PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Novel rapid identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by real-time RT-PCR using BD Max Open System in Taiwan
items: Contribution of prokaryotes and eukaryotes to CO2 emissions in the wastewater treatment process
items: Factors promoting the natural regeneration of Larix principis-rupprechtii plantation in the Lvliang Mountains of central China
items: Isolation, diversity, and antimicrobial activity of fungal endophytes from Rohdea chinensis (Baker) N.Tanaka (synonym Tupistra chinensis Baker) of Qinling Mountains, China
items: Identification of candidate genes and prognostic value analysis in patients with PDL1-positive and PDL1-negative lung adenocarcinoma
items: Near-infrared-light pre-treatment attenuates noise-induced hearing loss in mice
items: Identification of SPRR3 as a novel diagnostic/prognostic biomarker for oral squamous cell carcinoma via RNA sequencing and bioinformatic analyses
items: CRISPR 2 PCR and high resolution melting profiling for identification and characterization of clinically-relevant Salmonella enterica subsp. enterica
items: Quality of life after hip fracture: a 12-month prospective study
items: Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils

Novel rapid identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by real-time RT-PCR using BD Max Open System in Taiwan
type: item
type: AcademicArticle
description: Coronavirus disease 2019 has become a worldwide pandemic. By April 7, 2020, approximately 1,279,722 confirmed cases were reported worldwide including those in Asia, European Region, African Region and Region of the Americas. Rapid and accurate detection of Severe Acute Respiratory Syndrome Virus 2 (SARS-CoV-2) is critical for patient care and implementing public health measures to control the spread of infection. In this study, we developed and validated a rapid total nucleic acid extraction method based on real‐time RT-PCR for reliable, high‐throughput identification of SARS-CoV-2 using the BD MAX platform. For clinical validation, 300 throat swab and 100 sputum clinical samples were examined by both the BD MAX platform and in-house real-time RT-PCR methods, which showed 100% concordant results. This BD MAX protocol is fully automated and the turnaround time from sample to results is approximately 2.5 h for 24 samples compared to 4.8 h by in-house real-time RT-PCR. Our developed BD MAX RT-PCR assay can accurately identify SARS-CoV-2 infection and shorten the turnaround time to increase the effectiveness of control and prevention measures for this emerging infectious disease.
format: application/pdf
format: text/html
creator: Cherng-Lih Perng
creator: Ming-Jr Jian
creator: Chih-Kai Chang
creator: Jung-Chung Lin
creator: Kuo-Ming Yeh
creator: Chien-Wen Chen
creator: Sheng-Kang Chiu
creator: Hsing-Yi Chung
creator: Yi-Hui Wang
creator: Shu-Jung Liao
creator: Shih-Yi Li
creator: Shan-Shan Hsieh
creator: Shih-Hung Tsai
creator: Feng-Yee Chang
creator: Hung-Sheng Shang
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.9318
publisher: PeerJ Inc.
rights: © 2020 Perng et al.
abstract: Coronavirus disease 2019 has become a worldwide pandemic. By April 7, 2020, approximately 1,279,722 confirmed cases were reported worldwide including those in Asia, European Region, African Region and Region of the Americas. Rapid and accurate detection of Severe Acute Respiratory Syndrome Virus 2 (SARS-CoV-2) is critical for patient care and implementing public health measures to control the spread of infection. In this study, we developed and validated a rapid total nucleic acid extraction method based on real‐time RT-PCR for reliable, high‐throughput identification of SARS-CoV-2 using the BD MAX platform. For clinical validation, 300 throat swab and 100 sputum clinical samples were examined by both the BD MAX platform and in-house real-time RT-PCR methods, which showed 100% concordant results. This BD MAX protocol is fully automated and the turnaround time from sample to results is approximately 2.5 h for 24 samples compared to 4.8 h by in-house real-time RT-PCR. Our developed BD MAX RT-PCR assay can accurately identify SARS-CoV-2 infection and shorten the turnaround time to increase the effectiveness of control and prevention measures for this emerging infectious disease.
bibliographic citation: Perng et al. (2020) Novel rapid identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by real-time RT-PCR using BD Max Open System in Taiwan. PeerJ 8:e9318 https://doi.org/10.7717/peerj.9318
date submitted: 2020-04-20
date accepted: 2020-05-17
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Perng
  given name: Cherng-Lih
author list: Agent
  family name: Jian
  given name: Ming-Jr
author list: Agent
  family name: Chang
  given name: Chih-Kai
author list: Agent
  family name: Lin
  given name: Jung-Chung
author list: Agent
  family name: Yeh
  given name: Kuo-Ming
author list: Agent
  family name: Chen
  given name: Chien-Wen
author list: Agent
  family name: Chiu
  given name: Sheng-Kang
author list: Agent
  family name: Chung
  given name: Hsing-Yi
author list: Agent
  family name: Wang
  given name: Yi-Hui
author list: Agent
  family name: Liao
  given name: Shu-Jung
author list: Agent
  family name: Li
  given name: Shih-Yi
author list: Agent
  family name: Hsieh
  given name: Shan-Shan
author list: Agent
  family name: Tsai
  given name: Shih-Hung
author list: Agent
  family name: Chang
  given name: Feng-Yee
author list: Agent
  family name: Shang
  given name: Hung-Sheng
doi: 10.7717/peerj.9318
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: © 2020 Perng et al.
attribution name: Perng et al.

