Association of sleep duration and sleep quality with hypertension in oil workers in Xinjiang
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 the group > 45 years old (OR 30–45 years old = 1.71, 95% CI [1.10–2.66]; OR > 45 years old = 1.60, 95% CI [1.09–2.34]). Conclusion Insufficient sleep duration and poor sleep quality are the potential factors affecting hypertension in Xinjiang oil workers.
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
Outcomes of critically ill end-stage kidney disease patients who underwent major surgery
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 adjusted for age and SOFA non-renal score demonstrated that ESKD had a significant association with ICU and hospital mortality (adjOR = 5.59; 95%CI [1.49–20.88], p = 0.01 and adjOR = 4.55; 95%CI[1.67–12.44], p = 0.003, respectively). Conclusion Patients who underwent a major operation and needed intensive care admission with pre-existing ESKD requiring long-term dialysis were associated with greater mortality than patients without ESKD. More careful assessment before, during, and after major surgical procedures should be performed in this group of patients to improve post-operative outcomes.
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
Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide
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.
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
Local patterns of arbuscular mycorrhizal fungal diversity and community structure in a natural Toona ciliata var. pubescens forest in South Central China
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 application design of AMF in vegetation restoration.
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
re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files
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).
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
Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma
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 experiments showed that knocking down CENPN expression decreased the proliferation and colony-forming abilities of HepG2 and Huh7 cells as well as Ki67 expression in these cell lines. The cell cycle was arrested in G1 phase, which is consistent with previous experiments on CENPN downregulation., but neither migration nor invasion were significantly affected. Western blot results revealed that the expression of p53, p27, p21, CDK4, cyclin D1, CDK2, cyclin E, pRb, E2F1 and c-myc decreased after CENPN knockdown, but there was no significant change in total Rb levels. In addition, CENPN-knockdown cells subjected to irradiation showed significantly enhanced of γ-H2AX expression and reduced colony formation. Conclusion CENPN functions as an oncogene in HCC and may be a therapeutic target and promising prognostic marker for HCC.
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
Serum metabolomic profiling reveals an increase in homocitrulline in Chinese patients with nonalcoholic fatty liver disease: a retrospective study
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.
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
Sphenofontis velserae gen. et sp. nov., a new rhynchocephalian from the Late Jurassic of Brunn (Solnhofen Archipelago, southern Germany)
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.
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
Ecosystem services show variable responses to future climate conditions in the Colombian páramos
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.
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
DXA reference values of the humanoid sheep model in preclinical studies
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 density increases with the age of the animals. Around the fourth year of life, a first peak could be observed. Also, after the seventh year of life, a further peak with the beginning plateau phase was observed. When compiling a group of animals for an osteoporosis model, animals from the age of seven years should, therefore, be used.
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