1,720,971 research outputs found
Label core for understanding RNA structure
Full text linkThe RNA structure, the main predictor of biological function, is the result of the folding process. While the nucleotides in the RNA sequence rapidly coupled forming weak bonds, the spatial arrangement is a slow process. Although many computational approaches have been proposed to study the folding process of RNA, most of them do not consider the hierarchical aspect existing among the bonds. In this work, we propose to collapse nucleotides and bonds underpinning the primary and secondary structure of RNA in a unique label core congruent with the spatial configuration. A label core is represented as a term of generalized context-free grammar properly defined to support RNA structural reduction and analysis
A Loop Grammar to Understand the roles of miRNAs in the Tumor Cell
Full text linkA miRNA is a small non-coding RNA molecule that regulates gene expression. Current studies showed that miRNAs may function both as oncogenes and as tumor suppressors, but not revealed the precise conditions that cause miRNAs to alter gene expression of the cancer cells. In this study, we introduce a context-free grammar, Loop Grammar, that formalizes the primary and secondary structure as a composition of loops, corresponding to concatenation or nesting of hairpins. We also formalize the concatenation and nesting on fatgraphs, oriented surfaces with boundary, and we define a Surface Loop Grammar, whose algebraic expressions uniquely identify such surfaces associated to given RNA structures. The Loop Grammar has been used to model tumor and healthy miRNAs of the mir-515 family, and we observed that the mutations of elements of primary structure involved in loops formation changed the secondary structure of tumor miRNAs. The Surface Loop Grammar is useful to classify RNA structures in terms of loops and relations among them.
References:
1) Peng, Y., Croce, C. M. The role of MicroRNAs in human cancer. Signal transduction and targeted
therapy, 2016, 1, 15004.
2) Penner, R.C., Knudsen, M., Wiuf, C., Andersen, J.E., Fatgraph models of proteins. Communications on Pure and Applied Mathematics, 2010, 63(10), 1249–1297
3) Quadrini, M., Culmone, R., Merelli, E.: Topological Classification of RNA Structures via Intersection Graph. In: International Conference on Theory and Practice of Natural Computing, Springer, 2017, 203–215
4) Quadrini, M., Merelli, E.: Loop-loop interaction metrics on RNA secondary structures with pseudoknotsth International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 11th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2018 3, 2018
Branched coverings of CP^2 and other basic 4-manifolds
Full text linkWe give necessary and sufficient conditions for a 4-manifold to be a branched covering of CP2, S2xS2, S2x similar to S2 or S3xS1, which are expressed in terms of the Betti numbers and the signature of the 4-manifold. Moreover, we extend these results to include branched coverings of connected sums of the above manifolds. This leads to some new examples of closed simply connected quasiregularly elliptic 4-manifolds
Localization in the Discrete Non-linear Schrodinger Equation and Geometric Properties of the Microcanonical Surface
Full text linkIt is well known that, if the initial conditions have sufficiently high energy density, the dynamics of the classical Discrete Non-Linear Schrodinger Equation (DNLSE) on a lattice shows a form of breaking of ergodicity, with a finite fraction of the total charge accumulating on a few sites and residing there for times that diverge quickly in the thermodynamic limit. In this paper we show that this kind of localization can be attributed to some geometric properties of the microcanonical potential energy surface, and that it can be associated to a phase transition in the lowest eigenvalue of the Laplacian on said surface. We also show that the approximation of considering the phase space motion on the potential energy surface only, with effective decoupling of the potential and kinetic partition functions, is justified in the large connectivity limit, or fully connected model. In this model we further observe a synchronization transition, with a synchronized phase at low temperatures
Loop grammars to identify RNA structural patterns
No full textThe biological functions of an RNA molecule are largely determined by molecular configuration. Understanding the link between the structure and the biological functions has been considered one of the challenges in biology. In this study, we face the problem of identifying a given structural pattern into an RNA pseudoknotfree secondary structure. We introduce a context-free grammar, Loop Grammar, that formalizes the primary and secondary structure of an RNA molecule as a composition of loops. Such composition is expressed as to concatenation or nesting of the simplest structural elements, hairpins, generated during the folding process when a bond between two nonconsecutive nucleotides is established. Then, we formalize the concatenation and nesting on Fatgraphs, oriented surfaces with boundary, and we define a Surface Loop Grammar, whose algebraic expressions uniquely identify such surfaces associated with given RNA structures. The terms of the Loop Grammar allow us to face the problems of identifying substructures considering both the primary and secondary structures, while the strings generated by Surface Loop Grammar permit to identify a given structural pattern in a secondary structure in terms of relations among hairpins. Both use the string pattern matching
The simplest erasing substitution
Full text linkIn this work, we begin the study of a new class of dynamical systems
determined by interval maps generated by the symbolic action of erasing
substitution rules. We do this by discussing in some detail the geometric,
analytical, dynamical and arithmetic properties of a particular example, which
has the virtue of being arguably the simplest and that at the same time
produces interesting properties and new challenging problems
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
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