Pathos: a web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry

This work describes a freely available web-based facility which can be used to analyse raw or processed mass spectrometric data from metabolomics experiments and display the metabolites identified – and changes in their experimental abundance – in the context of the metabolic pathways in which they occur. The facility, Pathos (http://motif.gla.ac.uk/Pathos/), employs Java servlets and is underpinned by a relational database populated from the Kyoto Encyclopaedia of Genes and Genomes (KEGG). Input files can contain either raw m/z values from experiments conducted in different modes, or KEGG or MetaCyc IDs assigned by the user on the basis of the m/z values and other criteria. The textual output lists the KEGG pathways on an XHTML page according to the number of metabolites or potential metabolites that they contain. Filtering by organism is also available. For metabolic pathways of interest, the user is able to retrieve a pathway map with identified metabolites highlighted. A particular feature of Pathos is its ability to process relative quantification data for metabolites identified under different experimental conditions, and to present this in an easily comprehensible manner. Results are colour-coded according to the degree of experimental change, and bar charts of the results can be generated interactively from either the text listings or the pathway maps. The visual presentation of the output from Pathos is designed to allow the rapid identification of metabolic areas of potential interest, after which particular results may be examined in detail

A new approach to labor law

Thesis (B.S.) Massachusetts Institute of Technology. Dept. of Business and Engineering Administration, 1947.Bibliography: leaf [66].by Robert Creek.B.S

mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data

<p>Motivation: Stable isotope-labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography–mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here, we describe mzMatch–ISO, a new extension to the metabolomics analysis pipeline mzMatch.R.</p> <p>Results: Targeted and untargeted isotope profiling using mzMatch–ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono-isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab-delimited file. We demonstrate the power and versatility of mzMatch–ISO by analysing a 13C-labelled metabolome dataset from trypanosomal parasites.</p&gt

mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data

<p>Motivation: Stable isotope-labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography–mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here, we describe mzMatch–ISO, a new extension to the metabolomics analysis pipeline mzMatch.R.</p> <p>Results: Targeted and untargeted isotope profiling using mzMatch–ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono-isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab-delimited file. We demonstrate the power and versatility of mzMatch–ISO by analysing a 13C-labelled metabolome dataset from trypanosomal parasites.</p&gt

Engaging the hard to engage: What contribution can occupational therapy make to an interdisciplinary approach?

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Evaluation of HIV counseling and testing in ANC settings and adherence to short course antiretroviral prophylaxis for PMTCT in Francistown, Botswana

Worldwide, it is estimated that two million children are infected with HIV (USAID 2005). The vast majority of these infections are the result of mother-to-child transmission (MTCT) of the virus during pregnancy, labor, or breastfeeding. However, there are effective methods for prevention of mother-to-child transmission (PMTCT). Botswana is one of the first countries in the developing world with a national PMTCT program that uses an efficacious and complex regimen to reduce vertical transmission. At the time of this evaluation (August - December 2005), the standard of care for prevention of MTCT of HIV in Botswana included three-drug antiretroviral therapy for HIV-infected women with a CD4 count of 200 (300 mg AZT in the morning and 300 mg AZT in the evening); four weeks of AZT for their infants; single-dose maternal and infant nevirapine (NVP); and 12 months of free infant formula. Botswana's PMTCT program also provided routine HIV testing for all pregnant women during antenatal care (ANC) to identify HIV-positive women for prophylaxis or treatment. While programs often report the number of individuals beginning AZT and receiving nevirapine for PMTCT, effectiveness is dependent on the level of adherence of individuals to these regimens. To describe adherence of pregnant women to the current PMTCT regimen, the Horizons Program of the Population Council, in collaboration with the Centers for Disease Control and Prevention (CDC) and Premiere Personnel in Botswana, conducted an evaluation to describe HIV-related services provided to women during their pregnancies, document the content of post-test counseling sessions for HIV-positive pregnant women, whether HIV-positive women remembered what had been discussed, the extent of AZT adherence based on self-reports, and the operational successes and barriers to adherence to AZT for PMTCT