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Добірка наукової літератури з теми "Homologie distante"

Автор: Grafiati

Опубліковано: 14 грудня 2024

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Статті в журналах з теми "Homologie distante"

Patthy, László. "Detecting distant homologies of mosaic proteins." Journal of Molecular Biology 202, no. 4 (August 1988): 689–96. http://dx.doi.org/10.1016/0022-2836(88)90550-5.

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Kwessi, Eddy. "Topological Comparison of Some Dimension Reduction Methods Using Persistent Homology on EEG Data." Axioms 12, no. 7 (July 18, 2023): 699. http://dx.doi.org/10.3390/axioms12070699.

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In this paper, we explore how to use topological tools to compare dimension reduction methods. We first make a brief overview of some of the methods often used in dimension reduction such as isometric feature mapping, Laplacian Eigenmaps, fast independent component analysis, kernel ridge regression, and t-distributed stochastic neighbor embedding. We then give a brief overview of some of the topological notions used in topological data analysis, such as barcodes, persistent homology, and Wasserstein distance. Theoretically, when these methods are applied on a data set, they can be interpreted differently. From EEG data embedded into a manifold of high dimension, we discuss these methods and we compare them across persistent homologies of dimensions 0, 1, and 2, that is, across connected components, tunnels and holes, shells around voids, or cavities. We find that from three dimension clouds of points, it is not clear how distinct from each other the methods are, but Wasserstein and Bottleneck distances, topological tests of hypothesis, and various methods show that the methods qualitatively and significantly differ across homologies. We can infer from this analysis that topological persistent homologies do change dramatically at seizure, a finding already obtained in previous analyses. This suggests that looking at changes in homology landscapes could be a predictor of seizure.

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Cruz, Sergio Manuel Serra Da, Vanessa Batista, Edno Silva, Frederico Tosta, Clarissa Vilela, Rafael Cuadrat, Diogo Tschoeke, Alberto M. R. Davila, Maria Luiza Machado Campos, and Marta Mattoso. "Detecting distant homologies on protozoans metabolic pathways using scientific workflows." International Journal of Data Mining and Bioinformatics 4, no. 3 (2010): 256. http://dx.doi.org/10.1504/ijdmb.2010.033520.

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Gardiner, John, Robyn Overall, and Jan Marc. "Distant plant homologues: don’t throw out the baby." Trends in Plant Science 17, no. 3 (March 2012): 126–28. http://dx.doi.org/10.1016/j.tplants.2011.12.007.

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Spielberg, N., Z. Luz, R. Poupko, K. Praefcke, B. Kohne, J. Pickardt, and K. Horn. "The Crystal and Mesophase Structure of Hexakis(alkylsulfono)- benzene Homologues by X-Ray Diffractometry." Zeitschrift für Naturforschung A 41, no. 6 (June 1, 1986): 855–60. http://dx.doi.org/10.1515/zna-1986-0612.

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A powder X-ray diffractometer study of hexakis(tridecylsulfono)benzene (HASB13) has been carried out over the temperature range 20 to above 80 °C. In this range three phase transitions are observed by sharp discontinuities in the diffraction pattern indicating a solid-solid, solidmesophase, and mesophase-liquid transition. The mesomorphic phase is identified as a hexagonal columnar discotic mesophase, Dhd, with intercolumnar spacing of 25.7 Å and average stacking distance of 4.9 Å. Both distances are independent of temperature but there appears to be a gradual increase in the stacking disorder as the temperature is increased. The magnitude of the intercolumnar distance suggests a considerable degree of side chain disorder. A detailed X-ray diffraction study was also performed at room temperature on a single crystal of hexakis(propylsulfono) benzene (HASB3), which is not mesogenic. The results provide detailed information on the structure of HASB 3 which is used in the interpretation of HASB 13 results.

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Shay, C. E., P. G. Foster, and J. M. Neelin. "Predictability of sequence homologies among lysine-rich histones by immunological distance." Comparative Biochemistry and Physiology Part B: Comparative Biochemistry 86, no. 1 (January 1987): 193–99. http://dx.doi.org/10.1016/0305-0491(87)90197-0.

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SNIPAS, Scott J., Henning R. STENNICKE, Stefan RIEDL, Jan POTEMPA, James TRAVIS, Alan J. BARRETT, and Guy S. SALVESEN. "Inhibition of distant caspase homologues by natural caspase inhibitors." Biochemical Journal 357, no. 2 (July 15, 2001): 575. http://dx.doi.org/10.1042/0264-6021:3570575.

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SNIPAS, Scott J., Henning R. STENNICKE, Stefan RIEDL, Jan POTEMPA, James TRAVIS, Alan J. BARRETT, and Guy S. SALVESEN. "Inhibition of distant caspase homologues by natural caspase inhibitors." Biochemical Journal 357, no. 2 (July 9, 2001): 575–80. http://dx.doi.org/10.1042/bj3570575.

