Exploration of comorbidity mechanisms and potential therapeutic targets of rheumatoid arthritis and pigmented villonodular synovitis using machine learning and bioinformatics analysis

Background: Rheumatoid arthritis (RA) is a chronic autoimmune disease. Pigmented villonodular synovitis (PVNS) is a tenosynovial giant cell tumor that can involve joints. The mechanisms of co-morbidity between the two diseases have not been thoroughly explored. Therefore, this study focused on investigating the functions, immunological differences, and potential therapeutic targets of common genes between RA and PVNS.Methods: Through the dataset GSE3698 obtained from the Gene Expression Omnibus (GEO) database, the differentially expressed genes (DEGs) were screened by R software, and weighted gene coexpression network analysis (WGCNA) was performed to discover the modules most relevant to the clinical features. The common genes between the two diseases were identified. The molecular functions and biological processes of the common genes were analyzed. The protein-protein interaction (PPI) network was constructed using the STRING database, and the results were visualized in Cytoscape software. Two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) logistic regression and random forest (RF) were utilized to identify hub genes and predict the diagnostic efficiency of hub genes as well as the correlation between immune infiltrating cells.Results: We obtained a total of 107 DEGs, a module (containing 250 genes) with the highest correlation with clinical characteristics, and 36 common genes after taking the intersection. Moreover, using two machine learning algorithms, we identified three hub genes (PLIN, PPAP2A, and TYROBP) between RA and PVNS and demonstrated good diagnostic performance using ROC curve and nomogram plots. Single sample Gene Set Enrichment Analysis (ssGSEA) was used to analyze the biological functions in which three genes were mostly engaged. Finally, three hub genes showed a substantial association with 28 immune infiltrating cells.Conclusion: PLIN, PPAP2A, and TYROBP may influence RA and PVNS by modulating immunity and contribute to the diagnosis and therapy of the two diseases

Study of Promoter Methylation Patterns of HOXA2, HOXA5, and HOXA6 and Its Clinicopathological Characteristics in Colorectal Cancer

Research on DNA methylation offers great potential for the identification of biomarkers that can be applied for accurately assessing an individual's risk for cancer. In this article, we try to find the ideal epigenetic genes involved in colorectal cancer (CRC) based on a CRC database and our CRC cohort. The top 20 genes with an extremely high frequency of hypermethylation in CRC were identified in the latest database. Remarkably, 3 HOXA genes were included in this list and ranked at the top. The percentage of methylation in the HOXA5, HOXA2, and HOXA6 genes in CRC were up to 67.62, 58.36, and 31.32%, respectively, and ranked first in CRC among all human tumor tissues. Paired colorectal tumor samples and adjacent non-tumor colorectal tissue samples and four CRC cell lines were selected for MethylTarget™ assays. The results demonstrated that CRC tissues and cells had a stronger methylation status around the 3 HOXA gene promoter regions compared with adjacent non-tumor colonic tissue samples. The Receiver operator characteristic curve (ROC) curves for HOXA genes show excellent diagnostic ability in distinguishing tissue from healthy individuals and CRC patients, especially for Stage I patients (AUC = 0.9979 in HOXA2, 0.9309 in HOXA5, and 0.8025 in HOXA6). An association analysis between the methylation pattern of HOXA genes and clinical indicators was performed and found that HOXA2 methylation was significantly associated with age, N, stage, M, lymphovascular invasion, perineural invasion, lymph node number. HOXA5 methylation was associated with age, T, M, stage, and tumor status, and HOXA6 methylation was associated with age and KRAS mutation. Notably, we found that the highest methylation of HOXA5 and HOXA2 occurs in the early stages of colorectal cancer tissues such as stage I, N0, MO, and non-invasive tissues. The methylation levels declined as tumors progressed. However, methylation level at any stage of the tumor was still significantly higher than in normal tissues (p < 0.0001). The mRNA of the 3 HOXA genes was downregulated in early tumor stages due to hypermethylation of CpG islands adjacent to the promoters of the genes. In addition, hypermethylation of HOXA5 and HOXA6 mainly occurred in patients < 60 years old and with MSI-L, MSS, CIMP.L and non-CIMP tumors. Together, this suggests that epigenetic silencing of 3 adjacent HOXA genes may be an important event in the progression of colorectal cancer

YTHDF1 Regulates Tumorigenicity and Cancer Stem Cell-Like Activity in Human Colorectal Carcinoma

