PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: CYP2C11 played a significant role in down-regulating rat blood pressure under the challenge of a high-salt diet
items: Identification of a putative competitive endogenous RNA network for lung adenocarcinoma using TCGA datasets
items: Identification of optimal endogenous reference RNAs for RT-qPCR normalization in hindgut of rat models with anorectal malformations
items: Next-generation sequencing of BRCA1 and BRCA2 genes for rapid detection of germline mutations in hereditary breast/ovarian cancer
items: MicroRNA profiling of mouse liver in response to DENV-1 infection by deep sequencing
items: Integrated analysis of two-lncRNA signature as a potential prognostic biomarker in cervical cancer: a study based on public database
items: Extinction and the U.S. Endangered Species Act
items: eHealth adoption and use among healthcare professionals in a tertiary hospital in Sub-Saharan Africa: a Qmethodology study
items: Rapid ecological specialization despite constant population sizes
items: Ability emotional intelligence in young people and older adults with and without depressive symptoms, considering gender and educational level

CYP2C11 played a significant role in down-regulating rat blood pressure under the challenge of a high-salt diet
type: item
type: AcademicArticle
description: Background Arachidonic acid (AA) is oxidized by cytochrome P450s (CYPs) to form epoxyeicosatrienoic acids (EETs), compounds that modulate ion transport, gene expression, and vasorelaxation. Both CYP2Cs and CYP2Js are involved in kidney EET epoxidation. Methods In this study, we used a CYP2C11-null rat model to explore the in vivo effects of CYP2C11 on vasorelaxation. For 2 months, CYP2C11-null and wild-type (WT) Sprague-Dawley rats were either fed normal lab (0.3% (w/w) sodium chloride) or high-salt (8% (w/w) sodium chloride) diets. Subsequently, an invasive method was used to determine blood pressure. Next, western blots, quantitative PCR, and immunohistochemistry were used to determine renal expression of CYPs involved in AA metabolism. Results Among CYP2C11-null rats, a high-salt diet (females: 156.79 ± 15.89 mm Hg, males: 130.25 ± 16.76 mm Hg, n = 10) resulted in significantly higher blood pressure than a normal diet (females: 118.05 ± 8.43 mm Hg, P < 0.01; males: 115.15 ± 11.45 mm Hg, P < 0.05, n = 10). Compared with WT rats under the high-salt diet, western blots showed that CYP2C11-null rats had higher renal expression of CYP2J2 and CYP4A. This was consistent with the results of immunohistochemistry and the qPCR, respectively. The two rat strains did not differ in the renal expression of CYP2C23 or CYP2C24. Conclusion Our findings suggested that CYP2C11 plays an important role in lowering blood pressure under the challenge of a high-salt diet.
format: application/pdf
format: text/html
creator: Wei Liu
creator: Danjuan Sui
creator: Huanying Ye
creator: Zhen Ouyang
creator: Yuan Wei
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.6807
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Background Arachidonic acid (AA) is oxidized by cytochrome P450s (CYPs) to form epoxyeicosatrienoic acids (EETs), compounds that modulate ion transport, gene expression, and vasorelaxation. Both CYP2Cs and CYP2Js are involved in kidney EET epoxidation. Methods In this study, we used a CYP2C11-null rat model to explore the in vivo effects of CYP2C11 on vasorelaxation. For 2 months, CYP2C11-null and wild-type (WT) Sprague-Dawley rats were either fed normal lab (0.3% (w/w) sodium chloride) or high-salt (8% (w/w) sodium chloride) diets. Subsequently, an invasive method was used to determine blood pressure. Next, western blots, quantitative PCR, and immunohistochemistry were used to determine renal expression of CYPs involved in AA metabolism. Results Among CYP2C11-null rats, a high-salt diet (females: 156.79 ± 15.89 mm Hg, males: 130.25 ± 16.76 mm Hg, n = 10) resulted in significantly higher blood pressure than a normal diet (females: 118.05 ± 8.43 mm Hg, P < 0.01; males: 115.15 ± 11.45 mm Hg, P < 0.05, n = 10). Compared with WT rats under the high-salt diet, western blots showed that CYP2C11-null rats had higher renal expression of CYP2J2 and CYP4A. This was consistent with the results of immunohistochemistry and the qPCR, respectively. The two rat strains did not differ in the renal expression of CYP2C23 or CYP2C24. Conclusion Our findings suggested that CYP2C11 plays an important role in lowering blood pressure under the challenge of a high-salt diet.
bibliographic citation: Liu et al. (2019) CYP2C11 played a significant role in down-regulating rat blood pressure under the challenge of a high-salt diet. PeerJ 7:e6807 https://doi.org/10.7717/peerj.6807
date submitted: 2018-12-02
date accepted: 2019-03-18
issued: 2019-04-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Sui
  given name: Danjuan
author list: Agent
  family name: Ye
  given name: Huanying
author list: Agent
  family name: Ouyang
  given name: Zhen
author list: Agent
  family name: Wei
  given name: Yuan
doi: 10.7717/peerj.6807
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-23
copyright: © 2019 Liu et al.
attribution name: Liu et al.

