PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma
items: A new moradisaurine captorhinid reptile (Amniota: Eureptilia) from the upper Permian of India
items: https://peerj.com/articles/18397
items: The fall of the mycobacterial cell wall: interrogating peptidoglycan synthesis for novel anti-TB agents
items: Digital eye strain syndrome among higher education health sciences students in Saudi Arabia: severity and preventive ergonomic practices
items: A review of advancements in the theory and characterization of soil macropore structure
items: Comparative electromyography analysis of subphase gait disorder in chronic stroke survivors
items: New insights into the impact of wood vinegar on the growth and rhizosphere microorganisms of cherry radish (Raphanus sativus L.)
items: An experimental analysis of graph representation learning for Gene Ontology based protein function prediction
items: Intra-rater and inter-rater reliability of the fixed plumb line for postural and scoliosis assessment in the sagittal plane: a pilot study

Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Lung adenocarcinoma (LUAD) is a widely occurring cancer with a high death rate. Radiomics, as a high-throughput method, has a wide range of applications in different aspects of the management of multiple cancers. However, the molecular mechanism of LUAD by combining transcriptomics and radiomics in order to probe LUAD remains unclear. Methods The transcriptome data and radiomics features of LUAD were extracted from the public database. Subsequently, we used weighted gene co-expression network analysis (WGCNA) and a series of machine learning algorithms including Random Forest (RF), Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression, and Support Vector Machines Recursive Feature Elimination (SVM-RFE) to proceed with the screening of diagnostic genes for LUAD. In addition, the CIBERSORT and ESTIMATE algorithms were utilized to assess the association of these genes with immune profiles. The LASSO algorithm further identified the features most relevant to the expression levels of LUAD diagnostic genes and validated the model based on receiver operating characteristic (ROC), precision-recall (PR), calibration curves and decision curve analysis (DCA) curves. Finally, RT-qPCR, transwell and cell counting kit-8 (CCK8) based assays were performed to assess the expression levels and potential functions of the screened genes in LUAD cell lines. Results We screened a total of 214 modular genes with the highest correlation with LUAD samples based on WGCNA, of which 192 genes were shown to be highly expressed in LUAD patients. Subsequently, three machine learning algorithms identified a total of four genes, including UBE2T, TEDC2, RCC1, and FAM136A, as diagnostic molecules for LUAD, and the ROC curves showed that these diagnostic molecules had good diagnostic performance (AUC values of 0.989, 0.989, 989, and 0.987, respectively). The expression of these diagnostic molecules was significantly higher in tumor samples than in normal para-cancerous…
format: application/pdf
format: text/html
creator: Qian Huang
creator: Peng Zhang
creator: Zhixu Guo
creator: Min Li
creator: Chao Tao
creator: Zongyang Yu
subject: Bioinformatics
subject: Immunology
subject: Respiratory Medicine
description: doi:10.7717/peerj.18310
publisher: PeerJ Inc.
rights: © 2024 Huang et al.
abstract: Background Lung adenocarcinoma (LUAD) is a widely occurring cancer with a high death rate. Radiomics, as a high-throughput method, has a wide range of applications in different aspects of the management of multiple cancers. However, the molecular mechanism of LUAD by combining transcriptomics and radiomics in order to probe LUAD remains unclear. Methods The transcriptome data and radiomics features of LUAD were extracted from the public database. Subsequently, we used weighted gene co-expression network analysis (WGCNA) and a series of machine learning algorithms including Random Forest (RF), Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression, and Support Vector Machines Recursive Feature Elimination (SVM-RFE) to proceed with the screening of diagnostic genes for LUAD. In addition, the CIBERSORT and ESTIMATE algorithms were utilized to assess the association of these genes with immune profiles. The LASSO algorithm further identified the features most relevant to the expression levels of LUAD diagnostic genes and validated the model based on receiver operating characteristic (ROC), precision-recall (PR), calibration curves and decision curve analysis (DCA) curves. Finally, RT-qPCR, transwell and cell counting kit-8 (CCK8) based assays were performed to assess the expression levels and potential functions of the screened genes in LUAD cell lines. Results We screened a total of 214 modular genes with the highest correlation with LUAD samples based on WGCNA, of which 192 genes were shown to be highly expressed in LUAD patients. Subsequently, three machine learning algorithms identified a total of four genes, including UBE2T, TEDC2, RCC1, and FAM136A, as diagnostic molecules for LUAD, and the ROC curves showed that these diagnostic molecules had good diagnostic performance (AUC values of 0.989, 0.989, 989, and 0.987, respectively). The expression of these diagnostic molecules was significantly higher in tumor samples than in normal para-cancerous…
bibliographic citation: Huang et al. (2024) Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma. PeerJ 12:e18310 https://doi.org/10.7717/peerj.18310
date submitted: 2024-03-25
date accepted: 2024-09-24
issued: 2024-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Qian
author list: Agent
  family name: Zhang
  given name: Peng
author list: Agent
  family name: Guo
  given name: Zhixu
author list: Agent
  family name: Li
  given name: Min
author list: Agent
  family name: Tao
  given name: Chao
author list: Agent
  family name: Yu
  given name: Zongyang
doi: 10.7717/peerj.18310
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-14
copyright: © 2024 Huang et al.
attribution name: Huang et al.

