PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Research progress on V delta 1+ T cells and their effect on pathogen infection
items: Meta-analysis of the efficacy of the erector spinae plane block after spinal fusion surgery
items: The critical need for child and youth perceptions of active living in India: capturing context complexity in rural and urban regions
items: Differences in cardiovascular disease mortality between northern and southern China under exposure to different temperatures: a systematic review
items: Identification and validation of autophagy-related genes in Hirschsprung’s disease
items: Optimization of fermentation conditions for physcion production of Aspergillus chevalieri BYST01 by response surface methodology
items: The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil
items: Using vessels of opportunity for determining important habitats of bottlenose dolphins in Port Phillip Bay, south-eastern Australia
items: Kinematic differences between female national and provincial athletes in the tennis serve
items: Development and internal and external validation of a nomogram model for predicting the risk of chronic kidney disease progression in IgA nephropathy patients

Research progress on V delta 1+ T cells and their effect on pathogen infection
type: item
type: AcademicArticle
description: The ongoing high occurrence of harmful infectious diseases significantly threatens human health. Existing methods used to control such diseases primarily involve targeting the pathogens, usually neglecting the vital role of host factors in disease advancement. Gamma delta (γδ) T cells act as a bridge between innate and adaptive immunity, playing a crucial role in combating pathogen invasion. Among these γδT cell subsets, which are categorized based on T cell receptor delta variable expression patterns, V delta (δ) 1+ T cells possess unique recognition abilities and regulatory characteristics and actively engage in various immune responses. The differentiation, development, and immune reactivity of Vδ1+ T cells are closely associated with the initial and progressive stages of infectious diseases. This article provides an overview of the classification, distribution, differentiation, and development of Vδ1+ T cells and their mechanisms in combating pathogenic infections, offering new insights for disease diagnosis and treatment.
format: application/pdf
format: text/html
creator: Yuxia Li
creator: Yanfei Liu
creator: Xiaoxiao Bu
creator: Yuanyuan Qin
creator: Yanyan Zhang
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.18313
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: The ongoing high occurrence of harmful infectious diseases significantly threatens human health. Existing methods used to control such diseases primarily involve targeting the pathogens, usually neglecting the vital role of host factors in disease advancement. Gamma delta (γδ) T cells act as a bridge between innate and adaptive immunity, playing a crucial role in combating pathogen invasion. Among these γδT cell subsets, which are categorized based on T cell receptor delta variable expression patterns, V delta (δ) 1+ T cells possess unique recognition abilities and regulatory characteristics and actively engage in various immune responses. The differentiation, development, and immune reactivity of Vδ1+ T cells are closely associated with the initial and progressive stages of infectious diseases. This article provides an overview of the classification, distribution, differentiation, and development of Vδ1+ T cells and their mechanisms in combating pathogenic infections, offering new insights for disease diagnosis and treatment.
bibliographic citation: Li et al. (2024) Research progress on V delta 1+ T cells and their effect on pathogen infection. PeerJ 12:e18313 https://doi.org/10.7717/peerj.18313
date submitted: 2024-07-26
date accepted: 2024-09-24
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: Yuxia
author list: Agent
  family name: Liu
  given name: Yanfei
author list: Agent
  family name: Bu
  given name: Xiaoxiao
author list: Agent
  family name: Qin
  given name: Yuanyuan
author list: Agent
  family name: Zhang
  given name: Yanyan
doi: 10.7717/peerj.18313
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: © 2024 Li et al.
attribution name: Li et al.

Meta-analysis of the efficacy of the erector spinae plane block after spinal fusion surgery
type: item
type: AcademicArticle
description: Objective To investigate the efficacy of erector spinal plane block (ESPB) after spinal fusion surgery in this study. Methods The PubMed, Embase, Cochrane library, and Web of Science databases were searched with a search deadline of March 30, 2024, and Stata 15.0 was used to analyze the data from the included studies. Result Nine randomized controlled trials involving 663 patients were included. Meta-analysis showed that EPSB could reduce pain scores at 2h (standard mean difference (SMD) = −0.78, 95% CI [−1.38 to −0.19], GRADE: Moderate), 6 h (SMD = −0.81, 95% CI [−1.23 to −0.38], GRADE: Moderate), 12 h (SMD = −0.59, 95% CI [−1.05 to −0.13], GRADE: Moderate), 24 h (SMD = −0.54, 95% CI [−0.86 to −0.21], GRADE: Moderate), 48 h (SMD = −0.40, 95% CI [−0.75 to −0.05], GRADE: Moderate) after spinal fusion surgery, as well as the PCA (analgesia medication use) (SMD = −1.67, 95% CI [−2.67 to −0.67], GRADE: Moderate). However, EPSB had no effect on intraoperative blood loss (SMD = −0.28, 95% CI [−1.03 to 0.47], GRADE: Low) and length of hospital stay (SMD = −0.27, 95% CI [−0.60–0.06], GRADE: Low). Conclusion Combined with the current findings, EPSB may reduce pain scores in spinal fusion surgery, possibly reducing the use of postoperative analgesics. However, due to the limitations of the study, we need more high-quality, multi-center, large sample randomized controlled trials to merge.
