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/18532
items: miR-101-3p suppresses proliferation of orbital fibroblasts by targeting pentraxin-3 in thyroid eye disease
items: Microglial depletion rescues spatial memory impairment caused by LPS administration in adult mice
items: Biopsy-based normalizations of gill monogenean-infected European catfish (Silurus glanis L., 1758) stocks for laboratory-based experiments
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

https://peerj.com/articles/18532
type: item
type: AcademicArticle
title: Clinical outcomes of arthroscopic suture fixation combined with loop plate vs. posterior approach open reduction and cannulated screw fixation for treating tibial avulsion fractures of the posterior cruciate ligament: a retrospective study
description: Background Comparison of the efficacy of arthroscopic suture fixation combined with loop plate vs. the posterior approach involving open reduction and intramedullary nail fixation in treating posterior cruciate ligament tibial avulsion fractures (PCLTAFs). Methods A retrospective analysis was conducted on the clinical data of patients diagnosed with PCLTAF who were admitted to Northern Jiangsu People’s Hospital between June 2019 and March 2022. Based on distinct surgical procedures, the patients were categorized into two groups: arthroscopic group (33 cases), involving a single bone tunnel, high-strength suture, loop plate, and anchor screw fixed under arthroscopy, and open reduction and internal fixation (ORIF) group (13 cases), involving a modified posterior medial approach and fixation using 1–2 cannulated screws. Key parameters, including surgical duration, postoperative fracture alignment, fracture-healing duration, range of motion changes, postoperative Lysholm scores, and VAS scores were documented and compared between the two groups. Results The study cohort comprised 46 patients, with 28 males and 18 females, and the median age was 29 years old (range: 15–69). There were no significant differences in the baseline characteristics, including knee Lysholm scores, between the two groups. The arthroscopic group exhibited significant improvement in all eight Lysholm score indicators (all P < 0.001). The total Lysholm score also exhibited significant improvement before and after surgery in both groups (P < 0.001). Following surgery, the arthroscopic group demonstrated improvements in all indicators, but had a slightly longer operating time compared to the ORIF group. No significant differences were observed in the Lysholm scores for the knee joint between the two patient groups before and after surgery (P > 0.05). Conclusions Arthroscopic suture fixation in conjunction with looped plate binding can significantly improve knee function and clinical effect for patien…
format: application/pdf
format: text/html
creator: Lan Zhang
creator: Dan Guo
subject: Anatomy and Physiology
subject: Orthopedics
subject: Rheumatology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.18532
publisher: PeerJ Inc.
rights: © 2024 Zhang and Guo
abstract: Background Comparison of the efficacy of arthroscopic suture fixation combined with loop plate vs. the posterior approach involving open reduction and intramedullary nail fixation in treating posterior cruciate ligament tibial avulsion fractures (PCLTAFs). Methods A retrospective analysis was conducted on the clinical data of patients diagnosed with PCLTAF who were admitted to Northern Jiangsu People’s Hospital between June 2019 and March 2022. Based on distinct surgical procedures, the patients were categorized into two groups: arthroscopic group (33 cases), involving a single bone tunnel, high-strength suture, loop plate, and anchor screw fixed under arthroscopy, and open reduction and internal fixation (ORIF) group (13 cases), involving a modified posterior medial approach and fixation using 1–2 cannulated screws. Key parameters, including surgical duration, postoperative fracture alignment, fracture-healing duration, range of motion changes, postoperative Lysholm scores, and VAS scores were documented and compared between the two groups. Results The study cohort comprised 46 patients, with 28 males and 18 females, and the median age was 29 years old (range: 15–69). There were no significant differences in the baseline characteristics, including knee Lysholm scores, between the two groups. The arthroscopic group exhibited significant improvement in all eight Lysholm score indicators (all P < 0.001). The total Lysholm score also exhibited significant improvement before and after surgery in both groups (P < 0.001). Following surgery, the arthroscopic group demonstrated improvements in all indicators, but had a slightly longer operating time compared to the ORIF group. No significant differences were observed in the Lysholm scores for the knee joint between the two patient groups before and after surgery (P > 0.05). Conclusions Arthroscopic suture fixation in conjunction with looped plate binding can significantly improve knee function and clinical effect for patien…