Contribution of prokaryotes and eukaryotes to CO2 emissions in the wastewater treatment process
type: item
type: AcademicArticle
description: Reduction of the greenhouse effect is primarily associated with the reduction of greenhouse gas (GHG) emissions. Carbon dioxide (CO2) is one of the gases that increases the greenhouse effect - it is responsible for about half of the greenhouse effect. Significant sources of CO2 are wastewater treatment plants (WWTPs) and waste management, with about 3% contribution to global emissions. CO2 is produced mainly in the aerobic stage of wastewater purification and is a consequence of activated sludge activity. Although the roles of activated sludge components in the purification process have been studied quite well, their quantitative contribution to CO2 emissions is still unknown. The emission of CO2 caused by prokaryotes and eukaryotes over the course of a year (taking into account subsequent seasons) in model sequencing batch reactors (SBR) is presented in this study. In this work, for the first time, we aimed to quantify this contribution of eukaryotic organisms to total CO2 emissions during the WWTP process. It is of the order of several or more ppm. The contribution of CO2 produced by different components of activated sludge in WWTPs can improve estimation of the emissions of GHGs in this area of human activity.
format: application/pdf
format: text/html
creator: Katarzyna Jaromin-Gleń
creator: Roman Babko
creator: Tatiana Kuzmina
creator: Yaroslav Danko
creator: Grzegorz Łagód
creator: Cezary Polakowski
creator: Joanna Szulżyk-Cieplak
creator: Andrzej Bieganowski
subject: Agricultural Science
subject: Climate Change Biology
description: doi:10.7717/peerj.9325
publisher: PeerJ Inc.
rights: © 2020 Jaromin-Gleń et al.
abstract: Reduction of the greenhouse effect is primarily associated with the reduction of greenhouse gas (GHG) emissions. Carbon dioxide (CO2) is one of the gases that increases the greenhouse effect - it is responsible for about half of the greenhouse effect. Significant sources of CO2 are wastewater treatment plants (WWTPs) and waste management, with about 3% contribution to global emissions. CO2 is produced mainly in the aerobic stage of wastewater purification and is a consequence of activated sludge activity. Although the roles of activated sludge components in the purification process have been studied quite well, their quantitative contribution to CO2 emissions is still unknown. The emission of CO2 caused by prokaryotes and eukaryotes over the course of a year (taking into account subsequent seasons) in model sequencing batch reactors (SBR) is presented in this study. In this work, for the first time, we aimed to quantify this contribution of eukaryotic organisms to total CO2 emissions during the WWTP process. It is of the order of several or more ppm. The contribution of CO2 produced by different components of activated sludge in WWTPs can improve estimation of the emissions of GHGs in this area of human activity.
bibliographic citation: Jaromin-Gleń et al. (2020) Contribution of prokaryotes and eukaryotes to CO2 emissions in the wastewater treatment process. PeerJ 8:e9325 https://doi.org/10.7717/peerj.9325
date submitted: 2019-12-03
date accepted: 2020-05-18
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jaromin-Gleń
  given name: Katarzyna
author list: Agent
  family name: Babko
  given name: Roman
author list: Agent
  family name: Kuzmina
  given name: Tatiana
author list: Agent
  family name: Danko
  given name: Yaroslav
author list: Agent
  family name: Łagód
  given name: Grzegorz
author list: Agent
  family name: Polakowski
  given name: Cezary
author list: Agent
  family name: Szulżyk-Cieplak
  given name: Joanna
author list: Agent
  family name: Bieganowski
  given name: Andrzej
doi: 10.7717/peerj.9325
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: © 2020 Jaromin-Gleń et al.
attribution name: Jaromin-Gleń et al.

Factors promoting the natural regeneration of Larix principis-rupprechtii plantation in the Lvliang Mountains of central China
type: item
type: AcademicArticle
description: Given their complexity, targeted care and management of different areas and tree species are necessary for enhancing the natural regeneration of forests. Thus, an understanding of changes in the overstory and understory is essential for ensuring successful regeneration. Promoting the natural regeneration of Larix principis-rupprechtii plantations is considered challenging; indeed, regional sustainable development through natural regeneration of many stands has often been considered unattainable. Here, we studied several plots with varying extents of regeneration to identify the most important factors that affect regeneration. The plots were divided into three forest types based on the number of regenerating plants. For each type of plot, we measured various factors that might potentially affect regeneration. Representational difference analysis was used to identify the most important factors >9% contribution). Based on these factors, multiple corrections were made to construct a structural equation model of topography, stand structure, soil properties and litter to identify the most important factors driving variation in regeneration. Positive correlations were detected between regeneration with diameter at breast height (0.21) and litter thickness (0.57). Regeneration was negatively correlated with soil (−0.54) and slope (−0.48). Additionally, the number of regenerating plants and the height of regenerating plants were strongly positively correlated. However, there was no significant relationship between regeneration and litter accumulation, stand density, altitude, average tree height, total P and total N. Overall, our study showed that key factors for promoting natural regeneration include appropriate litter thickness, strong parent trees, a gentle slope and sufficient quantities of soil nutrients. Moreover, our findings provide a reference for the design of effective management and restoration plans.
format: application/pdf
format: text/html
creator: Wenjun Liang
creator: Xi Wei
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.9339
publisher: PeerJ Inc.