format: application/pdf
format: text/html
creator: Yi He
creator: Heng Liu
creator: Peng Ma
creator: Jing Zhang
creator: Qiulian He
subject: Anesthesiology and Pain Management
subject: Epidemiology
description: doi:10.7717/peerj.18332
publisher: PeerJ Inc.
rights: © 2024 He et al.
abstract: Objective To investigate the efficacy of erector spinal plane block (ESPB) after spinal fusion surgery in this study. Methods The PubMed, Embase, Cochrane library, and Web of Science databases were searched with a search deadline of March 30, 2024, and Stata 15.0 was used to analyze the data from the included studies. Result Nine randomized controlled trials involving 663 patients were included. Meta-analysis showed that EPSB could reduce pain scores at 2h (standard mean difference (SMD) = −0.78, 95% CI [−1.38 to −0.19], GRADE: Moderate), 6 h (SMD = −0.81, 95% CI [−1.23 to −0.38], GRADE: Moderate), 12 h (SMD = −0.59, 95% CI [−1.05 to −0.13], GRADE: Moderate), 24 h (SMD = −0.54, 95% CI [−0.86 to −0.21], GRADE: Moderate), 48 h (SMD = −0.40, 95% CI [−0.75 to −0.05], GRADE: Moderate) after spinal fusion surgery, as well as the PCA (analgesia medication use) (SMD = −1.67, 95% CI [−2.67 to −0.67], GRADE: Moderate). However, EPSB had no effect on intraoperative blood loss (SMD = −0.28, 95% CI [−1.03 to 0.47], GRADE: Low) and length of hospital stay (SMD = −0.27, 95% CI [−0.60–0.06], GRADE: Low). Conclusion Combined with the current findings, EPSB may reduce pain scores in spinal fusion surgery, possibly reducing the use of postoperative analgesics. However, due to the limitations of the study, we need more high-quality, multi-center, large sample randomized controlled trials to merge.
bibliographic citation: He et al. (2024) Meta-analysis of the efficacy of the erector spinae plane block after spinal fusion surgery. PeerJ 12:e18332 https://doi.org/10.7717/peerj.18332
date submitted: 2024-05-02
date accepted: 2024-09-25
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Yi
author list: Agent
  family name: Liu
  given name: Heng
author list: Agent
  family name: Ma
  given name: Peng
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: He
  given name: Qiulian
doi: 10.7717/peerj.18332
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: ©2024 He et al.
attribution name: He et al.

The critical need for child and youth perceptions of active living in India: capturing context complexity in rural and urban regions
type: item
type: AcademicArticle
description: Background The physical inactivity pandemic not only has a negative impact on the physical and mental health of children and youth, but it is also a key contributor to the non-communicable disease (NCD) burden, particularly among low- and middle-income countries. The widespread effects of climate change, ranging from extreme weather events to worsening air quality, are exacerbating the physical inactivity pandemic, highlighting the need to undertake holistic interventions to address environmental barriers while promoting physical activity. Despite the potential benefits of active school transportation (AST) on physical activity and the environment, no study has examined the intersection between perceptions of AST, environmental perceptions, and moderate-to-vigorous physical activity (MVPA) among children and youth in India from a child and youth perspective. Methods As a part of this cross-sectional, observational study, digital survey links were administered to 1,042 children and youth aged 5 to 17 (50.3% boys; 49.7% girls). Participants were recruited from 41 schools across 28 rural and urban regions in India. Children and youth provided information on various sociodemographic factors, perceptions of crime and air pollution, and peer support factors. MVPA data were collected using an adapted version of the IPAQ short-form questionnaire. The overall sample was stratified by age, gender, and location, resulting in a total of seven multiple linear regression models to assess the association between AST and MVPA. Results Children and youth who engaged in AST were associated with higher MVPA than those who did not engage in AST (β = 18.020, 95% CI [5.890 to 30.149], p = 0.004), after adjusting for age, gender, and location. In contrast, perceptions of high crime in the neighbourhood (β = − 21.921, CI [−36.195 to −7.647], p = 0.003) and perceptions of air pollution (β = − 12.472, CI [−23.797 to −1.147], p = 0.031) were associated with lower MVPA. Moreover, having active…
format: application/pdf
format: text/html
creator: Tarun Reddy Katapally
creator: Jamin Patel
creator: Anuradha Khadilkar
creator: Jasmin Bhawra
subject: Epidemiology
subject: Global Health
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.18350
publisher: PeerJ Inc.
