PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Assessment of autonomous nerve system through non-linear heart rate variability outcomes in sedentary healthy adults
items: Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages
items: Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections
items: Optimizing and purifying extracellular amylase from soil bacteria to inhibit clinical biofilm-forming bacteria
items: The current knowledge gap on metallothionein mediated metal-detoxification in Elasmobranchs
items: Changing health compliance through message repetition based on the extended parallel process model in the COVID-19 pandemic
items: The efficacy of IL-6 inhibitor Tocilizumab in reducing severe COVID-19 mortality: a systematic review
items: Integrated network pharmacology and molecular docking approaches to reveal the synergistic mechanism of multiple components in Venenum Bufonis for ameliorating heart failure
items: Biases in genome reconstruction from metagenomic data
items: Revalidation of morphological characteristics and multiplex PCR for the identification of three congener invasive Liriomyza species (Diptera: Agromyzidae) in China

Assessment of autonomous nerve system through non-linear heart rate variability outcomes in sedentary healthy adults
type: item
type: AcademicArticle
description: Background Heart rate variability (HRV) is a psycho-physiological phenomenon with broad health implications. Different data analysis methods have been used to assess the autonomic nervous system activity, but the validation of new indexes that accurately describe its balance through non-invasive methods (i.e., HRV analysis) is of clinical interest. This study aimed: (i) to evaluate the association of the Stress Score (SS) and the Sympathetic/Parasympathetic Ratio (S/PS) with time domain and frequency domain analysis of HRV, and (ii) to set reference values of SS and S/PS in sedentary healthy adults. Methods A total of 156 sedentary healthy adults (38.4 ± 15.57 years old, 81 women), aged were involved in this study. HRV was measured for 15 min in a supine position at rest. SS and S/PS were calculated from the non-linear HRV analyses based on Poincare Plot. Results Stress Score showed a non-linear negative power-law relationship with SDNN (β = −0.969; R2 = 0.963; P < 0.001), RMSSD (β = −0.867; R2 = 0.722; P < 0.001), high frequency (β = −0.834; R2 = 0.752; P =< 0.001), low frequency (β = −0.627; R2 = 0.330; P < 0.001), SD1 (β = −0.867; R2 = 0.722; P < 0.001) and SD2 (β = −1.000; R2 > 0.999; P < 0.001). There was observed a negative cubic relationship between SS with PNN50 (β = −1.972; R2 = 0.644; P < 0.001). A linear regression model was conducted between SS with Ratio Low/High Frequency (β = 0.026; R2 < 0.001; P = 0.750). Non-linear power-law regression models were built between S/PS and SDNN (β = −0.990; R2 = 0.981; P < 0.001), RMSSD (β = −0.973; R2 = 0.939; P < 0.001), high frequency (β = −0.928; R2 = 0.970; P < 0.001), low frequency (β = −2.344; R2 = 0.557; P < 0.001), SD1 (β = −0.973; R2 = 0.939; P < 0.001) and SD2 (β = −0.611; R2 = 0.908; P < 0.001). A non-linear negative regression model was built between S/PS and PNN50 (β = −3.412; R2 = 0.868; P < 0.001). A linear regression model was conducted between S/PS and SD2/SD1 (β = 0.075; R2 = 0.006; P < 0.001). Concl…
format: application/pdf
format: text/html
creator: Gines Navarro-Lomas
creator: Alejandro De-la-O
creator: Lucas Jurado-Fasoli
creator: Manuel J. Castillo
creator: Pedro Femia
creator: Francisco J. Amaro-Gahete
subject: Neuroscience
subject: Cardiology
subject: Global Health
subject: Public Health
description: doi:10.7717/peerj.10178
publisher: PeerJ Inc.
rights: © 2020 Navarro-Lomas et al.
