PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Association of sleep duration and sleep quality with hypertension in oil workers in Xinjiang
items: Outcomes of critically ill end-stage kidney disease patients who underwent major surgery
items: Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide
items: Local patterns of arbuscular mycorrhizal fungal diversity and community structure in a natural Toona ciliata var. pubescens forest in South Central China
items: re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files
items: Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma
items: Serum metabolomic profiling reveals an increase in homocitrulline in Chinese patients with nonalcoholic fatty liver disease: a retrospective study
items: Sphenofontis velserae gen. et sp. nov., a new rhynchocephalian from the Late Jurassic of Brunn (Solnhofen Archipelago, southern Germany)
items: Ecosystem services show variable responses to future climate conditions in the Colombian páramos
items: DXA reference values of the humanoid sheep model in preclinical studies

Association of sleep duration and sleep quality with hypertension in oil workers in Xinjiang
type: item
type: AcademicArticle
description: Objective The aim of this study is to explore sleep status and hypertension among oil workers in Xinjiang, China. It may provide new ideas and basis for the precise prevention and treatment of hypertension in occupational population. Methods Sleep status and hypertension were investigated in 3,040 workers by a multi-stage cluster sampling method in six oil field bases in Karamay City, Xinjiang. The Pittsburgh Sleep Quality Index was used to evaluate the sleep status of workers. Logistic regression was used to analyze the relationship between sleep duration and sleep quality, and hypertension. Stratified analysis was also performed. Results Our results show: 1. Insufficient sleep duration (OR = 1.51, 95% CI [1.19–1.90]) and poor sleep quality (OR = 1.78, 95% CI [1.33–2.38] were positively associated with hypertension. 2. Stratified analysis indicated insufficient sleep duration was associated with increased risk of hypertension in females (OR = 1.54, 95% CI [1.16–2.04]) than males (OR = 1.49, 95% CI [1.00–2.23]), and the risk of hypertension in the group <30 years old (OR = 9.03, 95% CI [2.32–35.15]) was higher than that in the group of 30–45 years old (OR = 1.59, 95% CI [1.14–2.20]). However, in the group > 45 years old, sleeping > 8 h was associated with increased risk of hypertension (OR = 3.36, 95% CI [1.42–7.91]). Oil workers doing shift work had a higher risk of hypertension (OR = 1.55, 95% CI [1.16–2.07]) to no shift work (OR = 1.48, 95% CI [1.02–2.15]). The risk of hypertension in the group with < 10 years of service (OR = 4.08, 95% CI [1.92–8.83]) was higher than that in the group with length of service of 10–20 years (OR = 2.79, 95% CI [1.59–4.86]). Poor sleep quality was associated with risk for hypertension in females (OR = 1.78, 95% CI [1.26–2.49]), those doing shift work (OR = 1.70, 95% CI [1.17–2.47]), those with length of service of > 20 years (OR = 1.64, 95% CI [1.18–2.27]). The risk of hypertension in the group 30–45 years old is higher than that in…
format: application/pdf
format: text/html
creator: Fen Yang
creator: Yuanyue Zhang
creator: Ruiying Qiu
creator: Ning Tao
subject: Cognitive Disorders
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11318
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Objective The aim of this study is to explore sleep status and hypertension among oil workers in Xinjiang, China. It may provide new ideas and basis for the precise prevention and treatment of hypertension in occupational population. Methods Sleep status and hypertension were investigated in 3,040 workers by a multi-stage cluster sampling method in six oil field bases in Karamay City, Xinjiang. The Pittsburgh Sleep Quality Index was used to evaluate the sleep status of workers. Logistic regression was used to analyze the relationship between sleep duration and sleep quality, and hypertension. Stratified analysis was also performed. Results Our results show: 1. Insufficient sleep duration (OR = 1.51, 95% CI [1.19–1.90]) and poor sleep quality (OR = 1.78, 95% CI [1.33–2.38] were positively associated with hypertension. 2. Stratified analysis indicated insufficient sleep duration was associated with increased risk of hypertension in females (OR = 1.54, 95% CI [1.16–2.04]) than males (OR = 1.49, 95% CI [1.00–2.23]), and the risk of hypertension in the group <30 years old (OR = 9.03, 95% CI [2.32–35.15]) was higher than that in the group of 30–45 years old (OR = 1.59, 95% CI [1.14–2.20]). However, in the group > 45 years old, sleeping > 8 h was associated with increased risk of hypertension (OR = 3.36, 95% CI [1.42–7.91]). Oil workers doing shift work had a higher risk of hypertension (OR = 1.55, 95% CI [1.16–2.07]) to no shift work (OR = 1.48, 95% CI [1.02–2.15]). The risk of hypertension in the group with < 10 years of service (OR = 4.08, 95% CI [1.92–8.83]) was higher than that in the group with length of service of 10–20 years (OR = 2.79, 95% CI [1.59–4.86]). Poor sleep quality was associated with risk for hypertension in females (OR = 1.78, 95% CI [1.26–2.49]), those doing shift work (OR = 1.70, 95% CI [1.17–2.47]), those with length of service of > 20 years (OR = 1.64, 95% CI [1.18–2.27]). The risk of hypertension in the group 30–45 years old is higher than that in…
bibliographic citation: Yang et al. (2021) Association of sleep duration and sleep quality with hypertension in oil workers in Xinjiang. PeerJ 9:e11318 https://doi.org/10.7717/peerj.11318
date submitted: 2020-08-10
date accepted: 2021-03-30
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Fen
author list: Agent
  family name: Zhang
  given name: Yuanyue
author list: Agent
  family name: Qiu
  given name: Ruiying
author list: Agent
  family name: Tao
  given name: Ning
doi: 10.7717/peerj.11318
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Yang et al.
attribution name: Yang et al.

