Development of an R script for simple lipidomic and metabolomic data analysis

Background: Metabolomic and lipidomic studies generate vast quantities of data that are often analysed in a closed software environment with little to no access to the underlying algorithms. As a result, data processed via different software pipelines yield different results thus leading to a widespread problem of low reproducibility within these fields. To address this problem, we are developing LipidAnalyst; an R based lipidomics software pipeline. As a part of this project, we are creating a simple statistical analysis and graphing module in R to generate accurate, reproducible, high-resolution figures. Methods: R scripts were developed under version 3.5.3 with the capability to undertake statistical analyses (e.g. ANOVA) and post-hoc tests (e.g. Tukey). Additional code plotted resultant information as high resolution violin and box plots that depicted statistical significance. Thereafter, lipidomic and metabolomic data were analysed by this code and compared against commercial software and Metaboanalyst, a primary software used in metabolomic and lipidomic research. Results: Code generated in house demonstrated the same results as those generated using commercial software (e.g. JMP 14.0 Pro) but were different from results obtained by using the MetaboAnalyst pipeline. Conclusions: This study demonstrated the prevalent danger of using closed-source software pipelines for the analysis of lipidomic and metabolomic data without validating the analysis outcomes via open-source software. Open source software such as LipidAnalyst, that has also been independently validated using multiple data sets, can then be published with the results to enable transparency of data analysis and improve the replicability of results across different labs.https://scholarscompass.vcu.edu/gradposters/1092/thumbnail.jp

A New Penalty Function Algorithm For Convex Quadratic Programming

In this paper, we develop an exterior point algorithm for convex quadratic programming using a penalty function approach. Each iteration in the algorithm consists of a single Newton step followed by a reduction in the value of the penalty parameter. The points generated by the algorithm follow an exterior path that we define. Convergence of the algorithm is established. The proposed algorithm was motivated by the work of Al-Sultan and Murty on nearest point problems, a special quadratic program. A preliminary implementation of the algorithm produced encouraging results. In particular, the algorithm requires a small and almost constant number of iterations to solve the small to medium size problems tested. (C) 1997 Elsevier Science B.V

A New Penalty Function Algorithm For Convex Quadratic Programming

In this paper, we develop an exterior point algorithm for convex quadratic programming using a penalty function approach. Each iteration in the algorithm consists of a single Newton step followed by a reduction in the value of the penalty parameter. The points generated by the algorithm follow an exterior path that we define. Convergence of the algorithm is established. The proposed algorithm was motivated by the work of Al-Sultan and Murty on nearest point problems, a special quadratic program. A preliminary implementation of the algorithm produced encouraging results. In particular, the algorithm requires a small and almost constant number of iterations to solve the small to medium size problems tested. (C) 1997 Elsevier Science B.V

Application Of Digital Camera Data For Air Quality Detection.

Air pollution problem becomes increasingly critical in this present-day, whether in the developed or developing countries. Air management is one of the important issues in this 21st century. Malaysia is also affected by this problem

Remote Sensing Of Pm10 From Landsat Tm Imagery.

Air pollution concentration has been estimated over Penang Island from Landsat TM 7. In-situ measurements of the corresponding air pollution parameter (particulate matter less than 10 micron, PM10) were carried out simultaneously with the acquisition of the satellite imagery

High frequency of carbapenem-resistant Acinetobacter baumannii in patients with diabetes mellitus in Saudi Arabia

Carbapenem-resistant Acinetobacter baumannii is becoming increasingly prevalent in patients with diabetes mellitus in the Middle East. We examined the relationship of these bacteria and their resistance mechanisms to the diabetic disease status of patients in Saudi Arabia. Susceptibilities of 271 isolates to carbapenems, tigecycline and colistin were determined, followed by detection of carbapenemase genes. A blaVIM gene was detected in ~95 % of isolates; blaOXA-23 and blaOXA-40 genes were also prevalent. Diabetic patients were significantly more likely to carry carbapenem-resistant isolates. Carbapenem-resistant A. baumannii is a serious problem in diabetic patients, and molecular detection of resistance mechanisms in these isolates is required

Molecular Predictors of Anakinra Treatment Success in Heart Failure Patients with Reduced Ejection Fraction

Background. Kineret (Anakinra) is an interleukin-1 antagonist that is under investigation for its novel clinical application treating patients that have heart failure with reduced (\u3c50%) ejection fraction (HFrEF). A prior study from our group indicated that Anakinra may restore heart function by addressing dysregulations in HFrEF metabolic pathways. Herein, we attempt to elicit Anakinra’s effects on both metabolome and lipidome. Methods. Lipids and metabolites that had previously been quantified by mass spectrometry (MS) from patients (n=49) who had ≥2 mg/L of high-sensitivity C-reactive protein (hs-CRP) were mTIC normalized and transformed. We conducted a stepwise Linear Discriminant Analysis (r- LDA) to test Anakinra (2 and 12 weeks) vs placebo for separation from combined baseline. Metabolic pathway analysis was performed with Fisher’s exact test algorithm for detection of over-represented and enriched analytes. Univariate analysis (one tailed t-test p\u3c0.05) compared placebo and Anakinra after 12-weeks for effect(s). Metaboanalyst 4.0, JMP Pro 14.0, and a proprietary package in R (version 3.4.4) were the software for all analyses and data wrangling. Results. Analytes such as acylcarnitines C10:0 and C16:0 and hsCRP showed significant improvements after 12 weeks of Anakinra, leading to improved mitochondrial function, reduced inflammation, and overall better health outcomes. Statistically significant (p\u3c0.05) pathways including the citrate cycle, cysteine and methionine metabolism, galactose metabolism among others were associated with treatment. Conclusions. We were able to determine significant alterations to metabolomic and lipidomic concentrations after 12 weeks of Anakinra therapy. Our biochemical analyses verifies that Anakinra did improve heart function within our HFrEF pilot cohort.https://scholarscompass.vcu.edu/gradposters/1081/thumbnail.jp