PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: https://peerj.com/articles/15397
items: A new miniMOS tool kit capable of visualizing single copy insertion in C. elegans
items: Assessment of multi-population polygenic risk scores for lipid traits in African Americans
items: Identification of immune-related genes in acute myocardial infarction based on integrated bioinformatical methods and experimental verification
items: Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture
items: Antibiotic resistance characteristics and risk factors analysis of Helicobacter pylori strains isolated from patients in Liaoning Province, an area in North China
items: Karst grassland forage quality and its determinants in Guizhou Province of Southwest China
items: Prognostic significance of thyroid hormone T3 in patients with septic shock: a retrospective cohort study
items: New genicular joint angle criteria for flexor muscle (Musculus Semimembranosus) during the terrestrial mammals walking
items: Autistic traits are associated with individual differences in finger tapping: an online study

https://peerj.com/articles/15397
type: item
type: AcademicArticle
title: Weight-shifting-based robot control system improves the weight-bearing rate and balance ability of the static standing position in hip osteoarthritis patients: a randomized controlled trial focusing on outcomes after total hip arthroplasty
description: Background After a total hip arthroplasty (THA), standing and walking balance are greatly affected in the early stages of recovery, so it is important to increase the weight-bearing amount (WBA) on the operated side. Sometimes, traditional treatments may not be enough to improve WBA and weight-bearing ratio (WBR) on the operated side in a satisfactory way. To solve this problem, we came up with a new weight-shifting-based robot control system called LOCOBOT. This system can control a spherical robot on a floor by changing the center of pressure (COP) on a force-sensing board in rehabilitation after THA. The goal of this study was to find out how rehabilitation with the LOCOBOT affects the WBR and balance in a static standing position in patients with unilateral hip osteoarthritis (OA) who had a primary uncemented THA. Methods This randomized controlled trial included 20 patients diagnosed with Kellgren–Lawrence (K–L) grade 3 or 4 hip OA on the operative side and K–L grade 0 normal hip on the nonoperative side. We used the minimization method for allocation and randomly assigned patients to either the LOCOBOT group or the control group. As a result, 10 patient seach were randomly assigned to the LOCOBOT and control groups. Both groups received 40 min of rehabilitation treatment. Out of the 40 min, the LOCOBOT group underwent treatment for 10 min with LOCOBOT. The control group performed COP-controlled exercises on a flat floor instead of using LOCOBOT for 10 of the 40 min. All theoutcome measures were performed pre-THA and 11.9 ± 1.6 days after THA (12 days after THA). The primary outcome measure included WBR in the static standing position. Results After12 days of THA, the LOCOBOT group exhibited significantly higher mean WBR and WBA (operated side) values than the control group. Furthermore, the LOCOBOT group exhibited significantly lower mean WBA (non-operated side) and outer diameter area (ODA) values than the control group. From pre-THA to 12 days after THA, the…
format: application/pdf
format: text/html
creator: Shigeaki Miyazaki
creator: Go Yamako
creator: Hideki Arakawa
creator: Takero Sakamoto
creator: Tsubasa Kawaguchi
creator: Kirari Ito
creator: Etsuo Chosa
subject: Clinical Trials
subject: Drugs and Devices
subject: Geriatrics
subject: Orthopedics
subject: Rheumatology
description: doi:10.7717/peerj.15397
publisher: PeerJ Inc.
rights: © 2023 Miyazaki et al.
abstract: Background After a total hip arthroplasty (THA), standing and walking balance are greatly affected in the early stages of recovery, so it is important to increase the weight-bearing amount (WBA) on the operated side. Sometimes, traditional treatments may not be enough to improve WBA and weight-bearing ratio (WBR) on the operated side in a satisfactory way. To solve this problem, we came up with a new weight-shifting-based robot control system called LOCOBOT. This system can control a spherical robot on a floor by changing the center of pressure (COP) on a force-sensing board in rehabilitation after THA. The goal of this study was to find out how rehabilitation with the LOCOBOT affects the WBR and balance in a static standing position in patients with unilateral hip osteoarthritis (OA) who had a primary uncemented THA. Methods This randomized controlled trial included 20 patients diagnosed with Kellgren–Lawrence (K–L) grade 3 or 4 hip OA on the operative side and K–L grade 0 normal hip on the nonoperative side. We used the minimization method for allocation and randomly assigned patients to either the LOCOBOT group or the control group. As a result, 10 patient seach were randomly assigned to the LOCOBOT and control groups. Both groups received 40 min of rehabilitation treatment. Out of the 40 min, the LOCOBOT group underwent treatment for 10 min with LOCOBOT. The control group performed COP-controlled exercises on a flat floor instead of using LOCOBOT for 10 of the 40 min. All theoutcome measures were performed pre-THA and 11.9 ± 1.6 days after THA (12 days after THA). The primary outcome measure included WBR in the static standing position. Results After12 days of THA, the LOCOBOT group exhibited significantly higher mean WBR and WBA (operated side) values than the control group. Furthermore, the LOCOBOT group exhibited significantly lower mean WBA (non-operated side) and outer diameter area (ODA) values than the control group. From pre-THA to 12 days after THA, the…
bibliographic citation: Miyazaki et al. (2023) Weight-shifting-based robot control system improves the weight-bearing rate and balance ability of the static standing position in hip osteoarthritis patients: a randomized controlled trial focusing on outcomes after total hip arthroplasty. PeerJ 11:e15397 https://doi.org/10.7717/peerj.15397
date submitted: 2022-12-06
date accepted: 2023-04-20
issued: 2023-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miyazaki
  given name: Shigeaki
author list: Agent
  family name: Yamako
  given name: Go
author list: Agent
  family name: Arakawa
  given name: Hideki
author list: Agent
  family name: Sakamoto
  given name: Takero
author list: Agent
  family name: Kawaguchi
  given name: Tsubasa
author list: Agent
  family name: Ito
  given name: Kirari
author list: Agent
  family name: Chosa
  given name: Etsuo
doi: 10.7717/peerj.15397
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-17
copyright: ©2023 Miyazaki et al.
