PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Studying turn performance, trunk control, and mobility in acute stroke subjects: a cross-sectional study
items: Phytochemical screening and in vitro antibacterial activity of Echinops kebericho Mesfin tuber extracts: experimental studies
items: https://peerj.com/articles/18618
items: Effect of mulching and organic manure on maize yield, water, and nitrogen use efficiency in the Loess Plateau of China
items: Investigation of the relationships between peri-implant diseases, periodontal diseases, and conditions: a cross-sectional study
items: Surgery-induced neuroinflammatory transcriptional programs in medial prefrontal cortex of mice during early phase of perioperative neurocognitive disorders
items: Comparative genomics analysis of the MYB gene family in barley: preliminary insights into evolution and biological function in Blue Qingke
items: Pelvic floor muscle training associated with the photobiomodulation therapy for women affected by the genitourinary syndrome of menopause: a study protocol
items: Impacts of abiotic factors and pesticide on the development, phenology, and reproductive biology of pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae)
items: A retrospective approach for evaluating ecological niche modeling transferability over time: the case of Mexican endemic rodents

Studying turn performance, trunk control, and mobility in acute stroke subjects: a cross-sectional study
type: item
type: AcademicArticle
description: Background Stroke leads to various impairments like motor deficits, impaired trunk control and restricted mobility. However, rehabilitation professionals often underestimate the fundamental function of turning, which is essential for daily living activities like walking, cooking, or performing household chores. Impaired turning can be attributed to motor deficits post-stroke, resulting in restricted mobility and impaired trunk movement. Therefore, the present study aimed to determine the relationship between turn performance, trunk control, and mobility in stroke patients. Materials and Methods A total of 63 first-time supratentorial stroke (i.e., anterior circulation stroke) patients aged 18–90 years were recruited for the study. Turn performance was assessed by asking patients to walk for 10 feet comfortably, then take a 180° turn and return to the starting position. In addition, the duration and number of steps were recorded. Following this, the Trunk Impairment Scale (TIS) and Stroke Rehabilitation Assessment of Movement (STREAM) were used to assess trunk impairment and mobility, respectively. The group turn performance was analyzed using the Kruskal–Wallis test with a post hoc Mann–Whitney U test for between-group comparisons. The turn duration and turn steps were correlated with age, trunk control, and mobility using Spearman’s rank correlation. A regression analysis was performed to determine the association of turn performance with age, trunk control, and mobility among stroke patients. Results Thirty stroke patients had turning difficulty, and 33 did not. Hence, they were categorized into the turning difficulty (TD) and non-turning difficulty (NTD) groups. When correlated with turn duration and the number of steps taken by the stroke patients while turning, the STREAM and TIS scores revealed a significant negative correlation (p < 0.001). The subjects’ age showed a significant positive correlation with the turn duration and number of steps taken by stroke p…
format: application/pdf
format: text/html
creator: Mahima Vasyani
creator: Akshatha Nayak
creator: K. Vijaya Kumar
creator: Zulkifli Misri
creator: Pema Choezom
creator: Rinita Mascarenhas
creator: Jaya Shanker Tedla
creator: Srikant Natarajan
subject: Neurology
subject: Healthcare Services
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.18501
publisher: PeerJ Inc.
rights: © 2024 Vasyani et al.
abstract: Background Stroke leads to various impairments like motor deficits, impaired trunk control and restricted mobility. However, rehabilitation professionals often underestimate the fundamental function of turning, which is essential for daily living activities like walking, cooking, or performing household chores. Impaired turning can be attributed to motor deficits post-stroke, resulting in restricted mobility and impaired trunk movement. Therefore, the present study aimed to determine the relationship between turn performance, trunk control, and mobility in stroke patients. Materials and Methods A total of 63 first-time supratentorial stroke (i.e., anterior circulation stroke) patients aged 18–90 years were recruited for the study. Turn performance was assessed by asking patients to walk for 10 feet comfortably, then take a 180° turn and return to the starting position. In addition, the duration and number of steps were recorded. Following this, the Trunk Impairment Scale (TIS) and Stroke Rehabilitation Assessment of Movement (STREAM) were used to assess trunk impairment and mobility, respectively. The group turn performance was analyzed using the Kruskal–Wallis test with a post hoc Mann–Whitney U test for between-group comparisons. The turn duration and turn steps were correlated with age, trunk control, and mobility using Spearman’s rank correlation. A regression analysis was performed to determine the association of turn performance with age, trunk control, and mobility among stroke patients. Results Thirty stroke patients had turning difficulty, and 33 did not. Hence, they were categorized into the turning difficulty (TD) and non-turning difficulty (NTD) groups. When correlated with turn duration and the number of steps taken by the stroke patients while turning, the STREAM and TIS scores revealed a significant negative correlation (p < 0.001). The subjects’ age showed a significant positive correlation with the turn duration and number of steps taken by stroke p…
bibliographic citation: Vasyani et al. (2024) Studying turn performance, trunk control, and mobility in acute stroke subjects: a cross-sectional study. PeerJ 12:e18501 https://doi.org/10.7717/peerj.18501
date submitted: 2024-05-24
date accepted: 2024-10-18
issued: 2024-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vasyani
  given name: Mahima
author list: Agent
  family name: Nayak
  given name: Akshatha
author list: Agent
  family name: Kumar
  given name: K. Vijaya
author list: Agent
  family name: Misri
  given name: Zulkifli
author list: Agent
  family name: Choezom
  given name: Pema
author list: Agent
  family name: Mascarenhas
  given name: Rinita
author list: Agent
  family name: Tedla
  given name: Jaya Shanker
author list: Agent
  family name: Natarajan
  given name: Srikant
doi: 10.7717/peerj.18501
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-03
copyright: © 2024 Vasyani et al.
attribution name: Vasyani et al.

