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Bio Systems

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https://www.readbyqxmd.com/read/28062323/biosystem-models-generated-from-a-complex-rule-reaction-influence-network-and-from-two-functionality-prototypes
#1
M Varga, A Prokop, B Csukas
In this work we have further developed the Direct Computer Mapping (DCM) based modelling and simulation methodology. A unified, transition-based representation of complex rule, reaction and influence networks has been introduced and two prototypes (one general state- and another general transition-prototype) have been developed for the unified functional modelling of the state and transition nodes. Starting from the network and from the functional prototypes, an automatic generation method of the graphically editable and extensible GraphML description of biosystem models has been elaborated...
January 3, 2017: Bio Systems
https://www.readbyqxmd.com/read/28041845/inverse-bayesian-inference-as-a-key-of-consciousness-featuring-a-macroscopic-quantum-logical-structure
#2
Yukio-Pegio Gunji, Shuji Shinohara, Taichi Haruna, Vasileios Basios
To overcome the dualism between mind and matter and to implement consciousness in science, a physical entity has to be embedded with a measurement process. Although quantum mechanics has been regarded as a candidate for implementing consciousness, nature at its macroscopic level is inconsistent with quantum mechanics. We propose a measurement-oriented inference system comprising Bayesian and inverse Bayesian inferences. While Bayesian inference contracts probability space, the newly defined inverse one relaxes the space...
December 29, 2016: Bio Systems
https://www.readbyqxmd.com/read/28034644/effects-of-size-refuge-specificity-on-a-predator-prey-model
#3
Hong Zhang, Feng Tian, Prince Harvim, Paul Georgescu
Predation is a major cause of early-stage mortality for prey individuals, which are often forced to use refuges in order to reduce the risk of being consumed. The ability of certain genotypes in a prey population to reach a size refuge from predation may contribute significantly to the preservation of community diversity. We investigate how the specificity of this behavior affects the evolution of a given population by using a modified Lotka-Volterra model, in which the proportion of each genotype available for predation consists of two components: an intrinsic part and a combination from all genotypes present in the population...
December 26, 2016: Bio Systems
https://www.readbyqxmd.com/read/28027958/chasing-the-tail-the-emergence-of-autocatalytic-networks
#4
REVIEW
Wim Hordijk, Mike Steel
A ubiquitous feature of all living systems is their ability to sustain a biochemistry in which all reactions are coordinated by catalysts, and all reactants (along with the catalysts) are either produced by the system itself or are available from the environment. This led to the hypothesis that 'autocatalytic networks' play a key role in both the origin and the organization of life, which was first proposed in the early 1970s, and has been enriched in recent years by a combination of experimental studies and the application of mathematical and computational techniques...
December 25, 2016: Bio Systems
https://www.readbyqxmd.com/read/27939914/corrigendum-to-dynamics-of-an-sir-model-with-vaccination-dependent-on-past-prevalence-with-high-order-distributed-delay-biosystems-129-2015-50-65
#5
John C Eckalbar, Walter L Eckalbar
No abstract text is available yet for this article.
December 7, 2016: Bio Systems
https://www.readbyqxmd.com/read/27914944/an-efficient-finite-difference-strategy-for-sensitivity-analysis-of-stochastic-models-of-biochemical-systems
#6
Monjur Morshed, Brian Ingalls, Silvana Ilie
Sensitivity analysis characterizes the dependence of a model's behaviour on system parameters. It is a critical tool in the formulation, characterization, and verification of models of biochemical reaction networks, for which confident estimates of parameter values are often lacking. In this paper, we propose a novel method for sensitivity analysis of discrete stochastic models of biochemical reaction systems whose dynamics occur over a range of timescales. This method combines finite-difference approximations and adaptive tau-leaping strategies to efficiently estimate parametric sensitivities for stiff stochastic biochemical kinetics models, with negligible loss in accuracy compared with previously published approaches...
November 30, 2016: Bio Systems
https://www.readbyqxmd.com/read/27902924/simple-mechanisms-of-early-life-simulation-model-on-the-origin-of-semi-cells
#7
Adrian Klein, Martin Bock, Wolfgang Alt
The development of first cellular structures played an important role in the early evolution of life. Early evolution of life probably took place on a molecular level in a reactive environment. The iron-sulfur theory postulates the formation of cell-like structures on catalytic surfaces. Experiments show that H2S together with FeS and other metallic centers drive auto-catalytic surface reactions, in which organic molecules such as pyruvic and amino acids occur. It is questionable which mechanisms are needed to form cell-like structures under these conditions...