attribution name: Miyazaki et al.

A new miniMOS tool kit capable of visualizing single copy insertion in C. elegans
type: item
type: AcademicArticle
description: The miniMOS technique has been widely used in the C. elegans community to generate single copy insertions. A worm is considered as a potential insertion candidate if it is resistant to G418 antibiotics and does not express a co-injected fluorescence marker. If the expression of the extrachromosomal array is very low, it is possible for a worm to be mistakenly identified as a miniMOS candidate, as this low expression level can still confer resistance to G418 without producing a detectable fluorescence signal from the co-injection marker. This may increase the workload for identifying the insertion locus in the subsequent steps. In the present study, we modified the plasmid platform for miniMOS insertion by incorporating a myo-2 promoter-driven TagRFP or a ubiquitous H2B::GFP expression cassette into the targeting vector and introducing two loxP sites flanking the selection cassettes. Based on this new miniMOS tool kit, the removable fluorescence reporters can be used to visualize the single copy insertions, greatly reducing insertion locus identification efforts. In our experience, this new platform greatly facilitates the isolation of the miniMOS mutants.
format: application/pdf
format: text/html
creator: Jiangyun Li
creator: Yuang Qin
creator: Chengchen Shen
creator: Jun Zhang
creator: Shasha Tu
creator: Jingxuan Yang
creator: Yu Wang
creator: Ruyun Zhou
creator: Kui Zhang
creator: Jianping Chen
creator: Wenxing Yang
subject: Biochemistry
subject: Biotechnology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.15433
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: The miniMOS technique has been widely used in the C. elegans community to generate single copy insertions. A worm is considered as a potential insertion candidate if it is resistant to G418 antibiotics and does not express a co-injected fluorescence marker. If the expression of the extrachromosomal array is very low, it is possible for a worm to be mistakenly identified as a miniMOS candidate, as this low expression level can still confer resistance to G418 without producing a detectable fluorescence signal from the co-injection marker. This may increase the workload for identifying the insertion locus in the subsequent steps. In the present study, we modified the plasmid platform for miniMOS insertion by incorporating a myo-2 promoter-driven TagRFP or a ubiquitous H2B::GFP expression cassette into the targeting vector and introducing two loxP sites flanking the selection cassettes. Based on this new miniMOS tool kit, the removable fluorescence reporters can be used to visualize the single copy insertions, greatly reducing insertion locus identification efforts. In our experience, this new platform greatly facilitates the isolation of the miniMOS mutants.
bibliographic citation: Li et al. (2023) A new miniMOS tool kit capable of visualizing single copy insertion in C. elegans. PeerJ 11:e15433 https://doi.org/10.7717/peerj.15433
date submitted: 2022-10-31
date accepted: 2023-04-26
issued: 2023-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jiangyun
author list: Agent
  family name: Qin
  given name: Yuang
author list: Agent
  family name: Shen
  given name: Chengchen
author list: Agent
  family name: Zhang
  given name: Jun
author list: Agent
  family name: Tu
  given name: Shasha
author list: Agent
  family name: Yang
  given name: Jingxuan
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Zhou
  given name: Ruyun
author list: Agent
  family name: Zhang
  given name: Kui
author list: Agent
  family name: Chen
  given name: Jianping
author list: Agent
  family name: Yang
  given name: Wenxing
doi: 10.7717/peerj.15433
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-17
copyright: © 2023 Li et al.
attribution name: Li et al.