abstract: Background Heart rate variability (HRV) is a psycho-physiological phenomenon with broad health implications. Different data analysis methods have been used to assess the autonomic nervous system activity, but the validation of new indexes that accurately describe its balance through non-invasive methods (i.e., HRV analysis) is of clinical interest. This study aimed: (i) to evaluate the association of the Stress Score (SS) and the Sympathetic/Parasympathetic Ratio (S/PS) with time domain and frequency domain analysis of HRV, and (ii) to set reference values of SS and S/PS in sedentary healthy adults. Methods A total of 156 sedentary healthy adults (38.4 ± 15.57 years old, 81 women), aged were involved in this study. HRV was measured for 15 min in a supine position at rest. SS and S/PS were calculated from the non-linear HRV analyses based on Poincare Plot. Results Stress Score showed a non-linear negative power-law relationship with SDNN (β = −0.969; R2 = 0.963; P < 0.001), RMSSD (β = −0.867; R2 = 0.722; P < 0.001), high frequency (β = −0.834; R2 = 0.752; P =< 0.001), low frequency (β = −0.627; R2 = 0.330; P < 0.001), SD1 (β = −0.867; R2 = 0.722; P < 0.001) and SD2 (β = −1.000; R2 > 0.999; P < 0.001). There was observed a negative cubic relationship between SS with PNN50 (β = −1.972; R2 = 0.644; P < 0.001). A linear regression model was conducted between SS with Ratio Low/High Frequency (β = 0.026; R2 < 0.001; P = 0.750). Non-linear power-law regression models were built between S/PS and SDNN (β = −0.990; R2 = 0.981; P < 0.001), RMSSD (β = −0.973; R2 = 0.939; P < 0.001), high frequency (β = −0.928; R2 = 0.970; P < 0.001), low frequency (β = −2.344; R2 = 0.557; P < 0.001), SD1 (β = −0.973; R2 = 0.939; P < 0.001) and SD2 (β = −0.611; R2 = 0.908; P < 0.001). A non-linear negative regression model was built between S/PS and PNN50 (β = −3.412; R2 = 0.868; P < 0.001). A linear regression model was conducted between S/PS and SD2/SD1 (β = 0.075; R2 = 0.006; P < 0.001). Concl…
bibliographic citation: Navarro-Lomas et al. (2020) Assessment of autonomous nerve system through non-linear heart rate variability outcomes in sedentary healthy adults. PeerJ 8:e10178 https://doi.org/10.7717/peerj.10178
date submitted: 2020-08-14
date accepted: 2020-09-23
issued: 2020-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Navarro-Lomas
  given name: Gines
author list: Agent
  family name: De-la-O
  given name: Alejandro
author list: Agent
  family name: Jurado-Fasoli
  given name: Lucas
author list: Agent
  family name: Castillo
  given name: Manuel J.
author list: Agent
  family name: Femia
  given name: Pedro
author list: Agent
  family name: Amaro-Gahete
  given name: Francisco J.
doi: 10.7717/peerj.10178
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-02
copyright: © 2020 Navarro-Lomas et al.
attribution name: Navarro-Lomas et al.

Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages
type: item
type: AcademicArticle
description: Background Red palm weevil, Rhynchophorus ferrugineus Olivier, is one of the most destructive pests harming palm trees. However, genomic resources for R. ferrugineus are still lacking, limiting the ability to discover molecular and genetic means of pest control. Methods In this study, PacBio Iso-Seq and Illumina RNA-seq were used to generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th-instar larva, adult) to increase the understanding of the life cycle and molecular characteristics of the pest. Results Sequencing generated 625,983,256 clean reads, from which 63,801 full-length transcripts were assembled with N50 of 3,547 bp. Expression analyses revealed 8,583 differentially expressed genes (DEGs). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mainly related to the peroxisome pathway which associated with metabolic pathways, material transportation and organ tissue formation. In summary, this work provides a valuable basis for further research on the growth and development, gene expression and gene prediction, and pest control of R. ferrugineus.
format: application/pdf
format: text/html
creator: Hongjun Yang
creator: Danping Xu
creator: Zhihang Zhuo
creator: Jiameng Hu
creator: Baoqian Lu
subject: Agricultural Science
subject: Entomology
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10223
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Background Red palm weevil, Rhynchophorus ferrugineus Olivier, is one of the most destructive pests harming palm trees. However, genomic resources for R. ferrugineus are still lacking, limiting the ability to discover molecular and genetic means of pest control. Methods In this study, PacBio Iso-Seq and Illumina RNA-seq were used to generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th-instar larva, adult) to increase the understanding of the life cycle and molecular characteristics of the pest. Results Sequencing generated 625,983,256 clean reads, from which 63,801 full-length transcripts were assembled with N50 of 3,547 bp. Expression analyses revealed 8,583 differentially expressed genes (DEGs). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mainly related to the peroxisome pathway which associated with metabolic pathways, material transportation and organ tissue formation. In summary, this work provides a valuable basis for further research on the growth and development, gene expression and gene prediction, and pest control of R. ferrugineus.