rights: © 2024 Katapally et al.
abstract: Background The physical inactivity pandemic not only has a negative impact on the physical and mental health of children and youth, but it is also a key contributor to the non-communicable disease (NCD) burden, particularly among low- and middle-income countries. The widespread effects of climate change, ranging from extreme weather events to worsening air quality, are exacerbating the physical inactivity pandemic, highlighting the need to undertake holistic interventions to address environmental barriers while promoting physical activity. Despite the potential benefits of active school transportation (AST) on physical activity and the environment, no study has examined the intersection between perceptions of AST, environmental perceptions, and moderate-to-vigorous physical activity (MVPA) among children and youth in India from a child and youth perspective. Methods As a part of this cross-sectional, observational study, digital survey links were administered to 1,042 children and youth aged 5 to 17 (50.3% boys; 49.7% girls). Participants were recruited from 41 schools across 28 rural and urban regions in India. Children and youth provided information on various sociodemographic factors, perceptions of crime and air pollution, and peer support factors. MVPA data were collected using an adapted version of the IPAQ short-form questionnaire. The overall sample was stratified by age, gender, and location, resulting in a total of seven multiple linear regression models to assess the association between AST and MVPA. Results Children and youth who engaged in AST were associated with higher MVPA than those who did not engage in AST (β = 18.020, 95% CI [5.890 to 30.149], p = 0.004), after adjusting for age, gender, and location. In contrast, perceptions of high crime in the neighbourhood (β = − 21.921, CI [−36.195 to −7.647], p = 0.003) and perceptions of air pollution (β = − 12.472, CI [−23.797 to −1.147], p = 0.031) were associated with lower MVPA. Moreover, having active…
bibliographic citation: Katapally et al. (2024) The critical need for child and youth perceptions of active living in India: capturing context complexity in rural and urban regions. PeerJ 12:e18350 https://doi.org/10.7717/peerj.18350
date submitted: 2024-04-25
date accepted: 2024-09-27
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Katapally
  given name: Tarun Reddy
author list: Agent
  family name: Patel
  given name: Jamin
author list: Agent
  family name: Khadilkar
  given name: Anuradha
author list: Agent
  family name: Bhawra
  given name: Jasmin
doi: 10.7717/peerj.18350
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: ©2024 Katapally et al.
attribution name: Katapally et al.

Differences in cardiovascular disease mortality between northern and southern China under exposure to different temperatures: a systematic review
type: item
type: AcademicArticle
description: Background Due to differences in climate and other environmental factors, exposure to different temperatures in China has different effects on the relative risk (RR) of cardiovascular disease (CVD) mortality. It is therefore important to compare the effects of exposure to different temperatures on CVD mortality in different regions of China. Methods To compare these effects, we performed a meta-analysis of 21 studies identified by a search of the Web of Science and China National Knowledge Infrastructure databases from January 1, 2014 to January 1, 2024. We performed the Cochran Q test and I2 statistics test to evaluate heterogeneity and Egger’s test to evaluate publication bias. Results The pooled estimated size of the relationship between exposure to different temperatures and CVD mortality was 1.60 (95% confidence interval [CI]: [1.42–1.80]) for the extreme cold, 1.17 (95% CI [1.10–1.25]) for the extreme heat, and 1.16 (95% CI [1.10–1.24]) for extremely high diurnal temperature range (DTR). The Egger’s test showed potential publication bias in studies analyzing both the extreme cold and the extreme heat. Discussion Extreme cold, extreme heat, and extremely high DTR are associated with an increase in CVD mortality in China, with extreme cold having the most significant effect. Residents of northern regions are more susceptible to high temperatures, while residents of southern regions are more sensitive to low temperatures.
format: application/pdf
format: text/html
creator: Guangyu Zhai
creator: Ziqing Jiang
creator: Wenjuan Zhou
subject: Cardiology
subject: Statistics
subject: Environmental Health
description: doi:10.7717/peerj.18355
publisher: PeerJ Inc.
rights: © 2024 Zhai et al.
abstract: Background Due to differences in climate and other environmental factors, exposure to different temperatures in China has different effects on the relative risk (RR) of cardiovascular disease (CVD) mortality. It is therefore important to compare the effects of exposure to different temperatures on CVD mortality in different regions of China. Methods To compare these effects, we performed a meta-analysis of 21 studies identified by a search of the Web of Science and China National Knowledge Infrastructure databases from January 1, 2014 to January 1, 2024. We performed the Cochran Q test and I2 statistics test to evaluate heterogeneity and Egger’s test to evaluate publication bias. Results The pooled estimated size of the relationship between exposure to different temperatures and CVD mortality was 1.60 (95% confidence interval [CI]: [1.42–1.80]) for the extreme cold, 1.17 (95% CI [1.10–1.25]) for the extreme heat, and 1.16 (95% CI [1.10–1.24]) for extremely high diurnal temperature range (DTR). The Egger’s test showed potential publication bias in studies analyzing both the extreme cold and the extreme heat. Discussion Extreme cold, extreme heat, and extremely high DTR are associated with an increase in CVD mortality in China, with extreme cold having the most significant effect. Residents of northern regions are more susceptible to high temperatures, while residents of southern regions are more sensitive to low temperatures.
