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Bio Systems

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...
October 19, 2016: Bio Systems
Joachim Niehren, Cristian Versari, Mathias John, François Coutte, Philippe Jacques
We wish to predict changes of reaction networks with partial kinetic information that lead to target changes of their steady states. The changes may be either increases or decreases of influxes, reaction knockouts, or multiple changes of these two kinds. Our prime applications are knockout prediction tasks for metabolic and regulation networks. In a first step, we propose a formal modeling language for reaction networks with partial kinetic information. The modeling language has a graphical syntax reminiscent to Petri nets...
October 18, 2016: Bio Systems
Fabíola Araújo, José Filho, Aldebaro Klautau
Voice imitation basically consists in estimating a synthesizer 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 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...
October 18, 2016: Bio Systems
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)...
October 17, 2016: Bio Systems
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...
October 8, 2016: Bio Systems
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...
September 28, 2016: Bio Systems
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...
September 28, 2016: Bio Systems
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...
September 22, 2016: Bio Systems
Alexander Andreychenko, Morgan Magnin, Katsumi Inoue
Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper we show how parametric time model checking can be applied to define the time behavior of biological oscillatory systems more precisely. In particular, we focus on the resilience properties of such systems. This notion was introduced to understand the behavior of biological systems (e.g. the mammalian circadian rhythm) that are reactive and adaptive enough to endorse major changes in their environment (e...
September 13, 2016: Bio Systems
Samiha Marwan, Ahmed Shawish, Khaled Nagaty
Information security can be achieved using cryptography, steganography or a combination of them, where data is firstly encrypted using any of the available cryptography techniques and then hid into any hiding medium. Recently, the famous genomic DNA has been introduced as a hiding medium, known as DNA steganography, due to its notable ability to hide huge data sets with a high level of randomness and hence security. Despite the numerous cryptography techniques, to our knowledge only the vigenere cipher and the DNA-based playfair cipher have been combined with the DNA steganography, which keeps space for investigation of other techniques and coming up with new improvements...
September 12, 2016: Bio Systems
Wassim Abou-Jaoudé, Denis Thieffry, Jérôme Feret
As technological advances allow a better identification of cellular networks, large-scale molecular data are swiftly produced, allowing the construction of large and detailed molecular interaction maps. One approach to unravel the dynamical properties of such complex systems consists in deriving coarse-grained dynamical models from these maps, which would make the salient properties emerge. We present here a method to automatically derive such models, relying on the abstract interpretation framework to formally relate model behaviour at different levels of description...
September 9, 2016: Bio Systems
Shounak Baksi, Sangram Bagh, Sandip Sarkar, Debashis Mukhopadhyay
Aggregation prone Huntingtin (Htt) protein and its aberrations, causing protein misfolding, have been the prototype of intense research for several decades. Misfolded aggregates or oligomers of different sizes not only deregulate the homeostasis, cellular machinery also counterbalances the effects at least at the initial stages, till the balance tilts towards toxicity and degeneration. In this paper, we combine experimental approaches with system based computational modeling to decipher the molecular mechanisms as well as the hidden dynamics leading to neuronal death in HD...
August 30, 2016: Bio Systems
Lu-Qiang Zhang, Qian-Zhong Li, Wen-Xia Su, Wen Jin
The transcription factor (TF) binding signals play important role in the control of gene expression. In this study, to elucidate the relationship between the transcription factor binding signals and gene expression, we firstly analyze the distributions of 57 kinds of TFs' binding signals in human H1 embryonic stem cells. Their distributions in highly and lowly expressed genes are further compared. On this basis, a statistic model of predicting gene expression level is constructed by using 57 kinds of transcription factor synthetic indexes (TFSIs)...
August 23, 2016: Bio Systems
Laura Hindersin, Marius Möller, Arne Traulsen, Benedikt Bauer
The Moran process on graphs is a popular model to study the dynamics of evolution in a spatially structured population. Exact analytical solutions for the fixation probability and time of a new mutant have been found for only a few classes of graphs so far. Simulations are time-expensive and many realizations are necessary, as the variance of the fixation times is high. We present an algorithm that numerically computes these quantities for arbitrary small graphs by an approach based on the transition matrix...
August 20, 2016: Bio Systems
Paweł Błażej, Małgorzata Wnȩtrzak, Paweł Mackiewicz
One of theories explaining the present structure of canonical genetic code assumes that it was optimized to minimize harmful effects of amino acid replacements resulting from nucleotide substitutions and translational errors. A way to testify this concept is to find the optimal code under given criteria and compare it with the canonical genetic code. Unfortunately, the huge number of possible alternatives makes it impossible to find the optimal code using exhaustive methods in sensible time. Therefore, heuristic methods should be applied to search the space of possible solutions...
August 20, 2016: Bio Systems
Célia Biane, Franck Delaplace, Hanna Klaudel
Recent advances in omics technologies provide the leverage for the emergence of precision medicine that aims at personalizing therapy to patient. In this undertaking, computational methods play a central role for assisting physicians in their clinical decision-making by combining data analysis and systems biology modelling. Complex diseases such as cancer or diabetes arise from the intricate interplay of various biological molecules. Therefore, assessing drug efficiency requires to study the effects of elementary perturbations caused by diseases on relevant biological networks...
August 16, 2016: Bio Systems
Tom Ziemke
Embodied cognition is a hot topic in both cognitive science and AI, despite the fact that there still is relatively little consensus regarding what exactly constitutes 'embodiment'. While most embodied AI and cognitive robotics research views the body as the physical/sensorimotor interface that allows to ground computational cognitive processes in sensorimotor interactions with the environment, more biologically-based notions of embodied cognition emphasize the fundamental role that the living body - and more specifically its homeostatic/allostatic self-regulation - plays in grounding both sensorimotor interactions and embodied cognitive processes...
August 16, 2016: Bio Systems
Carlos Baladrón, Andrei Khrennikov
The similarities between biological and physical systems as respectively defined in quantum information biology (QIB) and in a Darwinian approach to quantum mechanics (DAQM) have been analysed. In both theories the processing of information is a central feature characterising the systems. The analysis highlights a mutual support on the thesis contended by each theory. On the one hand, DAQM provides a physical basis that might explain the key role played by quantum information at the macroscopic level for bio-systems in QIB...
August 13, 2016: Bio Systems
Min Li, Yu Tang, Xuehong Wu, Jianxin Wang, Fang-Xiang Wu, Yi Pan
With the progress of studies and researches on the biological networks, plenty of excellent clustering algorithms have been proposed. Nevertheless, not only different algorithms but also the same algorithms with different characteristics result in different performances on the same biological networks. Therefore, it might be difficult for researchers to choose an appropriate clustering algorithm to use for a specific network. Here we present C-DEVA, a comprehensive platform for Detecting clusters from biological networks and its Evaluation, Visualization and Annotation analysis...
August 13, 2016: Bio Systems
Dino G Salinas, Mauricio O Gallardo, Manuel I Osorio
The polar requirement is an attribute of amino acids that is a major determinant of the structure and function of the proteins, and it plays a role in the flexibility and robustness of the genetic code. The viability of an organism depends on flexibility, which allows the exploration of new functions. However, robustness is necessary to protect the organism from deleterious changes derived from misreading errors and single-point mutations. Compared with random codes, the standard genetic code is one of the most robust against such errors...
August 12, 2016: Bio Systems
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