Identification of a putative competitive endogenous RNA network for lung adenocarcinoma using TCGA datasets
type: item
type: AcademicArticle
description: The mechanisms underlying the oncogenesis and progression of lung adenocarcinoma (LUAD) are currently unclear. The discovery of competitive endogenous RNA (ceRNA) regulatory networks has provided a new direction for the treatment and prognosis of patients with LUAD. However, the mechanism of action of ceRNA in LUAD remains elusive. In the present study, differentially expressed mRNAs, microRNAs (miRs) and long non-coding RNAs from the cancer genome atlas database were screened. CeRNAs for LUAD were then identified using online prediction software. Among the ceRNAs identified, family with sequence similarity 83 member A (FAM83A), miR-34c-5p, KCNQ1OT1 and FLJ26245 were observed to be significantly associated with the overall survival of patients with LUAD. Of note, FAM83A has potential significance in drug resistance, and may present a candidate biomarker for the prognosis and treatment of patients with LUAD.
format: application/pdf
format: text/html
creator: Yuanyong Wang
creator: Tong Lu
creator: Yang Wo
creator: Xiao Sun
creator: Shicheng Li
creator: Shuncheng Miao
creator: Yanting Dong
creator: Xiaoliang Leng
creator: Wenjie Jiao
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
description: doi:10.7717/peerj.6809
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: The mechanisms underlying the oncogenesis and progression of lung adenocarcinoma (LUAD) are currently unclear. The discovery of competitive endogenous RNA (ceRNA) regulatory networks has provided a new direction for the treatment and prognosis of patients with LUAD. However, the mechanism of action of ceRNA in LUAD remains elusive. In the present study, differentially expressed mRNAs, microRNAs (miRs) and long non-coding RNAs from the cancer genome atlas database were screened. CeRNAs for LUAD were then identified using online prediction software. Among the ceRNAs identified, family with sequence similarity 83 member A (FAM83A), miR-34c-5p, KCNQ1OT1 and FLJ26245 were observed to be significantly associated with the overall survival of patients with LUAD. Of note, FAM83A has potential significance in drug resistance, and may present a candidate biomarker for the prognosis and treatment of patients with LUAD.
bibliographic citation: Wang et al. (2019) Identification of a putative competitive endogenous RNA network for lung adenocarcinoma using TCGA datasets. PeerJ 7:e6809 https://doi.org/10.7717/peerj.6809
date submitted: 2018-11-11
date accepted: 2019-03-18
issued: 2019-04-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yuanyong
author list: Agent
  family name: Lu
  given name: Tong
author list: Agent
  family name: Wo
  given name: Yang
author list: Agent
  family name: Sun
  given name: Xiao
author list: Agent
  family name: Li
  given name: Shicheng
author list: Agent
  family name: Miao
  given name: Shuncheng
author list: Agent
  family name: Dong
  given name: Yanting
author list: Agent
  family name: Leng
  given name: Xiaoliang
author list: Agent
  family name: Jiao
  given name: Wenjie
doi: 10.7717/peerj.6809
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-23
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Identification of optimal endogenous reference RNAs for RT-qPCR normalization in hindgut of rat models with anorectal malformations
type: item
type: AcademicArticle
description: Background Quantitative real-time polymerase chain reaction (RT-qPCR) is a sensitive method for quantifying mRNA abundance. With relative expression analysis, however, reliable data output is dependent on stably expressed reference genes across the samples being studied. In anorectal malformations (ARMs), there is limited data on the selection of appropriate reference genes. Purpose This study was aimed to investigate the optimal reference genes for PCR in ARM rat models. Methods We selected 15 commonly used reference genes (Rps18, Actb, B2m, Gapdh, Ppia, Hprt1, Pgk1, Ywhaz, Tbp, Ubc, Rps16, Rpl13a, Rplp1, Sdha, and Hmbs) as candidate reference genes and detected their mRNA expression in ARM samples by RT-qPCR. The expression stability and variability of these transcripts were subsequently evaluated using four methods (geNorm, NormFinder, comparative ΔCt, and BestKeeper). Results The abundance of the candidate reference genes was qualified by RT-qPCR and the cycle threshold (Ct) values ranged between 14.07 (Rplp1) and 21.89 (Sdha). In the overall candidate genes, different variations existed across the different algorithms. A comprehensive analysis revealed that Rpl13a ranked first among the relatively stable genes, followed by Ywhaz, Rps18, Sdha, and Hmbs. Conclusions The most stable reference genes for RT-qPCR were Rpl13a, Ywhaz, and Rps18 in ETU-induced ARMs in rat fetus. This study provided a foundation for reference gene selection for future gene expression analyses.
format: application/pdf
format: text/html
creator: Caiyun Long
creator: Yunxia Xiao
creator: Siying Li
creator: Xiaobing Tang
creator: Zhengwei Yuan
creator: Yuzuo Bai
subject: Developmental Biology
subject: Molecular Biology
subject: Pediatrics
description: doi:10.7717/peerj.6829
publisher: PeerJ Inc.
rights: © 2019 Long et al.
abstract: Background Quantitative real-time polymerase chain reaction (RT-qPCR) is a sensitive method for quantifying mRNA abundance. With relative expression analysis, however, reliable data output is dependent on stably expressed reference genes across the samples being studied. In anorectal malformations (ARMs), there is limited data on the selection of appropriate reference genes. Purpose This study was aimed to investigate the optimal reference genes for PCR in ARM rat models. Methods We selected 15 commonly used reference genes (Rps18, Actb, B2m, Gapdh, Ppia, Hprt1, Pgk1, Ywhaz, Tbp, Ubc, Rps16, Rpl13a, Rplp1, Sdha, and Hmbs) as candidate reference genes and detected their mRNA expression in ARM samples by RT-qPCR. The expression stability and variability of these transcripts were subsequently evaluated using four methods (geNorm, NormFinder, comparative ΔCt, and BestKeeper). Results The abundance of the candidate reference genes was qualified by RT-qPCR and the cycle threshold (Ct) values ranged between 14.07 (Rplp1) and 21.89 (Sdha). In the overall candidate genes, different variations existed across the different algorithms. A comprehensive analysis revealed that Rpl13a ranked first among the relatively stable genes, followed by Ywhaz, Rps18, Sdha, and Hmbs. Conclusions The most stable reference genes for RT-qPCR were Rpl13a, Ywhaz, and Rps18 in ETU-induced ARMs in rat fetus. This study provided a foundation for reference gene selection for future gene expression analyses.