A new moradisaurine captorhinid reptile (Amniota: Eureptilia) from the upper Permian of India
type: item
type: AcademicArticle
description: Upper Permian rocks of the former supercontinent Gondwana record climax late Paleozoic terrestrial vertebrate faunas that were dominated numerically and ecologically by therapsid synapsids. Older faunal elements of earlier Paleozoic faunas, such as captorhinid reptiles, are rare and scattered components of the first amniote faunas to inhabit high-latitude regions. Here we describe a new genus and species of moradisaurine captorhinid that represents an archaic faunal element of the high-fibre herbivore fauna of the late Permian of what is now peninsular India. The presence of a relatively broad parietal and three rows of conical teeth on the maxilla and the dentary distinguishes Indosauriscus kuttyi gen. et sp. nov. from other moradisaurines. The hypodigm of I. kuttyi comprises skulls that range in length from 39 mm to 54 mm, and high ossification of the braincase elements and well developed skull-roof sutures, indicate that I. kuttyi adults were smaller than those of most moradisaurines. Results of our phylogenetic analyses suggest that moradisaurines, despite appearing first in the paleotropics, dispersed into temperate, high-latitude regions of Pangea early in their evolutionary history. Moradisaurines in dicynodont-dominated faunas, viz. Indosauriscus kuttyi and Gansurhinus naobaogouensis, were the smallest high-fibre herbivores in their respective faunas. This suggests that small body size may have evolved in these moradisaurines as they co-evolved with the more numerous and diverse dicynodont therapsids.
format: application/pdf
format: text/html
creator: Robert R. Reisz
creator: Sankar Chatterjee
creator: Sean P. Modesto
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.18394
publisher: PeerJ Inc.
rights: © 2024 Reisz et al.
abstract: Upper Permian rocks of the former supercontinent Gondwana record climax late Paleozoic terrestrial vertebrate faunas that were dominated numerically and ecologically by therapsid synapsids. Older faunal elements of earlier Paleozoic faunas, such as captorhinid reptiles, are rare and scattered components of the first amniote faunas to inhabit high-latitude regions. Here we describe a new genus and species of moradisaurine captorhinid that represents an archaic faunal element of the high-fibre herbivore fauna of the late Permian of what is now peninsular India. The presence of a relatively broad parietal and three rows of conical teeth on the maxilla and the dentary distinguishes Indosauriscus kuttyi gen. et sp. nov. from other moradisaurines. The hypodigm of I. kuttyi comprises skulls that range in length from 39 mm to 54 mm, and high ossification of the braincase elements and well developed skull-roof sutures, indicate that I. kuttyi adults were smaller than those of most moradisaurines. Results of our phylogenetic analyses suggest that moradisaurines, despite appearing first in the paleotropics, dispersed into temperate, high-latitude regions of Pangea early in their evolutionary history. Moradisaurines in dicynodont-dominated faunas, viz. Indosauriscus kuttyi and Gansurhinus naobaogouensis, were the smallest high-fibre herbivores in their respective faunas. This suggests that small body size may have evolved in these moradisaurines as they co-evolved with the more numerous and diverse dicynodont therapsids.
bibliographic citation: Reisz et al. (2024) A new moradisaurine captorhinid reptile (Amniota: Eureptilia) from the upper Permian of India. PeerJ 12:e18394 https://doi.org/10.7717/peerj.18394
date submitted: 2024-03-12
date accepted: 2024-10-03
issued: 2024-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reisz
  given name: Robert R.
author list: Agent
  family name: Chatterjee
  given name: Sankar
author list: Agent
  family name: Modesto
  given name: Sean P.
doi: 10.7717/peerj.18394
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-14
copyright: ©2024 Reisz et al.
attribution name: Reisz et al.

https://peerj.com/articles/18397
type: item
type: AcademicArticle
title: Evaluation of traditional and bootstrapped methods for assessing data-poor fisheries: a case study on tropical seabob shrimp (Xiphopenaeus kroyeri) with an improved length-based mortality estimation method
description: Background Unrealistic model assumptions or improper quantitative methods reduce the reliability of data-limited fisheries assessments. Here, we evaluate how traditional length-based methods perform in estimating growth and mortality parameters in comparison with unconstrained bootstrapped methods, based on a virtual population and a case study of seabob shrimp (Xiphopenaeus kroyeri, Heller, 1862). Methods Size data were obtained for 5,725 seabob shrimp caught in four distinct fishing grounds in the Southwestern Atlantic. Also, a synthetic population with known parameter values was simulated. These datasets were analyzed using different length-based methods: the traditional Powell-Wetheral plot method and novel bootstrapped methods. Results Analysis with bootstrapped ELEFAN (fishboot package) resulted in considerably lower estimates for asymptotic size (L∞), instantaneous growth rate (K), total mortalities (Z) and Z/K values compared to traditional methods. These parameters were highly influenced by L∞ estimates, which exhibited median values far below maximum lengths for all samples. Contrastingly, traditional methods (PW method and Lmax approach) resulted in much larger L∞ estimates, with average bias >70%. This caused multiplicative errors when estimating both Z and Z/K, with an astonishing average bias of roughly 200%, with deleterious consequences for stock assessment and management. We also present an improved version of the length-converted catch-curve method (the iLCCC) that allows for populations with L∞ > Lmax and propagates the uncertainty in growth parameters into mortality estimates. Our results highlight the importance of unbiased growth estimates to robustly evaluate mortality rates, with significant implications for length-based assessments of data-poor stocks. Thus, we underscore the call for standardized, unconstrained use of fishboot routines.