bibliographic citation: Zhai et al. (2024) Differences in cardiovascular disease mortality between northern and southern China under exposure to different temperatures: a systematic review. PeerJ 12:e18355 https://doi.org/10.7717/peerj.18355
date submitted: 2024-06-17
date accepted: 2024-09-27
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhai
  given name: Guangyu
author list: Agent
  family name: Jiang
  given name: Ziqing
author list: Agent
  family name: Zhou
  given name: Wenjuan
doi: 10.7717/peerj.18355
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: ©2024 Zhai et al.
attribution name: Zhai et al.

Identification and validation of autophagy-related genes in Hirschsprung’s disease
type: item
type: AcademicArticle
description: Background Hirschsprung’s disease (HSCR) is a congenital disorder characterized by aganglionosis in the intermuscular and submucosal nerve plexuses of the gut, leading to impaired gastrointestinal function. Although the precise cause and pathophysiology of HSCR remain elusive, increasing evidence points to a significant role of autophagy in its development, warranting further investigation into its underlying mechanisms. Methods This study utilized publicly available microarray expression profiling datasets, GSE96854 and GSE98502, from the Gene Expression Omnibus (GEO). The R software (version 4.2.0) was employed to identify autophagy-related genes potentially showing differential expression in HSCR. Subsequent analyses included correlation analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) network analysis using the STRING database (version 11.0) and Cytoscape software (version 3.8.2). Ultimately, HSCR samples were used to verify the mRNA levels of important genes by quantitative real-time polymerase chain reaction (qRT-PCR) in a laboratory setting. Results We have discovered 20 genes that are involved in autophagy and show variable expression. Among these genes, 15 are up-regulated and five are down-regulated. The enrichment analysis using the GO and KEGG pathways revealed a notable enrichment in pathways related to the control of autophagy. Nine hub genes were found via the investigation of the PPI network constructed from STRING database and module analysis using Cytoscape. Moreover, the concordance between SIRT1 expression in the HSCR model and the bioinformatics analysis of mRNA chip findings was validated using qRT-PCR. Conclusion Utilizing bioinformatics analysis, we identified 20 potential genes associated with Hirschsprung’s disease that play a role in autophagy. Notably, the upregulation of SIRT1 may profoundly influence the progression of HSCR by regulating autophagy-r…
format: application/pdf
format: text/html
creator: Ting Yao
creator: Zenghui Hao
creator: Wei Fan
creator: Jinbao Han
creator: Shuyu Wang
creator: Zaiqun Jiang
creator: Yunting Wang
creator: Xiao Qian Yang
creator: Zhilin Xu
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Pediatrics
description: doi:10.7717/peerj.18376
publisher: PeerJ Inc.
rights: © 2024 Yao et al.
abstract: Background Hirschsprung’s disease (HSCR) is a congenital disorder characterized by aganglionosis in the intermuscular and submucosal nerve plexuses of the gut, leading to impaired gastrointestinal function. Although the precise cause and pathophysiology of HSCR remain elusive, increasing evidence points to a significant role of autophagy in its development, warranting further investigation into its underlying mechanisms. Methods This study utilized publicly available microarray expression profiling datasets, GSE96854 and GSE98502, from the Gene Expression Omnibus (GEO). The R software (version 4.2.0) was employed to identify autophagy-related genes potentially showing differential expression in HSCR. Subsequent analyses included correlation analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) network analysis using the STRING database (version 11.0) and Cytoscape software (version 3.8.2). Ultimately, HSCR samples were used to verify the mRNA levels of important genes by quantitative real-time polymerase chain reaction (qRT-PCR) in a laboratory setting. Results We have discovered 20 genes that are involved in autophagy and show variable expression. Among these genes, 15 are up-regulated and five are down-regulated. The enrichment analysis using the GO and KEGG pathways revealed a notable enrichment in pathways related to the control of autophagy. Nine hub genes were found via the investigation of the PPI network constructed from STRING database and module analysis using Cytoscape. Moreover, the concordance between SIRT1 expression in the HSCR model and the bioinformatics analysis of mRNA chip findings was validated using qRT-PCR. Conclusion Utilizing bioinformatics analysis, we identified 20 potential genes associated with Hirschsprung’s disease that play a role in autophagy. Notably, the upregulation of SIRT1 may profoundly influence the progression of HSCR by regulating autophagy-r…
bibliographic citation: Yao et al. (2024) Identification and validation of autophagy-related genes in Hirschsprung’s disease. PeerJ 12:e18376 https://doi.org/10.7717/peerj.18376
date submitted: 2024-05-21
date accepted: 2024-10-01
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Ting
author list: Agent
  family name: Hao
  given name: Zenghui
author list: Agent
  family name: Fan
  given name: Wei
author list: Agent
  family name: Han
  given name: Jinbao
author list: Agent
  family name: Wang
  given name: Shuyu
author list: Agent
  family name: Jiang
  given name: Zaiqun
author list: Agent
  family name: Wang
  given name: Yunting
author list: Agent
  family name: Yang
  given name: Xiao Qian
author list: Agent
  family name: Xu
  given name: Zhilin
doi: 10.7717/peerj.18376
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: ©2024 Yao et al.