bibliographic citation: Long et al. (2019) Identification of optimal endogenous reference RNAs for RT-qPCR normalization in hindgut of rat models with anorectal malformations. PeerJ 7:e6829 https://doi.org/10.7717/peerj.6829
date submitted: 2018-12-14
date accepted: 2019-03-20
issued: 2019-04-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Long
  given name: Caiyun
author list: Agent
  family name: Xiao
  given name: Yunxia
author list: Agent
  family name: Li
  given name: Siying
author list: Agent
  family name: Tang
  given name: Xiaobing
author list: Agent
  family name: Yuan
  given name: Zhengwei
author list: Agent
  family name: Bai
  given name: Yuzuo
doi: 10.7717/peerj.6829
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-23
copyright: © 2019 Long et al.
attribution name: Long et al.

Next-generation sequencing of BRCA1 and BRCA2 genes for rapid detection of germline mutations in hereditary breast/ovarian cancer
type: item
type: AcademicArticle
description: Background Conventional methods used to identify BRCA1 and BRCA2 germline mutations in hereditary cancers, such as Sanger sequencing/multiplex ligation-dependent probe amplification (MLPA), are time-consuming and expensive, due to the large size of the genes. The recent introduction of next-generation sequencing (NGS) benchtop platforms offered a powerful alternative for mutation detection, dramatically improving the speed and the efficiency of DNA testing. Here we tested the performance of the Ion Torrent PGM platform with the Ion AmpliSeq BRCA1 and BRCA2 Panel in our clinical routine of breast/ovarian hereditary cancer syndrome assessment. Methods We first tested the NGS approach in a cohort of 11 patients (training set) who had previously undergone genetic diagnosis in our laboratory by conventional methods. Then, we applied the optimized pipeline to the consecutive cohort of 136 uncharacterized probands (validation set). Results By minimal adjustments in the analytical pipeline of Torrent Suite Software we obtained a 100% concordance with Sanger results regarding the identification of single nucleotide alterations, insertions, and deletions with the exception of three large genomic rearrangements (LGRs) contained in the training set. The optimized pipeline applied to the validation set (VS), identified pathogenic and polymorphic variants, including a novel BRCA2 pathogenic variant at exon 3, 100% of which were confirmed by Sanger in their correct zygosity status. To identify LGRs, all negative samples of the VS were subjected to MLPA analysis. Discussion Our experience strongly supports that the Ion Torrent PGM technology in BRCA1 and BRCA2 germline variant identification, combined with MLPA analysis, is highly sensitive, easy to use, faster, and cheaper than traditional (Sanger sequencing/MLPA) approaches.
format: application/pdf
format: text/html
creator: Arianna Nicolussi
creator: Francesca Belardinilli
creator: Yasaman Mahdavian
creator: Valeria Colicchia
creator: Sonia D’Inzeo
creator: Marialaura Petroni
creator: Massimo Zani
creator: Sergio Ferraro
creator: Virginia Valentini
creator: Laura Ottini
creator: Giuseppe Giannini
creator: Carlo Capalbo
creator: Anna Coppa
subject: Genetics
subject: Genomics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.6661
publisher: PeerJ Inc.
rights: © 2019 Nicolussi et al.
abstract: Background Conventional methods used to identify BRCA1 and BRCA2 germline mutations in hereditary cancers, such as Sanger sequencing/multiplex ligation-dependent probe amplification (MLPA), are time-consuming and expensive, due to the large size of the genes. The recent introduction of next-generation sequencing (NGS) benchtop platforms offered a powerful alternative for mutation detection, dramatically improving the speed and the efficiency of DNA testing. Here we tested the performance of the Ion Torrent PGM platform with the Ion AmpliSeq BRCA1 and BRCA2 Panel in our clinical routine of breast/ovarian hereditary cancer syndrome assessment. Methods We first tested the NGS approach in a cohort of 11 patients (training set) who had previously undergone genetic diagnosis in our laboratory by conventional methods. Then, we applied the optimized pipeline to the consecutive cohort of 136 uncharacterized probands (validation set). Results By minimal adjustments in the analytical pipeline of Torrent Suite Software we obtained a 100% concordance with Sanger results regarding the identification of single nucleotide alterations, insertions, and deletions with the exception of three large genomic rearrangements (LGRs) contained in the training set. The optimized pipeline applied to the validation set (VS), identified pathogenic and polymorphic variants, including a novel BRCA2 pathogenic variant at exon 3, 100% of which were confirmed by Sanger in their correct zygosity status. To identify LGRs, all negative samples of the VS were subjected to MLPA analysis. Discussion Our experience strongly supports that the Ion Torrent PGM technology in BRCA1 and BRCA2 germline variant identification, combined with MLPA analysis, is highly sensitive, easy to use, faster, and cheaper than traditional (Sanger sequencing/MLPA) approaches.