Phytochemical screening and in vitro antibacterial activity of Echinops kebericho Mesfin tuber extracts: experimental studies
type: item
type: AcademicArticle
description: Background The application of plant extracts and their phytochemicals as potential treatments for bacterial illnesses has increased significantly in the last few decades. In Ethiopia, Echinops kebericho Mesfin is widely used to treat a range of illnesses in humans and animals. This study aimed to evaluate the antibacterial activity and phytochemical screening of Echinops kebericho Mesfin. Methods We carried out an in vitro experimental study after collecting the plants from their natural habitats. Then macerated in absolute methanol and petroleum ether solvents and concentrated the extracts using a rotary evaporator. In the experiment, we used Standard cultures of E. coli, K. pneumoniae, S. aureus, and P. aeruginosa. The agar-well diffusion method evaluated the antibacterial activity of the plants. The agar dilution method determined the minimum inhibitory concentration of the plant extract. Results The percentage yield of the plant extracts ranged from 6.25% to 7.85%. The methanol extract of Echinops kebericho Mesfin had the highest inhibitory effect on S. aureus (ATCC 25923) (16.67 ± 0.58 mm), followed by E. coli (ATCC 25922) (11.0 ± 1.73 mm). Phytochemical screening of leaves from the methanol and petroleum ether extracts of the plant revealed the presence of phytochemicals such as alkaloids, flavonoids, tannins, and cardiac glycosides. The present study revealed that the extracts of these plants have antibacterial activity. However, researchers should conduct further studies on the safety margin and quantitative bioactive isolation of selected medicinal plants.
format: application/pdf
format: text/html
creator: Jiregna Gari Negasa
creator: Ibsa Teshome
creator: Edilu Jorga Sarba
creator: Bekiyad Shasho Daro
subject: Microbiology
subject: Veterinary Medicine
subject: Pharmacology
description: doi:10.7717/peerj.18554
publisher: PeerJ Inc.
rights: © 2024 Negasa et al.
abstract: Background The application of plant extracts and their phytochemicals as potential treatments for bacterial illnesses has increased significantly in the last few decades. In Ethiopia, Echinops kebericho Mesfin is widely used to treat a range of illnesses in humans and animals. This study aimed to evaluate the antibacterial activity and phytochemical screening of Echinops kebericho Mesfin. Methods We carried out an in vitro experimental study after collecting the plants from their natural habitats. Then macerated in absolute methanol and petroleum ether solvents and concentrated the extracts using a rotary evaporator. In the experiment, we used Standard cultures of E. coli, K. pneumoniae, S. aureus, and P. aeruginosa. The agar-well diffusion method evaluated the antibacterial activity of the plants. The agar dilution method determined the minimum inhibitory concentration of the plant extract. Results The percentage yield of the plant extracts ranged from 6.25% to 7.85%. The methanol extract of Echinops kebericho Mesfin had the highest inhibitory effect on S. aureus (ATCC 25923) (16.67 ± 0.58 mm), followed by E. coli (ATCC 25922) (11.0 ± 1.73 mm). Phytochemical screening of leaves from the methanol and petroleum ether extracts of the plant revealed the presence of phytochemicals such as alkaloids, flavonoids, tannins, and cardiac glycosides. The present study revealed that the extracts of these plants have antibacterial activity. However, researchers should conduct further studies on the safety margin and quantitative bioactive isolation of selected medicinal plants.
bibliographic citation: Negasa et al. (2024) Phytochemical screening and in vitro antibacterial activity of Echinops kebericho Mesfin tuber extracts: experimental studies. PeerJ 12:e18554 https://doi.org/10.7717/peerj.18554
date submitted: 2024-01-24
date accepted: 2024-10-29
issued: 2024-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Negasa
  given name: Jiregna Gari
author list: Agent
  family name: Teshome
  given name: Ibsa
author list: Agent
  family name: Sarba
  given name: Edilu Jorga
author list: Agent
  family name: Daro
  given name: Bekiyad Shasho
doi: 10.7717/peerj.18554
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-03
copyright: ©2024 Negasa et al.
attribution name: Negasa et al.

https://peerj.com/articles/18618
type: item
type: AcademicArticle
title: Predicting epidermal growth factor receptor (EGFR) mutation status in non-small cell lung cancer (NSCLC) patients through logistic regression: a model incorporating clinical characteristics, computed tomography (CT) imaging features, and tumor marker levels
description: Background Approximately 60% of Asian populations with non-small cell lung cancer (NSCLC) harbor epidermal growth factor receptor (EGFR) gene mutations, marking it as a pivotal target for genotype-directed therapies. Currently, determining EGFR mutation status relies on DNA sequencing of histological or cytological specimens. This study presents a predictive model integrating clinical parameters, computed tomography (CT) characteristics, and serum tumor markers to forecast EGFR mutation status in NSCLC patients. Methods Retrospective data collection was conducted on NSCLC patients diagnosed between January 2018 and June 2019 at the First Affiliated Hospital of Zhengzhou University, with available molecular pathology results. Clinical information, CT imaging features, and serum tumor marker levels were compiled. Four distinct models were employed in constructing the diagnostic model. Model diagnostic efficacy was assessed through receiver operating characteristic (ROC) area under the curve (AUC) values and calibration curves. DeLong’s test was administered to validate model robustness. Results Our study encompassed 748 participants. Logistic regression modeling, trained with the aforementioned variables, demonstrated remarkable predictive capability, achieving an AUC of 0.805 (95% confidence interval (CI) [0.766–0.844]) in the primary cohort and 0.753 (95% CI [0.687–0.818]) in the validation cohort. Calibration plots suggested a favorable fit of the model to the data. Conclusions The developed logistic regression model emerges as a promising tool for forecasting EGFR mutation status. It holds potential to aid clinicians in more precisely identifying patients likely to benefit from EGFR molecular testing and facilitating targeted therapy decision-making, particularly in scenarios where molecular testing is impractical or inaccessible.
