PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A within-subject comparison of different relaxation therapies in eliciting physiological and psychological changes in young women
items: Bioinformatics analyses of retinoblastoma reveal the retinoblastoma progression subtypes
items: VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo
items: SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)
items: Isolation, characterization, and comparative genomic analysis of a phage infecting high-level aminoglycoside-resistant (HLAR) Enterococcus faecalis
items: Transcriptome profiling of avian pathogenic Escherichia coli and the mouse microvascular endothelial cell line bEnd.3 during interaction
items: Development and validation of a prognostic nomogram to predict overall survival and cancer-specific survival for patients with anaplastic thyroid carcinoma
items: Extensive protein expression changes induced by pamidronate in RAW 264.7 cells as determined by IP-HPLC
items: Comparison between radiofrequency ablation and sublobar resections for the therapy of stage I non-small cell lung cancer: a meta-analysis
items: Evaluation of the effective dose of amygdalin for the improvement of antioxidant gene expression and suppression of oxidative damage in mice

A within-subject comparison of different relaxation therapies in eliciting physiological and psychological changes in young women
type: item
type: AcademicArticle
description: Background Stress reactivity can be different in women compared to men, which might consequently influence disease risk.Stress in women may also generate adverse physiological effects on their offspring during pregnancy or lactation. The objective of this study was to compare the effects of different relaxation interventions on physiological outcomes and perceived relaxation in healthy young women, to assist in identifying the most appropriate intervention(s) for use in a subsequent trial for mothers who deliver prematurely. Methods A within-subject study was conducted in 17 women of reproductive age comparing five different relaxation interventions (guided-imagery meditation audio (GIM), music listening (ML), relaxation lighting (RL), GIM+RL, ML+RL), with control (silence/sitting), assigned in random order over a 3–6 week period. Subjective feelings of relaxation (10-point scale), heart rate (HR), systolic and diastolic blood pressure (SBP, DBP), and fingertip temperature (FT) were measured before and after each technique Results All interventions significantly increased perceived relaxation and FT, while music also significantly reduced SBP (p < 0.05). Compared to control, HR significantly decreased following GIM (mean difference = 3.2 bpm, p < 0.05), and FT increased (mean difference = 2.2 °C, p < 0.05) and SBP decreased (mean difference = 3.3 mmHg, p < 0.01) following ML. GIM + RL followed by GIM were the most preferred interventions. Conclusions Based on preference, simplicity, and the physiological and psychological effects, GIM and ML were identified as the most effective tools for reducing stress and improving relaxation. These techniques warrant further research in larger samples and other populations.
format: application/pdf
format: text/html
creator: Sarah Dib
creator: Jonathan C.K. Wells
creator: Mary Fewtrell
subject: Clinical Trials
subject: Psychiatry and Psychology
subject: Women’s Health
description: doi:10.7717/peerj.9217
publisher: PeerJ Inc.
rights: © 2020 Dib et al.
abstract: Background Stress reactivity can be different in women compared to men, which might consequently influence disease risk.Stress in women may also generate adverse physiological effects on their offspring during pregnancy or lactation. The objective of this study was to compare the effects of different relaxation interventions on physiological outcomes and perceived relaxation in healthy young women, to assist in identifying the most appropriate intervention(s) for use in a subsequent trial for mothers who deliver prematurely. Methods A within-subject study was conducted in 17 women of reproductive age comparing five different relaxation interventions (guided-imagery meditation audio (GIM), music listening (ML), relaxation lighting (RL), GIM+RL, ML+RL), with control (silence/sitting), assigned in random order over a 3–6 week period. Subjective feelings of relaxation (10-point scale), heart rate (HR), systolic and diastolic blood pressure (SBP, DBP), and fingertip temperature (FT) were measured before and after each technique Results All interventions significantly increased perceived relaxation and FT, while music also significantly reduced SBP (p < 0.05). Compared to control, HR significantly decreased following GIM (mean difference = 3.2 bpm, p < 0.05), and FT increased (mean difference = 2.2 °C, p < 0.05) and SBP decreased (mean difference = 3.3 mmHg, p < 0.01) following ML. GIM + RL followed by GIM were the most preferred interventions. Conclusions Based on preference, simplicity, and the physiological and psychological effects, GIM and ML were identified as the most effective tools for reducing stress and improving relaxation. These techniques warrant further research in larger samples and other populations.
bibliographic citation: Dib et al. (2020) A within-subject comparison of different relaxation therapies in eliciting physiological and psychological changes in young women. PeerJ 8:e9217 https://doi.org/10.7717/peerj.9217
date submitted: 2019-09-18
date accepted: 2020-04-28
issued: 2020-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dib
  given name: Sarah
author list: Agent
  family name: Wells
  given name: Jonathan C.K.
author list: Agent
  family name: Fewtrell
  given name: Mary
doi: 10.7717/peerj.9217
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-22
copyright: ©2020 Dib et al.
attribution name: Dib et al.