Outcomes of critically ill end-stage kidney disease patients who underwent major surgery
type: item
type: AcademicArticle
description: Purpose End-stage kidney disease (ESKD) is a major worldwide health problem. Patients with ESKD are thought to have a significant risk for development of complications following an operation. However, the study of ESKD and its outcomes following major operations remains rare, particularly in critical illness. Therefore, this study aimed to demonstrate how the outcomes of ESKD patients were affected when they underwent a major operation and were admitted to the intensive care unit (ICU), compared with non-ESKD patients. Methods A retrospective matched case cohort study was conducted in 122 critically ill surgical patients who underwent a major operation and were admitted to the ICU, during 2013 and 2016. Sixty-one ESKD patients who required long-term dialysis were enrolled and compared with 61 matched non-ESKD patients. The matching criteria were the same age interval (±5 years), gender, and type of operation. The ICU mortality was compared to the primary outcome of the study. Results Patients’ baseline characteristics between ESKD and non-ESKD were similar to a priori matching criteria and other demographics, except for pre-existing diabetes mellitus and hypertension, which were found significantly more in ESKD (p = 0.03 and 0.04, respectively). For operations, ESKD showed a higher grade of the American Society of Anesthesiologist (ASA) physical status (p < 0.001), but there were no differences for emergency surgery (p = 0.71) and duration of operation (p = 0.34). At ICU admission, the severity of illness measured by the Sequential Organ Failure Assessment (SOFA) score was greater in ESKD (8.9 ± 2.6 vs 5.6 ± 2.5; p < 0.001). However, after eliminating renal domain, SOFA non-renal score was equivalent (5.7 ± 2.2 vs 5.2 ± 2.3, p = 0.16). The ICU mortality was significantly higher in critically-ill surgical patients with ESKD than non-ESKD (23% vs 5%, p=0.007), along with hospital mortality rates (34% vs 10%, p = 0.002). The multivariable logistic regression analyses a…
format: application/pdf
format: text/html
creator: Peerawitch Petchmak
creator: Yuthapong Wongmahisorn
creator: Konlawij Trongtrakul
subject: Emergency and Critical Care
subject: Internal Medicine
subject: Nephrology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.11324
publisher: PeerJ Inc.
rights: © 2021 Petchmak et al.
abstract: Purpose End-stage kidney disease (ESKD) is a major worldwide health problem. Patients with ESKD are thought to have a significant risk for development of complications following an operation. However, the study of ESKD and its outcomes following major operations remains rare, particularly in critical illness. Therefore, this study aimed to demonstrate how the outcomes of ESKD patients were affected when they underwent a major operation and were admitted to the intensive care unit (ICU), compared with non-ESKD patients. Methods A retrospective matched case cohort study was conducted in 122 critically ill surgical patients who underwent a major operation and were admitted to the ICU, during 2013 and 2016. Sixty-one ESKD patients who required long-term dialysis were enrolled and compared with 61 matched non-ESKD patients. The matching criteria were the same age interval (±5 years), gender, and type of operation. The ICU mortality was compared to the primary outcome of the study. Results Patients’ baseline characteristics between ESKD and non-ESKD were similar to a priori matching criteria and other demographics, except for pre-existing diabetes mellitus and hypertension, which were found significantly more in ESKD (p = 0.03 and 0.04, respectively). For operations, ESKD showed a higher grade of the American Society of Anesthesiologist (ASA) physical status (p < 0.001), but there were no differences for emergency surgery (p = 0.71) and duration of operation (p = 0.34). At ICU admission, the severity of illness measured by the Sequential Organ Failure Assessment (SOFA) score was greater in ESKD (8.9 ± 2.6 vs 5.6 ± 2.5; p < 0.001). However, after eliminating renal domain, SOFA non-renal score was equivalent (5.7 ± 2.2 vs 5.2 ± 2.3, p = 0.16). The ICU mortality was significantly higher in critically-ill surgical patients with ESKD than non-ESKD (23% vs 5%, p=0.007), along with hospital mortality rates (34% vs 10%, p = 0.002). The multivariable logistic regression analyses a…
bibliographic citation: Petchmak et al. (2021) Outcomes of critically ill end-stage kidney disease patients who underwent major surgery. PeerJ 9:e11324 https://doi.org/10.7717/peerj.11324
date submitted: 2020-04-22
date accepted: 2021-03-31
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Petchmak
  given name: Peerawitch
author list: Agent
  family name: Wongmahisorn
  given name: Yuthapong
author list: Agent
  family name: Trongtrakul
  given name: Konlawij
doi: 10.7717/peerj.11324
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Petchmak et al.
attribution name: Petchmak et al.

Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide
type: item
type: AcademicArticle
description: White clover is an important temperate legume forage with high nutrition. In the present study, 448 worldwide accessions were evaluated for the genetic variation and polymorphisms using 22 simple sequence repeat (SSR) markers. All the markers were highly informative, a total of 341 scored bands were amplified, out of which 337 (98.83%) were polymorphic. The PIC values ranged from 0.89 to 0.97 with an average of 0.95. For the AMOVA analysis, 98% of the variance was due to differences within the population and the remaining 2% was due to differences among populations. The white clover accessions were divided into different groups or subgroups based on PCoA, UPGMA, and STRUCTURE analyses. The existence of genetic differentiation between the originally natural and introduced areas according to the PCoA analysis of the global white clover accessions. There was a weak correlation between genetic relationships and geographic distribution according to UPGMA and STRUCTURE analyses. The results of the present study will provide the foundation for future breeding programs, genetic improvement, core germplasm collection establishment for white clover.
format: application/pdf
format: text/html
creator: Feifei Wu
creator: Sainan Ma
creator: Jie Zhou
creator: Chongyang Han
creator: Ruchang Hu
creator: Xinying Yang
creator: Gang Nie
creator: Xinquan Zhang
subject: Agricultural Science
subject: Biodiversity
subject: Bioinformatics
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.11325
publisher: PeerJ Inc.
rights: © 2021 Wu et al.
abstract: White clover is an important temperate legume forage with high nutrition. In the present study, 448 worldwide accessions were evaluated for the genetic variation and polymorphisms using 22 simple sequence repeat (SSR) markers. All the markers were highly informative, a total of 341 scored bands were amplified, out of which 337 (98.83%) were polymorphic. The PIC values ranged from 0.89 to 0.97 with an average of 0.95. For the AMOVA analysis, 98% of the variance was due to differences within the population and the remaining 2% was due to differences among populations. The white clover accessions were divided into different groups or subgroups based on PCoA, UPGMA, and STRUCTURE analyses. The existence of genetic differentiation between the originally natural and introduced areas according to the PCoA analysis of the global white clover accessions. There was a weak correlation between genetic relationships and geographic distribution according to UPGMA and STRUCTURE analyses. The results of the present study will provide the foundation for future breeding programs, genetic improvement, core germplasm collection establishment for white clover.
bibliographic citation: Wu et al. (2021) Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide. PeerJ 9:e11325 https://doi.org/10.7717/peerj.11325
date submitted: 2020-11-11
date accepted: 2021-03-31
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Feifei
author list: Agent
  family name: Ma
  given name: Sainan
author list: Agent
  family name: Zhou
  given name: Jie
author list: Agent
  family name: Han
  given name: Chongyang
author list: Agent
  family name: Hu
  given name: Ruchang
author list: Agent
  family name: Yang
  given name: Xinying
author list: Agent
  family name: Nie
  given name: Gang
author list: Agent
  family name: Zhang
  given name: Xinquan
doi: 10.7717/peerj.11325
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Wu et al.
attribution name: Wu et al.

Local patterns of arbuscular mycorrhizal fungal diversity and community structure in a natural Toona ciliata var. pubescens forest in South Central China
type: item
type: AcademicArticle
description: Toona ciliata var. pubescens (Toona in Meliaceae) (Tc) is listed as an endangered species, and there are natural regeneration obstacles due to its long-term excessive exploitation and utilization. Arbuscular mycorrhizal fungi (AMF) can produce beneficial effects for plant growth and natural regeneration. However, the characteristics of the AMF community in natural Tc forests are poorly understood. The Illumina PE250 high-throughput sequencing method was used to study the characteristics of the AMF community in the rhizosphere soil and roots associated with three dominant tree species (Tc; Padus buergeriana, Pb; and Maesa japonica, Mj) in a natural Tc forest in Guanshan National Natural Reserve, South Central China. The results found that Glomeraceae was the most abundant AMF family in the rhizosphere soil and roots. Moreover, the relative abundance of Archaeosporaceae in rhizosphere soil was significantly larger than that in the roots; in contrast, the relative abundance of Glomeraceae in rhizosphere soil was significantly lower than that in the roots (p < 0.05). Regarding different tree species, the relative abundances of Acaulosporaceae and Geosiphonaceae were larger in Mj and Tc than in Pb. AMF operational taxonomic units (OTUs) were 1.30-, 1.43-, and 1.71-fold higher in the Tc, Pb, and Mj rhizosphere soil, respectively, than in the corresponding roots. Nevertheless, higher AMF community richness was found in the roots compared to that in the rhizosphere soil based on the Chao index. This finding indicated that AMF of a relatively high aggregation degree were in roots, and more AMF groups with relatively low abundance occurred in the rhizosphere soil, which correspondingly lowered the calculated richness index of the AMF community. A redundancy analysis showed that different soil chemical properties impacted variations in the AMF community characteristics differently. This study has great significance for the interpretation of AMF diversity survey and the applica…
format: application/pdf
format: text/html
creator: Jianfeng Pan
creator: Qiong Wang
creator: Xiaoyan Guo
creator: Xueru Jiang
creator: Qiangqiang Cheng
creator: Li Fu
creator: Wei Liu
creator: Lu Zhang
subject: Biodiversity
subject: Ecology
subject: Molecular Biology
subject: Mycology
subject: Forestry
description: doi:10.7717/peerj.11331
publisher: PeerJ Inc.
