Search results for "Bayesian [statistical analysis]"
showing 10 items of 299 documents
The substitution rate of HIV-1 subtypes: a genomic approach
2017
Abstract HIV-1M causes most infections in the AIDS pandemic. Its genetic diversity is defined by nine pure subtypes and more than sixty recombinant forms. We have performed a comparative analysis of the evolutionary rate of five pure subtypes (A1, B, C, D, and G) and two circulating recombinant forms (CRF01_AE and CRF02 AG) using data obtained from nearly complete genome coding sequences. Times to the most recent common ancestor (tMRCA) and substitution rates of these HIV genomes, and their genomic partitions, were estimated by Bayesian coalescent analyses. Genomic substitution rate estimates were compared between the HIV-1 datasets analyzed by means of randomization tests. Significant diff…
Toward a direct and scalable identification of reduced models for categorical processes.
2017
The applicability of many computational approaches is dwelling on the identification of reduced models defined on a small set of collective variables (colvars). A methodology for scalable probability-preserving identification of reduced models and colvars directly from the data is derived—not relying on the availability of the full relation matrices at any stage of the resulting algorithm, allowing for a robust quantification of reduced model uncertainty and allowing us to impose a priori available physical information. We show two applications of the methodology: (i) to obtain a reduced dynamical model for a polypeptide dynamics in water and (ii) to identify diagnostic rules from a standar…
The Monoclonal Antitoxin Antibodies (Actoxumab–Bezlotoxumab) Treatment Facilitates Normalization of the Gut Microbiota of Mice with Clostridium diffi…
2016
Antibiotics have significant and long-lasting impacts on the intestinal microbiota and consequently reduce colonization resistance against Clostridium difficile infection (CDI). Standard therapy using antibiotics is associated with a high rate of disease recurrence, highlighting the need for novel treatment strategies that target toxins, the major virulence factors, rather than the organism itself. Human monoclonal antibodies MK-3415A (actoxumab–bezlotoxumab) to C. difficile toxin A and toxin B, as an emerging non-antibiotic approach, significantly reduced the recurrence of CDI in animal models and human clinical trials. Although the main mechanism of protection is through direct neutraliza…
Efficient Online Laplacian Eigenmap Computation for Dimensionality Reduction in Molecular Phylogeny via Optimisation on the Sphere
2019
Reconstructing the phylogeny of large groups of large divergent genomes remains a difficult problem to solve, whatever the methods considered. Methods based on distance matrices are blocked due to the calculation of these matrices that is impossible in practice, when Bayesian inference or maximum likelihood methods presuppose multiple alignment of the genomes, which is itself difficult to achieve if precision is required. In this paper, we propose to calculate new distances for randomly selected couples of species over iterations, and then to map the biological sequences in a space of small dimension based on the partial knowledge of this genome similarity matrix. This mapping is then used …
Distributed channel prediction for multi-agent systems
2017
Los sistemas multiagente (MAS) se comunican a través de una red inalámbrica para coordinar sus acciones e informar sobre el estado de su misión. La conectividad y el rendimiento del sistema pueden mejorarse mediante la predicción de la ganancia del canal. Presentamos un esquema basado en regresión de procesos gaussianos (GPR) distribuidos para predecir el canal inalámbrico en términos de la potencia recibida en el MAS. El esquema combina una máquina de comité bayesiano con un esquema de consenso medio, distribuyendo así no sólo la memoria sino también la carga computacional y de comunicación. A través de simulaciones de Monte Carlo, demostramos el rendimiento del GPR propuesto. RACHEL TEC20…
Particle identification in ALICE: a Bayesian approach
2016
We present a Bayesian approach to particle identification (PID) within the ALICE experiment. The aim is to more effectively combine the particle identification capabilities of its various detectors. After a brief explanation of the adopted methodology and formalism, the performance of the Bayesian PID approach for charged pions, kaons and protons in the central barrel of ALICE is studied. PID is performed via measurements of specific energy loss ($\mathrm{d}E/\mathrm{d}x$) and time-of-flight. PID efficiencies and misidentification probabilities are extracted and compared with Monte Carlo simulations using high-purity samples of identified particles in the decay channels ${\rm K}^0_S \righta…
New insights in Bayesian Survival Analysis in Ecology
2020
La fauna silvestre está asediada. Y ésta no es solo una frase impactante con la que empezar una tesis, tristemente, es una realidad. En el último siglo, muchas especies han disminuido drásticamente, mientras que otras afrontan su extinción debido, principalmente, a los rápidos cambios (y a gran escala) ocurridos tanto en hábitats como en ecosistemas. El cambio climático, las especies invasoras, la caza ilegal y la sobrepesca son sólo algunas de las principales amenazas que afectan a las poblaciones de animales silvestres en la actualidad. Para abordar este problema, se requiere de un compromiso a todos los niveles, desde las comunidades locales hasta los gobiernos, pasando por los expertos,…
Importance of proper conduct of clinical trials
2021
Genetic structure and differentiation from early bronze age in the mediterranean island of sicily: Insights from ancient mitochondrial genomes
2022
Sicily is one of the main islands of the Mediterranean Sea, and it is characterized by a variety of archaeological records, material culture and traditions, reflecting the history of migrations and populations’ interaction since its first colonization, during the Paleolithic. These deep and complex demographic and cultural dynamics should have affected the genomic landscape of Sicily at different levels; however, the relative impact of these migrations on the genomic structure and differentiation within the island remains largely unknown. The available Sicilian modern genetic data gave a picture of the current genetic structure, but the paucity of ancient data did not allow so far to make p…
Facilitating Effect of Natural Frequencies: Size Does Not Matter
2009
The question of whether humans are able to work in a Bayesian way is currently a topic of substantial investigation. An important finding, reported by Gigerenzer and Hoffrage in 1995 is that Bayesian reasoning is facilitated when the information format corresponds to natural frequencies. The present concern was whether the facilitating effect of frequencies persists when natural frequencies relate to samples which are not convenient multiples of 10. 150 undergraduates participated as volunteers (42 men, 108 women; M age = 23 yr.). Analysis showed the effect of natural frequency formats was not dependent on size of reference class. Theoretical and practical implications are discussed.