Machine learning-based identification of a novel prognosis-related long noncoding RNA signature for gastric cancer.

Gastric cancer (GC) is one of the most common malignancies with a poor prognosis. Immunotherapy has attracted much attention as a treatment for a wide range of cancers, including GC. However, not all patients respond to immunotherapy. New models are urgently needed to accurately predict the prognosis and the efficacy of immunotherapy in patients with GC. Long noncoding RNAs (lncRNAs) play crucial roles in the occurrence and progression of cancers. Recent studies have identified a variety of prognosis-related lncRNA signatures in multiple cancers. However, these studies have some limitations. In the present study, we developed an integrative analysis to screen risk prediction models using various feature selection methods, such as univariate and multivariate Cox regression, least absolute shrinkage and selection operator (LASSO), stepwise selection techniques, subset selection, and a combination of the aforementioned methods. We constructed a 9-lncRNA signature for predicting the prognosis of GC patients in The Cancer Genome Atlas (TCGA) cohort using a machine learning algorithm. After obtaining a risk model from the training cohort, we further validated the model for predicting the prognosis in the test cohort, the entire dataset and two external GEO datasets. Then we explored the roles of the risk model in predicting immune cell infiltration, immunotherapeutic responses and genomic mutations. The results revealed that this risk model held promise for predicting the prognostic outcomes and immunotherapeutic responses of GC patients. Our findings provide ideas for integrating multiple screening methods for risk modeling through machine learning algorithms.

Effects of influent salinity on water purification and greenhouse gas emissions in lab-scale constructed wetlands.

Salinity has a significant impact on the sewage treatment efficiency of constructed wetlands (CWs), as well as affecting the greenhouse gas emissions of CWs. A lab-scale CW simulation system was constructed to observe the treatment efficiency and greenhouse gas flux occurring in CWs at different influent salinities (0%, 0.5%, 1.0%, 1.5%, and 2.0%). The results show that (1) the removal rates of COD, TN, NH4+-N, NO3--N, and TP reach the highest at salinity of 0 or 0.5%. And the lowest removal rates are all at a salinity of 2.0%. (2) The emission flux of CO2, CH4, and N2O in CWs varies with an increase in salinity. The trends of CO2 and CH4 emission flux were consistent with those of COD reduction rate. However, it was opposite for N2O flux to that of TN, NH4+-N, and NO3--N removal rate. Affected by salinity, the greenhouse gas emission flux in this study is generally lower than what was reported in literature. (3) Correlation analysis showed that CO2 and CH4 emission fluxes were positively correlated with the COD reduction rate. N2O emission flux was negatively correlated with the removal rates of TN, NH4+-N, and NO3--N. The results suggest that different pollutants are inhibited by salinity to different degrees. COD is more affected by salinity than nitrogen and phosphorus, while nitrogen is more easily inhibited by salinity than phosphorus. CWs can have a high removal rate of pollutants in treating low-salinity wastewater. Although increased salinity reduces treatment efficiency of wastewater to some extent, it also inhibits the emission of CO2 and CH4.

Comparative proteomic and genomic analyses of Brucella abortus biofilm and planktonic cells.

The present study aimed to explore the differences in protein and gene expression of Brucella abortus cultured under biofilm and planktonic conditions. The proteins unique to biofilms and planktonic B. abortus were separated by two­dimensional (2­D) electrophoresis and then identified by matrix­assisted laser desorption/ionization­tandem time of flight­mass spectrometry (MALDI­TOF/TOF­MS). High­throughput sequencing and bioinformatic analyses were performed to identify differentially expressed genes between B. abortus cultured under biofilm and planktonic conditions. The proteins and genes identified by proteomic and genomic analyses were further evaluated via western blot and reverse transcription­quantitative polymerase chain reaction (RT­qPCR) analyses. 2­D electrophoresis identified 20 differentially expressed protein spots between biofilms and planktonic cells, which corresponded to 18 individual proteins (12 downregulated and 6 upregulated) after MALDI­TOF/TOF­MS analysis, including elongation factor Tu and enolase. RT­qPCR analysis revealed that all of the 18 genes were downregulated in biofilms compared with planktonic cells. Western blot analysis identified 9 downregulated and 3 upregulated proteins. High­throughput sequencing and bioinformatic analyses identified 14 function and pathway­associated genes (e.g., BAbS19_I14970). RT­qPCR analysis of the 14 genes showed that they were upregulated in biofilm compared with in planktonic state. In conclusion, these differentially expressed genes may play important roles in bacterial defense, colonization, invasion, and virulence.