rights: © 2020 Liang and Wei
abstract: Given their complexity, targeted care and management of different areas and tree species are necessary for enhancing the natural regeneration of forests. Thus, an understanding of changes in the overstory and understory is essential for ensuring successful regeneration. Promoting the natural regeneration of Larix principis-rupprechtii plantations is considered challenging; indeed, regional sustainable development through natural regeneration of many stands has often been considered unattainable. Here, we studied several plots with varying extents of regeneration to identify the most important factors that affect regeneration. The plots were divided into three forest types based on the number of regenerating plants. For each type of plot, we measured various factors that might potentially affect regeneration. Representational difference analysis was used to identify the most important factors >9% contribution). Based on these factors, multiple corrections were made to construct a structural equation model of topography, stand structure, soil properties and litter to identify the most important factors driving variation in regeneration. Positive correlations were detected between regeneration with diameter at breast height (0.21) and litter thickness (0.57). Regeneration was negatively correlated with soil (−0.54) and slope (−0.48). Additionally, the number of regenerating plants and the height of regenerating plants were strongly positively correlated. However, there was no significant relationship between regeneration and litter accumulation, stand density, altitude, average tree height, total P and total N. Overall, our study showed that key factors for promoting natural regeneration include appropriate litter thickness, strong parent trees, a gentle slope and sufficient quantities of soil nutrients. Moreover, our findings provide a reference for the design of effective management and restoration plans.
bibliographic citation: Liang et al. (2020) Factors promoting the natural regeneration of Larix principis-rupprechtii plantation in the Lvliang Mountains of central China. PeerJ 8:e9339 https://doi.org/10.7717/peerj.9339
date submitted: 2020-02-17
date accepted: 2020-05-20
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Wenjun
author list: Agent
  family name: Wei
  given name: Xi
doi: 10.7717/peerj.9339
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: ©2020 Liang and Wei
attribution name: Liang and Wei

Isolation, diversity, and antimicrobial activity of fungal endophytes from Rohdea chinensis (Baker) N.Tanaka (synonym Tupistra chinensis Baker) of Qinling Mountains, China
type: item
type: AcademicArticle
description: Endophytic fungi have been emerged as fruitful resources for producing structurally fascinating and biologically active secondary metabolites. However, endophytic fungi from medicinal plants of Qinling Mountains–the most important natural climatic boundary between the subtropical and warm temperate zones of China with an astonishingly high level of biodiversity–have rarely been explored as potential sources of novel fungal species and active secondary metabolites. In this study, a total of 371 fungal colonies were successfully isolated from 510 tissue segments of the medicinal Tupistra chinensis Baker collected from Qinling Mountains, China. Roots of T. chinensis Baker are used as a folk medicine to ameliorate pharyngitis and treat rheumatic diseases. A total of 100 representative morphotype strains were identified according to ITS rDNA sequence analyses and were grouped into three phyla (Ascomycota, Basidiomycota, Mucoromycota), seven classes (Dothideomycetes, Sordariomycetes, Eurotiomycetes, Microbotryomycetes, Agaricomycetes, Leotiomycetes, Mortierellomycetes), and at least 35 genera. The genera of Collectotrichum (IF, 29.92%), Fusarium (IF, 8.36%), Aspergillus (IF, 8.09%), and Dactylonectria (IF, 5.39%) were most frequently isolated from the tissues of T. chinensis Baker. The Species Richness Index (S, 65) and the Shannon-Wiener Index (H′, 3.7914) indicated that T. chinensis Baker harbored abundant fungal resources. Moreover, five isolates were potential new taxa because of low similarity of ITS sequences ranged from 95.09%∼96.61%. Fifteen out of 100 endophytic fungal ethyl acetate extracts exhibited inhibitory activities against at least one pathogenic bacterium or fungus. Two important lead compounds produced by two stains (F8047 and F8075) with high antimicrobial activities were identified using high performance liquid chromatography (HPLC) and ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC–QTOF MS) analyses. In addi…
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creator: Chao An
creator: Saijian Ma
creator: Xinwei Shi
creator: Wenjiao Xue
creator: Chen Liu
creator: Hao Ding
subject: Biodiversity
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.9342
publisher: PeerJ Inc.
rights: © 2020 An et al.
abstract: Endophytic fungi have been emerged as fruitful resources for producing structurally fascinating and biologically active secondary metabolites. However, endophytic fungi from medicinal plants of Qinling Mountains–the most important natural climatic boundary between the subtropical and warm temperate zones of China with an astonishingly high level of biodiversity–have rarely been explored as potential sources of novel fungal species and active secondary metabolites. In this study, a total of 371 fungal colonies were successfully isolated from 510 tissue segments of the medicinal Tupistra chinensis Baker collected from Qinling Mountains, China. Roots of T. chinensis Baker are used as a folk medicine to ameliorate pharyngitis and treat rheumatic diseases. A total of 100 representative morphotype strains were identified according to ITS rDNA sequence analyses and were grouped into three phyla (Ascomycota, Basidiomycota, Mucoromycota), seven classes (Dothideomycetes, Sordariomycetes, Eurotiomycetes, Microbotryomycetes, Agaricomycetes, Leotiomycetes, Mortierellomycetes), and at least 35 genera. The genera of Collectotrichum (IF, 29.92%), Fusarium (IF, 8.36%), Aspergillus (IF, 8.09%), and Dactylonectria (IF, 5.39%) were most frequently isolated from the tissues of T. chinensis Baker. The Species Richness Index (S, 65) and the Shannon-Wiener Index (H′, 3.7914) indicated that T. chinensis Baker harbored abundant fungal resources. Moreover, five isolates were potential new taxa because of low similarity of ITS sequences ranged from 95.09%∼96.61%. Fifteen out of 100 endophytic fungal ethyl acetate extracts exhibited inhibitory activities against at least one pathogenic bacterium or fungus. Two important lead compounds produced by two stains (F8047 and F8075) with high antimicrobial activities were identified using high performance liquid chromatography (HPLC) and ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC–QTOF MS) analyses. In addi…
bibliographic citation: An et al. (2020) Isolation, diversity, and antimicrobial activity of fungal endophytes from Rohdea chinensis (Baker) N.Tanaka (synonym Tupistra chinensis Baker) of Qinling Mountains, China. PeerJ 8:e9342 https://doi.org/10.7717/peerj.9342
date submitted: 2019-08-30
date accepted: 2020-05-21
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: An
  given name: Chao
author list: Agent
  family name: Ma
  given name: Saijian
author list: Agent
  family name: Shi
  given name: Xinwei
author list: Agent
  family name: Xue
  given name: Wenjiao
author list: Agent
  family name: Liu
  given name: Chen
author list: Agent
  family name: Ding
  given name: Hao
doi: 10.7717/peerj.9342
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: ©2020 An et al.