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Caspases play an important role in the ability of animal cells to kill themselves by apoptosis. Caspase activity is regulated in vivo by members of three distinct protease inhibitor families, two of which, baculovirus p35 and members of the inhibitor of apoptosis (IAP) family, are thought to be caspase specific. However, caspases are members of the clan of cysteine proteases designated CD, which also includes animal and plant legumains, and the bacterial proteases clostripain, gingipain-R and gingipain-K. Since these proteases have been proposed to have a common mechanism and evolutionary origin, we hypothesized that the caspase inhibitors may also regulate these other proteases. We tested this hypothesis by examining the effect of the natural caspase inhibitors on other members of protease clan CD. The IAP family proteins were found to have only a slight inhibitory effect on gingipain-R. The cowpox viral cytokine-response modifier A (CrmA) serpin had no effect on any of the proteases tested but a single point mutation of CrmA (Asp → Lys) resulted in strong inhibition of gingipain-K. More substantial, with respect to the hypothesis, was the strong inhibition of gingipain-K by wild-type p35. The site in p35, required for inhibition of gingipain-K, was mapped to Lys94, seven residues C-terminal to the caspase inhibitory site. Our data indicate that the virally encoded caspase inhibitors have adopted a mechanism that allows them to regulate disparate members of clan CD proteases.

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Rigden, Daniel J., Jens M. H. Thomas, Felix Simkovic, Adam Simpkin, Martyn D. Winn, Olga Mayans, and Ronan M. Keegan. "Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases inAMPLE." Acta Crystallographica Section D Structural Biology 74, no. 3 (March 1, 2018): 183–93. http://dx.doi.org/10.1107/s2059798318002310.

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Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Although routine in many cases, it becomes more effortful and often impossible when the available experimental structures typically used as search models are only distantly homologous to the target. Nevertheless, with current powerful MR software, relatively small core structures shared between the target and known structure, of 20–40% of the overall structure for example, can succeed as search models where they can be isolated. Manual sculpting of such small structural cores is rarely attempted and is dependent on the crystallographer's expertise and understanding of the protein family in question. Automated search-model editing has previously been performed on the basis of sequence alignment, in order to eliminate, for example, side chains or loops that are not present in the target, or on the basis of structural features (e.g.solvent accessibility) or crystallographic parameters (e.g.Bfactors). Here, based on recent work demonstrating a correlation between evolutionary conservation and protein rigidity/packing, novel automated ways to derive edited search models from a given distant homologue over a range of sizes are presented. A variety of structure-based metrics, many readily obtained from online webservers, can be fed to the MR pipelineAMPLEto produce search models that succeed with a set of test cases where expertly manually edited comparators, further processed in diverse ways withMrBUMP, fail. Further significant performance gains result when the structure-based distance geometry methodCONCOORDis used to generate ensembles from the distant homologue. To our knowledge, this is the first such approach whereby a single structure is meaningfully transformed into an ensemble for the purposes of MR. Additional cases further demonstrate the advantages of the approach.CONCOORDis freely available and computationally inexpensive, so these novel methods offer readily available new routes to solve difficult MR cases.

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Dorer, Douglas R., and Steven Henikoff. "Transgene Repeat Arrays Interact With Distant Heterochromatin and Cause Silencing in cis and trans." Genetics 147, no. 3 (November 1, 1997): 1181–90. http://dx.doi.org/10.1093/genetics/147.3.1181.

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Tandem repeats of Drosophila transgenes can cause heterochromatic variegation for transgene expression in a copy-number and orientation-dependent manner. Here, we demonstrate different ways in which these transgene repeat arrays interact with other sequences at a distance, displaying properties identical to those of a naturally occurring block of interstitial heterochromatin. Arrays consisting of tandemly repeated white transgenes are strongly affected by proximity to constitutive heterochromatin. Moving an array closer to heterochromatin enhanced variegation, and enhancement was reverted by recombination of the array onto a normal sequence chromosome. Rearrangements that lack the array enhanced variegation of white on a homologue bearing the array. Therefore, silencing of white genes within a repeat array depends on its distance from heterochromatin of the same chromosome or of its paired homologue. In addition, white transgene arrays cause variegation of a nearby gene in cis, a hallmark of classical position-effect variegation. Such spreading of heterochromatic silencing correlates with array size. Finally, white transgene arrays cause pairing-dependent silencing of a non-variegating white insertion at the homologous position.

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Більше джерел

Дисертації з теми "Homologie distante"

Sussfeld, Duncan. "Identifying remote homology and gene remodelling using network-based approaches." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASL112.

