title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1123 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification of DEGs and transcription factors involved in H. pylori-associated inflammation and their relevance with gastric cancer link: https://peerj.com/articles/9223 last-modified: 2020-06-03 description: BackgroundPrevious studies have indicated that chronic inflammation linked to H. pylori infection is the leading causes for gastric cancer (GC). However, the exact mechanism is not entirely clear until now.PurposeTo identify the key molecules and TFs involved in H. pylori infection and to provide new insights into H. pylori-associated carcinogenesis and lay the groundwork for the prevention of GC.ResultsGO and KEGG analysis revealed that the DEGs of Hp+-NAG were mainly associated with the immune response, chemokine activity, extracellular region and rheumatoid arthritis pathway. The DEGs of Hp+-AG-IM were related to the apical plasma membrane, intestinal cholesterol absorption, transporter activity and fat digestion and absorption pathway. In Hp+-NAG network, the expression of TNF, CXCL8, MMP9, CXCL9, CXCL1, CCL20, CTLA4, CXCL2, C3, SAA1 and FOXP3, JUN had statistical significance between normal and cancer in TCGA database. In Hp+-AG-IM network the expression of APOA4, GCG, CYP3A4, XPNPEP2 and FOXP3, JUN were statistically different in the comparison of normal and cancer in TCGA database. FOXP3 were negatively associated with overall survival, and the association for JUN was positive.ConclusionThe current study identified key DEGs and their transcriptional regulatory networks involved in H. pylori-associated NAG, AG-IM and GC and found that patients with higher expressed FOXP3 or lower expressed JUN had shorter overall survival time. Our study provided new directions for inflammation-associated oncogenic transformation involved in H. pylori infection. creator: Honghao Yin creator: Aining Chu creator: Songyi Liu creator: Yuan Yuan creator: Yuehua Gong uri: https://doi.org/10.7717/peerj.9223 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yin et al. title: Incorporating reef fish avoidance behavior improves accuracy of species distribution models link: https://peerj.com/articles/9246 last-modified: 2020-06-03 description: Species distribution models (SDMs) are used to interpret and map fish distributions based on habitat variables and other drivers. Reef fish avoidance behavior has been shown to vary in the presence of divers and is primarily driven by spearfishing pressure. Diver avoidance behavior or fish wariness may spatially influence counts and other descriptive measures of fish assemblages. Because fish assemblage metrics are response variables for SDMs, measures of fish wariness may be useful as predictors in SDMs of fishes targeted by spearfishing. We used a diver operated stereo-video system to conduct fish surveys and record minimum approach distance (MAD) of targeted reef fishes inside and outside of two marine reserves on the island of Oʻahu in the main Hawaiian Islands. By comparing MAD between sites and management types we tested the assumption that it provides a proxy for fish wariness related to spearfishing pressure. We then compared the accuracy of SDMs which included MAD as a predictor with SDMs that did not. Individual measures of MAD differed between sites though not management types. When included as a predictor, MAD averaged at the transect level greatly improved the accuracy of SDMs of targeted fish biomass. creator: Kostantinos A. Stamoulis creator: Jade M.S. Delevaux creator: Ivor D. Williams creator: Alan M. Friedlander creator: Jake Reichard creator: Keith Kamikawa creator: Euan S. Harvey uri: https://doi.org/10.7717/peerj.9246 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Stamoulis et al. title: Addressing initialisation uncertainty for end-to-end ecosystem models: application to the Chatham Rise Atlantis model link: https://peerj.com/articles/9254 last-modified: 2020-06-03 description: Ecosystem models require the specification of initial conditions, and these initial conditions have some level of uncertainty. It is important to allow for uncertainty when presenting model results, because it reduces the risk of errant or non-representative results. It is crucial that model results are presented as an envelope of what is likely, rather than presenting only one instance. We perturbed the initial conditions of the Chatham Rise Atlantis model and analysed the effect of this uncertainty on the model’s dynamics by comparing the model outputs resulting from many initial condition perturbations. At the species group level, we found some species groups were more sensitive than others, with lower trophic level species groups generally more sensitive to perturbations of the initial conditions. We recommend testing for robust system dynamics by assessing the consistency of ecosystem indicators in response to fishing pressure under perturbed initial conditions. In any set of scenarios explored using complex end-to-end