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.12914
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Background Gene-environment interaction is related to the prevalence of hypertension, but the impact of genetic polymorphisms on hypertension may vary due to different geography and population. Objective To explore the impact of the interaction among occupational stress and MTHFR gene and SELE gene polymorphism on the prevalence of hypertension in Xinjiang oil workers. Methods A case-control study was conducted on 310 oil workers. In an oilfield base in Karamay City, Xinjiang, 155 hypertensive patients aged 18~60 years old with more than one year of service were selected as the case group, and 155 oil workers without hypertension were selected as the control group according to the 1:1 matching principle (matching conditions: the gender and shift were the same. The age is around 2 years old). The Occupational Stress Scale was used to evaluate the degree of occupational stress, PCR technique was used to detect MTHFR and SELE gene polymorphism, Logistic regression analysis was used to analyze the effects of gene and occupational stress on hypertension, and gene-gene and gene-environment interactions were analyzed by generalized multi-factor dimension reduction method. Results The G98T polymorphism of SELE gene (χ2 = 6.776, P = 0.034), the C677T (χ2 = 7.130, P = 0.028) and A1298C (χ2 = 12.036, P = 0.002) loci of MTHFR gene and the degree of occupational stress (χ2 = 11.921, P = 0.003) were significantly different between the case group and the control group. The genotypes GT at the G98T polymorphism of the SELE gene (OR = 2.151, 95% CI [1.227–3.375]), and the dominant model (AC/CC vs AA, OR = 1.925, 95% CI [1.613–3.816]); AC and CC at the A1298C polymorphism of the MTHFR gene (ORAC = 1.917, 95% CI [1.064–3.453]; ORCC = 2.233, 95% CI [1.082–4.609]), the additive model (CC vs AA, OR = 2.497, 95% CI [1.277–4.883]) and the dominant model (AC/CC vs AA, OR = 2.012, 95% CI [1.200–3.373]); at the C677T polymorphism of the MTHFR gene CT and TT (ORCT = 1.913, 95% CI [1.085–3.375]…
bibliographic citation: Yang et al. (2022) Effect of interaction between occupational stress and polymorphisms of MTHFR gene and SELE gene on hypertension. PeerJ 10:e12914 https://doi.org/10.7717/peerj.12914
date submitted: 2021-08-31
date accepted: 2022-01-19
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Fen
author list: Agent
  family name: Qiu
  given name: Ruiying
author list: Agent
  family name: Abudoubari
  given name: Saimaitikari
author list: Agent
  family name: Tao
  given name: Ning
author list: Agent
  family name: An
  given name: Hengqing
doi: 10.7717/peerj.12914
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: © 2022 Yang et al.
attribution name: Yang et al.

Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China
type: item
type: AcademicArticle
description: Long-term and widespread cotton production in Xinjiang, China, has resulted in significant soil degradation, thereby leading to continuous cropping obstacles; cotton stalk biochar (CSB) addition may be an effective countermeasure to this issue, with effects that are felt immediately by root systems in direct contact with the soil. In this study, we assess the effects of different CSB application rates on soil nutrient contents, root morphology, and root physiology in two soil types commonly used for cotton production in the region. Compared with CK (no CSB addition), a 1% CSB addition increased total nitrogen (TN), available phosphorus (AP), and organic matter (OM) by 13.3%, 7.2%, and 50% in grey desert soil, respectively , and 36.5%, 19.9%, and 176.4%, respectively, in aeolian sandy soil. A 3% CSB addition increased TN, AP, and OM by 38.8%, 23.8%, and 208.1%, respectively, in grey desert soil, and 36%, 13%, and 183.2%, respectively, in aeolian sandy soil. Compared with the aeolian sandy soil, a 1% CSB addition increased TN, OM, and AP by 95%, 94.8%, and 33.3%, respectively, in the grey desert soil , while in the same soil 3% CSB addition increased TN, OM, and AP by 108%, 21.1%, and 73.9%, respectively. In the grey desert soil, compared with CK, a 1% CSB application increased the root length (RL) (34%), specific root length (SRL) (27.9%), and root volume (RV) (32.6%) during the bud stage, increased glutamine synthetase (GS) (13.9%) and nitrate reductase (NR) activities (237%), decreased the RV (34%) and average root diameter (ARD) (36.2%) during the harvesting stage. A 3% CSB addition increased the RL (44%), SRL (20%), and RV (41.2%) during the bud stage and decreased the RV (29%) and ARD (27%) during the harvesting stage. In the aeolian sandy soil, 1% CSB increased the RL (38.3%), SRL (73.7%), and RV (17%), while a 3% caused a greater increase in the RL (55%), SRL (89%), RV (28%), soluble sugar content (128%), and underground biomass (33.8%). Compared with the grey…
format: application/pdf
format: text/html
creator: Xiuxiu Dong
creator: Zhiyong Zhang
creator: Shaoming Wang
creator: Zihui Shen
creator: Xiaojiao Cheng
creator: Xinhua Lv
creator: Xiaozhen Pu
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Natural Resource Management
description: doi:10.7717/peerj.12928
publisher: PeerJ Inc.