Assessment of multi-population polygenic risk scores for lipid traits in African Americans
type: item
type: AcademicArticle
description: Polygenic risk scores (PRS) based on genome-wide discoveries are promising predictors or classifiers of disease development, severity, and/or progression for common clinical outcomes. A major limitation of most risk scores is the paucity of genome-wide discoveries in diverse populations, prompting an emphasis to generate these needed data for trans-population and population-specific PRS construction. Given diverse genome-wide discoveries are just now being completed, there has been little opportunity for PRS to be evaluated in diverse populations independent from the discovery efforts. To fill this gap, we leverage here summary data from a recent genome-wide discovery study of lipid traits (HDL-C, LDL-C, triglycerides, and total cholesterol) conducted in diverse populations represented by African Americans, Hispanics, Asians, Native Hawaiians, Native Americans, and others by the Population Architecture using Genomics and Epidemiology (PAGE) Study. We constructed lipid trait PRS using PAGE Study published genetic variants and weights in an independent African American adult patient population linked to de-identified electronic health records and genotypes from the Illumina Metabochip (n = 3,254). Using multi-population lipid trait PRS, we assessed levels of association for their respective lipid traits, clinical outcomes (cardiovascular disease and type 2 diabetes), and common clinical labs. While none of the multi-population PRS were strongly associated with the tested trait or outcome, PRSLDL-Cwas nominally associated with cardiovascular disease. These data demonstrate the complexity in applying PRS to real-world clinical data even when data from multiple populations are available.
format: application/pdf
format: text/html
creator: Domenica E. Drouet
creator: Shiying Liu
creator: Dana C. Crawford
subject: Genetics
subject: Genomics
subject: Medical Genetics
description: doi:10.7717/peerj.14910
publisher: PeerJ Inc.
rights: © 2023 Drouet et al.
abstract: Polygenic risk scores (PRS) based on genome-wide discoveries are promising predictors or classifiers of disease development, severity, and/or progression for common clinical outcomes. A major limitation of most risk scores is the paucity of genome-wide discoveries in diverse populations, prompting an emphasis to generate these needed data for trans-population and population-specific PRS construction. Given diverse genome-wide discoveries are just now being completed, there has been little opportunity for PRS to be evaluated in diverse populations independent from the discovery efforts. To fill this gap, we leverage here summary data from a recent genome-wide discovery study of lipid traits (HDL-C, LDL-C, triglycerides, and total cholesterol) conducted in diverse populations represented by African Americans, Hispanics, Asians, Native Hawaiians, Native Americans, and others by the Population Architecture using Genomics and Epidemiology (PAGE) Study. We constructed lipid trait PRS using PAGE Study published genetic variants and weights in an independent African American adult patient population linked to de-identified electronic health records and genotypes from the Illumina Metabochip (n = 3,254). Using multi-population lipid trait PRS, we assessed levels of association for their respective lipid traits, clinical outcomes (cardiovascular disease and type 2 diabetes), and common clinical labs. While none of the multi-population PRS were strongly associated with the tested trait or outcome, PRSLDL-Cwas nominally associated with cardiovascular disease. These data demonstrate the complexity in applying PRS to real-world clinical data even when data from multiple populations are available.
bibliographic citation: Drouet et al. (2023) Assessment of multi-population polygenic risk scores for lipid traits in African Americans. PeerJ 11:e14910 https://doi.org/10.7717/peerj.14910
date submitted: 2022-08-22
date accepted: 2023-01-25
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Drouet
  given name: Domenica E.
author list: Agent
  family name: Liu
  given name: Shiying
author list: Agent
  family name: Crawford
  given name: Dana C.
doi: 10.7717/peerj.14910
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: ©2023 Drouet et al.
attribution name: Drouet et al.

Identification of immune-related genes in acute myocardial infarction based on integrated bioinformatical methods and experimental verification
type: item
type: AcademicArticle
description: Background Acute myocardial infarction (AMI) is one of the leading causes of death worldwide. The etiology of AMI is complex and has not been fully defined. In recent years, the role of immune response in the development, progression and prognosis of AMI has received increasing attention. The aim of this study was to identify key genes associated with the immune response in AMI and to analyze their immune infiltration. Methods The study included a total of two GEO databases, containing 83 patients with AMI and 54 healthy individuals. We used the linear model of microarray data (limma) package to find the differentially expressed genes associated with AMI, performing weighted gene co-expression analysis (WGCNA) to further identify the genes associated with inflammatory response to AMI. We found the final hub genes through the protein-protein interaction (PPI) network and least absolute shrinkage and selection operator (LASSO) regression model. To verify the above conclusions, we constructed mice AMI model, extracting myocardial tissue to perform qRT-PCR. Furthermore, the CIBERSORT tool for immune cells infiltration analysis was also carried out. Results A total of 5,425 significant up-regulated and 2,126 down-regulated genes were found in GSE66360 and GSE24519. A total of 116 immune-related genes in close association with AMI were screened by WGCNA analysis. These genes were mostly clustered in the immune response on the basis of GO and KEGG enrichment. With construction of PPI network and LASSO regression analysis, this research found three hub genes (SOCS2, FFAR2, MYO10) among these differentially expressed genes. The immune cell infiltration results revealed that significant differences could be found on T cells CD4 memory activated, Tregs (regulatory T cells), macrophages M2, neutrophils, T cells CD8, T cells CD4 naive, eosinophils between controls and AMI patients.