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L'augmentation toujours plus importante de données génomiques et métagénomiques appelle de nouveaux développements méthodologiques et bio-informatiques, afin de caractériser avec davantage de précision les phénomènes évolutifs dans leur ensemble. En particulier, certaines des méthodes usuelles pour étudier l'évolution des (familles de) gènes s'avèrent inadaptées lorsque la parenté entre séquences n'est que partiellement supportée. Ainsi, la définition et la reconstruction de familles de gènes se heurtent à l'obstacle de l'homologie distante, qui passe sous le seuil de détection des alignements de séquences. De même, les mécanismes d'évolution combinatoire, tels que les fusions et fissions de gènes, remettent en cause les représentations purement arborescentes de l'évolution des familles de gènes. L'application de méthodes complémentaires basées sur les réseaux de similarité de séquences permet de contourner certaines de ces lacunes, en proposant une représentation holistique des similarités entre gènes. La détection et l'analyse d'homologues très divergents de familles de gènes fortement conservées dans des jeux de données environnementaux est notamment facilitée par la recherche itérative d'homologie fondée sur les réseaux. Cette fouille itérative de métagénomes révèle une immense diversité de variants environnementaux dans ces familles, qui divergent de la diversité connue tant par leur séquence que par la structure des protéines qu'ils encodent, et elle permet de suggérer des pistes pour guider de futures explorations de la matière noire microbienne. En outre, en prenant en compte des liens d'homologie partielle entre séquences génétiques, les réseaux de similarité de séquences permettent une identification systématique des évènements de fusion et de fission de gènes. Il devient ainsi possible d'évaluer l'impact de ces processus au cours de l'évolution de lignées biologiques d'intérêt, permettant de comparer le rôle qu'ils ont joué lors de l'émergence de phénotypes multicellulaires complexes dans plusieurs telles lignées. Plus généralement, ces approches basées sur les réseaux illustrent l'intérêt de prendre en compte une pluralité de modèles pour étudier une plus grande variété de processus évolutifs
The ever-increasing accumulation of genomic and metagenomic data calls for new methodological developments in bioinformatics, in order to characterise evolutionary phenomena as a whole with better accuracy. In particular, some of the canonical methods to study the evolution of genes and gene families may be ill-suited when the relatedness of sequences is only partially supported. For instance, the definition and reconstruction of gene families face the hurdle of remote homology, which falls beneath the detection thresholds of sequence alignments. Likewise, combinatorial mechanisms of evolution, such as gene fusion and gene fission, challenge the purely tree-based representations of gene family evolution. The use of complementary methods based on sequence similarity networks allows us to circumvent some of these shortcomings, by offering a more holistic representation of similarities between genes. The detection and analysis of highly divergent homologues of strongly conserved families in environmental sequence datasets, in particular, is facilitated by iterative homology search protocols based on networks. This iterative mining of metagenomes reveals an immense diversity of environmental variants in these families, diverging from the known diversity in primary sequence as well as in the tertiary structure of the proteins they encode. It is thus able to suggest possible directions of future explorations into microbial dark matter. Furthermore, by factoring in relationships of partial homology between gene sequences, sequence similarity networks allow for a systematic identification of gene fusion and fission events. It thus becomes possible to assess the effects of these processes on the evolution of biological lineages of interest, enabling us for instance to compare the role that they played in the emergence of complex multicellular phenotypes between several such lineages. More generally, these network-based approaches illustrate the benefits of taking a plurality of models into account, in order to study a broader range of evolutionary processes

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Tinarrage, Raphaël. "Inférence topologique à partir de mesures et de fibrés vectoriels." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASM001.

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Nous contribuons à l'inférence topologique, basée sur la théorie de l'homologie persistante, en proposant trois familles de filtrations.Nous établissons pour chacune d'elles des résultats de consistance---c'est-à-dire de qualité d'approximation d'un objet géométrique sous-jacent---, et de stabilité---c'est-à-dire que robustesse face à des erreurs de mesures initiales.Nous proposons des algorithmes concrets afin de pouvoir utiliser ces méthodes en pratique.La première famille, les filtrations-DTM, est une alternative robuste à la classique filtration de Cech lorsque le nuage de points est bruité ou contient des points aberrants.Elle repose sur la notion de distance à la mesure qui permet d'obtenir une stabilité au sens de la distance de Wasserstein.Deuxièmement, nous proposons les filtrations relevées, qui permettent d'estimer l'homologie des variétés immergées, même quand leur portée est nulle.Nous introduisons la notion de portée normale, et montrons qu'elle conduit à un contrôle quantitatif de la variété.Nous étudions l'estimation des espaces tangents par les matrices de covariance locale.En troisième lieu, nous développons un cadre pour les filtrations de fibrés vectoriels, et définissons les classes de Stiefel-Whitney persistantes.Nous montrons que les classes persistantes associées aux filtrations de fibrés de Cech sont consistantes et stables en distance de Hausdorff.Pour permettre leur mise en œuvre algorithmique, nous introduisons la notion de condition étoile faible
We contribute to the theory of topological inference, based on the theory of persistent homology, by proposing three families of filtrations.For each of them, we prove consistency results---that is, the quality of approximation of an underlying geometric object---, and stability results---that is, robustness against initial measurement errors.We propose concrete algorithms in order to use these methods in practice.The first family, the DTM-filtration, is a robust alternative to the classical Cech filtration when the point cloud is noisy or contains outliers.It is based on the notion of distance to measure, which allows to obtain stability in the sense of the Wasserstein distance.Secondly, we propose the lifted filtrations, which make it possible to estimate the homology of immersed manifolds, even when their reach is zero.We introduce the notion of normal reach, and show that it leads to a quantitative control of the manifold.We study the estimation of tangent spaces by local covariance matrices.Thirdly, we develop a framework for vector bundle filtrations, and define the persistent Stiefel-Whitney classes.We show that the persistent classes associated to the Cech bundle filtrations are Hausdorff-stable and consistent.To allow their algorithmic implementation, we introduce the notion of weak star condition

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Lee, Marianne M. "A two-pronged approach to improve distant homology detection." Columbus, Ohio : Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1242235868.