Association between hypokalemia and small bowel capsule endoscopy completion rates in patients in South China: A prospective single-center study.

BACKGROUND/AIMS: Approximately 20-30% of small bowel capsule endoscopies (SBCEs) do not reach the cecum at the completion of the examination. We aimed to determine whether hypokalemia influences the completion rate and small bowel transit time (SBTT) of SBCE. PATIENTS AND METHODS: From January to December 2017, 112 patients (18-75 years old) who underwent SBCE were assessed consecutively for enrolment in our study. On the day of the procedure, a blood test was performed prior to capsule ingestion. The completion rate, gastric transit time (GTT), SBTT, and diagnostic yield were recorded for each SBCE. RESULTS: The SBCE completion rate was lower in the hypokalemia group than that in the normal potassium group (55.6% (15/27) vs. 76.5% (65/85), P = 0.036). The median GTT was 55.5 ± 47.1 min in the hypokalemia group and 46.7 ± 44.5 min in the normal potassium group (P > 0.05). The median SBTT was 412.8 ± 123.3 min in the hypokalemia group and 367.3 ± 172.5 min in the normal potassium group (P > 0.05). The diagnostic yields of the hypokalemia and normal potassium groups were 74.1% and 78.8%, respectively (P = 1.00). CONCLUSION: Hypokalemia may decrease the SBCE completion rate. Physicians should consider the possibility of hypokalemia after bowel preparation because this condition is not rare. Potassium deficiencies should be rectified prior to performing SBCE procedures to increase the SBCE completion rate.

[Effects of Different Substrates and Particle Sizes on Wastewater Purification].

Choosing suitable substrate is key to improving the efficiency of wetland decontamination. However, little is known about the effect of particle size. In order to study the effect of substrate type and size on COD, TN, and TP removal from sewage, 1-2, 2-4, and 4-8 mm zeolite, 2-4, 4-8, and 8-16 mm gravel, and 2-4, 3-5, and 6-8 mm anthracite were selected for establishment of the constructed system of experimental media with three replications. Results showed that removal efficiency of COD, TN, and TP varied with different particle sizes of the same material. The greatest COD removal was achieved with 4-8 mm zeolite and gravel and 6-8 mm anthracite, with removal rates of 53.74%, 60.76%, and 62.93%, respectively. Denitrification is the main pattern of nitrogen removal in the artificial test column; results show that smaller particle size is more effective for removal of TN. The removal rate of TP is also higher with smaller sizes of gravel and anthracite, but the opposite pattern occurred with zeolite. The removal of COD, TP, and TN also varied by substrate type. Anthracite led to good removal of COD, TP, and TN. Zeolite was most effective for removal of TN but had lower removal of TP. Gravel has high removal rate for COD, and has a general removal effect on TP.

Efficacy of two different dosages of levofloxacin in curing Helicobacter pylori infection: A Prospective, Single-Center, randomized clinical trial.

Bismuth + proton pump inhibitor (PPI) + amoxicillin + levofloxacin is one of the bismuth quadruple therapy regimens widely used for the eradication of H. pylori infection. The recommended dosage of levofloxacin is 500 mg once daily or 200 mg twice daily to eradicate H. pylori infection. The aim of the present open-label, randomized control trial was to compare the effectiveness, safety, and compliance of different dosages of levofloxacin used to cure Helicobacter pylori infection. Eligible patients were randomly assigned to receive esomeprazole, amoxicillin, colloidal bismuth pectin and levofloxacin 500 mg once/day (group A) or levofloxacin 200 mg twice/day (group B) for 14 days. The primary outcome was the eradication rates in the intention-to-treat (ITT) and per protocol (PP) analyses. Overall, 400 patients were enrolled. The eradication rates in group A and group B were 77.5% and 79.5% respectively, in the ITT analysis, and 82.9% and 86.4%, respectively, in the PP analysis. No significant differences were found between two groups in terms of eradication rate, adverse effects or compliance. Oral levofloxacin 200 mg twice daily was similar in efficacy for eradicating H. pylori infection to oral levofloxacin 500 mg once daily but with lower mean total costs.

The effects of air pollution on mortality and clinicopathological features of esophageal cancer.