format: application/pdf
format: text/html
creator: Matheus de Barros
creator: Ronaldo Oliveira-Filho
creator: Alexandre Aschenbrenner
creator: Mauricio Hostim-Silva
creator: Julien Chiquieri
creator: Ralf Schwamborn
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
subject: Population Biology
description: doi:10.7717/peerj.18397
publisher: PeerJ Inc.
rights: © 2024 de Barros et al.
abstract: Background Unrealistic model assumptions or improper quantitative methods reduce the reliability of data-limited fisheries assessments. Here, we evaluate how traditional length-based methods perform in estimating growth and mortality parameters in comparison with unconstrained bootstrapped methods, based on a virtual population and a case study of seabob shrimp (Xiphopenaeus kroyeri, Heller, 1862). Methods Size data were obtained for 5,725 seabob shrimp caught in four distinct fishing grounds in the Southwestern Atlantic. Also, a synthetic population with known parameter values was simulated. These datasets were analyzed using different length-based methods: the traditional Powell-Wetheral plot method and novel bootstrapped methods. Results Analysis with bootstrapped ELEFAN (fishboot package) resulted in considerably lower estimates for asymptotic size (L∞), instantaneous growth rate (K), total mortalities (Z) and Z/K values compared to traditional methods. These parameters were highly influenced by L∞ estimates, which exhibited median values far below maximum lengths for all samples. Contrastingly, traditional methods (PW method and Lmax approach) resulted in much larger L∞ estimates, with average bias >70%. This caused multiplicative errors when estimating both Z and Z/K, with an astonishing average bias of roughly 200%, with deleterious consequences for stock assessment and management. We also present an improved version of the length-converted catch-curve method (the iLCCC) that allows for populations with L∞ > Lmax and propagates the uncertainty in growth parameters into mortality estimates. Our results highlight the importance of unbiased growth estimates to robustly evaluate mortality rates, with significant implications for length-based assessments of data-poor stocks. Thus, we underscore the call for standardized, unconstrained use of fishboot routines.
bibliographic citation: de Barros et al. (2024) Evaluation of traditional and bootstrapped methods for assessing data-poor fisheries: a case study on tropical seabob shrimp (Xiphopenaeus kroyeri) with an improved length-based mortality estimation method. PeerJ 12:e18397 https://doi.org/10.7717/peerj.18397
date submitted: 2023-01-18
date accepted: 2024-10-04
issued: 2024-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Barros
  given name: Matheus
author list: Agent
  family name: Oliveira-Filho
  given name: Ronaldo
author list: Agent
  family name: Aschenbrenner
  given name: Alexandre
author list: Agent
  family name: Hostim-Silva
  given name: Mauricio
author list: Agent
  family name: Chiquieri
  given name: Julien
author list: Agent
  family name: Schwamborn
  given name: Ralf
doi: 10.7717/peerj.18397
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-14
copyright: ©2024 de Barros et al.
attribution name: de Barros et al.

The fall of the mycobacterial cell wall: interrogating peptidoglycan synthesis for novel anti-TB agents
type: item
type: AcademicArticle
description: Tuberculosis (TB) caused by Mycobacterium tuberculosis has been a threat to human health for thousands of years and still leads to millions of deaths each year. TB is a disease that is refractory to treatment, partially due to its capacity for in-host persistence. The cell wall of mycobacteria, rich in mycolic acid, is broadly associated with bacterial persistence together with antimicrobial and immunological resistance. Enzymes for the biosynthesis of bacterial peptidoglycan, an essential component of the cell wall, have been addressed and considered as appealing drug targets in pathogens. Significant effort has been dedicated to finding inhibitors that hinder peptidoglycan biosynthesis, many with demonstrated enzymatic inhibition in vitro being published. One family of critical biosynthetic enzymes are the Mur enzymes, with many enzyme specific inhibitors having been reported. However, a lesser developed strategy which may have positive clinical implications is to take advantage of the common structural and catalytic characteristics among Mur enzymes and to allow simultaneous, multiple Mur inhibition, and avert the development of drug resistance. M. tuberculosis relies on these essential Mur enzymes, with the best-known subset being Mur ligases, but also utilizes unique functions of atypical transpeptidases resulting in peptidoglycan peptide cross-linking beneficial to the bacteria’s capacity for chronic persistence in humans. A systematic review is now needed, with an emphasis on M. tuberculosis. The urgent development of novel anti-TB agents to counter rapidly developing drug resistance requires a revisit of the literature, past successes and failures, in an attempt to reveal liabilities in critical cellular functions and drive innovation.
format: application/pdf
format: text/html
creator: Cheng-Yu Chiang
creator: Nicholas P. West
subject: Biochemistry
subject: Microbiology
subject: Infectious Diseases
subject: Pharmacology
description: doi:10.7717/peerj.18404
publisher: PeerJ Inc.
