PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Phytotoxic effects of Acacia saligna dry leachates on germination, seedling growth, photosynthetic performance, and gene expression of economically important crops
items: Effectiveness of physical activity on immunity markers and quality of life in cancer patient: a systematic review
items: Prevalence of sarcopenia was higher in women than in men: a cross-sectional study from a rural area in eastern China
items: Differential gene expression analysis after DAPK1 knockout in hepatocellular carcinoma cells
items: Ray-finned fishes (Actinopterygii) from the Upper Jurassic (Oxfordian) of the Atacama Desert, Northern Chile
items: https://peerj.com/articles/13762
items: Digital technology for orthognathic surgery training promotion: a randomized comparative study
items: Hydrological and lock operation conditions associated with paddlefish and bigheaded carp dam passage on a large and small scale in the Upper Mississippi River (Pools 14–18)
items: Advanced oxidation protein products induce annulus fibrosus cell senescence through a NOX4-dependent, MAPK-mediated pathway and accelerate intervertebral disc degeneration
items: Comparative transcriptome analysis of Lupinus polyphyllus Lindl. provides a rich molecular resource for research on coloration mechanism

Phytotoxic effects of Acacia saligna dry leachates on germination, seedling growth, photosynthetic performance, and gene expression of economically important crops
type: item
type: AcademicArticle
description: The influence of dry leachates of Acasia saligna was tested on the seedling growth, photosynthesis, biochemical attributes, and gene expression of the economically important crops, including wheat (Triticum aestivum L.), radish (Raphanus sativus L.), barley (Hordeum vulgare L.) and arugula (Eruca sativa L.). Different concentrations (5%, 10%, 15%, 20%, and 25%) of stem extract (SE) and leaf extract (LE) of A. saligna were prepared, and seedlings were allowed to grow in Petri plates for 8 days. The results showed that all plant species exhibited reduced germination rate, plant height, and fresh and dry weight due to leachates extracts of A. saligna. Moreover, the activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX), exhibited differential regulation due to the extract treatment. The SOD was increased with increasing the concentration of extracts, while CAT and APX activities were decreased with increasing the extract concentrations. In addition, leachate extract treatment decrease chlorophyll content, photosynthesis, PSII activity, and water use efficiency, with evident effects at their higher concentrations. Furthermore, the content of proline, sugars, protein, total phenols, and flavonoids were reduced considerably due to leachates extract treatments. Furthermore, seedlings treated with high concentrations of LE increased the expression of genes. The present results lead to the conclusion that A. saligna contains significant allelochemicals that interfere with the growth and development of the tested crop species and reduced the crops biomass and negatively affected other related parameters. However, further studies are suggested to determine the isolation and purification of the active compounds present in A. saligna extracts.
format: application/pdf
format: text/html
creator: Haifa Abdulaziz Sakit ALHaithloul
creator: Muhammad Ishfaq Khan
creator: Arafa Musa
creator: Mohammed M. Ghoneim
creator: Ayshah Aysh ALrashidi
creator: Imtiaz Khan
creator: Ehab Azab
creator: Adil A. Gobouri
creator: Mahmoud R. Sofy
creator: Mohamed El-Sherbiny
creator: Mona H. Soliman
subject: Agricultural Science
subject: Biochemistry
subject: Biodiversity
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13623
publisher: PeerJ Inc.
rights: © 2022 S. Alhaithloul et al.
abstract: The influence of dry leachates of Acasia saligna was tested on the seedling growth, photosynthesis, biochemical attributes, and gene expression of the economically important crops, including wheat (Triticum aestivum L.), radish (Raphanus sativus L.), barley (Hordeum vulgare L.) and arugula (Eruca sativa L.). Different concentrations (5%, 10%, 15%, 20%, and 25%) of stem extract (SE) and leaf extract (LE) of A. saligna were prepared, and seedlings were allowed to grow in Petri plates for 8 days. The results showed that all plant species exhibited reduced germination rate, plant height, and fresh and dry weight due to leachates extracts of A. saligna. Moreover, the activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX), exhibited differential regulation due to the extract treatment. The SOD was increased with increasing the concentration of extracts, while CAT and APX activities were decreased with increasing the extract concentrations. In addition, leachate extract treatment decrease chlorophyll content, photosynthesis, PSII activity, and water use efficiency, with evident effects at their higher concentrations. Furthermore, the content of proline, sugars, protein, total phenols, and flavonoids were reduced considerably due to leachates extract treatments. Furthermore, seedlings treated with high concentrations of LE increased the expression of genes. The present results lead to the conclusion that A. saligna contains significant allelochemicals that interfere with the growth and development of the tested crop species and reduced the crops biomass and negatively affected other related parameters. However, further studies are suggested to determine the isolation and purification of the active compounds present in A. saligna extracts.
bibliographic citation: Sakit ALHaithloul et al. (2022) Phytotoxic effects of Acacia saligna dry leachates on germination, seedling growth, photosynthetic performance, and gene expression of economically important crops. PeerJ 10:e13623 https://doi.org/10.7717/peerj.13623
date submitted: 2021-11-16
date accepted: 2022-06-02
issued: 2022-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sakit ALHaithloul
  given name: Haifa Abdulaziz
author list: Agent
  family name: Khan
  given name: Muhammad Ishfaq
author list: Agent
  family name: Musa
  given name: Arafa
author list: Agent
  family name: Ghoneim
  given name: Mohammed M.
author list: Agent
  family name: Aysh ALrashidi
  given name: Ayshah
author list: Agent
  family name: Khan
  given name: Imtiaz
author list: Agent
  family name: Azab
  given name: Ehab
author list: Agent
  family name: Gobouri
  given name: Adil A.
author list: Agent
  family name: Sofy
  given name: Mahmoud R.
author list: Agent
  family name: El-Sherbiny
  given name: Mohamed
author list: Agent
  family name: Soliman
  given name: Mona H.
doi: 10.7717/peerj.13623
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-02
copyright: © 2022 ALHaithloul et al.
attribution name: S. Alhaithloul et al.

