PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Seasonal variation characteristics of water quality in the Sunxi River Watershed, Three Gorges Reservoir Area
items: Intensive hunting changes human-wildlife relationships
items: Estimation methods for the ratio of medians of three-parameter lognormal distributions containing zero values and their application to wind speed data from northern Thailand
items: Association between hypomagnesemia and mortality among dialysis patients: a systematic review and meta-analysis
items: Impact of silver nanoparticles on the nutritional properties of Arthrospira platensis
items: Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups
items: Effectiveness of a community-based peer support service among persons suffering severe mental illness in China
items: Differentially expressed genes related to plant height and yield in two alfalfa cultivars based on RNA-seq
items: Rapid and convenient detection of SARS-CoV-2 using a colorimetric triple-target reverse transcription loop-mediated isothermal amplification method
items: The impact of children’s temperament on recurrent unintentional injuries: the role of paternal parenting styles as a mediator

Seasonal variation characteristics of water quality in the Sunxi River Watershed, Three Gorges Reservoir Area
type: item
type: AcademicArticle
description: The seasonal change characteristics of water quality in the Sunxi River watershed, which is a typical watershed in the tail area of the Three Gorges Reservoir Area, must be studied to provide remediation ideas and specific measures for agricultural nonpoint source pollution in the reservoir area. A two-way repeated measures ANOVA was used to analyze the variation characteristics of chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) concentrations in the upstream and downstream of the Sunxi River watershed in spring, summer, and autumn of 2018–2021. With data from autumn 2018 taken as an example, path analysis was applied to study the effect degree of influencing factors on TN concentrations. The two-way repeated measures ANOVA illustrated that the COD, TN, and TP concentrations in the downstream were significantly higher than those in the upstream (P < 0.05). In addition, the COD concentrations were the highest in summer 2019, followed by spring of 2019 and 2021, and TN and TP concentrations were higher in spring and summer. The TN and TP concentrations were comparatively lower in the autumn. The path analysis showed that electrical conductance and dissolved oxygen directly affected the TN concentrations, and water temperature mainly affected the TN concentrations via the indirect effects of electrical conductance and dissolved oxygen. The water quality of upstream Sunxi River watershed was better than that of downstream, and the water quality in autumn was better than spring and summer in 2018–2021. For water quality management and ecological restoration of the Sunxi River watershed, further attention should be paid to the water quality changes in the downstream and in spring and summer and to the impact of water temperature, electrical conductivity, and dissolved oxygen on the water quality.
format: application/pdf
format: text/html
creator: Wenning Hou
creator: Haiyan Wang
creator: Yonglin Zheng
creator: Yige Wang
creator: Dandan Yang
creator: Hai Meng
subject: Ecosystem Science
subject: Aquatic and Marine Chemistry
subject: Ecohydrology
subject: Environmental Impacts
description: doi:10.7717/peerj.14233
publisher: PeerJ Inc.
rights: © 2022 Hou et al.
abstract: The seasonal change characteristics of water quality in the Sunxi River watershed, which is a typical watershed in the tail area of the Three Gorges Reservoir Area, must be studied to provide remediation ideas and specific measures for agricultural nonpoint source pollution in the reservoir area. A two-way repeated measures ANOVA was used to analyze the variation characteristics of chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) concentrations in the upstream and downstream of the Sunxi River watershed in spring, summer, and autumn of 2018–2021. With data from autumn 2018 taken as an example, path analysis was applied to study the effect degree of influencing factors on TN concentrations. The two-way repeated measures ANOVA illustrated that the COD, TN, and TP concentrations in the downstream were significantly higher than those in the upstream (P < 0.05). In addition, the COD concentrations were the highest in summer 2019, followed by spring of 2019 and 2021, and TN and TP concentrations were higher in spring and summer. The TN and TP concentrations were comparatively lower in the autumn. The path analysis showed that electrical conductance and dissolved oxygen directly affected the TN concentrations, and water temperature mainly affected the TN concentrations via the indirect effects of electrical conductance and dissolved oxygen. The water quality of upstream Sunxi River watershed was better than that of downstream, and the water quality in autumn was better than spring and summer in 2018–2021. For water quality management and ecological restoration of the Sunxi River watershed, further attention should be paid to the water quality changes in the downstream and in spring and summer and to the impact of water temperature, electrical conductivity, and dissolved oxygen on the water quality.
bibliographic citation: Hou et al. (2022) Seasonal variation characteristics of water quality in the Sunxi River Watershed, Three Gorges Reservoir Area. PeerJ 10:e14233 https://doi.org/10.7717/peerj.14233
date submitted: 2022-04-26
date accepted: 2022-09-22
issued: 2022-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Wenning
author list: Agent
  family name: Wang
  given name: Haiyan
author list: Agent
  family name: Zheng
  given name: Yonglin
author list: Agent
  family name: Wang
  given name: Yige
author list: Agent
  family name: Yang
  given name: Dandan
author list: Agent
  family name: Meng
  given name: Hai
doi: 10.7717/peerj.14233
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-12
copyright: ©2022 Hou et al.
attribution name: Hou et al.