rights: © 2021 Pan et al.
abstract: Toona ciliata var. pubescens (Toona in Meliaceae) (Tc) is listed as an endangered species, and there are natural regeneration obstacles due to its long-term excessive exploitation and utilization. Arbuscular mycorrhizal fungi (AMF) can produce beneficial effects for plant growth and natural regeneration. However, the characteristics of the AMF community in natural Tc forests are poorly understood. The Illumina PE250 high-throughput sequencing method was used to study the characteristics of the AMF community in the rhizosphere soil and roots associated with three dominant tree species (Tc; Padus buergeriana, Pb; and Maesa japonica, Mj) in a natural Tc forest in Guanshan National Natural Reserve, South Central China. The results found that Glomeraceae was the most abundant AMF family in the rhizosphere soil and roots. Moreover, the relative abundance of Archaeosporaceae in rhizosphere soil was significantly larger than that in the roots; in contrast, the relative abundance of Glomeraceae in rhizosphere soil was significantly lower than that in the roots (p < 0.05). Regarding different tree species, the relative abundances of Acaulosporaceae and Geosiphonaceae were larger in Mj and Tc than in Pb. AMF operational taxonomic units (OTUs) were 1.30-, 1.43-, and 1.71-fold higher in the Tc, Pb, and Mj rhizosphere soil, respectively, than in the corresponding roots. Nevertheless, higher AMF community richness was found in the roots compared to that in the rhizosphere soil based on the Chao index. This finding indicated that AMF of a relatively high aggregation degree were in roots, and more AMF groups with relatively low abundance occurred in the rhizosphere soil, which correspondingly lowered the calculated richness index of the AMF community. A redundancy analysis showed that different soil chemical properties impacted variations in the AMF community characteristics differently. This study has great significance for the interpretation of AMF diversity survey and the applica…
bibliographic citation: Pan et al. (2021) Local patterns of arbuscular mycorrhizal fungal diversity and community structure in a natural Toona ciliata var. pubescens forest in South Central China. PeerJ 9:e11331 https://doi.org/10.7717/peerj.11331
date submitted: 2020-08-21
date accepted: 2021-04-01
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Jianfeng
author list: Agent
  family name: Wang
  given name: Qiong
author list: Agent
  family name: Guo
  given name: Xiaoyan
author list: Agent
  family name: Jiang
  given name: Xueru
author list: Agent
  family name: Cheng
  given name: Qiangqiang
author list: Agent
  family name: Fu
  given name: Li
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Zhang
  given name: Lu
doi: 10.7717/peerj.11331
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Pan et al.
attribution name: Pan et al.

re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files
type: item
type: AcademicArticle
description: Background High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples. Results Existing tools for processing VCF files don’t usually have an intuitive graphical interface, but instead have just a command-line interface that may be challenging to use for the broader biomedical community interested in genomics data analysis. re-Searcher solves this problem by pre-processing VCF files by chunks to not load RAM of computer. The tool can be used as standalone user-friendly multiplatform GUI application as well as web application (https://nla-lbsb.nu.edu.kz). The software including source code as well as tested VCF files and additional information are publicly available on the GitHub repository (https://github.com/LabBandSB/re-Searcher).
format: application/pdf
format: text/html
creator: Daniyar Karabayev
creator: Askhat Molkenov
creator: Kaiyrgali Yerulanuly
creator: Ilyas Kabimoldayev
creator: Asset Daniyarov
creator: Aigul Sharip
creator: Ainur Ashenova
creator: Zhaxybay Zhumadilov
creator: Ulykbek Kairov
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Medical Genetics
description: doi:10.7717/peerj.11333
publisher: PeerJ Inc.
rights: © 2021 Karabayev et al.
abstract: Background High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples. Results Existing tools for processing VCF files don’t usually have an intuitive graphical interface, but instead have just a command-line interface that may be challenging to use for the broader biomedical community interested in genomics data analysis. re-Searcher solves this problem by pre-processing VCF files by chunks to not load RAM of computer. The tool can be used as standalone user-friendly multiplatform GUI application as well as web application (https://nla-lbsb.nu.edu.kz). The software including source code as well as tested VCF files and additional information are publicly available on the GitHub repository (https://github.com/LabBandSB/re-Searcher).
bibliographic citation: Karabayev et al. (2021) re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files. PeerJ 9:e11333 https://doi.org/10.7717/peerj.11333
date submitted: 2020-09-17
date accepted: 2021-04-01
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Karabayev
  given name: Daniyar
author list: Agent
  family name: Molkenov
  given name: Askhat
author list: Agent
  family name: Yerulanuly
  given name: Kaiyrgali
author list: Agent
  family name: Kabimoldayev
  given name: Ilyas
author list: Agent
  family name: Daniyarov
  given name: Asset
author list: Agent
  family name: Sharip
  given name: Aigul
author list: Agent
  family name: Ashenova
  given name: Ainur
author list: Agent
  family name: Zhumadilov
  given name: Zhaxybay
author list: Agent
  family name: Kairov
  given name: Ulykbek
doi: 10.7717/peerj.11333
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Karabayev et al.
attribution name: Karabayev et al.

Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Hepatocellular carcinoma (HCC) is one of the deadliest tumors. The majority of HCC is detected in the late stage, and the clinical results for HCC patients are poor. There is an urgent need to discover early diagnostic biomarkers and potential therapeutic targets for HCC. Methods The GSE87630 and GSE112790 datasets from the Gene Expression Omnibus (GEO) database were downloaded to analyze the differentially expressed genes (DEGs) between HCC and normal tissues. R packages were used for Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses of the DEGs. A Search Tool for Retrieval of Interacting Genes (STRING) database was used to develop a protein-protein interaction (PPI) network, and also cytoHubba, Molecular Complex Detection (MCODE), EMBL-EBI, CCLE, Gene Expression Profiling Interactive Analysis (GEPIA), and Oncomine analyses were performed to identify hub genes. Gene expression was verified with a third GEO dataset, GSE25097. The Cancer Genome Atlas (TCGA) database was used to explore the correlations between the hub genes and clinical indexes of HCC patients. The functions of the hub genes were enriched by gene set enrichment analysis (GSEA), and the biological significance of the hub genes was explored by real-time polymerase chain reaction (qRT-PCR), western blot, immunofluorescence, CCK-8, colony formation, Transwell and flow cytometry assays with loss-of-function experiments in vitro. Results Centromere protein N (CENPN) was screened as a hub gene affecting HCC tumorigenesis. Evaluation by Cox regression showed that a high level of CENPN expression was an independent danger variable for poor prognosis of HCC. GSEA showed that high CENPN expression was linked to the following pathways: liver cancer subclass proliferation, cell cycle, p53 signaling pathway, Rb1 pathway, positive regulation of cell cycle G1/S phase transition, and DNA damage response signal transduction by p53 class moderators. Further cell experi…
format: application/pdf
format: text/html
creator: Qingqing Wang
creator: Xiaoyan Yu
creator: Zhewen Zheng
creator: Fengxia Chen
creator: Ningning Yang
creator: Yunfeng Zhou
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.11342
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background Hepatocellular carcinoma (HCC) is one of the deadliest tumors. The majority of HCC is detected in the late stage, and the clinical results for HCC patients are poor. There is an urgent need to discover early diagnostic biomarkers and potential therapeutic targets for HCC. Methods The GSE87630 and GSE112790 datasets from the Gene Expression Omnibus (GEO) database were downloaded to analyze the differentially expressed genes (DEGs) between HCC and normal tissues. R packages were used for Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses of the DEGs. A Search Tool for Retrieval of Interacting Genes (STRING) database was used to develop a protein-protein interaction (PPI) network, and also cytoHubba, Molecular Complex Detection (MCODE), EMBL-EBI, CCLE, Gene Expression Profiling Interactive Analysis (GEPIA), and Oncomine analyses were performed to identify hub genes. Gene expression was verified with a third GEO dataset, GSE25097. The Cancer Genome Atlas (TCGA) database was used to explore the correlations between the hub genes and clinical indexes of HCC patients. The functions of the hub genes were enriched by gene set enrichment analysis (GSEA), and the biological significance of the hub genes was explored by real-time polymerase chain reaction (qRT-PCR), western blot, immunofluorescence, CCK-8, colony formation, Transwell and flow cytometry assays with loss-of-function experiments in vitro. Results Centromere protein N (CENPN) was screened as a hub gene affecting HCC tumorigenesis. Evaluation by Cox regression showed that a high level of CENPN expression was an independent danger variable for poor prognosis of HCC. GSEA showed that high CENPN expression was linked to the following pathways: liver cancer subclass proliferation, cell cycle, p53 signaling pathway, Rb1 pathway, positive regulation of cell cycle G1/S phase transition, and DNA damage response signal transduction by p53 class moderators. Further cell experi…
bibliographic citation: Wang et al. (2021) Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma. PeerJ 9:e11342 https://doi.org/10.7717/peerj.11342
date submitted: 2021-01-04
date accepted: 2021-04-03
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qingqing
author list: Agent
  family name: Yu
  given name: Xiaoyan
author list: Agent
  family name: Zheng
  given name: Zhewen
author list: Agent
  family name: Chen
  given name: Fengxia
author list: Agent
  family name: Yang
  given name: Ningning
author list: Agent
  family name: Zhou
  given name: Yunfeng
doi: 10.7717/peerj.11342
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Serum metabolomic profiling reveals an increase in homocitrulline in Chinese patients with nonalcoholic fatty liver disease: a retrospective study
type: item
type: AcademicArticle
description: Backgrounds Nonalcoholic fatty liver disease (NAFLD) has multiple causes, is triggered by individual genetic susceptibility, environmental factors, and metabolic disturbances, and may be triggered by acquired metabolic stress. The metabolic profiles of NAFLD show significant ethnic differences, and the metabolic characteristics of NAFLD in Chinese individuals are unclear. Our study aimed to identify the metabolites and pathways associated with NAFLD in a Chinese cohort. Methods One hundred participants, including 50 NAFLD patients and 50 healthy controls, were enrolled in this retrospective observational study at Jinling Hospital in Nanjing; serum samples were collected from the patients and healthy subjects. The metabolome was determined in all samples by liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-Q/TOF-MS). Univariate and multivariate statistical analyses were used to compare the metabolic profiles between the two groups. Results The comparison indicated that the levels of 89 metabolites were different between the two groups. The glycerophospholipid family of metabolites was the most abundant family of metabolites that demonstrated significant differences. L-acetylcarnitine, L-homocitrulline, and glutamic acid were the top three metabolites ranked by VIP score and had favorable effective functions for diagnosis. Moreover, pathway enrichment analysis suggested 14 potentially different metabolic pathways between NAFLD patients and healthy controls based on their impact value. Biological modules involved in the lipid and carbohydrate metabolism had the highest relevance to the conditions of NAFLD. Glycerophospholipid metabolism had the strongest associations with the conditions of NAFLD. Conclusions Our data suggest that the serum metabolic profiles of NAFLD patients and healthy controls are different. L-Homocitrulline was remarkably increased in NAFLD patients.