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Hamdi, Chaima. "Applications de l’homologie persistante pour la reconnaissance des formes." Mémoire, Université de Sherbrooke, 2017. http://hdl.handle.net/11143/10675.

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L’homologie persistante est un outil fondamental dans la topologie computationnelle. Cette méthode est utilisée pour reconnaître et comparer les formes. Dans ce travail nous étudions d’abord l’homologie persistante dans le cas unidimensionnel d’ordre 0 qu’on appelle aussi fonction de taille. Nous présentons une démonstration du fait que toute fonction de taille peut être représentée comme un ensemble de points et de lignes dans le plan réel, avec des multiplicités. Cela permet une approche algébrique aux fonctions de taille et la construction de nouvelles pseudo distances entre les fonctions de taille pour comparer les formes. Nous calculons ensuite l’homologie persistante unidimensionnelle d’ordre n avec différentes méthodes de filtration de l’espace correspondant à l’histoire d’un complexe croissant. Nous classons un changement topologique qui se produit pendant la croissance soit comme une caractéristique ou un bruit, en fonction de sa durée de vie ou de sa persistance dans la filtration. Une présentation avec des codes barres affiche alors la persistance de ces invariants. L’homologie persistante multidimensionnelle nous permet de soutirer plus d’informations sur les formes en utilisant la fonction de filtration avec des valeurs dans [nombre réel]k. Pour fournir un descripteur de forme concis et complet dans le cas multidimensionnel nous réduisons le calcul de l’homologie persistante multidimensionnelle au calcul de l’homologie persistante ordinaire pour une famille paramétrée de fonctions à valeur dans [nombre réel].

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Mauricio, Mauro. "Distance bounding and Heegaard Floer homology methods in reducible Dehn surgery." Thesis, Imperial College London, 2012. http://hdl.handle.net/10044/1/10226.

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Motivated by the formation of certain link types during Hin-mediated DNA recombination experiments, we consider tangle equations where one of the products is a connect-sum of 2-bridge links. We are thus led to study Dehn surgeries on knots in lens spaces that yield connect-sums of lens spaces. Using 3-manifold methods, we prove, for certain classes of knot exteriors, a distance bound on Dehn surgery slopes. (This proof complements an algebraic-geometric proof of a more general statement due to Boyer and Zhang [6]). Analysing the known examples of connect-sums of lens spaces surgeries, together with some sample calculations, we conjecture that if surgery on a knot K [Symbol appears here. To view, please open pdf attachment] L(p, q), with p, q [Symbol appears here. To view, please open pdf attachment]1, 2, yields L(p, q)#L(t, 1), then the knot has reducible exterior. Using Heegaard Floer homology, we prove a special case of the conjecture, as well as some surgery obstructions. We then apply our results, in the spirit of the tangle model of Ernst and Sumners [67], to the problem of Hin-mediated DNA recombination, where we characterise its distributive recombination step.

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Quercioli, Nicola. "A compactness theorem in group invariant persistent homology." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2017. http://amslaurea.unibo.it/13485/.

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In this thesis we present a new result concerning the theory of group invariant persistent homology. This theory adapts persistent homology in the presence of the action on a space of functions Phi of a subgroup G of the group H of all self-homeomorphisms of a topological space X. Its model is based on a space of suitable operators defined on Phi. After describing the mathematical setting and recalling some basic results, we prove that the space of these operators is compact with respect to a suitable topology. In order to prove this result, we require that Phi, G, X are compact.

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Elchesen, Alex. "Stability of Zigzag Persistence with Respect to a Reflection-type Distance." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1492707343134983.

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Chowdhury, Samir. "Metric and Topological Approaches to Network Data Analysis." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1555420352147114.

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Oruc-Ratinaud, Zéliha. "Interactions de longue distance et commutation de classe dans le locus des chaînes lourdes d’immunoglobulines." Limoges, 2006. https://aurore.unilim.fr/theses/nxfile/default/c5f89700-ef67-402e-ad1b-559e8e524b0c/blobholder:0/2006LIMO0066.pdf.

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La commutation isotypique au sein du locus des chaînes lourdes d'immunoglobulines (IgH) nécessite la transcription geffi1inale, l'intervention de AID (Activation-Induced cytidine Deaminase) et des éléments régulateurs en aval du locus (3 'RR). Pour analyser l'effet des interactions de longue distance sur la commutation isotypique, nous avons généré 3 modèles murins par recombinaison homologue. Dans le premier modèle, nous avons inséré un isolateur sauvage ou muté entre la 3'RR et le locus IgH. Dans le deuxième modèle, nous avons inséré un site de polyadénylation et de pause transcriptionnelle en aval des promoteurs germinaux Imu ou de Igamma3 pour un arrêt prématuré de la transcription germinale. Enfin dans le troisième modèle, nous avons remplacé le promoteur Igamma3 par Igamma1. Ces 3 approches nous ont permiis de mieux comprendre les interactions à longue distance au cours de la régulation de la transcription germinale, de la commutation isotypique et de l'élongation transcriptionnelle
Class switch recombination is a process in the immunoglobulin heavy chain locus (IgH) which requires germline transcription, Activated-Induced cytidine Deaminase (AID) and the 3' regulatory region (3'RR). In order to investigate the effect of long-range interactions on the class switch recombination, we generated three models in the mouse thanks to homologous recombination. In the first model, the entire or mutated core element of the chicken HS4 insulator was inserted between the 3'RR and the IgH locus. In the second, a polyadenylation and pause site was inserted downstream of germline promoters Imu or Igamma3 to attempt a premature termination of the germline transcription. In the last, the Igamma3 germline promoter was replaced by Igamma1. Thanks to these models, a better understanding is possible about the long-range interactions during the regulation of the germline transcription, the class switch recombination and the transcriptional elongation

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Buchet, Mickaël. "Topological inference from measures." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA112367/document.

