Tropical Geometry of Statistical Models

This paper presents a unified mathematical framework for inference in graphical models, building on the observation that graphical models are algebraic varieties. From this geometric viewpoint, observations generated from a model are coordinates of a point in the variety, and the sum-product algorithm is an efficient tool for evaluating specific coordinates. The question addressed here is how the solutions to various inference problems depend on the model parameters. The proposed answer is expressed in terms of tropical algebraic geometry. A key role is played by the Newton polytope of a statistical model. Our results are applied to the hidden Markov model and to the general Markov model on a binary tree.Comment: 14 pages, 3 figures. Major revision. Applications now in companion paper, "Parametric Inference for Biological Sequence Analysis

Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans

Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR) sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM) that originated from the rsp- 2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM moti

Optimal stopping of oscillating Brownian motion

We solve optimal stopping problems for an oscillating Brownian motion, i.e. a diffusion with positive piecewise constant volatility changing at the point x=0. Let σ1 and σ 2 denote the volatilities on the negative and positive half-lines, respectively. Our main result is that continuation region of the optimal stopping problem with reward ((1+x)+)2 can be disconnected for some values of the discount rate when 2 σ 21 <σ22. Based on the fact that the skew Brownian motion in natural scale is an oscillating Brownian motion, the obtained results are translated into corresponding results for the skew Brownian motion

Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms

BACKGROUND: While the premise that lateral gene transfer (LGT) is a dominant evolutionary force is still in considerable dispute, the case for widespread LGT in the family of aminoacyl-tRNA synthetases (aaRS) is no longer contentious. aaRSs are ancient enzymes, guarding the fidelity of the genetic code. They are clustered in two structurally unrelated classes. Only lysine aminoacyl-tRNA synthetase (LysRS) is found both as a class 1 and a class 2 enzyme (LysRS1-2). Remarkably, in several extant prokaryotes both classes of the enzyme coexist, a unique phenomenon that has yet to receive its due attention. RESULTS: We applied a phylogenetic approach for determining the extent and origin of LGT in prokaryotic LysRS. Reconstructing species trees for Archaea and Bacteria, and inferring that their last common ancestors encoded LysRS1 and LysRS2, respectively, we studied the gains and losses of both classes. A complex pattern of LGT events emerged. In specific groups of organisms LysRS1 was replaced by LysRS2 (and vice versa). In one occasion, within the alpha proteobacteria, a LysRS2 to LysRS1 LGT was followed by reversal to LysRS2. After establishing the most likely LGT paths, we studied the possible origins of the laterally transferred genes. To this end, we reconstructed LysRS gene trees and evaluated the likely origins of the laterally transferred genes. While the sources of LysRS1 LGTs were readily identified, those for LysRS2 remain, for now, uncertain. The replacement of one LysRS by another apparently transits through a stage simultaneously coding for both synthetases, probably conferring a selective advantage to the affected organisms. CONCLUSION: The family of LysRSs features complex LGT events. The currently available data were sufficient for identifying unambiguously the origins of LysRS1 but not of LysRS2 gene transfers. A selective advantage is suggested to organisms encoding simultaneously LysRS1-2

Social support and self care in diabetes type 2

Se realizó un estudio descriptivo y transversal con el objetivo de identificar la relación entre el ámbito laboral y familiar con las prácticas de autoatención y autocuidado de pacientes con diagnóstico de diabetes tipo 2, que concurren a los consultorios externos de diabetología de hospitales públicos dependientes del Gobierno de la Ciudad de Buenos Aires. Se tomó una muestra probabilística al azar sistemático de 337 pacientes entre 40 y 79 años que fueron encuestados con los siguientes instrumentos: cuestionario de datos personales y laborales, escala de frecuencias sobre prácticas de autoatención y autocuidado, ambos construidos ad hoc y validados previamente. Los datos fueron analizados estadísticamente con análisis descriptivos y pruebas bivariadas, según el nivel de medición de las variables. Los hallazgos del presente estudio evidencian que el apoyo social favorece una mayor adherencia a los tratamientos a través del cumplimiento de pautas de autocuidado.A descriptive and transversal study was made with the aim of identifying the relationship between the working and the family environment with the self attention and self care of patients with diabetes type 2 who are treated in Public Hospitals of Buenos Aires. A systematic sample of 337 people was randomly chosen. These people, aged since 40 to79 years old, had to answer the following: a questionnaire about personal and working issues, a frequency scale about self care and self attentions' practices, all of them built ad hoc and previously val idated. Data was analyzed statistically with descriptive and bivariated tests. According to the breakthroughs, social support helps the compliance to treatments through the fulillment of the self care prescriptions.Fil: Azzollini, Susana Celeste. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Psicología; ArgentinaFil: Bail Pupko, Vera. No especifica;Fil: Vidal, Victoria Alejandra. No especifica

