Search results for "Theory"
showing 10 items of 24627 documents
Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data
2016
Next-generation sequencing technologies have led to the sequencing of more and more genomes, propelling related research into the era of big data. In this paper, we present ParaBWT, a parallelized Burrows-Wheeler transform (BWT) and suffix array construction algorithm for big genome data. In ParaBWT, we have investigated a progressive construction approach to constructing the BWT of single genome sequences in linear space complexity, but with a small constant factor. This approach has been further parallelized using multi-threading based on a master-slave coprocessing model. After gaining the BWT, the suffix array is constructed in a memory-efficient manner. The performance of ParaBWT has b…
A detailed experimental study of a DNA computer with two endonucleases
2017
Abstract Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro’s group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity – increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effe…
Biomolecular computers with multiple restriction enzymes
2017
Abstract The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and the von Neumann “bottleneck”. Biomolecular computers based on DNA and proteins are largely free of these disadvantages and, along with quantum computers, are reasonable alternatives to their conventional counterparts in some applications. The idea of a DNA computer proposed by Ehud Shapiro’s group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software and input/output signals. This computer represented a two-state two-symbol finite automaton t…
Minors and Transexuality
2020
[ES] En el ámbito de la transexualidad los poderes públicos han ejercido desde un principio una política claramente restrictiva que ha requerido de años para poder abrirse a las nuevas necesidades y a la sociedad actual. Así, la normativa en la materia era totalmente excluyente de los menores de edad, considerándolos carentes de aptitud alguna para poder decidir sobre su identidad sexual y todo lo que ello conllevaba, quizá porque como afirman algunos autores “la finalidad básica de esa prohibición es la de garantizar que la decisión de la rectificación registral sea una decisión firme y coherente, evitando así cambios arbitrarios o no fundados en el sexo” (Vázquez-Pastor, 2010).Esta idea p…
Stability of stationary solutions in models of the Calvin cycle
2017
Abstract In this paper results are obtained concerning the number of positive stationary solutions in simple models of the Calvin cycle of photosynthesis and the stability of these solutions. It is proved that there are open sets of parameters in the model of Zhu et al. (2009) for which there exist two positive stationary solutions. There are never more than two isolated positive stationary solutions but under certain explicit special conditions on the parameters there is a whole continuum of positive stationary solutions. It is also shown that in the set of parameter values for which two isolated positive stationary solutions exist there is an open subset where one of the solutions is asym…
A study on time discretization and adaptive mesh refinement methods for the simulation of cancer invasion: The urokinase model
2016
In the present work we investigate a model that describes the chemotactically and proteolytically driven tissue invasion by cancer cells. The model is a system of advection-reaction-diffusion equations that takes into account the role of the serine protease urokinase-type plasminogen activator. The analytical and numerical study of such a system constitutes a challenge due to the merging, emerging, and traveling concentrations that the solutions exhibit. Classical numerical methods applied to this system necessitate very fine discretization grids to resolve these dynamics in an accurate way. To reduce the computational cost without sacrificing the accuracy of the solution, we apply adaptive…
Negative transfer effects between reference memory and working memory training in the water maze in C57BL/6 mice
2017
The water maze is one of the most widely employed spatial learning paradigms in the cognitive profiling of genetically modified mice. Oftentimes, tests of reference memory (RM) and working memory (WM) in the water maze are sequentially evaluated in the same animals. However, critical difference in the rules governing efficient escape from the water between WM and RM tests is expected to promote the adoption of incompatible mnemonic or navigational strategies. Hence, performance in a given test is likely poorer if it follows the other test instead of being conducted first. Yet, the presence of such negative transfer effects (or proactive interference) between WM and RM training in the water …
Hypothesis: Etiologic and Molecular Mechanistic Leads for Sporadic Neurodegenerative Diseases Based on Experience With Western Pacific ALS/PDC
2019
Seventy years of research on Western Pacific amyotrophic lateral sclerosis and Parkinsonism-dementia Complex (ALS/PDC) have provided invaluable data on the etiology, molecular pathogenesis and latency of this disappearing, largely environmental neurodegenerative disease. ALS/PDC is linked to genotoxic chemicals (notably methylazoxymethanol, MAM) derived from seed of the cycad plant (Cycas spp.) that were used as a traditional food and/or medicine in all three disease-affected Western Pacific populations. MAM, nitrosamines and hydrazines generate methyl free radicals that damage DNA (in the form of O6-methylguanine lesions) that can induce mutations in cycling cells and degenerative changes …
An Integrative Framework for the Construction of Big Functional Networks
2018
We present a methodology for biological data integration, aiming at building and analysing large functional networks which model complex genotype-phenotype associations. A functional network is a graph where nodes represent cellular components (e.g., genes, proteins, mRNA, etc.) and edges represent associations among such molecules. Different types of components may cohesist in the same network, and associations may be related to physical[biochemical interactions or functional/phenotipic relationships. Due to both the large amount of involved information and the computational complexity typical of the problems in this domain, the proposed framework is based on big data technologies (Spark a…
A Basic Architecture of an Autonomous Adaptive System With Conscious-Like Function for a Humanoid Robot.
2018
In developing a humanoid robot, there are two major objectives. One is developing a physical robot having body, hands, and feet resembling those of human beings and being able to similarly control them. The other is to develop a control system that works similarly to our brain, to feel, think, act, and learn like ours. In this article, an architecture of a control system with a brain-oriented logical structure for the second objective is proposed. The proposed system autonomously adapts to the environment and implements a clearly defined “consciousness” function, through which both habitual behavior and goal-directed behavior are realized. Consciousness is regarded as a function for effecti…