PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Retrospective study on the correlation between serum MIF level and the condition and prognosis of patients with traumatic head injury
items: Identification of novel key markers that are induced during traumatic brain injury in mice
items: Development and validation of the Exteroceptive Body Awareness (EBA-q) questionnaire
items: Signatures of prescribed fire in the microbial communities of Cornus florida are largely undetectable five months post-fire
items: Exogenous hydrogen sulfide improves salt stress tolerance of Reaumuria soongorica seedlings by regulating active oxygen metabolism
items: Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction
items: Genetic diversity analysis and molecular characteristics of wild centipedegrass using sequence-related amplified polymorphism (SRAP) markers
items: Characteristics of water jump for better performance in collegiate male 3000 m steeplechase
items: Bacillus amyloliquefaciens 11B91 inoculation enhances the growth of quinoa (Chenopodium quinoa Willd.) under salt stress
items: A decision tree model to predict liver cirrhosis in hepatocellular carcinoma patients: a retrospective study

Retrospective study on the correlation between serum MIF level and the condition and prognosis of patients with traumatic head injury
type: item
type: AcademicArticle
description: Objective This study aimed to investigate the correlation between serum levels of macrophage migration inhibitory factor (MIF) and the condition and prognosis of patients with traumatic brain injury (TBI). Methods A retrospective study design was used, and the clinical data of 131 TBI patients from February 2019 to January 2022 were analyzed. Patients were divided into mild (13–15 points), moderate (9–12 points), or severe (3–8 points) groups according to their Glasgow Coma Scale (GCS) score after admission. The serum levels of BDNF, MIF, and MBP in the three groups were compared, and their correlation with the severity of TBI was analyzed. Patients were then separated into a good prognosis group (4–5 points) and a poor prognosis group (≤3 points) based on their Glasgow Prognostic Score (GOS) after 6 months of follow-up. The predictive power of serum indexes and combined detection on prognosis was analyzed. Results Patients were classified into a mild group (n = 63), moderate group (n = 47), and severe group (n = 21) based on their GCS, with a significant difference noted in serum levels of MIF, MBP, and BDNF among patients with different degrees of severity (all P < 0.001). The MIF, MBP, and BDNF levels were lower in the mild group compared to the moderate (all P < 0.001) and severe group (all P < 0.001). Additionally, the MIF and BDNF levels in the moderate group were lower compared to the severe group (P = 0.011, P = 0.002). Patients with mild severity had lower serum MIF, MBP, and BDNF levels than those with other degrees, and these indexes were positively correlated with the severity of TBI (all P < 0.001, r = 0.62, r = 0.48, r = 0.58). Based on the GOS, patients were divided into a good prognosis group (n = 107) and a poor prognosis group (n = 24), with the levels of MIF, MBP, and BDNF in the good prognosis group being significantly lower than those in the poor prognosis group (P < 0.001, P = 0.007, P = 0.003). The area under the curve (AUC) of MIF was higher …
format: application/pdf
format: text/html
creator: Zhentong Liu
creator: Chengwu Liu
creator: Kegao Ma
subject: Hematology
subject: Neurology
description: doi:10.7717/peerj.15933
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Objective This study aimed to investigate the correlation between serum levels of macrophage migration inhibitory factor (MIF) and the condition and prognosis of patients with traumatic brain injury (TBI). Methods A retrospective study design was used, and the clinical data of 131 TBI patients from February 2019 to January 2022 were analyzed. Patients were divided into mild (13–15 points), moderate (9–12 points), or severe (3–8 points) groups according to their Glasgow Coma Scale (GCS) score after admission. The serum levels of BDNF, MIF, and MBP in the three groups were compared, and their correlation with the severity of TBI was analyzed. Patients were then separated into a good prognosis group (4–5 points) and a poor prognosis group (≤3 points) based on their Glasgow Prognostic Score (GOS) after 6 months of follow-up. The predictive power of serum indexes and combined detection on prognosis was analyzed. Results Patients were classified into a mild group (n = 63), moderate group (n = 47), and severe group (n = 21) based on their GCS, with a significant difference noted in serum levels of MIF, MBP, and BDNF among patients with different degrees of severity (all P < 0.001). The MIF, MBP, and BDNF levels were lower in the mild group compared to the moderate (all P < 0.001) and severe group (all P < 0.001). Additionally, the MIF and BDNF levels in the moderate group were lower compared to the severe group (P = 0.011, P = 0.002). Patients with mild severity had lower serum MIF, MBP, and BDNF levels than those with other degrees, and these indexes were positively correlated with the severity of TBI (all P < 0.001, r = 0.62, r = 0.48, r = 0.58). Based on the GOS, patients were divided into a good prognosis group (n = 107) and a poor prognosis group (n = 24), with the levels of MIF, MBP, and BDNF in the good prognosis group being significantly lower than those in the poor prognosis group (P < 0.001, P = 0.007, P = 0.003). The area under the curve (AUC) of MIF was higher …
bibliographic citation: Liu et al. (2023) Retrospective study on the correlation between serum MIF level and the condition and prognosis of patients with traumatic head injury. PeerJ 11:e15933 https://doi.org/10.7717/peerj.15933
date submitted: 2023-03-15
date accepted: 2023-07-30
issued: 2023-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Zhentong
author list: Agent
  family name: Liu
  given name: Chengwu
author list: Agent
  family name: Ma
  given name: Kegao
doi: 10.7717/peerj.15933
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-25
copyright: © 2023 Liu et al.
attribution name: Liu et al.

