1,720,962 research outputs found
Modélisation de la pepsinolyse in vitro en conditions gastriques et inférence de réseaux de filiation de peptides à partir de données de peptidomique
No full textAddressing the current demographic challenges, “civilization diseases” and the possible depletion of food resources, require optimization of food utilization and adapting their conception to the specific needs of each target population. This requires a better understanding of the different stages of the digestion process. In particular, how proteins are hydrolyzed is a major issue, due to their crucial role in human nutrition. However, the probabilistic laws governing the action of pepsin, the first protease to act in the gastrointestinal tract, are still unclear.In a first approach based on peptidomic data, we demonstrate that the hydrolysis by pepsin of a peptidebond depends on the nature of the amino acid residues in its large neighborhood, but also on physicochemical and structural variables describing its environment. In a second step, and considering the physicochemical environment at the peptide level, we propose a nonparametric model of the hydrolysis by pepsin of these peptides, and an Expectation-Maximization type estimation algorithm, offering novel perspectives for the valorization of peptidomic data. In this dynamic approach, we integrate the peptide kinship network into the estimation procedure, which leads to a more parsimonious model that is also more relevant regarding biological interpretations.Pour faire face aux enjeux démographiques actuels, aux « maladies de civilisation » et à la possible raréfaction des ressources alimentaires, il est impératif d’optimiser l’utilisation effective des aliments et d’adapter leur conception aux besoins spécifiques des différentes populations. Cela demande d’accroître notre compréhension des différentes étapes de la digestion. En particulier, en raison du rôle majeur des protéines dans notre alimentation, leur devenir au cours de la digestion est au coeur des préoccupations. Or, les lois probabilistes qui régissent l’action de la pepsine, première protéase à agir dans le tractus gastro-intestinal, ne sont pas encore clairement identifiées.Dans une première approche s’appuyant sur des données de peptidomique, nous démontrons que l’hydrolyse parla pepsine d’une liaison peptidique dépend de la nature des résidus d’acides aminés dans son large voisinage, mais aussi de variables physicochimiques et de structure décrivant son environnement. Nous proposons dans un second temps, tenant compte de l’environnement physicochimique à l’échelle de séquences peptidiques, un modèle non-paramétrique de l’hydrolyse de ces séquences par la pepsine et un algorithme d’estimation de type Expectation-Maximisation, offrant des perspectives de valorisation des données de peptidomique. Dans cette approche dynamique, nous intégrons les réseaux de filiation des peptides dans la procédure d’estimation, ce qui conduit à un modèle plus parcimonieux et plus pertinent au regard des interprétations biologiques
Modelling in vitro pepsinolysis in gastric conditions and inferring peptide filiation networks from peptidomics data
No full textPour faire face aux enjeux démographiques actuels, aux « maladies de civilisation » et à la possible raréfaction des ressources alimentaires, il est impératif d’optimiser l’utilisation effective des aliments et d’adapter leur conception aux besoins spécifiques des différentes populations. Cela demande d’accroître notre compréhension des différentes étapes de la digestion. En particulier, en raison du rôle majeur des protéines dans notre alimentation, leur devenir au cours de la digestion est au coeur des préoccupations. Or, les lois probabilistes qui régissent l’action de la pepsine, première protéase à agir dans le tractus gastro-intestinal, ne sont pas encore clairement identifiées.Dans une première approche s’appuyant sur des données de peptidomique, nous démontrons que l’hydrolyse parla pepsine d’une liaison peptidique dépend de la nature des résidus d’acides aminés dans son large voisinage, mais aussi de variables physicochimiques et de structure décrivant son environnement. Nous proposons dans un second temps, tenant compte de l’environnement physicochimique à l’échelle de séquences peptidiques, un modèle non-paramétrique de l’hydrolyse de ces séquences par la pepsine et un algorithme d’estimation de type Expectation-Maximisation, offrant des perspectives de valorisation des données de peptidomique. Dans cette approche dynamique, nous intégrons les réseaux de filiation des peptides dans la procédure d’estimation, ce qui conduit à un modèle plus parcimonieux et plus pertinent au regard des interprétations biologiques.Addressing the current demographic challenges, “civilization diseases” and the possible depletion of food resources, require optimization of food utilization and adapting their conception to the specific needs of each target population. This requires a better understanding of the different stages of the digestion process. In particular, how proteins are hydrolyzed is a major issue, due to their crucial role in human nutrition. However, the probabilistic laws governing the action of pepsin, the first protease to act in the gastrointestinal tract, are still unclear.In a first approach based on peptidomic data, we demonstrate that the hydrolysis by pepsin of a peptidebond depends on the nature of the amino acid residues in its large neighborhood, but also on physicochemical and structural variables describing its environment. In a second step, and considering the physicochemical environment at the peptide level, we propose a nonparametric model of the hydrolysis by pepsin of these peptides, and an Expectation-Maximization type estimation algorithm, offering novel perspectives for the valorization of peptidomic data. In this dynamic approach, we integrate the peptide kinship network into the estimation procedure, which leads to a more parsimonious model that is also more relevant regarding biological interpretations