attribution name: Yao et al.

Optimization of fermentation conditions for physcion production of Aspergillus chevalieri BYST01 by response surface methodology
type: item
type: AcademicArticle
description: This study aimed to optimize the culture conditions of the termite-derived fungus Aspergillus chevalieri BYST01 for the production of physcion, a characteristic component of the traditional herb rhubarb, which has been commercially approved as a botanical fungicide in China. First, potato dextrose broth was screened as the suitable basal medium for further optimization, with an initial yield of 28.0 mg/L. Then, the suitable carbon source, fermentation time, temperature, pH value, and the rotary shaker speed for physcion production were determined using the one-variable-at-a-time method. Based on the results of single factors experiments, the variables with statistically significant effects on physcion production were further confirmed using the Plackett-Burman design (PBD). Among the five variables, temperature, initial pH, and rotary shaker speed were identified as significant factors (P < 0.05) for physcion productivity in the PDB and were further analyzed by response surface methodology (RSM). Finally, we found that the maximum physcion production (82.0 mg/L) was achieved under the following optimized conditions:initial pH 6.6, rotary shaker speed of 177 rpm, temperature of 28 °C, and glucose concentration of 30 g/L in PDB medium after 11 d of fermentation. The yield of physcion under the optimized culture conditions was approximately threefold higher than that obtained using the basal culture medium. Furthermore, the optimum fermentation conditions in the 5-L bioreactor achieved a maximal physcion yield of 85.2 mg/L within 8 d of fermentation. Hence, response surface methodology proved to be a powerful tool for optimizing physcion production by A. chevalieri BYST01. This study may be helpful in promoting the application of physcion produced by A. chevalieri BYST01 to manage plant diseases.
format: application/pdf
format: text/html
creator: Shuxiang Zhang
creator: Zhou Jiang
creator: Suwen An
creator: Xiaolan Jiang
creator: Yinglao Zhang
subject: Agricultural Science
subject: Biochemistry
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.18380
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: This study aimed to optimize the culture conditions of the termite-derived fungus Aspergillus chevalieri BYST01 for the production of physcion, a characteristic component of the traditional herb rhubarb, which has been commercially approved as a botanical fungicide in China. First, potato dextrose broth was screened as the suitable basal medium for further optimization, with an initial yield of 28.0 mg/L. Then, the suitable carbon source, fermentation time, temperature, pH value, and the rotary shaker speed for physcion production were determined using the one-variable-at-a-time method. Based on the results of single factors experiments, the variables with statistically significant effects on physcion production were further confirmed using the Plackett-Burman design (PBD). Among the five variables, temperature, initial pH, and rotary shaker speed were identified as significant factors (P < 0.05) for physcion productivity in the PDB and were further analyzed by response surface methodology (RSM). Finally, we found that the maximum physcion production (82.0 mg/L) was achieved under the following optimized conditions:initial pH 6.6, rotary shaker speed of 177 rpm, temperature of 28 °C, and glucose concentration of 30 g/L in PDB medium after 11 d of fermentation. The yield of physcion under the optimized culture conditions was approximately threefold higher than that obtained using the basal culture medium. Furthermore, the optimum fermentation conditions in the 5-L bioreactor achieved a maximal physcion yield of 85.2 mg/L within 8 d of fermentation. Hence, response surface methodology proved to be a powerful tool for optimizing physcion production by A. chevalieri BYST01. This study may be helpful in promoting the application of physcion produced by A. chevalieri BYST01 to manage plant diseases.
bibliographic citation: Zhang et al. (2024) Optimization of fermentation conditions for physcion production of Aspergillus chevalieri BYST01 by response surface methodology. PeerJ 12:e18380 https://doi.org/10.7717/peerj.18380
date submitted: 2024-05-20
date accepted: 2024-10-01
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shuxiang
author list: Agent
  family name: Jiang
  given name: Zhou
author list: Agent
  family name: An
  given name: Suwen
author list: Agent
  family name: Jiang
  given name: Xiaolan
author list: Agent
  family name: Zhang
  given name: Yinglao
doi: 10.7717/peerj.18380
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil
type: item
type: AcademicArticle
description: Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices.