bibliographic citation: Yang et al. (2020) Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages. PeerJ 8:e10223 https://doi.org/10.7717/peerj.10223
date submitted: 2020-03-05
date accepted: 2020-09-29
issued: 2020-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Hongjun
author list: Agent
  family name: Xu
  given name: Danping
author list: Agent
  family name: Zhuo
  given name: Zhihang
author list: Agent
  family name: Hu
  given name: Jiameng
author list: Agent
  family name: Lu
  given name: Baoqian
doi: 10.7717/peerj.10223
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-02
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections
type: item
type: AcademicArticle
description: Background In December 2019, an ongoing outbreak of pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/ 2019-nCoV) infection was initially reported in Wuhan, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be a Public Health Emergency of International Concern (PHEIC). Cellular co-infection is a critical determinant of viral fitness and infection outcomes and plays a crucial role in shaping the host immune response to infections. Methods In this study, 68 public next-generation sequencing data from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Data screening was performed using an alignment-free method based on k-mer mapping and extension, fastv. Taxonomic classification was performed using Kraken 2 on all reads containing one or more virus sequences other than SARS-CoV-2. Results SARS-CoV-2 was identified in all except three patients. Influenza type A (H7N9) virus, human immunodeficiency virus, rhabdovirus, human metapneumovirus, Human adenovirus, Human herpesvirus 1, coronavirus NL63, parvovirus, simian virus 40, and hepatitis virus genomes sequences were detected in SARS-CoV-2 infected patients. Besides, a very diverse group of bacterial populations were observed in the samples.
format: application/pdf
format: text/html
creator: Mohamed A. Abouelkhair
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.10246
publisher: PeerJ Inc.
rights: © 2020 Abouelkhair
abstract: Background In December 2019, an ongoing outbreak of pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/ 2019-nCoV) infection was initially reported in Wuhan, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be a Public Health Emergency of International Concern (PHEIC). Cellular co-infection is a critical determinant of viral fitness and infection outcomes and plays a crucial role in shaping the host immune response to infections. Methods In this study, 68 public next-generation sequencing data from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Data screening was performed using an alignment-free method based on k-mer mapping and extension, fastv. Taxonomic classification was performed using Kraken 2 on all reads containing one or more virus sequences other than SARS-CoV-2. Results SARS-CoV-2 was identified in all except three patients. Influenza type A (H7N9) virus, human immunodeficiency virus, rhabdovirus, human metapneumovirus, Human adenovirus, Human herpesvirus 1, coronavirus NL63, parvovirus, simian virus 40, and hepatitis virus genomes sequences were detected in SARS-CoV-2 infected patients. Besides, a very diverse group of bacterial populations were observed in the samples.
bibliographic citation: Abouelkhair (2020) Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections. PeerJ 8:e10246 https://doi.org/10.7717/peerj.10246
date submitted: 2020-06-19
date accepted: 2020-10-06
issued: 2020-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abouelkhair
  given name: Mohamed A.
doi: 10.7717/peerj.10246
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-02
copyright: © 2020 Abouelkhair
attribution name: Abouelkhair

Optimizing and purifying extracellular amylase from soil bacteria to inhibit clinical biofilm-forming bacteria
type: item
type: AcademicArticle
description: Background Bacterial biofilms have become a major threat to human health. The objective of this study was to isolate amylase-producing bacteria from soil to determine the overall inhibition of certain pathogenic bacterial biofilms. Methods We used serial dilution and the streaking method to obtain a total of 75 positive amylase isolates. The starch-agar plate method was used to screen the amylolytic activities of these isolates, and we used morphological and biochemical methods to characterize the isolates. Optimal conditions for amylase production and purification using Sephadex G-200 and SDS-PAGE were monitored. We screened these isolates’ antagonistic activities and the purified amylase against pathogenic and multi-drug-resistant human bacteria using the agar disk diffusion method. Some standard antibiotics were controlled according to their degree of sensitivity. Finally, we used spectrophotometric methods to screen the antibiofilm 24 and 48 h after application of filtering and purifying enzymes in order to determine its efficacy at human pathogenic bacteria. Results The isolated Bacillus species were Bacillus megaterium (26.7%), Bacillus subtilis (16%), Bacillus cereus (13.3%), Bacillus thuringiesis (10.7%), Bacillus lentus (10.7%), Bacillus mycoides (5.3%), Bacillus alvei (5.3%), Bacillus polymyxa (4%), Bacillus circulans (4%), and Micrococcus roseus (4%). Interestingly, all isolates showed a high antagonism to target pathogens. B. alevi had the highest recorded activity (48 mm) and B. polymyxa had the lowest recorded activity (12 mm) against Staphylococcus aureus (MRSA) and Escherichia coli, respectively. On the other hand, we detected no antibacterial activity for purified amylase. The supernatant of the isolated amylase-producing bacteria and its purified amylase showed significant inhibition for biofilm: 93.7% and 78.8%, respectively. This suggests that supernatant and purified amylase may be effective for clinical and environmental biofilm control. Discus…
format: application/pdf
format: text/html
creator: Rokaia Elamary
creator: Wesam M. Salem
subject: Biotechnology
subject: Microbiology
description: doi:10.7717/peerj.10288
publisher: PeerJ Inc.