ecosystem models, we recommend that associated uncertainty analysis be included with perturbations of the initial conditions. creator: Vidette L. McGregor creator: Elizabeth A. Fulton creator: Matthew R. Dunn uri: https://doi.org/10.7717/peerj.9254 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 McGregor et al. title: Identification of gene expression and DNA methylation of SERPINA5 and TIMP1 as novel prognostic markers in lower-grade gliomas link: https://peerj.com/articles/9262 last-modified: 2020-06-03 description: BackgroundLower-grade gliomas (LGGs) is characteristic with great difference in prognosis. Due to limited prognostic biomarkers, it is urgent to identify more molecular markers to provide a more objective and accurate tumor classification system for LGGs.MethodsIn the current study, we performed an integrated analysis of gene expression data and genome-wide methylation data to determine novel prognostic genes and methylation sites in LGGs.ResultsTo determine genes that differentially expressed between 44 short-term survivors (<2 years) and 48 long-term survivors (≥2 years), we searched LGGs TCGA RNA-seq dataset and identified 106 differentially expressed genes. SERPINA5 and TIMP1 were selected for further study. Kaplan–Meier plots showed that SERPINA5 and TIMP1 expression were significantly correlated with overall survival (OS) and relapse-free survival (RFS) in TCGA LGGs patients. We next validated the correlation between the candidate genes expression and clinical outcome in CGGA LGGs patients. Multivariate analysis showed that TIMP1 mRNA expression had a significant prognostic value independent of other variables (HR = 4.825, 95% CI = 1.370–17.000, P = 0.014). Then, differential methylation sites were identified from differentially candidate gene expression groups, and all four methylation sites were significantly negatively correlated with gene expression (spearman r <  − 0.5, P < 0.0001). Moreover, hyper-methylation of four methylation sites indicated better OS (P < 0.05), and three of them also shown statistical significantly association with better RFS, except for SERPINA5 cg15509705 (P = 0.0762).ConclusionTaken together, these findings indicated that the gene expression and methylation of SERPINA5 and TIMP1 may serve as prognostic predictors in LGGs and may help to precise the current histology-based tumors classification system and to provide better stratification for future clinical trials. creator: Wen-Jing Zeng creator: Yong-Long Yang creator: Zhi-Peng Wen creator: Peng Chen creator: Xiao-Ping Chen creator: Zhi-Cheng Gong uri: https://doi.org/10.7717/peerj.9262 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zeng et al. title: Identification of differentially expressed methylated genes in melanoma versus nevi using bioinformatics methods link: https://peerj.com/articles/9273 last-modified: 2020-06-03 description: BackgroundMelanoma is a highly invasive malignant skin tumor. While melanoma may share some similarities with that of melanocytic nevi, there also exist a number of distinct differences between these conditions. An analysis of these differences may provide a means to more effectively evaluate the etiology and pathogenesis of melanoma. In particular, differences in aberrant methylation expression may prove to represent a critical distinction.MethodsData from gene expression datasets (GSE3189 and GSE46517) and gene methylation datasets (GSE86355 and GSE120878) were downloaded from the GEO database. GEO2R was used to obtain differentially expressed genes (DEGs) and differentially methylation genes (DMGs). Function and pathway enrichment of selected genes were performed using the DAVID database. A protein-protein interaction (PPI) network was constructed by STRING while its visualization was achieved with use of cytoscape. Primary melanoma samples from TCGA were used to identify significant survival genes.ResultsThere was a total of 199 genes in the hypermethylation-low expression group, while 136 genes in the hypomethylation-high expression group were identified. The former were enriched in the biological processes of transcription regulation, RNA metabolism and regulation of cell proliferation. The later were highly involved in cell cycle regulation. 13 genes were screened out after survival analysis and included: ISG20, DTL, TRPV2, PLOD3, KIF3C, DLGAP4, PI4K2A, WIPI1, SHANK2, SLC16A10, GSTA4O, LFML2A and TMEM47.ConclusionThese findings reveal some of the methylated differentially expressed genes and pathways that exist between melonoma and melanocytic nevi. Moreover, we have identified some critical genes that may help to improve the diagnosis and treatment of melanoma. creator: Congcong He creator: Yujing Zhang creator: Hanghang Jiang creator: Xueli Niu creator: Ruiqun Qi creator: Xinghua Gao uri: https://doi.org/10.7717/peerj.9273 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 He et al. title: The linkages of plant, litter and soil C:N:P stoichiometry and nutrient stock in different secondary mixed forest types