rights: © 2024 Chiang and West
abstract: Tuberculosis (TB) caused by Mycobacterium tuberculosis has been a threat to human health for thousands of years and still leads to millions of deaths each year. TB is a disease that is refractory to treatment, partially due to its capacity for in-host persistence. The cell wall of mycobacteria, rich in mycolic acid, is broadly associated with bacterial persistence together with antimicrobial and immunological resistance. Enzymes for the biosynthesis of bacterial peptidoglycan, an essential component of the cell wall, have been addressed and considered as appealing drug targets in pathogens. Significant effort has been dedicated to finding inhibitors that hinder peptidoglycan biosynthesis, many with demonstrated enzymatic inhibition in vitro being published. One family of critical biosynthetic enzymes are the Mur enzymes, with many enzyme specific inhibitors having been reported. However, a lesser developed strategy which may have positive clinical implications is to take advantage of the common structural and catalytic characteristics among Mur enzymes and to allow simultaneous, multiple Mur inhibition, and avert the development of drug resistance. M. tuberculosis relies on these essential Mur enzymes, with the best-known subset being Mur ligases, but also utilizes unique functions of atypical transpeptidases resulting in peptidoglycan peptide cross-linking beneficial to the bacteria’s capacity for chronic persistence in humans. A systematic review is now needed, with an emphasis on M. tuberculosis. The urgent development of novel anti-TB agents to counter rapidly developing drug resistance requires a revisit of the literature, past successes and failures, in an attempt to reveal liabilities in critical cellular functions and drive innovation.
bibliographic citation: Chiang et al. (2024) The fall of the mycobacterial cell wall: interrogating peptidoglycan synthesis for novel anti-TB agents. PeerJ 12:e18404 https://doi.org/10.7717/peerj.18404
date submitted: 2024-06-10
date accepted: 2024-10-04
issued: 2024-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chiang
  given name: Cheng-Yu
author list: Agent
  family name: West
  given name: Nicholas P.
doi: 10.7717/peerj.18404
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-14
copyright: ©2024 Chiang and West
attribution name: Chiang and West

Digital eye strain syndrome among higher education health sciences students in Saudi Arabia: severity and preventive ergonomic practices
type: item
type: AcademicArticle
description: Background The increased utilization of digital screens is an unavoidable consequence of the technology era. Digital eye strain (DES) is a prevalent health problem among higher education students in Saudi Arabia, especially health sciences students due to the frequent use of digital sources and virtual classes. Thus, this study aimed to assess the severity of digital eye strain syndrome (DESS) symptoms and preventive ergonomic practices among higher education health science students in Saudi Arabia. Methods A cross-sectional study using multistage cluster sampling in three cities (Dammam, Riyadh, Jeddah) in Saudi Arabia. A convenient sample of 328 health science students was selected using an equal allocation technique. The researchers designed and used an online survey of three sections: personal and digital device use-related data, the DESS questionnaire, and the self-reported preventive ergonomic practices scale. Results DESS is a widespread problem among 72.0% of health science students, and 58.2% had unsatisfactory ergonomics. The frequently reported symptoms were blurred vision (32.9%) and increased sensitivity to light (33.5%). The severe eye-related symptoms were headache (45.85%), foreign body inside the eye (43.71%), eye burning (40.19%), and dryness (39.76%). Logistic regression analysis revealed that the female sex, years of screen utilization and the number of hours per day, screen use without rest, and frequency of virtual classes per week, eye disease, digital screen utilization for studying, nonuse of protective eye measures, and using numerous digital devices were significant predictors of DESS risk (P < 0.05). Conclusions DESS is a common problem among many health science students, with headaches and foreign body sensations in the eye being the most frequent symptoms. Screen utilization time and eye disease are significant predictors of DESS, while most items’ application of ergonomic practices was low. Educational programs are needed to increase s…
format: application/pdf
format: text/html
creator: Olfat Abdulgafoor Gushgari
creator: Samiha Hamdi Sayed
creator: Wafaa Taha Elgzar
subject: Global Health
subject: Ophthalmology
subject: Public Health
subject: Human-Computer Interaction
description: doi:10.7717/peerj.18423
publisher: PeerJ Inc.
rights: © 2024 Gushgari et al.