bibliographic citation: Nicolussi et al. (2019) Next-generation sequencing of BRCA1 and BRCA2 genes for rapid detection of germline mutations in hereditary breast/ovarian cancer. PeerJ 7:e6661 https://doi.org/10.7717/peerj.6661
date submitted: 2018-12-07
date accepted: 2019-02-19
issued: 2019-04-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nicolussi
  given name: Arianna
author list: Agent
  family name: Belardinilli
  given name: Francesca
author list: Agent
  family name: Mahdavian
  given name: Yasaman
author list: Agent
  family name: Colicchia
  given name: Valeria
author list: Agent
  family name: D’Inzeo
  given name: Sonia
author list: Agent
  family name: Petroni
  given name: Marialaura
author list: Agent
  family name: Zani
  given name: Massimo
author list: Agent
  family name: Ferraro
  given name: Sergio
author list: Agent
  family name: Valentini
  given name: Virginia
author list: Agent
  family name: Ottini
  given name: Laura
author list: Agent
  family name: Giannini
  given name: Giuseppe
author list: Agent
  family name: Capalbo
  given name: Carlo
author list: Agent
  family name: Coppa
  given name: Anna
doi: 10.7717/peerj.6661
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-22
copyright: © 2019 Nicolussi et al.
attribution name: Nicolussi et al.

MicroRNA profiling of mouse liver in response to DENV-1 infection by deep sequencing
type: item
type: AcademicArticle
description: Background Dengue caused by dengue virus (DENV) serotypes −1 to −4 is the most important mosquito-borne viral disease in the tropical and sub-tropical countries worldwide. Yet many of the pathophysiological mechanisms of host responses during DENV infection remain largely unknown and incompletely understood. Methods Using a mouse model, the miRNA expressions in liver during DENV-1 infection was investigated using high throughput miRNA sequencing. The differential expressions of miRNAs were then validated by qPCR, followed by target genes prediction. The identified miRNA targets were subjected to gene ontology (GO) annotation and pathway enrichment analysis to elucidate the potential biological pathways and molecular mechanisms associated with DENV-1 infection. Results A total of 224 and 372 miRNAs out of 433 known mouse miRNAs were detected in the livers of DENV-1-infected and uninfected mice, respectively; of these, 207 miRNAs were present in both libraries. The miR-148a-3p and miR-122-5p were the two most abundant miRNAs in both groups. Thirty-one miRNAs were found to have at least 2-fold change in upregulation or downregulation, in which seven miRNAs were upregulated and 24 miRNAs were downregulated in the DENV-1-infected mouse livers. The miR-1a-3p was found to be the most downregulated miRNA in the DENV-1-infected mouse livers, with a significant fold change of 0.10. To validate the miRNA sequencing result, the expression pattern of 12 miRNAs, which were highly differentially expressed or most abundant, were assessed by qPCR and nine of them correlated positively with the one observed in deep sequencing. In silico functional analysis revealed that the adaptive immune responses involving TGF-beta, MAPK, PI3K-Akt, Rap1, Wnt and Ras signalling pathways were modulated collectively by 23 highly differentially expressed miRNAs during DENV-1 infection. Conclusion This study provides the first insight into the global miRNA expressions of mouse livers in response to DEN…
format: application/pdf
format: text/html
creator: Lian Yih Pong
creator: Sinikka Parkkinen
creator: Amreeta Dhanoa
creator: Han Ming Gan
creator: Indeevari Abisheka Chiharu Wickremesinghe
creator: Sharifah Syed Hassan
subject: Bioinformatics
subject: Genomics
subject: Virology
subject: Infectious Diseases
description: doi:10.7717/peerj.6697
publisher: PeerJ Inc.
rights: © 2019 Pong et al.
abstract: Background Dengue caused by dengue virus (DENV) serotypes −1 to −4 is the most important mosquito-borne viral disease in the tropical and sub-tropical countries worldwide. Yet many of the pathophysiological mechanisms of host responses during DENV infection remain largely unknown and incompletely understood. Methods Using a mouse model, the miRNA expressions in liver during DENV-1 infection was investigated using high throughput miRNA sequencing. The differential expressions of miRNAs were then validated by qPCR, followed by target genes prediction. The identified miRNA targets were subjected to gene ontology (GO) annotation and pathway enrichment analysis to elucidate the potential biological pathways and molecular mechanisms associated with DENV-1 infection. Results A total of 224 and 372 miRNAs out of 433 known mouse miRNAs were detected in the livers of DENV-1-infected and uninfected mice, respectively; of these, 207 miRNAs were present in both libraries. The miR-148a-3p and miR-122-5p were the two most abundant miRNAs in both groups. Thirty-one miRNAs were found to have at least 2-fold change in upregulation or downregulation, in which seven miRNAs were upregulated and 24 miRNAs were downregulated in the DENV-1-infected mouse livers. The miR-1a-3p was found to be the most downregulated miRNA in the DENV-1-infected mouse livers, with a significant fold change of 0.10. To validate the miRNA sequencing result, the expression pattern of 12 miRNAs, which were highly differentially expressed or most abundant, were assessed by qPCR and nine of them correlated positively with the one observed in deep sequencing. In silico functional analysis revealed that the adaptive immune responses involving TGF-beta, MAPK, PI3K-Akt, Rap1, Wnt and Ras signalling pathways were modulated collectively by 23 highly differentially expressed miRNAs during DENV-1 infection. Conclusion This study provides the first insight into the global miRNA expressions of mouse livers in response to DEN…
bibliographic citation: Pong et al. (2019) MicroRNA profiling of mouse liver in response to DENV-1 infection by deep sequencing. PeerJ 7:e6697 https://doi.org/10.7717/peerj.6697
date submitted: 2018-12-07
date accepted: 2019-02-28
issued: 2019-04-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pong
  given name: Lian Yih
author list: Agent
  family name: Parkkinen
  given name: Sinikka
author list: Agent
  family name: Dhanoa
  given name: Amreeta
author list: Agent
  family name: Gan
  given name: Han Ming
author list: Agent
  family name: Wickremesinghe
  given name: Indeevari Abisheka Chiharu
author list: Agent
  family name: Syed Hassan
  given name: Sharifah
doi: 10.7717/peerj.6697
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-22
copyright: ©2019 Pong et al.
