MEMOSys: Bioinformatics platform for genome-scale metabolic models

<p>Abstract</p> <p>Background</p> <p>Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in order to gain novel biological insights. One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models.</p> <p>Results</p> <p>MEMOSys (MEtabolic MOdel research and development System) is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains six annotated microbial metabolic models.</p> <p>Conclusions</p> <p>We have developed a web-based system designed to provide researchers a novel application facilitating the management and development of metabolic models. The system is freely available at <url>http://www.icbi.at/MEMOSys</url>.</p

Oral Apolipoprotein A-I Mimetic D-4F Lowers HDL-Inflammatory Index in High-Risk Patients: A First-in-Human Multiple-Dose, Randomized Controlled Trial.

A single dose of the apolipoprotein (apo)A-I mimetic peptide D-4F rendered high-density lipoprotein (HDL) less inflammatory, motivating the first multiple-dose study. We aimed to assess safety/tolerability, pharmacokinetics, and pharmacodynamics of daily, orally administered D-4F. High-risk coronary heart disease (CHD) subjects added double-blinded placebo or D-4F to statin for 13 days, randomly assigned 1:3 to ascending cohorts of 100, 300, then 500 mg (n = 62; 46 men/16 women). D-4F was safe and well-tolerated. Mean ± SD plasma D-4F area under the curve (AUC, 0-8h) was 6.9 ± 5.7 ng/mL*h (100 mg), 22.7 ± 19.6 ng/mL*h (300 mg), and 104.0 ± 60.9 ng/mL*h (500 mg) among men, higher among women. Whereas placebo dropped HDL inflammatory index (HII) 28% 8 h postdose (range, 1.25-0.86), 300-500 mg D-4F effectively halved HII: 1.35-0.57 and 1.22-0.63, respectively (P \u3c 0.03 vs. placebo). Oral D-4F peptide dose predicted HII suppression, whereas plasma D-4F exposure was dissociated, suggesting plasma penetration is unnecessary. In conclusion, oral D-4F dosing rendered HDL less inflammatory, affirming oral D-4F as a potential therapy to improve HDL function

QPCR: Application for real-time PCR data management and analysis

BACKGROUND: Since its introduction quantitative real-time polymerase chain reaction (qPCR) has become the standard method for quantification of gene expression. Its high sensitivity, large dynamic range, and accuracy led to the development of numerous applications with an increasing number of samples to be analyzed. Data analysis consists of a number of steps, which have to be carried out in several different applications. Currently, no single tool is available which incorporates storage, management, and multiple methods covering the complete analysis pipeline. RESULTS: QPCR is a versatile web-based Java application that allows to store, manage, and analyze data from relative quantification qPCR experiments. It comprises a parser to import generated data from qPCR instruments and includes a variety of analysis methods to calculate cycle-threshold and amplification efficiency values. The analysis pipeline includes technical and biological replicate handling, incorporation of sample or gene specific efficiency, normalization using single or multiple reference genes, inter-run calibration, and fold change calculation. Moreover, the application supports assessment of error propagation throughout all analysis steps and allows conducting statistical tests on biological replicates. Results can be visualized in customizable charts and exported for further investigation. CONCLUSION: We have developed a web-based system designed to enhance and facilitate the analysis of qPCR experiments. It covers the complete analysis workflow combining parsing, analysis, and generation of charts into one single application. The system is freely available a

Nocturia as an Unrecognized Symptom of Uncontrolled Hypertension in Black Men Aged 35 to 49&nbsp;Years.

Background Hypertension is assumed to be asymptomatic. Yet, clinically significant nocturia (≥2 nightly voids) constitutes a putative symptom of uncontrolled hypertension. Black men with hypertension may be prone to nocturia because of blunted nocturnal blood pressure ( BP ) dipping, diuretic drug use for hypertension, and comorbidity that predisposes to nocturia. Here, we test the hypothesis that nocturia is a common and potentially reversible symptom of uncontrolled hypertension in black men. Methods and Results We determined the strength of association between nocturia (≥2 nightly voids) and high BP (≥135/85&nbsp;mm&nbsp;Hg) by conducting in-person health interviews and measuring BP with an automated monitor in a large community-based sample of black men in their barbershops. Because nocturia is prevalent and steeply age-dependent after age 50&nbsp;years, we studied men aged 35 to 49&nbsp;years. Among 1673 black men (mean age, 43±4&nbsp;years [ SD ]), those with hypertension were 56% more likely than men with normotension to have nocturia after adjustment for diabetes mellitus and sleep apnea (adjusted odds ratio, 1.56; 95% CI , 1.25-1.94 [ P&lt;0.0001]). Nocturia prevalence varied by hypertension status, ranging from 24% in men with normotension to 49% in men whose hypertension was medically treated but uncontrolled. Men with untreated hypertension were 39% more likely than men with normotension to report nocturia ( P=0.02), whereas men whose hypertension was treated and controlled were no more likely than men with normotension to report nocturia ( P=0.69). Conclusions Uncontrolled hypertension was an independent determinant of clinically important nocturia in a large cross-sectional community-based study of non-Hispanic black men aged 35 to 49&nbsp;years. Clinical Trial Registration URL : http://www.clinicaltrials.gov . Unqiue identifier: NCT 02321618

Explicit Lie-Poisson integration and the Euler equations

We give a wide class of Lie-Poisson systems for which explicit, Lie-Poisson integrators, preserving all Casimirs, can be constructed. The integrators are extremely simple. Examples are the rigid body, a moment truncation, and a new, fast algorithm for the sine-bracket truncation of the 2D Euler equations.Comment: 7 pages, compile with AMSTEX; 2 figures available from autho

Method Development for Determining the Removal of Metals from the Water Column under Transformation/Dissolution Conditions for Chronic Hazard Classification

An extension of the transformation/dissolution protocol (T/DP) was developed and evaluated as a tool to measure the removal of metals from the water column for chronic aquatic hazard classification. The T/DP extension (T/DP‐E) consists of 2 parts: T/DP‐E part 1, to measure metal removal from the water column via binding of metals to a substrate and subsequent settling, and T/DP‐E part 2, to assess the potential for remobilization of metals following resuspension. The T/DP‐E methodology (672‐h [28‐d] removal period, 1‐h resuspension event, and 96‐h resettling period) was tested using Cu, Co, and Sr solutions in the presence of a substrate. The metal removal rates varied from rapid removal for Cu to slower rates of removal for Co and Sr. The resuspension event did not trigger any increase in dissolved Cu, Co, or Sr. Additional 96‐h experiments were conducted using dissolved Ni, Pb, Zn, and Ag and supported the conclusion that the T/DP‐E is sufficiently robust to distinguish removal rates between metals with a wide range of reactivities. The proposed method provides a means to quantify the rate of metal removal from the water column and evaluate remobilization potential in a standardized and reliable way. Environ Toxicol Chem 2019;38:2032–2042. © 2019 SETAC.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151361/1/etc4471.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151361/2/etc4471_am.pd