format: application/pdf
format: text/html
creator: Yarong Yang
creator: Zexin Huang
creator: Zhao Yang
creator: Ying Qi
creator: Hui Shi
creator: Yifei Zhou
creator: Fangyu Wang
creator: Miaofang Yang
subject: Gastroenterology and Hepatology
subject: Hematology
subject: Metabolic Sciences
description: doi:10.7717/peerj.11346
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Backgrounds Nonalcoholic fatty liver disease (NAFLD) has multiple causes, is triggered by individual genetic susceptibility, environmental factors, and metabolic disturbances, and may be triggered by acquired metabolic stress. The metabolic profiles of NAFLD show significant ethnic differences, and the metabolic characteristics of NAFLD in Chinese individuals are unclear. Our study aimed to identify the metabolites and pathways associated with NAFLD in a Chinese cohort. Methods One hundred participants, including 50 NAFLD patients and 50 healthy controls, were enrolled in this retrospective observational study at Jinling Hospital in Nanjing; serum samples were collected from the patients and healthy subjects. The metabolome was determined in all samples by liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-Q/TOF-MS). Univariate and multivariate statistical analyses were used to compare the metabolic profiles between the two groups. Results The comparison indicated that the levels of 89 metabolites were different between the two groups. The glycerophospholipid family of metabolites was the most abundant family of metabolites that demonstrated significant differences. L-acetylcarnitine, L-homocitrulline, and glutamic acid were the top three metabolites ranked by VIP score and had favorable effective functions for diagnosis. Moreover, pathway enrichment analysis suggested 14 potentially different metabolic pathways between NAFLD patients and healthy controls based on their impact value. Biological modules involved in the lipid and carbohydrate metabolism had the highest relevance to the conditions of NAFLD. Glycerophospholipid metabolism had the strongest associations with the conditions of NAFLD. Conclusions Our data suggest that the serum metabolic profiles of NAFLD patients and healthy controls are different. L-Homocitrulline was remarkably increased in NAFLD patients.
bibliographic citation: Yang et al. (2021) Serum metabolomic profiling reveals an increase in homocitrulline in Chinese patients with nonalcoholic fatty liver disease: a retrospective study. PeerJ 9:e11346 https://doi.org/10.7717/peerj.11346
date submitted: 2020-10-07
date accepted: 2021-04-03
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yarong
author list: Agent
  family name: Huang
  given name: Zexin
author list: Agent
  family name: Yang
  given name: Zhao
author list: Agent
  family name: Qi
  given name: Ying
author list: Agent
  family name: Shi
  given name: Hui
author list: Agent
  family name: Zhou
  given name: Yifei
author list: Agent
  family name: Wang
  given name: Fangyu
author list: Agent
  family name: Yang
  given name: Miaofang
doi: 10.7717/peerj.11346
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Yang et al.
attribution name: Yang et al.

Sphenofontis velserae gen. et sp. nov., a new rhynchocephalian from the Late Jurassic of Brunn (Solnhofen Archipelago, southern Germany)
type: item
type: AcademicArticle
description: The Solnhofen Archipelago is well known for its fossil vertebrates of Late Jurassic age, among which figure numerous rhynchocephalian specimens, representing at least six and up to nine genera. A new taxon, named Sphenofontis velserae gen. et sp. nov., increases rhynchocephalian diversity in the Solnhofen Archipelago and is herein described based on a single, well-preserved specimen originating from the Late Kimmeridgian of the Brunn quarry, near Regensburg. The exquisite preservation of the holotype allowed a detailed description of the animal, revealing a skeletal morphology that includes both plesiomorphic and derived features within rhynchocephalians. Sphenofontis is herein referred to Neosphenodontia and tentatively to sphenodontine sphenodontids. It notably differs from all other rhynchocephalians known from the Jurassic of Europe, showing instead closer resemblance with the Middle Jurassic Cynosphenodon from Mexico and especially the extant Sphenodon. This is evidence for a wide distribution of taxa related to the extant tuatara early in the Mesozoic, and also for the presence of less-specialized rhynchocephalians coexisting with more derived forms during the earliest time in the history of the Solnhofen Archipelago.
format: application/pdf
format: text/html
creator: Andrea Villa
creator: Roel Montie
creator: Martin Röper
creator: Monika Rothgaenger
creator: Oliver W.M. Rauhut
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11363
publisher: PeerJ Inc.
rights: © 2021 Villa et al.