Identification of novel key markers that are induced during traumatic brain injury in mice
type: item
type: AcademicArticle
description: Background Traumatic brain injury (TBI) has emerged as an increasing public health problem but has not been well studied, particularly the mechanisms of brain cellular behaviors during TBI. Methods In this study, we established an ischemia/reperfusion (I/R) brain injury mice model using transient middle cerebral artery occlusion (tMCAO) strategy. After then, RNA-sequencing of frontal lobes was performed to screen key inducers during TBI. To further verify the selected genes, we collected peripheral blood mononuclear cells (PBMCs) from TBI patients within 24 h who attended intensive care unit (ICU) in the Affiliated Hospital of Yangzhou University and analyzed the genes expression using RT-qPCR. Finally, the receiver operator characteristic (ROC) curves and co-expression with cellular senescence markers were applied to evaluate the predictive value of the genes. Results A total of six genes were screened out from the RNA-sequencing based on their novelty in TBI and implications in apoptosis and cellular senescence signaling. RT-qPCR analysis of PBMCs from patients showed the six genes were all up-regulated during TBI after comparing with healthy volunteers who attended the hospital for physical examination. The area under ROC (AUC) curves were all >0.7, and the co-expression scores of the six genes with senescence markers were all significantly positive. We thus identified TGM1, TGM2, ATF3, RCN3, ORAI1 and ITPR3 as novel key markers that are induced during TBI, and these markers may also serve as potential predictors for the progression of TBI.
format: application/pdf
format: text/html
creator: Yucheng Li
creator: Ningbo Li
creator: Changjiao Luan
creator: Yunlong Pei
creator: Qingbin Zheng
creator: Bingchun Yan
creator: Xingjie Ma
creator: Weili Liu
subject: Biochemistry
subject: Molecular Biology
subject: Epidemiology
subject: Neurology
subject: Histology
description: doi:10.7717/peerj.15981
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background Traumatic brain injury (TBI) has emerged as an increasing public health problem but has not been well studied, particularly the mechanisms of brain cellular behaviors during TBI. Methods In this study, we established an ischemia/reperfusion (I/R) brain injury mice model using transient middle cerebral artery occlusion (tMCAO) strategy. After then, RNA-sequencing of frontal lobes was performed to screen key inducers during TBI. To further verify the selected genes, we collected peripheral blood mononuclear cells (PBMCs) from TBI patients within 24 h who attended intensive care unit (ICU) in the Affiliated Hospital of Yangzhou University and analyzed the genes expression using RT-qPCR. Finally, the receiver operator characteristic (ROC) curves and co-expression with cellular senescence markers were applied to evaluate the predictive value of the genes. Results A total of six genes were screened out from the RNA-sequencing based on their novelty in TBI and implications in apoptosis and cellular senescence signaling. RT-qPCR analysis of PBMCs from patients showed the six genes were all up-regulated during TBI after comparing with healthy volunteers who attended the hospital for physical examination. The area under ROC (AUC) curves were all >0.7, and the co-expression scores of the six genes with senescence markers were all significantly positive. We thus identified TGM1, TGM2, ATF3, RCN3, ORAI1 and ITPR3 as novel key markers that are induced during TBI, and these markers may also serve as potential predictors for the progression of TBI.
bibliographic citation: Li et al. (2023) Identification of novel key markers that are induced during traumatic brain injury in mice. PeerJ 11:e15981 https://doi.org/10.7717/peerj.15981
date submitted: 2023-05-01
date accepted: 2023-08-08
issued: 2023-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yucheng
author list: Agent
  family name: Li
  given name: Ningbo
author list: Agent
  family name: Luan
  given name: Changjiao
author list: Agent
  family name: Pei
  given name: Yunlong
author list: Agent
  family name: Zheng
  given name: Qingbin
author list: Agent
  family name: Yan
  given name: Bingchun
author list: Agent
  family name: Ma
  given name: Xingjie
author list: Agent
  family name: Liu
  given name: Weili
doi: 10.7717/peerj.15981
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-25
copyright: © 2023 Li et al.
attribution name: Li et al.

Development and validation of the Exteroceptive Body Awareness (EBA-q) questionnaire
type: item
type: AcademicArticle
description: The conscious processing of body signals influences higher-order psychological and cognitive functions, including self-awareness. Dysfunctions in the processing of these signals has been connected to neurological and psychiatric disorders characterized by altered states of self-consciousness. Studies indicate that perceiving the body through interoceptive signals (e.g., from internal organs such as heartbeat and breathing) is distinct from perceiving the body through exteroceptive signals (e.g., by relying on visual, tactile and olfactory cues). While questionnaires are available for assessing interoception, there are no validated self-report instruments for measuring bodily exterception. To fill this gap, we performed three studies to develop and validate a novel scale designed to assess bodily self-consciousness based on the processing of exteroceptive bodily signals. Exploratory factor analysis (Study 1, N = 302) led to an 18-item questionnaire comprised of four factors. We called this instrument Exteroceptive Body Awareness questionnaire (EBA-q). Confirmatory factor analysis (Study 2, N = 184) run on a second sample showed an acceptable fit for a bifactor model, suggesting researchers may use the questionnaire as a unidimensional scale reflecting exteroceptive bodily self-consciousness, or use each of its four sub-scales, reflecting “visuo-tactile body awareness”, “spatial coordination”, “awareness of body changes” and “awareness of clothing fit”. Overall EBA-q showed good internal consistency. Convergent and divergent validity were assessed via cross-validation with existing body awareness questionnaires (Study 3, N = 366) and behavioral measures (Study 3, N = 64) of exteroceptive and interoceptive bodily self-consciousness. Research applications are discussed within a multi-faceted model of exteroception and interoception as distinct, but at the same time interconnected, dimensions of bodily self-consciousness.