attribution name: An et al.

Identification of candidate genes and prognostic value analysis in patients with PDL1-positive and PDL1-negative lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Increasing bodies of evidence reveal that targeting a programmed cell death protein 1 (PD-1) monoclonal antibody is a promising immunotherapy for lung adenocarcinoma. Although PD receptor ligand 1 (PDL1) expression is widely recognized as the most powerful predictive biomarker for anti-PD-1 therapy, its regulatory mechanisms in lung adenocarcinoma remain unclear. Therefore, we conducted this study to explore differentially expressed genes (DEGs) and elucidate the regulatory mechanism of PDL1 in lung adenocarcinoma. Methods The GSE99995 data set was obtained from the Gene Expression Omnibus (GEO) database. Patients with and without PDL1 expression were divided into PDL1-positive and PDL1-negative groups, respectively. DEGs were screened using R. The Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) were analyzed using the Database for Annotation, Visualization and Integrated Discovery. Protein–protein interaction (PPI) networks of DEGs was visualized using Cytoscape, and the MNC algorithm was applied to screen hub genes. A survival analysis involving Gene Expression Profiling Interactive Analysis was used to verify the GEO results. Mutation characteristics of the hub genes were further analyzed in a combined study of five datasets in The Cancer Genome Atlas (TCGA) database. Results In total, 869 DEGs were identified, 387 in the PDL1-positive group and 482 in the PDL1-negative group. GO and KEGG analysis results of the PDL1-positive group mainly exhibited enrichment of biological processes and pathways related to cell adhesion and the peroxisome proliferators-activated receptors (PPAR) signaling pathway, whereas biological process and pathways associated with cell division and repair were mainly enriched in the PDL1-negative group. The top 10 hub genes were screened during the PPI network analysis. Notably, survival analysis revealed BRCA1, mainly involved in cell cycle and DNA damage responses, to be a novel prognostic indicato…
format: application/pdf
format: text/html
creator: Xiaoguang Qi
creator: Chunyan Qi
creator: Xindan Kang
creator: Yi Hu
creator: Weidong Han
subject: Bioinformatics
subject: Immunology
subject: Oncology
subject: Respiratory Medicine
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.9362
publisher: PeerJ Inc.
rights: © 2020 Qi et al.
abstract: Background Increasing bodies of evidence reveal that targeting a programmed cell death protein 1 (PD-1) monoclonal antibody is a promising immunotherapy for lung adenocarcinoma. Although PD receptor ligand 1 (PDL1) expression is widely recognized as the most powerful predictive biomarker for anti-PD-1 therapy, its regulatory mechanisms in lung adenocarcinoma remain unclear. Therefore, we conducted this study to explore differentially expressed genes (DEGs) and elucidate the regulatory mechanism of PDL1 in lung adenocarcinoma. Methods The GSE99995 data set was obtained from the Gene Expression Omnibus (GEO) database. Patients with and without PDL1 expression were divided into PDL1-positive and PDL1-negative groups, respectively. DEGs were screened using R. The Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) were analyzed using the Database for Annotation, Visualization and Integrated Discovery. Protein–protein interaction (PPI) networks of DEGs was visualized using Cytoscape, and the MNC algorithm was applied to screen hub genes. A survival analysis involving Gene Expression Profiling Interactive Analysis was used to verify the GEO results. Mutation characteristics of the hub genes were further analyzed in a combined study of five datasets in The Cancer Genome Atlas (TCGA) database. Results In total, 869 DEGs were identified, 387 in the PDL1-positive group and 482 in the PDL1-negative group. GO and KEGG analysis results of the PDL1-positive group mainly exhibited enrichment of biological processes and pathways related to cell adhesion and the peroxisome proliferators-activated receptors (PPAR) signaling pathway, whereas biological process and pathways associated with cell division and repair were mainly enriched in the PDL1-negative group. The top 10 hub genes were screened during the PPI network analysis. Notably, survival analysis revealed BRCA1, mainly involved in cell cycle and DNA damage responses, to be a novel prognostic indicato…
bibliographic citation: Qi et al. (2020) Identification of candidate genes and prognostic value analysis in patients with PDL1-positive and PDL1-negative lung adenocarcinoma. PeerJ 8:e9362 https://doi.org/10.7717/peerj.9362
date submitted: 2020-02-14
date accepted: 2020-05-25
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Xiaoguang
author list: Agent
  family name: Qi
  given name: Chunyan
author list: Agent
  family name: Kang
  given name: Xindan
author list: Agent
  family name: Hu
  given name: Yi
author list: Agent
  family name: Han
  given name: Weidong
doi: 10.7717/peerj.9362
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: ©2020 Qi et al.
attribution name: Qi et al.