Epitopia: a web-server for predicting B-cell epitopes

<p>Abstract</p> <p>Background</p> <p>Detecting candidate B-cell epitopes in a protein is a basic and fundamental step in many immunological applications. Due to the impracticality of experimental approaches to systematically scan the entire protein, a computational tool that predicts the most probable epitope regions is desirable.</p> <p>Results</p> <p>The Epitopia server is a web-based tool that aims to predict immunogenic regions in either a protein three-dimensional structure or a linear sequence. Epitopia implements a machine-learning algorithm that was trained to discern antigenic features within a given protein. The Epitopia algorithm has been compared to other available epitope prediction tools and was found to have higher predictive power. A special emphasis was put on the development of a user-friendly graphical interface for displaying the results.</p> <p>Conclusion</p> <p>Epitopia is a user-friendly web-server that predicts immunogenic regions for both a protein structure and a protein sequence. Its accuracy and functionality make it a highly useful tool. Epitopia is available at <url>http://epitopia.tau.ac.il</url> and includes extensive explanations and example predictions.</p

The Alternative Choice of Constitutive Exons throughout Evolution

Alternative cassette exons are known to originate from two processes exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced exons become alternative cassette exons during evolution. We compiled a dataset of orthologous exons from human and mouse that are constitutively spliced in one species but alternatively spliced in the other. Examination of these exons suggests that the common ancestors were constitutively spliced. We show that relaxation of the 59 splice site during evolution is one of the molecular mechanisms by which exons shift from constitutive to alternative splicing. This shift is associated with the fixation of exonic splicing regulatory sequences (ESRs) that are essential for exon definition and control the inclusion level only after the transition to alternative splicing. The effect of each ESR on splicing and the combinatorial effects between two ESRs are conserved from fish to human. Our results uncover an evolutionary pathway that increases transcriptome diversity by shifting exons from constitutive to alternative splicin

Applications of Psychological First Aid in Disaster and Emergency Situations: Its Relationship with Decision-Making

Many people in the world are highly vulnerable to being affected by events of great vitalimpact. A disaster, which is known as an unexpected and brutal event, causes great socialdisorganization and significant psychological disorders. The protocol on PsychologicalFirst Aid (PFA) establishes certain actions to take on victims who are in the area of theevent. Through these actions, the victims are assisted in a non-invasive protocol and theyare helped to feel calm but not passive. The study of the processes of decision-making is atopic of great interest for the advancement of Cognitive Psychology and Neuroscience.Regarding the implementation of PFA in disaster situations, the type of decision-making,analytic or intuitive, could represent an important factor for the effectiveness of theactions of aid provided by volunteers. Thus, the evaluation and decision-making trainingwould be taken as a key factor. In this sense, intuitive or emotional decisions are moreeffective than analytical ones according to cultural experts who have studied similarsituations. This paper presents results and conclusions regarding the associations betweenthe implementation of PFA and the types of decisions made by the volunteers in asimulated disaster. To do so, the use of software, which stages a transport accident,provides the necessary instructions to the users through a set of four videos to be chosen.Fil: Azzollini, Susana Celeste. Universidad de Buenos Aires. Facultad de Psicología. Instituto de Investigaciones; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Depaula, Pablo Domingo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Psicología. Instituto de Investigaciones; ArgentinaFil: Cosentino, Alejandro César. Universidad de Buenos Aires. Facultad de Psicología; ArgentinaFil: Bail Pupko, Vera. Universidad de Buenos Aires. Facultad de Psicología. Instituto de Investigaciones; Argentin