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Search Results: 1 - 10 of 11772 matches for " Elena;Rivas "
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Evolutionary models for insertions and deletions in a probabilistic modeling framework
Elena Rivas
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-63
Abstract: Probabilistic models of substitution events are well established, but there has not been a completely satisfactory theoretical framework for modeling insertion and deletion events.I have developed a method for extending standard Markov substitution models to include gap characters, and another method for the evolution of state transition probabilities in a probabilistic model. These methods use instantaneous rate matrices in a way that is more general than those used for substitution processes, and are sufficient to provide time-dependent models for standard linear and affine gap penalties, respectively.Given a probabilistic model, we can make all of its emission probabilities (including gap characters) and all its transition probabilities conditional on a chosen divergence time. To do this, we only need to know the parameters of the model at one particular divergence time instance, as well as the parameters of the model at the two extremes of zero and infinite divergence.I have implemented these methods in a new generation of the RNA genefinder QRNA (eQRNA).These methods can be applied to incorporate evolutionary models of insertions and deletions into any hidden Markov model or stochastic context-free grammar, in a pair or profile form, for sequence modeling.Probabilistic models are widely used for sequence analysis [1]. Hidden Markov models (HMMs) are a very large class of probabilistic models used for many problems in biological sequence analysis such as sequence homology searches [2-4], sequence alignment [5], or protein genefinding [6-8]. Stochastic context-free grammars (SCFGs) are another class of probabilistic models used for structural RNAs for problems such as RNA homology searches [9-13], RNA structure prediction [14,15], and RNA genefinding [16].Sequence similarity methods based on HMMs or SCFGs can take the form of profile or pair models and are very important for comparative genomics. These probabilistic methods for sequence comparison assume a certai
Probabilistic Phylogenetic Inference with Insertions and Deletions
Elena Rivas ,Sean R. Eddy
PLOS Computational Biology , 2008, DOI: 10.1371/journal.pcbi.1000172
Abstract: A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth–death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new “concordance test” benchmark on real ribosomal RNA alignments, we show that the extended program dnamlε improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm.
Noncoding RNA gene detection using comparative sequence analysis
Elena Rivas, Sean R Eddy
BMC Bioinformatics , 2001, DOI: 10.1186/1471-2105-2-8
Abstract: We describe a comparative sequence analysis algorithm for detecting novel structural RNA genes. The key idea is to test the pattern of substitutions observed in a pairwise alignment of two homologous sequences. A conserved coding region tends to show a pattern of synonymous substitutions, whereas a conserved structural RNA tends to show a pattern of compensatory mutations consistent with some base-paired secondary structure. We formalize this intuition using three probabilistic "pair-grammars": a pair stochastic context free grammar modeling alignments constrained by structural RNA evolution, a pair hidden Markov model modeling alignments constrained by coding sequence evolution, and a pair hidden Markov model modeling a null hypothesis of position-independent evolution. Given an input pairwise sequence alignment (e.g. from a BLASTN comparison of two related genomes) we classify the alignment into the coding, RNA, or null class according to the posterior probability of each class.We have implemented this approach as a program, QRNA, which we consider to be a prototype structural noncoding RNA genefinder. Tests suggest that this approach detects noncoding RNA genes with a fair degree of reliability.Some genes produce functional noncoding RNAs (ncRNAs) instead of coding for proteins [1,2]. For protein-coding genes, we have computational genefinding tools [3] that predict novel genes in genome sequence data with reasonable efficiency [4]. For ncRNA genes, there are as yet no general genefinding algorithms. The number and diversity of ncRNA genes remains poorly understood, despite the availability of many complete genome sequences. Gene discovery methods (whether experimental or computational) typically assume that the target is a protein coding gene that produces a messenger RNA.New noncoding RNA genes continue to be discovered by less systematic means, which makes it seem likely that a systematic RNA genefinding algorithm would be of use. Recent discoveries have inclu
A dynamic programming algorithm for RNA structure prediction including pseudoknots
Elena Rivas,Sean R. Eddy
Physics , 1998,
Abstract: We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the algorithm is complex, which led us to adopt a useful graphical representation (Feynman diagrams) borrowed from quantum field theory. We present an implementation of the algorithm that generates the optimal minimum energy structure for a single RNA sequence, using standard RNA folding thermodynamic parameters augmented by a few parameters describing the thermodynamic stability of pseudoknots. We demonstrate the properties of the algorithm by using it to predict structures for several small pseudoknotted and non-pseudoknotted RNAs. Although the time and memory demands of the algorithm are steep, we believe this is the first algorithm to be able to fold optimal (minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model.