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La quantité de données disponibles n'a jamais été aussi grande. Se poser les bonnes questions, c'est-à-dire des questions qui soient à la fois pertinentes et dont la réponse est accessible est difficile. L'analyse topologique de données tente de contourner le problème en ne posant pas une question trop précise mais en recherchant une structure sous-jacente aux données. Une telle structure est intéressante en soi mais elle peut également guider le questionnement de l'analyste et le diriger vers des questions pertinentes. Un des outils les plus utilisés dans ce domaine est l'homologie persistante. Analysant les données à toutes les échelles simultanément, la persistance permet d'éviter le choix d'une échelle particulière. De plus, ses propriétés de stabilité fournissent une manière naturelle pour passer de données discrètes à des objets continus. Cependant, l'homologie persistante se heurte à deux obstacles. Sa construction se heurte généralement à une trop large taille des structures de données pour le travail en grandes dimensions et sa robustesse ne s'étend pas au bruit aberrant, c'est-à-dire à la présence de points non corrélés avec la structure sous-jacente.Dans cette thèse, je pars de ces deux constatations et m'applique tout d'abord à rendre le calcul de l'homologie persistante robuste au bruit aberrant par l'utilisation de la distance à la mesure. Utilisant une approximation du calcul de l'homologie persistante pour la distance à la mesure, je fournis un algorithme complet permettant d'utiliser l'homologie persistante pour l'analyse topologique de données de petite dimension intrinsèque mais pouvant être plongées dans des espaces de grande dimension. Précédemment, l'homologie persistante a également été utilisée pour analyser des champs scalaires. Ici encore, le problème du bruit aberrant limitait son utilisation et je propose une méthode dérivée de l'utilisation de la distance à la mesure afin d'obtenir une robustesse au bruit aberrant. Cela passe par l'introduction de nouvelles conditions de bruit et l'utilisation d'un nouvel opérateur de régression. Ces deux objets font l'objet d'une étude spécifique. Le travail réalisé au cours de cette thèse permet maintenant d'utiliser l'homologie persistante dans des cas d'applications réelles en grandes dimensions, que ce soit pour l'inférence topologique ou l'analyse de champs scalaires
Massive amounts of data are now available for study. Asking questions that are both relevant and possible to answer is a difficult task. One can look for something different than the answer to a precise question. Topological data analysis looks for structure in point cloud data, which can be informative by itself but can also provide directions for further questioning. A common challenge faced in this area is the choice of the right scale at which to process the data.One widely used tool in this domain is persistent homology. By processing the data at all scales, it does not rely on a particular choice of scale. Moreover, its stability properties provide a natural way to go from discrete data to an underlying continuous structure. Finally, it can be combined with other tools, like the distance to a measure, which allows to handle noise that are unbounded. The main caveat of this approach is its high complexity.In this thesis, we will introduce topological data analysis and persistent homology, then show how to use approximation to reduce the computational complexity. We provide an approximation scheme to the distance to a measure and a sparsifying method of weighted Vietoris-Rips complexes in order to approximate persistence diagrams with practical complexity. We detail the specific properties of these constructions.Persistent homology was previously shown to be of use for scalar field analysis. We provide a way to combine it with the distance to a measure in order to handle a wider class of noise, especially data with unbounded errors. Finally, we discuss interesting opportunities opened by these results to study data where parts are missing or erroneous

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Книги з теми "Homologie distante"

Nieder, Andreas. Neuronal Correlates of Non-verbal Numerical Competence in Primates. Edited by Roi Cohen Kadosh and Ann Dowker. Oxford University Press, 2014. http://dx.doi.org/10.1093/oxfordhb/9780199642342.013.027.

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Non-verbal numerical competence, such as the estimation of set size, is rooted in biological primitives that can also be explored in animals. Over the past years, the anatomical substrates and neuronal mechanisms of numerical cognition in primates have been unravelled down to the level of single neurons. Studies with behaviourally-trained monkeys have identified a parietofrontal network of individual neurons selectively tuned to the number of items (cardinal aspect) or the rank of items in a sequence (ordinal aspect). The properties of these neurons’ numerosity tuning curves can explain fundamental psychophysical phenomena, such as the numerical distance and size effect. Functionally overlapping groups of parietal neurons represent not only numerable-discrete quantity (numerosity), but also innumerable-continuous quantity (extent) and relations between quantities (proportions), supporting the idea of a generalized magnitude system in the brain. Moreover, many neurons in the prefrontal cortex establish semantic associations between signs and abstract numerical categories, a neuronal precursor mechanisms that may ultimately give rise to symbolic number processing in humans. These studies establish putative homologies between the monkey and human brain, and demonstrate the suitability of non-human primates as model system to explore the neurobiological roots of the brain’s non-verbal quantification system, which may constitute the phylogenetic and ontogenetic foundation of all further, more elaborate numerical skills in humans.