rights: © 2020 Elamary and Salem
abstract: Background Bacterial biofilms have become a major threat to human health. The objective of this study was to isolate amylase-producing bacteria from soil to determine the overall inhibition of certain pathogenic bacterial biofilms. Methods We used serial dilution and the streaking method to obtain a total of 75 positive amylase isolates. The starch-agar plate method was used to screen the amylolytic activities of these isolates, and we used morphological and biochemical methods to characterize the isolates. Optimal conditions for amylase production and purification using Sephadex G-200 and SDS-PAGE were monitored. We screened these isolates’ antagonistic activities and the purified amylase against pathogenic and multi-drug-resistant human bacteria using the agar disk diffusion method. Some standard antibiotics were controlled according to their degree of sensitivity. Finally, we used spectrophotometric methods to screen the antibiofilm 24 and 48 h after application of filtering and purifying enzymes in order to determine its efficacy at human pathogenic bacteria. Results The isolated Bacillus species were Bacillus megaterium (26.7%), Bacillus subtilis (16%), Bacillus cereus (13.3%), Bacillus thuringiesis (10.7%), Bacillus lentus (10.7%), Bacillus mycoides (5.3%), Bacillus alvei (5.3%), Bacillus polymyxa (4%), Bacillus circulans (4%), and Micrococcus roseus (4%). Interestingly, all isolates showed a high antagonism to target pathogens. B. alevi had the highest recorded activity (48 mm) and B. polymyxa had the lowest recorded activity (12 mm) against Staphylococcus aureus (MRSA) and Escherichia coli, respectively. On the other hand, we detected no antibacterial activity for purified amylase. The supernatant of the isolated amylase-producing bacteria and its purified amylase showed significant inhibition for biofilm: 93.7% and 78.8%, respectively. This suggests that supernatant and purified amylase may be effective for clinical and environmental biofilm control. Discus…
bibliographic citation: Elamary et al. (2020) Optimizing and purifying extracellular amylase from soil bacteria to inhibit clinical biofilm-forming bacteria. PeerJ 8:e10288 https://doi.org/10.7717/peerj.10288
date submitted: 2020-03-19
date accepted: 2020-10-11
issued: 2020-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elamary
  given name: Rokaia
author list: Agent
  family name: Salem
  given name: Wesam M.
doi: 10.7717/peerj.10288
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-02
copyright: ©2020 Elamary and Salem
attribution name: Elamary and Salem

The current knowledge gap on metallothionein mediated metal-detoxification in Elasmobranchs
type: item
type: AcademicArticle
description: Elasmobranchs are particularly vulnerable to environmental contamination, especially pollutants that may bioaccumulate and biomagnify, throughout the trophic web, such as metals. However, Elasmobranch management and conservation plans are challenging, and this group is often neglected regarding ecotoxicological analyses, particularly concerning metal detoxification mechanisms. This article discusses metallothionein (MT) mediated metal detoxification in Elasmobranchs and reflects on the current knowledge gap in this regard.
format: application/pdf
format: text/html
creator: Rachel Ann Hauser-Davis
subject: Biochemistry
subject: Conservation Biology
subject: Zoology
subject: Ecotoxicology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.10293
publisher: PeerJ Inc.
rights: © 2020 Hauser-Davis
abstract: Elasmobranchs are particularly vulnerable to environmental contamination, especially pollutants that may bioaccumulate and biomagnify, throughout the trophic web, such as metals. However, Elasmobranch management and conservation plans are challenging, and this group is often neglected regarding ecotoxicological analyses, particularly concerning metal detoxification mechanisms. This article discusses metallothionein (MT) mediated metal detoxification in Elasmobranchs and reflects on the current knowledge gap in this regard.
bibliographic citation: Hauser-Davis (2020) The current knowledge gap on metallothionein mediated metal-detoxification in Elasmobranchs. PeerJ 8:e10293 https://doi.org/10.7717/peerj.10293
date submitted: 2020-08-15
date accepted: 2020-10-12
issued: 2020-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hauser-Davis
  given name: Rachel Ann
doi: 10.7717/peerj.10293
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-02
copyright: © 2020 Hauser-Davis
attribution name: Hauser-Davis

Changing health compliance through message repetition based on the extended parallel process model in the COVID-19 pandemic
type: item
type: AcademicArticle
description: When people are confronted with health proposals during the coronavirus disease 2019 (COVID-19) pandemic, it has been suggested that fear of COVID-19 can serve protective functions and ensure public health compliance. However, health proposal repetition and its perceived efficacy also influence the behavior intention toward the proposal, which has not yet been confirmed in the COVID-19 context. The present study aims to examine whether the extended parallel process model (EPPM) can be generalized to a naturalistic context like the COVID-19 pandemic. Additionally, we will explore how repetition of a health proposal is involved with the EPPM. In this study, two groups of participants are exposed to the same health proposal related to COVID-19, where one group is exposed once and another group twice. They then fill out a questionnaire consisting of items concerning behavior intention and adapted from the Risk Behavior Diagnosis Scale. Structural equation modeling will be used to determine the multivariate associations between the variables. We predict that repetition of the health proposal will associate with response efficacy (i.e., a belief about the effectiveness of the health proposal in deterring the threat) and perceived susceptibility (i.e., a belief about the risk of experiencing the threat). It is also predicted that following the EPPM, behavior intention will associate with both perceived efficacy of the health proposal, which will underlie response efficacy, and perceived threat of COVID-19, which will underlie perceived susceptibility. We will discuss the process, based on the model, where health message repetition affects behavior intention during the COVID-19 pandemic.