November 27, 2016: Bio Systems
https://www.readbyqxmd.com/read/27894970/genome-wide-characterization-of-the-sidof-gene-family-in-foxtail-millet-setaria-italica
#8
Li Zhang, Baoling Liu, Gewen Zheng, Aiying Zhang, Runzhi Li
Dof (DNA binding with one finger) proteins, which constitute a class of transcription factors found exclusively in plants, are involved in numerous physiological and biochemical reactions affecting growth and development. A genome-wide analysis of SiDof genes was performed in this study. Thirty five SiDof genes were identified and those genes were unevenly distributed across nine chromosomes in the Seteria italica genome. Protein lengths, molecular weights, and theoretical isoelectric points of SiDofs all vary greatly...
November 25, 2016: Bio Systems
https://www.readbyqxmd.com/read/27887904/a-new-integrated-symmetrical-table-for-genetic-codes
#9
Jian-Jun Shu
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact, because the conventional wisdom avoids the question, there is little agreement as to whether the symmetrical nature actually even exists. A better understanding of symmetry and an appreciation for its essential role in the genetic code formation can improve our understanding of nature's coding processes...
November 23, 2016: Bio Systems
https://www.readbyqxmd.com/read/27884620/effect-of-dispersal-in-two-patch-prey-predator-system-with-positive-density-dependence-growth-of-preys
#10
Sourav Kumar Sasmal, Dibakar Ghosh
Prey-predator systems in patchy environment, connected through dispersal between patches is a very common phenomenon observed in nature, which have a significant impact in ecology, species persistence and extinction, etc. In the present paper, we consider a two patch prey-predator system where the patches are connected through dispersal between preys populations only. We consider positive density dependence growth for preys population. In addition, we consider the time scale difference (different life span) between preys and predator populations...
November 21, 2016: Bio Systems
https://www.readbyqxmd.com/read/27863978/predicting-the-physiological-response-of-tivela-stultorum-hearts-with-digoxin-from-cardiac-parameters-using-artificial-neural-networks
#11
Dora-Luz Flores, Claudia Gómez, David Cervantes, Alberto Abaroa, Carlos Castro, Rubén A Castañeda-Martínez
Multi-layer perceptron artificial neural networks (MLP-ANNs) were used to predict the concentration of digoxin needed to obtain a cardio-activity of specific biophysical parameters in Tivela stultorum hearts. The inputs of the neural networks were the minimum and maximum values of heart contraction force, the time of ventricular filling, the volume used for dilution, heart rate and weight, volume, length and width of the heart, while the output was the digoxin concentration in dilution necessary to obtain a desired physiological response...
November 15, 2016: Bio Systems
https://www.readbyqxmd.com/read/27984171/stochastic-analysis-of-chemical-reaction-networks-using-linear-noise-approximation
#12
Luca Cardelli, Marta Kwiatkowska, Luca Laurenti
Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analysed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some molecules occur in low numbers. Unfortunately, both approaches become infeasible if the system is complex and/or it cannot be ensured that initial populations are small. We develop a probabilistic logic for CRNs that enables stochastic analysis of the evolution of populations of molecular species...
October 28, 2016: Bio Systems
https://www.readbyqxmd.com/read/27784624/multiple-sequence-alignment-using-multi-objective-based-bacterial-foraging-optimization-algorithm
#13
R Ranjani Rani, D Ramyachitra
Multiple sequence alignment (MSA) is a widespread approach in computational biology and bioinformatics. MSA deals with how the sequences of nucleotides and amino acids are sequenced with possible alignment and minimum number of gaps between them, which directs to the functional, evolutionary and structural relationships among the sequences. Still the computation of MSA is a challenging task to provide an efficient accuracy and statistically significant results of alignments. In this work, the Bacterial Foraging Optimization Algorithm was employed to align the biological sequences which resulted in a non-dominated optimal solution...
December 2016: Bio Systems
https://www.readbyqxmd.com/read/27771386/kinetic-aspects-of-enzyme-mediated-repair-of-dna-single-strand-breaks
#14
Vladimir P Zhdanov
In cells and bacteria, DNA can be damaged in different ways. The efficient damage repair, mediated by various enzymes, is crucial for their survival. Most frequently, the damage is reduced to single-strand breaks. In human cells, according to the experiments, the repair of such breaks can mechanistically be divided into four steps including (i) the break detection, (ii) processing of damaged ends, (iii) gap filling, and (iv) ligation of unbound ends of the broken strand. The first and second steps run in parallel while the third and fourth steps are sequential...