Intensive hunting changes human-wildlife relationships
type: item
type: AcademicArticle
description: Wildlife alter their behaviors in a trade-off between consuming food and fear of becoming food themselves. The risk allocation hypothesis posits that variation in the scale, intensity and longevity of predation threats can influence the magnitude of antipredator behavioral responses. Hunting by humans represents a threat thought to be perceived by wildlife similar to how they perceive a top predator, although hunting intensity and duration varys widely around the world. Here we evaluate the effects of hunting pressure on wildlife by comparing how two communities of mammals under different management schemes differ in their relative abundance and response to humans. Using camera traps to survey wildlife across disturbance levels (yards, farms, forests) in similar landscapes in southern Germany and southeastern USA, we tested the prediction of the risk allocation hypothesis: that the higher intensity and longevity of hunting in Germany (year round vs 3 months, 4x higher harvest/km2/year) would reduce relative abundance of hunted species and result in a larger fear-based response to humans (i.e., more spatial and temporal avoidance). We further evaluated how changes in animal abundance and behavior would result in potential changes to ecological impacts (i.e., herbivory and predation). We found that hunted species were relatively less abundant in Germany and less associated with humans on the landscape (i.e., yards and urban areas), but did not avoid humans temporally in hunted areas while hunted species in the USA showed the opposite pattern. These results are consistent with the risk allocation hypothesis where we would expect more spatial avoidance in response to threats of longer duration (i.e., year-round hunting in Germany vs. 3-month duration in USA) and less spatial avoidance but more temporal avoidance for threats of shorter duration. The expected ecological impacts of mammals in all three habitats were quite different between countries, most strikingly due to…
format: application/pdf
format: text/html
creator: Arielle Waldstein Parsons
creator: Martin Wikelski
creator: Brigitta Keeves von Wolff
creator: Jan Dodel
creator: Roland Kays
subject: Animal Behavior
subject: Ecology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.14159
publisher: PeerJ Inc.
rights: © 2022 Parsons et al.
abstract: Wildlife alter their behaviors in a trade-off between consuming food and fear of becoming food themselves. The risk allocation hypothesis posits that variation in the scale, intensity and longevity of predation threats can influence the magnitude of antipredator behavioral responses. Hunting by humans represents a threat thought to be perceived by wildlife similar to how they perceive a top predator, although hunting intensity and duration varys widely around the world. Here we evaluate the effects of hunting pressure on wildlife by comparing how two communities of mammals under different management schemes differ in their relative abundance and response to humans. Using camera traps to survey wildlife across disturbance levels (yards, farms, forests) in similar landscapes in southern Germany and southeastern USA, we tested the prediction of the risk allocation hypothesis: that the higher intensity and longevity of hunting in Germany (year round vs 3 months, 4x higher harvest/km2/year) would reduce relative abundance of hunted species and result in a larger fear-based response to humans (i.e., more spatial and temporal avoidance). We further evaluated how changes in animal abundance and behavior would result in potential changes to ecological impacts (i.e., herbivory and predation). We found that hunted species were relatively less abundant in Germany and less associated with humans on the landscape (i.e., yards and urban areas), but did not avoid humans temporally in hunted areas while hunted species in the USA showed the opposite pattern. These results are consistent with the risk allocation hypothesis where we would expect more spatial avoidance in response to threats of longer duration (i.e., year-round hunting in Germany vs. 3-month duration in USA) and less spatial avoidance but more temporal avoidance for threats of shorter duration. The expected ecological impacts of mammals in all three habitats were quite different between countries, most strikingly due to…
bibliographic citation: Parsons et al. (2022) Intensive hunting changes human-wildlife relationships. PeerJ 10:e14159 https://doi.org/10.7717/peerj.14159
date submitted: 2022-06-20
date accepted: 2022-09-08
issued: 2022-10-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parsons
  given name: Arielle Waldstein
author list: Agent
  family name: Wikelski
  given name: Martin
author list: Agent
  family name: Keeves von Wolff
  given name: Brigitta
author list: Agent
  family name: Dodel
  given name: Jan
author list: Agent
  family name: Kays
  given name: Roland
doi: 10.7717/peerj.14159
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-11
copyright: ©2022 Parsons et al.
attribution name: Parsons et al.

Estimation methods for the ratio of medians of three-parameter lognormal distributions containing zero values and their application to wind speed data from northern Thailand
type: item
type: AcademicArticle
description: Wind speed has an important impact on the formation and dispersion of fine particulate matter (PM), which can cause several health problems. During the transition from the winter to the summer season in northern Thailand, the wind speed has been low for longer than usual, which has resulted in fine PM accumulating in the air. Motivated by this, we have identified a need to investigate wind speed due to its effect on PM formation and dispersion and to raise awareness among the general public. The hourly windspeed can be approximated by using confidence intervals for the ratio of the medians of three-parameter lognormal distributions containing zero values. Thus, we constructed them by using fiducial, normal approximation, and Bayesian methods. By way of comparison, the performance measures for all ofthe proposed methods (the coverage percentage, lower and upper error probabilities (LEP and UEP,respectively), and expected length) were assessed via Monte Carlo simulation. The results of Monte Carlo simulation studies show that the Bayesian method provided coverage percentages close to the nominal confidence level and shorter intervals than the other methods. Importantly, it maintained a good balance between LEP and UEP even for large variation and percentage of zero-valued observations. To illustrate the efficacy of our proposed methods, we applied them to hourly wind speed data from northern Thailand.