Near-infrared-light pre-treatment attenuates noise-induced hearing loss in mice
type: item
type: AcademicArticle
description: Noise induced hearing loss (NIHL) is accompanied by a reduction of cochlear hair cells and spiral ganglion neurons. Different approaches have been applied to prevent noise induced apoptosis / necrosis. Physical intervention is one technique currently under investigation. Specific wavelengths within the near-infrared light (NIR)-spectrum are known to influence cytochrome-c-oxidase activity, which leads in turn to a decrease in apoptotic mechanisms. It has been shown recently that NIR can significantly decrease the cochlear hair cell loss if applied daily for 12 days after a noise exposure. However, it is still unclear if a single NIR-treatment, just before a noise exposure, could induce similar protective effects. Therefore, the present study was conducted to investigate the effect of a single NIR-pre-treatment aimed at preventing or limiting NIHL. The cochleae of adult NMRI-mice were pre-treated with NIR-light (808 nm, 120 mW) for 5, 10, 20, 30 or 40 minutes via the external ear canal. All animals were noised exposed immediately after the pre-treatment by broad band noise (5–20 kHz) for 30 minutes at 115 dB SPL. Frequency specific ABR-recordings to determine auditory threshold shift were carried out before the pre-treatment and two weeks after the noise exposure. The amplitude increase for wave IV and cochlear hair cell loss were determined. A further group of similar mice was noise exposed only and served as a control for the NIR pre-exposed groups. Two weeks after noise exposure, the ABR threshold shifts of NIR-treated animals were significantly lower (p < 0.05) than those of the control animals. The significance was at three frequencies for the 5-minute pre-treatment group and across the entire frequency range for all other treatment groups. Due to NIR light, the amplitude of wave four deteriorates significantly less after noise exposure than in controls. The NIR pre-treatment had no effect on the loss of outer hair cells, which was just as high with or without N…
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format: text/html
creator: Dietmar Basta
creator: Moritz Gröschel
creator: Ira Strübing
creator: Patrick Boyle
creator: Felix Fröhlich
creator: Arne Ernst
creator: Rainer Seidl
subject: Neuroscience
subject: Neurology
subject: Otorhinolaryngology
description: doi:10.7717/peerj.9384
publisher: PeerJ Inc.
rights: © 2020 Basta et al.
abstract: Noise induced hearing loss (NIHL) is accompanied by a reduction of cochlear hair cells and spiral ganglion neurons. Different approaches have been applied to prevent noise induced apoptosis / necrosis. Physical intervention is one technique currently under investigation. Specific wavelengths within the near-infrared light (NIR)-spectrum are known to influence cytochrome-c-oxidase activity, which leads in turn to a decrease in apoptotic mechanisms. It has been shown recently that NIR can significantly decrease the cochlear hair cell loss if applied daily for 12 days after a noise exposure. However, it is still unclear if a single NIR-treatment, just before a noise exposure, could induce similar protective effects. Therefore, the present study was conducted to investigate the effect of a single NIR-pre-treatment aimed at preventing or limiting NIHL. The cochleae of adult NMRI-mice were pre-treated with NIR-light (808 nm, 120 mW) for 5, 10, 20, 30 or 40 minutes via the external ear canal. All animals were noised exposed immediately after the pre-treatment by broad band noise (5–20 kHz) for 30 minutes at 115 dB SPL. Frequency specific ABR-recordings to determine auditory threshold shift were carried out before the pre-treatment and two weeks after the noise exposure. The amplitude increase for wave IV and cochlear hair cell loss were determined. A further group of similar mice was noise exposed only and served as a control for the NIR pre-exposed groups. Two weeks after noise exposure, the ABR threshold shifts of NIR-treated animals were significantly lower (p < 0.05) than those of the control animals. The significance was at three frequencies for the 5-minute pre-treatment group and across the entire frequency range for all other treatment groups. Due to NIR light, the amplitude of wave four deteriorates significantly less after noise exposure than in controls. The NIR pre-treatment had no effect on the loss of outer hair cells, which was just as high with or without N…
bibliographic citation: Basta et al. (2020) Near-infrared-light pre-treatment attenuates noise-induced hearing loss in mice. PeerJ 8:e9384 https://doi.org/10.7717/peerj.9384
date submitted: 2020-01-07
date accepted: 2020-05-28
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Basta
  given name: Dietmar
author list: Agent
  family name: Gröschel
  given name: Moritz
author list: Agent
  family name: Strübing
  given name: Ira
author list: Agent
  family name: Boyle
  given name: Patrick
author list: Agent
  family name: Fröhlich
  given name: Felix
author list: Agent
  family name: Ernst
  given name: Arne
author list: Agent
  family name: Seidl
  given name: Rainer
doi: 10.7717/peerj.9384
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: ©2020 Basta et al.
attribution name: Basta et al.