Effectiveness of physical activity on immunity markers and quality of life in cancer patient: a systematic review
type: item
type: AcademicArticle
description: Background Cancer is a huge group of diseases that can affect various body parts of humans but also has a psychological, societal, and economic impact. Physical activity can improve the quality of life (QOL) and immunity, while moderate intensity exercise can reduce the probability of this lethal disease. The current study aimed to determine the effect of physical activity on immune markers and QOL in cancer patients as well as to evaluate cancer-related fatigue (CRF) and its association with physical activity. Methodology Before starting the study, the study protocol was registered in PROSPERO (registration number CRD42021273292). An electronic literature search was performed by combining MeSH terminology and keywords used with the Boolean operators “OR” and “AND” to find relevant published studies on PubMed, Scopus, Cochrane, and ScienceDirect databases. The Joanna Briggs Institute (JBI) critical evaluation checklist was used to assess the quality of selected studies, while the GRADE approach was used to see the quality of evidence. Results A total of 13,931 studies were retrieved after the search on databases. After the scrutiny of studies by reading the title of articles and the inclusion/exclusion criteria, a total of 54 studies were selected for further screening by reading the full texts. In the final, a total of nine studies were selected for the current systematic review and proceeded for data extraction. The patients who were doing different exercises showed improvements in immunity, QOL, and reduction in CRF. A significant reduction in tumour necrosis factor-α (TNF-α), C reactive protein (CRP), interleukin-8 (IL-8), IL-6, and an increase in natural killer (NK) cells levels was also observed. Conclusions The exercise program is safe and beneficial to improve the quality of life and immunity markers before, during, and after cancer treatment. Physical exercise may also help patients to overcome the adverse effects of the treatment and to reduce the chance o…
format: application/pdf
format: text/html
creator: Sameer Badri AL-Mhanna
creator: Wan Syaheedah Wan Ghazali
creator: Mahaneem Mohamed
creator: Ali A. Rabaan
creator: Eman Y. Santali
creator: Jeehan H. Alestad
creator: Enas Y. Santali
creator: Sohaib Arshad
creator: Naveed Ahmed
creator: Hafeez Abiola Afolabi
subject: Kinesiology
subject: Healthcare Services
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.13664
publisher: PeerJ Inc.
rights: © 2022 AL-Mhanna et al.
abstract: Background Cancer is a huge group of diseases that can affect various body parts of humans but also has a psychological, societal, and economic impact. Physical activity can improve the quality of life (QOL) and immunity, while moderate intensity exercise can reduce the probability of this lethal disease. The current study aimed to determine the effect of physical activity on immune markers and QOL in cancer patients as well as to evaluate cancer-related fatigue (CRF) and its association with physical activity. Methodology Before starting the study, the study protocol was registered in PROSPERO (registration number CRD42021273292). An electronic literature search was performed by combining MeSH terminology and keywords used with the Boolean operators “OR” and “AND” to find relevant published studies on PubMed, Scopus, Cochrane, and ScienceDirect databases. The Joanna Briggs Institute (JBI) critical evaluation checklist was used to assess the quality of selected studies, while the GRADE approach was used to see the quality of evidence. Results A total of 13,931 studies were retrieved after the search on databases. After the scrutiny of studies by reading the title of articles and the inclusion/exclusion criteria, a total of 54 studies were selected for further screening by reading the full texts. In the final, a total of nine studies were selected for the current systematic review and proceeded for data extraction. The patients who were doing different exercises showed improvements in immunity, QOL, and reduction in CRF. A significant reduction in tumour necrosis factor-α (TNF-α), C reactive protein (CRP), interleukin-8 (IL-8), IL-6, and an increase in natural killer (NK) cells levels was also observed. Conclusions The exercise program is safe and beneficial to improve the quality of life and immunity markers before, during, and after cancer treatment. Physical exercise may also help patients to overcome the adverse effects of the treatment and to reduce the chance o…
bibliographic citation: AL-Mhanna et al. (2022) Effectiveness of physical activity on immunity markers and quality of life in cancer patient: a systematic review. PeerJ 10:e13664 https://doi.org/10.7717/peerj.13664
date submitted: 2021-12-28
date accepted: 2022-06-10
issued: 2022-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: AL-Mhanna
  given name: Sameer Badri
author list: Agent
  family name: Wan Ghazali
  given name: Wan Syaheedah
author list: Agent
  family name: Mohamed
  given name: Mahaneem
author list: Agent
  family name: Rabaan
  given name: Ali A.
author list: Agent
  family name: Santali
  given name: Eman Y.
author list: Agent
  family name: H. Alestad
  given name: Jeehan
author list: Agent
  family name: Santali
  given name: Enas Y.
author list: Agent
  family name: Arshad
  given name: Sohaib
author list: Agent
  family name: Ahmed
  given name: Naveed
author list: Agent
  family name: Afolabi
  given name: Hafeez Abiola
doi: 10.7717/peerj.13664
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-02
copyright: ©2022 AL-Mhanna et al.
attribution name: AL-Mhanna et al.