format: application/pdf
format: text/html
creator: Patcharee Maneerat
creator: Pisit Nakjai
creator: Sa-Aat Niwitpong
subject: Statistics
subject: Computational Science
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.14194
publisher: PeerJ Inc.
rights: © 2022 Maneerat et al.
abstract: Wind speed has an important impact on the formation and dispersion of fine particulate matter (PM), which can cause several health problems. During the transition from the winter to the summer season in northern Thailand, the wind speed has been low for longer than usual, which has resulted in fine PM accumulating in the air. Motivated by this, we have identified a need to investigate wind speed due to its effect on PM formation and dispersion and to raise awareness among the general public. The hourly windspeed can be approximated by using confidence intervals for the ratio of the medians of three-parameter lognormal distributions containing zero values. Thus, we constructed them by using fiducial, normal approximation, and Bayesian methods. By way of comparison, the performance measures for all ofthe proposed methods (the coverage percentage, lower and upper error probabilities (LEP and UEP,respectively), and expected length) were assessed via Monte Carlo simulation. The results of Monte Carlo simulation studies show that the Bayesian method provided coverage percentages close to the nominal confidence level and shorter intervals than the other methods. Importantly, it maintained a good balance between LEP and UEP even for large variation and percentage of zero-valued observations. To illustrate the efficacy of our proposed methods, we applied them to hourly wind speed data from northern Thailand.
bibliographic citation: Maneerat et al. (2022) Estimation methods for the ratio of medians of three-parameter lognormal distributions containing zero values and their application to wind speed data from northern Thailand. PeerJ 10:e14194 https://doi.org/10.7717/peerj.14194
date submitted: 2022-06-16
date accepted: 2022-09-15
issued: 2022-10-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maneerat
  given name: Patcharee
author list: Agent
  family name: Nakjai
  given name: Pisit
author list: Agent
  family name: Niwitpong
  given name: Sa-Aat
doi: 10.7717/peerj.14194
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-11
copyright: ©2022 Maneerat et al.
attribution name: Maneerat et al.

Association between hypomagnesemia and mortality among dialysis patients: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Malnutrition-inflammation-atherosclerosis (MIA) syndrome is caused by the inflammatory cytokines in end stage renal disease (ESRD) patients, and MIA complex-related factors may be associated with hypomagnesemia and mortality. However, the association between serum magnesium level and mortality for dialysis patients is still not clear. Additionally, no meta-analysis has investigated the impact of serum magnesium on peritoneal dialysis and hemodialysis, separately. Methods We searched published studies in PubMed, Embase, Cochrane, Collaboration Central Register of Controlled Clinical Trials, and Cochrane Systematic Reviews through April 2022. Studies associated with serum magnesium and all-cause mortality or cardiovascular (CV) mortality in ESRD on kidney replacement therapy (KRT) patients were included. A hazard ratio (HR) with 95% confidence intervals (CI) was used to report the outcomes. Results Twenty-one studies involving 55,232 patients were included. Overall, there was a significant association between hypomagnesemia and all-cause mortality for dialysis patients (HR: 1.67, 95% CI [1.412–2.00], p < 0.001; certainty of evidence: moderate) using a mixed unadjusted and adjusted HR for analysis. There was also a significantly increased risk of CV mortality for individuals with hypomagnesemia compared with the non-hypomagnesemia group (HR 1.56, 95% CI [1.08–2.25], p < 0.001; certainty of evidence: moderate). In addition, a subgroup analysis demonstrated that hypomagnesemia was associated with a high risk of both all-cause mortality and CV mortality (all-cause mortality, HR:1.80, 95% CI [1.48–2.19]; CV mortality, HR:1.84, 95% CI [1.10–3.07]) in hemodialysis (HD) patients, but not in participants receiving peritoneal dialysis (PD; all-cause mortality, HR:1.26, 95% CI [0.84–1.91]; CV mortality, HR:0.66, 95% CI [0.22–2.00]). The systematic review protocol was prespecified and registered in PROSPERO [CRD42021256187]. Conclusions Hypomagnesemia may be a signific…
format: application/pdf
format: text/html
creator: Chi-Ya Huang
creator: Chi-Chen Yang
creator: Kuo-Chuan Hung
creator: Ming-Yan Jiang
creator: Yun-Ting Huang
creator: Jyh-Chang Hwang
creator: Chih-Chieh Hsieh
creator: Min-Hsiang Chuang
creator: Jui-Yi Chen
subject: Biochemistry
subject: Hematology
subject: Internal Medicine
subject: Nephrology
description: doi:10.7717/peerj.14203
publisher: PeerJ Inc.
rights: © 2022 Huang et al.