bibliographic citation: Zhang et al. (2024) Clinical outcomes of arthroscopic suture fixation combined with loop plate vs. posterior approach open reduction and cannulated screw fixation for treating tibial avulsion fractures of the posterior cruciate ligament: a retrospective study. PeerJ 12:e18532 https://doi.org/10.7717/peerj.18532
date submitted: 2023-11-15
date accepted: 2024-10-24
issued: 2024-11-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhang
  given name: Lan
author list: Agent
  family name: Guo
  given name: Dan
doi: 10.7717/peerj.18532
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-15
copyright: © 2024 Zhang and Guo
attribution name: Zhang and Guo

miR-101-3p suppresses proliferation of orbital fibroblasts by targeting pentraxin-3 in thyroid eye disease
type: item
type: AcademicArticle
description: Background Excessive proliferation of orbital fibroblasts (OFs) is an essential factor in the pathogenesis of thyroid eye disease (TED). While existing evidence indicates that various microRNAs (miRNAs) significantly contribute to TED development, the precise function and targets of miR-101-3p in TED pathogenesis remain unknown. This research aims to elucidate the effects of miR-101-3p on TED-OFs and identify its potential targets. Methods Orbital adipose tissues were harvested from both TED patients and healthy controls to culture their fibroblasts. MiR-101-3p mimic or mimic negative control (mimic NC) was transfected into OFs from TED patients, with untreated OFs serving as an additional blank control group. Cell proliferation was assessed using cell counting kit-8 (CCK-8) assay, Ki-67 immunofluorescence staining, and the EdU assay, while apoptosis was evaluated via flow cytometry. Quantitative real-time polymerase chain reaction (qRT-PCR) was employed to measure the expression levels of miR-101-3p and pentraxin-3 (PTX3), and PTX3 protein levels were quantified using western blot. A dual-luciferase assay was conducted to ascertain how miR-101-3p and PTX3 interacted. Results The results demonstrated a significant downregulation of miR-101-3p in fibroblasts and TED orbital adipose tissues. Transfection with the miR-101-3p mimic upregulated miR-101-3p levels, significantly reducing OFs proliferation without affecting apoptosis. Overexpression of miR-101-3p led to the downregulation of PTX3 in OFs. The dual-luciferase assay validated miR-101-3p binding to PTX3’s 3’UTR, thereby repressing its expression. Moreover, overexpression of PTX3 partially rescued the miR-101-3p mimic’s inhibitory effect on TED-OFs proliferation. Conclusion Our findings illustrate miR-101-3p’s role in targeting PTX3 to regulate TED-OFs proliferation, providing novel insights into the pathological mechanisms underlying TED development.
format: application/pdf
format: text/html
creator: Yanfei Zhu
creator: Yuqing Chen
creator: Xingyi Shu
creator: Ruili Wei
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Ophthalmology
description: doi:10.7717/peerj.18535
publisher: PeerJ Inc.
rights: © 2024 Zhu et al.
abstract: Background Excessive proliferation of orbital fibroblasts (OFs) is an essential factor in the pathogenesis of thyroid eye disease (TED). While existing evidence indicates that various microRNAs (miRNAs) significantly contribute to TED development, the precise function and targets of miR-101-3p in TED pathogenesis remain unknown. This research aims to elucidate the effects of miR-101-3p on TED-OFs and identify its potential targets. Methods Orbital adipose tissues were harvested from both TED patients and healthy controls to culture their fibroblasts. MiR-101-3p mimic or mimic negative control (mimic NC) was transfected into OFs from TED patients, with untreated OFs serving as an additional blank control group. Cell proliferation was assessed using cell counting kit-8 (CCK-8) assay, Ki-67 immunofluorescence staining, and the EdU assay, while apoptosis was evaluated via flow cytometry. Quantitative real-time polymerase chain reaction (qRT-PCR) was employed to measure the expression levels of miR-101-3p and pentraxin-3 (PTX3), and PTX3 protein levels were quantified using western blot. A dual-luciferase assay was conducted to ascertain how miR-101-3p and PTX3 interacted. Results The results demonstrated a significant downregulation of miR-101-3p in fibroblasts and TED orbital adipose tissues. Transfection with the miR-101-3p mimic upregulated miR-101-3p levels, significantly reducing OFs proliferation without affecting apoptosis. Overexpression of miR-101-3p led to the downregulation of PTX3 in OFs. The dual-luciferase assay validated miR-101-3p binding to PTX3’s 3’UTR, thereby repressing its expression. Moreover, overexpression of PTX3 partially rescued the miR-101-3p mimic’s inhibitory effect on TED-OFs proliferation. Conclusion Our findings illustrate miR-101-3p’s role in targeting PTX3 to regulate TED-OFs proliferation, providing novel insights into the pathological mechanisms underlying TED development.