format: application/pdf
format: text/html
creator: Alisha Vabba
creator: Giuseppina Porciello
creator: Maria Serena Panasiti
creator: Salvatore Maria Aglioti
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.15382
publisher: PeerJ Inc.
rights: © 2023 Vabba et al.
abstract: The conscious processing of body signals influences higher-order psychological and cognitive functions, including self-awareness. Dysfunctions in the processing of these signals has been connected to neurological and psychiatric disorders characterized by altered states of self-consciousness. Studies indicate that perceiving the body through interoceptive signals (e.g., from internal organs such as heartbeat and breathing) is distinct from perceiving the body through exteroceptive signals (e.g., by relying on visual, tactile and olfactory cues). While questionnaires are available for assessing interoception, there are no validated self-report instruments for measuring bodily exterception. To fill this gap, we performed three studies to develop and validate a novel scale designed to assess bodily self-consciousness based on the processing of exteroceptive bodily signals. Exploratory factor analysis (Study 1, N = 302) led to an 18-item questionnaire comprised of four factors. We called this instrument Exteroceptive Body Awareness questionnaire (EBA-q). Confirmatory factor analysis (Study 2, N = 184) run on a second sample showed an acceptable fit for a bifactor model, suggesting researchers may use the questionnaire as a unidimensional scale reflecting exteroceptive bodily self-consciousness, or use each of its four sub-scales, reflecting “visuo-tactile body awareness”, “spatial coordination”, “awareness of body changes” and “awareness of clothing fit”. Overall EBA-q showed good internal consistency. Convergent and divergent validity were assessed via cross-validation with existing body awareness questionnaires (Study 3, N = 366) and behavioral measures (Study 3, N = 64) of exteroceptive and interoceptive bodily self-consciousness. Research applications are discussed within a multi-faceted model of exteroception and interoception as distinct, but at the same time interconnected, dimensions of bodily self-consciousness.
bibliographic citation: Vabba et al. (2023) Development and validation of the Exteroceptive Body Awareness (EBA-q) questionnaire. PeerJ 11:e15382 https://doi.org/10.7717/peerj.15382
date submitted: 2022-11-16
date accepted: 2023-04-18
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Vabba
  given name: Alisha
author list: Agent
  family name: Porciello
  given name: Giuseppina
author list: Agent
  family name: Panasiti
  given name: Maria Serena
author list: Agent
  family name: Aglioti
  given name: Salvatore Maria
doi: 10.7717/peerj.15382
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: ©2023 Vabba et al.
attribution name: Vabba et al.

Signatures of prescribed fire in the microbial communities of Cornus florida are largely undetectable five months post-fire
type: item
type: AcademicArticle
description: Prescribed burn is a management tool that influences the physical structure and composition of forest plant communities and their associated microorganisms. Plant-associated microorganisms aid in host plant disease tolerance and increase nutrient availability. The effects of prescribed burn on microorganisms associated with native ecologically and economically important tree species, such as Cornus florida L. (flowering dogwood), are not well understood, particularly in aboveground plant tissues (e.g., leaf, stem, and bark tissues). The objective of this study was to use 16S rRNA gene and ITS2 region sequencing to evaluate changes in bacterial and fungal communities of five different flowering dogwood-associated niches (soil, roots, bark, stem, and leaves) five months following a prescribed burn treatment. The alpha- and beta-diversity of root bacterial/archaeal communities differed significantly between prescribed burn and unburned control-treated trees. In these bacterial/archaeal root communities, we also detected a significantly higher relative abundance of sequences identified as Acidothermaceae, a family of thermophilic bacteria. No significant differences were detected between prescribed burn-treated and unburned control trees in bulk soils or bark, stem, or leaf tissues. The findings of our study suggest that prescribed burn does not significantly alter the aboveground plant-associated microbial communities of flowering dogwood trees five months following the prescribed burn application. Further studies are required to better understand the short- and long-term effects of prescribed burns on the microbial communities of forest trees.
format: application/pdf
format: text/html
creator: Beant Kapoor
creator: Aaron Onufrak
creator: William Klingeman III
creator: Jennifer M. DeBruyn
creator: Melissa A. Cregger
creator: Emma Willcox
creator: Robert Trigiano
creator: Denita Hadziabdic
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.15822
publisher: PeerJ Inc.
rights: © 2023 Kapoor et al.