Bioinformatics analyses of retinoblastoma reveal the retinoblastoma progression subtypes
type: item
type: AcademicArticle
description: Introduction Retinoblastoma (RB) is one common pediatric malignant tumor with dismal outcomes. Heterogeneity of RB and subtypes of RB were identified but the association between the subtypes of RB and RB progression have not been fully investigated. Methods Four public datasets were downloaded from Gene expression omnibus and normalization was performed to remove batch effect. Two public datasets were explored to obtain the RB progression gene signatures by differentially expression analysis while another two datasets were iterated for RB subtypes identification using consensus clustering. After the RB progressive subtype gene signatures were identified, we tested the diagnostic capacity of these gene signatures by receiver operation curve. Results Three hundreds and forty six genes that were enriched in cell cycle were identified as the progression signature in RB from two independent datasets. Four subtypes of RB were stratified by consensus clustering. A total of 21 genes from RB progression signature were differentially expressed between RB subtypes. One subtype with low expression cell division genes have less progression of all four subtypes. A panel of five RB subtype genes (CLUL1, CNGB1, ROM1, LRRC39 and RDH12) predict progression of RB. Conclusion Retinoblastoma is a highly heterogeneous tumor and the level of cell cycle related gene expression is associated with RB progression. A subpopulation of RB with high expression of visual perception has less progressive features. LRRC39 is potentially the RB progression subtype biomarker.
format: application/pdf
format: text/html
creator: Manjing Cao
creator: Sha Wang
creator: Jing Zou
creator: Wanpeng Wang
subject: Bioinformatics
subject: Ophthalmology
description: doi:10.7717/peerj.8873
publisher: PeerJ Inc.
rights: © 2020 Cao et al.
abstract: Introduction Retinoblastoma (RB) is one common pediatric malignant tumor with dismal outcomes. Heterogeneity of RB and subtypes of RB were identified but the association between the subtypes of RB and RB progression have not been fully investigated. Methods Four public datasets were downloaded from Gene expression omnibus and normalization was performed to remove batch effect. Two public datasets were explored to obtain the RB progression gene signatures by differentially expression analysis while another two datasets were iterated for RB subtypes identification using consensus clustering. After the RB progressive subtype gene signatures were identified, we tested the diagnostic capacity of these gene signatures by receiver operation curve. Results Three hundreds and forty six genes that were enriched in cell cycle were identified as the progression signature in RB from two independent datasets. Four subtypes of RB were stratified by consensus clustering. A total of 21 genes from RB progression signature were differentially expressed between RB subtypes. One subtype with low expression cell division genes have less progression of all four subtypes. A panel of five RB subtype genes (CLUL1, CNGB1, ROM1, LRRC39 and RDH12) predict progression of RB. Conclusion Retinoblastoma is a highly heterogeneous tumor and the level of cell cycle related gene expression is associated with RB progression. A subpopulation of RB with high expression of visual perception has less progressive features. LRRC39 is potentially the RB progression subtype biomarker.
bibliographic citation: Cao et al. (2020) Bioinformatics analyses of retinoblastoma reveal the retinoblastoma progression subtypes. PeerJ 8:e8873 https://doi.org/10.7717/peerj.8873
date submitted: 2019-08-05
date accepted: 2020-03-09
issued: 2020-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Manjing
author list: Agent
  family name: Wang
  given name: Sha
author list: Agent
  family name: Zou
  given name: Jing
author list: Agent
  family name: Wang
  given name: Wanpeng
doi: 10.7717/peerj.8873
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: © 2020 Cao et al.
attribution name: Cao et al.

VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo
type: item
type: AcademicArticle
description: Vitiligo is a chronic asymptomatic disorder affecting melanocytes from the basal layer of the epidermis which leads to a patchy loss of skin color. Even though it is one of the neglected disease conditions, people suffering from vitiligo are more prone to psychological disorders. As of now, various studies have been done in order to project auto-immune implications as the root cause. To understand the complexity of vitiligo, we propose the Vitiligo Information Resource (VIRdb) that integrates both the drug-target and systems approach to produce a comprehensive repository entirely devoted to vitiligo, along with curated information at both protein level and gene level along with potential therapeutics leads. These 25,041 natural compounds are curated from Natural Product Activity and Species Source Database. VIRdb is an attempt to accelerate the drug discovery process and laboratory trials for vitiligo through the computationally derived potential drugs. It is an exhaustive resource consisting of 129 differentially expressed genes, which are validated through gene ontology and pathway enrichment analysis. We also report 22 genes through enrichment analysis which are involved in the regulation of epithelial cell differentiation. At the protein level, 40 curated protein target molecules along with their natural hits that are derived through virtual screening. We also demonstrate the utility of the VIRdb by exploring the Protein–Protein Interaction Network and Gene–Gene Interaction Network of the target proteins and differentially expressed genes. For maintaining the quality and standard of the data in the VIRdb, the gold standard in bioinformatics toolkits like Cytoscape, Schrödinger’s GLIDE, along with the server installation of MATLAB, are used for generating results. VIRdb can be accessed through “http://www.vitiligoinfores.com/”.
format: application/pdf
format: text/html
creator: Priyansh Srivastava
creator: Alakto Choudhury
creator: Mehak Talwar
creator: Sabyasachi Mohanty
creator: Priyanka Narad
creator: Abhishek Sengupta
subject: Bioinformatics
subject: Computational Biology
subject: Dermatology
subject: Computational Science
description: doi:10.7717/peerj.9119
publisher: PeerJ Inc.
