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SUMMARY MIAMI (Mass Isotopolome Analysis for Mode of action Identification) combines the strengths of targeted and non-targeted approaches to detect metabolic flux changes in gas chromatography/mass spectrometry datasets. Based on stable isotope labeling experiments, MIAMI determines a mass isotopomer distribution (MID) based similarity network and incorporates the data into metabolic reference networks. By identifying MID variations of all labeled conpounds between different conditions, targets of metabolic changes can be detected. AVAILABILITY AND IMPLEMENTATION We implemented the data processing in C ++17 with Qt5 back-end using MetaboliteDetector and NTFD libraries. The data visualization is implemented as web application. Executable binaries and visualization are freely available for Linux operating systems, the source code is licensed under General Public License version 3. SUPPLEMENTARY INFORMATION Source code, documentation and sample data are available at http//miami.tu-bs.de. © The Author(s) 2020. Published by Oxford University Press.BACKGROUND Gastric and gastro-oesophageal junction cancers (GCs) frequently recur after resection but markers to predict recurrence risk are missing. T-cell infiltrates have been validated as prognostic markers in other cancer types, but not in GC due to methodological limitations of past studies. We aimed to define and validate the prognostic role of major T-cell subtypes in GC by objective computational quantification. METHODS Surgically resected chemotherapy-naïve GCs were split into discovery (n = 327) and validation (n = 147) cohorts. CD8 (cytotoxic), CD45RO (memory) and FOXP3 (regulatory) T-cell densities were measured through multicolour immunofluorescence and computational image analysis. Cancer specific survival (CSS) was assessed. All statistical tests were two-sided. RESULTS CD45RO-cell and FOXP3-cell densities statistically significantly predicted CSS in both cohorts. Stage, CD45RO-cell and FOXP3-cell densities were independent predictors of CSS in multivariable analysis; mismatch repair (MMR) and Epstein-Barr Virus (EBV) status were not statistically significant. Combining CD45RO-cell and FOXP3-cell densities into the Stomach Cancer Immune Score showed highly statistically significant (all p ≤ 0.002) CSS differences (0.9y median CSS to not reached). T-cell infiltrates were highest in EBV-positive GCs and similar in MMR-deficient and MMR-proficient GCs. CONCLUSION The validation of CD45RO-cell and FOXP3-cell densities as prognostic markers in GC may guide personalized follow-up or (neo)adjuvant treatment strategies. Only those 20% of GCs with the highest T-cell infiltrates showed particularly good CSS, suggesting that a small subgroup of GCs is highly immunogenic. read more The potential for T-cell densities to predict immunotherapy responses should be assessed. The association of high FOXP3-cell densities with longer CSS warrants studies into the biology of regulatory T-cells in GC. © The Author(s) 2020. Published by Oxford University Press.SUMMARY Glycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is critical. This application note describes the GlyGen data model, processing workflow and the data access interfaces featuring programmatic use case example queries based on specific biological questions. The GlyGen project is a data integration, harmonization, and dissemination project for carbohydrate and glycoconjugate related data retrieved from multiple international data sources including UniProtKB, GlyTouCan, UniCarbKB and other key resources. AVAILABILITY AND IMPLEMENTATION GlyGen web portal is freely available to access at https//glygen.org. The data portal, web services, SPARQL endpoint, and GitHub repository are also freely available at https//data.glygen.org, https//api.glygen.org, https//sparql.glygen.org, and https//github.com/glygener, respectively. All code is released under license GNU General Public License version 3 (GNU GPLv3) and is available on GitHub https//github.com/glygener. The datasets are made available under Creative Commons Attribution 4.0 International (CC BY 4.0) license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. © The Author(s) 2020. Published by Oxford University Press.Purpose Previous studies on the association between choroidal thickness (CT) and severity of diabetic retinopathy (DR) gave conflicting results. The aim of this study was to evaluate the CT changes in diabetic patients and associated factors in a large sample of Chinese patients with diabetes. Methods Type 2 diabetes mellitus patients without history of ocular treatment were recruited from the community health system in Guangzhou, China. The swept source OCT instrument was used to obtain high-definition retina and choroid images. The diabetic retinopathy (DR) status was graded based on the guidelines of the United Kingdom National Diabetic Eye Screening Programme. Univariate and multivariate linear regression analyses was used to explore the association of CT with DR severity, diabetic macular edema (DME), hemoglobin A1c, and vision function. Results A total of 1347 patients were included in the final analysis. After adjusting for other factors, the patients with stage R3 DR had significantly thinner CT (β = -29.1 µm, 95% CI -53.8 to -4.4, P = 0.021) in comparison in those with R0. After adjusting for other factors, the CTs were thicker than those in R0 patients with difference of 15.6 µm (95% CI 4.3-26.9, P = 0.007) for outer nasal sector, 15.7 µm (95% CI 3.8-25.5, P = 0.008) for outer inferior, and 12.2 µm (95% CI 0.4-24.0, P = 0.042) for inner inferior sector. The presence of DME and hemoglobin A1c levels did not significantly affect average CT. Higher average CT was significantly associated with better best corrected visual acuity, with a -0.02 LogMAR unit per 100 µm increase in average CT (95% CI -0.03 to -0.01, P less then 0.001). Conclusions CT increased in the early stage of DR, and further decreased with DR progression. DME was not significantly associated with CT. These findings provide more clues to suggest that choroid alterations play a role in the pathogenesis of DR.