abstract: Background The increased utilization of digital screens is an unavoidable consequence of the technology era. Digital eye strain (DES) is a prevalent health problem among higher education students in Saudi Arabia, especially health sciences students due to the frequent use of digital sources and virtual classes. Thus, this study aimed to assess the severity of digital eye strain syndrome (DESS) symptoms and preventive ergonomic practices among higher education health science students in Saudi Arabia. Methods A cross-sectional study using multistage cluster sampling in three cities (Dammam, Riyadh, Jeddah) in Saudi Arabia. A convenient sample of 328 health science students was selected using an equal allocation technique. The researchers designed and used an online survey of three sections: personal and digital device use-related data, the DESS questionnaire, and the self-reported preventive ergonomic practices scale. Results DESS is a widespread problem among 72.0% of health science students, and 58.2% had unsatisfactory ergonomics. The frequently reported symptoms were blurred vision (32.9%) and increased sensitivity to light (33.5%). The severe eye-related symptoms were headache (45.85%), foreign body inside the eye (43.71%), eye burning (40.19%), and dryness (39.76%). Logistic regression analysis revealed that the female sex, years of screen utilization and the number of hours per day, screen use without rest, and frequency of virtual classes per week, eye disease, digital screen utilization for studying, nonuse of protective eye measures, and using numerous digital devices were significant predictors of DESS risk (P < 0.05). Conclusions DESS is a common problem among many health science students, with headaches and foreign body sensations in the eye being the most frequent symptoms. Screen utilization time and eye disease are significant predictors of DESS, while most items’ application of ergonomic practices was low. Educational programs are needed to increase s…
bibliographic citation: Gushgari et al. (2024) Digital eye strain syndrome among higher education health sciences students in Saudi Arabia: severity and preventive ergonomic practices. PeerJ 12:e18423 https://doi.org/10.7717/peerj.18423
date submitted: 2024-06-21
date accepted: 2024-10-08
issued: 2024-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gushgari
  given name: Olfat Abdulgafoor
author list: Agent
  family name: Sayed
  given name: Samiha Hamdi
author list: Agent
  family name: Elgzar
  given name: Wafaa Taha
doi: 10.7717/peerj.18423
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-14
copyright: © 2024 Gushgari et al.
attribution name: Gushgari et al.

A review of advancements in the theory and characterization of soil macropore structure
type: item
type: AcademicArticle
description: Soil has an intricate pore structure, with the macropore structure serving as a pivotal component of gas exchange, liquid flow, and solute transport within the soil matrix. Scientifically understanding the macropore structure is important for the exploration of soil ecological functions. Drawing upon research literature from diverse nations, this study presents a comprehensive summary of past research findings, thoroughly examining the definition and taxonomy of soil macropores. Additionally, we delve into the factors that affect macropore structure, the effects of macropores on soil ecological functions, and the indicators that describe the nature of macropores. Furthermore, the principles, suitability conditions, benefits, and limitations of the widely utilized techniques for characterizing soil macropore structure were outlined, including staining observation, soil water retention curve, mercury intrusion porosimetry, gas adsorption, nuclear magnetic resonance, scanning electron microscopy, and computed tomography (CT). A comparative analysis was conducted to assist scholars in comprehending the theory of soil macropores, facilitating the selection of suitable macropore structure characterization techniques, and enabling the development of collaborative application modes among these techniques. Using the Web of Science core collection database, bibliometric software such as VOSviewer and CiteSpace were employed to explore the research hotspots and trends in CT, which is currently the most popular technique for characterizing soil macropore structure. This analysis offers insights into the future prospects of CT in the field of soil macropore structure characterization techniques. This article is of particular interest to readers engaged in the characterization of soil macropores.
format: application/pdf
format: text/html
creator: Yanwen Cao
creator: Kai Zhang
creator: Shuyu Liu
creator: Yilin Wang
subject: Agricultural Science
subject: Ecology
subject: Soil Science
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.18442
publisher: PeerJ Inc.
rights: © 2024 Cao et al.
abstract: Soil has an intricate pore structure, with the macropore structure serving as a pivotal component of gas exchange, liquid flow, and solute transport within the soil matrix. Scientifically understanding the macropore structure is important for the exploration of soil ecological functions. Drawing upon research literature from diverse nations, this study presents a comprehensive summary of past research findings, thoroughly examining the definition and taxonomy of soil macropores. Additionally, we delve into the factors that affect macropore structure, the effects of macropores on soil ecological functions, and the indicators that describe the nature of macropores. Furthermore, the principles, suitability conditions, benefits, and limitations of the widely utilized techniques for characterizing soil macropore structure were outlined, including staining observation, soil water retention curve, mercury intrusion porosimetry, gas adsorption, nuclear magnetic resonance, scanning electron microscopy, and computed tomography (CT). A comparative analysis was conducted to assist scholars in comprehending the theory of soil macropores, facilitating the selection of suitable macropore structure characterization techniques, and enabling the development of collaborative application modes among these techniques. Using the Web of Science core collection database, bibliometric software such as VOSviewer and CiteSpace were employed to explore the research hotspots and trends in CT, which is currently the most popular technique for characterizing soil macropore structure. This analysis offers insights into the future prospects of CT in the field of soil macropore structure characterization techniques. This article is of particular interest to readers engaged in the characterization of soil macropores.
bibliographic citation: Cao et al. (2024) A review of advancements in the theory and characterization of soil macropore structure. PeerJ 12:e18442 https://doi.org/10.7717/peerj.18442
date submitted: 2024-04-30
date accepted: 2024-10-11
issued: 2024-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Yanwen
author list: Agent
  family name: Zhang
  given name: Kai
author list: Agent
  family name: Liu
  given name: Shuyu
author list: Agent
  family name: Wang
  given name: Yilin
doi: 10.7717/peerj.18442
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-14
copyright: ©2024 Cao et al.
attribution name: Cao et al.