Prevalence of sarcopenia was higher in women than in men: a cross-sectional study from a rural area in eastern China
type: item
type: AcademicArticle
description: Background There were limited studies specifically evaluating whether the difference of the prevalence of sarcopenia exists in men and women in older adults from rural areas in China. The aim of this study was to compare the prevalence of sarcopenia between men and women in a rural area in eastern China and to explore the underlying causes. Methods This study included 1,105 participants aged 60-89 years. Muscle mass was measured by bio-electrical impedance analysis. Hand grip strength was measured by Jamar Hydraulic Hand Dynamometer. Sarcopenia was diagnosed according to the Asian Working Group for Sarcopenia-2019 Consensus. Data were analyzed using log-binomial and linear regression. Results The prevalence of sarcopenia was 21.7% in women and 12.9% in men among the study cohort. After adjusting for age, education level, number of diseases, income level, smoking, drinking, and eating habits, proportion of people with sarcopenia was 1.49-fold greater in women than in men (PR = 1.49, 95% CI [1.01–2.26], P = 0.055). Conclusions The prevalence of sarcopenia in elderly women in this rural area of eastern China is higher than in men, suggesting that women in rural areas in China seem to be more vulnerable for sarcopenia, thus early screening and prevention need to be provided for them to address such gender disparity in health.
format: application/pdf
format: text/html
creator: Yichen Yang
creator: Qin Zhang
creator: Caihong He
creator: Jing Chen
creator: Danfeng Deng
creator: Wenwen Lu
creator: Yuming Wang
subject: Epidemiology
subject: Geriatrics
subject: Kinesiology
subject: Orthopedics
subject: Women’s Health
description: doi:10.7717/peerj.13678
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Background There were limited studies specifically evaluating whether the difference of the prevalence of sarcopenia exists in men and women in older adults from rural areas in China. The aim of this study was to compare the prevalence of sarcopenia between men and women in a rural area in eastern China and to explore the underlying causes. Methods This study included 1,105 participants aged 60-89 years. Muscle mass was measured by bio-electrical impedance analysis. Hand grip strength was measured by Jamar Hydraulic Hand Dynamometer. Sarcopenia was diagnosed according to the Asian Working Group for Sarcopenia-2019 Consensus. Data were analyzed using log-binomial and linear regression. Results The prevalence of sarcopenia was 21.7% in women and 12.9% in men among the study cohort. After adjusting for age, education level, number of diseases, income level, smoking, drinking, and eating habits, proportion of people with sarcopenia was 1.49-fold greater in women than in men (PR = 1.49, 95% CI [1.01–2.26], P = 0.055). Conclusions The prevalence of sarcopenia in elderly women in this rural area of eastern China is higher than in men, suggesting that women in rural areas in China seem to be more vulnerable for sarcopenia, thus early screening and prevention need to be provided for them to address such gender disparity in health.
bibliographic citation: Yang et al. (2022) Prevalence of sarcopenia was higher in women than in men: a cross-sectional study from a rural area in eastern China. PeerJ 10:e13678 https://doi.org/10.7717/peerj.13678
date submitted: 2022-03-11
date accepted: 2022-06-13
issued: 2022-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yichen
author list: Agent
  family name: Zhang
  given name: Qin
author list: Agent
  family name: He
  given name: Caihong
author list: Agent
  family name: Chen
  given name: Jing
author list: Agent
  family name: Deng
  given name: Danfeng
author list: Agent
  family name: Lu
  given name: Wenwen
author list: Agent
  family name: Wang
  given name: Yuming
doi: 10.7717/peerj.13678
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-02
copyright: ©2022 Yang et al.
attribution name: Yang et al.

Differential gene expression analysis after DAPK1 knockout in hepatocellular carcinoma cells
type: item
type: AcademicArticle
description: Background The mechanism through which death-associated protein kinase 1 (DAPK1) causes hepatocellular carcinoma (HCC) progression remains unclear. In this study, we aimed to identify key proteins that were altered after DAPK1 knockout. Methods Stable DAPK1 knockout HCC cell lines were established, then the differentially expressed genes (DEGs) of HCC were screened using the NetworkAnalyst database and enriched using the Metascape software. Protein-protein interaction networks (PPIs) were analyzed and visualized using the STRING database expansion. Results In total, 732 differentially expressed genes were identified, including 415 upregulated genes and 317 downregulated genes. Through Cytoscape software scoring, 10 pivotal genes were found to be closely related to changes in DAPK1 expression; Kininogen-1 (KNG1), Complement C3 (C3), Metalloproteinase inhibitor 1 (TIMP1), and Alpha-2-HS-glycoprotein (AHSG) were the most strongly associated with DAPK1 expression changes. Moreover, western blot analysis results revealed that changes in the levels of proteins encoded by the four key genes after DAPK1 knockout were consistent with those seen in the database screening. Conclusions These results provide a direction for further studies on the DAPK1 gene and on the mechanism through which DAPK1 leads to hepatocellular carcinoma development.