abstract: Prescribed burn is a management tool that influences the physical structure and composition of forest plant communities and their associated microorganisms. Plant-associated microorganisms aid in host plant disease tolerance and increase nutrient availability. The effects of prescribed burn on microorganisms associated with native ecologically and economically important tree species, such as Cornus florida L. (flowering dogwood), are not well understood, particularly in aboveground plant tissues (e.g., leaf, stem, and bark tissues). The objective of this study was to use 16S rRNA gene and ITS2 region sequencing to evaluate changes in bacterial and fungal communities of five different flowering dogwood-associated niches (soil, roots, bark, stem, and leaves) five months following a prescribed burn treatment. The alpha- and beta-diversity of root bacterial/archaeal communities differed significantly between prescribed burn and unburned control-treated trees. In these bacterial/archaeal root communities, we also detected a significantly higher relative abundance of sequences identified as Acidothermaceae, a family of thermophilic bacteria. No significant differences were detected between prescribed burn-treated and unburned control trees in bulk soils or bark, stem, or leaf tissues. The findings of our study suggest that prescribed burn does not significantly alter the aboveground plant-associated microbial communities of flowering dogwood trees five months following the prescribed burn application. Further studies are required to better understand the short- and long-term effects of prescribed burns on the microbial communities of forest trees.
bibliographic citation: Kapoor et al. (2023) Signatures of prescribed fire in the microbial communities of Cornus florida are largely undetectable five months post-fire. PeerJ 11:e15822 https://doi.org/10.7717/peerj.15822
date submitted: 2023-02-20
date accepted: 2023-07-10
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kapoor
  given name: Beant
author list: Agent
  family name: Onufrak
  given name: Aaron
author list: Agent
  family name: Klingeman III
  given name: William
author list: Agent
  family name: DeBruyn
  given name: Jennifer M.
author list: Agent
  family name: Cregger
  given name: Melissa A.
author list: Agent
  family name: Willcox
  given name: Emma
author list: Agent
  family name: Trigiano
  given name: Robert
author list: Agent
  family name: Hadziabdic
  given name: Denita
doi: 10.7717/peerj.15822
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: © 2023 Kapoor et al.
attribution name: Kapoor et al.

Exogenous hydrogen sulfide improves salt stress tolerance of Reaumuria soongorica seedlings by regulating active oxygen metabolism
type: item
type: AcademicArticle
description: Hydrogen sulfide (H2S), as an endogenous gas signaling molecule, plays an important role in plant growth regulation and resistance to abiotic stress. This study aims to investigate the mechanism of exogenous H2S on the growth and development of Reaumuria soongorica seedlings under salt stress and to determine the optimal concentration for foliar application. To investigate the regulatory effects of exogenous H2S (donor sodium hydrosulfide, NaHS) at concentrations ranging from 0 to 1 mM on reactive oxygen species (ROS), antioxidant system, and osmoregulation in R. soongorica seedlings under 300 mM NaCl stress. The growth of R. soongorica seedlings was inhibited by salt stress, which resulted in a decrease in the leaf relative water content (LRWC), specific leaf area (SLA), and soluble sugar content in leaves, elevated activity levels of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT); and accumulated superoxide anion (O2–), proline, malondialdehyde (MDA), and soluble protein content in leaves; and increased L-cysteine desulfhydrase (LCD) activity and endogenous H2S content. This indicated that a high level of ROS was produced in the leaves of R. soongorica seedlings and seriously affected the growth and development of R. soongorica seedlings. The exogenous application of different concentrations of NaHS reduced the content of O 2–, proline and MDA, increased the activity of antioxidant enzymes and the content of osmoregulators (soluble sugars and soluble proteins), while the LCD enzyme activity and the content of endogenous H2S were further increased with the continuous application of exogenous H2S. The inhibitory effects of salt stress on the growth rate of plant height and ground diameter, the LRWC, biomass, and SLA were effectively alleviated. A comprehensive analysis showed that the LRWC, POD, and proline could be used as the main indicators to evaluate the alleviating effect of exogenous H2S on R. soongorica seedlings under salt stress. The opti…
format: application/pdf
format: text/html
creator: Hanghang Liu
creator: Peifang Chong
creator: Zehua Liu
creator: Xinguang Bao
creator: Bingbing Tan
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.15881
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Hydrogen sulfide (H2S), as an endogenous gas signaling molecule, plays an important role in plant growth regulation and resistance to abiotic stress. This study aims to investigate the mechanism of exogenous H2S on the growth and development of Reaumuria soongorica seedlings under salt stress and to determine the optimal concentration for foliar application. To investigate the regulatory effects of exogenous H2S (donor sodium hydrosulfide, NaHS) at concentrations ranging from 0 to 1 mM on reactive oxygen species (ROS), antioxidant system, and osmoregulation in R. soongorica seedlings under 300 mM NaCl stress. The growth of R. soongorica seedlings was inhibited by salt stress, which resulted in a decrease in the leaf relative water content (LRWC), specific leaf area (SLA), and soluble sugar content in leaves, elevated activity levels of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT); and accumulated superoxide anion (O2–), proline, malondialdehyde (MDA), and soluble protein content in leaves; and increased L-cysteine desulfhydrase (LCD) activity and endogenous H2S content. This indicated that a high level of ROS was produced in the leaves of R. soongorica seedlings and seriously affected the growth and development of R. soongorica seedlings. The exogenous application of different concentrations of NaHS reduced the content of O 2–, proline and MDA, increased the activity of antioxidant enzymes and the content of osmoregulators (soluble sugars and soluble proteins), while the LCD enzyme activity and the content of endogenous H2S were further increased with the continuous application of exogenous H2S. The inhibitory effects of salt stress on the growth rate of plant height and ground diameter, the LRWC, biomass, and SLA were effectively alleviated. A comprehensive analysis showed that the LRWC, POD, and proline could be used as the main indicators to evaluate the alleviating effect of exogenous H2S on R. soongorica seedlings under salt stress. The opti…
bibliographic citation: Liu et al. (2023) Exogenous hydrogen sulfide improves salt stress tolerance of Reaumuria soongorica seedlings by regulating active oxygen metabolism. PeerJ 11:e15881 https://doi.org/10.7717/peerj.15881
date submitted: 2023-03-31
date accepted: 2023-07-20
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hanghang
author list: Agent
  family name: Chong
  given name: Peifang
author list: Agent
  family name: Liu
  given name: Zehua
author list: Agent
  family name: Bao
  given name: Xinguang
author list: Agent
  family name: Tan
  given name: Bingbing
doi: 10.7717/peerj.15881
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: ©2023 Liu et al.