format: application/pdf
format: text/html
creator: Jingwen Yang
creator: Xue Wu
creator: Kyoshiro Sasaki
creator: Yuki Yamada
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.10318
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: When people are confronted with health proposals during the coronavirus disease 2019 (COVID-19) pandemic, it has been suggested that fear of COVID-19 can serve protective functions and ensure public health compliance. However, health proposal repetition and its perceived efficacy also influence the behavior intention toward the proposal, which has not yet been confirmed in the COVID-19 context. The present study aims to examine whether the extended parallel process model (EPPM) can be generalized to a naturalistic context like the COVID-19 pandemic. Additionally, we will explore how repetition of a health proposal is involved with the EPPM. In this study, two groups of participants are exposed to the same health proposal related to COVID-19, where one group is exposed once and another group twice. They then fill out a questionnaire consisting of items concerning behavior intention and adapted from the Risk Behavior Diagnosis Scale. Structural equation modeling will be used to determine the multivariate associations between the variables. We predict that repetition of the health proposal will associate with response efficacy (i.e., a belief about the effectiveness of the health proposal in deterring the threat) and perceived susceptibility (i.e., a belief about the risk of experiencing the threat). It is also predicted that following the EPPM, behavior intention will associate with both perceived efficacy of the health proposal, which will underlie response efficacy, and perceived threat of COVID-19, which will underlie perceived susceptibility. We will discuss the process, based on the model, where health message repetition affects behavior intention during the COVID-19 pandemic.
bibliographic citation: Yang et al. (2020) Changing health compliance through message repetition based on the extended parallel process model in the COVID-19 pandemic. PeerJ 8:e10318 https://doi.org/10.7717/peerj.10318
date submitted: 2020-07-14
date accepted: 2020-10-16
issued: 2020-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Jingwen
author list: Agent
  family name: Wu
  given name: Xue
author list: Agent
  family name: Sasaki
  given name: Kyoshiro
author list: Agent
  family name: Yamada
  given name: Yuki
doi: 10.7717/peerj.10318
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-02
copyright: © 2020 Yang et al.
attribution name: Yang et al.

The efficacy of IL-6 inhibitor Tocilizumab in reducing severe COVID-19 mortality: a systematic review
type: item
type: AcademicArticle
description: Background In the absence of highly effective antiviral therapies against SARS-CoV-2, it is crucial to counter the known pathophysiological causes of severe COVID-19. Evaluating the efficacy existing drugs may expedite the development of such therapeutics. Severe COVID-19 is largely the result of a dysregulated immune response characterized by lymphocytopenia, neutrophilia and critical hypercytokinemia, or “cytokine storm,” which is largely mediated by the cytokine interleukin-6 (IL-6). The IL-6 inhibitor tocilizumab (TCZ) could potentially suppress the effects of the pro-inflammatory cytokine and thereby lower mortality from the disease. This systematic analysis aimed to investigate and synthesize existing evidence for the efficacy of TCZ in reducing COVID-19 mortality. Methodology PubMed and SearchWorks searches were performed to locate clinical studies with primary data on TCZ treatment for severe COVID-19. Sixteen case-control studies comparing mortality between TCZ and standard of care (SOC) were identified for quantitative synthesis. The systematic analysis was pre-approved through PROSPERO (CRD42020193479). Results Combined mortality for the TCZ-treated and SOC groups were 26.0% and 43.4% respectively. In all but one of the studies, the odds ratio of mortality from COVID-19 pointed towards lower fatality with TCZ vs the SOC. A combined random effects odds ratio calculation yielded an odds ratio of 0.453 (95% CI [0.376–0.547], p < 0.001). Additionally, 18 uncontrolled trials were identified for qualitative analysis producing a raw combined mortality rate of 16.0%. Conclusions Important caveats to this research include the lack of prospective randomized control trials and the absence of data from the large COVATA study from the published literature. However, results from this systematic analysis of published research provide positive evidence for the potential efficacy of TCZ to treat severe COVID-19, validating the ethical basis and merit of ongoing randomized…
format: application/pdf
format: text/html
creator: Avi Gurion Kaye
creator: Robert Siegel
subject: Virology
subject: Drugs and Devices
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.10322
publisher: PeerJ Inc.