format: application/pdf
format: text/html
creator: Yuanqi Li
creator: Hui Huang
creator: Huajun Yu
creator: Ting Mo
creator: Ting Wei
creator: Guodan Li
creator: Yufang Jia
creator: Xiaoqin Huang
creator: Mingjin Tu
creator: Xiuwen Yan
creator: Haitao Zhang
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13711
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background The mechanism through which death-associated protein kinase 1 (DAPK1) causes hepatocellular carcinoma (HCC) progression remains unclear. In this study, we aimed to identify key proteins that were altered after DAPK1 knockout. Methods Stable DAPK1 knockout HCC cell lines were established, then the differentially expressed genes (DEGs) of HCC were screened using the NetworkAnalyst database and enriched using the Metascape software. Protein-protein interaction networks (PPIs) were analyzed and visualized using the STRING database expansion. Results In total, 732 differentially expressed genes were identified, including 415 upregulated genes and 317 downregulated genes. Through Cytoscape software scoring, 10 pivotal genes were found to be closely related to changes in DAPK1 expression; Kininogen-1 (KNG1), Complement C3 (C3), Metalloproteinase inhibitor 1 (TIMP1), and Alpha-2-HS-glycoprotein (AHSG) were the most strongly associated with DAPK1 expression changes. Moreover, western blot analysis results revealed that changes in the levels of proteins encoded by the four key genes after DAPK1 knockout were consistent with those seen in the database screening. Conclusions These results provide a direction for further studies on the DAPK1 gene and on the mechanism through which DAPK1 leads to hepatocellular carcinoma development.
bibliographic citation: Li et al. (2022) Differential gene expression analysis after DAPK1 knockout in hepatocellular carcinoma cells. PeerJ 10:e13711 https://doi.org/10.7717/peerj.13711
date submitted: 2022-01-27
date accepted: 2022-06-20
issued: 2022-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yuanqi
author list: Agent
  family name: Huang
  given name: Hui
author list: Agent
  family name: Yu
  given name: Huajun
author list: Agent
  family name: Mo
  given name: Ting
author list: Agent
  family name: Wei
  given name: Ting
author list: Agent
  family name: Li
  given name: Guodan
author list: Agent
  family name: Jia
  given name: Yufang
author list: Agent
  family name: Huang
  given name: Xiaoqin
author list: Agent
  family name: Tu
  given name: Mingjin
author list: Agent
  family name: Yan
  given name: Xiuwen
author list: Agent
  family name: Zhang
  given name: Haitao
doi: 10.7717/peerj.13711
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-02
copyright: ©2022 Li et al.
attribution name: Li et al.

Ray-finned fishes (Actinopterygii) from the Upper Jurassic (Oxfordian) of the Atacama Desert, Northern Chile
type: item
type: AcademicArticle
description: This contribution presents novel records of ray-finned fishes from the Oxfordian of Cerritos Bayos, northern Chile. This includes a Pachycormiformes diversity represented by macropredatory forms (aff. Hypsocormus sp. and a still indeterminate form) and by suspension-feeding forms (Leedsichthys sp). The assemblage also includes the first Upper Jurassic local record of a Lepisosteidae, the latter being the oldest known to date in Gondwana. This diversity is complemented by new material of the lepidotid genus Scheenstia. The ray-finned fish assemblage from the Oxfordian of Cerritos Bayos is dominated by Lepisosteiformes and Pachycormiformes, complementing previous local coeval records from El Profeta Formation (ca. 250 km south from the localities here studied), mostly comprised by small Teleostei (e.g., Protoclupea chilensis, Varasichthys ariasi, Chongichthys dentatus, among others), indeterminate Pachycormiformes and Pycnodontiformes (Gyrodus sp.). The new records extend the known actinopterygian diversity from the Upper Jurassic of southeastern Panthalassa.
format: application/pdf
format: text/html
creator: Rodrigo A. Otero
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13739
publisher: PeerJ Inc.
rights: © 2022 Otero
abstract: This contribution presents novel records of ray-finned fishes from the Oxfordian of Cerritos Bayos, northern Chile. This includes a Pachycormiformes diversity represented by macropredatory forms (aff. Hypsocormus sp. and a still indeterminate form) and by suspension-feeding forms (Leedsichthys sp). The assemblage also includes the first Upper Jurassic local record of a Lepisosteidae, the latter being the oldest known to date in Gondwana. This diversity is complemented by new material of the lepidotid genus Scheenstia. The ray-finned fish assemblage from the Oxfordian of Cerritos Bayos is dominated by Lepisosteiformes and Pachycormiformes, complementing previous local coeval records from El Profeta Formation (ca. 250 km south from the localities here studied), mostly comprised by small Teleostei (e.g., Protoclupea chilensis, Varasichthys ariasi, Chongichthys dentatus, among others), indeterminate Pachycormiformes and Pycnodontiformes (Gyrodus sp.). The new records extend the known actinopterygian diversity from the Upper Jurassic of southeastern Panthalassa.
bibliographic citation: Otero (2022) Ray-finned fishes (Actinopterygii) from the Upper Jurassic (Oxfordian) of the Atacama Desert, Northern Chile. PeerJ 10:e13739 https://doi.org/10.7717/peerj.13739
date submitted: 2021-11-19
date accepted: 2022-06-25
issued: 2022-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Otero
  given name: Rodrigo A.