rights: © 2020 Srivastava et al.
abstract: Vitiligo is a chronic asymptomatic disorder affecting melanocytes from the basal layer of the epidermis which leads to a patchy loss of skin color. Even though it is one of the neglected disease conditions, people suffering from vitiligo are more prone to psychological disorders. As of now, various studies have been done in order to project auto-immune implications as the root cause. To understand the complexity of vitiligo, we propose the Vitiligo Information Resource (VIRdb) that integrates both the drug-target and systems approach to produce a comprehensive repository entirely devoted to vitiligo, along with curated information at both protein level and gene level along with potential therapeutics leads. These 25,041 natural compounds are curated from Natural Product Activity and Species Source Database. VIRdb is an attempt to accelerate the drug discovery process and laboratory trials for vitiligo through the computationally derived potential drugs. It is an exhaustive resource consisting of 129 differentially expressed genes, which are validated through gene ontology and pathway enrichment analysis. We also report 22 genes through enrichment analysis which are involved in the regulation of epithelial cell differentiation. At the protein level, 40 curated protein target molecules along with their natural hits that are derived through virtual screening. We also demonstrate the utility of the VIRdb by exploring the Protein–Protein Interaction Network and Gene–Gene Interaction Network of the target proteins and differentially expressed genes. For maintaining the quality and standard of the data in the VIRdb, the gold standard in bioinformatics toolkits like Cytoscape, Schrödinger’s GLIDE, along with the server installation of MATLAB, are used for generating results. VIRdb can be accessed through “http://www.vitiligoinfores.com/”.
bibliographic citation: Srivastava et al. (2020) VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo. PeerJ 8:e9119 https://doi.org/10.7717/peerj.9119
date submitted: 2020-01-02
date accepted: 2020-04-13
issued: 2020-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Srivastava
  given name: Priyansh
author list: Agent
  family name: Choudhury
  given name: Alakto
author list: Agent
  family name: Talwar
  given name: Mehak
author list: Agent
  family name: Mohanty
  given name: Sabyasachi
author list: Agent
  family name: Narad
  given name: Priyanka
author list: Agent
  family name: Sengupta
  given name: Abhishek
doi: 10.7717/peerj.9119
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: © 2020 Srivastava et al.
attribution name: Srivastava et al.

SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)
type: item
type: AcademicArticle
description: Background Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus. Results A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.
format: application/pdf
format: text/html
creator: Hongjun Yang
creator: Danping Xu
creator: Zhihang Zhuo
creator: Jiameng Hu
creator: Baoqian Lu
subject: Biodiversity
subject: Entomology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.9133
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Background Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus. Results A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.
bibliographic citation: Yang et al. (2020) SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae). PeerJ 8:e9133 https://doi.org/10.7717/peerj.9133
date submitted: 2020-01-13
date accepted: 2020-04-14
issued: 2020-05-21
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.9133
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Isolation, characterization, and comparative genomic analysis of a phage infecting high-level aminoglycoside-resistant (HLAR) Enterococcus faecalis
type: item
type: AcademicArticle
description: Enterococcus is a genus of Gram-positive bacteria that are commensal to the gastrointestinal tracts of humans but some species have been increasingly implicated as agents of nosocomial infections. The increase in infections and the spread of antibiotic-resistant strains have contributed to renewed interest in the discovery of Enterococcus phages. The aims of this study were (1) the isolation, characterization, and genome sequencing of a phage capable of infecting an antibiotic-resistant E. faecalis strain, and (2) the comparative genomic analysis of publicly-available Enterococcus phages. For this purpose, multiple phages were isolated from wastewater treatment plant (WWTP) influent using a high-level aminoglycoside-resistant (HLAR) E. faecalis strain as the host. One phage, phiNASRA1, demonstrated a high lytic efficiency (∼97.52%). Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) showed that phiNASRA1 belongs to the Siphoviridae family of double-stranded DNA viruses. The phage was approximately 250 nm in length and its complete genome (40,139 bp, 34.7% GC) contained 62 open reading frames (ORFs). Phylogenetic comparisons of phiNASRA1 and 31 publicly-available Enterococcus phages, based on the large subunit terminase and portal proteins, grouped phage by provenance, size, and GC content. In particular, both phylogenies grouped phages larger than 100 kbp into distinct clades. A phylogeny based on a pangenome analysis of the same 32 phages also grouped phages by provenance, size, and GC content although agreement between the two single-locus phylogenies was higher. Per the pangenome phylogeny, phiNASRA1 was most closely related to phage LY0322 that was similar in size, GC content, and number of ORFs (40,139 and 40,934 bp, 34.77 and 34.80%, and 60 and 64 ORFs, respectively). The pangenome analysis did illustrate the high degree of sequence diversity and genome plasticity as no coding sequence was homologous across all 32 phages, and even ‘conser…
format: application/pdf
format: text/html
creator: Danial Nasr Azadani
creator: Daiyuan Zhang
creator: J. Robert Hatherill
creator: David Silva
creator: Jeffrey W. Turner
subject: Genomics
subject: Taxonomy
subject: Virology
subject: Infectious Diseases
description: doi:10.7717/peerj.9171
publisher: PeerJ Inc.