format: application/pdf
format: text/html
creator: Jian Liu
creator: Lu Chen
creator: Xiang Zheng
creator: Caixia Guo
subject: Bioinformatics
subject: Molecular Biology
subject: Cardiology
subject: Immunology
subject: Medical Genetics
description: doi:10.7717/peerj.15058
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Background Acute myocardial infarction (AMI) is one of the leading causes of death worldwide. The etiology of AMI is complex and has not been fully defined. In recent years, the role of immune response in the development, progression and prognosis of AMI has received increasing attention. The aim of this study was to identify key genes associated with the immune response in AMI and to analyze their immune infiltration. Methods The study included a total of two GEO databases, containing 83 patients with AMI and 54 healthy individuals. We used the linear model of microarray data (limma) package to find the differentially expressed genes associated with AMI, performing weighted gene co-expression analysis (WGCNA) to further identify the genes associated with inflammatory response to AMI. We found the final hub genes through the protein-protein interaction (PPI) network and least absolute shrinkage and selection operator (LASSO) regression model. To verify the above conclusions, we constructed mice AMI model, extracting myocardial tissue to perform qRT-PCR. Furthermore, the CIBERSORT tool for immune cells infiltration analysis was also carried out. Results A total of 5,425 significant up-regulated and 2,126 down-regulated genes were found in GSE66360 and GSE24519. A total of 116 immune-related genes in close association with AMI were screened by WGCNA analysis. These genes were mostly clustered in the immune response on the basis of GO and KEGG enrichment. With construction of PPI network and LASSO regression analysis, this research found three hub genes (SOCS2, FFAR2, MYO10) among these differentially expressed genes. The immune cell infiltration results revealed that significant differences could be found on T cells CD4 memory activated, Tregs (regulatory T cells), macrophages M2, neutrophils, T cells CD8, T cells CD4 naive, eosinophils between controls and AMI patients.
bibliographic citation: Liu et al. (2023) Identification of immune-related genes in acute myocardial infarction based on integrated bioinformatical methods and experimental verification. PeerJ 11:e15058 https://doi.org/10.7717/peerj.15058
date submitted: 2022-08-23
date accepted: 2023-02-22
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Jian
author list: Agent
  family name: Chen
  given name: Lu
author list: Agent
  family name: Zheng
  given name: Xiang
author list: Agent
  family name: Guo
  given name: Caixia
doi: 10.7717/peerj.15058
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: ©2023 Liu et al.
attribution name: Liu et al.

Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture
type: item
type: AcademicArticle
description: Background Aquacultured animals are reared in water hosting various microorganisms with which they are in close relationships during their whole lifecycle as some of these microorganisms can be involved in their host’s health or physiology. In aquaculture hatcheries, understanding the interactions existing between the natural seawater microbiota, the rearing water microbiota, the larval stage and the larval health status, may allow the establishment of microbial proxies to monitor the rearing ecosystems. Indeed, these proxies could help to define the optimal microbiota for shrimp larval development and could ultimately help microbial management. Methods In this context, we monitored the daily composition of the active microbiota of the rearing water in a hatchery of the Pacific blue shrimp Penaeus stylirostris. Two distinct rearing conditions were analyzed; one with antibiotics added to the rearing water and one without antibiotics. During this rearing, healthy larvae with a high survival rate and unhealthy larvae with a high mortality rate were observed. Using HiSeq sequencing of the V4 region of the 16S rRNA gene of the water microbiota, coupled with zootechnical and statistical analysis, we aimed to distinguish the microbial taxa related to high mortality rates at a given larval stage. Results We highlight that the active microbiota of the rearing water is highly dynamic whatever the larval survival rate. A clear distinction of the microbial composition is shown between the water harboring heathy larvae reared with antibiotics versus the unhealthy larvae reared without antibiotics. However, it is hard to untangle the effects of the antibiotic addition and of the larval death on the active microbiota of the rearing water. Various active taxa of the rearing water are specific to a given larval stage and survival rate except for the zoea with a good survival rate. Comparing these communities to those of the lagoon, it appears that many taxa were originally detected …
format: application/pdf
format: text/html
creator: Nolwenn Callac
creator: Carolane Giraud
creator: Viviane Boulo
creator: Nelly Wabete
creator: Dominique Pham
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.15201
publisher: PeerJ Inc.
rights: © 2023 Callac et al.