attribution name: Liu et al.

Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction
type: item
type: AcademicArticle
description: Background A growing number of experiments have shown that microRNAs (miRNAs) can be used as target of small molecules (SMs) to regulate gene expression for treating diseases. Therefore, identifying SM-related miRNAs is helpful for the treatment of diseases in the domain of medical investigation. Methods This article presents a new computational model, called NIRBMSMMA (neighborhood-based inference (NI) and restricted Boltzmann machine (RBM)), which we developed to identify potential small molecule-miRNA associations (NIRBMSMMA). First, grounded on known SM-miRNAs associations, SM similarity and miRNA similarity, NI was used to predict score of an unknown SM-miRNA pair by reckoning the sum of known associations between neighbors of the SM (miRNA) and the miRNA (SM). Second, utilizing a two-layered generative stochastic artificial neural network, RBM was used to predict SM-miRNA association by learning potential probability distribution from known SM-miRNA associations. At last, an ensemble learning model was conducted to combine NI and RBM for identifying potential SM-miRNA associations. Results Furthermore, we conducted global leave one out cross validation (LOOCV), miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation to assess performance of NIRBMSMMA based on three datasets. Results showed that NIRBMSMMA obtained areas under the curve (AUC) of 0.9912, 0.9875, 0.8376 and 0.9898 ± 0.0009 under global LOOCV, miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation based on dataset 1, respectively. For dataset 2, the AUCs are 0.8645, 0.8720, 0.7066 and 0.8547 ± 0.0046 in turn. For dataset 3, the AUCs are 0.9884, 0.9802, 0.8239 and 0.9870 ± 0.0015 in turn. Also, we conducted case studies to further assess the predictive performance of NIRBMSMMA. These results illustrated the proposed model is a useful tool in predicting potential SM-miRNA associations.
format: application/pdf
format: text/html
creator: Jia Qu
creator: Zihao Song
creator: Xiaolong Cheng
creator: Zhibin Jiang
creator: Jie Zhou
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.15889
publisher: PeerJ Inc.
rights: © 2023 Qu et al.
abstract: Background A growing number of experiments have shown that microRNAs (miRNAs) can be used as target of small molecules (SMs) to regulate gene expression for treating diseases. Therefore, identifying SM-related miRNAs is helpful for the treatment of diseases in the domain of medical investigation. Methods This article presents a new computational model, called NIRBMSMMA (neighborhood-based inference (NI) and restricted Boltzmann machine (RBM)), which we developed to identify potential small molecule-miRNA associations (NIRBMSMMA). First, grounded on known SM-miRNAs associations, SM similarity and miRNA similarity, NI was used to predict score of an unknown SM-miRNA pair by reckoning the sum of known associations between neighbors of the SM (miRNA) and the miRNA (SM). Second, utilizing a two-layered generative stochastic artificial neural network, RBM was used to predict SM-miRNA association by learning potential probability distribution from known SM-miRNA associations. At last, an ensemble learning model was conducted to combine NI and RBM for identifying potential SM-miRNA associations. Results Furthermore, we conducted global leave one out cross validation (LOOCV), miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation to assess performance of NIRBMSMMA based on three datasets. Results showed that NIRBMSMMA obtained areas under the curve (AUC) of 0.9912, 0.9875, 0.8376 and 0.9898 ± 0.0009 under global LOOCV, miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation based on dataset 1, respectively. For dataset 2, the AUCs are 0.8645, 0.8720, 0.7066 and 0.8547 ± 0.0046 in turn. For dataset 3, the AUCs are 0.9884, 0.9802, 0.8239 and 0.9870 ± 0.0015 in turn. Also, we conducted case studies to further assess the predictive performance of NIRBMSMMA. These results illustrated the proposed model is a useful tool in predicting potential SM-miRNA associations.
bibliographic citation: Qu et al. (2023) Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction. PeerJ 11:e15889 https://doi.org/10.7717/peerj.15889
date submitted: 2023-05-16
date accepted: 2023-07-21
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qu
  given name: Jia
author list: Agent
  family name: Song
  given name: Zihao
author list: Agent
  family name: Cheng
  given name: Xiaolong
author list: Agent
  family name: Jiang
  given name: Zhibin
author list: Agent
  family name: Zhou
  given name: Jie
doi: 10.7717/peerj.15889
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: ©2023 Qu et al.
attribution name: Qu et al.