rights: © 2022 Dong et al.
abstract: Long-term and widespread cotton production in Xinjiang, China, has resulted in significant soil degradation, thereby leading to continuous cropping obstacles; cotton stalk biochar (CSB) addition may be an effective countermeasure to this issue, with effects that are felt immediately by root systems in direct contact with the soil. In this study, we assess the effects of different CSB application rates on soil nutrient contents, root morphology, and root physiology in two soil types commonly used for cotton production in the region. Compared with CK (no CSB addition), a 1% CSB addition increased total nitrogen (TN), available phosphorus (AP), and organic matter (OM) by 13.3%, 7.2%, and 50% in grey desert soil, respectively , and 36.5%, 19.9%, and 176.4%, respectively, in aeolian sandy soil. A 3% CSB addition increased TN, AP, and OM by 38.8%, 23.8%, and 208.1%, respectively, in grey desert soil, and 36%, 13%, and 183.2%, respectively, in aeolian sandy soil. Compared with the aeolian sandy soil, a 1% CSB addition increased TN, OM, and AP by 95%, 94.8%, and 33.3%, respectively, in the grey desert soil , while in the same soil 3% CSB addition increased TN, OM, and AP by 108%, 21.1%, and 73.9%, respectively. In the grey desert soil, compared with CK, a 1% CSB application increased the root length (RL) (34%), specific root length (SRL) (27.9%), and root volume (RV) (32.6%) during the bud stage, increased glutamine synthetase (GS) (13.9%) and nitrate reductase (NR) activities (237%), decreased the RV (34%) and average root diameter (ARD) (36.2%) during the harvesting stage. A 3% CSB addition increased the RL (44%), SRL (20%), and RV (41.2%) during the bud stage and decreased the RV (29%) and ARD (27%) during the harvesting stage. In the aeolian sandy soil, 1% CSB increased the RL (38.3%), SRL (73.7%), and RV (17%), while a 3% caused a greater increase in the RL (55%), SRL (89%), RV (28%), soluble sugar content (128%), and underground biomass (33.8%). Compared with the grey…
bibliographic citation: Dong et al. (2022) Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China. PeerJ 10:e12928 https://doi.org/10.7717/peerj.12928
date submitted: 2021-09-06
date accepted: 2022-01-20
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Xiuxiu
author list: Agent
  family name: Zhang
  given name: Zhiyong
author list: Agent
  family name: Wang
  given name: Shaoming
author list: Agent
  family name: Shen
  given name: Zihui
author list: Agent
  family name: Cheng
  given name: Xiaojiao
author list: Agent
  family name: Lv
  given name: Xinhua
author list: Agent
  family name: Pu
  given name: Xiaozhen
doi: 10.7717/peerj.12928
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Dong et al.
attribution name: Dong et al.

New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea)
type: item
type: AcademicArticle
description: Piipironus grandis gen. et sp. nov. is described from Piip submarine volcano, the Bering Sea. Piipironus gen. nov. shows all main characters of Thalassironinae but differs from all known ironids in the form of the amphid (spiral vs pocket-like) and the simultaneous presence of precloacal papilliform supplements and tubular postcloacal organs. Pared tubular postcloacal organs have never been described before for the family Ironidae. The combination of papilliform precloacal supplements and the pair of tubular postcloacal organs described for Piipironus grandis gen. et sp. nov. is unique among nematodes. The study of the nematofauna of the Piip submarine volcano began quite recently, and Piipironus is the second new genus of nematodes described from here from one sample of bottom sediments. This can be taken as one of the examples of the hyper-high diversity of marine nematodes.