format: application/pdf
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creator: Jimin Hao
creator: Man Liu
creator: Zhigang Zhou
creator: Chunling Zhao
creator: Liping Dai
creator: Songyun Ouyang
subject: Cardiology
subject: Radiology and Medical Imaging
subject: Respiratory Medicine
description: doi:10.7717/peerj.18618
publisher: PeerJ Inc.
rights: © 2024 Hao et al.
abstract: Background Approximately 60% of Asian populations with non-small cell lung cancer (NSCLC) harbor epidermal growth factor receptor (EGFR) gene mutations, marking it as a pivotal target for genotype-directed therapies. Currently, determining EGFR mutation status relies on DNA sequencing of histological or cytological specimens. This study presents a predictive model integrating clinical parameters, computed tomography (CT) characteristics, and serum tumor markers to forecast EGFR mutation status in NSCLC patients. Methods Retrospective data collection was conducted on NSCLC patients diagnosed between January 2018 and June 2019 at the First Affiliated Hospital of Zhengzhou University, with available molecular pathology results. Clinical information, CT imaging features, and serum tumor marker levels were compiled. Four distinct models were employed in constructing the diagnostic model. Model diagnostic efficacy was assessed through receiver operating characteristic (ROC) area under the curve (AUC) values and calibration curves. DeLong’s test was administered to validate model robustness. Results Our study encompassed 748 participants. Logistic regression modeling, trained with the aforementioned variables, demonstrated remarkable predictive capability, achieving an AUC of 0.805 (95% confidence interval (CI) [0.766–0.844]) in the primary cohort and 0.753 (95% CI [0.687–0.818]) in the validation cohort. Calibration plots suggested a favorable fit of the model to the data. Conclusions The developed logistic regression model emerges as a promising tool for forecasting EGFR mutation status. It holds potential to aid clinicians in more precisely identifying patients likely to benefit from EGFR molecular testing and facilitating targeted therapy decision-making, particularly in scenarios where molecular testing is impractical or inaccessible.
bibliographic citation: Hao et al. (2024) Predicting epidermal growth factor receptor (EGFR) mutation status in non-small cell lung cancer (NSCLC) patients through logistic regression: a model incorporating clinical characteristics, computed tomography (CT) imaging features, and tumor marker levels. PeerJ 12:e18618 https://doi.org/10.7717/peerj.18618
date submitted: 2024-07-16
date accepted: 2024-11-09
issued: 2024-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Jimin
author list: Agent
  family name: Liu
  given name: Man
author list: Agent
  family name: Zhou
  given name: Zhigang
author list: Agent
  family name: Zhao
  given name: Chunling
author list: Agent
  family name: Dai
  given name: Liping
author list: Agent
  family name: Ouyang
  given name: Songyun
doi: 10.7717/peerj.18618
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-03
copyright: © 2024 Hao et al.
attribution name: Hao et al.

Effect of mulching and organic manure on maize yield, water, and nitrogen use efficiency in the Loess Plateau of China
type: item
type: AcademicArticle
description: Current agricultural practices prioritize intensive food production, often at the expense of environmental sustainability. This approach results in greenhouse gas emissions and groundwater pollution due to over-fertilization. In contrast, organic agriculture promotes a more efficient use of non-renewable energy, improves soil quality, and reduces ecological damage. However, the effects of mulching and organic manure on maize yield, water use efficiency (WUE), and nitrogen use efficiency (NUE) in China’s Loess Plateau have not been sufficiently researched. In 2017 and 2018, an experiment utilizing a randomized complete block design with two factors (two mulching levels × three organic nitrogen application rates) was conducted. The water content of the upper soil layer was found to be 12.6% to 19.4% higher than that of the subsoil layer. Across all soil depths and years, the soil nitrate-N content in mulched treatments was 10% to 31.8% greater than in non-mulched treatments with varying organic nitrogen rates. Additionally, mulching resulted in an increase in grain yield of 9.4% in 2017 and 8.9% in 2018 compared to non-mulched treatments. A significant interaction was observed between mulching and organic nitrogen application rate concerning WUE, alongside a negative correlation between WUE and NUE. These findings suggest that the application of 270 kg N ha−1 of sheep manure in conjunction with mulching is a highly recommended practice for the Loess Plateau, thereby supporting sustainable agricultural strategies.
