PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Lanspora dorisauae, a new marine fungus from rocky shores in Taiwan
items: Seed bio-priming with beneficial Trichoderma harzianum alleviates cold stress in maize
items: Characterization of endoplasmic reticulum-associated degradation in the human fungal pathogen Candida albicans
items: NEAL: an open-source tool for audio annotation
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

Lanspora dorisauae, a new marine fungus from rocky shores in Taiwan
type: item
type: AcademicArticle
description: This article reports a new marine fungus, Lanspora dorisauae (Phomatosporales, Sordariomycetes, Ascomycota), on trapped wood collected in coastal sites of Taiwan. This new fungus was subjected to a morphological examination and a phylogenetic study based on a combined analysis of the 18S, 28S, ITS rDNA, TEF1-α and RPB2 genes. Lanspora dorisauae is characterized by dark-coloured ascomata with a short neck, periphysate ostioles, subclavate, deliquescing asci without an apical ring, presence of wide paraphyses, striated wall ascospores with crown-like appendages on one pole of the ascospores. Phylogenetically, L. dorisauae grouped with Lanspora coronata (type species) with strong support. Lanspora coronata lacks paraphyses and appendages occur on both ends of the ascospores, while paraphyses are present and ascospore appendage is unipolar in L. dorisauae. Lanspora cylindrospora formed a sister clade with L. coronata and L. dorisauae, but it significantly differs in morphology with the latter two species in having cylindrical asci with an apical J- ring, smooth ascospore wall and no ascospore appendages, and may be better referred to a new genus. Lanspora, together with Phomatospora and Tenuimurus, belong to the Phomatosporaceae, Phomatosporales. Phomatospora berkeleyi should be sequenced to test the validity of the order Phomatosporales and the family Phomatosporaceae.
format: application/pdf
format: text/html
creator: Ka-Lai Pang
creator: Sheng-Yu Guo
creator: Ami Shaumi
creator: Satinee Suetrong
creator: Anupong Klaysuban
creator: Michael W. L. Chiang
creator: E. B. Gareth Jones
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Mycology
description: doi:10.7717/peerj.15958
publisher: PeerJ Inc.
rights: © 2023 Pang et al.
abstract: This article reports a new marine fungus, Lanspora dorisauae (Phomatosporales, Sordariomycetes, Ascomycota), on trapped wood collected in coastal sites of Taiwan. This new fungus was subjected to a morphological examination and a phylogenetic study based on a combined analysis of the 18S, 28S, ITS rDNA, TEF1-α and RPB2 genes. Lanspora dorisauae is characterized by dark-coloured ascomata with a short neck, periphysate ostioles, subclavate, deliquescing asci without an apical ring, presence of wide paraphyses, striated wall ascospores with crown-like appendages on one pole of the ascospores. Phylogenetically, L. dorisauae grouped with Lanspora coronata (type species) with strong support. Lanspora coronata lacks paraphyses and appendages occur on both ends of the ascospores, while paraphyses are present and ascospore appendage is unipolar in L. dorisauae. Lanspora cylindrospora formed a sister clade with L. coronata and L. dorisauae, but it significantly differs in morphology with the latter two species in having cylindrical asci with an apical J- ring, smooth ascospore wall and no ascospore appendages, and may be better referred to a new genus. Lanspora, together with Phomatospora and Tenuimurus, belong to the Phomatosporaceae, Phomatosporales. Phomatospora berkeleyi should be sequenced to test the validity of the order Phomatosporales and the family Phomatosporaceae.
bibliographic citation: Pang et al. (2023) Lanspora dorisauae, a new marine fungus from rocky shores in Taiwan. PeerJ 11:e15958 https://doi.org/10.7717/peerj.15958
date submitted: 2023-04-25
date accepted: 2023-08-03
issued: 2023-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pang
  given name: Ka-Lai
author list: Agent
  family name: Guo
  given name: Sheng-Yu
author list: Agent
  family name: Shaumi
  given name: Ami
author list: Agent
  family name: Suetrong
  given name: Satinee
author list: Agent
  family name: Klaysuban
  given name: Anupong
author list: Agent
  family name: Chiang
  given name: Michael W. L.
author list: Agent
  family name: Jones
  given name: E. B. Gareth
doi: 10.7717/peerj.15958
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-28
copyright: © 2023 Pang et al.
attribution name: Pang et al.