format: application/pdf
format: text/html
creator: Julia Zograf
creator: Vladimir Mordukhovich
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12946
publisher: PeerJ Inc.
rights: © 2022 Zograf and Mordukhovich
abstract: Piipironus grandis gen. et sp. nov. is described from Piip submarine volcano, the Bering Sea. Piipironus gen. nov. shows all main characters of Thalassironinae but differs from all known ironids in the form of the amphid (spiral vs pocket-like) and the simultaneous presence of precloacal papilliform supplements and tubular postcloacal organs. Pared tubular postcloacal organs have never been described before for the family Ironidae. The combination of papilliform precloacal supplements and the pair of tubular postcloacal organs described for Piipironus grandis gen. et sp. nov. is unique among nematodes. The study of the nematofauna of the Piip submarine volcano began quite recently, and Piipironus is the second new genus of nematodes described from here from one sample of bottom sediments. This can be taken as one of the examples of the hyper-high diversity of marine nematodes.
bibliographic citation: Zograf et al. (2022) New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea). PeerJ 10:e12946 https://doi.org/10.7717/peerj.12946
date submitted: 2021-11-19
date accepted: 2022-01-25
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zograf
  given name: Julia
author list: Agent
  family name: Mordukhovich
  given name: Vladimir
doi: 10.7717/peerj.12946
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: © 2022 Zograf and Mordukhovich
attribution name: Zograf and Mordukhovich

The impact of COVID-19 and control measures on public health in Thailand, 2020
type: item
type: AcademicArticle
description: Background The COVID-19 virus has been an emerging disease causing global outbreaks for over a year. In Thailand, transmission may be controlled by strict measures that could positively and negatively impact physical health and suicidal behavior. Methods The incidence of COVID-19 was retrieved from the Department of Disease Control (DDC). The impact of viral diseases was retrieved from the open-source of the DDC and King Chulalongkorn Memorial Hospital. The road accidents data were from the Thai Ministry of Transport. The suicidal behavior data were obtained from the Department of Mental Health. We compared data from the year 2019 with the pandemic COVID-19 outbreak period in 2020, before lockdown, during lockdown, easing, and new wave period using unpaired t-test and least-squares linear regression. We compared the impact of the outbreak on various data records in 2020 with corresponding non-outbreak from 2019. Results There was a significant decline in cases of influenza (p < 0.001) and norovirus (p = 0.01). However, there was no significant difference in RSV cases (p = 0.17). There was a dramatic increase in attempt to suicides and suicides (p < 0.001). There was no impact on roadside accidents and outpatient department visits. Discussion The extensive intervention measures during lockdown during the first wave positively impacted total cases for each period for acute respiratory and gastrointestinal tract diseases, car accidents, and injuries and negatively impacted indicators of suicidal behavior. The data support government policies that would be effective against the next outbreak by promoting the “new normal” lifestyle.
format: application/pdf
format: text/html
creator: Ritthideach Yorsaeng
creator: Nungruthai Suntronwong
creator: Ilada Thongpan
creator: Watchaporn Chuchaona
creator: Fajar Budi Lestari
creator: Siripat Pasittungkul
creator: Jiratchaya Puenpa
creator: Kamolthip Atsawawaranunt
creator: Chollasap Sharma
creator: Natthinee Sudhinaraset
creator: Anek Mungaomklang
creator: Rungrueng Kitphati
creator: Nasamon Wanlapakorn
creator: Yong Poovorawan
subject: Epidemiology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.12960
publisher: PeerJ Inc.
rights: © 2022 Yorsaeng et al.
abstract: Background The COVID-19 virus has been an emerging disease causing global outbreaks for over a year. In Thailand, transmission may be controlled by strict measures that could positively and negatively impact physical health and suicidal behavior. Methods The incidence of COVID-19 was retrieved from the Department of Disease Control (DDC). The impact of viral diseases was retrieved from the open-source of the DDC and King Chulalongkorn Memorial Hospital. The road accidents data were from the Thai Ministry of Transport. The suicidal behavior data were obtained from the Department of Mental Health. We compared data from the year 2019 with the pandemic COVID-19 outbreak period in 2020, before lockdown, during lockdown, easing, and new wave period using unpaired t-test and least-squares linear regression. We compared the impact of the outbreak on various data records in 2020 with corresponding non-outbreak from 2019. Results There was a significant decline in cases of influenza (p < 0.001) and norovirus (p = 0.01). However, there was no significant difference in RSV cases (p = 0.17). There was a dramatic increase in attempt to suicides and suicides (p < 0.001). There was no impact on roadside accidents and outpatient department visits. Discussion The extensive intervention measures during lockdown during the first wave positively impacted total cases for each period for acute respiratory and gastrointestinal tract diseases, car accidents, and injuries and negatively impacted indicators of suicidal behavior. The data support government policies that would be effective against the next outbreak by promoting the “new normal” lifestyle.