Comparative electromyography analysis of subphase gait disorder in chronic stroke survivors
type: item
type: AcademicArticle
description: Abnormal lower limb muscle activity is the most common cause of the alterative pattern of gait in stroke survivors, resulting from spastic and paralytic muscles around the hip, knee, and ankle joints. However, the activity of the major lower limb muscles that control the legs to facilitate walking in stroke patients have not been clearly understood in each subphase of the gait. This study differentiated the characteristics of surface electromyography (sEMG) signals of lower limb muscles during four subphases of gait cycle between stroke patients and healthy subjects. Sixteen chronic stroke patients and sixteen healthy subjects were recruited. All participants completed three walking trials with a self-selected walking speed. The sEMG signals were recorded on the gluteus medius, rectus femoris, long head of biceps femoris, medial gastrocnemius, tibialis anterior, and peroneus longus muscles. The characteristics of sEMG signals were processed and analyzed in the time and frequency features, considering the first double support, single support, second double support, and swing phases of the gait cycle.The stroke patients had altered sEMG characteristics on both paretic and non-paretic sides compared to healthy subjects across the sub-phases of gait cycle for all six muscles. All time domain features of sEMG signal showed that the medial gastrocnemius muscle has the most significant impaired activity (p < 0.05) and affected gait disturbance during all four subphases of the gait cycle. The findings demonstrated that the medial gastrocnemius muscle had impaired activity and was most affected during all four sub-phases of the gait cycle. This indicates that sEMG of medial gastrocnemius muscle can be used to measure the improvement of gait rehabilitation.
format: application/pdf
format: text/html
creator: Nusreena Hohsoh
creator: Thanita Sanghan
creator: Desmond Y.R. Chong
creator: Goran Stojanovic
creator: Surapong Chatpun
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.18473
publisher: PeerJ Inc.
rights: © 2024 Hohsoh et al.
abstract: Abnormal lower limb muscle activity is the most common cause of the alterative pattern of gait in stroke survivors, resulting from spastic and paralytic muscles around the hip, knee, and ankle joints. However, the activity of the major lower limb muscles that control the legs to facilitate walking in stroke patients have not been clearly understood in each subphase of the gait. This study differentiated the characteristics of surface electromyography (sEMG) signals of lower limb muscles during four subphases of gait cycle between stroke patients and healthy subjects. Sixteen chronic stroke patients and sixteen healthy subjects were recruited. All participants completed three walking trials with a self-selected walking speed. The sEMG signals were recorded on the gluteus medius, rectus femoris, long head of biceps femoris, medial gastrocnemius, tibialis anterior, and peroneus longus muscles. The characteristics of sEMG signals were processed and analyzed in the time and frequency features, considering the first double support, single support, second double support, and swing phases of the gait cycle.The stroke patients had altered sEMG characteristics on both paretic and non-paretic sides compared to healthy subjects across the sub-phases of gait cycle for all six muscles. All time domain features of sEMG signal showed that the medial gastrocnemius muscle has the most significant impaired activity (p < 0.05) and affected gait disturbance during all four subphases of the gait cycle. The findings demonstrated that the medial gastrocnemius muscle had impaired activity and was most affected during all four sub-phases of the gait cycle. This indicates that sEMG of medial gastrocnemius muscle can be used to measure the improvement of gait rehabilitation.
bibliographic citation: Hohsoh et al. (2024) Comparative electromyography analysis of subphase gait disorder in chronic stroke survivors. PeerJ 12:e18473 https://doi.org/10.7717/peerj.18473
date submitted: 2024-06-24
date accepted: 2024-10-15
issued: 2024-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hohsoh
  given name: Nusreena
author list: Agent
  family name: Sanghan
  given name: Thanita
author list: Agent
  family name: Chong
  given name: Desmond Y.R.
author list: Agent
  family name: Stojanovic
  given name: Goran
author list: Agent
  family name: Chatpun
  given name: Surapong
doi: 10.7717/peerj.18473
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-14
copyright: ©2024 Hohsoh et al.
attribution name: Hohsoh et al.

New insights into the impact of wood vinegar on the growth and rhizosphere microorganisms of cherry radish (Raphanus sativus L.)
type: item
type: AcademicArticle
description: Understanding the impact of wood vinegar on the growth of cherry radish is indispensable for use in crop production and environmental safety. Our study explored the regulation of rhizosphere microbial abundance and activity by wood vinegar, as well as the relationship between microbial community and growth factors in-depth and systematically. Bacterial communities at the phylum and genus levels were significantly changed after wood vinegar treatment. Application of 200-fold diluted wood vinegar significantly boosted Actinobacteriota and Firmicutes abundances by 40.88% and 126.67%, respectively, while Proteobacteria was promoted in carbon-rich soil. Fungi positively responded to cherry radish root traits and were correlated with aboveground biomass and fruit production. The fungi that correlated with photosynthesis included Albifimbria, Allomyces, Calcarisporiella, Clonostachys, Fusarium, Fusicolla, Knufia, Nigrospora, Paraconiothyrium, Preussia, Talaromyces, and Mortierellomycota. Wood vinegar treatment significantly affected the composition and abundance of soil bacterial and fungal communities in cherry radish rhizosphere, while simultaneously enhancing photosynthetic efficiency (e.g., Pn: 80.45% and Tr: 56.75%) and resulting in a 44.91% increase in crop yield. The promotion of cherry radish growth by wood vinegar may be attributed to the stimulation of soil microorganisms that degraded aromatic compounds and drove nitrogen cycling. This study provided novel insights into the significant promotion of cherry radish growth using wood vinegar diluted 200 times and identified potential microbial targets for agricultural applications.