Absence of Chiral Fermions in the Eichten--Preskill Model
Maarten Golterman,Don Petcher,Elena Rivas
Physics , 1992, DOI: 10.1016/0550-3213(93)90049-U
Abstract: The model proposed by Eichten and Preskill for obtaining theories with chiral fermions from the lattice is shown to undergo spontaneous symmetry breaking. In addition, the fermions appear to be Dirac-like everywhere in the phase diagram with no room for undoubled Weyl fermions. The phase diagram of a closely related Higgs-Yukawa model is similar to that of the Smit--Swift model, which also does not give rise to chiral fermions. These results cast serious doubts on the original scenario for the emergence of chiral fermions.
Guadalupe Mares,Héctor Rocha,Olga Rivas,Elena Rueda
Ense?anza e Investigación en Psicología , 2012,
Abstract: El propósito de este estudio fue identificar si las competencias académicas de los alumnos, la motivación por sus estudios y su condición laboral se correlacionan con su trayectoria universitaria. A 552 estudiantes de la carrera de Psicología se les aplicó un cuestionario y la Prueba de Aptitud para la Ciencia al ingresar a la institución; tres semestres después se obtuvo el promedio universitario, el registro de las asignaturas aprobadas y la deserción observada. Se encontró que las competencias académicas se relacionaron positivamente con el promedio y con la continuidad en los estudios, pero no con la deserción; la motivación por los estudios se relacionó positivamente con las mismas variables y negativamente con la deserción, y la situación laboral se relacionó positivamente con deserción. Se propone un modelo que describe la manera de interacción de los factores que afectan la trayectoria universitaria y la deserción.
Extended Dualization: a method for the Bosonization of Anomalous Fermion Systems in Arbitrary Dimension
José Luis Cortés,Elena Rivas,Luis Velázquez
Physics , 1995, DOI: 10.1103/PhysRevD.53.5952
Abstract: The technique of extended dualization developed in this paper is used to bosonize quantized fermion systems in arbitrary dimension $D$ in the low energy regime. In its original (minimal) form, dualization is restricted to models wherein it is possible to define a dynamical quantized conserved charge. We generalize the usual dualization prescription to include systems with dynamical non--conserved quantum currents. Bosonization based on this extended dualization requires the introduction of an additional rank $0$ (scalar) field together with the usual antisymmetric tensor field of rank $(D-2)$. Our generalized dualization prescription permits one to clearly distinguish the arbitrariness in the bosonization from the arbitrariness in the quantization of the system. We study the bosonization of four--fermion interactions with large mass in arbitrary dimension. First, we observe that dualization permits one to formally bosonize these models by invoking the bosonization of the free massive Dirac fermion and adding some extra model--dependent bosonic terms. Secondly, we explore the potential of extended dualization by considering the particular case of \underbar{chiral} four--fermion interactions. Here minimal dualization is inadequate for calculating the extra bosonic terms. We demonstrate the utility of extended dualization by successfully completing the bosonization of this chiral model. Finally, we consider two examples in two dimensions which illuminate the utility of using extended dualization by showing how quantization ambiguities in a fermionic theory propagate into the bosonized version. An explicit parametrization of the quantization ambiguities of the chiral current in the Chiral Schwinger model is obtained. Similarly, for the sine--Gordon interaction in the massive Thirring model the quantization
Implementation of an in vitro bioassay as an indicator of the bionutrient FitoMas E