format: application/pdf
format: text/html
creator: Nattanan Rueangmongkolrat
creator: Pichahpuk Uthaipaisanwong
creator: Kanthida Kusonmano
creator: Sasipa Pruksangkul
creator: Prinpida Sonthiphand
subject: Genomics
subject: Microbiology
subject: Soil Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.18383
publisher: PeerJ Inc.
rights: © 2024 Rueangmongkolrat et al.
abstract: Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices.
bibliographic citation: Rueangmongkolrat et al. (2024) The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil. PeerJ 12:e18383 https://doi.org/10.7717/peerj.18383
date submitted: 2024-08-01
date accepted: 2024-10-01
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rueangmongkolrat
  given name: Nattanan
author list: Agent
  family name: Uthaipaisanwong
  given name: Pichahpuk
author list: Agent
  family name: Kusonmano
  given name: Kanthida
author list: Agent
  family name: Pruksangkul
  given name: Sasipa
author list: Agent
  family name: Sonthiphand
  given name: Prinpida
doi: 10.7717/peerj.18383
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: ©2024 Rueangmongkolrat et al.
attribution name: Rueangmongkolrat et al.

Using vessels of opportunity for determining important habitats of bottlenose dolphins in Port Phillip Bay, south-eastern Australia
type: item
type: AcademicArticle
description: Understanding species’ critical habitat requirements is crucial for effective conservation and management. However, such information can be challenging to obtain, particularly for highly mobile, wide-ranging species such as cetaceans. In the absence of systematic surveys, alternative economically viable methods are needed, such as the use of data collected from platforms of opportunity, and modelling techniques to predict species distribution in un-surveyed areas. The present study used data collected by ecotourism and other vessels of opportunity to investigate important habitats of a small, poorly studied population of bottlenose dolphins in Port Phillip Bay, south-eastern Australia. Using 16 years of dolphin sighting location data, an ensemble habitat suitability model was built from which physical factors influencing dolphin distribution were identified. Results indicated that important habitats were those areas close to shipping channels and coastlines with these factors primarily influencing the variation in the likelihood of dolphin presence. The relatively good performance of the ensemble model suggests that simple presence-background data may be sufficient for predicting the species distribution where sighting data are limited. However, additional data from the center of Port Phillip Bay is required to further support this contention. Important habitat features identified in the study are likely to relate to favorable foraging conditions for dolphins as they are known to provide feeding, breeding, and spawning habitat for a diverse range of fish and cephalopod prey species. The results of the present study highlight the importance of affordable community-based data collection, such as ecotourism vessels, for obtaining information critical for effective management.
format: application/pdf
format: text/html
creator: Maddison J. Ledwidge
creator: Jacquomo Monk
creator: Suzanne J. Mason
creator: John P. Y. Arnould
subject: Biogeography
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.18400
publisher: PeerJ Inc.
rights: © 2024 Ledwidge et al.
abstract: Understanding species’ critical habitat requirements is crucial for effective conservation and management. However, such information can be challenging to obtain, particularly for highly mobile, wide-ranging species such as cetaceans. In the absence of systematic surveys, alternative economically viable methods are needed, such as the use of data collected from platforms of opportunity, and modelling techniques to predict species distribution in un-surveyed areas. The present study used data collected by ecotourism and other vessels of opportunity to investigate important habitats of a small, poorly studied population of bottlenose dolphins in Port Phillip Bay, south-eastern Australia. Using 16 years of dolphin sighting location data, an ensemble habitat suitability model was built from which physical factors influencing dolphin distribution were identified. Results indicated that important habitats were those areas close to shipping channels and coastlines with these factors primarily influencing the variation in the likelihood of dolphin presence. The relatively good performance of the ensemble model suggests that simple presence-background data may be sufficient for predicting the species distribution where sighting data are limited. However, additional data from the center of Port Phillip Bay is required to further support this contention. Important habitat features identified in the study are likely to relate to favorable foraging conditions for dolphins as they are known to provide feeding, breeding, and spawning habitat for a diverse range of fish and cephalopod prey species. The results of the present study highlight the importance of affordable community-based data collection, such as ecotourism vessels, for obtaining information critical for effective management.
bibliographic citation: Ledwidge et al. (2024) Using vessels of opportunity for determining important habitats of bottlenose dolphins in Port Phillip Bay, south-eastern Australia. PeerJ 12:e18400 https://doi.org/10.7717/peerj.18400
date submitted: 2023-11-08
date accepted: 2024-10-04
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ledwidge
  given name: Maddison J.
author list: Agent
  family name: Monk
  given name: Jacquomo
author list: Agent
  family name: Mason
  given name: Suzanne J.
author list: Agent
  family name: Arnould
  given name: John P. Y.
doi: 10.7717/peerj.18400
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: © 2024 Ledwidge et al.
attribution name: Ledwidge et al.