bibliographic citation: Zhu et al. (2024) miR-101-3p suppresses proliferation of orbital fibroblasts by targeting pentraxin-3 in thyroid eye disease. PeerJ 12:e18535 https://doi.org/10.7717/peerj.18535
date submitted: 2024-08-08
date accepted: 2024-10-25
issued: 2024-11-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhu
  given name: Yanfei
author list: Agent
  family name: Chen
  given name: Yuqing
author list: Agent
  family name: Shu
  given name: Xingyi
author list: Agent
  family name: Wei
  given name: Ruili
doi: 10.7717/peerj.18535
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-15
copyright: © 2024 Zhu et al.
attribution name: Zhu et al.

Microglial depletion rescues spatial memory impairment caused by LPS administration in adult mice
type: item
type: AcademicArticle
description: Recent studies have highlighted the importance of microglia, the resident macrophages in the brain, in regulating cognitive functions such as learning and memory in both healthy and diseased states. However, there are conflicting results and the underlying mechanisms are not fully understood. In this study, we examined the effect of depleting adult microglia on spatial learning and memory under both physiological conditions and lipopolysaccharide (LPS)-induced neuroinflammation. Our results revealed that microglial depletion by PLX5622 caused mild spatial memory impairment in mice under physiological conditions; however, it prevented memory deficits induced by systemic LPS insult. Inactivating microglia through minocycline administration replicated the protective effect of microglial depletion on LPS-induced memory impairment. Furthermore, our study showed that PLX5622 treatment suppressed LPS-induced neuroinflammation, microglial activation, and synaptic dysfunction. These results strengthen the evidence for the involvement of microglial immunoactivation in LPS-induced synaptic and cognitive malfunctions. They also suggest that targeting microglia may be a potential approach to treating neuroinflammation-associated cognitive dysfunction seen in neurodegenerative diseases.
format: application/pdf
format: text/html
creator: Tao Zong
creator: Na Li
creator: Fubing Han
creator: Junru Liu
creator: Mingru Deng
creator: Vincent Li
creator: Meng Zhang
creator: Yu Zhou
creator: Ming Yu
subject: Animal Behavior
subject: Cell Biology
subject: Neuroscience
description: doi:10.7717/peerj.18552
publisher: PeerJ Inc.
rights: © 2024 Zong et al.
abstract: Recent studies have highlighted the importance of microglia, the resident macrophages in the brain, in regulating cognitive functions such as learning and memory in both healthy and diseased states. However, there are conflicting results and the underlying mechanisms are not fully understood. In this study, we examined the effect of depleting adult microglia on spatial learning and memory under both physiological conditions and lipopolysaccharide (LPS)-induced neuroinflammation. Our results revealed that microglial depletion by PLX5622 caused mild spatial memory impairment in mice under physiological conditions; however, it prevented memory deficits induced by systemic LPS insult. Inactivating microglia through minocycline administration replicated the protective effect of microglial depletion on LPS-induced memory impairment. Furthermore, our study showed that PLX5622 treatment suppressed LPS-induced neuroinflammation, microglial activation, and synaptic dysfunction. These results strengthen the evidence for the involvement of microglial immunoactivation in LPS-induced synaptic and cognitive malfunctions. They also suggest that targeting microglia may be a potential approach to treating neuroinflammation-associated cognitive dysfunction seen in neurodegenerative diseases.
bibliographic citation: Zong et al. (2024) Microglial depletion rescues spatial memory impairment caused by LPS administration in adult mice. PeerJ 12:e18552 https://doi.org/10.7717/peerj.18552
date submitted: 2024-08-13
date accepted: 2024-10-29
issued: 2024-11-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zong
  given name: Tao
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Han
  given name: Fubing
author list: Agent
  family name: Liu
  given name: Junru
author list: Agent
  family name: Deng
  given name: Mingru
author list: Agent
  family name: Li
  given name: Vincent
author list: Agent
  family name: Zhang
  given name: Meng
author list: Agent
  family name: Zhou
  given name: Yu
author list: Agent
  family name: Yu
  given name: Ming
doi: 10.7717/peerj.18552
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-15
copyright: © 2024 Zong et al.
attribution name: Zong et al.