Díaz de Villegas,María Elena; Delgado,Grizel; Rivas,Mauricio; Torres,Esmérida; Saura,Maribel;
Ciencia e investigación agraria , 2011, DOI: 10.4067/S0718-16202011000200005
Abstract: seed bioassays are employed to determine the stimulatory effect of various biological products on the seed germination of plants used for the detection and control of toxic environmental contaminants. the objective of the present study was to design an in vitro bioassay to monitor the quality of the final production of fitomas e, a bionutrient derived from the sugar industry and produced by the instituto cubano de investigaciones de los derivados de la ca?a de azúcar by-products (icidca), by determining rates of seed germination and growth of lettuce (lactuca sativa l.) as an indicator plant. a significant effect of controllable factors under study (fitomas e concentration in lots and replicates of petri dishes) was determined by one-way and multifactor anova analysis. in all cases, the highest values of relative germination and growth occurred at a concentration of fitomas e of 0.1 ml l-1, with a marked increase in the growth of hypocotyl (rhg), which decreased at concentrations of 2.5 and 5 ml l-1. these results can be explained by the hormesis phenomenon, which is characterized by stimulation at low doses and inhibition at high doses. for a confidence level of p ≤ 0.05, there were no significant differences between petri dishes with lettuce seeds and lots in all responses tested. the bioassay method implemented in this study was fast, simple and reliable.
Obtención y Caracterización de dos Concentrados Proteicos a partir de Biomasa de Kluyveromyces marxianus var. marxianus cultivada en suero lácteo Desproteinizado
Cori de Mendoza,Marta Elena; Rivas,Nilo; Dorta,Blas; Pacheco de Delahaye,Emperatriz; Bertsch,Antonio;
Revista Científica , 2006,
Abstract: this work was carried out with the purpose of attain a protein concentrate from microbial biomass with low content of nucleic acids. the yeast kluyveromyces marxianus var. marxianus was grown on deproteinized and supplemented whey with nitrogen and vitamins sources at ph 4.5; 32 to 35°c and an aeration rate of 1.22 volumes of air fed for volume of broth per minute (vvm). the average biomass yield obtained was 0.30 g/g lactose, a lactose consumption of 93.21% and a cellular concentration of 4.15 g/l at the end of the fermentation. two protein concentrates were obtained: the first one by alkaline extraction and isoelectric precipitation (c1) and the second one by alkaline extraction, phosphorylation and isoelectric precipitation (c2). chemical analysis of both concentrates shown significant differences (p < 0.05) in the content of ash, fat, crude protein, non protein nitrogen, rna and carbohydrates. there was significant (p < 0.05) the decrease in the rna content from 4.59% (c1) to 2.71% (c2), important fact for the use of this protein concentrates for human consumption. phosphorylation of the protein (c2) produced an increase in the water holding capacity (4.21 to 4.64 g water/g protein), solubility (32.43 to 41.74 g solubilized protein/g total protein) and emulsifying capacity (903.38 to 971.91 g oil/g protein), as well as a decrease in the oil absorption capacity (1.79 to 1.65 g oil/g protein). these characteristics are important when considering the use of such protein concentrates as ingredients in bakery or meat products.
Los dolores abdominales psicógenos de la infancia: una revisión
Otero Rodríguez,Juan; Rodado Martínez,Juan; Sanz Rivas,Elena;
Revista de la Asociación Espa?ola de Neuropsiquiatría , 2001, DOI: 10.4321/S0211-57352001000400002
Abstract: thorough bibliographic review about the functional abdominal pain in childhood. it's described its clinic expression, differential diagnosis, epidemiology and the biopsychosocial and developmental-psychodinamic explanatory models.
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