bibliographic citation: Yorsaeng et al. (2022) The impact of COVID-19 and control measures on public health in Thailand, 2020. PeerJ 10:e12960 https://doi.org/10.7717/peerj.12960
date submitted: 2021-08-27
date accepted: 2022-01-27
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yorsaeng
  given name: Ritthideach
author list: Agent
  family name: Suntronwong
  given name: Nungruthai
author list: Agent
  family name: Thongpan
  given name: Ilada
author list: Agent
  family name: Chuchaona
  given name: Watchaporn
author list: Agent
  family name: Lestari
  given name: Fajar Budi
author list: Agent
  family name: Pasittungkul
  given name: Siripat
author list: Agent
  family name: Puenpa
  given name: Jiratchaya
author list: Agent
  family name: Atsawawaranunt
  given name: Kamolthip
author list: Agent
  family name: Sharma
  given name: Chollasap
author list: Agent
  family name: Sudhinaraset
  given name: Natthinee
author list: Agent
  family name: Mungaomklang
  given name: Anek
author list: Agent
  family name: Kitphati
  given name: Rungrueng
author list: Agent
  family name: Wanlapakorn
  given name: Nasamon
author list: Agent
  family name: Poovorawan
  given name: Yong
doi: 10.7717/peerj.12960
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Yorsaeng et al.
attribution name: Yorsaeng et al.

In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury
type: item
type: AcademicArticle
description: Lipopolysaccharide (LPS) is a glycolipid component of the cell wall of Gram-negative bacteria, which induces multiple organ dysfunctions, eventually leading to septic shock and death. Arjunolic acid (AA) has been shown to have therapeutic benefits against various organ pathophysiologies, although its role in sepsis remains unclear. Here, we evaluated the effects of AA on LPS-induced free radical production and cardiotoxicity. Male albino mice were allocated to four groups: normal, 1.5 µg/30 g b.w. of LPS (LPS), 20 mg/kg b.w. AA with LPS (AA+LPS) and 20 mg/kg b.w. of AA (AA). Subsequently, blood and heart samples were harvested for biochemical and histopathological examinations. Pretreatment with AA attenuated LPS-induced increased serum levels of cardiac troponin I, lactate dehydrogenase and creatine kinase. In the meantime, AA pretreatment before LPS resulted in a significant increase in endogenous antioxidants (superoxide dismutase, catalase, glutathione peroxidase and reduced glutathione) and a significant decrease in the level of lipid peroxidation product (malondialdehyde) in the heart as compared to the LPS group, while cardiac cytochrome c activity were significantly increased. In addition, in the AA-pretreated mice, C-reactive protein and proinflammatory cytokines (interlukin-1 and tumor necrosis factor-alpha) were significantly reduced, and anti-inflammatory cytokines (interleukin-4 and -10) were significantly increased in cardiac tissues as compared to the LPS-treated animals. Furthermore, prior administration of AA to LPS exposed mice led to a significant a significant decrease in heart caspase-3, -8, and -9 as compared to the LPS group. Interestingly, AA was also able to improve LPS-induced histopathological changes in the cardiomyocytes. In conclusion, these in vivo findings indicate that AA may be a promising cardioprotective agent against LPS-stimulated cardiotoxicity, at least in part, through upregulation of cardiac antioxidants, reduction of lipid …
format: application/pdf
format: text/html
creator: Hany Elsawy
creator: Mohammed Almalki
creator: Omar Elmenshawy
creator: Ashraf Abdel-Moneim
subject: Biochemistry
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.12986
publisher: PeerJ Inc.
rights: © 2022 Elsawy et al.