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format: text/html
creator: Yingying Xing
creator: Jintao Fu
creator: Xiukang Wang
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.18644
publisher: PeerJ Inc.
rights: © 2024 Xing et al.
abstract: Current agricultural practices prioritize intensive food production, often at the expense of environmental sustainability. This approach results in greenhouse gas emissions and groundwater pollution due to over-fertilization. In contrast, organic agriculture promotes a more efficient use of non-renewable energy, improves soil quality, and reduces ecological damage. However, the effects of mulching and organic manure on maize yield, water use efficiency (WUE), and nitrogen use efficiency (NUE) in China’s Loess Plateau have not been sufficiently researched. In 2017 and 2018, an experiment utilizing a randomized complete block design with two factors (two mulching levels × three organic nitrogen application rates) was conducted. The water content of the upper soil layer was found to be 12.6% to 19.4% higher than that of the subsoil layer. Across all soil depths and years, the soil nitrate-N content in mulched treatments was 10% to 31.8% greater than in non-mulched treatments with varying organic nitrogen rates. Additionally, mulching resulted in an increase in grain yield of 9.4% in 2017 and 8.9% in 2018 compared to non-mulched treatments. A significant interaction was observed between mulching and organic nitrogen application rate concerning WUE, alongside a negative correlation between WUE and NUE. These findings suggest that the application of 270 kg N ha−1 of sheep manure in conjunction with mulching is a highly recommended practice for the Loess Plateau, thereby supporting sustainable agricultural strategies.
bibliographic citation: Xing et al. (2024) Effect of mulching and organic manure on maize yield, water, and nitrogen use efficiency in the Loess Plateau of China. PeerJ 12:e18644 https://doi.org/10.7717/peerj.18644
date submitted: 2024-05-22
date accepted: 2024-11-14
issued: 2024-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xing
  given name: Yingying
author list: Agent
  family name: Fu
  given name: Jintao
author list: Agent
  family name: Wang
  given name: Xiukang
doi: 10.7717/peerj.18644
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-03
copyright: © 2024 Xing et al.
attribution name: Xing et al.

Investigation of the relationships between peri-implant diseases, periodontal diseases, and conditions: a cross-sectional study
type: item
type: AcademicArticle
description: Introduction Peri-implant and periodontal conditions share common underlying factors, including risk factors, microbiology, immunology, and treatment approaches. Aims This study aims to investigate the potential co-occurrence of peri-implant and periodontal conditions. Design One hundred twenty-three implants were divided into three groups: peri-implantitis (41 implants), peri-implant mucositis (41 implants), and peri-implant health (41 implants). Peri-implant and periodontal statuses were assessed using the 2017 AAP/EFP World Workshop on Classification of Periodontal and Peri-implant Diseases and Conditions. All measurements were performed by a single clinician (T.Ş.). One-way analysis of variance was used to compare the study groups according to the data. An assessment was conducted regarding the coexistence of periodontal and peri-implant conditions. Results Patients with peri-implant mucositis predominantly had gingivitis, whereas those with peri-implant health exhibited periodontal health. In contrast, patients with peri-implantitis mostly had gingivitis, with a lower occurrence of periodontitis. A significant difference was observed between the peri-implant and periodontal groups (p = 0.003). Significant differences were observed between peri-implant and periodontal evaluations for plaque indices, gingival indices, probing depth, gingival recession, and clinical attachment level (p = 0.001), (p = 0.006). Conclusions The findings of this study underscore the intricate influence of implant treatment on periodontal health. This observation emphasizes the importance of elucidating the underlying factors to improve clinical management and outcomes in patients with periodontal and peri-implant diseases, highlighting the relevance and potential impact of this research in the field.
format: application/pdf
format: text/html
creator: Tuğba Şahin
subject: Dentistry
description: doi:10.7717/peerj.18663
publisher: PeerJ Inc.
rights: © 2024 Şahin
abstract: Introduction Peri-implant and periodontal conditions share common underlying factors, including risk factors, microbiology, immunology, and treatment approaches. Aims This study aims to investigate the potential co-occurrence of peri-implant and periodontal conditions. Design One hundred twenty-three implants were divided into three groups: peri-implantitis (41 implants), peri-implant mucositis (41 implants), and peri-implant health (41 implants). Peri-implant and periodontal statuses were assessed using the 2017 AAP/EFP World Workshop on Classification of Periodontal and Peri-implant Diseases and Conditions. All measurements were performed by a single clinician (T.Ş.). One-way analysis of variance was used to compare the study groups according to the data. An assessment was conducted regarding the coexistence of periodontal and peri-implant conditions. Results Patients with peri-implant mucositis predominantly had gingivitis, whereas those with peri-implant health exhibited periodontal health. In contrast, patients with peri-implantitis mostly had gingivitis, with a lower occurrence of periodontitis. A significant difference was observed between the peri-implant and periodontal groups (p = 0.003). Significant differences were observed between peri-implant and periodontal evaluations for plaque indices, gingival indices, probing depth, gingival recession, and clinical attachment level (p = 0.001), (p = 0.006). Conclusions The findings of this study underscore the intricate influence of implant treatment on periodontal health. This observation emphasizes the importance of elucidating the underlying factors to improve clinical management and outcomes in patients with periodontal and peri-implant diseases, highlighting the relevance and potential impact of this research in the field.