Kinematic differences between female national and provincial athletes in the tennis serve
type: item
type: AcademicArticle
description: Background Tennis, the second-largest ball game in the world, has a particularly wide audience. To date, little research has been conducted on the biomechanics of female serves. Purpose The purpose of this study was to capture the key moments by using 1,000 frames/s high-speed video analysis, to analyze the kinematics of the serving techniques of national athletes and provincial athletes, to determine the differences between the two levels of athletes, and to provide theoretical references for the improvement of scientific training level. Methods Ten female athletes were selected as participants for this study, five of whom are national athletes, and the other are provincial athletes. Three-dimensional filming techniques were employed to capture videos of the first and second serve techniques. Simi Motion was applied to obtain the 3D kinematic data. Statistical analyses were performed using IBM SPSS Statistics 27.0, and Mann–Whitney U tests were conducted to determine differences between groups. Results Significant differences in kinematics were found between national and provincial athletes. At the moment of the left knee’s minimum flexion (T2), in the first serve, national athletes had a smaller shoulder-hip vertical plane angle (−18.281 ± 6.142° vs. −25.631 ± 3.497°; p = 0.047) and a larger hip vertical plane rotation angle (−9.378 ± 4.263° vs. −0.470 ± 4.724°; p = 0.047). In the second serve, national athletes had a smaller hip horizontal plane rotation angle (−1.720 ± 4.683° vs. 24.146 ± 24.014°; p = 0.047) but a larger hip vertical plane rotation angle (−11.553 ± 1.949° vs. −0.422 ± 4.958°; p = 0.009). At the moment of impact (T4), in the second serve, national athletes’ batting position (0.296 ± 0.088 m vs. 0.446 ± 0.094 m; p = 0.047) was further back. Additionally, in the second serve, national athletes consistently had their body center of gravity further back at T2 (−0.106 ± 0.052 m vs. −0.018 ± 0.048 m; p = 0.028), T3 (0.002 ± 0.038 m vs. 0.132 ± 0.039 m;…
format: application/pdf
format: text/html
creator: Yan Chen
creator: Tianyang Wang
creator: Yuyan Zhao
creator: Genghao Zhan
creator: Yinchao Tang
creator: Zefeng Wang
subject: Biomechanics
description: doi:10.7717/peerj.18410
publisher: PeerJ Inc.
rights: © 2024 Chen et al.
abstract: Background Tennis, the second-largest ball game in the world, has a particularly wide audience. To date, little research has been conducted on the biomechanics of female serves. Purpose The purpose of this study was to capture the key moments by using 1,000 frames/s high-speed video analysis, to analyze the kinematics of the serving techniques of national athletes and provincial athletes, to determine the differences between the two levels of athletes, and to provide theoretical references for the improvement of scientific training level. Methods Ten female athletes were selected as participants for this study, five of whom are national athletes, and the other are provincial athletes. Three-dimensional filming techniques were employed to capture videos of the first and second serve techniques. Simi Motion was applied to obtain the 3D kinematic data. Statistical analyses were performed using IBM SPSS Statistics 27.0, and Mann–Whitney U tests were conducted to determine differences between groups. Results Significant differences in kinematics were found between national and provincial athletes. At the moment of the left knee’s minimum flexion (T2), in the first serve, national athletes had a smaller shoulder-hip vertical plane angle (−18.281 ± 6.142° vs. −25.631 ± 3.497°; p = 0.047) and a larger hip vertical plane rotation angle (−9.378 ± 4.263° vs. −0.470 ± 4.724°; p = 0.047). In the second serve, national athletes had a smaller hip horizontal plane rotation angle (−1.720 ± 4.683° vs. 24.146 ± 24.014°; p = 0.047) but a larger hip vertical plane rotation angle (−11.553 ± 1.949° vs. −0.422 ± 4.958°; p = 0.009). At the moment of impact (T4), in the second serve, national athletes’ batting position (0.296 ± 0.088 m vs. 0.446 ± 0.094 m; p = 0.047) was further back. Additionally, in the second serve, national athletes consistently had their body center of gravity further back at T2 (−0.106 ± 0.052 m vs. −0.018 ± 0.048 m; p = 0.028), T3 (0.002 ± 0.038 m vs. 0.132 ± 0.039 m;…
bibliographic citation: Chen et al. (2024) Kinematic differences between female national and provincial athletes in the tennis serve. PeerJ 12:e18410 https://doi.org/10.7717/peerj.18410
date submitted: 2024-03-08
date accepted: 2024-10-07
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yan
author list: Agent
  family name: Wang
  given name: Tianyang
author list: Agent
  family name: Zhao
  given name: Yuyan
author list: Agent
  family name: Zhan
  given name: Genghao
author list: Agent
  family name: Tang
  given name: Yinchao
author list: Agent
  family name: Wang
  given name: Zefeng
doi: 10.7717/peerj.18410
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: © 2024 Chen et al.
attribution name: Chen et al.