abstract: Background Aquacultured animals are reared in water hosting various microorganisms with which they are in close relationships during their whole lifecycle as some of these microorganisms can be involved in their host’s health or physiology. In aquaculture hatcheries, understanding the interactions existing between the natural seawater microbiota, the rearing water microbiota, the larval stage and the larval health status, may allow the establishment of microbial proxies to monitor the rearing ecosystems. Indeed, these proxies could help to define the optimal microbiota for shrimp larval development and could ultimately help microbial management. Methods In this context, we monitored the daily composition of the active microbiota of the rearing water in a hatchery of the Pacific blue shrimp Penaeus stylirostris. Two distinct rearing conditions were analyzed; one with antibiotics added to the rearing water and one without antibiotics. During this rearing, healthy larvae with a high survival rate and unhealthy larvae with a high mortality rate were observed. Using HiSeq sequencing of the V4 region of the 16S rRNA gene of the water microbiota, coupled with zootechnical and statistical analysis, we aimed to distinguish the microbial taxa related to high mortality rates at a given larval stage. Results We highlight that the active microbiota of the rearing water is highly dynamic whatever the larval survival rate. A clear distinction of the microbial composition is shown between the water harboring heathy larvae reared with antibiotics versus the unhealthy larvae reared without antibiotics. However, it is hard to untangle the effects of the antibiotic addition and of the larval death on the active microbiota of the rearing water. Various active taxa of the rearing water are specific to a given larval stage and survival rate except for the zoea with a good survival rate. Comparing these communities to those of the lagoon, it appears that many taxa were originally detected …
bibliographic citation: Callac et al. (2023) Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture. PeerJ 11:e15201 https://doi.org/10.7717/peerj.15201
date submitted: 2022-10-04
date accepted: 2023-03-17
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Callac
  given name: Nolwenn
author list: Agent
  family name: Giraud
  given name: Carolane
author list: Agent
  family name: Boulo
  given name: Viviane
author list: Agent
  family name: Wabete
  given name: Nelly
author list: Agent
  family name: Pham
  given name: Dominique
doi: 10.7717/peerj.15201
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: ©2023 Callac et al.
attribution name: Callac et al.

Antibiotic resistance characteristics and risk factors analysis of Helicobacter pylori strains isolated from patients in Liaoning Province, an area in North China
type: item
type: AcademicArticle
description: Background The prevalence of Helicobacter pylori (H. pylori) keeps rising while the eradication rate continues to decline due to the increasing antibiotic resistance. Regional variations of antimicrobial resistance to H. pylori have been recommended by guidelines in recent years. This study aims to investigate the antibiotic resistance rate of H. pylori and its association with infected subjects’ characteristics in Liaoning Province, an area in north China. Methods Gastric tissues from 178 H. pylori positive participants without previous antibiotic use within four weeks were collected for H. pylori culture. Antibiotic susceptibility to furazolidone (AOZ), tetracycline (TC), levofloxacin (LFX), metronidazole (MET), clarithromycin (CLA), and amoxicillin (AMX) were examined with the agar dilution method. Associations between H. pylori resistance and patient characteristics were further analysed. Results No resistance was observed in AOZ or TC. For LFX, MET, CLA, and AMX, the overall resistance rates were 41.10%, 79.14%, 71.78%, and 22.09% respectively. There were significant differences between resistance to CLA and MALToma (P = 0.021), and between resistance to MET and age (P < 0.001). Conclusions The primary resistant rates of LEX, MET, CLA, and AMX were relatively high in Liaoning. Treatment effectiveness improvement could be achieved by prior antimicrobial susceptibility tests before antibiotic prescription.
format: application/pdf
format: text/html
creator: Yanmeng Wang
creator: Yiling Li
creator: Yuehua Gong
creator: Yuzhen Dong
creator: Jing Sun
creator: Moye Chen
subject: Microbiology
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.15268
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Background The prevalence of Helicobacter pylori (H. pylori) keeps rising while the eradication rate continues to decline due to the increasing antibiotic resistance. Regional variations of antimicrobial resistance to H. pylori have been recommended by guidelines in recent years. This study aims to investigate the antibiotic resistance rate of H. pylori and its association with infected subjects’ characteristics in Liaoning Province, an area in north China. Methods Gastric tissues from 178 H. pylori positive participants without previous antibiotic use within four weeks were collected for H. pylori culture. Antibiotic susceptibility to furazolidone (AOZ), tetracycline (TC), levofloxacin (LFX), metronidazole (MET), clarithromycin (CLA), and amoxicillin (AMX) were examined with the agar dilution method. Associations between H. pylori resistance and patient characteristics were further analysed. Results No resistance was observed in AOZ or TC. For LFX, MET, CLA, and AMX, the overall resistance rates were 41.10%, 79.14%, 71.78%, and 22.09% respectively. There were significant differences between resistance to CLA and MALToma (P = 0.021), and between resistance to MET and age (P < 0.001). Conclusions The primary resistant rates of LEX, MET, CLA, and AMX were relatively high in Liaoning. Treatment effectiveness improvement could be achieved by prior antimicrobial susceptibility tests before antibiotic prescription.