attribution name: Pong et al.

Integrated analysis of two-lncRNA signature as a potential prognostic biomarker in cervical cancer: a study based on public database
type: item
type: AcademicArticle
description: Background Cervical cancer (CC) is a common gynecological malignancy in women worldwide. Evidence suggests that long non-coding RNAs (lncRNAs) can be used as biomarkers in patients with CC. However, prognostic biomarkers for CC are still lacking. The aim of our study was to find lncRNA biomarkers which are able to predict prognosis in CC based on the data from The Cancer Genome Atlas (TCGA). Methods The patients were divided into three groups according to FIGO stage. Differentially expressed lncRNAs were identified in CC tissue compared to adjacent normal tissues based on a fold change >2 and <0.5 at P < 0.05 for up- and downregulated lncRNA, respectively. The relationship between survival outcome and lncRNA expression was assessed with univariate and multivariate Cox proportional hazards regression analysis. We constructed a risk score as a method to evaluate prognosis. We used receiver operating characteristic (ROC) curve and the area under curve (AUC) analyses to assess the diagnostic value of a two-lncRNA signature. We detected the expression levels of the two lncRNAs in 31 pairs of newly diagnosed CC specimens and paired adjacent non-cancerous tissue specimens, and also in CC cell lines. Finally, the results were statistically compared using t-tests. Results In total, 289 RNA sequencing profiles and accompanying clinical data were obtained. We identified 49 differentially expressed lncRNAs, of which two related to overall survival (OS) in CC patients. These two lncRNAs (ILF3-AS1 and RASA4CP) were found together as a single prognostic signature. Meanwhile, the prognosis of patients with low-risk CC was better and positively correlated with OS (P < 0.001). Further analysis showed that the combined two-lncRNA expression signature could be used as an independent biomarker to evaluate the prognosis in CC. qRT-PCR results were consistent with TCGA, confirming downregulated expression of both lncRNAs. Furthermore, upon ROC curve analysis, the AUC of the combined lncRN…
format: application/pdf
format: text/html
creator: Wenjuan Wu
creator: Jing Sui
creator: Tong Liu
creator: Sheng Yang
creator: Siyi Xu
creator: Man Zhang
creator: Shaoping Huang
creator: Lihong Yin
creator: Yuepu Pu
creator: Geyu Liang
subject: Bioinformatics
subject: Genomics
subject: Gynecology and Obstetrics
subject: Oncology
subject: Public Health
description: doi:10.7717/peerj.6761
publisher: PeerJ Inc.
rights: © 2019 Wu et al.
abstract: Background Cervical cancer (CC) is a common gynecological malignancy in women worldwide. Evidence suggests that long non-coding RNAs (lncRNAs) can be used as biomarkers in patients with CC. However, prognostic biomarkers for CC are still lacking. The aim of our study was to find lncRNA biomarkers which are able to predict prognosis in CC based on the data from The Cancer Genome Atlas (TCGA). Methods The patients were divided into three groups according to FIGO stage. Differentially expressed lncRNAs were identified in CC tissue compared to adjacent normal tissues based on a fold change >2 and <0.5 at P < 0.05 for up- and downregulated lncRNA, respectively. The relationship between survival outcome and lncRNA expression was assessed with univariate and multivariate Cox proportional hazards regression analysis. We constructed a risk score as a method to evaluate prognosis. We used receiver operating characteristic (ROC) curve and the area under curve (AUC) analyses to assess the diagnostic value of a two-lncRNA signature. We detected the expression levels of the two lncRNAs in 31 pairs of newly diagnosed CC specimens and paired adjacent non-cancerous tissue specimens, and also in CC cell lines. Finally, the results were statistically compared using t-tests. Results In total, 289 RNA sequencing profiles and accompanying clinical data were obtained. We identified 49 differentially expressed lncRNAs, of which two related to overall survival (OS) in CC patients. These two lncRNAs (ILF3-AS1 and RASA4CP) were found together as a single prognostic signature. Meanwhile, the prognosis of patients with low-risk CC was better and positively correlated with OS (P < 0.001). Further analysis showed that the combined two-lncRNA expression signature could be used as an independent biomarker to evaluate the prognosis in CC. qRT-PCR results were consistent with TCGA, confirming downregulated expression of both lncRNAs. Furthermore, upon ROC curve analysis, the AUC of the combined lncRN…
bibliographic citation: Wu et al. (2019) Integrated analysis of two-lncRNA signature as a potential prognostic biomarker in cervical cancer: a study based on public database. PeerJ 7:e6761 https://doi.org/10.7717/peerj.6761
date submitted: 2018-01-02
date accepted: 2019-03-08
issued: 2019-04-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Wenjuan
author list: Agent
  family name: Sui
  given name: Jing
author list: Agent
  family name: Liu
  given name: Tong
author list: Agent
  family name: Yang
  given name: Sheng
author list: Agent
  family name: Xu
  given name: Siyi
author list: Agent
  family name: Zhang
  given name: Man
author list: Agent
  family name: Huang
  given name: Shaoping
author list: Agent
  family name: Yin
  given name: Lihong
author list: Agent
  family name: Pu
  given name: Yuepu
author list: Agent
  family name: Liang
  given name: Geyu
doi: 10.7717/peerj.6761
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-22
copyright: © 2019 Wu et al.
attribution name: Wu et al.