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Частини книг з теми "Homologie distante"

Gîrdea, Marta, Laurent Noé, and Gregory Kucherov. "Back-Translation for Discovering Distant Protein Homologies." In Lecture Notes in Computer Science, 108–20. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-04241-6_10.

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Cerri, Andrea, Marc Ethier, and Patrizio Frosini. "The Coherent Matching Distance in 2D Persistent Homology." In Computational Topology in Image Context, 216–27. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-39441-1_20.

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Songdechakraiwut, Tananun, Bryan M. Krause, Matthew I. Banks, Kirill V. Nourski, and Barry D. Van Veen. "Wasserstein Distance-Preserving Vector Space of Persistent Homology." In Lecture Notes in Computer Science, 277–86. Cham: Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-43993-3_27.

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Lausen, Berthold. "Exploration Homologer Sequenzdaten: Positionelle Mutationsrate, Genetische Distanz und Phylogenie." In Biometrie und Informatik — neue Wege zur Erkenntnisgewinnung in der Medizin, 138–41. Berlin, Heidelberg: Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-48167-3_27.

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Casadio, Rita, Pier Luigi Martelli, Lisa Bartoli, and Piero Fariselli. "Topology prediction of membrane proteins: how distantly related homologs come into play." In Structural Bioinformatics of Membrane Proteins, 61–82. Vienna: Springer Vienna, 2010. http://dx.doi.org/10.1007/978-3-7091-0045-5_4.

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Kumar, Gayatri, Narayanaswamy Srinivasan, and Sankaran Sandhya. "Profiles of Natural and Designed Protein-Like Sequences Effectively Bridge Protein Sequence Gaps: Implications in Distant Homology Detection." In Methods in Molecular Biology, 149–67. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2095-3_5.

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Lewis, Sally A., and Nicholas J. Cowan. "Tubulin-specific chaperones." In Guidebook to the Cytoskeletal and Motor Proteins, 247–48. Oxford University PressOxford, 1999. http://dx.doi.org/10.1093/oso/9780198599579.003.0080.

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Abstract Tubulin-specific chaperone A has also been termed p14.11 Homologues of chaperones A (RBL2), 12 B (ALF1), 8 D (CIN1), 13 and E (PAC2)14 exist in S. cerevisiae. There is no discernable homologue of chaperone C in S. cerevisiae, although homologues of this chaperone exist in distantly related eukaryotes (e.g. Arabidopsis, C. elegans).

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CHANDLER, V., M. STAM, and L. SIDORENKO. "7 Long-distance Cis and Trans interactions mediate paramutation." In Homology Effects, 215–34. Elsevier, 2002. http://dx.doi.org/10.1016/s0065-2660(02)46008-7.

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Rajeswari, V., and Dr T. Nithiya. "NONLINEAR QUANTUM ALGEBRAIC TOPOLOGICAL MODEL FOR COMPUTING MINIMUM TRANSITION HOMOLOGIES USING JOINT CLUSTER PAINLEVE NETWORK THEORY." In Futuristic Trends in Contemporary Mathematics & Applications Volume 3 Book 1, 97–103. Iterative International Publishers, Selfypage Developers Pvt Ltd, 2024. http://dx.doi.org/10.58532/v3bjcm1p1ch9.

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Developing immense in network communication, complex topology is one of main structural problem in Transition homologies. Due to this nonlinear structure creates a redundant network life time foe energy loses due to distance theory of connective nodes in network leads data transmission failures. Existing analytics model estimates the linear substance based distance theory to process the Data Transition Homologies (DTH) indeed of nonlinear structure because of dynamic topology in homotphy to improve the network communication. To resolve this problem, we propose a Nonlinear Quantum Algebraic Topological (NQAT) model for computing the minimum Transition homologies using painleve network theory to improve the homological network structure for network life time improvement. This proposed system forming best joint cluster network path 〖lim┬(t-→∞) 2 (x+y)〗⁡〖(2(n+1(t)))/(α (t))〗 at 'α' variance at x^' time to create network structure. To create joint cluster by estimating immediate consequence of the orthogonally node condition is the recurrence relation between transient node based on response rate. This chose the best energy level supporting node to construct a topology to improve the network lifetime maximization.

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Liu, Yayun, Zhijian Zhang, Lin Jiang, Hui Zhong, and Xinyang Li. "Identifying Key Nodes Based on TS Distance in Time-Varying Social Networks." In Fuzzy Systems and Data Mining IX. IOS Press, 2023. http://dx.doi.org/10.3233/faia231025.