doi: 10.7717/peerj.13739
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-02
copyright: © 2022 Otero
attribution name: Otero

https://peerj.com/articles/13762
type: item
type: AcademicArticle
title: Clinical characteristics of the severe acute respiratory syndrome coronavirus 2 omicron variant compared with the delta variant: a retrospective case-control study of 318 outpatients from a single sight institute in Japan
description: Background Clinical characteristics, including laboratory parameters, of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant have been limited. Methods This retrospective case-control study was conducted in a single hospital. Patients with coronavirus disease 2019 (COVID-19) who visited the Asahikawa City Hospital outpatient department as new patients and underwent blood tests were included in this study. We analyzed the data from January 2022 to April 2022 during the Omicron phase and from April 2021 to October 2021 during the Delta phase. Patients who were treated at other hospitals after visiting our hospital were excluded. All blood tests were performed before treatment for COVID-19 was initiated. Demographic information, laboratory data, and clinical courses were extracted from electronic medical records. We matched the two groups by age and comorbidities and compared their characteristics. We also analyzed factors associated with pneumonia in the Omicron phase. Results A total of 151 Omicron patients and 167 delta patients were analyzed in this study. The mean age, rate of comorbidities, and vaccination were significantly higher in the Omicron group. The number of patients with pneumonia or those requiring oxygen, admissions, or both was significantly lower in the Omicron group. Lactate dehydrogenase (LDH), C-reactive protein (CRP), ferritin, aspartate aminotransferase (AST), and neutrophil-to-lymphocyte ratio (NLR) levels were significantly lower in the Omicron group. Compared with the mild symptom and pneumonia groups in the Omicron group, older age, higher body mass index (BMI), higher non-vaccination, higher LDH, and higher CRP levels were associated with the pneumonia group. Conclusion The Omicron variant is associated with a reduction in hospitalization and the risk of pneumonia compared to the delta variant in a real-life clinical setting. In the Omicron variant, the risk of pneumonia is related to high-risk factors, laborat…
format: application/pdf
format: text/html
creator: Keiko Suzuki
creator: Takaya Ichikawa
creator: Satoshi Suzuki
creator: Yoko Tanino
creator: Yasutaka Kakinoki
subject: Epidemiology
subject: Hematology
subject: Infectious Diseases
subject: Internal Medicine
subject: COVID-19
description: doi:10.7717/peerj.13762
publisher: PeerJ Inc.
rights: © 2022 Suzuki et al.
abstract: Background Clinical characteristics, including laboratory parameters, of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant have been limited. Methods This retrospective case-control study was conducted in a single hospital. Patients with coronavirus disease 2019 (COVID-19) who visited the Asahikawa City Hospital outpatient department as new patients and underwent blood tests were included in this study. We analyzed the data from January 2022 to April 2022 during the Omicron phase and from April 2021 to October 2021 during the Delta phase. Patients who were treated at other hospitals after visiting our hospital were excluded. All blood tests were performed before treatment for COVID-19 was initiated. Demographic information, laboratory data, and clinical courses were extracted from electronic medical records. We matched the two groups by age and comorbidities and compared their characteristics. We also analyzed factors associated with pneumonia in the Omicron phase. Results A total of 151 Omicron patients and 167 delta patients were analyzed in this study. The mean age, rate of comorbidities, and vaccination were significantly higher in the Omicron group. The number of patients with pneumonia or those requiring oxygen, admissions, or both was significantly lower in the Omicron group. Lactate dehydrogenase (LDH), C-reactive protein (CRP), ferritin, aspartate aminotransferase (AST), and neutrophil-to-lymphocyte ratio (NLR) levels were significantly lower in the Omicron group. Compared with the mild symptom and pneumonia groups in the Omicron group, older age, higher body mass index (BMI), higher non-vaccination, higher LDH, and higher CRP levels were associated with the pneumonia group. Conclusion The Omicron variant is associated with a reduction in hospitalization and the risk of pneumonia compared to the delta variant in a real-life clinical setting. In the Omicron variant, the risk of pneumonia is related to high-risk factors, laborat…
bibliographic citation: Suzuki et al. (2022) Clinical characteristics of the severe acute respiratory syndrome coronavirus 2 omicron variant compared with the delta variant: a retrospective case-control study of 318 outpatients from a single sight institute in Japan. PeerJ 10:e13762 https://doi.org/10.7717/peerj.13762
date submitted: 2022-01-20
date accepted: 2022-06-29
issued: 2022-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Suzuki
  given name: Keiko
author list: Agent
  family name: Ichikawa
  given name: Takaya
author list: Agent
  family name: Suzuki
  given name: Satoshi
author list: Agent
  family name: Tanino
  given name: Yoko
author list: Agent
  family name: Kakinoki
  given name: Yasutaka
doi: 10.7717/peerj.13762
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-02
copyright: ©2022 Suzuki et al.
attribution name: Suzuki et al.