Biopsy-based normalizations of gill monogenean-infected European catfish (Silurus glanis L., 1758) stocks for laboratory-based experiments
type: item
type: AcademicArticle
description: Ectoparasites cause serious problems during the aquaculture production of food fishes. In this study, we set out to develop and test protocols for maintenance and sampling European catfish (Silurus glanis L., 1758) stocks infected with a gill monogenean, Thaparocleidus vistulensis (Siwak 1932) Lim 1996. When we compared the feasibility of two cohabitation-based parasite culture systems (i.e., static vs. flow-through), we found that the life cycle of T. vistulensis was completed in both habitats. In our experience, static tank systems with regular water exchange allowed better daily quality control of the parasite culture than continuous flow-through systems. We investigated the microhabitat preference of T. vistulensis on the gills of infected European catfish. A balanced distribution on the two lateral gill sets and a decreasing trend in parasite numbers from anterior gill holobranches towards the posterior ones was observed. Using these results, we developed a minimally invasive sampling protocol to estimate the parasite load of individuals. The biopsy aimed at four sectors (#6, #7, #10, and #11) situated within the distal and middle zones of the first holobranch on the left side, encompassing both rows of filaments. Biopsy-based estimates of parasite loads were validated by comparing them to full parasite counts of the same individuals and showed statistically significant correlations. Our biopsy-based method is designed to identify experimental animals with similar parasite loads and create groups of hosts with comparable burdens. This setup is expected to generate reduced between-group differences for expensive experiments (e.g., high throughput transcriptomic or epigenetic studies). We propose that the biopsy-based pre-sorting procedure should be considered in similar experiments with other cultured fish species and their gill monogeneans following a thorough fine-tuning of the experimental conditions.
format: application/pdf
format: text/html
creator: András Bognár
creator: Muhammad Hafiz Borkhanuddin
creator: Shion Nagase
creator: Boglárka Sellyei
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Parasitology
description: doi:10.7717/peerj.18288
publisher: PeerJ Inc.
rights: © 2024 Bognár et al.
abstract: Ectoparasites cause serious problems during the aquaculture production of food fishes. In this study, we set out to develop and test protocols for maintenance and sampling European catfish (Silurus glanis L., 1758) stocks infected with a gill monogenean, Thaparocleidus vistulensis (Siwak 1932) Lim 1996. When we compared the feasibility of two cohabitation-based parasite culture systems (i.e., static vs. flow-through), we found that the life cycle of T. vistulensis was completed in both habitats. In our experience, static tank systems with regular water exchange allowed better daily quality control of the parasite culture than continuous flow-through systems. We investigated the microhabitat preference of T. vistulensis on the gills of infected European catfish. A balanced distribution on the two lateral gill sets and a decreasing trend in parasite numbers from anterior gill holobranches towards the posterior ones was observed. Using these results, we developed a minimally invasive sampling protocol to estimate the parasite load of individuals. The biopsy aimed at four sectors (#6, #7, #10, and #11) situated within the distal and middle zones of the first holobranch on the left side, encompassing both rows of filaments. Biopsy-based estimates of parasite loads were validated by comparing them to full parasite counts of the same individuals and showed statistically significant correlations. Our biopsy-based method is designed to identify experimental animals with similar parasite loads and create groups of hosts with comparable burdens. This setup is expected to generate reduced between-group differences for expensive experiments (e.g., high throughput transcriptomic or epigenetic studies). We propose that the biopsy-based pre-sorting procedure should be considered in similar experiments with other cultured fish species and their gill monogeneans following a thorough fine-tuning of the experimental conditions.
bibliographic citation: Bognár et al. (2024) Biopsy-based normalizations of gill monogenean-infected European catfish (Silurus glanis L., 1758) stocks for laboratory-based experiments. PeerJ 12:e18288 https://doi.org/10.7717/peerj.18288
date submitted: 2023-07-13
date accepted: 2024-09-20
issued: 2024-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bognár
  given name: András
author list: Agent
  family name: Borkhanuddin
  given name: Muhammad Hafiz
author list: Agent
  family name: Nagase
  given name: Shion
author list: Agent
  family name: Sellyei
  given name: Boglárka
doi: 10.7717/peerj.18288
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-14
copyright: ©2024 Bognár et al.
attribution name: Bognár et al.

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.

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