abstract: Lipopolysaccharide (LPS) is a glycolipid component of the cell wall of Gram-negative bacteria, which induces multiple organ dysfunctions, eventually leading to septic shock and death. Arjunolic acid (AA) has been shown to have therapeutic benefits against various organ pathophysiologies, although its role in sepsis remains unclear. Here, we evaluated the effects of AA on LPS-induced free radical production and cardiotoxicity. Male albino mice were allocated to four groups: normal, 1.5 µg/30 g b.w. of LPS (LPS), 20 mg/kg b.w. AA with LPS (AA+LPS) and 20 mg/kg b.w. of AA (AA). Subsequently, blood and heart samples were harvested for biochemical and histopathological examinations. Pretreatment with AA attenuated LPS-induced increased serum levels of cardiac troponin I, lactate dehydrogenase and creatine kinase. In the meantime, AA pretreatment before LPS resulted in a significant increase in endogenous antioxidants (superoxide dismutase, catalase, glutathione peroxidase and reduced glutathione) and a significant decrease in the level of lipid peroxidation product (malondialdehyde) in the heart as compared to the LPS group, while cardiac cytochrome c activity were significantly increased. In addition, in the AA-pretreated mice, C-reactive protein and proinflammatory cytokines (interlukin-1 and tumor necrosis factor-alpha) were significantly reduced, and anti-inflammatory cytokines (interleukin-4 and -10) were significantly increased in cardiac tissues as compared to the LPS-treated animals. Furthermore, prior administration of AA to LPS exposed mice led to a significant a significant decrease in heart caspase-3, -8, and -9 as compared to the LPS group. Interestingly, AA was also able to improve LPS-induced histopathological changes in the cardiomyocytes. In conclusion, these in vivo findings indicate that AA may be a promising cardioprotective agent against LPS-stimulated cardiotoxicity, at least in part, through upregulation of cardiac antioxidants, reduction of lipid …
bibliographic citation: Elsawy et al. (2022) In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury. PeerJ 10:e12986 https://doi.org/10.7717/peerj.12986
date submitted: 2021-11-08
date accepted: 2022-02-01
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elsawy
  given name: Hany
author list: Agent
  family name: Almalki
  given name: Mohammed
author list: Agent
  family name: Elmenshawy
  given name: Omar
author list: Agent
  family name: Abdel-Moneim
  given name: Ashraf
doi: 10.7717/peerj.12986
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Elsawy et al.
attribution name: Elsawy et al.

A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)
type: item
type: AcademicArticle
description: To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data records is the associated taxon concept. Unlike Linnaean taxon names, the traditional way in which taxon concepts are provided, phylogenetic definitions are native to phylogenetic trees and offer well-defined semantics that can be transformed into formal, computationally evaluable logic expressions. These attributes make them highly suitable for phylogeny-driven comparative biology by allowing computationally verifiable and reproducible integration of taxon-linked data against Tree of Life-scale phylogenies. To achieve this, the first step is transforming phylogenetic definitions from the natural language text in which they are published to a structured interoperable data format that maintains strong ties to semantics and lends itself well to sharing, reuse, and long-term archival. To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software library, phyx.js, to streamline computational management of such files. Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades.
format: application/pdf
format: text/html
creator: Gaurav Vaidya
creator: Nico Cellinese
creator: Hilmar Lapp
subject: Bioinformatics
subject: Evolutionary Studies
subject: Taxonomy
subject: Computational Science
subject: Data Science
description: doi:10.7717/peerj.12618
publisher: PeerJ Inc.
rights: © 2022 Vaidya et al.
abstract: To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data records is the associated taxon concept. Unlike Linnaean taxon names, the traditional way in which taxon concepts are provided, phylogenetic definitions are native to phylogenetic trees and offer well-defined semantics that can be transformed into formal, computationally evaluable logic expressions. These attributes make them highly suitable for phylogeny-driven comparative biology by allowing computationally verifiable and reproducible integration of taxon-linked data against Tree of Life-scale phylogenies. To achieve this, the first step is transforming phylogenetic definitions from the natural language text in which they are published to a structured interoperable data format that maintains strong ties to semantics and lends itself well to sharing, reuse, and long-term archival. To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software library, phyx.js, to streamline computational management of such files. Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades.
bibliographic citation: Vaidya et al. (2022) A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx). PeerJ 10:e12618 https://doi.org/10.7717/peerj.12618
date submitted: 2021-03-23
date accepted: 2021-11-18
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vaidya
  given name: Gaurav
author list: Agent
  family name: Cellinese
  given name: Nico
author list: Agent
  family name: Lapp
  given name: Hilmar
doi: 10.7717/peerj.12618
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Vaidya et al.
attribution name: Vaidya et al.

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