Digital technology for orthognathic surgery training promotion: a randomized comparative study
type: item
type: AcademicArticle
description: Background This study aims to investigate whether a systematic digital training system can improve the learning efficiency of residents in the first-year orthognathic surgery training course and evaluate its effectiveness in teaching orthognathic surgery. Methods A digital training system was applied, and a comparative research approach was adopted. 24 first-year orthognathic surgery residents participated in the experiment as part of their professional skill training. The Experimental group was required to use a digital training system, and the Control group was trained in lectures without digital technologies. Three indicators, including theoretical knowledge and clinical operation, were assessed in tests, and evaluations from instructors were analyzed to evaluate learning efficiency. Results The results showed that the scores in theoretical tests, practical operations, and teacher evaluations, the Experimental groups were all higher than the Control group (P = 0.002 for anatomy, P = 0.000 for operation theory) after using digital technology, except for the understanding of complications (P = 0.771). In addition, the questionnaire survey results showed that the study interest (P = 0.001), self-confidence (P = 0.001), satisfaction (P = 0.002), and academic performance (P = 0.001) of the residents of the Experimental group were higher than those of the Control group. Conclusions The outcomes indicated that the digital training system could benefit orthognathic residents’ learning efficiency, and learning interest and teaching satisfaction will also improve.
format: application/pdf
format: text/html
creator: Zhan Su
creator: Yao Liu
creator: Wenli Zhao
creator: Yuanyan Bai
creator: Nan Jiang
creator: Songsong Zhu
subject: Dentistry
subject: Science and Medical Education
description: doi:10.7717/peerj.13810
publisher: PeerJ Inc.
rights: © 2022 Su et al.
abstract: Background This study aims to investigate whether a systematic digital training system can improve the learning efficiency of residents in the first-year orthognathic surgery training course and evaluate its effectiveness in teaching orthognathic surgery. Methods A digital training system was applied, and a comparative research approach was adopted. 24 first-year orthognathic surgery residents participated in the experiment as part of their professional skill training. The Experimental group was required to use a digital training system, and the Control group was trained in lectures without digital technologies. Three indicators, including theoretical knowledge and clinical operation, were assessed in tests, and evaluations from instructors were analyzed to evaluate learning efficiency. Results The results showed that the scores in theoretical tests, practical operations, and teacher evaluations, the Experimental groups were all higher than the Control group (P = 0.002 for anatomy, P = 0.000 for operation theory) after using digital technology, except for the understanding of complications (P = 0.771). In addition, the questionnaire survey results showed that the study interest (P = 0.001), self-confidence (P = 0.001), satisfaction (P = 0.002), and academic performance (P = 0.001) of the residents of the Experimental group were higher than those of the Control group. Conclusions The outcomes indicated that the digital training system could benefit orthognathic residents’ learning efficiency, and learning interest and teaching satisfaction will also improve.
bibliographic citation: Su et al. (2022) Digital technology for orthognathic surgery training promotion: a randomized comparative study. PeerJ 10:e13810 https://doi.org/10.7717/peerj.13810
date submitted: 2022-01-31
date accepted: 2022-07-07
issued: 2022-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Zhan
author list: Agent
  family name: Liu
  given name: Yao
author list: Agent
  family name: Zhao
  given name: Wenli
author list: Agent
  family name: Bai
  given name: Yuanyan
author list: Agent
  family name: Jiang
  given name: Nan
author list: Agent
  family name: Zhu
  given name: Songsong
doi: 10.7717/peerj.13810
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-02
copyright: ©2022 Su et al.
attribution name: Su et al.

Hydrological and lock operation conditions associated with paddlefish and bigheaded carp dam passage on a large and small scale in the Upper Mississippi River (Pools 14–18)
type: item
type: AcademicArticle
description: Movement and dispersal of migratory fish species is an important life-history characteristics that can be impeded by navigation dams. Although habitat fragmentation may be detrimental to native fish species, it might act as an effective and economical barrier for controlling the spread of invasive species in riverine systems. Various technologies have been proposed as potential fish deterrents at locks and dams to reduce bigheaded carp (i.e., silver carp and bighead carp (Hypophthalmichthys spp.)) range expansion in the Upper Mississippi River (UMR). Lock and Dam (LD) 15 is infrequently at open-river condition (spillway gates completely open; hydraulic head across the dam <0.4 m) and has been identified as a potential location for fish deterrent implementation. We used acoustic telemetry to evaluate paddlefish passage at UMR dams and to evaluate seasonal and diel movement of paddlefish and bigheaded carp relative to environmental conditions and lock operations at LD 15. We observed successful paddlefish passage at all dams, with the highest number of passages occurring at LDs 17 and 16. Paddlefish residency events in the downstream lock approach of LD 15 occurred more frequently and for longer durations than residency events of bigheaded carp. We documented upstream passages completed by two individual paddlefish through the lock chamber at LD 15, and a single bighead carp completed upstream passage through the lock chamber during two separate years of this study. We identified four bigheaded carp and 19 paddlefish that made upstream passages through the spillway gates at LD 15 during this study. The majority of the upstream passages through the spillway gates for both species occurred during open river conditions. When hydraulic head was approximately 1-m or greater, we observed these taxa opt for upstream passage through the lock chamber more often than the dam gates. In years with infrequent open-river condition, a deterrent placed in the downstream lock approach…
format: application/pdf
format: text/html
creator: Dominique D. Turney
creator: Andrea K. Fritts
creator: Brent C. Knights
creator: Jon M. Vallazza
creator: Douglas S. Appel
creator: James T. Lamer
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.13822
publisher: PeerJ Inc.
rights: © 2022 Turney et al.