Seed bio-priming with beneficial Trichoderma harzianum alleviates cold stress in maize
type: item
type: AcademicArticle
description: Maize is one of the major crops in the world and the most productive member of the Gramineae family. Since cold stress affects the germination, growth, and productivity of corn seeds, the present study aimed to investigate the effect of seed biopriming with Trichoderma harzianum on the tolerance of two genotypes of maize seedlings to cold stress. This study was conducted in triplicates in factorial experiment with a complete randomized block design (CRBD). The study was conducted in the greenhouse and laboratory of the University of Mohaghegh Ardabili, Ardabil, Iran. Experimental factors include two cultivars (AR68 cold-resistant and KSC703 cold-sensitive maize cultivars), four pretreatment levels (control, biopriming with T. harzianum, exogenous T. harzianum, and hydropriming), and two levels of cold stress (control and cold at 5 °C) in a hydroponic culture medium. The present study showed that maize leaves’ establishment rate and maximum fluorescence (Fm) are affected by triple effects (C*, P*, S). The highest establishment (99.66%) and Fm (994 units) rates were observed in the KP3 control treatment. Moreover, among the pretreatments, the highest (0.476 days) and the lowest (0.182 days) establishment rates were related to P0 and P3 treatments, respectively. Cultivar A showed higher chlorophyll a and b, carotenoid content, and establishment rate compared to cultivar K in both optimal and cold conditions. The highest root dry weight (11.84 units) was obtained in cultivar A with P3 pretreatment. The pretreatments with T. harzianum increased physiological parameters and seedling emergence of maize under cold and optimal stress conditions. Pretreatment and cultivar improved catalase activity in roots and leaves. Higher leaf and root catalase activity was observed in the roots and leaves of cultivar K compared to cultivar A. The cold treatment significantly differed in peroxidase activity from the control treatment. Cultivar K showed higher catalase activity than cultiv…
format: application/pdf
format: text/html
creator: Mehdi Afrouz
creator: R Z. Sayyed
creator: Bahman Fazeli-Nasab
creator: Ramin Piri
creator: WaleedHassan Almalki
creator: Betty Natalie Fitriatin
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.15644
publisher: PeerJ Inc.
rights: © 2023 Afrouz et al.
abstract: Maize is one of the major crops in the world and the most productive member of the Gramineae family. Since cold stress affects the germination, growth, and productivity of corn seeds, the present study aimed to investigate the effect of seed biopriming with Trichoderma harzianum on the tolerance of two genotypes of maize seedlings to cold stress. This study was conducted in triplicates in factorial experiment with a complete randomized block design (CRBD). The study was conducted in the greenhouse and laboratory of the University of Mohaghegh Ardabili, Ardabil, Iran. Experimental factors include two cultivars (AR68 cold-resistant and KSC703 cold-sensitive maize cultivars), four pretreatment levels (control, biopriming with T. harzianum, exogenous T. harzianum, and hydropriming), and two levels of cold stress (control and cold at 5 °C) in a hydroponic culture medium. The present study showed that maize leaves’ establishment rate and maximum fluorescence (Fm) are affected by triple effects (C*, P*, S). The highest establishment (99.66%) and Fm (994 units) rates were observed in the KP3 control treatment. Moreover, among the pretreatments, the highest (0.476 days) and the lowest (0.182 days) establishment rates were related to P0 and P3 treatments, respectively. Cultivar A showed higher chlorophyll a and b, carotenoid content, and establishment rate compared to cultivar K in both optimal and cold conditions. The highest root dry weight (11.84 units) was obtained in cultivar A with P3 pretreatment. The pretreatments with T. harzianum increased physiological parameters and seedling emergence of maize under cold and optimal stress conditions. Pretreatment and cultivar improved catalase activity in roots and leaves. Higher leaf and root catalase activity was observed in the roots and leaves of cultivar K compared to cultivar A. The cold treatment significantly differed in peroxidase activity from the control treatment. Cultivar K showed higher catalase activity than cultiv…
bibliographic citation: Afrouz et al. (2023) Seed bio-priming with beneficial Trichoderma harzianum alleviates cold stress in maize. PeerJ 11:e15644 https://doi.org/10.7717/peerj.15644
date submitted: 2023-02-14
date accepted: 2023-06-05
issued: 2023-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Afrouz
  given name: Mehdi
author list: Agent
  family name: Sayyed
  given name: R Z.