YTH N6-methyladenosine (m6A) RNA binding protein 1 (YTHDF1) is a core factor in RNA methylation modification. Recent studies have shown that m6A is closely related to multiple tumors, thus YTHDF1 may also play a role in tumorigenesis. This study, aimed to explore the role of YTHDF1 in the colorectal cancer (CRC). In this study, we identified YTHDF1 as being highly expressed at the mRNA and protein levels in TCGA, GEO CRC and primary CRC. Furthermore, the YTHDF1 gene copy number was positively correlated with YTHDF1 mRNA expression in CRC. Knocking down the expression of YTHDF1 significantly inhibited the CRC cell's tumorigenicity in vitro and murine xenograft tumor growth in vivo. Furthermore, silencing of YTHDF1 inhibited the colonosphere formation ability in vitro. Mechanistically, we found that silencing YTHDF1 significantly inhibited Wnt/β-catenin pathway activity in CRC cells. Together, YTHDF1 is overexpressed in CRC and plays a vital oncogenic role in CRC, and this novel finding may provide a potential therapeutic target for CRC

Sintering Temperature Induced Evolution of Microstructures and Enhanced Electrochemical Performances: Sol-Gel Derived LiFe(MoO4)2 Microcrystals as a Promising Anode Material for Lithium-Ion Batteries

A facile sol-gel process was used for synthesis of LiFe(MoO4)2 microcrystals. The effects of sintering temperature on the microstructures and electrochemical performances of the as-synthesized samples were systematically investigated through XRD, SEM and electrochemical performance characterization. When sintered at 650°C, the obtained LiFe(MoO4)2 microcrystals show regular shape and uniform size distribution with mean size of 1–2 μm. At the lower temperature (600°C), the obtained LiFe(MoO4)2 microcrystals possess relative inferior crystallinity, irregular morphology and vague grain boundary. At the higher temperatures (680 and 700°C), the obtained LiFe(MoO4)2 microcrystals are larger and thicker particles. The electrochemical results demonstrate that the optimized LiFe(MoO4)2 microcrystals (650°C) can deliver a high discharge specific capacity of 925 mAh g−1 even at a current rate of 1 C (1,050 mA g−1) after 500 cycles. Our work can provide a good guidance for the controllable synthesis of other transition metal NASICON-type electrode materials

Bioresour. Technol.

In this study, pinewood and corn stover pretreated with the ionic liquid (IL) 1-allyl-3-methylimidazolium chloride (AmimCl) were used as a feedstock for succinic acid production. Results reveal that 5% (v/v) AmimCl inhibited bacterial growth, whereas 0.01% (v/v) AmimCl inhibited succinic acid production. AmimCl was effective in extracting cellulose from pinewood and in degrading pinewood into a uniform pulp, as revealed by scanning electron microscopy (SEM). The rate of enzymatic hydrolysis of pinewood extract reached 72.16%. The combinations of AmimCl pretreatment with steam explosion or with hot compressed water were effective in treating corn stover, whereas AmimCl treatment alone did not result in a significant improvement. Pinewood extract produced 20.7 g/L succinic acid with an average yield of 0.37 g per gram of biomass. Workflow calculations indicated pine wood pretreated with IL has a theoretical yield of succinic acid of 57.1%. IL pretreatment led to increase in succinic acid yields. (C) 2014 Elsevier Ltd. All rights reserved.In this study, pinewood and corn stover pretreated with the ionic liquid (IL) 1-allyl-3-methylimidazolium chloride (AmimCl) were used as a feedstock for succinic acid production. Results reveal that 5% (v/v) AmimCl inhibited bacterial growth, whereas 0.01% (v/v) AmimCl inhibited succinic acid production. AmimCl was effective in extracting cellulose from pinewood and in degrading pinewood into a uniform pulp, as revealed by scanning electron microscopy (SEM). The rate of enzymatic hydrolysis of pinewood extract reached 72.16%. The combinations of AmimCl pretreatment with steam explosion or with hot compressed water were effective in treating corn stover, whereas AmimCl treatment alone did not result in a significant improvement. Pinewood extract produced 20.7 g/L succinic acid with an average yield of 0.37 g per gram of biomass. Workflow calculations indicated pine wood pretreated with IL has a theoretical yield of succinic acid of 57.1%. IL pretreatment led to increase in succinic acid yields. (C) 2014 Elsevier Ltd. All rights reserved

Research on the artificial control method of the gas nuclei spectrum in the small-scale experimental pool under atmospheric pressure