Extinction and the U.S. Endangered Species Act
type: item
type: AcademicArticle
description: The U.S. Endangered Species Act is one of the strongest laws of any nation for preventing species extinction, but quantifying the Act’s effectiveness has proven difficult. To provide one measure of effectiveness, we identified listed species that have gone extinct and used previously developed methods to update an estimate of the number of species extinctions prevented by the Act. To date, only four species have been confirmed extinct with another 22 possibly extinct following protection. Another 71 listed species are extinct or possibly extinct, but were last seen before protections were enacted, meaning the Act’s protections never had the opportunity to save these species. In contrast, a total of 39 species have been fully recovered, including 23 in the last 10 years. We estimate the Endangered Species Act has prevented the extinction of roughly 291 species since passage in 1973, and has to date saved more than 99% of species under its protection.
format: application/pdf
format: text/html
creator: Noah Greenwald
creator: Kieran F. Suckling
creator: Brett Hartl
creator: Loyal A. Mehrhoff
subject: Biodiversity
subject: Conservation Biology
subject: Science Policy
description: doi:10.7717/peerj.6803
publisher: PeerJ Inc.
rights: © 2019 Greenwald et al.
abstract: The U.S. Endangered Species Act is one of the strongest laws of any nation for preventing species extinction, but quantifying the Act’s effectiveness has proven difficult. To provide one measure of effectiveness, we identified listed species that have gone extinct and used previously developed methods to update an estimate of the number of species extinctions prevented by the Act. To date, only four species have been confirmed extinct with another 22 possibly extinct following protection. Another 71 listed species are extinct or possibly extinct, but were last seen before protections were enacted, meaning the Act’s protections never had the opportunity to save these species. In contrast, a total of 39 species have been fully recovered, including 23 in the last 10 years. We estimate the Endangered Species Act has prevented the extinction of roughly 291 species since passage in 1973, and has to date saved more than 99% of species under its protection.
bibliographic citation: Greenwald et al. (2019) Extinction and the U.S. Endangered Species Act. PeerJ 7:e6803 https://doi.org/10.7717/peerj.6803
date submitted: 2019-01-07
date accepted: 2019-03-16
issued: 2019-04-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Greenwald
  given name: Noah
author list: Agent
  family name: Suckling
  given name: Kieran F.
author list: Agent
  family name: Hartl
  given name: Brett
author list: Agent
  family name: A. Mehrhoff
  given name: Loyal
doi: 10.7717/peerj.6803
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-22
copyright: © 2019 Greenwald et al.
attribution name: Greenwald et al.

eHealth adoption and use among healthcare professionals in a tertiary hospital in Sub-Saharan Africa: a Qmethodology study
type: item
type: AcademicArticle
description: Background The aim of the study was to explore the viewpoints of healthcare professionals (HCPs) on the adoption and use of eHealth in clinical practice in sub-Saharan Africa (SSA). Information and communication technologies (ICTs) including eHealth provide HCPs the opportunity to provide quality healthcare to their patients while also improving their own clinical practices. Despite this, previous research has identified these technologies have their associated challenges when adopting them for clinical practice. But more research is needed to identify how these eHealth resources influence clinical practice. In addition, there is still little information about adoption and use of these technologies by HCPs inclinical practice in Sub-Saharan Africa. Method An exploratory descriptive design was adopted for this study. Thirty-six (36) HCPs (18 nurses and 18 physicians) working in the clinical area in a tertiary health institution in SSA participated in this study. Using Qmethodology, study participants rank-ordered forty-six statementsin relation to their adoption and use of eHealth within their clinical practice.This was analysed using by-person factor analysis and complemented with audio-taped interviews. Results The analysis yielded four factors i.e., distinct viewpoints the HCPs hold about adoption and use of eHealth within their clinical practice. These factors include: “Patient-focused eHealth advocates” who use the eHealth because they are motivated by patients and their families preferences; “Task-focused eHealth advocates” use eHealth because it helps them complete clinical tasks; “Traditionalistic-pragmatists” recognise contributions eHealth makes in clinical practice but separate from their routine clinical activities; and the “Tech-focused eHealth advocates” who use the eHealth because they are motivated by the technology itself. Conclusion The study shows the equivocal viewpoints that HCPs have about eHealth within their clinical practice. This, in additio…
format: application/pdf
format: text/html
creator: Muhammad Awwal Ladan
creator: Heather Wharrad
creator: Richard Windle
subject: Nursing
subject: Human–Computer Interaction
description: doi:10.7717/peerj.6326
publisher: PeerJ Inc.
rights: © 2019 Ladan et al.