rights: © 2020 Kaye and Siegel
abstract: Background In the absence of highly effective antiviral therapies against SARS-CoV-2, it is crucial to counter the known pathophysiological causes of severe COVID-19. Evaluating the efficacy existing drugs may expedite the development of such therapeutics. Severe COVID-19 is largely the result of a dysregulated immune response characterized by lymphocytopenia, neutrophilia and critical hypercytokinemia, or “cytokine storm,” which is largely mediated by the cytokine interleukin-6 (IL-6). The IL-6 inhibitor tocilizumab (TCZ) could potentially suppress the effects of the pro-inflammatory cytokine and thereby lower mortality from the disease. This systematic analysis aimed to investigate and synthesize existing evidence for the efficacy of TCZ in reducing COVID-19 mortality. Methodology PubMed and SearchWorks searches were performed to locate clinical studies with primary data on TCZ treatment for severe COVID-19. Sixteen case-control studies comparing mortality between TCZ and standard of care (SOC) were identified for quantitative synthesis. The systematic analysis was pre-approved through PROSPERO (CRD42020193479). Results Combined mortality for the TCZ-treated and SOC groups were 26.0% and 43.4% respectively. In all but one of the studies, the odds ratio of mortality from COVID-19 pointed towards lower fatality with TCZ vs the SOC. A combined random effects odds ratio calculation yielded an odds ratio of 0.453 (95% CI [0.376–0.547], p < 0.001). Additionally, 18 uncontrolled trials were identified for qualitative analysis producing a raw combined mortality rate of 16.0%. Conclusions Important caveats to this research include the lack of prospective randomized control trials and the absence of data from the large COVATA study from the published literature. However, results from this systematic analysis of published research provide positive evidence for the potential efficacy of TCZ to treat severe COVID-19, validating the ethical basis and merit of ongoing randomized…
bibliographic citation: Kaye et al. (2020) The efficacy of IL-6 inhibitor Tocilizumab in reducing severe COVID-19 mortality: a systematic review. PeerJ 8:e10322 https://doi.org/10.7717/peerj.10322
date submitted: 2020-09-04
date accepted: 2020-10-18
issued: 2020-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kaye
  given name: Avi Gurion
author list: Agent
  family name: Siegel
  given name: Robert
doi: 10.7717/peerj.10322
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-02
copyright: © 2020 Kaye and Siegel
attribution name: Kaye and Siegel

Integrated network pharmacology and molecular docking approaches to reveal the synergistic mechanism of multiple components in Venenum Bufonis for ameliorating heart failure
type: item
type: AcademicArticle
description: Venenum Bufonis (VB), also called Chan Su in China, has been extensively used as a traditional Chinese medicine (TCM) for treating heart failure (HF) since ancient time. However, the active components and the potential anti-HF mechanism of VB remain unclear. In the current study, the major absorbed components and metabolites of VB after oral administration in rats were first collected from literatures. A total of 17 prototypes and 25 metabolites were gathered. Next, a feasible network-based pharmacological approach was developed and employed to explore the therapeutic mechanism of VB on HF based on the collected constituents. In total, 158 main targets were screened out and considered as effective players in ameliorating HF. Then, the VB components–main HF putative targets–main pathways network was established, clarifying the underlying biological process of VB on HF. More importantly, the main hubs were found to be highly enriched in adrenergic signalling in cardio-myocytes. After verified by molecular docking studies, four key targets (ATP1A1, GNAS, MAPK1 and PRKCA) and three potential active leading compounds (bufotalin, cinobufaginol and 19-oxo-bufalin) were identified, which may play critical roles in cardiac muscle contraction. This study demonstrated that the integrated strategy based on network pharmacology and molecular docking was helpful to uncover the synergistic mechanism of multiple constituents in TCM.
format: application/pdf
format: text/html
creator: Wei Ren
creator: Zhiqiang Luo
creator: Fulu Pan
creator: Jiali Liu
creator: Qin Sun
creator: Gang Luo
creator: Raoqiong Wang
creator: Haiyu Zhao
creator: Baolin Bian
creator: Xiao Xiao
creator: Qingrong Pu
creator: Sijin Yang
creator: Guohua Yu
subject: Bioinformatics
subject: Molecular Biology
subject: Drugs and Devices
subject: Pharmacology
subject: Computational Science
description: doi:10.7717/peerj.10107
publisher: PeerJ Inc.