Genetic diversity analysis and molecular characteristics of wild centipedegrass using sequence-related amplified polymorphism (SRAP) markers
type: item
type: AcademicArticle
description: Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is commonly used as a low-maintenance warm-season turfgrass owing to its excellent adaptation to various soil types. A better understanding of the genetic diversity pattern of centipedegrass is essential for the efficient development and utilization of accessions. This study used fifty-five pairs of primers to detect the genetic variation and genetic structure of twenty-three wild centipedegrass accessions by Sequence-related amplified polymorphism (SRAP) markers. A total of 919 reliable bands were amplified, among which 606 (65.80%) were polymorphic and 160 (2.91%) were the monomorphic loci. The average polymorphic information content (PIC) value was 0.228. The unweighted pair group method with arithmetic mean (UPGMA) clustering analysis grouped the twenty-three accessions into two clusters. Meanwhile, the structure analysis showed that the tested accessions possessed two main genetic memberships (K = 2). The Mantel test significantly correlated the genetic and geographic distance matrices (r = 0.3854, p = 0.000140). Furthermore, geographical groups showed moderate genetic differentiation, and the highest intragroup genetic diversity was found in the Sichuan group (He = 0.201). Overall, the present research findings could promote the protection and collection of centipedegrass and provide comprehensive information to develop novel breeding strategies.
format: application/pdf
format: text/html
creator: Xiaoyun Wang
creator: Wenlong Gou
creator: Ting Wang
creator: Yanli Xiong
creator: Yi Xiong
creator: Qingqing Yu
creator: Zhixiao Dong
creator: Xiao Ma
creator: Nanqing Liu
creator: Junming Zhao
subject: Biodiversity
subject: Genetics
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.15900
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is commonly used as a low-maintenance warm-season turfgrass owing to its excellent adaptation to various soil types. A better understanding of the genetic diversity pattern of centipedegrass is essential for the efficient development and utilization of accessions. This study used fifty-five pairs of primers to detect the genetic variation and genetic structure of twenty-three wild centipedegrass accessions by Sequence-related amplified polymorphism (SRAP) markers. A total of 919 reliable bands were amplified, among which 606 (65.80%) were polymorphic and 160 (2.91%) were the monomorphic loci. The average polymorphic information content (PIC) value was 0.228. The unweighted pair group method with arithmetic mean (UPGMA) clustering analysis grouped the twenty-three accessions into two clusters. Meanwhile, the structure analysis showed that the tested accessions possessed two main genetic memberships (K = 2). The Mantel test significantly correlated the genetic and geographic distance matrices (r = 0.3854, p = 0.000140). Furthermore, geographical groups showed moderate genetic differentiation, and the highest intragroup genetic diversity was found in the Sichuan group (He = 0.201). Overall, the present research findings could promote the protection and collection of centipedegrass and provide comprehensive information to develop novel breeding strategies.
bibliographic citation: Wang et al. (2023) Genetic diversity analysis and molecular characteristics of wild centipedegrass using sequence-related amplified polymorphism (SRAP) markers. PeerJ 11:e15900 https://doi.org/10.7717/peerj.15900
date submitted: 2023-03-29
date accepted: 2023-07-25
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiaoyun
author list: Agent
  family name: Gou
  given name: Wenlong
author list: Agent
  family name: Wang
  given name: Ting
author list: Agent
  family name: Xiong
  given name: Yanli
author list: Agent
  family name: Xiong
  given name: Yi
author list: Agent
  family name: Yu
  given name: Qingqing
author list: Agent
  family name: Dong
  given name: Zhixiao
author list: Agent
  family name: Ma
  given name: Xiao
author list: Agent
  family name: Liu
  given name: Nanqing
author list: Agent
  family name: Zhao
  given name: Junming
doi: 10.7717/peerj.15900
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Characteristics of water jump for better performance in collegiate male 3000 m steeplechase
type: item
type: AcademicArticle
description: Background The 3000 m steeplechase consists of 28 barriers and seven water-jumping obstacles. The water jump in the 3000 m steeplechase makes it different from the sprint hurdle events. It is important for coaches and athletes to understand how to clear the water jump successfully. I aimed to investigate whether the takeoff and landing distances for the water jump per lap differ between participants with good and worse records. Methods Data were collected from the men’s 3000 m steeplechase races (heats) at Kanto Intercollegiate race. A total of 48 men’s performances were analyzed (24 upper group, 24 lower group). Takeoff distance, landing distance and clearance time were analyzed. Takeoff distance, landing distance, total water jump distance and clearance time were subjected to mixed two-way ANOVAs with repeated factors of Lap (lap 1/lap 2/lap 3/lap 4/lap 5/lap 6/lap 7) with Group (upper group/lower group) as a between group factor. Results Takeoff distance was longer for upper group (1.43 m) than lower group (1.34 m) (p = .01). Landing distance was longer for upper group (2.95 m) than for lower group (2.74 m) (p = .01) and was longer for lap 1 (2.95 m) than last three laps (lap 5: 2.83 m, lap 6: 2.82 m, lap 7: 2.76 m) (p = .01). Discussion Individuals who were faster in 3000 m steeplechase exhibited longer water jump distance. The effect of fatigue might be greater for landing distance than for takeoff distance. Because the landing distance becomes shorter in the second half of the 3000 m steeplechase, it is important to note that athletes should aim to land as far away from the water pit as possible.