rights: © 2020 Nasr Azadani et al.
abstract: Enterococcus is a genus of Gram-positive bacteria that are commensal to the gastrointestinal tracts of humans but some species have been increasingly implicated as agents of nosocomial infections. The increase in infections and the spread of antibiotic-resistant strains have contributed to renewed interest in the discovery of Enterococcus phages. The aims of this study were (1) the isolation, characterization, and genome sequencing of a phage capable of infecting an antibiotic-resistant E. faecalis strain, and (2) the comparative genomic analysis of publicly-available Enterococcus phages. For this purpose, multiple phages were isolated from wastewater treatment plant (WWTP) influent using a high-level aminoglycoside-resistant (HLAR) E. faecalis strain as the host. One phage, phiNASRA1, demonstrated a high lytic efficiency (∼97.52%). Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) showed that phiNASRA1 belongs to the Siphoviridae family of double-stranded DNA viruses. The phage was approximately 250 nm in length and its complete genome (40,139 bp, 34.7% GC) contained 62 open reading frames (ORFs). Phylogenetic comparisons of phiNASRA1 and 31 publicly-available Enterococcus phages, based on the large subunit terminase and portal proteins, grouped phage by provenance, size, and GC content. In particular, both phylogenies grouped phages larger than 100 kbp into distinct clades. A phylogeny based on a pangenome analysis of the same 32 phages also grouped phages by provenance, size, and GC content although agreement between the two single-locus phylogenies was higher. Per the pangenome phylogeny, phiNASRA1 was most closely related to phage LY0322 that was similar in size, GC content, and number of ORFs (40,139 and 40,934 bp, 34.77 and 34.80%, and 60 and 64 ORFs, respectively). The pangenome analysis did illustrate the high degree of sequence diversity and genome plasticity as no coding sequence was homologous across all 32 phages, and even ‘conser…
bibliographic citation: Nasr Azadani et al. (2020) Isolation, characterization, and comparative genomic analysis of a phage infecting high-level aminoglycoside-resistant (HLAR) Enterococcus faecalis. PeerJ 8:e9171 https://doi.org/10.7717/peerj.9171
date submitted: 2019-09-09
date accepted: 2020-04-20
issued: 2020-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nasr Azadani
  given name: Danial
author list: Agent
  family name: Zhang
  given name: Daiyuan
author list: Agent
  family name: Hatherill
  given name: J. Robert
author list: Agent
  family name: Silva
  given name: David
author list: Agent
  family name: Turner
  given name: Jeffrey W.
doi: 10.7717/peerj.9171
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: ©2020 Nasr Azadani et al.
attribution name: Nasr Azadani et al.

Transcriptome profiling of avian pathogenic Escherichia coli and the mouse microvascular endothelial cell line bEnd.3 during interaction
type: item
type: AcademicArticle
description: Background Avian pathogenic Escherichia coli (APEC), an important extraintestinal pathogenic E. coli, causes colibacillosis, an acute and mostly systemic disease involving multiple organ lesions such as meningitis. Meningitis-causing APEC can invade the host central nervous system by crossing the blood–brain barrier (BBB), which is a critical step in the development of meningitis. However, the bacteria-host interaction mechanism in this process remains unclear. Methods In this study, we examined E. coli and bEnd.3 cells transcriptomes during infection and mock infection to investigate the global transcriptional changes in both organisms using RNA sequencing approach. Results When APEC infected the bEnd.3 cells, several significant changes in the expression of genes related to cell junctional complexes, extracellular matrix degradation, actin cytoskeleton rearrangement, immune activation and the inflammatory response in bEnd.3 cells were observed as compared to the mock infection group. Thus, the immune activation of bEnd.3 cells indicated that APEC infection activated host defenses. Furthermore, APEC may exploit cell junction degradation to invade the BBB. In addition, amino acid metabolism and energy metabolism related genes were downregulated and the protein export pathway related genes were upregulated in APEC cultured with bEnd.3 cells, compared to that in control. Thus, APEC may encounter starvation and express virulence factors during incubation with bEnd.3 cells. Conclusion This study provides a comprehensive overview of transcriptomic changes that occur during APEC infection of bEnd.3 cells, and offers insights into the bacterial invasion strategies and the subsequent host defense mechanism.