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Key nodes are important for analyzing the evolution of time-varying networks. Persistent homology can calculate topological information of the network in different dimensions and encode it into a persistence diagram. This paper first defines the Topological Similarity (TS) distance based on the theory of persistent homology to describe the topological similarity of the networks. The smaller the TS distance, the more similar the network is. Secondly, an algorithm for identifying key nodes based on TS distance (KITS) is proposed to obtain the sequence of key nodes in time-varying network. Finally, the paper analyses the TS distance on two real time-varying social networks and compares it with the degree centrality. The experimental results show that the TS distance can effectively characterize the topological similarity between two networks and that the KITS algorithm accurately and comprehensively identifies key nodes.

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Тези доповідей конференцій з теми "Homologie distante"

Vieira, Diogo Munaro, Elvismary Molina de Armas, Maria L. G. Jaramillo, Marcos Catanho, Antonio B. Miranda, Edward Hermann Haeusler, and Sérgio Lifschitz. "A New Data Modeling Approach for Alignment-free Biological Applications." In Simpósio Brasileiro de Banco de Dados. Sociedade Brasileira de Computação - SBC, 2023. http://dx.doi.org/10.5753/sbbd.2023.232471.

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Finding homologous proteins and grouping them are tasks of utmost importance in biology, which currently rely on tools based on information from these proteins' DNA or amino acid sequences. These tasks require identifying evolutionary patterns that are challenging to obtain automatically using traditional methods. This work proposes a data modeling approach to leverage evolutionary patterns in homology searching, ranking, and clustering tasks through an alignment-free process using image similarity algorithms. This strategy is valuable even for distant homologs and contributes to data privacy and security.

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Aljawad, Osama, Yanni Sun, Alex Liu, and Jikai Lei. "NcRNA homology search using Hamming distance seeds." In the 2nd ACM Conference. New York, New York, USA: ACM Press, 2011. http://dx.doi.org/10.1145/2147805.2147828.

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Ahmed, Mahmuda, Brittany Terese Fasy, and Carola Wenk. "Local persistent homology based distance between maps." In SIGSPATIAL '14: 22nd SIGSPATIAL International Conference on Advances in Geographic Information Systems. New York, NY, USA: ACM, 2014. http://dx.doi.org/10.1145/2666310.2666390.

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Huang, Weiyu, and Alejandro Ribeiro. "Persistent homology approximations of network distances." In 2015 IEEE Global Conference on Signal and Information Processing (GlobalSIP). IEEE, 2015. http://dx.doi.org/10.1109/globalsip.2015.7418348.

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Huang, Weiyu, and Alejandro Ribeiro. "Persistent homology lower bounds on network distances." In 2016 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). IEEE, 2016. http://dx.doi.org/10.1109/icassp.2016.7472598.

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Sheehy, Donald R. "The Persistent Homology of Distance Functions under Random Projection." In Annual Symposium. New York, New York, USA: ACM Press, 2014. http://dx.doi.org/10.1145/2582112.2582126.

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Huang, Weiyu, and Alejandro Ribeiro. "Persistent homology lower bounds on distances in the space of networks." In 2016 50th Asilomar Conference on Signals, Systems and Computers. IEEE, 2016. http://dx.doi.org/10.1109/acssc.2016.7868996.

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Jia, Yan, Runheng Li, Liang Gan, and Guangqiang Chen. "IRC Botnets' Homology Identifying Method Based on Improved LB_PAA Distance of Communication Characteristic Curves." In 2010 Third International Symposium on Intelligent Information Technology and Security Informatics (IITSI). IEEE, 2010. http://dx.doi.org/10.1109/iitsi.2010.69.

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Prokhorova, E. E., and R. R. Usmanova. "GENETIC POLYMORPHISM OF SNAILS SUCCINEA PUTRIS (GASTROPODA, PULMONATA)." In V International Scientific Conference CONCEPTUAL AND APPLIED ASPECTS OF INVERTEBRATE SCIENTIFIC RESEARCH AND BIOLOGICAL EDUCATION. Tomsk State University Press, 2020. http://dx.doi.org/10.17223/978-5-94621-931-0-2020-33.

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Genotypic diversity of snails Succinea putris L. (Linnaeus, 1758) collected in the north-west of Russia and in the Republic of Belarus was analysed. Homology between the nucleotide sequences of snails from different population made up 100% by the nucleotide sequence of ITS1-5.8S-ITS2 region of rDNA. Genetic variability based on mitochondrial markers was insignificant. Average genetic distances between samples made up 0,009 for СOI gene loci and 0.008 for CytB gene loci. Was found ten haplotypes of the mitochondrial gene CytB and nine haplotypes of the mitochondrial gene СOI. Perhaps the genetic homogeneity of snails S. putris found in the study explains a low variability of their parasites, trematodes from the genus Leucochloridium.

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Shigeta, Yuji, Masatoshi Aramaki, Kentaro Kudo, Kazunari Shinagawa, Naoyuki Nomura, Katsuyoshi Kondoh, Masato Hoshino, Kentaro Uesugi, and Yukiko Ozaki. "Understanding The Effect Of Process Parameters On Three-dimensional Pore Configurations And Mechanical Properties Of Laser Additive Manufactured Ti Using Synchrotron X-ray Computed Tomography And Homology." In World Powder Metallurgy 2022 Congress & Exhibition. EPMA, 2022. http://dx.doi.org/10.59499/wp225369761.

