1,720,967 research outputs found
The Development and Applications of NMR Metabolomics Analysis of Bacterial Metabolomes
No full textMetabolomics is a relatively new field that involves the study of metabolic responses that are occurring within a biological system. Metabolite profiles of an organism, tissue extract, and biofluids are important indicators to determine the physiological state of a biological profile. Comparison of such profiles from different phenotypes can be used to identify specific metabolic changes leading to the understanding of metabolic pathways, disease progression, drug toxicity and efficacy, and cellular responses to different intracellular and extracellular conditions. Metabolomics investigations often use sophisticated analytical techniques such as NMR spectroscopy to provide an unbiased and comprehensive approach to evaluate metabolic perturbation in different cell lysates.
This dissertation will focus on the development and applications of NMR-based metabolomics methodologies to generate reliable and reproducible results. The protocol has been expanded greatly, optimizing all aspects of the metabolomics process including cell growth, sample preparation, sample handling, data collection, data processing, and data analysis. There are two main approaches in the protocol to decipher NMR metabolomics data: pattern recognition, such as PCA and OPLS-DA, comparing numerous 1-dimensional 1H NMR datasets to analyze biofluids at a global scale, and quantitative profiling of 13C-labeled metabolites using 2-dimensional 1H-13C HSQC. As a result, our protocol provides a comprehensive analysis, describing unique characteristics and relationships between various samples that differ in their source or treatment.
We applied our protocol to predict the in vivo mechanism of action for drug leads from NMR metabolomics data. The NMR analysis resulted in distinct clustering which would be classified by an in vivo mechanism. Also, we demonstrated the similarity of Staphylococcus epidermidis metabolomes resulting from exposure to divergent environmental stressors that are known to facilitate biofilm formation. Our results suggest that the tricarboxlic acid cycle acts as a metabolic signaling mechanism for the activation of biofilm formation. Also investigated was the mechanism of action of D-cycloserine in M. smegmatis and M. tuberculosis. Our findings proved that D-alanine-D-alanine ligase is the primary target as cell growth is inhibited when the production of D-alanyl-D-alanine is halted. Furthermore, we were able to identify an alternate path for the production of D-alanine via a possible transaminase mechanism.
Adviser: Robert Power
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
No full text“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Negative impact of noise on the principal component analysis of NMR data
No full textPrincipal component analysis (PCA) is routinely applied to the study of NMR based metabolomic data. PCA is used to simplify the examination of complex metabolite mixtures obtained from biological samples that may be composed of hundreds or thousands of chemical components. PCA is primarily used to identify relative changes in the concentration of metabolites to identify trends or characteristics within the NMR data that permits discrimination between various samples that differ in their source or treatment. A common concern with PCA of NMR data is the potential over emphasis of small changes in high concentration metabolites that would over-shadow signifi cant and large changes in low-concentration components that may lead to a skewed or irrelevant clustering of the NMR data. We have identifi ed an additional concern, very small and random fl uctuations within the noise of the NMR spectrum can also result in large and irrelevant variations in the PCA clustering. Alleviation of this problem is obtained by simply excluding the noise region from the PCA by a judicious choice of a threshold above the spectral noise
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