format: application/pdf
format: text/html
creator: Peili Wang
creator: Xia Meng
creator: Jianji Li
creator: Yanfei Chen
creator: Dong Zhang
creator: Haoran Zhong
creator: Pengpeng Xia
creator: Luying Cui
creator: Guoqiang Zhu
creator: Heng Wang
subject: Bioinformatics
subject: Microbiology
subject: Veterinary Medicine
subject: Infectious Diseases
description: doi:10.7717/peerj.9172
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background Avian pathogenic Escherichia coli (APEC), an important extraintestinal pathogenic E. coli, causes colibacillosis, an acute and mostly systemic disease involving multiple organ lesions such as meningitis. Meningitis-causing APEC can invade the host central nervous system by crossing the blood–brain barrier (BBB), which is a critical step in the development of meningitis. However, the bacteria-host interaction mechanism in this process remains unclear. Methods In this study, we examined E. coli and bEnd.3 cells transcriptomes during infection and mock infection to investigate the global transcriptional changes in both organisms using RNA sequencing approach. Results When APEC infected the bEnd.3 cells, several significant changes in the expression of genes related to cell junctional complexes, extracellular matrix degradation, actin cytoskeleton rearrangement, immune activation and the inflammatory response in bEnd.3 cells were observed as compared to the mock infection group. Thus, the immune activation of bEnd.3 cells indicated that APEC infection activated host defenses. Furthermore, APEC may exploit cell junction degradation to invade the BBB. In addition, amino acid metabolism and energy metabolism related genes were downregulated and the protein export pathway related genes were upregulated in APEC cultured with bEnd.3 cells, compared to that in control. Thus, APEC may encounter starvation and express virulence factors during incubation with bEnd.3 cells. Conclusion This study provides a comprehensive overview of transcriptomic changes that occur during APEC infection of bEnd.3 cells, and offers insights into the bacterial invasion strategies and the subsequent host defense mechanism.
bibliographic citation: Wang et al. (2020) Transcriptome profiling of avian pathogenic Escherichia coli and the mouse microvascular endothelial cell line bEnd.3 during interaction. PeerJ 8:e9172 https://doi.org/10.7717/peerj.9172
date submitted: 2019-10-21
date accepted: 2020-04-21
issued: 2020-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Peili
author list: Agent
  family name: Meng
  given name: Xia
author list: Agent
  family name: Li
  given name: Jianji
author list: Agent
  family name: Chen
  given name: Yanfei
author list: Agent
  family name: Zhang
  given name: Dong
author list: Agent
  family name: Zhong
  given name: Haoran
author list: Agent
  family name: Xia
  given name: Pengpeng
author list: Agent
  family name: Cui
  given name: Luying
author list: Agent
  family name: Zhu
  given name: Guoqiang
author list: Agent
  family name: Wang
  given name: Heng
doi: 10.7717/peerj.9172
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Development and validation of a prognostic nomogram to predict overall survival and cancer-specific survival for patients with anaplastic thyroid carcinoma
type: item
type: AcademicArticle
description: Background Anaplastic thyroid carcinoma (ATC) is a rare malignant tumor with a poor prognosis. However, there is no useful clinical prognostic predictive tool for ATC so far. Our study identified risk factors for survival of ATC and created a reliable nomogram to predict overall survival (OS) and cancer-specific survival (CSS) of patients with ATC. Methods A total of 1,404 cases of ATC diagnosed between 1983 and 2013 were extracted from on the Surveillance, Epidemiology and End Results database based on our inclusion criteria. OS and CSS were compared among patients between each variable by Kaplan–Meier methods. The Cox proportional hazards model was used to evaluate multiple prognostic factors and obtain independent predictors. All independent risk factors were included to build nomograms, whose accuracy and practicability were tested by concordance index (C-index), calibration curves, ROC curves, DCA, net reclassification improvement (NRI) and integrated discrimination improvement (IDI). Results Historic stage, tumor size, surgery and radiotherapy were independent risk factors associated with ATC according to multivariate Cox regression analysis of OS. However, gender was also an important prognostic predictor in CSS besides the factors mentioned above. These characteristics were included in the nomograms predicting OS and CSS of patients with ATC. The nomograms predicting OS and CSS performed well with a C-index of 0.765 and 0.773. ROC curves, DCA, NRI and IDI suggested that the nomogram was superior to TNM staging and age. Conclusion The proposed nomogram is a reliable tool based on the prediction of OS and CSS for patients with ATC. Such a predictive tool can help to predict the survival of the patients.
format: application/pdf
format: text/html
creator: Weiwei Gui
creator: Weifen Zhu
creator: Weina Lu
creator: Chengxin Shang
creator: Fenping Zheng
creator: Xihua Lin
creator: Hong Li
subject: Bioinformatics
subject: Diabetes and Endocrinology
subject: Internal Medicine
subject: Metabolic Sciences
description: doi:10.7717/peerj.9173
publisher: PeerJ Inc.
rights: © 2020 Gui et al.
abstract: Background Anaplastic thyroid carcinoma (ATC) is a rare malignant tumor with a poor prognosis. However, there is no useful clinical prognostic predictive tool for ATC so far. Our study identified risk factors for survival of ATC and created a reliable nomogram to predict overall survival (OS) and cancer-specific survival (CSS) of patients with ATC. Methods A total of 1,404 cases of ATC diagnosed between 1983 and 2013 were extracted from on the Surveillance, Epidemiology and End Results database based on our inclusion criteria. OS and CSS were compared among patients between each variable by Kaplan–Meier methods. The Cox proportional hazards model was used to evaluate multiple prognostic factors and obtain independent predictors. All independent risk factors were included to build nomograms, whose accuracy and practicability were tested by concordance index (C-index), calibration curves, ROC curves, DCA, net reclassification improvement (NRI) and integrated discrimination improvement (IDI). Results Historic stage, tumor size, surgery and radiotherapy were independent risk factors associated with ATC according to multivariate Cox regression analysis of OS. However, gender was also an important prognostic predictor in CSS besides the factors mentioned above. These characteristics were included in the nomograms predicting OS and CSS of patients with ATC. The nomograms predicting OS and CSS performed well with a C-index of 0.765 and 0.773. ROC curves, DCA, NRI and IDI suggested that the nomogram was superior to TNM staging and age. Conclusion The proposed nomogram is a reliable tool based on the prediction of OS and CSS for patients with ATC. Such a predictive tool can help to predict the survival of the patients.