abstract: The Solnhofen Archipelago is well known for its fossil vertebrates of Late Jurassic age, among which figure numerous rhynchocephalian specimens, representing at least six and up to nine genera. A new taxon, named Sphenofontis velserae gen. et sp. nov., increases rhynchocephalian diversity in the Solnhofen Archipelago and is herein described based on a single, well-preserved specimen originating from the Late Kimmeridgian of the Brunn quarry, near Regensburg. The exquisite preservation of the holotype allowed a detailed description of the animal, revealing a skeletal morphology that includes both plesiomorphic and derived features within rhynchocephalians. Sphenofontis is herein referred to Neosphenodontia and tentatively to sphenodontine sphenodontids. It notably differs from all other rhynchocephalians known from the Jurassic of Europe, showing instead closer resemblance with the Middle Jurassic Cynosphenodon from Mexico and especially the extant Sphenodon. This is evidence for a wide distribution of taxa related to the extant tuatara early in the Mesozoic, and also for the presence of less-specialized rhynchocephalians coexisting with more derived forms during the earliest time in the history of the Solnhofen Archipelago.
bibliographic citation: Villa et al. (2021) Sphenofontis velserae gen. et sp. nov., a new rhynchocephalian from the Late Jurassic of Brunn (Solnhofen Archipelago, southern Germany). PeerJ 9:e11363 https://doi.org/10.7717/peerj.11363
date submitted: 2020-12-07
date accepted: 2021-04-06
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Villa
  given name: Andrea
author list: Agent
  family name: Montie
  given name: Roel
author list: Agent
  family name: Röper
  given name: Martin
author list: Agent
  family name: Rothgaenger
  given name: Monika
author list: Agent
  family name: Rauhut
  given name: Oliver W.M.
doi: 10.7717/peerj.11363
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: © 2021 Villa et al.
attribution name: Villa et al.

Ecosystem services show variable responses to future climate conditions in the Colombian páramos
type: item
type: AcademicArticle
description: Background The páramos, the high-elevation ecosystems of the northern Andes, are well-known for their high species richness and provide a variety of ecosystem services to local subsistence-based communities and regional urbanizations. Climate change is expected to negatively affect the provision of these services, but the level of this impact is still unclear. Here we assess future climate change impact on the ecosystem services provided by the critically important páramos of the department of Boyacá in Colombia, of which over 25% of its territory is páramo. Methods We first performed an extensive literature review to identify useful species of Boyacá, and selected 103 key plant species that, based on their uses, support the provision of ecosystem services in the páramos. We collated occurrence information for each key species and using a Mahalanobis distance approach we applied climate niche modelling for current and future conditions. Results We show an overall tendency of reduction in area for all ecosystem services under future climate conditions (mostly a loss of 10% but reaching up to a loss of 40%), but we observe also increases, and responses differ in intensity loss. Services such as Food for animals, Material and Medicinal, show a high range of changes that includes both positive and negative outcomes, while for Food for humans the responses are mostly substantially negative. Responses are less extreme than those projected for individual species but are often complex because a given ecosystem service is provided by several species. As the level of functional or ecological redundancy between species is not yet known, there is an urgency to expand our knowledge on páramos ecosystem services for more species. Our results are crucial for decision-makers, social and conservation organizations to support sustainable strategies to monitor and mitigate the potential consequences of climate change for human livelihoods in mountainous settings.
format: application/pdf
format: text/html
creator: Mauricio Diazgranados
creator: Carolina Tovar
creator: Thomas R. Etherington
creator: Paula A. Rodríguez-Zorro
creator: Carolina Castellanos-Castro
creator: Manuel Galvis Rueda
creator: Suzette G.A. Flantua
subject: Biogeography
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.11370
publisher: PeerJ Inc.
rights: © 2021 Diazgranados et al.
abstract: Background The páramos, the high-elevation ecosystems of the northern Andes, are well-known for their high species richness and provide a variety of ecosystem services to local subsistence-based communities and regional urbanizations. Climate change is expected to negatively affect the provision of these services, but the level of this impact is still unclear. Here we assess future climate change impact on the ecosystem services provided by the critically important páramos of the department of Boyacá in Colombia, of which over 25% of its territory is páramo. Methods We first performed an extensive literature review to identify useful species of Boyacá, and selected 103 key plant species that, based on their uses, support the provision of ecosystem services in the páramos. We collated occurrence information for each key species and using a Mahalanobis distance approach we applied climate niche modelling for current and future conditions. Results We show an overall tendency of reduction in area for all ecosystem services under future climate conditions (mostly a loss of 10% but reaching up to a loss of 40%), but we observe also increases, and responses differ in intensity loss. Services such as Food for animals, Material and Medicinal, show a high range of changes that includes both positive and negative outcomes, while for Food for humans the responses are mostly substantially negative. Responses are less extreme than those projected for individual species but are often complex because a given ecosystem service is provided by several species. As the level of functional or ecological redundancy between species is not yet known, there is an urgency to expand our knowledge on páramos ecosystem services for more species. Our results are crucial for decision-makers, social and conservation organizations to support sustainable strategies to monitor and mitigate the potential consequences of climate change for human livelihoods in mountainous settings.
bibliographic citation: Diazgranados et al. (2021) Ecosystem services show variable responses to future climate conditions in the Colombian páramos. PeerJ 9:e11370 https://doi.org/10.7717/peerj.11370
date submitted: 2020-11-01
date accepted: 2021-04-07
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Diazgranados
  given name: Mauricio
author list: Agent
  family name: Tovar
  given name: Carolina
author list: Agent
  family name: Etherington
  given name: Thomas R.
author list: Agent
  family name: Rodríguez-Zorro
  given name: Paula A.
author list: Agent
  family name: Castellanos-Castro
  given name: Carolina
author list: Agent
  family name: Galvis Rueda
  given name: Manuel
author list: Agent
  family name: Flantua
  given name: Suzette G.A.
doi: 10.7717/peerj.11370
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: © 2021 Diazgranados et al.
attribution name: Diazgranados et al.