in the Qinling Mountains, China link: https://peerj.com/articles/9274 last-modified: 2020-06-03 description: BackgroundCarbon (C), nitrogen (N) and phosphorus (P) stoichiometric ratios are important indicators of ecosystem function and productivity. However, few studies have assessed the nutrient relationship between plant, litter and soil, and the nutrient stock in different secondary mixed forest types.MethodsWe investigated the C, N and P concentrations and stoichiometric ratios in trees, understory plants, litter and soil layers in three different secondary mixed forest types (broadleaf mixed forests (BM), broadleaf-conifer mixed forests (BCM) and coniferous mixed forests (CM)) in the Qinling Mountains.ResultsThe results showed that significant differences in C:N:P stoichiometry were detected in multiple organs in the vegetation layers in the different forest types. Trees, shrubs and herbs all allocated more N and P in leaves and had a higher N:P ratio in leaves than in other organs. The C concentrations, C:N ratios and C:P ratios of all tree organs showed a decreasing order: BM < BCM < CM, while the N and P concentrations showed an increasing order: BM > BCM > CM. For litter and soil, BM had generally higher N and P concentrations than those of BCM and CM. The highest N and P stock was in tree branches-not in the stem, which had the highest biomass (except for P in CM). Compared with other forest types, CM stored more nutrients in the labile litter layer, while BM stored more nutrients in the stable soil layer. The net ecosystem nutrient element stock in BM was generally higher than that in BCM and CM. The C, N and P concentrations and stoichiometry in the plant organs, litter and soil were significantly correlated.ConclusionOur findings demonstrate that nutrient concentrations in plant organs, litter and soil are tightly linked in secondary mixed forests. creator: Yue Pang creator: Jing Tian creator: Xuan Zhao creator: Zhi Chao creator: Yuchao Wang creator: Xinping Zhang creator: Dexiang Wang uri: https://doi.org/10.7717/peerj.9274 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Pang et al. title: Association of carotid intima-media thickness with the risk of sudden sensorineural hearing loss link: https://peerj.com/articles/9276 last-modified: 2020-06-03 description: Cardiovascular factors are associated with the pathophysiological features and risk of sudden sensorineural hearing loss (SSNHL). However, little is known about the link between carotid intima-media thickness (IMT), SSNHL risk, and their respective treatment outcomes. In this study, we retrospectively reviewed 47 SSNHL cases and 33 control subjects from a single medical center and compared their demographic data and clinical characteristics, including their carotid IMT and audiological data. Of the 80 enrolled subjects, the proportion of those with high carotid IMT was greater in the SSNHL group (53.2%) than in the control group (21.2%), with an odds ratio (OR) of 4.22 (95% confidence interval (CI) [1.53–11.61], P = 0.004). Notably, high carotid IMT was more common in female SSNHL patients than females in the control group (54.2% vs. 12.5%; OR, 8.27 (95% CI [1.53–44.62]), P = 0.008), particularly in female patients ≥50 years of age (75% vs. 25%; OR, 9.0 (95% CI [1.27–63.9]), P = 0.032). The multivariate regression analyses showed the association between high carotid IMT and SSNHL with an adjusted OR of 4.655 (95% CI [1.348–16.076], P = 0.015), particularly in female SSNHL patients (adjusted OR, 9.818 (95% CI [1.064–90.587], P = 0.044). The carotid IMT was not associated with the treatment outcomes of SSNHL. Our results indicate that early-stage atherosclerosis may be associated with SSNHL, particularly in female patients more than 50 years old. creator: Chun-Hsien Ho creator: Teng-Yeow Tan creator: Chung-Feng Hwang creator: Wei-Che Lin creator: Ching-Nung Wu creator: Chao-Hui Yang uri: https://doi.org/10.7717/peerj.9276 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ho et al. title: Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2 link: https://peerj.com/articles/9278 last-modified: 2020-06-03 description: BackgroundHighly sensitive real-time reverse transcription polymerase chain reaction (RT-qPCR) methods have been developed for the detection of SARS-CoV-2. However, they are costly. Loop-mediated isothermal amplification (LAMP) assay has emerged as a novel alternative isothermal amplification method for the detection of nucleic acid.MethodsA rapid, sensitive and specific real-time reverse transcription LAMP (RT-LAMP) assay was developed for SARS-CoV-2 detection.ResultsThis assay detected one copy/reaction of SARS-CoV-2 RNA in 30 min. Both the clinical sensitivity and specificity of this assay were 100%. The RT-LAMP showed comparable performance with RT-qPCR. Combining simplicity and cost-effectiveness, this assay is therefore recommended for use in resource resource-limited settings. creator: Yee Ling Lau creator: Ilyiana Ismail creator: Nur Izati Mustapa creator: Meng Yee