format: application/pdf
format: text/html
creator: Shiguo Gu
creator: Wei Zhu
creator: Liying Ren
creator: Binbin Sun
creator: Yuying Ren
creator: Yongkang Niu
creator: Xiaokang Li
creator: Qingshan He
subject: Agricultural Science
subject: Ecology
subject: Ecosystem Science
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.18505
publisher: PeerJ Inc.
rights: © 2024 Gu et al.
abstract: Understanding the impact of wood vinegar on the growth of cherry radish is indispensable for use in crop production and environmental safety. Our study explored the regulation of rhizosphere microbial abundance and activity by wood vinegar, as well as the relationship between microbial community and growth factors in-depth and systematically. Bacterial communities at the phylum and genus levels were significantly changed after wood vinegar treatment. Application of 200-fold diluted wood vinegar significantly boosted Actinobacteriota and Firmicutes abundances by 40.88% and 126.67%, respectively, while Proteobacteria was promoted in carbon-rich soil. Fungi positively responded to cherry radish root traits and were correlated with aboveground biomass and fruit production. The fungi that correlated with photosynthesis included Albifimbria, Allomyces, Calcarisporiella, Clonostachys, Fusarium, Fusicolla, Knufia, Nigrospora, Paraconiothyrium, Preussia, Talaromyces, and Mortierellomycota. Wood vinegar treatment significantly affected the composition and abundance of soil bacterial and fungal communities in cherry radish rhizosphere, while simultaneously enhancing photosynthetic efficiency (e.g., Pn: 80.45% and Tr: 56.75%) and resulting in a 44.91% increase in crop yield. The promotion of cherry radish growth by wood vinegar may be attributed to the stimulation of soil microorganisms that degraded aromatic compounds and drove nitrogen cycling. This study provided novel insights into the significant promotion of cherry radish growth using wood vinegar diluted 200 times and identified potential microbial targets for agricultural applications.
bibliographic citation: Gu et al. (2024) New insights into the impact of wood vinegar on the growth and rhizosphere microorganisms of cherry radish (Raphanus sativus L.). PeerJ 12:e18505 https://doi.org/10.7717/peerj.18505
date submitted: 2024-06-18
date accepted: 2024-10-21
issued: 2024-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gu
  given name: Shiguo
author list: Agent
  family name: Zhu
  given name: Wei
author list: Agent
  family name: Ren
  given name: Liying
author list: Agent
  family name: Sun
  given name: Binbin
author list: Agent
  family name: Ren
  given name: Yuying
author list: Agent
  family name: Niu
  given name: Yongkang
author list: Agent
  family name: Li
  given name: Xiaokang
author list: Agent
  family name: He
  given name: Qingshan
doi: 10.7717/peerj.18505
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-14
copyright: ©2024 Gu et al.
attribution name: Gu et al.

An experimental analysis of graph representation learning for Gene Ontology based protein function prediction
type: item
type: AcademicArticle
description: Understanding protein function is crucial for deciphering biological systems and facilitating various biomedical applications. Computational methods for predicting Gene Ontology functions of proteins emerged in the 2000s to bridge the gap between the number of annotated proteins and the rapidly growing number of newly discovered amino acid sequences. Recently, there has been a surge in studies applying graph representation learning techniques to biological networks to enhance protein function prediction tools. In this review, we provide fundamental concepts in graph embedding algorithms. This study described graph representation learning methods for protein function prediction based on four principal data categories, namely PPI network, protein structure, Gene Ontology graph, and integrated graph. The commonly used approaches for each category were summarized and diagrammed, with the specific results of each method explained in detail. Finally, existing limitations and potential solutions were discussed, and directions for future research within the protein research community were suggested.
format: application/pdf
format: text/html
creator: Thi Thuy Duong Vu
creator: Jeongho Kim
creator: Jaehee Jung
subject: Bioinformatics
subject: Computational Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.18509
publisher: PeerJ Inc.
rights: © 2024 Vu et al.
abstract: Understanding protein function is crucial for deciphering biological systems and facilitating various biomedical applications. Computational methods for predicting Gene Ontology functions of proteins emerged in the 2000s to bridge the gap between the number of annotated proteins and the rapidly growing number of newly discovered amino acid sequences. Recently, there has been a surge in studies applying graph representation learning techniques to biological networks to enhance protein function prediction tools. In this review, we provide fundamental concepts in graph embedding algorithms. This study described graph representation learning methods for protein function prediction based on four principal data categories, namely PPI network, protein structure, Gene Ontology graph, and integrated graph. The commonly used approaches for each category were summarized and diagrammed, with the specific results of each method explained in detail. Finally, existing limitations and potential solutions were discussed, and directions for future research within the protein research community were suggested.
bibliographic citation: Vu et al. (2024) An experimental analysis of graph representation learning for Gene Ontology based protein function prediction. PeerJ 12:e18509 https://doi.org/10.7717/peerj.18509
date submitted: 2024-09-05
date accepted: 2024-10-21
issued: 2024-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vu
  given name: Thi Thuy Duong
author list: Agent
  family name: Kim
  given name: Jeongho
author list: Agent
  family name: Jung
  given name: Jaehee
doi: 10.7717/peerj.18509
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-14
copyright: © 2024 Vu et al.
attribution name: Vu et al.

