1,720,960 research outputs found
Protéotypage haut-débit de microorganismes par spectrométrie de masse en tandem
No full textRapid identification of microorganisms is essential in clinical diagnostics, health and food quality controls, and screening for biotechnology applications. Improving identification methods to make them faster and more sensitive is a major challenge. Currently, proteotyping by MALDI-TOF mass spectrometry is the reference method for isolates. However, this methodology is unable to handle most environmental isolates and opportunistic pathogens due to an incomplete database of experimental spectra. By recording much more sequence information at the peptide level, proteotyping by tandem mass spectrometry is able to identify the taxonomic position of any microorganism in the tree of life, and can be highly discriminating at the subspecies level. The aim of this thesis is to adapt and render high-throughput an approach without any a priori for microorganism identification by proteotyping developed in the laboratory. Phylopeptidomics is based on the recording of peptide sequence data by tandem mass spectrometry and their association with taxonomic information, enabling the organism to be identified. In order to reduce costs and analysis time, two methods were invented and tested during my thesis's work to identify any microorganism in just a few minutes of analysis. The first method enables sample multiplexing without labeling, by creating a mixture containing fractions for each isolate differing in hydrophobicity. The robustness, reproducibility and limitations of this method were evaluated. The second method takes advantage of the speed of direct infusion analysis, reducing analysis time to 36 seconds of spectrometry measurement.Identifier rapidement des microorganismes est essentiel dans le domaine du diagnostic clinique, des contrôles sanitaires et alimentaires, et du criblage pour applications biotechnologiques. Améliorer les méthodes d'identification afin qu'elles soient plus rapides et sensibles est un enjeu de taille. Actuellement, le protéotypage par spectrométrie de masse MALDI-TOF est la méthode de référence pour les isolats bactériens dans les laboratoires de microbiologie clinique. Toutefois, cette méthodologie n'est pas en mesure de traiter la plupart des isolats environnementaux et des agents pathogènes opportunistes en raison d'une base de données de spectres expérimentaux incomplète. En enregistrant beaucoup plus d'informations sur les séquences au niveau des peptides, le protéotypage par spectrométrie de masse en tandem est capable d'identifier la position taxonomique de n'importe quel micro-organisme dans l'arbre de la vie, et peut s'avérer hautement discriminant au niveau des sous-espèces. Cette thèse a pour objectif d'adapter et rendre haut-débit une approche d'identification de microorganismes sans a priori par protéotypage de microorganismes, développée au laboratoire. La phylopeptidomique repose sur l'enregistrement de données de séquences peptidiques par spectrométrie de masse en tandem et l'association de ces données taxonomiques, permettant d'identifier l'organisme. Afin de réduire les coûts et le temps d'analyse, deux méthodes ont été inventées et testées durant ma thèse pour identifier tout type de microorganismes en quelques minutes d'analyse. La première méthode permet de multiplexer sans marquage plusieurs échantillons en créant un mélange contenant des fractions de chaque isolat qui différent en hydrophobicité. La robustesse, la reproductibilité et les limites de cette méthode ont été évaluées. La seconde méthode utilise les capacités de rapidité d'une analyse par infusion directe, permettant de réduire le temps d'analyse à 36 secondes de spectrométrie
Protéotypage haut-débit de microorganismes par spectrométrie de masse en tandem
No full textRapid identification of microorganisms is essential in clinical diagnostics, health and food quality controls, and screening for biotechnology applications. Improving identification methods to make them faster and more sensitive is a major challenge. Currently, proteotyping by MALDI-TOF mass spectrometry is the reference method for isolates. However, this methodology is unable to handle most environmental isolates and opportunistic pathogens due to an incomplete database of experimental spectra. By recording much more sequence information at the peptide level, proteotyping by tandem mass spectrometry is able to identify the taxonomic position of any microorganism in the tree of life, and can be highly discriminating at the subspecies level. The aim of this thesis is to adapt and render high-throughput an approach without any a priori for microorganism identification by proteotyping developed in the laboratory. Phylopeptidomics is based on the recording of peptide sequence data by tandem mass spectrometry and their association with taxonomic information, enabling the organism to be identified. In order to reduce costs and analysis time, two methods were invented and tested during my thesis's work to identify any microorganism in just a few minutes of analysis. The first method enables sample multiplexing without labeling, by creating a mixture containing fractions for each isolate differing in hydrophobicity. The robustness, reproducibility and limitations of this method were evaluated. The second method takes advantage of the speed of direct infusion analysis, reducing analysis time to 36 seconds of spectrometry measurement.Identifier rapidement des microorganismes est essentiel dans le domaine du diagnostic clinique, des contrôles sanitaires et alimentaires, et du criblage pour applications biotechnologiques. Améliorer les méthodes d'identification afin qu'elles soient plus rapides et sensibles est un enjeu de taille. Actuellement, le protéotypage par spectrométrie de masse MALDI-TOF est la méthode de référence pour les isolats bactériens dans les laboratoires de microbiologie clinique. Toutefois, cette méthodologie n'est pas en mesure de traiter la plupart des isolats environnementaux et des agents pathogènes opportunistes en raison d'une base de données de spectres expérimentaux incomplète. En enregistrant beaucoup plus d'informations sur les séquences au niveau des peptides, le protéotypage par spectrométrie de masse en tandem est capable d'identifier la position taxonomique de n'importe quel micro-organisme dans l'arbre de la vie, et peut s'avérer hautement discriminant au niveau des sous-espèces. Cette thèse a pour objectif d'adapter et rendre haut-débit une approche d'identification de microorganismes sans a priori par protéotypage de microorganismes, développée au laboratoire. La phylopeptidomique repose sur l'enregistrement de données de séquences peptidiques par spectrométrie de masse en tandem et l'association de ces données taxonomiques, permettant d'identifier l'organisme. Afin de réduire les coûts et le temps d'analyse, deux méthodes ont été inventées et testées durant ma thèse pour identifier tout type de microorganismes en quelques minutes d'analyse. La première méthode permet de multiplexer sans marquage plusieurs échantillons en créant un mélange contenant des fractions de chaque isolat qui différent en hydrophobicité. La robustesse, la reproductibilité et les limites de cette méthode ont été évaluées. La seconde méthode utilise les capacités de rapidité d'une analyse par infusion directe, permettant de réduire le temps d'analyse à 36 secondes de spectrométrie
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Get PDF“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
Get PDFWe 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
Get PDFWe 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
A Simplified Label-Free Method for Proteotyping Sets of Six Isolates in a Single Liquid Chromatography-High-Resolution Tandem Mass Spectrometry Analysis
No full textInternational audienceClinical diagnostics and microbiology require high-throughput identification of microorganisms. Sample multiplexing prior to detection is an attractive means to reduce analysis costs and time-to-result. Recent studies have demonstrated the discriminative power of tandem mass spectrometry-based proteotyping. This technology can rapidly identify the most likely taxonomical position of any microorganism, even uncharacterized organisms. Here, we present a simplified label-free multiplexing method to proteotype isolates by tandem mass spectrometry that can identify six microorganisms in a single 20 min analytical run. The strategy involves the production of peptide fractions with distinct hydrophobicity profiles using spin column fractionation. Assemblages of different fractions can then be analyzed using mass spectrometry. Results are subsequently interpreted based on the hydrophobic characteristics of the peptides detected, which make it possible to link each taxon identified to the initial sample. The methodology was tested on 32 distinct sets of six organisms including several worst-scenario assemblages-with differences in sample quantities or the presence of the same organisms in multiple fractions-and proved to be robust. These results pave the way for the deployment of tandem mass spectrometry-based proteotyping in microbiology laboratories
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