abstract: Background Malnutrition-inflammation-atherosclerosis (MIA) syndrome is caused by the inflammatory cytokines in end stage renal disease (ESRD) patients, and MIA complex-related factors may be associated with hypomagnesemia and mortality. However, the association between serum magnesium level and mortality for dialysis patients is still not clear. Additionally, no meta-analysis has investigated the impact of serum magnesium on peritoneal dialysis and hemodialysis, separately. Methods We searched published studies in PubMed, Embase, Cochrane, Collaboration Central Register of Controlled Clinical Trials, and Cochrane Systematic Reviews through April 2022. Studies associated with serum magnesium and all-cause mortality or cardiovascular (CV) mortality in ESRD on kidney replacement therapy (KRT) patients were included. A hazard ratio (HR) with 95% confidence intervals (CI) was used to report the outcomes. Results Twenty-one studies involving 55,232 patients were included. Overall, there was a significant association between hypomagnesemia and all-cause mortality for dialysis patients (HR: 1.67, 95% CI [1.412–2.00], p < 0.001; certainty of evidence: moderate) using a mixed unadjusted and adjusted HR for analysis. There was also a significantly increased risk of CV mortality for individuals with hypomagnesemia compared with the non-hypomagnesemia group (HR 1.56, 95% CI [1.08–2.25], p < 0.001; certainty of evidence: moderate). In addition, a subgroup analysis demonstrated that hypomagnesemia was associated with a high risk of both all-cause mortality and CV mortality (all-cause mortality, HR:1.80, 95% CI [1.48–2.19]; CV mortality, HR:1.84, 95% CI [1.10–3.07]) in hemodialysis (HD) patients, but not in participants receiving peritoneal dialysis (PD; all-cause mortality, HR:1.26, 95% CI [0.84–1.91]; CV mortality, HR:0.66, 95% CI [0.22–2.00]). The systematic review protocol was prespecified and registered in PROSPERO [CRD42021256187]. Conclusions Hypomagnesemia may be a signific…
bibliographic citation: Huang et al. (2022) Association between hypomagnesemia and mortality among dialysis patients: a systematic review and meta-analysis. PeerJ 10:e14203 https://doi.org/10.7717/peerj.14203
date submitted: 2022-04-13
date accepted: 2022-09-19
issued: 2022-10-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Chi-Ya
author list: Agent
  family name: Yang
  given name: Chi-Chen
author list: Agent
  family name: Hung
  given name: Kuo-Chuan
author list: Agent
  family name: Jiang
  given name: Ming-Yan
author list: Agent
  family name: Huang
  given name: Yun-Ting
author list: Agent
  family name: Hwang
  given name: Jyh-Chang
author list: Agent
  family name: Hsieh
  given name: Chih-Chieh
author list: Agent
  family name: Chuang
  given name: Min-Hsiang
author list: Agent
  family name: Chen
  given name: Jui-Yi
doi: 10.7717/peerj.14203
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-11
copyright: © 2022 Huang et al.
attribution name: Huang et al.

Impact of silver nanoparticles on the nutritional properties of Arthrospira platensis
type: item
type: AcademicArticle
description: Background Arthrospira platensis is farmed worldwide due to its nutrient-rich properties and provides multiple benefits to human health. However, the wide usage of silver nanoparticles (Ag NPs) causes pollution which may affect the nutritional quality of A. platensis. Hence, this study aimed to investigate the interaction and accumulation of Ag NPs on A. platensis, and determine the changes in biomass and nutritional value of A. platensis due to the exposure to Ag NPs. Methods The interaction and accumulation of Ag NPs on A. platensis were examined through Fourier transformed infrared (FTIR) spectroscopy and scanning electron microscope (SEM). The loss in biomass together with the macromolecules, pigments, and phenolic compounds of A. platensis was investigated upon treating with various concentrations of Ag NPs (5, 10, 25, 50 and 100 µg/mL) for 24, 48, 72 and 96 h. Results The results showed that the treatment of A. platensis with Ag NPs caused a dose and time-dependent reduction in biomass, macronutrients, pigments and phenolic compounds. The highest detrimental effects were found at 96 h with the reported values of 65.71 ± 2.79%, 67.21 ± 3.98%, 48.99 ± 4.39% and 59.62 ± 3.96% reduction in biomass, proteins, carbohydrates and lipids, respectively, along with 82.99 ± 7.81%, 67.55 ± 2.63%, 75.03 ± 1.55%, and 63.43 ± 2.89% loss in chlorophyll-a, carotenoids, C-phycocyanin, and total phenolic compounds of A. platensis for 100 µg/mL of Ag NPs. The EDX analysis confirmed the surface accumulation of Ag NPs on Arthrospira cells, while SEM images evidenced the surface alterations and damage of the treated cells. The functional groups such as hydroxyl, amine, methyl, amide I, amide II, carboxyl, carbonyl and phosphate groups from the cell wall of the A. platensis were identified to be possibly involved in the interaction of Ag NPs with A. platensis. Conclusion The study confirmed that the exposure of Ag NPs is detrimental to A. platensis where the interaction and accumulati…
format: application/pdf
format: text/html
creator: Sharolynne Xiao Tong Liang
creator: Sinouvassane Djearamane
creator: Anto Cordelia Tanislaus Antony Dhanapal
creator: Ling Shing Wong
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
subject: Toxicology
subject: Ecotoxicology
description: doi:10.7717/peerj.13972
publisher: PeerJ Inc.
rights: © 2022 Liang et al.