bibliographic citation: Şahin (2024) Investigation of the relationships between peri-implant diseases, periodontal diseases, and conditions: a cross-sectional study. PeerJ 12:e18663 https://doi.org/10.7717/peerj.18663
date submitted: 2024-09-18
date accepted: 2024-11-18
issued: 2024-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Şahin
  given name: Tuğba
doi: 10.7717/peerj.18663
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-03
copyright: © 2024 Şahin
attribution name: Şahin

Surgery-induced neuroinflammatory transcriptional programs in medial prefrontal cortex of mice during early phase of perioperative neurocognitive disorders
type: item
type: AcademicArticle
description: Patients receiving anesthesia and surgery may experience cognitive dysfunction, memory deficits, and mental disturbances, which are referred to as perioperative neurocognitive disorders (PND). The function of the medial prefrontal cortex (mPFC) is disrupted during early phase of PND. To gain insight into the mechanisms of PND, we collected mouse mPFC tissues 6 h post-surgery and performed RNA sequencing analysis. In total, 178 differentially expressed genes (DEGs) were identified, including 105 upregulated and 73 downregulated genes. Bioinformatic analysis highlighted the significant enrichment of these DEGs in several immune-related biological processes and signaling pathways, suggesting that pronounced neuroinflammatory transcriptional programming in the mPFC was evoked during early phase of PND. Interleukin-6 level increased in both serum and mPFC, while the mRNA levels of Il-6, Tnf-α, and Il-1β remained unchanged. Taken together, our findings suggest that a distinct and acute neuroinflammatory response in the mPFC is evoked after peripheral surgery, which might play a key role in the development of PND.
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creator: Xiaodong Tang
creator: Xuwu Xiang
creator: Yang Yu
creator: Shuyuan Huang
creator: Caifei Pan
creator: Shuyuan Gan
creator: Yongxing Yao
subject: Genomics
subject: Molecular Biology
subject: Neuroscience
subject: Cognitive Disorders
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.18664
publisher: PeerJ Inc.
rights: © 2024 Tang et al.
abstract: Patients receiving anesthesia and surgery may experience cognitive dysfunction, memory deficits, and mental disturbances, which are referred to as perioperative neurocognitive disorders (PND). The function of the medial prefrontal cortex (mPFC) is disrupted during early phase of PND. To gain insight into the mechanisms of PND, we collected mouse mPFC tissues 6 h post-surgery and performed RNA sequencing analysis. In total, 178 differentially expressed genes (DEGs) were identified, including 105 upregulated and 73 downregulated genes. Bioinformatic analysis highlighted the significant enrichment of these DEGs in several immune-related biological processes and signaling pathways, suggesting that pronounced neuroinflammatory transcriptional programming in the mPFC was evoked during early phase of PND. Interleukin-6 level increased in both serum and mPFC, while the mRNA levels of Il-6, Tnf-α, and Il-1β remained unchanged. Taken together, our findings suggest that a distinct and acute neuroinflammatory response in the mPFC is evoked after peripheral surgery, which might play a key role in the development of PND.
bibliographic citation: Tang et al. (2024) Surgery-induced neuroinflammatory transcriptional programs in medial prefrontal cortex of mice during early phase of perioperative neurocognitive disorders. PeerJ 12:e18664 https://doi.org/10.7717/peerj.18664
date submitted: 2024-09-20
date accepted: 2024-11-18
issued: 2024-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Tang
  given name: Xiaodong
author list: Agent
  family name: Xiang
  given name: Xuwu
author list: Agent
  family name: Yu
  given name: Yang
author list: Agent
  family name: Huang
  given name: Shuyuan
author list: Agent
  family name: Pan
  given name: Caifei
author list: Agent
  family name: Gan
  given name: Shuyuan
author list: Agent
  family name: Yao
  given name: Yongxing
doi: 10.7717/peerj.18664
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-03
copyright: © 2024 Tang et al.
attribution name: Tang et al.

Comparative genomics analysis of the MYB gene family in barley: preliminary insights into evolution and biological function in Blue Qingke
type: item
type: AcademicArticle
description: Background The Myeloblastosis related (MYB) family is one of the most widely distributed transcription factor families in plants and plays a significant role in plant growth and development, hormone signal transduction, and stress response. There are many reports on MYB family species, but the research on Qingke is still limited. Methods This study used comparative genomics methods to analyze gene and protein structure, protein physicochemical properties, chromosome localization, and evolution. A bioinformatics approach was used to systematically analyze the HvMYB gene family. At the milk stage, soft dough stage, and mature stage, White and Blue Qingke grains were selected for RNA sequencing (RNA-seq), among which two proteins interacted (HvMYB and HvMYC). The expression of this gene family was analyzed through RNA-seq, and the expression levels of HvMYB and HvMYC in the grains of two different color varieties were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, the interaction between HvMYB and HvMYC was verified by bimolecular fluorescence complementation (BiFC) experiments. Results A total of 92 Qingke HvMYB genes were identified and analyzed, and 92 HvMYB proteins were classified into five categories. Cis-acting elements associated with abscisic acid response, light response, and methyl jasmonate (MeJA) response were found in the promoter regions of most MYB genes. Using qRT-PCR combined with RNA-seq analysis showed that MYB gene was highly expressed in the soft dough stage and was varietal specific. Subcellular localization indicated that HvMYB was located in the nucleus and cell membrane, HvMYC was located in the nucleus, cell membrane, and cytoplasm. Through BiFC analysis, it has been proven that HvMYB in the MYB family and HvMYC in the basic helix–loop–helix (bHLH) family can interact. This study provides a preliminary theoretical basis for understanding the function and role of the Qingke MYB gene family and prov…