abstract: Movement and dispersal of migratory fish species is an important life-history characteristics that can be impeded by navigation dams. Although habitat fragmentation may be detrimental to native fish species, it might act as an effective and economical barrier for controlling the spread of invasive species in riverine systems. Various technologies have been proposed as potential fish deterrents at locks and dams to reduce bigheaded carp (i.e., silver carp and bighead carp (Hypophthalmichthys spp.)) range expansion in the Upper Mississippi River (UMR). Lock and Dam (LD) 15 is infrequently at open-river condition (spillway gates completely open; hydraulic head across the dam <0.4 m) and has been identified as a potential location for fish deterrent implementation. We used acoustic telemetry to evaluate paddlefish passage at UMR dams and to evaluate seasonal and diel movement of paddlefish and bigheaded carp relative to environmental conditions and lock operations at LD 15. We observed successful paddlefish passage at all dams, with the highest number of passages occurring at LDs 17 and 16. Paddlefish residency events in the downstream lock approach of LD 15 occurred more frequently and for longer durations than residency events of bigheaded carp. We documented upstream passages completed by two individual paddlefish through the lock chamber at LD 15, and a single bighead carp completed upstream passage through the lock chamber during two separate years of this study. We identified four bigheaded carp and 19 paddlefish that made upstream passages through the spillway gates at LD 15 during this study. The majority of the upstream passages through the spillway gates for both species occurred during open river conditions. When hydraulic head was approximately 1-m or greater, we observed these taxa opt for upstream passage through the lock chamber more often than the dam gates. In years with infrequent open-river condition, a deterrent placed in the downstream lock approach…
bibliographic citation: Turney et al. (2022) Hydrological and lock operation conditions associated with paddlefish and bigheaded carp dam passage on a large and small scale in the Upper Mississippi River (Pools 14–18). PeerJ 10:e13822 https://doi.org/10.7717/peerj.13822
date submitted: 2022-03-11
date accepted: 2022-07-10
issued: 2022-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Turney
  given name: Dominique D.
author list: Agent
  family name: Fritts
  given name: Andrea K.
author list: Agent
  family name: Knights
  given name: Brent C.
author list: Agent
  family name: Vallazza
  given name: Jon M.
author list: Agent
  family name: Appel
  given name: Douglas S.
author list: Agent
  family name: Lamer
  given name: James T.
doi: 10.7717/peerj.13822
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-02
copyright: ©2022 Turney et al.
attribution name: Turney et al.

Advanced oxidation protein products induce annulus fibrosus cell senescence through a NOX4-dependent, MAPK-mediated pathway and accelerate intervertebral disc degeneration
type: item
type: AcademicArticle
description: Background Intervertebral disc degeneration (IVDD) is closely associated with senescence. Annulus fibrosus (AF) cell senescence is a crucial driver of AF tissue tearing and fissures, thereby exacerbating IVDD. Increased advanced oxidative protein products (AOPPs) were found in human degenerative discs and aged rat discs and may be involved in IVDD. This study aimed to explore the mechanism of AOPPs-induced senescence in AF cells. Methods The pathological effects of AOPPs in vivo were investigated using a rat lumbar disc persistent degeneration model and a rat caudal disc puncture model. Rat primary AF cells were selected as in vitro models, and AOPPs were used as direct stimulation to observe their pathological effects. Setanaxb (NOX1/4 inhibitor), apocynin (NADPH oxidase inhibitor) and adenovirus (ADV) packed NADPH oxidase 4 (NOX4) specific shRNAs were used for pathway inhibition, respectively. Finally, adeno-associated viruses (AAVs) packed with NOX4-specific blocking sequences were used to inhibit the in vivo pathway. Results AOPPs accumulated in the rat lumbar and caudal degenerative discs. Intra-discal loading of AOPPs up-regulated the expression of NOX4, p53, p21, p16, IL-1β, and TNF-α, ultimately accelerating IVDD. Exposure of AOPPs to AF primary cells up-regulated NOX4 expression, induced phosphorylation of mitogen-activated protein kinases (MAPK), triggered senescence and increased IL-1β and TNF-α. Apocynin, setanaxib, and ADV pre-cultured AF cells abrogated AOPPs-induced senescence. AAV-mediated inhibition of NOX4 expression in vivo reduced the expression of p53, p21, p16, IL-1β and TNF-α in vivo and delayed IVDD. Conclusions AOPPs induced AF cell senescence through a NOX4-dependent and MAPK-mediated pathway.
format: application/pdf
format: text/html
creator: Xiangheng Dai
creator: Yu Chen
creator: Zihan Yu
creator: Congrui Liao
creator: Zhongyuan Liu
creator: Jianting Chen
creator: Qian Wu
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.13826
publisher: PeerJ Inc.
rights: © 2022 Dai et al.