Development and internal and external validation of a nomogram model for predicting the risk of chronic kidney disease progression in IgA nephropathy patients
type: item
type: AcademicArticle
description: Background IgA nephropathy (IgAN) is the most common primary glomerular disease in chronic kidney disease (CKD), exhibiting significant heterogeneity in both clinical and pathological presentations. We aimed to explore the risk factors influencing short-term prognosis (≥90 days) and to construct a nomogram model for evaluating the risk of CKD progression in IgAN patients. Methods Clinical and pathological data of patients diagnosed with IgAN through biopsy at two centers were retrospectively collected. Logistic regression was employed to analyze the training cohort dataset and identify the independent predictors to construct a nomogram model based on the final variables. The predictive model was validated both internally and externally, with its performance assessed using the area under the curve (AUC), calibration curves, and decision curve analysis. Results Out of the patients in the modeling group, 129 individuals (41.6%) did not achieve remission following 3 months of treatment, indicating a high risk of CKD progression. A multivariate logistic regression analysis demonstrated that body mass index, urinary protein excretion, and tubular atrophy/interstitial fibrosis were identified as independent predictors for risk stratification. A nomogram model was formulated utilizing the final variables. The AUCs for the training set, internal validation set, and external validation set were 0.746 (95% confidence intervals (CI) [0.691–0.8]), 0.764 (95% CI [0.68–0.85]), and 0.749 (95% CI [0.65–0.85]), respectively. The validation of the subgroup analysis also demonstrated a satisfactory AUC. Conclusion This study developed and validated a practical nomogram that can individually predict short-term treatment outcomes (≥90 days) and the risk of CKD progression in IgAN patients. It provides reliable guidance for timely and personalized intervention and treatment strategies.
format: application/pdf
format: text/html
creator: Ying Zhang
creator: Zhixin Wang
creator: Wenwu Tang
creator: Xinzhu Yuan
creator: Xisheng Xie
subject: Internal Medicine
subject: Nephrology
description: doi:10.7717/peerj.18416
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Background IgA nephropathy (IgAN) is the most common primary glomerular disease in chronic kidney disease (CKD), exhibiting significant heterogeneity in both clinical and pathological presentations. We aimed to explore the risk factors influencing short-term prognosis (≥90 days) and to construct a nomogram model for evaluating the risk of CKD progression in IgAN patients. Methods Clinical and pathological data of patients diagnosed with IgAN through biopsy at two centers were retrospectively collected. Logistic regression was employed to analyze the training cohort dataset and identify the independent predictors to construct a nomogram model based on the final variables. The predictive model was validated both internally and externally, with its performance assessed using the area under the curve (AUC), calibration curves, and decision curve analysis. Results Out of the patients in the modeling group, 129 individuals (41.6%) did not achieve remission following 3 months of treatment, indicating a high risk of CKD progression. A multivariate logistic regression analysis demonstrated that body mass index, urinary protein excretion, and tubular atrophy/interstitial fibrosis were identified as independent predictors for risk stratification. A nomogram model was formulated utilizing the final variables. The AUCs for the training set, internal validation set, and external validation set were 0.746 (95% confidence intervals (CI) [0.691–0.8]), 0.764 (95% CI [0.68–0.85]), and 0.749 (95% CI [0.65–0.85]), respectively. The validation of the subgroup analysis also demonstrated a satisfactory AUC. Conclusion This study developed and validated a practical nomogram that can individually predict short-term treatment outcomes (≥90 days) and the risk of CKD progression in IgAN patients. It provides reliable guidance for timely and personalized intervention and treatment strategies.
bibliographic citation: Zhang et al. (2024) Development and internal and external validation of a nomogram model for predicting the risk of chronic kidney disease progression in IgA nephropathy patients. PeerJ 12:e18416 https://doi.org/10.7717/peerj.18416
date submitted: 2024-06-05
date accepted: 2024-10-07
issued: 2024-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ying
author list: Agent
  family name: Wang
  given name: Zhixin
author list: Agent
  family name: Tang
  given name: Wenwu
author list: Agent
  family name: Yuan
  given name: Xinzhu
author list: Agent
  family name: Xie
  given name: Xisheng
doi: 10.7717/peerj.18416
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-30
copyright: ©2024 Zhang et al.
attribution name: Zhang et al.

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