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creator: Hongyan Li
creator: Youhua Yao
creator: Xin Li
creator: Yongmei Cui
creator: Likun An
creator: Baojun Ding
creator: Xiaohua Yao
creator: Kunlun Wu
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.18443
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background The Myeloblastosis related (MYB) family is one of the most widely distributed transcription factor families in plants and plays a significant role in plant growth and development, hormone signal transduction, and stress response. There are many reports on MYB family species, but the research on Qingke is still limited. Methods This study used comparative genomics methods to analyze gene and protein structure, protein physicochemical properties, chromosome localization, and evolution. A bioinformatics approach was used to systematically analyze the HvMYB gene family. At the milk stage, soft dough stage, and mature stage, White and Blue Qingke grains were selected for RNA sequencing (RNA-seq), among which two proteins interacted (HvMYB and HvMYC). The expression of this gene family was analyzed through RNA-seq, and the expression levels of HvMYB and HvMYC in the grains of two different color varieties were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, the interaction between HvMYB and HvMYC was verified by bimolecular fluorescence complementation (BiFC) experiments. Results A total of 92 Qingke HvMYB genes were identified and analyzed, and 92 HvMYB proteins were classified into five categories. Cis-acting elements associated with abscisic acid response, light response, and methyl jasmonate (MeJA) response were found in the promoter regions of most MYB genes. Using qRT-PCR combined with RNA-seq analysis showed that MYB gene was highly expressed in the soft dough stage and was varietal specific. Subcellular localization indicated that HvMYB was located in the nucleus and cell membrane, HvMYC was located in the nucleus, cell membrane, and cytoplasm. Through BiFC analysis, it has been proven that HvMYB in the MYB family and HvMYC in the basic helix–loop–helix (bHLH) family can interact. This study provides a preliminary theoretical basis for understanding the function and role of the Qingke MYB gene family and prov…
bibliographic citation: Li et al. (2024) Comparative genomics analysis of the MYB gene family in barley: preliminary insights into evolution and biological function in Blue Qingke. PeerJ 12:e18443 https://doi.org/10.7717/peerj.18443
date submitted: 2024-07-11
date accepted: 2024-10-11
issued: 2024-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Hongyan
author list: Agent
  family name: Yao
  given name: Youhua
author list: Agent
  family name: Li
  given name: Xin
author list: Agent
  family name: Cui
  given name: Yongmei
author list: Agent
  family name: An
  given name: Likun
author list: Agent
  family name: Ding
  given name: Baojun
author list: Agent
  family name: Yao
  given name: Xiaohua
author list: Agent
  family name: Wu
  given name: Kunlun
doi: 10.7717/peerj.18443
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-02
copyright: © 2024 Li et al.
attribution name: Li et al.

Pelvic floor muscle training associated with the photobiomodulation therapy for women affected by the genitourinary syndrome of menopause: a study protocol
type: item
type: AcademicArticle
description: Background Frequently, the women affected by the genitourinary syndrome of menopause experience genitourinary dysfunctions that profoundly influence their overall health. Even though the symptoms do not jeopardize the women’s lives, the urinary and sexual dysfunctions significantly impact their quality of life. Isolated treatments focused on the main causes of the dysfunctions, such as pelvic floor muscle training (PFMT) and photobiomodulation have shown significant improvements in genitourinary dysfunctions. So, the association of PFMT with photobiomodulation may generate additional effects in the genitourinary area. This study aims to create a PFMT protocol isolated and associated with photobiomodulation therapy in women affected by the genitourinary syndrome of menopause. Methods It is a randomized, controlled, double-blind clinical trial protocol study that will include women experiencing genitourinary symptoms related to menopause, sexually active, never practiced pelvic floor muscle exercise or photobiomodulation treatment, and do not use hormone replacement therapy for at least 3 months. The randomization will allocate the women to three groups: PFMT group, PFMT associated with active intracavitary photobiomodulation group, and PFMT associated with sham intracavitary photobiomodulation group. A total of 16 sessions will be conducted twice a week. The assessments will occur before interventions, after the sixteenth session, and 1 month after the sixteenth session (follow-up). The evaluation will include the pelvic floor muscle vaginal manometry as the primary outcome. Also, the international consultation on incontinence questionnaire—short form, the female sexual function index, the Utian Quality of Life scale, the patient global impression of improvement, the modified Oxford scale, and the vaginal health index will be the secondary outcomes. Discussion Despite there are gold standard treatments such as PFMT, to alleviate genitourinary symptoms, interventions …
format: application/pdf
format: text/html
creator: Lívia Oliveira Bezerra
creator: Maria Letícia Araújo Silva de Carvalho
creator: Edson Silva-Filho
creator: Maria Clara Eugênia de Oliveira
creator: Palloma Rodrigues de Andrade
creator: Maria Thereza Albuquerque Barbosa Cabral Micussi
subject: Clinical Trials
subject: Gynecology and Obstetrics
subject: Urology
subject: Women’s Health
subject: Rehabilitation
description: doi:10.7717/peerj.17848
publisher: PeerJ Inc.
rights: © 2024 Oliveira Bezerra et al.