DXA reference values of the humanoid sheep model in preclinical studies
type: item
type: AcademicArticle
description: Background Merino land sheep are a popular pre-clinical large animal model in research on systemic skeletal diseases such as osteoporosis. Interpretation of studies is difficult because many reference parameters are missing or not established. This study aims to determine the reference parameters of the skeletal system (peak bone mass = PBM, T-Score). A defined standard allows an easier comparison of the study data of the animal model with human studies (T-Score). Materials and methods A total of 116 Dual Energy X-ray Absorptiometry DXA measurements were performed on 74 untreated sheep. The average age of the animals was 57 months. The BMD, BMC, and fat content of the sheep were determined by the relevant human region of interest (ROI). From this, the PBM and from this the T-score for each of the animals were calculated. Results Using 682 DXA measurements BMD and BMC were determined to provide an indication to PBM. For BMD a significant correlation to the age of the animals was observed (p = 0.043). A significant correlation was also seen for BMC (B) (p ≤ 0.001). In the age-dependent analysis, a widespread of values above the linear regression line was measured for both BMD and BMC between the 50th and 90th months of life. From an age of about 90 months, a wider spread of values below the linear regression line was found, although the average values continued to rise. Discussion The evaluation of the 116 DXA measurements allowed the determination of the PBM for merino land sheep. With the help of the PBM, a T-score was calculated for each animal. The statistical analysis shows significant differences in BMD values between the different animal groups in each of the four ROIs investigated. Individual control or sham groups per study are therefore not sufficient. To improve comparability, an independent reference group should be established. Conclusion An independent reference group for PBM and a T-score was established from four to six-year-old animals. The bone densi…
format: application/pdf
format: text/html
creator: Christoph Biehl
creator: Jakob Schmitt
creator: Sabine Stoetzel
creator: Deeksha Malhan
creator: Fathi Hassan
creator: Gero Knapp
creator: Christian Heiss
creator: Thaqif El Khassawna
subject: Orthopedics
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.11183
publisher: PeerJ Inc.
rights: © 2021 Biehl et al.
abstract: Background Merino land sheep are a popular pre-clinical large animal model in research on systemic skeletal diseases such as osteoporosis. Interpretation of studies is difficult because many reference parameters are missing or not established. This study aims to determine the reference parameters of the skeletal system (peak bone mass = PBM, T-Score). A defined standard allows an easier comparison of the study data of the animal model with human studies (T-Score). Materials and methods A total of 116 Dual Energy X-ray Absorptiometry DXA measurements were performed on 74 untreated sheep. The average age of the animals was 57 months. The BMD, BMC, and fat content of the sheep were determined by the relevant human region of interest (ROI). From this, the PBM and from this the T-score for each of the animals were calculated. Results Using 682 DXA measurements BMD and BMC were determined to provide an indication to PBM. For BMD a significant correlation to the age of the animals was observed (p = 0.043). A significant correlation was also seen for BMC (B) (p ≤ 0.001). In the age-dependent analysis, a widespread of values above the linear regression line was measured for both BMD and BMC between the 50th and 90th months of life. From an age of about 90 months, a wider spread of values below the linear regression line was found, although the average values continued to rise. Discussion The evaluation of the 116 DXA measurements allowed the determination of the PBM for merino land sheep. With the help of the PBM, a T-score was calculated for each animal. The statistical analysis shows significant differences in BMD values between the different animal groups in each of the four ROIs investigated. Individual control or sham groups per study are therefore not sufficient. To improve comparability, an independent reference group should be established. Conclusion An independent reference group for PBM and a T-score was established from four to six-year-old animals. The bone densi…
bibliographic citation: Biehl et al. (2021) DXA reference values of the humanoid sheep model in preclinical studies. PeerJ 9:e11183 https://doi.org/10.7717/peerj.11183
date submitted: 2020-08-10
date accepted: 2021-03-08
issued: 2021-04-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Biehl
  given name: Christoph
author list: Agent
  family name: Schmitt
  given name: Jakob
author list: Agent
  family name: Stoetzel
  given name: Sabine
author list: Agent
  family name: Malhan
  given name: Deeksha
author list: Agent
  family name: Hassan
  given name: Fathi
author list: Agent
  family name: Knapp
  given name: Gero
author list: Agent
  family name: Heiss
  given name: Christian
author list: Agent
  family name: El Khassawna
  given name: Thaqif
doi: 10.7717/peerj.11183
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-30
copyright: ©2021 Biehl et al.
attribution name: Biehl et al.

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