rights: © 2020 Ren et al.
abstract: Venenum Bufonis (VB), also called Chan Su in China, has been extensively used as a traditional Chinese medicine (TCM) for treating heart failure (HF) since ancient time. However, the active components and the potential anti-HF mechanism of VB remain unclear. In the current study, the major absorbed components and metabolites of VB after oral administration in rats were first collected from literatures. A total of 17 prototypes and 25 metabolites were gathered. Next, a feasible network-based pharmacological approach was developed and employed to explore the therapeutic mechanism of VB on HF based on the collected constituents. In total, 158 main targets were screened out and considered as effective players in ameliorating HF. Then, the VB components–main HF putative targets–main pathways network was established, clarifying the underlying biological process of VB on HF. More importantly, the main hubs were found to be highly enriched in adrenergic signalling in cardio-myocytes. After verified by molecular docking studies, four key targets (ATP1A1, GNAS, MAPK1 and PRKCA) and three potential active leading compounds (bufotalin, cinobufaginol and 19-oxo-bufalin) were identified, which may play critical roles in cardiac muscle contraction. This study demonstrated that the integrated strategy based on network pharmacology and molecular docking was helpful to uncover the synergistic mechanism of multiple constituents in TCM.
bibliographic citation: Ren et al. (2020) Integrated network pharmacology and molecular docking approaches to reveal the synergistic mechanism of multiple components in Venenum Bufonis for ameliorating heart failure. PeerJ 8:e10107 https://doi.org/10.7717/peerj.10107
date submitted: 2020-05-26
date accepted: 2020-09-15
issued: 2020-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Wei
author list: Agent
  family name: Luo
  given name: Zhiqiang
author list: Agent
  family name: Pan
  given name: Fulu
author list: Agent
  family name: Liu
  given name: Jiali
author list: Agent
  family name: Sun
  given name: Qin
author list: Agent
  family name: Luo
  given name: Gang
author list: Agent
  family name: Wang
  given name: Raoqiong
author list: Agent
  family name: Zhao
  given name: Haiyu
author list: Agent
  family name: Bian
  given name: Baolin
author list: Agent
  family name: Xiao
  given name: Xiao
author list: Agent
  family name: Pu
  given name: Qingrong
author list: Agent
  family name: Yang
  given name: Sijin
author list: Agent
  family name: Yu
  given name: Guohua
doi: 10.7717/peerj.10107
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-30
copyright: ©2020 Ren et al.
attribution name: Ren et al.

Biases in genome reconstruction from metagenomic data
type: item
type: AcademicArticle
description: Background Advances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction of genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly and binning techniques are accurate when applied to environmental metagenomes due to a lack of complete reference genome sequences against which to check the resulting MAGs. Methods We compared MAGs derived from an enrichment culture containing ~20 organisms to complete genome sequences of 10 organisms isolated from the enrichment culture. Factors commonly considered in binning software—nucleotide composition and sequence repetitiveness—were calculated for both the correctly binned and not-binned regions. This direct comparison revealed biases in sequence characteristics and gene content in the not-binned regions. Additionally, the composition of three public data sets representing MAGs reconstructed from the Tara Oceans metagenomic data was compared to a set of representative genomes available through NCBI RefSeq to verify that the biases identified were observable in more complex data sets and using three contemporary binning software packages. Results Repeat sequences were frequently not binned in the genome reconstruction processes, as were sequence regions with variant nucleotide composition. Genes encoded on the not-binned regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function. Our results support genome reconstruction as a robust process and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function; however, population-level genotypic heterogeneity in natural populations, such as uneven distribution of plasmids, can lead to incorrect inferences.
format: application/pdf
format: text/html
creator: William C. Nelson
creator: Benjamin J. Tully
creator: Jennifer M. Mobberley
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.10119
publisher: PeerJ Inc.
rights: © 2020 Nelson et al.
abstract: Background Advances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction of genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly and binning techniques are accurate when applied to environmental metagenomes due to a lack of complete reference genome sequences against which to check the resulting MAGs. Methods We compared MAGs derived from an enrichment culture containing ~20 organisms to complete genome sequences of 10 organisms isolated from the enrichment culture. Factors commonly considered in binning software—nucleotide composition and sequence repetitiveness—were calculated for both the correctly binned and not-binned regions. This direct comparison revealed biases in sequence characteristics and gene content in the not-binned regions. Additionally, the composition of three public data sets representing MAGs reconstructed from the Tara Oceans metagenomic data was compared to a set of representative genomes available through NCBI RefSeq to verify that the biases identified were observable in more complex data sets and using three contemporary binning software packages. Results Repeat sequences were frequently not binned in the genome reconstruction processes, as were sequence regions with variant nucleotide composition. Genes encoded on the not-binned regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function. Our results support genome reconstruction as a robust process and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function; however, population-level genotypic heterogeneity in natural populations, such as uneven distribution of plasmids, can lead to incorrect inferences.