This study aimed to estimate the associations between air pollution and esophageal cancer. In the ecologic cross-sectional study, correlation analyses were made between city-level mean concentrations of particulate matter less than 10µm in aerodynamic diameter (PM10), SO2, NO2 and city-level age-standardized mortality rates of esophageal cancer in Shandong Province, China. PM10 (p=0.046) and NO2 (p=0.03) both had significant linear correlations with esophageal cancer mortality rates. After introducing smoking as a risk factor in models of multiple linear regression analyses, PM10 was still an independent risk factor that increased esophageal cancer mortality rates. This study further compared clinicopathological features of 1,255 eligible esophageal squamous cell carcinoma patients by dividing them into different pollution level groups. There was statistically significant difference in gender distributions (p=0.02) between groups after subgroup analysis. Female patients accounted for a higher proportion in the high PM10 level group than in the low PM10 level group. It suggested that females were more sensitive to higher PM10 level pollution. The features that manifested the degree of malignancy of esophageal cancer, including primary tumor invasion, regional lymph nodes metastasis, histological grade, stage, lymph-vascular invasion and tumor size demonstrated no statistically significant difference between groups.

Prognostic and diagnostic potential of isocitrate dehydrogenase 1 in esophageal squamous cell carcinoma.

We aimed to investigate the pattern of expression and clinical significance of isocitrate dehydrogenase 1(IDH1) in esophageal squamous cell carcinoma (ESCC). The IDH1 expression was determined by quantitative real-time polymerase chain reaction, immunohistochemistry, and Western blot analysis using 38 pairs of frozen tissues. Enzyme-linked immunosorbent assay was employed to measure 67 pairs of serum samples from patients and their controls to evaluate its diagnostic value. Immunohistochemistry analysis of 111 formalin-fixed paraffin embedded tissue samples was conducted for explaining its prognostic value. After shRNA transfection, CCK8 and clonal efficiency assays were carried on for verifying the function of IDH1 in vitro. Increased expression at mRNA (P < 0.001) and protein levels (immunohistochemistry: P < 0.001, Western blot analysis: P < 0.001) were observed. Similarly, the IDH1 expression in serum from patients with ESCC was significantly upregulated relative to that from healthy controls (P < 0.001). Kaplan-Meier curve indicated that IDH1 upregulation predicted worse overall survival (OS) and progression-free survival (PFS). Univariate and multivariate analyses identified IDH1 expression as an independent prognostic factor for OS and PFS. Furthermore, OD450 values and colony numbers were decreased in sh-IDH1 groups (all P < 0.05). In conclusion, IDH1 is upregulated in patients with ESCC and can be used as a good potential biomarker for diagnosis and prognosis.

Prevalence and spectrum of BRCA germline variants in mainland Chinese familial breast and ovarian cancer patients.

Germline mutations in BRCA1 and BRCA2 are the most penetrating genetic predispositions for breast and ovarian cancer, and their presence is largely ethnic-specific. Comprehensive information about the prevalence and spectrum of BRCA mutations has been collected in European and North American populations. However, similar information is lacking in other populations, including the mainland Chinese population despite its large size of 1.4 billion accounting for one fifth of the world's population. Herein, we performed an extensive literature analysis to collect BRCA variants identified from mainland Chinese familial breast and ovarian cancer patients. We observed 137 distinct BRCA1 variants in 409 of 3,844 and 80 distinct BRCA2 variants in 157 of 3,024 mainland Chinese patients, with an estimated prevalence of 10.6% for BRCA1 and 5.2% for BRCA2. Of these variants, only 40.3% in BRCA1 and 42.5% in BRCA2 are listed in current Breast Cancer Information Core database. We observed higher frequent variation in BRCA1 exons 11A, 11C, 11D, and 24 and BRCA2 exon 10 in Chinese patients than in the patients of other populations. The most common pathogenic variant in BRCA1 wasc.981_982delAT in exon 11A, and in BRCA2 c.3195_3198delTAAT in exon 11B and c.5576_5579delTTAA in exon 11E; the most common novel variant in BRCA1 was c.919A>G in exon 10A, and in BRCA2 c.7142delC in exon 14. None of the variants overlap with the founder mutations in other populations. Our analysis indicates that the prevalence of BRCA variation in mainland Chinese familial breast and ovarian cancer patients is at a level similar to but the spectrum is substantially different from the ones of other populations.