Identification of SPRR3 as a novel diagnostic/prognostic biomarker for oral squamous cell carcinoma via RNA sequencing and bioinformatic analyses
type: item
type: AcademicArticle
description: Oral squamous cell carcinoma (OSCC) has always been one of the most aggressive and invasive cancers among oral and maxillofacial malignancies. As the morbidity and mortality of the disease have increased year by year, the search for a promising diagnostic and prognostic biomarker for the disease is becoming increasingly urgent. Tumorous and adjacent tissues were collected from three OSCC sufferers and we obtained 229 differentially expressed genes (DEGs) between tumor and normal tissues via high-throughput RNA sequence. Function and pathway enrichment analyses for DEGs were conducted to find a correlation between tumorigenesis status and DEGs. Protein interaction network and molecular complex detection (MCODE) were constructed to detect core modules. Two modules were enriched in MCODE. The diagnostic and prognostic values of the candidate genes were analyzed, which provided evidence for the candidate genes as new tumor markers. Small Proline Rich Protein 3 (SPRR3), a potential tumor marker that may be useful for the diagnosis of OSCC, was screened out. The survival analysis showed that SPRR3 under expression predicted the poor prognosis of OSCC patients. Further experiments have also shown that the expression of SPRR3 decreased as the malignancy of OSCC increased. Therefore, we believe that SPRR3 could be used as a novel diagnostic and prognostic tumor marker.
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creator: Lu Yu
creator: Zongcheng Yang
creator: Yingjiao Liu
creator: Fen Liu
creator: Wenjing Shang
creator: Wei Shao
creator: Yue Wang
creator: Man Xu
creator: Ya-nan Wang
creator: Yue Fu
creator: Xin Xu
subject: Bioinformatics
subject: Genomics
subject: Dentistry
subject: Oncology
description: doi:10.7717/peerj.9393
publisher: PeerJ Inc.
rights: © 2020 Yu et al.
abstract: Oral squamous cell carcinoma (OSCC) has always been one of the most aggressive and invasive cancers among oral and maxillofacial malignancies. As the morbidity and mortality of the disease have increased year by year, the search for a promising diagnostic and prognostic biomarker for the disease is becoming increasingly urgent. Tumorous and adjacent tissues were collected from three OSCC sufferers and we obtained 229 differentially expressed genes (DEGs) between tumor and normal tissues via high-throughput RNA sequence. Function and pathway enrichment analyses for DEGs were conducted to find a correlation between tumorigenesis status and DEGs. Protein interaction network and molecular complex detection (MCODE) were constructed to detect core modules. Two modules were enriched in MCODE. The diagnostic and prognostic values of the candidate genes were analyzed, which provided evidence for the candidate genes as new tumor markers. Small Proline Rich Protein 3 (SPRR3), a potential tumor marker that may be useful for the diagnosis of OSCC, was screened out. The survival analysis showed that SPRR3 under expression predicted the poor prognosis of OSCC patients. Further experiments have also shown that the expression of SPRR3 decreased as the malignancy of OSCC increased. Therefore, we believe that SPRR3 could be used as a novel diagnostic and prognostic tumor marker.
bibliographic citation: Yu et al. (2020) Identification of SPRR3 as a novel diagnostic/prognostic biomarker for oral squamous cell carcinoma via RNA sequencing and bioinformatic analyses. PeerJ 8:e9393 https://doi.org/10.7717/peerj.9393
date submitted: 2019-12-27
date accepted: 2020-05-29
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Yu
  given name: Lu
author list: Agent
  family name: Yang
  given name: Zongcheng
author list: Agent
  family name: Liu
  given name: Yingjiao
author list: Agent
  family name: Liu
  given name: Fen
author list: Agent
  family name: Shang
  given name: Wenjing
author list: Agent
  family name: Shao
  given name: Wei
author list: Agent
  family name: Wang
  given name: Yue
author list: Agent
  family name: Xu
  given name: Man
author list: Agent
  family name: Wang
  given name: Ya-nan
author list: Agent
  family name: Fu
  given name: Yue
author list: Agent
  family name: Xu
  given name: Xin
doi: 10.7717/peerj.9393
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: © 2020 Yu et al.
attribution name: Yu et al.

CRISPR 2 PCR and high resolution melting profiling for identification and characterization of clinically-relevant Salmonella enterica subsp. enterica
type: item
type: AcademicArticle
description: Background Nontyphoidal Salmonella spp. constitute a major bacterial cause of food poisoning. Each Salmonella serotype causes distinct virulence to humans. Method A small cohort study was conducted to characterize several aspects of Salmonella isolates obtained from stool of diarrheal patients (n = 26) admitted to Phayao Ram Hospital, Phayao province, Thailand. A simple CRISPR 2 molecular analysis was developed to rapidly type Salmonella isolates employing both uniplex and high resolution melting (HRM) curve analysis. Results CRISPR 2 monoplex PCR generated a single Salmonella serotype-specific amplicon, showing S. 4,[5],12:i:- with highest frequency (42%), S. Enteritidis (15%) and S. Stanley (11%); S. Typhimurium was not detected. CRISPR 2 HRM-PCR allowed further classification of S. 4,[5],12:i:- isolates based on their specific CRISPR 2 signature sequences. The highest prevalence of Salmonella infection was during the summer season (April to August). Additional studies were conducted using standard multiplex HRM-PCR typing, which confirmed CRISPR 2 PCR results and, using a machine-learning algorithm, clustered the majority of Salmonella serotypes into six clades; repetitive element-based (ERIC) PCR, which clustered the serotypes into three clades only; antibiogram profiling, which revealed the majority resistant to ampicillin (69%); and test for extended spectrum β-lactamase production (two isolates) and PCR-based detection of bla alleles. Conclusion CRISPR 2 PCR provided a simple assay for detection and identification of clinically-relevant Salmonella serotypes. In conjunction with antibiogram profiling and rapid assay for β-lactamase producers, this approach should facilitate detection and appropriate treatment of Salmonellosis in a local hospital setting. In addition, CRISPR 2 HRM-PCR profiling enabled clustering of S. 4,[5],12:i:-isolates according to CRISPR 2 locus signature sequences, indicative of their different evolutionary trajectories, thereby providing…
format: application/pdf
format: text/html
creator: Nuttachat Wisittipanit
creator: Chaiwat Pulsrikarn
creator: Sudarat Srisong
creator: Rungthiwa Srimora
creator: Nattinee Kittiwan
creator: Kritchai Poonchareon
subject: Microbiology
subject: Epidemiology
description: doi:10.7717/peerj.9113
publisher: PeerJ Inc.