Modélisation de la pepsinolyse in vitro en conditions gastriques et inférence de réseaux de filiation de peptides à partir de données de peptidomique
No full textAddressing the current demographic challenges, “civilization diseases” and the possible depletion of food resources, require optimization of food utilization and adapting their conception to the specific needs of each target population. This requires a better understanding of the different stages of the digestion process. In particular, how proteins are hydrolyzed is a major issue, due to their crucial role in human nutrition. However, the probabilistic laws governing the action of pepsin, the first protease to act in the gastrointestinal tract, are still unclear.In a first approach based on peptidomic data, we demonstrate that the hydrolysis by pepsin of a peptidebond depends on the nature of the amino acid residues in its large neighborhood, but also on physicochemical and structural variables describing its environment. In a second step, and considering the physicochemical environment at the peptide level, we propose a nonparametric model of the hydrolysis by pepsin of these peptides, and an Expectation-Maximization type estimation algorithm, offering novel perspectives for the valorization of peptidomic data. In this dynamic approach, we integrate the peptide kinship network into the estimation procedure, which leads to a more parsimonious model that is also more relevant regarding biological interpretations.Pour faire face aux enjeux démographiques actuels, aux « maladies de civilisation » et à la possible raréfaction des ressources alimentaires, il est impératif d’optimiser l’utilisation effective des aliments et d’adapter leur conception aux besoins spécifiques des différentes populations. Cela demande d’accroître notre compréhension des différentes étapes de la digestion. En particulier, en raison du rôle majeur des protéines dans notre alimentation, leur devenir au cours de la digestion est au coeur des préoccupations. Or, les lois probabilistes qui régissent l’action de la pepsine, première protéase à agir dans le tractus gastro-intestinal, ne sont pas encore clairement identifiées.Dans une première approche s’appuyant sur des données de peptidomique, nous démontrons que l’hydrolyse parla pepsine d’une liaison peptidique dépend de la nature des résidus d’acides aminés dans son large voisinage, mais aussi de variables physicochimiques et de structure décrivant son environnement. Nous proposons dans un second temps, tenant compte de l’environnement physicochimique à l’échelle de séquences peptidiques, un modèle non-paramétrique de l’hydrolyse de ces séquences par la pepsine et un algorithme d’estimation de type Expectation-Maximisation, offrant des perspectives de valorisation des données de peptidomique. Dans cette approche dynamique, nous intégrons les réseaux de filiation des peptides dans la procédure d’estimation, ce qui conduit à un modèle plus parcimonieux et plus pertinent au regard des interprétations biologiques
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
Identification of the physicochemical characteristics of peptides that influence their hydrolysis by pepsin
No full textChanging the structure of foods can modulate their nutritional quality by modifying the digestion process, a complex process that is still imperfectly understood. In particular, digestion dynamics have been poorly studied, although it can has significant metabolic consequences. The objective of this study is to model the proteolytic cascade by pepsin, and to highlight a potential "structural effect".
Egg white is an interesting model to meet this dual objective, as it offers the possibility of obtaining gels with different structures. In a probabilistic modeling approach of the peptide cleavage dynamics, we sought to identify leverages for the cleavage of a peptide after a given digestion time. For this purpose, peptides are identified and quantified at different time points in an in vitro digestion experiment. A Generalized Additive Modeling of the probability of a cleavage based on the physicochemical profile of peptides is proposed, considering either all kinds of cleavages made by the pepsin or only those made on preferential peptide bonds. The most significant variables are related to the length of the peptide and its location on the ovalbumin sequence. These results suggest that the action of pepsin depends more on structural criteria than on the presence of specific cleavage sites
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