author list: Agent
  family name: Fazeli-Nasab
  given name: Bahman
author list: Agent
  family name: Piri
  given name: Ramin
author list: Agent
  family name: Almalki
  given name: WaleedHassan
author list: Agent
  family name: Fitriatin
  given name: Betty Natalie
doi: 10.7717/peerj.15644
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-25
copyright: ©2023 Afrouz et al.
attribution name: Afrouz et al.

Characterization of endoplasmic reticulum-associated degradation in the human fungal pathogen Candida albicans
type: item
type: AcademicArticle
description: Background Candida albicans is the most prevalent human fungal pathogen. In immunocompromised individuals, C. albicans can cause serious systemic disease, and patients infected with drug-resistant isolates have few treatment options. The ubiquitin-proteasome system has not been thoroughly characterized in C. albicans. Research from other organisms has shown ubiquitination is important for protein quality control and regulated protein degradation at the endoplasmic reticulum (ER) via ER-associated protein degradation (ERAD). Methods Here we perform the first characterization, to our knowledge, of ERAD in a human fungal pathogen. We generated functional knockouts of C. albicans genes encoding three proteins predicted to play roles in ERAD, the ubiquitin ligases Hrd1 and Doa10 and the ubiquitin-conjugating enzyme Ubc7. We assessed the fitness of each mutant in the presence of proteotoxic stress, and we used quantitative tandem mass tag mass spectrometry to characterize proteomic alterations in yeast lacking each gene. Results Consistent with a role in protein quality control, yeast lacking proteins thought to contribute to ERAD displayed hypersensitivity to proteotoxic stress. Furthermore, each mutant displayed distinct proteomic profiles, revealing potential physiological ERAD substrates, co-factors, and compensatory stress response factors. Among candidate ERAD substrates are enzymes contributing to ergosterol synthesis, a known therapeutic vulnerability of C. albicans. Together, our results provide the first description of ERAD function in C. albicans, and, to our knowledge, any pathogenic fungus.
format: application/pdf
format: text/html
creator: Ellen M. Doss
creator: Joshua M. Moore
creator: Bryce H. Harman
creator: Emma H. Doud
creator: Eric M. Rubenstein
creator: Douglas A. Bernstein
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.15897
publisher: PeerJ Inc.
rights: © 2023 Doss et al.
abstract: Background Candida albicans is the most prevalent human fungal pathogen. In immunocompromised individuals, C. albicans can cause serious systemic disease, and patients infected with drug-resistant isolates have few treatment options. The ubiquitin-proteasome system has not been thoroughly characterized in C. albicans. Research from other organisms has shown ubiquitination is important for protein quality control and regulated protein degradation at the endoplasmic reticulum (ER) via ER-associated protein degradation (ERAD). Methods Here we perform the first characterization, to our knowledge, of ERAD in a human fungal pathogen. We generated functional knockouts of C. albicans genes encoding three proteins predicted to play roles in ERAD, the ubiquitin ligases Hrd1 and Doa10 and the ubiquitin-conjugating enzyme Ubc7. We assessed the fitness of each mutant in the presence of proteotoxic stress, and we used quantitative tandem mass tag mass spectrometry to characterize proteomic alterations in yeast lacking each gene. Results Consistent with a role in protein quality control, yeast lacking proteins thought to contribute to ERAD displayed hypersensitivity to proteotoxic stress. Furthermore, each mutant displayed distinct proteomic profiles, revealing potential physiological ERAD substrates, co-factors, and compensatory stress response factors. Among candidate ERAD substrates are enzymes contributing to ergosterol synthesis, a known therapeutic vulnerability of C. albicans. Together, our results provide the first description of ERAD function in C. albicans, and, to our knowledge, any pathogenic fungus.