bibliographic citation: Nelson et al. (2020) Biases in genome reconstruction from metagenomic data. PeerJ 8:e10119 https://doi.org/10.7717/peerj.10119
date submitted: 2017-04-25
date accepted: 2020-09-16
issued: 2020-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nelson
  given name: William C.
author list: Agent
  family name: Tully
  given name: Benjamin J.
author list: Agent
  family name: Mobberley
  given name: Jennifer M.
doi: 10.7717/peerj.10119
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-30
copyright: © 2020 Nelson et al.
attribution name: Nelson et al.

Revalidation of morphological characteristics and multiplex PCR for the identification of three congener invasive Liriomyza species (Diptera: Agromyzidae) in China
type: item
type: AcademicArticle
description: Due to varietal differences, diminutive size, and similar morphological characters, it is difficult to classify and identify Liriomyza spp., a genus comprised of economically-important, highly-polyphagous insect pests. In this study, we reconfirmed the morphological characteristics of three closely-related invasive leafminers, L. trifolii, L. sativae, and L. huidobrensis. Morphological results showed that characteristics imparted by the male genitalia were the most reliable morphological features for identification. The colors exhibited by vertical setae were variable among species, and the ratio of the length of the ultimate section of vein CuA1 divided by penultimate section also varied within species. Although the patterns of abdominal tergites were diverse among Liriomyza spp., L. trifolii exhibited a unique pattern with a yellow patch at the 5th black visible tergite; this pattern can be profiled as a prominent characteristic for morphological identification. In order to identify the three Liriomyza spp. quickly and accurately, we developed an improved molecular identification method using multiplex PCR based on the gene encoding mitochondrial cytochrome oxidase I (COI); this method enabled direct identification based on the size of amplified products. The results of this study provide a valuable reference for the identification of Liriomyza spp., which will ultimately improve our ability to control individual species.
format: application/pdf
format: text/html
creator: Ya-Wen Chang
creator: Jing-Yun Chen
creator: Si-Zhu Zheng
creator: Yuan Gao
creator: Yunfang Chen
creator: Yanfeng Deng
creator: Yu-Zhou Du
subject: Agricultural Science
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10138
publisher: PeerJ Inc.
rights: © 2020 Chang et al.
abstract: Due to varietal differences, diminutive size, and similar morphological characters, it is difficult to classify and identify Liriomyza spp., a genus comprised of economically-important, highly-polyphagous insect pests. In this study, we reconfirmed the morphological characteristics of three closely-related invasive leafminers, L. trifolii, L. sativae, and L. huidobrensis. Morphological results showed that characteristics imparted by the male genitalia were the most reliable morphological features for identification. The colors exhibited by vertical setae were variable among species, and the ratio of the length of the ultimate section of vein CuA1 divided by penultimate section also varied within species. Although the patterns of abdominal tergites were diverse among Liriomyza spp., L. trifolii exhibited a unique pattern with a yellow patch at the 5th black visible tergite; this pattern can be profiled as a prominent characteristic for morphological identification. In order to identify the three Liriomyza spp. quickly and accurately, we developed an improved molecular identification method using multiplex PCR based on the gene encoding mitochondrial cytochrome oxidase I (COI); this method enabled direct identification based on the size of amplified products. The results of this study provide a valuable reference for the identification of Liriomyza spp., which will ultimately improve our ability to control individual species.
bibliographic citation: Chang et al. (2020) Revalidation of morphological characteristics and multiplex PCR for the identification of three congener invasive Liriomyza species (Diptera: Agromyzidae) in China. PeerJ 8:e10138 https://doi.org/10.7717/peerj.10138
date submitted: 2020-06-26
date accepted: 2020-09-18
issued: 2020-10-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Ya-Wen
author list: Agent
  family name: Chen
  given name: Jing-Yun
author list: Agent
  family name: Zheng
  given name: Si-Zhu
author list: Agent
  family name: Gao
  given name: Yuan
author list: Agent
  family name: Chen
  given name: Yunfang
author list: Agent
  family name: Deng
  given name: Yanfeng
author list: Agent
  family name: Du
  given name: Yu-Zhou
doi: 10.7717/peerj.10138
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-30
copyright: ©2020 Chang et al.
attribution name: Chang et al.

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