Intra-rater and inter-rater reliability of the fixed plumb line for postural and scoliosis assessment in the sagittal plane: a pilot study
type: item
type: AcademicArticle
description: Background The plumb line (PL) is a common tool for assessing the sagittal curvatures of the spine, but its accuracy depends on the ability of the physician to use it correctly. This study aimed to present a fixed plumb line (FPL) no longer held by a physician but fixed to a support, evaluating the reliability in posture assessment, comparing it with PL in both adolescent with and without scoliosis. Methods The study evaluated the sagittal distances of the spine using a PL and a FPL in 80 young adults aged between 28.7 ± 7.2 and 55 adolescents aged between 12.4 ± 2.3, with and without scoliosis. Two expert and two novice clinicians tested the patients to evaluate the intra-rater and inter-rater reliability of FPL. Each clinician assessed participants twice on the same day, with a predetermined time interval (>1 h) to reduce recall bias. Multi-factor multivariate analysis of variance and two-way analysis of variance assessed the statistical significance, while intraclass correlation coefficient (ICC), standard error of measurement (SEM) and minimum detectable change (MDC) validated FPL consistency. Results FPL provided an ICC coefficient >0.90 for all the measures, while PL an average of 0.70. On AIS patients, PL and FPL showed a significant difference for C7 p < 0.001 and T12 p < 0.001. The measured parameters were sensitive to gender and age for the FPL, furthermore, the C7 and L3 measurements were statistically different between PL and FPL (p < 0.001). Intra-rater reliability results for FPL ranged from 0.94 to 0.98 across various parameters, while the SEM and MDC values underscore the valuable precision of the FPL with changes exceeding 1 cm being meaningful. These findings suggest that FPL could be a reliable and accurate tool for measuring sagittal distances of the spine in both scoliotic and non-scoliotic patients.
format: application/pdf
format: text/html
creator: Federico Roggio
creator: Bruno Trovato
creator: Martina Sortino
creator: Marta Zanghì
creator: Claudio Di Brigida
creator: Claudia Guglielmino
creator: Claudia Lombardo
creator: Carla Loreto
creator: Piero Pavone
creator: Giuseppe Musumeci
subject: Anatomy and Physiology
subject: Kinesiology
subject: Orthopedics
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.18121
publisher: PeerJ Inc.
rights: © 2024 Roggio et al.
abstract: Background The plumb line (PL) is a common tool for assessing the sagittal curvatures of the spine, but its accuracy depends on the ability of the physician to use it correctly. This study aimed to present a fixed plumb line (FPL) no longer held by a physician but fixed to a support, evaluating the reliability in posture assessment, comparing it with PL in both adolescent with and without scoliosis. Methods The study evaluated the sagittal distances of the spine using a PL and a FPL in 80 young adults aged between 28.7 ± 7.2 and 55 adolescents aged between 12.4 ± 2.3, with and without scoliosis. Two expert and two novice clinicians tested the patients to evaluate the intra-rater and inter-rater reliability of FPL. Each clinician assessed participants twice on the same day, with a predetermined time interval (>1 h) to reduce recall bias. Multi-factor multivariate analysis of variance and two-way analysis of variance assessed the statistical significance, while intraclass correlation coefficient (ICC), standard error of measurement (SEM) and minimum detectable change (MDC) validated FPL consistency. Results FPL provided an ICC coefficient >0.90 for all the measures, while PL an average of 0.70. On AIS patients, PL and FPL showed a significant difference for C7 p < 0.001 and T12 p < 0.001. The measured parameters were sensitive to gender and age for the FPL, furthermore, the C7 and L3 measurements were statistically different between PL and FPL (p < 0.001). Intra-rater reliability results for FPL ranged from 0.94 to 0.98 across various parameters, while the SEM and MDC values underscore the valuable precision of the FPL with changes exceeding 1 cm being meaningful. These findings suggest that FPL could be a reliable and accurate tool for measuring sagittal distances of the spine in both scoliotic and non-scoliotic patients.
bibliographic citation: Roggio et al. (2024) Intra-rater and inter-rater reliability of the fixed plumb line for postural and scoliosis assessment in the sagittal plane: a pilot study. PeerJ 12:e18121 https://doi.org/10.7717/peerj.18121
date submitted: 2024-03-08
date accepted: 2024-08-28
issued: 2024-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roggio
  given name: Federico
author list: Agent
  family name: Trovato
  given name: Bruno
author list: Agent
  family name: Sortino
  given name: Martina
author list: Agent
  family name: Zanghì
  given name: Marta
author list: Agent
  family name: Di Brigida
  given name: Claudio
author list: Agent
  family name: Guglielmino
  given name: Claudia
author list: Agent
  family name: Lombardo
  given name: Claudia
author list: Agent
  family name: Loreto
  given name: Carla
author list: Agent
  family name: Pavone
  given name: Piero
author list: Agent
  family name: Musumeci
  given name: Giuseppe
doi: 10.7717/peerj.18121
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-13
copyright: ©2024 Roggio et al.
attribution name: Roggio et al.

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