format: application/pdf
format: text/html
creator: Yuya Maruo
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.15918
publisher: PeerJ Inc.
rights: © 2023 Maruo
abstract: Background The 3000 m steeplechase consists of 28 barriers and seven water-jumping obstacles. The water jump in the 3000 m steeplechase makes it different from the sprint hurdle events. It is important for coaches and athletes to understand how to clear the water jump successfully. I aimed to investigate whether the takeoff and landing distances for the water jump per lap differ between participants with good and worse records. Methods Data were collected from the men’s 3000 m steeplechase races (heats) at Kanto Intercollegiate race. A total of 48 men’s performances were analyzed (24 upper group, 24 lower group). Takeoff distance, landing distance and clearance time were analyzed. Takeoff distance, landing distance, total water jump distance and clearance time were subjected to mixed two-way ANOVAs with repeated factors of Lap (lap 1/lap 2/lap 3/lap 4/lap 5/lap 6/lap 7) with Group (upper group/lower group) as a between group factor. Results Takeoff distance was longer for upper group (1.43 m) than lower group (1.34 m) (p = .01). Landing distance was longer for upper group (2.95 m) than for lower group (2.74 m) (p = .01) and was longer for lap 1 (2.95 m) than last three laps (lap 5: 2.83 m, lap 6: 2.82 m, lap 7: 2.76 m) (p = .01). Discussion Individuals who were faster in 3000 m steeplechase exhibited longer water jump distance. The effect of fatigue might be greater for landing distance than for takeoff distance. Because the landing distance becomes shorter in the second half of the 3000 m steeplechase, it is important to note that athletes should aim to land as far away from the water pit as possible.
bibliographic citation: Maruo (2023) Characteristics of water jump for better performance in collegiate male 3000 m steeplechase. PeerJ 11:e15918 https://doi.org/10.7717/peerj.15918
date submitted: 2023-06-01
date accepted: 2023-07-27
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maruo
  given name: Yuya
doi: 10.7717/peerj.15918
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: ©2023 Maruo
attribution name: Maruo

Bacillus amyloliquefaciens 11B91 inoculation enhances the growth of quinoa (Chenopodium quinoa Willd.) under salt stress
type: item
type: AcademicArticle
description: Quinoa (Chenopodium quinoa Willd.) is a highly nutritious food product with a comprehensive development prospect. Here, we discussed the effect of Bacillus amyloliquefaciens 11B91 on the growth, development and salt tolerance (salt concentrations: 0, 150, 300 mmol·L−1) of quinoa and highlighted a positive role for the application of plant growth-promoting rhizobacteria bacteria in quinoa. In this artical, the growth-promoting effect of Bacillus amyloliquefaciens 11B91 on quinoa (Longli No.1) and the changes in biomass, chlorophyll content, root activity and total phosphorus content under salt stress were measured. The results revealed that plants inoculated with 11B91 exhibited increased maximum shoot fresh weight (73.95%), root fresh weight (75.36%), root dry weight (136%), chlorophyll a (65.32%) contents and chlorophyll b (58.5%) contents, root activity (54.44%) and total phosphorus content (16.66%). Additionally, plants inoculated with 11B91 under salt stress plants showed significantly improved, fresh weight (107%), dry weight (133%), chlorophyll a (162%) contents and chlorophyll b (76.37%) contents, root activity (33.07%), and total phosphorus content (42.73%).
format: application/pdf
format: text/html
creator: Jing Li
creator: Xiaonong Guo
creator: Deyu Cai
creator: Ying Xu
creator: Yaling Wang
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15925
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Quinoa (Chenopodium quinoa Willd.) is a highly nutritious food product with a comprehensive development prospect. Here, we discussed the effect of Bacillus amyloliquefaciens 11B91 on the growth, development and salt tolerance (salt concentrations: 0, 150, 300 mmol·L−1) of quinoa and highlighted a positive role for the application of plant growth-promoting rhizobacteria bacteria in quinoa. In this artical, the growth-promoting effect of Bacillus amyloliquefaciens 11B91 on quinoa (Longli No.1) and the changes in biomass, chlorophyll content, root activity and total phosphorus content under salt stress were measured. The results revealed that plants inoculated with 11B91 exhibited increased maximum shoot fresh weight (73.95%), root fresh weight (75.36%), root dry weight (136%), chlorophyll a (65.32%) contents and chlorophyll b (58.5%) contents, root activity (54.44%) and total phosphorus content (16.66%). Additionally, plants inoculated with 11B91 under salt stress plants showed significantly improved, fresh weight (107%), dry weight (133%), chlorophyll a (162%) contents and chlorophyll b (76.37%) contents, root activity (33.07%), and total phosphorus content (42.73%).
bibliographic citation: Li et al. (2023) Bacillus amyloliquefaciens 11B91 inoculation enhances the growth of quinoa (Chenopodium quinoa Willd.) under salt stress. PeerJ 11:e15925 https://doi.org/10.7717/peerj.15925
date submitted: 2023-03-31
date accepted: 2023-07-30
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Guo
  given name: Xiaonong
author list: Agent
  family name: Cai
  given name: Deyu
author list: Agent
  family name: Xu
  given name: Ying
author list: Agent
  family name: Wang
  given name: Yaling
doi: 10.7717/peerj.15925
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: © 2023 Li et al.
attribution name: Li et al.