bibliographic citation: Gui et al. (2020) Development and validation of a prognostic nomogram to predict overall survival and cancer-specific survival for patients with anaplastic thyroid carcinoma. PeerJ 8:e9173 https://doi.org/10.7717/peerj.9173
date submitted: 2019-10-24
date accepted: 2020-04-21
issued: 2020-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gui
  given name: Weiwei
author list: Agent
  family name: Zhu
  given name: Weifen
author list: Agent
  family name: Lu
  given name: Weina
author list: Agent
  family name: Shang
  given name: Chengxin
author list: Agent
  family name: Zheng
  given name: Fenping
author list: Agent
  family name: Lin
  given name: Xihua
author list: Agent
  family name: Li
  given name: Hong
doi: 10.7717/peerj.9173
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: © 2020 Gui et al.
attribution name: Gui et al.

Extensive protein expression changes induced by pamidronate in RAW 264.7 cells as determined by IP-HPLC
type: item
type: AcademicArticle
description: Background Bisphosphonate therapy has become a popular treatment for osteoporosis, Paget’s disease, multiple myeloma, osteogenesis imperfecta, myocardial infarction, and cancer despite its serious side effects. Bisphosphonate-induced molecular signaling changes in cells are still not clearly elucidated. Methods As bisphosphonates are primarily engulfed by macrophages, we treated RAW 264.7 cells (a murine macrophage cell line) with pamidronate and investigated global protein expressional changes in cells by immunoprecipitation high performance liquid chromatography (IP-HPLC) using 218 antisera. Results Pamidronate upregulated proliferation-activating proteins associated with p53/Rb/E2F and Wnt/β-catenin pathways, but downregulated the downstream of RAS signaling, pAKT1/2/3, ERK-1, and p-ERK-1, and subsequently suppressed cMyc/MAX/MAD network. However, in situ proliferation index of pamidronate-treated RAW264.7 cells was slightly increased by 3.2% vs. non-treated controls. Pamidronate-treated cells showed increase in the expressions of histone- and DNA methylation-related proteins but decrease of protein translation-related proteins. NFkB signaling was also suppressed as indicated by the down-regulations of p38 and p-p38 and the up-regulation of mTOR, while the protein expressions related to cellular protection, HSP-70, NRF2, JNK-1, and LC3 were upregulated. Consequently, pamidronate downregulated the protein expressions related to immediate inflammation,cellular differentiation, survival, angiogenesis, and osteoclastogenesis, but upregulated PARP-1 and FAS-mediated apoptosis proteins. These observations suggest pamidronate affects global protein expressions in RAW 264.7 cells by stimulating cellular proliferation, protection, and apoptosis but suppressing immediate inflammation, differentiation, osteoclastogenesis, and angiogenesis. Accordingly, pamidronate appears to affect macrophages in several ways eliciting not only its therapeutic effects but also atypical epig…
format: application/pdf
format: text/html
creator: Sang Shin Lee
creator: Soung Min Kim
creator: Yeon Sook Kim
creator: Suk Keun Lee
subject: Biochemistry
subject: Biotechnology
subject: Cell Biology
subject: Pathology
subject: Pharmacology
description: doi:10.7717/peerj.9202
publisher: PeerJ Inc.
rights: © 2020 Lee et al.