rights: © 2020 Wisittipanit et al.
abstract: Background Nontyphoidal Salmonella spp. constitute a major bacterial cause of food poisoning. Each Salmonella serotype causes distinct virulence to humans. Method A small cohort study was conducted to characterize several aspects of Salmonella isolates obtained from stool of diarrheal patients (n = 26) admitted to Phayao Ram Hospital, Phayao province, Thailand. A simple CRISPR 2 molecular analysis was developed to rapidly type Salmonella isolates employing both uniplex and high resolution melting (HRM) curve analysis. Results CRISPR 2 monoplex PCR generated a single Salmonella serotype-specific amplicon, showing S. 4,[5],12:i:- with highest frequency (42%), S. Enteritidis (15%) and S. Stanley (11%); S. Typhimurium was not detected. CRISPR 2 HRM-PCR allowed further classification of S. 4,[5],12:i:- isolates based on their specific CRISPR 2 signature sequences. The highest prevalence of Salmonella infection was during the summer season (April to August). Additional studies were conducted using standard multiplex HRM-PCR typing, which confirmed CRISPR 2 PCR results and, using a machine-learning algorithm, clustered the majority of Salmonella serotypes into six clades; repetitive element-based (ERIC) PCR, which clustered the serotypes into three clades only; antibiogram profiling, which revealed the majority resistant to ampicillin (69%); and test for extended spectrum β-lactamase production (two isolates) and PCR-based detection of bla alleles. Conclusion CRISPR 2 PCR provided a simple assay for detection and identification of clinically-relevant Salmonella serotypes. In conjunction with antibiogram profiling and rapid assay for β-lactamase producers, this approach should facilitate detection and appropriate treatment of Salmonellosis in a local hospital setting. In addition, CRISPR 2 HRM-PCR profiling enabled clustering of S. 4,[5],12:i:-isolates according to CRISPR 2 locus signature sequences, indicative of their different evolutionary trajectories, thereby providing…
bibliographic citation: Wisittipanit et al. (2020) CRISPR 2 PCR and high resolution melting profiling for identification and characterization of clinically-relevant Salmonella enterica subsp. enterica. PeerJ 8:e9113 https://doi.org/10.7717/peerj.9113
date submitted: 2019-11-01
date accepted: 2020-04-10
issued: 2020-06-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wisittipanit
  given name: Nuttachat
author list: Agent
  family name: Pulsrikarn
  given name: Chaiwat
author list: Agent
  family name: Srisong
  given name: Sudarat
author list: Agent
  family name: Srimora
  given name: Rungthiwa
author list: Agent
  family name: Kittiwan
  given name: Nattinee
author list: Agent
  family name: Poonchareon
  given name: Kritchai
doi: 10.7717/peerj.9113
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-16
copyright: ©2020 Wisittipanit et al.
attribution name: Wisittipanit et al.

Quality of life after hip fracture: a 12-month prospective study
type: item
type: AcademicArticle
description: Background Hip fracture is an important and frequent health problem worldwide. To date, there are still limited studies focused on the analysis of health-related quality of life (HRQOL) after a hip fracture in the Spanish population, especially with long-term follow-up. Objective To determine the HRQOL at 12 months after hip fracture and to identify potential factors associated with HRQOL. Design Prospective observational study. Setting Traumatology units of two university hospitals in province Cáceres (Spain). Participants A total of 224 patients were admitted to the unit and required immediate surgery due to a hip fracture. Methods HRQOL was measured with the EuroQol-5D questionnaire (EQ-5D) and the SF-12 Health Survey. Results Scores from the visual analog scale EQ-5D decreased significantly (p < 0.001) from 72.8 at baseline to 48.3 after 1 month, to 48.2 after 6 months and to 46.1 after 12 months. The EQ-5D index score showed a similar significant reduction (p < 0.001) from 0.6 to 0.1, 0.3 and 0.3, respectively. Values of the physical component summary (PCS-12) significantly decreased (p < 0.001) from 38.6 at baseline to 31.0, 33.1 and 33.5. The mental component summary (MCS-12) decreased from 46.5 to 44.8 after 6 months (p = 0.022) and 44.3 after 12 months (p = 0.005). Factors potentially associated with HRQOL at 12 months after hip fracture were depression status after 12 months (B = 0–1.876; 95% CI [−2.409 to −1.343]; p < 0.001), functional ambulation classification after 12 months (B = −12.133; 95% CI [−17.970 to −6.297]; p < 0.001), EQ-5D VAS at baseline (B = 0.223; 95% CI [0.115–0.330]; p < 0.001), and age (B = −0.323; 95% CI [−0.594 to −0.053; p = 0.015). Conclusions Patients experience a significant impairment in HRQOL H after a hip fracture, especially in self-care, pain/discomfort, usual activities, mobility and anxiety/depression. The decline in the HRQOL is effective the first month and lasts at least 12 months after the surgical intervention.