abstract: Background Arthrospira platensis is farmed worldwide due to its nutrient-rich properties and provides multiple benefits to human health. However, the wide usage of silver nanoparticles (Ag NPs) causes pollution which may affect the nutritional quality of A. platensis. Hence, this study aimed to investigate the interaction and accumulation of Ag NPs on A. platensis, and determine the changes in biomass and nutritional value of A. platensis due to the exposure to Ag NPs. Methods The interaction and accumulation of Ag NPs on A. platensis were examined through Fourier transformed infrared (FTIR) spectroscopy and scanning electron microscope (SEM). The loss in biomass together with the macromolecules, pigments, and phenolic compounds of A. platensis was investigated upon treating with various concentrations of Ag NPs (5, 10, 25, 50 and 100 µg/mL) for 24, 48, 72 and 96 h. Results The results showed that the treatment of A. platensis with Ag NPs caused a dose and time-dependent reduction in biomass, macronutrients, pigments and phenolic compounds. The highest detrimental effects were found at 96 h with the reported values of 65.71 ± 2.79%, 67.21 ± 3.98%, 48.99 ± 4.39% and 59.62 ± 3.96% reduction in biomass, proteins, carbohydrates and lipids, respectively, along with 82.99 ± 7.81%, 67.55 ± 2.63%, 75.03 ± 1.55%, and 63.43 ± 2.89% loss in chlorophyll-a, carotenoids, C-phycocyanin, and total phenolic compounds of A. platensis for 100 µg/mL of Ag NPs. The EDX analysis confirmed the surface accumulation of Ag NPs on Arthrospira cells, while SEM images evidenced the surface alterations and damage of the treated cells. The functional groups such as hydroxyl, amine, methyl, amide I, amide II, carboxyl, carbonyl and phosphate groups from the cell wall of the A. platensis were identified to be possibly involved in the interaction of Ag NPs with A. platensis. Conclusion The study confirmed that the exposure of Ag NPs is detrimental to A. platensis where the interaction and accumulati…
bibliographic citation: Liang et al. (2022) Impact of silver nanoparticles on the nutritional properties of Arthrospira platensis. PeerJ 10:e13972 https://doi.org/10.7717/peerj.13972
date submitted: 2022-02-14
date accepted: 2022-08-09
issued: 2022-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Sharolynne Xiao Tong
author list: Agent
  family name: Djearamane
  given name: Sinouvassane
author list: Agent
  family name: Tanislaus Antony Dhanapal
  given name: Anto Cordelia
author list: Agent
  family name: Wong
  given name: Ling Shing
doi: 10.7717/peerj.13972
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-10
copyright: © 2022 Liang et al.
attribution name: Liang et al.

Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups
type: item
type: AcademicArticle
description: North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucl…
format: application/pdf
format: text/html
creator: Carla Stout
creator: Susana Schonhuth
creator: Richard Mayden
creator: Nicole L. Garrison
creator: Jonathan W. Armbruster
subject: Genomics
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.14072
publisher: PeerJ Inc.
rights: © 2022 Stout et al.
abstract: North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucl…
bibliographic citation: Stout et al. (2022) Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups. PeerJ 10:e14072 https://doi.org/10.7717/peerj.14072
date submitted: 2022-05-26
date accepted: 2022-08-27
issued: 2022-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stout
  given name: Carla
author list: Agent
  family name: Schonhuth
  given name: Susana
author list: Agent
  family name: Mayden
  given name: Richard
author list: Agent
  family name: Garrison
  given name: Nicole L.
author list: Agent
  family name: Armbruster
  given name: Jonathan W.
doi: 10.7717/peerj.14072
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-10
copyright: © 2022 Stout et al.
attribution name: Stout et al.

Effectiveness of a community-based peer support service among persons suffering severe mental illness in China
type: item
type: AcademicArticle
description: Background Community-based peer support service is widely and effectively deployed for persons suffering severe mental illness (SMI) in countries with well-developed outpatient mental health systems. The objective of this study is to evaluate the effectiveness of a 1-year peer service project among persons with SMI implemented in China. Methods A total of 101 consumers (service recipients) and 66 family caregivers were recruited at baseline from communities located in Beijing and Chengdu. Severity of psychiatric symptoms, personal and social functioning, self-esteem, life satisfaction, and medication adherence were evaluated among consumers. Self-esteem, life satisfaction, anxiety, and depressive symptoms were assessed among family caregivers. Participants were reevaluated at 1 year with the same measures. Changes in outcomes from baseline to 1-year follow-up were examined using paired sample t tests or Stuart-Maxwell tests. Results Consumers’ psychiatric symptoms were decreased at 1 year (p < 0.001). Their personal and social functioning (p = 0.003) and life satisfaction (p < 0.001) were increased. There were no improvements in self-esteem (p = 0.108) and medication adherence (ps ≥ 0.827) among consumers. For caregivers, no increases were presented in outcomes at the 1-year assessment (ps ≥ 0.164). Conclusions The findings suggest that peer support services could be sustainably implemented across China, with positive impacts on the psychiatric symptoms, social functioning, and life satisfaction of participants suffering SMI.