abstract: Background Frequently, the women affected by the genitourinary syndrome of menopause experience genitourinary dysfunctions that profoundly influence their overall health. Even though the symptoms do not jeopardize the women’s lives, the urinary and sexual dysfunctions significantly impact their quality of life. Isolated treatments focused on the main causes of the dysfunctions, such as pelvic floor muscle training (PFMT) and photobiomodulation have shown significant improvements in genitourinary dysfunctions. So, the association of PFMT with photobiomodulation may generate additional effects in the genitourinary area. This study aims to create a PFMT protocol isolated and associated with photobiomodulation therapy in women affected by the genitourinary syndrome of menopause. Methods It is a randomized, controlled, double-blind clinical trial protocol study that will include women experiencing genitourinary symptoms related to menopause, sexually active, never practiced pelvic floor muscle exercise or photobiomodulation treatment, and do not use hormone replacement therapy for at least 3 months. The randomization will allocate the women to three groups: PFMT group, PFMT associated with active intracavitary photobiomodulation group, and PFMT associated with sham intracavitary photobiomodulation group. A total of 16 sessions will be conducted twice a week. The assessments will occur before interventions, after the sixteenth session, and 1 month after the sixteenth session (follow-up). The evaluation will include the pelvic floor muscle vaginal manometry as the primary outcome. Also, the international consultation on incontinence questionnaire—short form, the female sexual function index, the Utian Quality of Life scale, the patient global impression of improvement, the modified Oxford scale, and the vaginal health index will be the secondary outcomes. Discussion Despite there are gold standard treatments such as PFMT, to alleviate genitourinary symptoms, interventions …
bibliographic citation: Oliveira Bezerra et al. (2024) Pelvic floor muscle training associated with the photobiomodulation therapy for women affected by the genitourinary syndrome of menopause: a study protocol. PeerJ 12:e17848 https://doi.org/10.7717/peerj.17848
date submitted: 2024-01-19
date accepted: 2024-07-10
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliveira Bezerra
  given name: Lívia
author list: Agent
  family name: de Carvalho
  given name: Maria Letícia Araújo Silva
author list: Agent
  family name: Silva-Filho
  given name: Edson
author list: Agent
  family name: Clara Eugênia de Oliveira
  given name: Maria
author list: Agent
  family name: de Andrade
  given name: Palloma Rodrigues
author list: Agent
  family name: Micussi
  given name: Maria Thereza Albuquerque Barbosa Cabral
doi: 10.7717/peerj.17848
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Oliveira Bezerra et al.
attribution name: Oliveira Bezerra et al.

Impacts of abiotic factors and pesticide on the development, phenology, and reproductive biology of pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae)
type: item
type: AcademicArticle
description: The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) is a serious insect pest of cotton crop. The studies to evaluate the impact of abiotic factors on cotton pests’ biology are limited. The current study was undertaken to determine the impact of abiotic factors (temperature, humidity, photoperiod) and an insecticide (lambda-cyhalothrin) on the biological aspects of P. gossypiella. The results revealed that all the treatments showed a significant impact on different life parameters of P. gossypiella. The temperature exposure at 27 °C revealed a total life span of about 33 days. Maximum mortality for larvae (51.11%), pupae (59.04%) and adults (61.92%) were recorded at 33 °C exposure. Both low and high humidity levels caused negative impacts on life parameters of P. gossypiella. The life span was completed in about 30 days at 60% relative humidity (RH). Maximum mortality for larvae (75.00%) and pupae (49.59%) were recorded at 80% RH level exposure, while adult mortality was maximum (63.09%) at 40% RH level followed by 80% RH level (55.52%). The P. gossypiella exhibited a life span of about 32 days at 14:10 light-dark period. The larval mortality was maximum (14.83%) at 12:12 light-dark period while pupal (47.36%) and adult (48.84%) mortality was maximum at 16:08 light-dark period. Lambdacyhalothrin (LC) showed dose dependent negative impacts on biological aspects of P. gossypiella. The P. gossypiella exhibited a life span of about 26 days at 0.5 ppm LC concentration. The P. gossypiella exposure to highest concentration (LC) revealed maximum mortality of larval (80.22%), pupal (64.63%) and adult (70.74%) stages. Conclusively, the best suited abiotic factor ranges were 27 °C (temperature), 60% (RH) and 14:10 (light-dark) which can be used for successful rearing and bioassay activities of P. gossypiella.
format: application/pdf
format: text/html
creator: Muhammad Jalal Arif
creator: Ahmad Nawaz
creator: Muhammad Sufyan
creator: Muhammad Dildar Gogi
creator: Zain UlAbdin
creator: Muhammad Tayyib
creator: Abid Ali
creator: Waqar Majeed
creator: Manel Ben Ali
creator: Amor Hedfi
subject: Agricultural Science
subject: Entomology
subject: Toxicology
subject: Zoology
description: doi:10.7717/peerj.18399
publisher: PeerJ Inc.
rights: © 2024 Arif et al.
abstract: The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) is a serious insect pest of cotton crop. The studies to evaluate the impact of abiotic factors on cotton pests’ biology are limited. The current study was undertaken to determine the impact of abiotic factors (temperature, humidity, photoperiod) and an insecticide (lambda-cyhalothrin) on the biological aspects of P. gossypiella. The results revealed that all the treatments showed a significant impact on different life parameters of P. gossypiella. The temperature exposure at 27 °C revealed a total life span of about 33 days. Maximum mortality for larvae (51.11%), pupae (59.04%) and adults (61.92%) were recorded at 33 °C exposure. Both low and high humidity levels caused negative impacts on life parameters of P. gossypiella. The life span was completed in about 30 days at 60% relative humidity (RH). Maximum mortality for larvae (75.00%) and pupae (49.59%) were recorded at 80% RH level exposure, while adult mortality was maximum (63.09%) at 40% RH level followed by 80% RH level (55.52%). The P. gossypiella exhibited a life span of about 32 days at 14:10 light-dark period. The larval mortality was maximum (14.83%) at 12:12 light-dark period while pupal (47.36%) and adult (48.84%) mortality was maximum at 16:08 light-dark period. Lambdacyhalothrin (LC) showed dose dependent negative impacts on biological aspects of P. gossypiella. The P. gossypiella exhibited a life span of about 26 days at 0.5 ppm LC concentration. The P. gossypiella exposure to highest concentration (LC) revealed maximum mortality of larval (80.22%), pupal (64.63%) and adult (70.74%) stages. Conclusively, the best suited abiotic factor ranges were 27 °C (temperature), 60% (RH) and 14:10 (light-dark) which can be used for successful rearing and bioassay activities of P. gossypiella.