bibliographic citation: Doss et al. (2023) Characterization of endoplasmic reticulum-associated degradation in the human fungal pathogen Candida albicans. PeerJ 11:e15897 https://doi.org/10.7717/peerj.15897
date submitted: 2023-05-22
date accepted: 2023-07-24
issued: 2023-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Doss
  given name: Ellen M.
author list: Agent
  family name: Moore
  given name: Joshua M.
author list: Agent
  family name: Harman
  given name: Bryce H.
author list: Agent
  family name: Doud
  given name: Emma H.
author list: Agent
  family name: Rubenstein
  given name: Eric M.
author list: Agent
  family name: Bernstein
  given name: Douglas A.
doi: 10.7717/peerj.15897
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-25
copyright: © 2023 Doss et al.
attribution name: Doss et al.

NEAL: an open-source tool for audio annotation
type: item
type: AcademicArticle
description: Passive acoustic monitoring is used widely in ecology, biodiversity, and conservation studies. Data sets collected via acoustic monitoring are often extremely large and built to be processed automatically using artificial intelligence and machine learning models, which aim to replicate the work of domain experts. These models, being supervised learning algorithms, need to be trained on high quality annotations produced by experts. Since the experts are often resource-limited, a cost-effective process for annotating audio is needed to get maximal use out of the data. We present an open-source interactive audio data annotation tool, NEAL (Nature+Energy Audio Labeller). Built using R and the associated Shiny framework, the tool provides a reactive environment where users can quickly annotate audio files and adjust settings that automatically change the corresponding elements of the user interface. The app has been designed with the goal of having both expert birders and citizen scientists contribute to acoustic annotation projects. The popularity and flexibility of R programming in bioacoustics means that the Shiny app can be modified for other bird labelling data sets, or even to generic audio labelling tasks. We demonstrate the app by labelling data collected from wind farm sites across Ireland.
format: application/pdf
format: text/html
creator: Anthony Gibbons
creator: Ian Donohue
creator: Courtney Gorman
creator: Emma King
creator: Andrew Parnell
subject: Bioinformatics
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.15913
publisher: PeerJ Inc.
rights: © 2023 Gibbons et al.
abstract: Passive acoustic monitoring is used widely in ecology, biodiversity, and conservation studies. Data sets collected via acoustic monitoring are often extremely large and built to be processed automatically using artificial intelligence and machine learning models, which aim to replicate the work of domain experts. These models, being supervised learning algorithms, need to be trained on high quality annotations produced by experts. Since the experts are often resource-limited, a cost-effective process for annotating audio is needed to get maximal use out of the data. We present an open-source interactive audio data annotation tool, NEAL (Nature+Energy Audio Labeller). Built using R and the associated Shiny framework, the tool provides a reactive environment where users can quickly annotate audio files and adjust settings that automatically change the corresponding elements of the user interface. The app has been designed with the goal of having both expert birders and citizen scientists contribute to acoustic annotation projects. The popularity and flexibility of R programming in bioacoustics means that the Shiny app can be modified for other bird labelling data sets, or even to generic audio labelling tasks. We demonstrate the app by labelling data collected from wind farm sites across Ireland.
bibliographic citation: Gibbons et al. (2023) NEAL: an open-source tool for audio annotation. PeerJ 11:e15913 https://doi.org/10.7717/peerj.15913
date submitted: 2023-04-13
date accepted: 2023-07-26
issued: 2023-08-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gibbons
  given name: Anthony
author list: Agent
  family name: Donohue
  given name: Ian
author list: Agent
  family name: Gorman
  given name: Courtney
author list: Agent
  family name: King
  given name: Emma
author list: Agent
  family name: Parnell
  given name: Andrew
doi: 10.7717/peerj.15913
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-25
copyright: ©2023 Gibbons et al.
attribution name: Gibbons et al.

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.
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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.

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