format: application/pdf
format: text/html
creator: Yunge Fan
creator: Ning Ma
creator: Aili Ouyang
creator: Wufang Zhang
creator: Manxi He
creator: Yong Chen
creator: Jin Liu
creator: Zhongxiang Li
creator: Junlan Yang
creator: Liang Ma
creator: Eric D. Caine
subject: Psychiatry and Psychology
subject: Mental Health
subject: Healthcare Services
subject: Rehabilitation
description: doi:10.7717/peerj.14091
publisher: PeerJ Inc.
rights: © 2022 Fan et al.
abstract: Background Community-based peer support service is widely and effectively deployed for persons suffering severe mental illness (SMI) in countries with well-developed outpatient mental health systems. The objective of this study is to evaluate the effectiveness of a 1-year peer service project among persons with SMI implemented in China. Methods A total of 101 consumers (service recipients) and 66 family caregivers were recruited at baseline from communities located in Beijing and Chengdu. Severity of psychiatric symptoms, personal and social functioning, self-esteem, life satisfaction, and medication adherence were evaluated among consumers. Self-esteem, life satisfaction, anxiety, and depressive symptoms were assessed among family caregivers. Participants were reevaluated at 1 year with the same measures. Changes in outcomes from baseline to 1-year follow-up were examined using paired sample t tests or Stuart-Maxwell tests. Results Consumers’ psychiatric symptoms were decreased at 1 year (p < 0.001). Their personal and social functioning (p = 0.003) and life satisfaction (p < 0.001) were increased. There were no improvements in self-esteem (p = 0.108) and medication adherence (ps ≥ 0.827) among consumers. For caregivers, no increases were presented in outcomes at the 1-year assessment (ps ≥ 0.164). Conclusions The findings suggest that peer support services could be sustainably implemented across China, with positive impacts on the psychiatric symptoms, social functioning, and life satisfaction of participants suffering SMI.
bibliographic citation: Fan et al. (2022) Effectiveness of a community-based peer support service among persons suffering severe mental illness in China. PeerJ 10:e14091 https://doi.org/10.7717/peerj.14091
date submitted: 2022-04-09
date accepted: 2022-08-30
issued: 2022-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Yunge
author list: Agent
  family name: Ma
  given name: Ning
author list: Agent
  family name: Ouyang
  given name: Aili
author list: Agent
  family name: Zhang
  given name: Wufang
author list: Agent
  family name: He
  given name: Manxi
author list: Agent
  family name: Chen
  given name: Yong
author list: Agent
  family name: Liu
  given name: Jin
author list: Agent
  family name: Li
  given name: Zhongxiang
author list: Agent
  family name: Yang
  given name: Junlan
author list: Agent
  family name: Ma
  given name: Liang
author list: Agent
  family name: Caine
  given name: Eric D.
doi: 10.7717/peerj.14091
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-10
copyright: ©2022 Fan et al.
attribution name: Fan et al.

Differentially expressed genes related to plant height and yield in two alfalfa cultivars based on RNA-seq
type: item
type: AcademicArticle
description: Background Alfalfa (Medicago sativa L.) is a kind of forage with high relative feeding value in farming and livestock breeding, and is of great significance to the development of animal husbandry. The growth of the aboveground part of alfalfa is an important factor that limits crop yield. Clarifying the molecular mechanisms that maintain vigorous growth in alfalfa may contribute to the development of molecular breeding for this crop. Methods Here, we evaluated the growth phenotypes of five cultivars of alfalfa (WL 712, WL 525HQ, Victoria, Knight 2, and Aohan). Then RNA-seq was performed on the stems of WL 712, chosen as a fast growing cultivar, and Aohan, chosen as a slow growing cultivar. GO enrichment analysis was conducted on all differentially expressed genes (DEGs). Result Among the differentially expressed genes that were up-regulated in the fast growing cultivar, GO analysis revealed enrichment in the following seven categories: formation of water-conducting tissue in vascular plants, biosynthesis and degradation of lignin, formation of the primary or secondary cell wall, cell enlargement and plant growth, cell division and shoot initiation, stem growth and induced germination, and cell elongation. KEGG analysis showed that differentially expressed genes were annotated as being involved in plant hormone signal transduction, photosynthesis, and phenylpropanoid biosynthesis. KEGG analysis also showed that up-regulated in the fast growing cultivar were members of the WRKY family of transcription factors related to plant growth and development, members of the NAC and MYB gene families related to the synthesis of cellulose and hemicellulose, and the development of secondary cell wall fibres, and finally, MYB family members that are involved in plant growth regulation. Our research results not only enrich the transcriptome database of alfalfa, but also provide valuable information for explaining the molecular mechanism of fast growth, and can provide reference for …
format: application/pdf
format: text/html
creator: Jiangjiao Qi
creator: Xue Yu
creator: Xuzhe Wang
creator: Fanfan Zhang
creator: Chunhui Ma
subject: Agricultural Science
subject: Biotechnology
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14096
publisher: PeerJ Inc.
rights: © 2022 Qi et al.