bibliographic citation: Wang et al. (2023) Antibiotic resistance characteristics and risk factors analysis of Helicobacter pylori strains isolated from patients in Liaoning Province, an area in North China. PeerJ 11:e15268 https://doi.org/10.7717/peerj.15268
date submitted: 2022-12-05
date accepted: 2023-03-29
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yanmeng
author list: Agent
  family name: Li
  given name: Yiling
author list: Agent
  family name: Gong
  given name: Yuehua
author list: Agent
  family name: Dong
  given name: Yuzhen
author list: Agent
  family name: Sun
  given name: Jing
author list: Agent
  family name: Chen
  given name: Moye
doi: 10.7717/peerj.15268
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Karst grassland forage quality and its determinants in Guizhou Province of Southwest China
type: item
type: AcademicArticle
description: Forage quality is a key property of grassland ecosystems. In this study, grassland forage qualities were measured at 373 sampling sites throughout Guizhou Province in the karst mountain region of Southwest China, and the factors affecting it were explored. The forage quality level of most plant species was categorized into four levels: (1) preferred forage species; (2) desirable forage species; (3) consumed but undesirable forage species; and (4) non-consumable or toxic forage species. High temperature and precipitation appeared to facilitate the growth of preferred forage species, but limited the growth of other plants. Increasing soil pH had a positive impact on the number and biomass of preferred forage plants, but a negative influence on other plants, especially non-consumable or toxic plants. Both GDP and population density had a positive correlation with the number and biomass of preferred forage species, while such correlations for other levels of forage species tended to be negative. Grazing could lead to a decrease in the preferred forage species. Therefore, it is suggested that by focusing on soil improvement in grassland and maintaining an appropriate grazing intensity, global warming and rapid economic growth in Guizhou Province will likely contribute to increase the forage quality of karst grasslands in Southwest China.
format: application/pdf
format: text/html
creator: Dengming He
creator: Baocheng Jin
creator: Xuechun Zhao
creator: Hua Cheng
creator: Chao Chen
creator: Huanhuan Wang
creator: Jinping Zhang
creator: Yaoyao Zhang
creator: Qin Yang
creator: Kun Liu
creator: Min Han
creator: Zhongcai Li
creator: Jing Peng
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.15323
publisher: PeerJ Inc.
rights: © 2023 He et al.
abstract: Forage quality is a key property of grassland ecosystems. In this study, grassland forage qualities were measured at 373 sampling sites throughout Guizhou Province in the karst mountain region of Southwest China, and the factors affecting it were explored. The forage quality level of most plant species was categorized into four levels: (1) preferred forage species; (2) desirable forage species; (3) consumed but undesirable forage species; and (4) non-consumable or toxic forage species. High temperature and precipitation appeared to facilitate the growth of preferred forage species, but limited the growth of other plants. Increasing soil pH had a positive impact on the number and biomass of preferred forage plants, but a negative influence on other plants, especially non-consumable or toxic plants. Both GDP and population density had a positive correlation with the number and biomass of preferred forage species, while such correlations for other levels of forage species tended to be negative. Grazing could lead to a decrease in the preferred forage species. Therefore, it is suggested that by focusing on soil improvement in grassland and maintaining an appropriate grazing intensity, global warming and rapid economic growth in Guizhou Province will likely contribute to increase the forage quality of karst grasslands in Southwest China.
bibliographic citation: He et al. (2023) Karst grassland forage quality and its determinants in Guizhou Province of Southwest China. PeerJ 11:e15323 https://doi.org/10.7717/peerj.15323
date submitted: 2022-08-01
date accepted: 2023-04-10
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Dengming
author list: Agent
  family name: Jin
  given name: Baocheng
author list: Agent
  family name: Zhao
  given name: Xuechun
author list: Agent
  family name: Cheng
  given name: Hua
author list: Agent
  family name: Chen
  given name: Chao
author list: Agent
  family name: Wang
  given name: Huanhuan
author list: Agent
  family name: Zhang
  given name: Jinping
author list: Agent
  family name: Zhang
  given name: Yaoyao
author list: Agent
  family name: Yang
  given name: Qin
author list: Agent
  family name: Liu
  given name: Kun
author list: Agent
  family name: Han
  given name: Min
author list: Agent
  family name: Li
  given name: Zhongcai
author list: Agent
  family name: Peng
  given name: Jing
doi: 10.7717/peerj.15323
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: ©2023 He et al.
attribution name: He et al.

Prognostic significance of thyroid hormone T3 in patients with septic shock: a retrospective cohort study
type: item
type: AcademicArticle
description: Background The role of thyroid hormones is crucial in the response to stress and critical illness, which has been reported to be closely associated with a poor prognosis in patients admitted to the intensive care unit (ICU). This study aimed to explore the relationship between thyroid hormone and prognosis in septic shock patients. Methods A total of 186 patients with septic shock were enrolled in the analytical study between December 2014 and September 2022. The baseline variables and thyroid hormone were collected. The patients were divided into survivor group and non-survivor group according to whether they died during the ICU hospitalization. Among 186 patients with septic shock, 123 (66.13%) were in the survivor group and 63 (33.87%) were in the non-survivor group. Results There were significant differences in the indictors of free triiodothyronine (FT3) (p = 0.000), triiodothyronine (T3) (p = 0.000), T3/FT3 (p = 0.000), acute physiology and chronic health evaluation II score (APACHE II) (p = 0.000), sequential organ failure assessment score (SOFA) (p = 0.000), pulse rate (p = 0.020), creatinine (p = 0.008), PaO2/FiO2 (p = 0.000), length of stay (p = 0.000) and hospitalization expenses (p = 0.000) in ICU between the two groups. FT3 [odds ratio (OR): 1.062, 95% confidence interval(CI): (0.021, 0.447), p = 0.003], T3 (OR: 0.291, 95% CI: 0.172-0.975, p = 0.037) and T3/FT3 (OR: 0.985, 95% CI:0.974-0.996, p = 0.006) were independent risk factors of the short-term prognosis of septic shock patients after adjustment. The areas under the receiver operating characteristic curves for T3 was associated with ICU mortality (AUC = 0.796, p < 0.05) and was higher than that for FT3 (AUC = 0.670, p < 0.05) and T3/FT3 (AUC = 0.712, p < 0.05). A Kaplan-Meier curve showed that patients with T3 greater than 0.48 nmol/L had a significantly higher survival rate than the patients with T3 less than 0.48 nmol/L. Conclusions The decrease in serum level of T3 in patients with septic shock…
format: application/pdf
format: text/html
creator: Caizhi Sun
creator: Lei Bao
creator: Lei Guo
creator: Jingjing Wei
creator: Yang Song
creator: Hua Shen
creator: Haidong Qin
subject: Diabetes and Endocrinology
subject: Emergency and Critical Care
subject: Metabolic Sciences
description: doi:10.7717/peerj.15335
publisher: PeerJ Inc.