With the improvement of the accuracy of experimental devices and measuring instruments, cavitation experiments such as cross-media vehicles and propellers have been carried out in small pools. However, the water quality in the laboratory and the engineering application waters differs, especially the concentration of the gas nuclei that cause cavitation, resulting in experimental results that differ from prototype experimental results, and the scale effect occurs. In order to reduce the influence of the scale effect, according to the conditions of cavitation, gas nuclei can be mixed with water before the experiment is formally implemented. Aeration behavior will affect the size and concentration of gas nuclei (gas nuclei spectrum) in water. In order to obtain better experimental results, it is necessary to clarify the variation of the gas nuclei spectrum in small-scale experimental pools before and after aeration, so as to master aeration technology. Through research, it is found that the artificial aeration method can effectively change the gas nuclei spectrum in water and increase the concentration of gas nuclei. By using the underwater acoustic measurement method, the change in the gas nuclei spectrum can be captured sensitively. The gas nuclei spectrum in water after aeration is in good agreement with the mathematical model of gas nuclei spectrum under non-artificial intervention, which shows that the distribution of gas nuclei in water under artificial aeration is similar to that under non-artificial intervention, which is conducive to the occurrence of cavitation. At the same time, it shows that the combination of experiment and numerical method can reduce the measuring state and the measurement cost and improve the measurement efficiency

Simultaneous Removal of Thiophene and Dibenzothiophene by Immobilized Pseudomonas delafieldii R-8 cells

Biodesulfurization (BDS) is a promising technology for deep desulfurization. In this work, Pseudomonas delafieldii R-8 cells are immobilized in calcium alginate beads and used for BDS of transportation fuels. It is found that thiophene and dibenzothiophene (DBT) can be simultaneously metabolized by immobilized R-8 cells. The initial sulfur content in the model oil is 300 mg·kg ?1 (thiophene: UDBT1:U1). After 10 h of treatment, the thiophene concentration is reduced by 40%, while DBT is reduced by 25%. The utilization rate of thiophene is faster than that of DBT. Moreover, the oi

A Novel Dual-Emission Fluorescence Probe Based on CDs and Eu3+ Functionalized UiO-66-(COOH)2 Hybrid for Visual Monitoring of Cu2+

In this work, CDs@Eu-UiO-66(COOH)2 (denoted as CDs-F2), a fluorescent material made up of carbon dots (CDs) and a Eu3+ functionalized metal–organic framework, has been designed and prepared via a post-synthetic modification method. The synthesized CDs-F2 presents dual emissions at 410 nm and 615 nm, which can effectively avoid environmental interference. CDs-F2 exhibits outstanding selectivity, great sensitivity, and good anti-interference for ratiometric sensing Cu2+ in water. The linear range is 0–200 µM and the limit of detection is 0.409 µM. Interestingly, the CDs-F2’s silicon plate achieves rapid and selective detection of Cu2+. The change in fluorescence color can be observed by the naked eye. These results reveal that the CDs-F2 hybrid can be employed as a simple, rapid, and sensitive fluorescent probe to detect Cu2+. Moreover, the possible sensing mechanism of this dual-emission fluorescent probe is discussed in detail

Simultaneous Removal of Thiophene and Dibenzothiophene by Immobilized Pseudomonas delafieldii R-8 cells

Biodesulfurization (BDS) is a promising technology for deep desulfurization. In this work, PseudomonaS delafieldii R-8 cells are immobilized in calcium alginate beads and used for BDS of transportation fuels. It is found that thiophene and dibenzothiophene (DBT) can be simultaneously metabolized by immobilized R-8 cells. The initial sulfur content in the model oil is 300 mg.kg(-1) (thiophene : DBT = 1 : 1). After 10 h of treatment, the thiophene concentration is reduced by 40%, while DBT is reduced by 25%. The utilization rate of thiophene is faster than that of DBT. Moreover, the oil/water ratio of alginate immobilized cells is studied to reduce the water volume in desulfurization systems. Long-term recycling of BDS by alginate immobilized cells is carried out with oil/water ratio at 5 : 1. The immobilized cells are successfully reused over 15 batch cycles. In the last batch, the desulfurization activity remains at least 75% of the first batch

Clarification of succinic acid fermentation broth by ultrafiltration in succinic acid biorefinery

BACKGROUND: Succinic acid is an important precursor chemical for the synthesis of high value-added products. In this work, ultrafiltration was first investigated to clarify succinic acid fermentation broth by integrating fermentation and separation and removal processes of the product in situ. Four different ultrafiltration membranes (PES 100 kDa, PES 30 kDa, PES 10 kDa and RC 10 kDa) were used in this work. RESULTS: Results indicate that ultrafiltration is feasible for clarifying succinic acid fermentation broth. Almost all the microorganism cells (99.6%) were removed from the fermentation broth. Proteins were also removed effectively by all the membranes studied. The removal rate was 79.86% for PES 100 kDa, 86.43% for PES 30 kDa, 86.83% for PES 10 kDa, and 80.06% for the RC 10 kDa. After ultrafiltration, a clearer permeate was obtained compared with that from centrifugation. CONCLUSION: Membranes operating at high flux are always susceptible to rapid fouling. Compared with molecular weight cut-offs (MWCO), membrane material has a significant influence on the flux. Membrane flux measured in this study shows industrial potential of this technology in treatment of succinic acid fermentation broth. (c) 2012 Society of Chemical Industr