abstract: Background The aim of the study was to explore the viewpoints of healthcare professionals (HCPs) on the adoption and use of eHealth in clinical practice in sub-Saharan Africa (SSA). Information and communication technologies (ICTs) including eHealth provide HCPs the opportunity to provide quality healthcare to their patients while also improving their own clinical practices. Despite this, previous research has identified these technologies have their associated challenges when adopting them for clinical practice. But more research is needed to identify how these eHealth resources influence clinical practice. In addition, there is still little information about adoption and use of these technologies by HCPs inclinical practice in Sub-Saharan Africa. Method An exploratory descriptive design was adopted for this study. Thirty-six (36) HCPs (18 nurses and 18 physicians) working in the clinical area in a tertiary health institution in SSA participated in this study. Using Qmethodology, study participants rank-ordered forty-six statementsin relation to their adoption and use of eHealth within their clinical practice.This was analysed using by-person factor analysis and complemented with audio-taped interviews. Results The analysis yielded four factors i.e., distinct viewpoints the HCPs hold about adoption and use of eHealth within their clinical practice. These factors include: “Patient-focused eHealth advocates” who use the eHealth because they are motivated by patients and their families preferences; “Task-focused eHealth advocates” use eHealth because it helps them complete clinical tasks; “Traditionalistic-pragmatists” recognise contributions eHealth makes in clinical practice but separate from their routine clinical activities; and the “Tech-focused eHealth advocates” who use the eHealth because they are motivated by the technology itself. Conclusion The study shows the equivocal viewpoints that HCPs have about eHealth within their clinical practice. This, in additio…
bibliographic citation: Ladan et al. (2019) eHealth adoption and use among healthcare professionals in a tertiary hospital in Sub-Saharan Africa: a Qmethodology study. PeerJ 7:e6326 https://doi.org/10.7717/peerj.6326
date submitted: 2018-10-12
date accepted: 2018-12-20
issued: 2019-04-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ladan
  given name: Muhammad Awwal
author list: Agent
  family name: Wharrad
  given name: Heather
author list: Agent
  family name: Windle
  given name: Richard
doi: 10.7717/peerj.6326
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-19
copyright: ©2019 Ladan et al.
attribution name: Ladan et al.

Rapid ecological specialization despite constant population sizes
type: item
type: AcademicArticle
description: Background The bushbuck, Tragelaphus scriptus, is a widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes. This species was recently found to consist of two genetically divergent but monophyletic lineages, which are paraphyletic at mitochondrial (mt)DNA owing to an ancient interspecific hybridization event. The Scriptus lineage (T. s. scriptus) inhabits the north-western half of the African continent while Sylvaticus (T. s. sylvaticus) is found in the south-eastern half. Here we test hypotheses of historical demography and adaptation in bushbuck using a higher-resolution framework, with four nuclear (MGF, PRKCI, SPTBN, and THY) and three new mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA). Methods Genealogies were reconstructed for the mitochondrial and nuclear data sets, with the latter dated using fossil calibration points. We also inferred the demographic history of Scriptus and Sylvaticus using coalescent-based methods. To obtain an overview of the origins and ancestral colonisation routes of ancestral bushbuck sequences across geographic space, we conducted discrete Bayesian phylogeographic and statistical dispersal-vicariance analyses on our nuclear DNA data set. Results Both nuclear DNA and mtDNA support previous findings of two genetically divergent Sylvaticus and Scriptus lineages. The three mtDNA loci confirmed 15 of the previously defined haplogroups, including those with convergent phenotypes. However, the nuclear tree showed less phylogenetic resolution at the more derived parts of the genealogy, possibly due to incomplete lineage sorting of the slower evolving nuclear genome. The only exception to this was the montane Menelik’s bushbuck (Sylvaticus) of the Ethiopian highlands, which formed a monophyletic group at three of four nuclear DNA loci. We dated the coalescence of the two lineages to a common ancestor ∼2.54 million years ago. Both marker sets revealed similar demographic histories of consta…
format: application/pdf
format: text/html
creator: Andrinajoro R. Rakotoarivelo
creator: Paul O’Donoghue
creator: Michael W. Bruford
creator: Yoshan Moodley
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.6476
publisher: PeerJ Inc.
rights: © 2019 Rakotoarivelo et al.
abstract: Background The bushbuck, Tragelaphus scriptus, is a widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes. This species was recently found to consist of two genetically divergent but monophyletic lineages, which are paraphyletic at mitochondrial (mt)DNA owing to an ancient interspecific hybridization event. The Scriptus lineage (T. s. scriptus) inhabits the north-western half of the African continent while Sylvaticus (T. s. sylvaticus) is found in the south-eastern half. Here we test hypotheses of historical demography and adaptation in bushbuck using a higher-resolution framework, with four nuclear (MGF, PRKCI, SPTBN, and THY) and three new mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA). Methods Genealogies were reconstructed for the mitochondrial and nuclear data sets, with the latter dated using fossil calibration points. We also inferred the demographic history of Scriptus and Sylvaticus using coalescent-based methods. To obtain an overview of the origins and ancestral colonisation routes of ancestral bushbuck sequences across geographic space, we conducted discrete Bayesian phylogeographic and statistical dispersal-vicariance analyses on our nuclear DNA data set. Results Both nuclear DNA and mtDNA support previous findings of two genetically divergent Sylvaticus and Scriptus lineages. The three mtDNA loci confirmed 15 of the previously defined haplogroups, including those with convergent phenotypes. However, the nuclear tree showed less phylogenetic resolution at the more derived parts of the genealogy, possibly due to incomplete lineage sorting of the slower evolving nuclear genome. The only exception to this was the montane Menelik’s bushbuck (Sylvaticus) of the Ethiopian highlands, which formed a monophyletic group at three of four nuclear DNA loci. We dated the coalescence of the two lineages to a common ancestor ∼2.54 million years ago. Both marker sets revealed similar demographic histories of consta…
bibliographic citation: Rakotoarivelo et al. (2019) Rapid ecological specialization despite constant population sizes. PeerJ 7:e6476 https://doi.org/10.7717/peerj.6476
date submitted: 2018-07-27
date accepted: 2019-01-17
issued: 2019-04-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rakotoarivelo
  given name: Andrinajoro R.