bibliographic citation: Arif et al. (2024) Impacts of abiotic factors and pesticide on the development, phenology, and reproductive biology of pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae). PeerJ 12:e18399 https://doi.org/10.7717/peerj.18399
date submitted: 2024-06-25
date accepted: 2024-10-04
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arif
  given name: Muhammad Jalal
author list: Agent
  family name: Nawaz
  given name: Ahmad
author list: Agent
  family name: Sufyan
  given name: Muhammad
author list: Agent
  family name: Gogi
  given name: Muhammad Dildar
author list: Agent
  family name: UlAbdin
  given name: Zain
author list: Agent
  family name: Tayyib
  given name: Muhammad
author list: Agent
  family name: Ali
  given name: Abid
author list: Agent
  family name: Majeed
  given name: Waqar
author list: Agent
  family name: Ali
  given name: Manel Ben
author list: Agent
  family name: Hedfi
  given name: Amor
doi: 10.7717/peerj.18399
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Arif et al.
attribution name: Arif et al.

A retrospective approach for evaluating ecological niche modeling transferability over time: the case of Mexican endemic rodents
type: item
type: AcademicArticle
description: Ecological niche modeling (ENM) is a valuable tool for inferring suitable environmental conditions and estimating species’ geographic distributions. ENM is widely used to assess the potential effects of climate change on species distributions; however, the choice of modeling algorithm introduces substantial uncertainty, especially since future projections cannot be properly validated. In this study, we evaluated the performance of seven popular modeling algorithms—Bioclim, generalized additive models (GAM), generalized linear models (GLM), boosted regression trees (BRT), Maxent, random forest (RF), and support vector machine (SVM)—in transferring ENM across time, using Mexican endemic rodents as a model system. We used a retrospective approach, transferring models from the near past (1950–1979) to more recent conditions (1980–2009) and vice versa, to evaluate their performance in both forecasting and hindcasting. Consistent with previous studies, our results highlight that input data quality and algorithm choice significantly impact model accuracy, but most importantly, we found that algorithm performance varied between forecasting and hindcasting. While no single algorithm outperformed the others in both temporal directions, RF generally showed better performance for forecasting, while Maxent performed better in hindcasting, though it was more sensitive to small sample sizes. Bioclim consistently showed the lowest performance. These findings underscore that not all species or algorithms are suited for temporal projections. Therefore, we strongly recommend conducting a thorough evaluation of the data quality—in terms of quantity and potential biases—of the species of interest. Based on this assessment, appropriate algorithm(s) should be carefully selected and rigorously tested before proceeding with temporal transfers.
format: application/pdf
format: text/html
creator: Claudia N. Moreno-Arzate
creator: Enrique Martínez-Meyer
subject: Biodiversity
subject: Biogeography
subject: Bioinformatics
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.18414
publisher: PeerJ Inc.
rights: © 2024 Moreno-Arzate and Martínez-Meyer
abstract: Ecological niche modeling (ENM) is a valuable tool for inferring suitable environmental conditions and estimating species’ geographic distributions. ENM is widely used to assess the potential effects of climate change on species distributions; however, the choice of modeling algorithm introduces substantial uncertainty, especially since future projections cannot be properly validated. In this study, we evaluated the performance of seven popular modeling algorithms—Bioclim, generalized additive models (GAM), generalized linear models (GLM), boosted regression trees (BRT), Maxent, random forest (RF), and support vector machine (SVM)—in transferring ENM across time, using Mexican endemic rodents as a model system. We used a retrospective approach, transferring models from the near past (1950–1979) to more recent conditions (1980–2009) and vice versa, to evaluate their performance in both forecasting and hindcasting. Consistent with previous studies, our results highlight that input data quality and algorithm choice significantly impact model accuracy, but most importantly, we found that algorithm performance varied between forecasting and hindcasting. While no single algorithm outperformed the others in both temporal directions, RF generally showed better performance for forecasting, while Maxent performed better in hindcasting, though it was more sensitive to small sample sizes. Bioclim consistently showed the lowest performance. These findings underscore that not all species or algorithms are suited for temporal projections. Therefore, we strongly recommend conducting a thorough evaluation of the data quality—in terms of quantity and potential biases—of the species of interest. Based on this assessment, appropriate algorithm(s) should be carefully selected and rigorously tested before proceeding with temporal transfers.
bibliographic citation: Moreno-Arzate et al. (2024) A retrospective approach for evaluating ecological niche modeling transferability over time: the case of Mexican endemic rodents. PeerJ 12:e18414 https://doi.org/10.7717/peerj.18414
date submitted: 2024-04-28
date accepted: 2024-10-07
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreno-Arzate
  given name: Claudia N.
author list: Agent
  family name: Martínez-Meyer
  given name: Enrique
doi: 10.7717/peerj.18414
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Moreno-Arzate and Martínez-Meyer
attribution name: Moreno-Arzate and Martínez-Meyer

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