abstract: Background Alfalfa (Medicago sativa L.) is a kind of forage with high relative feeding value in farming and livestock breeding, and is of great significance to the development of animal husbandry. The growth of the aboveground part of alfalfa is an important factor that limits crop yield. Clarifying the molecular mechanisms that maintain vigorous growth in alfalfa may contribute to the development of molecular breeding for this crop. Methods Here, we evaluated the growth phenotypes of five cultivars of alfalfa (WL 712, WL 525HQ, Victoria, Knight 2, and Aohan). Then RNA-seq was performed on the stems of WL 712, chosen as a fast growing cultivar, and Aohan, chosen as a slow growing cultivar. GO enrichment analysis was conducted on all differentially expressed genes (DEGs). Result Among the differentially expressed genes that were up-regulated in the fast growing cultivar, GO analysis revealed enrichment in the following seven categories: formation of water-conducting tissue in vascular plants, biosynthesis and degradation of lignin, formation of the primary or secondary cell wall, cell enlargement and plant growth, cell division and shoot initiation, stem growth and induced germination, and cell elongation. KEGG analysis showed that differentially expressed genes were annotated as being involved in plant hormone signal transduction, photosynthesis, and phenylpropanoid biosynthesis. KEGG analysis also showed that up-regulated in the fast growing cultivar were members of the WRKY family of transcription factors related to plant growth and development, members of the NAC and MYB gene families related to the synthesis of cellulose and hemicellulose, and the development of secondary cell wall fibres, and finally, MYB family members that are involved in plant growth regulation. Our research results not only enrich the transcriptome database of alfalfa, but also provide valuable information for explaining the molecular mechanism of fast growth, and can provide reference for …
bibliographic citation: Qi et al. (2022) Differentially expressed genes related to plant height and yield in two alfalfa cultivars based on RNA-seq. PeerJ 10:e14096 https://doi.org/10.7717/peerj.14096
date submitted: 2022-04-08
date accepted: 2022-08-30
issued: 2022-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Jiangjiao
author list: Agent
  family name: Yu
  given name: Xue
author list: Agent
  family name: Wang
  given name: Xuzhe
author list: Agent
  family name: Zhang
  given name: Fanfan
author list: Agent
  family name: Ma
  given name: Chunhui
doi: 10.7717/peerj.14096
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-10
copyright: ©2022 Qi et al.
attribution name: Qi et al.

Rapid and convenient detection of SARS-CoV-2 using a colorimetric triple-target reverse transcription loop-mediated isothermal amplification method
type: item
type: AcademicArticle
description: Coronavirus Disease 2019 (COVID-19) caused by SARS-CoV-2 poses a significant threat to global public health. Early detection with reliable, fast, and simple assays is crucial to contain the spread of SARS-CoV-2. The real-time reverse transcription-polymerase chain reaction (RT-PCR) assay is currently the gold standard for SARS-CoV-2 detection; however, the reverse transcription loop-mediated isothermal amplification method (RT-LAMP) assay may allow for faster, simpler and cheaper screening of SARS-CoV-2. In this study, the triple-target RT-LAMP assay was first established to simultaneously detect three different target regions (ORF1ab, N and E genes) of SARS-CoV-2. The results revealed that the developed triplex RT-LAMP assay was able to detect down to 11 copies of SARS-CoV-2 RNA per 25 µL reaction, with greater sensitivity than singleplex or duplex RT-LAMP assays. Moreover, two different indicators, hydroxy naphthol blue (HNB) and cresol red, were studied in the colorimetric RT-LAMP assay; our results suggest that both indicators are suitable for RT-LAMP reactions with an obvious color change. In conclusion, our developed triplex colorimetric RT-LAMP assay may be useful for the screening of COVID-19 cases in limited-resource areas.
format: application/pdf
format: text/html
creator: Zhu Yang
creator: Nicole Y. Liu
creator: Zhiwei Zhu
creator: Minmin Xiao
creator: Shuzhi Zhong
creator: Qiqi Xue
creator: Lina Nie
creator: Jinhong Zhao
subject: Biochemistry
subject: Biotechnology
subject: Molecular Biology
subject: Virology
subject: COVID-19
description: doi:10.7717/peerj.14121
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Coronavirus Disease 2019 (COVID-19) caused by SARS-CoV-2 poses a significant threat to global public health. Early detection with reliable, fast, and simple assays is crucial to contain the spread of SARS-CoV-2. The real-time reverse transcription-polymerase chain reaction (RT-PCR) assay is currently the gold standard for SARS-CoV-2 detection; however, the reverse transcription loop-mediated isothermal amplification method (RT-LAMP) assay may allow for faster, simpler and cheaper screening of SARS-CoV-2. In this study, the triple-target RT-LAMP assay was first established to simultaneously detect three different target regions (ORF1ab, N and E genes) of SARS-CoV-2. The results revealed that the developed triplex RT-LAMP assay was able to detect down to 11 copies of SARS-CoV-2 RNA per 25 µL reaction, with greater sensitivity than singleplex or duplex RT-LAMP assays. Moreover, two different indicators, hydroxy naphthol blue (HNB) and cresol red, were studied in the colorimetric RT-LAMP assay; our results suggest that both indicators are suitable for RT-LAMP reactions with an obvious color change. In conclusion, our developed triplex colorimetric RT-LAMP assay may be useful for the screening of COVID-19 cases in limited-resource areas.
bibliographic citation: Yang et al. (2022) Rapid and convenient detection of SARS-CoV-2 using a colorimetric triple-target reverse transcription loop-mediated isothermal amplification method. PeerJ 10:e14121 https://doi.org/10.7717/peerj.14121
date submitted: 2022-06-29
date accepted: 2022-09-05
issued: 2022-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Zhu
author list: Agent
  family name: Liu
  given name: Nicole Y.
author list: Agent
  family name: Zhu
  given name: Zhiwei
author list: Agent
  family name: Xiao
  given name: Minmin
author list: Agent
  family name: Zhong
  given name: Shuzhi
author list: Agent
  family name: Xue
  given name: Qiqi
author list: Agent
  family name: Nie
  given name: Lina
author list: Agent
  family name: Zhao
  given name: Jinhong
doi: 10.7717/peerj.14121
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-10
copyright: ©2022 Yang et al.
attribution name: Yang et al.