abstract: Background Bisphosphonate therapy has become a popular treatment for osteoporosis, Paget’s disease, multiple myeloma, osteogenesis imperfecta, myocardial infarction, and cancer despite its serious side effects. Bisphosphonate-induced molecular signaling changes in cells are still not clearly elucidated. Methods As bisphosphonates are primarily engulfed by macrophages, we treated RAW 264.7 cells (a murine macrophage cell line) with pamidronate and investigated global protein expressional changes in cells by immunoprecipitation high performance liquid chromatography (IP-HPLC) using 218 antisera. Results Pamidronate upregulated proliferation-activating proteins associated with p53/Rb/E2F and Wnt/β-catenin pathways, but downregulated the downstream of RAS signaling, pAKT1/2/3, ERK-1, and p-ERK-1, and subsequently suppressed cMyc/MAX/MAD network. However, in situ proliferation index of pamidronate-treated RAW264.7 cells was slightly increased by 3.2% vs. non-treated controls. Pamidronate-treated cells showed increase in the expressions of histone- and DNA methylation-related proteins but decrease of protein translation-related proteins. NFkB signaling was also suppressed as indicated by the down-regulations of p38 and p-p38 and the up-regulation of mTOR, while the protein expressions related to cellular protection, HSP-70, NRF2, JNK-1, and LC3 were upregulated. Consequently, pamidronate downregulated the protein expressions related to immediate inflammation,cellular differentiation, survival, angiogenesis, and osteoclastogenesis, but upregulated PARP-1 and FAS-mediated apoptosis proteins. These observations suggest pamidronate affects global protein expressions in RAW 264.7 cells by stimulating cellular proliferation, protection, and apoptosis but suppressing immediate inflammation, differentiation, osteoclastogenesis, and angiogenesis. Accordingly, pamidronate appears to affect macrophages in several ways eliciting not only its therapeutic effects but also atypical epig…
bibliographic citation: Lee et al. (2020) Extensive protein expression changes induced by pamidronate in RAW 264.7 cells as determined by IP-HPLC. PeerJ 8:e9202 https://doi.org/10.7717/peerj.9202
date submitted: 2020-01-29
date accepted: 2020-04-24
issued: 2020-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Sang Shin
author list: Agent
  family name: Kim
  given name: Soung Min
author list: Agent
  family name: Kim
  given name: Yeon Sook
author list: Agent
  family name: Lee
  given name: Suk Keun
doi: 10.7717/peerj.9202
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: © 2020 Lee et al.
attribution name: Lee et al.

Comparison between radiofrequency ablation and sublobar resections for the therapy of stage I non-small cell lung cancer: a meta-analysis
type: item
type: AcademicArticle
description: Background Sublobar resection (SLR) and radiofrequency ablation (RFA) are the two minimally invasive procedures performed for treating stage I non-small cell lung cancer (NSCLC). This study aimed to compare SLR and RFA for the treatment of stage I NSCLC using the meta-analytical method. Methods We searched PubMed and Embase for articles published till December 2019 to evaluate the comparative studies and assess the survival and progression-free survival rates and postoperative complications (PROSPERO registration number: CRD42018087587). A meta-analysis was performed by combining the outcomes of the reported incidences of short-term morbidity and long-term mortality. The fixed or random effects model was utilized to calculate the pooled odds ratios (OR) and the 95% confidence intervals. Results Four retrospective studies were considered in the course of this study. The studies included a total of 309 participants; 154 were assigned to the SLR group, and 155 were assigned to the RFA group. Moreover, there were statistically significant differences between the one- and three-year survival rates and one- and three-year progression-free survival rates for the two groups, which were in favor of the SLR group. Among the post-surgical complications, pneumothorax and pleural effusion were more common for the SLR group, while cardiac abnormalities were prevalent in the RFA group. There was no difference in prevalence of hemoptysis between SLR and RFA groups, which might be attributed to the limited study sample size. Conclusion Considering the higher survival rates and disease control in the evaluated cases, surgical resection is the preferred treatment method for stage I NSCLC. RFA can be considered a valid alternative in patients not eligible for surgery and in high-risk patients as it is less invasive and requires shorter hospital stay.
format: application/pdf
format: text/html
creator: Shuang Chen
creator: Shize Yang
creator: Shun Xu
creator: Siyuan Dong
subject: Oncology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.9228
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Background Sublobar resection (SLR) and radiofrequency ablation (RFA) are the two minimally invasive procedures performed for treating stage I non-small cell lung cancer (NSCLC). This study aimed to compare SLR and RFA for the treatment of stage I NSCLC using the meta-analytical method. Methods We searched PubMed and Embase for articles published till December 2019 to evaluate the comparative studies and assess the survival and progression-free survival rates and postoperative complications (PROSPERO registration number: CRD42018087587). A meta-analysis was performed by combining the outcomes of the reported incidences of short-term morbidity and long-term mortality. The fixed or random effects model was utilized to calculate the pooled odds ratios (OR) and the 95% confidence intervals. Results Four retrospective studies were considered in the course of this study. The studies included a total of 309 participants; 154 were assigned to the SLR group, and 155 were assigned to the RFA group. Moreover, there were statistically significant differences between the one- and three-year survival rates and one- and three-year progression-free survival rates for the two groups, which were in favor of the SLR group. Among the post-surgical complications, pneumothorax and pleural effusion were more common for the SLR group, while cardiac abnormalities were prevalent in the RFA group. There was no difference in prevalence of hemoptysis between SLR and RFA groups, which might be attributed to the limited study sample size. Conclusion Considering the higher survival rates and disease control in the evaluated cases, surgical resection is the preferred treatment method for stage I NSCLC. RFA can be considered a valid alternative in patients not eligible for surgery and in high-risk patients as it is less invasive and requires shorter hospital stay.
bibliographic citation: Chen et al. (2020) Comparison between radiofrequency ablation and sublobar resections for the therapy of stage I non-small cell lung cancer: a meta-analysis. PeerJ 8:e9228 https://doi.org/10.7717/peerj.9228
date submitted: 2020-01-23
date accepted: 2020-04-30
issued: 2020-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Shuang
author list: Agent
  family name: Yang
  given name: Shize
author list: Agent
  family name: Xu
  given name: Shun
author list: Agent
  family name: Dong
  given name: Siyuan
doi: 10.7717/peerj.9228
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: ©2020 Chen et al.
attribution name: Chen et al.