author list: Agent
  family name: O’Donoghue
  given name: Paul
author list: Agent
  family name: Bruford
  given name: Michael W.
author list: Agent
  family name: Moodley
  given name: Yoshan
doi: 10.7717/peerj.6476
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-19
copyright: ©2019 Rakotoarivelo et al.
attribution name: Rakotoarivelo et al.

Ability emotional intelligence in young people and older adults with and without depressive symptoms, considering gender and educational level
type: item
type: AcademicArticle
description: Background There is little research on differences in Emotional Intelligence (EI) ability at different stages of adult development. The few published studies tend not to use older adult samples. Previous studies on EI ability and age have shown contradictory results. Our main objective was to evaluate results in EI ability across different stages of adult development, taking into account gender, depressive symptoms, and educational level. Methods We interviewed 166 participants (108 women), 66 of whom were aged 18–30 years, 53 aged 31–60 years, and 40 aged 61–76 years. All were either working or enrolled in colleges at the time of the study. The assessment tools used were the Mayer-Salovey-Caruso Emotional Intelligence Test (MSCEIT), a test that assesses performance-based EI, and the Centre for Epidemiologic Studies-Depression (CES-D) scale, a tool to evaluate depressive symptoms. Results Young people, women, and participants with a higher educational level achieved higher scores on the MSCEIT. Additionally, depressive symptomatology was only partially associated with the MSCEIT (i.e., with the using emotions branch). However, a subsequent joint analysis of the independent effects of variables age, gender, educational level, and depressive symptomatology and their interactions on MSCEIT total suggests that only educational level and depressive symptomatology were associated with EI ability, with the direct relationship between age and gender with MSCEIT disappearing. Additionally, our study indicated an interaction effect between age and depressive symptoms, showing that participants in age cohorts 18–30 and 31–60 and without depressive symptoms have a higher EI ability. Discussion Our study suggests that the direct effects of age and gender on EI ability across adult development, using a wide age range, can change or disappear when effects of educational level and depressive symptomatology, and their interactions, are controlled for. Our results also suggest that E…
format: application/pdf
format: text/html
creator: Beatriz Navarro-Bravo
creator: José M. Latorre
creator: Ana Jiménez
creator: Rosario Cabello
creator: Pablo Fernández-Berrocal
subject: Geriatrics
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6595
publisher: PeerJ Inc.
rights: © 2019 Navarro-Bravo et al.
abstract: Background There is little research on differences in Emotional Intelligence (EI) ability at different stages of adult development. The few published studies tend not to use older adult samples. Previous studies on EI ability and age have shown contradictory results. Our main objective was to evaluate results in EI ability across different stages of adult development, taking into account gender, depressive symptoms, and educational level. Methods We interviewed 166 participants (108 women), 66 of whom were aged 18–30 years, 53 aged 31–60 years, and 40 aged 61–76 years. All were either working or enrolled in colleges at the time of the study. The assessment tools used were the Mayer-Salovey-Caruso Emotional Intelligence Test (MSCEIT), a test that assesses performance-based EI, and the Centre for Epidemiologic Studies-Depression (CES-D) scale, a tool to evaluate depressive symptoms. Results Young people, women, and participants with a higher educational level achieved higher scores on the MSCEIT. Additionally, depressive symptomatology was only partially associated with the MSCEIT (i.e., with the using emotions branch). However, a subsequent joint analysis of the independent effects of variables age, gender, educational level, and depressive symptomatology and their interactions on MSCEIT total suggests that only educational level and depressive symptomatology were associated with EI ability, with the direct relationship between age and gender with MSCEIT disappearing. Additionally, our study indicated an interaction effect between age and depressive symptoms, showing that participants in age cohorts 18–30 and 31–60 and without depressive symptoms have a higher EI ability. Discussion Our study suggests that the direct effects of age and gender on EI ability across adult development, using a wide age range, can change or disappear when effects of educational level and depressive symptomatology, and their interactions, are controlled for. Our results also suggest that E…
bibliographic citation: Navarro-Bravo et al. (2019) Ability emotional intelligence in young people and older adults with and without depressive symptoms, considering gender and educational level. PeerJ 7:e6595 https://doi.org/10.7717/peerj.6595
date submitted: 2018-07-31
date accepted: 2019-02-09
issued: 2019-04-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Navarro-Bravo
  given name: Beatriz
author list: Agent
  family name: Latorre
  given name: José M.
author list: Agent
  family name: Jiménez
  given name: Ana
author list: Agent
  family name: Cabello
  given name: Rosario
author list: Agent
  family name: Fernández-Berrocal
  given name: Pablo
doi: 10.7717/peerj.6595
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-19
copyright: ©2019 Navarro-Bravo et al.
attribution name: Navarro-Bravo et al.

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