The impact of children’s temperament on recurrent unintentional injuries: the role of paternal parenting styles as a mediator
type: item
type: AcademicArticle
description: Background Unintentional injuries (UIs) pose a threat to the health of children all over the world and are a major global health problem. The recurrence of UIs are influenced by the host itself or environmental factors. Children’s temperament and paternal parenting styles (PPS) are important potential factors for poor health outcomes, including recurrent unintentional injuries (recurrent UIs). Therefore, exploring the relationship among these variables may help reduce the likelihood of recurrent UIs in children. Purpose To elucidate the mediating effect of PPS in the relationship of children’s temperament characteristics and recurrent UIs among children. Methods By multistage random cluster sampling method, a total of 2,850 pupils in grades four and five from 10 different schools were included. The survey included the characteristics of UIs in the past year, parenting styles, and children’s temperament. Structural equation modeling (SEM) was used to examine the possible mediating effect of PPS between children’s temperament and recurrent UIs. Results In this study, the incidence rate of recurrent UIs was 3.8%. In temperament, children with recurrent UIs had higher mean scores than the non-recurrent UIs group (t = −3.40, −3.52, −3.45, respectively; p < 0.001) in the activity, predictability, persistence. Meanwhile, the scores of negative PPS (punishing, over-interference, rejection, and overprotection) were higher in the recurrent UIs group than in the non-recurrent UIs group (t = −5.78, −5.05, −5.56, and −3.29; p < 0.001, < 0.001, < 0.001, < 0.001, respectively). Using a stepwise binary logistic regression model, grade (OR = 0.23, 95% CI [0.12–0.41], p < 0.001), activity (OR = 1.61, 95% CI [1.14–2.26], p = 0.007) and over-interference (OR = 2.28, 95% CI [1.37–3.80], p = 0.002) had a significant independent relationship with recurrent UIs. The SEM results indicated that children’s temperament was significantly related to negative PPS (β = 0.26, p < 0.001) and recurre…
format: application/pdf
format: text/html
creator: Liuyuan Zhang
creator: Jin Liu
creator: Ying Tang
creator: Li Wang
subject: Pediatrics
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.14128
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Unintentional injuries (UIs) pose a threat to the health of children all over the world and are a major global health problem. The recurrence of UIs are influenced by the host itself or environmental factors. Children’s temperament and paternal parenting styles (PPS) are important potential factors for poor health outcomes, including recurrent unintentional injuries (recurrent UIs). Therefore, exploring the relationship among these variables may help reduce the likelihood of recurrent UIs in children. Purpose To elucidate the mediating effect of PPS in the relationship of children’s temperament characteristics and recurrent UIs among children. Methods By multistage random cluster sampling method, a total of 2,850 pupils in grades four and five from 10 different schools were included. The survey included the characteristics of UIs in the past year, parenting styles, and children’s temperament. Structural equation modeling (SEM) was used to examine the possible mediating effect of PPS between children’s temperament and recurrent UIs. Results In this study, the incidence rate of recurrent UIs was 3.8%. In temperament, children with recurrent UIs had higher mean scores than the non-recurrent UIs group (t = −3.40, −3.52, −3.45, respectively; p < 0.001) in the activity, predictability, persistence. Meanwhile, the scores of negative PPS (punishing, over-interference, rejection, and overprotection) were higher in the recurrent UIs group than in the non-recurrent UIs group (t = −5.78, −5.05, −5.56, and −3.29; p < 0.001, < 0.001, < 0.001, < 0.001, respectively). Using a stepwise binary logistic regression model, grade (OR = 0.23, 95% CI [0.12–0.41], p < 0.001), activity (OR = 1.61, 95% CI [1.14–2.26], p = 0.007) and over-interference (OR = 2.28, 95% CI [1.37–3.80], p = 0.002) had a significant independent relationship with recurrent UIs. The SEM results indicated that children’s temperament was significantly related to negative PPS (β = 0.26, p < 0.001) and recurre…
bibliographic citation: Zhang et al. (2022) The impact of children’s temperament on recurrent unintentional injuries: the role of paternal parenting styles as a mediator. PeerJ 10:e14128 https://doi.org/10.7717/peerj.14128
date submitted: 2022-05-12
date accepted: 2022-09-06
issued: 2022-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Liuyuan
author list: Agent
  family name: Liu
  given name: Jin
author list: Agent
  family name: Tang
  given name: Ying
author list: Agent
  family name: Wang
  given name: Li
doi: 10.7717/peerj.14128
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-10
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

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