December 2016: Bio Systems
https://www.readbyqxmd.com/read/27769749/genetic-algorithm-to-estimate-the-input-parameters-of-klatt-and-hlsyn-formant-based-speech-synthesizers
#15
Fabíola Araújo, José Filho, Aldebaro Klautau
Voice imitation basically consists in estimating a synthesizer's input parameters to mimic a target speech signal. This is a difficult inverse problem because the mapping is time-varying, non-linear and from many to one. It typically requires considerable amount of time to be done manually. This work presents the evolution of a system based on a genetic algorithm (GA) to automatically estimate the input parameters of the Klatt and HLSyn formant synthesizers using an analysis-by-synthesis process. Results are presented for natural (human-generated) speech for three male speakers...
December 2016: Bio Systems
https://www.readbyqxmd.com/read/27765600/fixed-points-in-random-boolean-networks-the-impact-of-parallelism-in-the-barab%C3%A3-si-albert-scale-free-topology-case
#16
P Moisset de Espanés, A Osses, I Rapaport
Fixed points are fundamental states in any dynamical system. In the case of gene regulatory networks (GRNs) they correspond to stable genes profiles associated to the various cell types. We use Kauffman's approach to model GRNs with random Boolean networks (RBNs). In this paper we explore how the topology affects the distribution of the number of fixed points in randomly generated networks. We also study the size of the basins of attraction of these fixed points if we assume the α-asynchronous dynamics (where every node is updated independently with probability 0≤α≤1)...
December 2016: Bio Systems
https://www.readbyqxmd.com/read/27725265/a-modified-estimation-distribution-algorithm-based-on-extreme-elitism
#17
Shujun Gao, Clarence W de Silva
An existing estimation distribution algorithm (EDA) with univariate marginal Gaussian model was improved by designing and incorporating an extreme elitism selection method. This selection method highlighted the effect of a few top best solutions in the evolution and advanced EDA to form a primary evolution direction and obtain a fast convergence rate. Simultaneously, this selection can also keep the population diversity to make EDA avoid premature convergence. Then the modified EDA was tested by means of benchmark low-dimensional and high-dimensional optimization problems to illustrate the gains in using this extreme elitism selection...
December 2016: Bio Systems
https://www.readbyqxmd.com/read/27693626/a-general-resolution-of-intractable-problems-in-polynomial-time-through-dna-computing
#18
C A A Sanches, N Y Soma
Based on a set of known biological operations, a general resolution of intractable problems in polynomial time through DNA Computing is presented. This scheme has been applied to solve two NP-Hard problems (Minimization of Open Stacks Problem and Matrix Bandwidth Minimization Problem) and three co-NP-Complete problems (associated with Hamiltonian Path, Traveling Salesman and Hamiltonian Circuit), which have not been solved with this model. Conclusions and open questions concerning the computational capacity of this model are presented, and research topics are suggested...
December 2016: Bio Systems
https://www.readbyqxmd.com/read/27693625/a-neural-mechanism-of-dynamic-gating-of-task-relevant-information-by-top-down-influence-in-primary-visual-cortex
#19
Akikazu Kamiyama, Kazuhisa Fujita, Yoshiki Kashimori
Visual recognition involves bidirectional information flow, which consists of bottom-up information coding from retina and top-down information coding from higher visual areas. Recent studies have demonstrated the involvement of early visual areas such as primary visual area (V1) in recognition and memory formation. V1 neurons are not passive transformers of sensory inputs but work as adaptive processor, changing their function according to behavioral context. Top-down signals affect tuning property of V1 neurons and contribute to the gating of sensory information relevant to behavior...
December 2016: Bio Systems
https://www.readbyqxmd.com/read/27666636/spike-timing-dependent-plasticity-enhanced-synchronization-transitions-induced-by-autapses-in-adaptive-newman-watts-neuronal-networks
#20
Yubing Gong, Baoying Wang, Huijuan Xie
In this paper, we numerically study the effect of spike-timing-dependent plasticity (STDP) on synchronization transitions induced by autaptic activity in adaptive Newman-Watts Hodgkin-Huxley neuron networks. It is found that synchronization transitions induced by autaptic delay vary with the adjusting rate Ap of STDP and become strongest at a certain Ap value, and the Ap value increases when network randomness or network size increases. It is also found that the synchronization transitions induced by autaptic delay become strongest at a certain network randomness and network size, and the values increase and related synchronization transitions are enhanced when Ap increases...
December 2016: Bio Systems
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