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To establish a quantitative relationship between fabrication parameters, pore-configuration, and mechanical properties in porous materials, the pore configurations were visualized by X-ray computed tomography (CT) about pure Ti-AM specimens fabricated under different laser beam conditions. Radius and sphericity of all pores were obtained by image analysis. Furthermore, using the 0th persistent homology, the pore configurations were qualified by the pair of birth and death values, b and d for all pores: |b| means a pore radius and d correspond to a half distance between adjacent pores. The significant correlations were confirmed between tensile strength|elongation and the parameters: the maximum value of |b|, the ratio of the mean values of |b| and d (neck geometry), and the sphericity of the largest pore. These were proposed as useful structural parameters representing 3D pore-structure in porous materials.

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Звіти організацій з теми "Homologie distante"

Terwilliger, Thomas C. Molecular replacement and model-building using distant homology models as templates. Office of Scientific and Technical Information (OSTI), November 2013. http://dx.doi.org/10.2172/1107986.

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Dolja, Valerian V., Amit Gal-On, and Victor Gaba. Suppression of Potyvirus Infection by a Closterovirus Protein. United States Department of Agriculture, March 2002. http://dx.doi.org/10.32747/2002.7580682.bard.

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The plant virus family Polyviridae is the largest and most destructive of all plant viruses. Despite the continuous effort to develop resistant plant varieties, there is a desperate need for novel approaches conferring wide-range potyvirus resistance. Based on experiments with the tobacco etch potyvirus (TEV)-derived gene expression vector, we suggested approach for screening of the candidate resistance genes. This approach relies on insertion of the genes into a virus vector and evaluation of the phenotypes of the resulting recombinant viruses. The genes which suppress infection by the recombinant virus are selected as candidates for engineering transgenic resistance. Our analysis of the TEV variants expressing proteins of the beet yellows closterovirus (BYV) revealed that one of those, the leader proteinase (L-Pro), strongly and specifically interfered with the hybrid TEV infection. Since closterovirus L-Pro is evolutionary related to potyviral helper component-proteinase (HC-Pro), we suggested that the L-Pro interfered with HC-Pro function via a trans-dominant inhibitory effect. Based on these findings, we proposed to test two major hypotheses. First, we suggested that L-Pro-mediated suppression of potyvirus infection is a general phenomenon effective against a range of potyviruses. The second hypothesis stated that the suppression effect can be reproduced in transgenic plants expressing L-Pro, and can be utilized for generation of resistance to potyviruses. In accord with these hypotheses, we developed two original objectives of our proposal: A) to determine the range of the closterovirus-derived suppression of potyviral infection, and B) to try and utilize the L-Pro-mediated suppression for the development of transgenic resistance to potyviruses. In the first phase of the project, we have developed all major tools and technologies required for successful completion of the proposed research. These included TEV and ZYMV vectors engineered to express several closteroviral L-Pro variants, and generation of the large collection of transgenic plants. To our satisfaction, characterization of the infection phenotypes exhibited by chimeric TEV and ZYMV variants confirmed our first hypothesis. For instance, similar to TEV-L- Pro(BYV) chimera, ZYMV-L-Pro(LIYV) chimera was debilitated in its systemic spread. In contrast, ZYMV-GUS chimera (positive control) was competent in establishing vigorous systemic infection. These and other results with chimeric viruses indicated that several closteroviral proteinases inhibit long-distance movement of the potyviruses upon co-expression in infected plants. In order to complete the second objective, we have generated ~90 tobacco lines transformed with closteroviral L-Pro variants, as well as ~100 lines transformed with BYV Hsp70-homolog (Hsp70h; a negative control). The presence and expression of the trans gene in each line was initially confirmed using RT-PCR and RNA preparations isolated from plants. However, since detection of the trans gene-specific RNA can not guarantee production of the corresponding protein, we have also generated L-Pro- and Hsp70h-specific antisera using corresponding synthetic peptides. These antisera allowed us to confirm that the transgenic plant lines produced detectable, although highly variable levels of the closterovirus antigens. In a final phase of the project, we tested susceptibility of the transgenic lines to TEV infection. To this end, we determined that the minimal dilution of the TEV inoculum that is still capable of infecting 100% of nontransgenic plants was 1:20, and used 10 plants per line (in total, ~2,000 plants). Unfortunately, none of the lines exhibited statistically significant reduction in susceptibility. Although discouraging, this outcome prompted us to expand our experimental plan and conduct additional experiments. Our aim was to test if closteroviral proteinases are capable of functioning in trans. We have developed agroinfection protocol for BYV, and tested if co- expression of the L-Pro is capable of rescuing corresponding null-mutant. The clear-cut, negative results of these experiments demonstrated that L-Pro acts only in cis, thus explaining the lack of resistance in our transgenic plants. We have also characterized a collection of the L-Pro alanine- scanning mutants and found direct genetic evidence of the requirement for L-Pro in virus systemic spread. To conclude, our research supported by BARD confirmed one but not another of our original hypotheses. Moreover, it provided an important insight into functional specialization of the viral proteinases and generated set of tools and data with which we will be able to address the molecular mechanisms by which these proteins provide a variety of critical functions during virus life cycle.

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