A decision tree model to predict liver cirrhosis in hepatocellular carcinoma patients: a retrospective study
type: item
type: AcademicArticle
description: Background The severity of liver cirrhosis in hepatocellular carcinoma (HCC) patients is essential for determining the scope of surgical resection. It also affects the long-term efficacy of systemic anti-tumor therapy and transcatheter arterial chemoembolization (TACE). Non-invasive tools, including aspartate aminotransferase to platelet ratio index (APRI), fibrosis-4 (FIB-4), and γ-glutamyl transferase to platelet ratio (GPR), are less accurate in predicting cirrhosis in HCC patients. We aimed to build a novel decision tree model to improve diagnostic accuracy of liver cirrhosis. Patients and Methods The Mann-Whitney U test, χ2 test, and multivariate logistic regression analysis were used to identify independent cirrhosis predictors. A decision tree model was developed using machine learning algorithms in a training cohort of 141 HCC patients. Internal validation was conducted in 99 HCC patients. The diagnostic accuracy and calibration of the established model were evaluated using receiver operating characteristic (ROC) and calibration curves, respectively. Results Sex and platelet count were identified as independent cirrhosis predictors. A decision tree model integrating imaging-reported cirrhosis, APRI, FIB-4, and GPR was established. The novel model had an excellent diagnostic performance in the training and validation cohorts, with area under the curve (AUC) values of 0.853 and 0.817, respectively. Calibration curves and the Hosmer-Lemeshow test showed good calibration of the novel model. The decision curve analysis (DCA) indicated that the decision tree model could provide a larger net benefit to predict liver cirrhosis. Conclusion Our developed decision tree model could successfully predict liver cirrhosis in HCC patients, which may be helpful in clinical decision-making.
format: application/pdf
format: text/html
creator: Zheyu Zhou
creator: Chaobo Chen
creator: Meiling Sun
creator: Xiaoliang Xu
creator: Yang Liu
creator: Qiaoyu Liu
creator: Jincheng Wang
creator: Yin Yin
creator: Beicheng Sun
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Pathology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.15950
publisher: PeerJ Inc.
rights: © 2023 Zhou et al.
abstract: Background The severity of liver cirrhosis in hepatocellular carcinoma (HCC) patients is essential for determining the scope of surgical resection. It also affects the long-term efficacy of systemic anti-tumor therapy and transcatheter arterial chemoembolization (TACE). Non-invasive tools, including aspartate aminotransferase to platelet ratio index (APRI), fibrosis-4 (FIB-4), and γ-glutamyl transferase to platelet ratio (GPR), are less accurate in predicting cirrhosis in HCC patients. We aimed to build a novel decision tree model to improve diagnostic accuracy of liver cirrhosis. Patients and Methods The Mann-Whitney U test, χ2 test, and multivariate logistic regression analysis were used to identify independent cirrhosis predictors. A decision tree model was developed using machine learning algorithms in a training cohort of 141 HCC patients. Internal validation was conducted in 99 HCC patients. The diagnostic accuracy and calibration of the established model were evaluated using receiver operating characteristic (ROC) and calibration curves, respectively. Results Sex and platelet count were identified as independent cirrhosis predictors. A decision tree model integrating imaging-reported cirrhosis, APRI, FIB-4, and GPR was established. The novel model had an excellent diagnostic performance in the training and validation cohorts, with area under the curve (AUC) values of 0.853 and 0.817, respectively. Calibration curves and the Hosmer-Lemeshow test showed good calibration of the novel model. The decision curve analysis (DCA) indicated that the decision tree model could provide a larger net benefit to predict liver cirrhosis. Conclusion Our developed decision tree model could successfully predict liver cirrhosis in HCC patients, which may be helpful in clinical decision-making.
bibliographic citation: Zhou et al. (2023) A decision tree model to predict liver cirrhosis in hepatocellular carcinoma patients: a retrospective study. PeerJ 11:e15950 https://doi.org/10.7717/peerj.15950
date submitted: 2023-06-16
date accepted: 2023-08-01
issued: 2023-08-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zheyu
author list: Agent
  family name: Chen
  given name: Chaobo
author list: Agent
  family name: Sun
  given name: Meiling
author list: Agent
  family name: Xu
  given name: Xiaoliang
author list: Agent
  family name: Liu
  given name: Yang
author list: Agent
  family name: Liu
  given name: Qiaoyu
author list: Agent
  family name: Wang
  given name: Jincheng
author list: Agent
  family name: Yin
  given name: Yin
author list: Agent
  family name: Sun
  given name: Beicheng
doi: 10.7717/peerj.15950
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-24
copyright: © 2023 Zhou et al.
attribution name: Zhou et al.

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