Evaluation of the effective dose of amygdalin for the improvement of antioxidant gene expression and suppression of oxidative damage in mice
type: item
type: AcademicArticle
description: Background Little is known regarding the toxic and therapeutic doses of amygdalin. Treatment regimens and schedules can vary between humans and animal models, and there have been reports of cyanide toxicity due to amygdalin use. Objective The aim of this study was to evaluate the effect of different doses of amygdalin on antioxidant gene expression and suppression of oxidative damage in mice. Methods Forty adult male mice were divided randomly into four groups (n = 10) as follows and treated orally for two weeks: a control group treated with saline solution, a group treated with amygdalin at 200 mg/kg body weight, a group treated with amygdalin at 100 mg/kg body weight, and a group treated with amygdalin at 50 mg/kg body weight. Liver and testis samples were collected for gene expression, biochemical and histopathological analyses. Results The mice treated with medium-dose amygdalin (100 mg/kg) showed upregulated mRNA expression of glutathione peroxidase (P < 0.01) and superoxide dismutase (P < 0.05) and significantly decreased lipid peroxidation (P < 0.05) in hepatic and testicular tissues compared to those in the untreated groups (controls), with mild histopathological effects. The mice treated with high-dose of amygdalin (200 mg/kg) showed downregulated mRNA expression of glutathione peroxidase and superoxide dismutase (P < 0.01) and significantly increased lipid peroxidation (P < 0.05) in both hepatic and testicular tissues compared to those in the untreated groups (controls), with an apparent effect at the histopathological level. No effects were observed in the mice treated with low-dose amygdalin (50 mg/kg) at the gene, protein and histopathological level. Conclusion Low-and medium-dose amygdalin did not induce toxicity in the hepatic and testicular tissues of male mice, unlike high-dose amygdalin, which had a negative effect on oxidative balance in mice. Therefore, amygdalin at a moderate dose may improve oxidative balance in mice.
format: application/pdf
format: text/html
creator: Sarah Albogami
creator: Aziza Hassan
creator: Nibal Ahmed
creator: Alaa Alnefaie
creator: Afnan Alattas
creator: Lama Alquthami
creator: Afaf Alharbi
subject: Biotechnology
subject: Molecular Biology
subject: Toxicology
subject: Pharmacology
subject: Histology
description: doi:10.7717/peerj.9232
publisher: PeerJ Inc.
rights: © 2020 Albogami et al.
abstract: Background Little is known regarding the toxic and therapeutic doses of amygdalin. Treatment regimens and schedules can vary between humans and animal models, and there have been reports of cyanide toxicity due to amygdalin use. Objective The aim of this study was to evaluate the effect of different doses of amygdalin on antioxidant gene expression and suppression of oxidative damage in mice. Methods Forty adult male mice were divided randomly into four groups (n = 10) as follows and treated orally for two weeks: a control group treated with saline solution, a group treated with amygdalin at 200 mg/kg body weight, a group treated with amygdalin at 100 mg/kg body weight, and a group treated with amygdalin at 50 mg/kg body weight. Liver and testis samples were collected for gene expression, biochemical and histopathological analyses. Results The mice treated with medium-dose amygdalin (100 mg/kg) showed upregulated mRNA expression of glutathione peroxidase (P < 0.01) and superoxide dismutase (P < 0.05) and significantly decreased lipid peroxidation (P < 0.05) in hepatic and testicular tissues compared to those in the untreated groups (controls), with mild histopathological effects. The mice treated with high-dose of amygdalin (200 mg/kg) showed downregulated mRNA expression of glutathione peroxidase and superoxide dismutase (P < 0.01) and significantly increased lipid peroxidation (P < 0.05) in both hepatic and testicular tissues compared to those in the untreated groups (controls), with an apparent effect at the histopathological level. No effects were observed in the mice treated with low-dose amygdalin (50 mg/kg) at the gene, protein and histopathological level. Conclusion Low-and medium-dose amygdalin did not induce toxicity in the hepatic and testicular tissues of male mice, unlike high-dose amygdalin, which had a negative effect on oxidative balance in mice. Therefore, amygdalin at a moderate dose may improve oxidative balance in mice.
bibliographic citation: Albogami et al. (2020) Evaluation of the effective dose of amygdalin for the improvement of antioxidant gene expression and suppression of oxidative damage in mice. PeerJ 8:e9232 https://doi.org/10.7717/peerj.9232
date submitted: 2019-11-19
date accepted: 2020-05-01
issued: 2020-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Albogami
  given name: Sarah
author list: Agent
  family name: Hassan
  given name: Aziza
author list: Agent
  family name: Ahmed
  given name: Nibal
author list: Agent
  family name: Alnefaie
  given name: Alaa
author list: Agent
  family name: Alattas
  given name: Afnan
author list: Agent
  family name: Alquthami
  given name: Lama
author list: Agent
  family name: Alharbi
  given name: Afaf
doi: 10.7717/peerj.9232
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-21
copyright: © 2020 Albogami et al.
attribution name: Albogami et al.

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