abstract: Background Intervertebral disc degeneration (IVDD) is closely associated with senescence. Annulus fibrosus (AF) cell senescence is a crucial driver of AF tissue tearing and fissures, thereby exacerbating IVDD. Increased advanced oxidative protein products (AOPPs) were found in human degenerative discs and aged rat discs and may be involved in IVDD. This study aimed to explore the mechanism of AOPPs-induced senescence in AF cells. Methods The pathological effects of AOPPs in vivo were investigated using a rat lumbar disc persistent degeneration model and a rat caudal disc puncture model. Rat primary AF cells were selected as in vitro models, and AOPPs were used as direct stimulation to observe their pathological effects. Setanaxb (NOX1/4 inhibitor), apocynin (NADPH oxidase inhibitor) and adenovirus (ADV) packed NADPH oxidase 4 (NOX4) specific shRNAs were used for pathway inhibition, respectively. Finally, adeno-associated viruses (AAVs) packed with NOX4-specific blocking sequences were used to inhibit the in vivo pathway. Results AOPPs accumulated in the rat lumbar and caudal degenerative discs. Intra-discal loading of AOPPs up-regulated the expression of NOX4, p53, p21, p16, IL-1β, and TNF-α, ultimately accelerating IVDD. Exposure of AOPPs to AF primary cells up-regulated NOX4 expression, induced phosphorylation of mitogen-activated protein kinases (MAPK), triggered senescence and increased IL-1β and TNF-α. Apocynin, setanaxib, and ADV pre-cultured AF cells abrogated AOPPs-induced senescence. AAV-mediated inhibition of NOX4 expression in vivo reduced the expression of p53, p21, p16, IL-1β and TNF-α in vivo and delayed IVDD. Conclusions AOPPs induced AF cell senescence through a NOX4-dependent and MAPK-mediated pathway.
bibliographic citation: Dai et al. (2022) Advanced oxidation protein products induce annulus fibrosus cell senescence through a NOX4-dependent, MAPK-mediated pathway and accelerate intervertebral disc degeneration. PeerJ 10:e13826 https://doi.org/10.7717/peerj.13826
date submitted: 2022-04-14
date accepted: 2022-07-11
issued: 2022-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dai
  given name: Xiangheng
author list: Agent
  family name: Chen
  given name: Yu
author list: Agent
  family name: Yu
  given name: Zihan
author list: Agent
  family name: Liao
  given name: Congrui
author list: Agent
  family name: Liu
  given name: Zhongyuan
author list: Agent
  family name: Chen
  given name: Jianting
author list: Agent
  family name: Wu
  given name: Qian
doi: 10.7717/peerj.13826
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-02
copyright: ©2022 Dai et al.
attribution name: Dai et al.

Comparative transcriptome analysis of Lupinus polyphyllus Lindl. provides a rich molecular resource for research on coloration mechanism
type: item
type: AcademicArticle
description: Lupinus polyphyllus is rich in color, making it a well-known horticultural ornamental plant. However, little is known about the genes related to anthocyanin and carotenoid biosynthesis in L. polyphyllus. In this study, transcriptome sequencing was performed on eight different colors of L. polyphyllus. A total of 1.13 billion clean reads were obtained and assembled into 89,124 unigenes, which were then aligned with six databases, resulting in the identification of 54,823 annotated unigenes. Among these unigenes, 76 and 101 were involved in the biosynthetic pathway of carotenoids and anthocyanins, respectively. In addition, 505 transcription factors were revealed, which belonged to the MYB, R2R3-MYB, NAC, bHLH, and WD40 families. A total of 6,700 differentially expressed genes (DEGs) were obtained by comparative transcriptome analysis. Among them, 17 candidate unigenes (four carotenoid genes, seven anthocyanin genes, and six TFs) were specifically up-regulated for one or more colors of L. polyphyllus. Eight representative candidate unigenes were analyzed by qRT-PCR. The findings enrich the transcriptome database of lupine, and provide a rich molecular resource for research on the coloration mechanism of L. polyphyllus.
format: application/pdf
format: text/html
creator: Zhu Gao
creator: Jipeng Mao
creator: Lu Chen
creator: Xiaoling Wang
creator: Lu Zhang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13836
publisher: PeerJ Inc.
rights: © 2022 Gao et al.
abstract: Lupinus polyphyllus is rich in color, making it a well-known horticultural ornamental plant. However, little is known about the genes related to anthocyanin and carotenoid biosynthesis in L. polyphyllus. In this study, transcriptome sequencing was performed on eight different colors of L. polyphyllus. A total of 1.13 billion clean reads were obtained and assembled into 89,124 unigenes, which were then aligned with six databases, resulting in the identification of 54,823 annotated unigenes. Among these unigenes, 76 and 101 were involved in the biosynthetic pathway of carotenoids and anthocyanins, respectively. In addition, 505 transcription factors were revealed, which belonged to the MYB, R2R3-MYB, NAC, bHLH, and WD40 families. A total of 6,700 differentially expressed genes (DEGs) were obtained by comparative transcriptome analysis. Among them, 17 candidate unigenes (four carotenoid genes, seven anthocyanin genes, and six TFs) were specifically up-regulated for one or more colors of L. polyphyllus. Eight representative candidate unigenes were analyzed by qRT-PCR. The findings enrich the transcriptome database of lupine, and provide a rich molecular resource for research on the coloration mechanism of L. polyphyllus.
bibliographic citation: Gao et al. (2022) Comparative transcriptome analysis of Lupinus polyphyllus Lindl. provides a rich molecular resource for research on coloration mechanism. PeerJ 10:e13836 https://doi.org/10.7717/peerj.13836
date submitted: 2022-04-28
date accepted: 2022-07-13
issued: 2022-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Zhu
author list: Agent
  family name: Mao
  given name: Jipeng
author list: Agent
  family name: Chen
  given name: Lu
author list: Agent
  family name: Wang
  given name: Xiaoling
author list: Agent
  family name: Zhang
  given name: Lu
doi: 10.7717/peerj.13836
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-02
copyright: ©2022 Gao et al.
attribution name: Gao et al.

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