rights: © 2023 Sun et al.
abstract: Background The role of thyroid hormones is crucial in the response to stress and critical illness, which has been reported to be closely associated with a poor prognosis in patients admitted to the intensive care unit (ICU). This study aimed to explore the relationship between thyroid hormone and prognosis in septic shock patients. Methods A total of 186 patients with septic shock were enrolled in the analytical study between December 2014 and September 2022. The baseline variables and thyroid hormone were collected. The patients were divided into survivor group and non-survivor group according to whether they died during the ICU hospitalization. Among 186 patients with septic shock, 123 (66.13%) were in the survivor group and 63 (33.87%) were in the non-survivor group. Results There were significant differences in the indictors of free triiodothyronine (FT3) (p = 0.000), triiodothyronine (T3) (p = 0.000), T3/FT3 (p = 0.000), acute physiology and chronic health evaluation II score (APACHE II) (p = 0.000), sequential organ failure assessment score (SOFA) (p = 0.000), pulse rate (p = 0.020), creatinine (p = 0.008), PaO2/FiO2 (p = 0.000), length of stay (p = 0.000) and hospitalization expenses (p = 0.000) in ICU between the two groups. FT3 [odds ratio (OR): 1.062, 95% confidence interval(CI): (0.021, 0.447), p = 0.003], T3 (OR: 0.291, 95% CI: 0.172-0.975, p = 0.037) and T3/FT3 (OR: 0.985, 95% CI:0.974-0.996, p = 0.006) were independent risk factors of the short-term prognosis of septic shock patients after adjustment. The areas under the receiver operating characteristic curves for T3 was associated with ICU mortality (AUC = 0.796, p < 0.05) and was higher than that for FT3 (AUC = 0.670, p < 0.05) and T3/FT3 (AUC = 0.712, p < 0.05). A Kaplan-Meier curve showed that patients with T3 greater than 0.48 nmol/L had a significantly higher survival rate than the patients with T3 less than 0.48 nmol/L. Conclusions The decrease in serum level of T3 in patients with septic shock…
bibliographic citation: Sun et al. (2023) Prognostic significance of thyroid hormone T3 in patients with septic shock: a retrospective cohort study. PeerJ 11:e15335 https://doi.org/10.7717/peerj.15335
date submitted: 2022-12-07
date accepted: 2023-04-11
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Caizhi
author list: Agent
  family name: Bao
  given name: Lei
author list: Agent
  family name: Guo
  given name: Lei
author list: Agent
  family name: Wei
  given name: Jingjing
author list: Agent
  family name: Song
  given name: Yang
author list: Agent
  family name: Shen
  given name: Hua
author list: Agent
  family name: Qin
  given name: Haidong
doi: 10.7717/peerj.15335
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: ©2023 Sun et al.
attribution name: Sun et al.

New genicular joint angle criteria for flexor muscle (Musculus Semimembranosus) during the terrestrial mammals walking
type: item
type: AcademicArticle
description: Background The genicular or knee joint angles of terrestrial mammals remain constant during the stance phase of walking; however, the angles differ among taxa. The knee joint angle is known to correlate with taxa and body mass among extant mammals, yet several extinct mammals, such as desmostylians, do not have closely related descendants. Furthermore, fossils lose their soft tissues by the time they are unearthed, making body mass estimates difficult. These factors cause significant problems when reconstructing the proper postures of extinct mammals. Terrestrial mammals use potential and kinetic energy for locomotion; particularly, an inverted pendulum mechanism is used for walking. This mechanism requires maintaining the rod length constant, therefore, terrestrial mammals maintain their joint angle in a small range. A muscle reaction referred to as co-contraction is known to increase joint stiffness; both the agonist and antagonist muscles work simultaneously on the same joint at the same time. The musculus semimembranosus flexes the knee joint and acts as an antagonist to muscles that extend it. Methods Twenty-one species of terrestrial mammals were examined to identify the elements that constitute the angle between the m. semimembranosus and the tibia based on the period between the hindlimb touching down and taking off from the ground. Measurements were captured from videos in high-speed mode (420 fps), selecting 13 pictures from the first 75% of each video while the animals were walking. The angles between the main force line of the m. semimembranosus and the tibia, which were defined as θsm−t, were measured. Results The maximum and minimum angles between the m. semimembranosus and the tibia (θsm−t) of the stance instance (SI) were successfully determined for more than 80% of the target animals (17 out of 21 species) during SI-1 to SI-13 within ±10° from the mean. The difference between each successive SI was small and, therefore, the θsm−t transition was smoo…
format: application/pdf
format: text/html
creator: Fumihiro Mizuno
creator: Naoki Kohno
subject: Animal Behavior
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.15379
publisher: PeerJ Inc.