format: application/pdf
format: text/html
creator: Francisco Javier Amarilla-Donoso
creator: Raul Roncero-Martin
creator: Jesus Maria Lavado-Garcia
creator: Rosaura Toribio-Felipe
creator: Jose Maria Moran-Garcia
creator: Fidel Lopez-Espuela
subject: Geriatrics
subject: Nursing
subject: Orthopedics
description: doi:10.7717/peerj.9215
publisher: PeerJ Inc.
rights: © 2020 Amarilla-Donoso et al.
abstract: Background Hip fracture is an important and frequent health problem worldwide. To date, there are still limited studies focused on the analysis of health-related quality of life (HRQOL) after a hip fracture in the Spanish population, especially with long-term follow-up. Objective To determine the HRQOL at 12 months after hip fracture and to identify potential factors associated with HRQOL. Design Prospective observational study. Setting Traumatology units of two university hospitals in province Cáceres (Spain). Participants A total of 224 patients were admitted to the unit and required immediate surgery due to a hip fracture. Methods HRQOL was measured with the EuroQol-5D questionnaire (EQ-5D) and the SF-12 Health Survey. Results Scores from the visual analog scale EQ-5D decreased significantly (p < 0.001) from 72.8 at baseline to 48.3 after 1 month, to 48.2 after 6 months and to 46.1 after 12 months. The EQ-5D index score showed a similar significant reduction (p < 0.001) from 0.6 to 0.1, 0.3 and 0.3, respectively. Values of the physical component summary (PCS-12) significantly decreased (p < 0.001) from 38.6 at baseline to 31.0, 33.1 and 33.5. The mental component summary (MCS-12) decreased from 46.5 to 44.8 after 6 months (p = 0.022) and 44.3 after 12 months (p = 0.005). Factors potentially associated with HRQOL at 12 months after hip fracture were depression status after 12 months (B = 0–1.876; 95% CI [−2.409 to −1.343]; p < 0.001), functional ambulation classification after 12 months (B = −12.133; 95% CI [−17.970 to −6.297]; p < 0.001), EQ-5D VAS at baseline (B = 0.223; 95% CI [0.115–0.330]; p < 0.001), and age (B = −0.323; 95% CI [−0.594 to −0.053; p = 0.015). Conclusions Patients experience a significant impairment in HRQOL H after a hip fracture, especially in self-care, pain/discomfort, usual activities, mobility and anxiety/depression. The decline in the HRQOL is effective the first month and lasts at least 12 months after the surgical intervention.
bibliographic citation: Amarilla-Donoso et al. (2020) Quality of life after hip fracture: a 12-month prospective study. PeerJ 8:e9215 https://doi.org/10.7717/peerj.9215
date submitted: 2019-10-23
date accepted: 2020-04-27
issued: 2020-06-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amarilla-Donoso
  given name: Francisco Javier
author list: Agent
  family name: Roncero-Martin
  given name: Raul
author list: Agent
  family name: Lavado-Garcia
  given name: Jesus Maria
author list: Agent
  family name: Toribio-Felipe
  given name: Rosaura
author list: Agent
  family name: Moran-Garcia
  given name: Jose Maria
author list: Agent
  family name: Lopez-Espuela
  given name: Fidel
doi: 10.7717/peerj.9215
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-16
copyright: © 2020 Amarilla-Donoso et al.
attribution name: Amarilla-Donoso et al.

Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils
type: item
type: AcademicArticle
description: Background Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species’ range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years. Methods We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression. Results Wefound that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population may be entering an extinction vortex and that to protect the population genetic rescue should be considered. This study provides conservation managers with useful information for managing wild devils and provides support for the “Wild Devil Recovery Program”, which is currently augmenting small, isolated populations.
format: application/pdf
format: text/html
creator: Rebecca M. Gooley
creator: Carolyn J. Hogg
creator: Samantha Fox
creator: David Pemberton
creator: Katherine Belov
creator: Catherine E. Grueber
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Population Biology
description: doi:10.7717/peerj.9220
publisher: PeerJ Inc.
rights: © 2020 Gooley et al.
abstract: Background Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species’ range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years. Methods We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression. Results Wefound that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population may be entering an extinction vortex and that to protect the population genetic rescue should be considered. This study provides conservation managers with useful information for managing wild devils and provides support for the “Wild Devil Recovery Program”, which is currently augmenting small, isolated populations.
bibliographic citation: Gooley et al. (2020) Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils. PeerJ 8:e9220 https://doi.org/10.7717/peerj.9220
date submitted: 2019-09-11
date accepted: 2020-04-28
issued: 2020-06-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gooley
  given name: Rebecca M.
author list: Agent
  family name: Hogg
  given name: Carolyn J.
author list: Agent
  family name: Fox
  given name: Samantha
author list: Agent
  family name: Pemberton
  given name: David
author list: Agent
  family name: Belov
  given name: Katherine
author list: Agent
  family name: Grueber
  given name: Catherine E.
doi: 10.7717/peerj.9220
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-16
copyright: ©2020 Gooley et al.
attribution name: Gooley et al.

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