Lai creator: Tuan Suhaila Tuan Soh creator: Afifah Hassan creator: Kalaiarasu M. Peariasamy creator: Yee Leng Lee creator: Yoong Min Chong creator: I-Ching Sam creator: Pik Pin Goh uri: https://doi.org/10.7717/peerj.9278 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lau et al. title: Ginsenoside panaxatriol reverses TNBC paclitaxel resistance by inhibiting the IRAK1/NF-κB and ERK pathways link: https://peerj.com/articles/9281 last-modified: 2020-06-03 description: BackgroundPaclitaxel (PTX) resistance is a major obstacle in the treatment of triple-negative breast cancer (TNBC). Previously, we have reported that interleukin-1 receptor-associated kinase 1 (IRAK1) and its downstream pathways are associated with PTX resistance in TNBC cells. In this study, we sought to investigate the combination treatment of ginsenoside panaxatriol (GPT), one of the main active components in Panax ginseng, with PTX on viability and apoptosis of TNBC PTX resistant cells, and explore the role of IRAK1 mediated signaling pathways in the therapeutic effects.MethodsCellTiter-Glo and colony formation assays were used to assess cell viability. Flow cytometry was used to analyze subG1 and apoptosis. Western blot was used to detect expressions of proteins involved in apoptosis and the IRAK1/NF-κB and ERK pathways. The mRNA expression of inflammatory cytokines, S100A7/8/9 and cancer stem cell (CSC)-related genes were examined by qPCR. Stem cells were identified by tumor sphere assay. Cell invasion ability was examined by transwell assay.ResultsWe show that GPT inhibits MDA-MB-231 PTX resistant (MB231-PR) cell viability in a dose-dependent manner. When combined with PTX, GPT synergistically causes more cell death, induces subG1 accumulation and cell apoptosis. Besides, up-regulation of BAX/BCL-2 ratio, and down-regulation of MCL-1 are also observed. Moreover, this combination inhibits IRAK1, NF-κB and ERK1/2 activation, and leads to down-regulation of inflammatory cytokines (IL6, IL8, CXCL1, CCL2), S100A7/9 and CSC-related genes (OCT4, SOX2, NANOG, ALDH1, CD44) expression. In addition, the combination treatment suppresses MB231-PR cell invasion ability, and impairs tumor sphere growth both in MB231-PR and SUM159 PTX resistant (SUM159-PR) cells.ConclusionOur study demonstrates that GPT can resensitize TNBC PTX resistant cells to PTX by inhibiting the IRAK1/NF-κB and ERK pathways and reducing stem cell characteristics. creator: Panpan Wang creator: Dan Song creator: Danhong Wan creator: Lingyu Li creator: Wenhui Mei creator: Xiaoyun Li creator: Li Han creator: Xiaofeng Zhu creator: Li Yang creator: Yu Cai creator: Ronghua Zhang uri: https://doi.org/10.7717/peerj.9281 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Association of FKBP5 polymorphisms with patient susceptibility to coronary artery disease comorbid with depression link: https://peerj.com/articles/9286 last-modified: 2020-06-03 description: BackgroundCoronary artery disease (CAD) and depression cause great burden to society and frequently co-occur. The exact mechanisms of this comorbidity are unclear. FK506-binding protein 51 (FKBP51) is correlated with cardiovascular disease and depression. The aim of this study was to determine the role of the seven single nucleotide polymorphisms (SNPs) of FKBP5 that code FKBP51, namely, rs1360780 (C>T), rs2817032 (T>C), rs2817035 (G>A), rs9296158 (G>A), rs9470079 (G>A), rs4713902 (T>C), and rs3800373 (C>T) in a patient’s susceptibility to comorbid CAD and depression.MethodsWe enrolled 271 Northern Chinese Han patients with CAD, including 123 patients with depression and 147 patients without depression. We also included 113 healthy controls that match the patients’ sex and age. Genomic DNA from whole blood was extracted, and seven SNPs were assessed using MassArray method. Patient Health Questionnaire-9 was applied to access the depression.ResultsThe GA genotype for rs9470079 was associated with a significantly decreased risk of CAD (odds ratio = 0.506, 95% confidence interval = 0.316–0.810, P = 0.005) when the GG genotype was used as reference. A statistically significant difference was observed among females but not among males in the rs9470079 genotype and allele frequency. Patients with CAD were further divided into CAD+D and CAD-D groups according to the presence of comorbid depression and were compared with the controls. Significant differences were found regarding the genotype and allele frequency of rs2817035 and rs9470079 in CAD+H groups compared with the control subjects in all groups and the female groups (P < 0.05).ConclusionsThe current study found a remarkable association between FKBP5 gene variations and the risk of comorbid CAD and depression in a north Chinese population. rs9470079 may be a potential gene locus for the incidence of comorbid CAD and depression. creator: Haidong Wang creator: Chao Wang creator: Xingfa Song creator: Hai Liu creator: Yun Zhang creator: Pei Jiang uri: https://doi.org/10.7717/peerj.9286 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al.