rights: © 2023 Mizuno and Kohno
abstract: Background The genicular or knee joint angles of terrestrial mammals remain constant during the stance phase of walking; however, the angles differ among taxa. The knee joint angle is known to correlate with taxa and body mass among extant mammals, yet several extinct mammals, such as desmostylians, do not have closely related descendants. Furthermore, fossils lose their soft tissues by the time they are unearthed, making body mass estimates difficult. These factors cause significant problems when reconstructing the proper postures of extinct mammals. Terrestrial mammals use potential and kinetic energy for locomotion; particularly, an inverted pendulum mechanism is used for walking. This mechanism requires maintaining the rod length constant, therefore, terrestrial mammals maintain their joint angle in a small range. A muscle reaction referred to as co-contraction is known to increase joint stiffness; both the agonist and antagonist muscles work simultaneously on the same joint at the same time. The musculus semimembranosus flexes the knee joint and acts as an antagonist to muscles that extend it. Methods Twenty-one species of terrestrial mammals were examined to identify the elements that constitute the angle between the m. semimembranosus and the tibia based on the period between the hindlimb touching down and taking off from the ground. Measurements were captured from videos in high-speed mode (420 fps), selecting 13 pictures from the first 75% of each video while the animals were walking. The angles between the main force line of the m. semimembranosus and the tibia, which were defined as θsm−t, were measured. Results The maximum and minimum angles between the m. semimembranosus and the tibia (θsm−t) of the stance instance (SI) were successfully determined for more than 80% of the target animals (17 out of 21 species) during SI-1 to SI-13 within ±10° from the mean. The difference between each successive SI was small and, therefore, the θsm−t transition was smoo…
bibliographic citation: Mizuno et al. (2023) New genicular joint angle criteria for flexor muscle (Musculus Semimembranosus) during the terrestrial mammals walking. PeerJ 11:e15379 https://doi.org/10.7717/peerj.15379
date submitted: 2022-08-26
date accepted: 2023-04-18
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mizuno
  given name: Fumihiro
author list: Agent
  family name: Kohno
  given name: Naoki
doi: 10.7717/peerj.15379
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: © 2023 Mizuno and Kohno
attribution name: Mizuno and Kohno

Autistic traits are associated with individual differences in finger tapping: an online study
type: item
type: AcademicArticle
description: In a novel online study, we explored whether finger tapping differences are evident in people with autistic traits in the general population. We hypothesised that those with higher autistic traits would show more impairment in finger tapping, and that age would moderate tapping output. The study included a non-diagnosed population of 159 participants aged 18–78 who completed an online measure of autistic traits (the AQ-10) and a measure of finger tapping (the FTT). Results showed those with higher AQ-10 scores recorded lower tapping scores in both hands. Moderation analysis showed younger participants with more autistic traits recorded lower tapping scores for the dominant hand. This suggests motor differences seen in autism studies are evident in the general population.
format: application/pdf
format: text/html
creator: Alycia Messing
creator: Deborah Apthorp
subject: Neuroscience
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.15406
publisher: PeerJ Inc.
rights: © 2023 Messing and Apthorp
abstract: In a novel online study, we explored whether finger tapping differences are evident in people with autistic traits in the general population. We hypothesised that those with higher autistic traits would show more impairment in finger tapping, and that age would moderate tapping output. The study included a non-diagnosed population of 159 participants aged 18–78 who completed an online measure of autistic traits (the AQ-10) and a measure of finger tapping (the FTT). Results showed those with higher AQ-10 scores recorded lower tapping scores in both hands. Moderation analysis showed younger participants with more autistic traits recorded lower tapping scores for the dominant hand. This suggests motor differences seen in autism studies are evident in the general population.
bibliographic citation: Messing et al. (2023) Autistic traits are associated with individual differences in finger tapping: an online study. PeerJ 11:e15406 https://doi.org/10.7717/peerj.15406
date submitted: 2022-12-16
date accepted: 2023-04-21
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Messing
  given name: Alycia
author list: Agent
  family name: Apthorp
  given name: Deborah
doi: 10.7717/peerj.15406
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: © 2023 Messing and Apthorp
attribution name: Messing and Apthorp

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