This paper presents a general theoretical framework for generating Boolean networks whose state transitions realize set of given biological pathways or minor variations thereof. ill-posed inverse problem, which is crucial importance across practically all areas biology, solved by using Karnaugh maps are classical tools digital system design. It shown that the incorporation prior knowledge, presented in form pathways, can bring about dramatic reduction cardinality network search space....

Abstract Background Oxidative stress is a consequence of normal and abnormal cellular metabolism linked to the development human diseases. The effective functioning pathway responding oxidative protects DNA against damage; conversely failure response mechanism can induce aberrant behavior leading diseases such as neurodegenerative disorders cancer. Thus, understanding signaling present in pathways determining possible alterations disease could provide us with useful pointers for therapeutic...

Abstract Motivation: Cancer encompasses various diseases associated with loss of cell cycle control, leading to uncontrolled proliferation and/or reduced apoptosis. is usually caused by malfunction(s) in the cellular signaling pathways. Malfunctions occur different ways and at locations a pathway. Consequently, therapy design should first identify location type malfunction arrive suitable drug combination. Results: We consider growth factor (GF) pathways, widely studied context cancer....

SUMMARY This paper presents a possible new direction for the design of adaptive controllers. It begins by outlining measurement‐based approach to analysis, synthesis, and unknown systems. The systems under consideration can typically be electrical, mechanical, hydraulic, continuous, discrete, real, artificial, or biological, societal origin. Our is novel in sense that we propose use measurement, measured data, directly control decision variables whereas current mainstream system theory...

Abstract Motivation: A basic problem of translational systems biology is to utilize gene regulatory networks as a vehicle design therapeutic intervention strategies beneficially alter network and, therefore, cellular dynamics. One strain research has this from the perspective control theory via optimal Markov chain decision processes, mainly in framework probabilistic Boolean (PBNs). Full optimization assumes that accurately modeled extent model inference inaccurate, which can be expected...

The study of diseases such as cancer requires the modeling gene regulations and loss control associated with it. Prior work has shown that genetic alterations in system can be suitably modeled using different fault models (like stuck-at faults) Boolean Network paradigm. By studying dynamics original faulty BN, it is possible to design intervention strategies which could drive from a diseased state less harmful one. In this paper, method detecting faults along demonstrated on couple real...

In this paper, a novel mathematical approach is proposed for the dynamics of progression and suppression cancer. We define mutant cell density, ρ(μ) (μ × ρ), as primary factor in cancer dynamics, use logistic growth model replicator equation defining total density (ρ) fraction (μ), respectively. Furthermore, model, we introduce an analytical expression control parameter D (drug), to suppress proliferation mutants with extra fitness level σ. Lastly, present comparison some existing models...

The emergence and abundance of public goods cooperation in the face selfish "cheaters" is an enduring puzzle realm evolutionary biology. synergistic antagonistic interactions within between cooperators free riders have immense impact on sustenance cooperation, which often maintains biodiversity nature. We, therefore, address problem to formulate theoretically analyze effects social population dynamics a primitive natural population, such as phenotypically variant monospecies pathogenic...

We present a GPU-based implementation of the saliency model proposed by Achanta et al. [1] to perform real-time and detailed map generation. all components algorithm kernels data structures. The parallel version is able accurately simulate desired results in very low time. describe streaming pipeline address many issues terms obtaining high throughput on multi-core GPUs. highlight performance three different generations On high-end NVIDIA Tesla K20m, we observe up 600x order magnitude...

This paper reports a new measurement based approach that can be used to determine the functional dependence of D.C. circuit variable interest on small set design variables. The makes use number measurements and generalizes well known Thévenin's Theorem theory.

Bacterial species are known to show chemotaxis, i.e., the directed motions in presence of certain chemicals, whereas motion is random absence those chemicals. The bacteria modulate their run time induce chemotactic drift towards attractant chemicals and away from repellent However, existing theoretical knowledge does not exhibit a proper match with experimental validation, hence there need for developing alternate models validating experimentally. In this paper more robust model proposed...

This paper presents a general theoretical framework for generating Boolean networks whose state transitions realize set of given biological pathways or minor variations thereof. ill-posed inverse problem, which is crucial importance across practically all areas biology, solved by using Karnaugh maps are classical tools digital system design. It shown that the incorporation prior knowledge, presented in form pathways, can bring about dramatic reduction cardinality network search space....

A new linear approach is proposed to model the dynamics of asynchronous Boolean networks (ABNs). The continuous-time discrete-state definition makes ABN a suitable formulation describe gene regulatory networks. semi-tensor product matrices used as algebraic tool for formulation. results on are elaborated with synthetic and biological examples.

This paper reports a new measurement based approach that can be used to determine the functional dependence of circuit variable interest on few design variables. The makes use small number measurements and generalizes well known Thévenin's Theorem theory. Results for both D.C. A.C. circuits are presented.

Diagnostics and therapeutic interventions in complex systemic diseases like cancer can be mapped to fault identification control problem. A complete linear framework has been developed this manuscript comprehend different classes of faults controllability the output for a class homeostatic inputs Boolean network framework. The problems undertaken are non-trivial. Interesting results have derived linearised model proliferating cellular system.

The generalized asynchronous Boolean network model proposed in this paper can reliably mimic the temporal behavior of Ordinary Differential Equation without compromising flexibility model.

The problem of inferring a stochastic model for gene regulatory networks is addressed here. prior biological data includes pathways and time-series expression data. We propose novel algorithm to use both these construct Probabilistic Boolean Network (PBN) which models the observed dynamics genes with high degree precision. Our constructs pathway tree uses select an optimal level tree, whose nodes are used infer PBN.

In this paper, a shape recognition method is proposed for few common geometrical shapes including straight line, circle, ellipse, triangle, quadrilateral, pentagon and hexagon. the present work, two indices namely Unique Shape Signature (USS) Condensibility (C) are employed of an object. Using USS index, all above mentioned non-circular neatly recognized, whereas, C index recognized circular objects. An added advantage that it can further differentiate triangles, quadrilaterals both...

The existence of phenotypic heterogeneity in single-species bacterial biofilms is well-established the published literature. However, modeling population dynamics from viewpoint social interactions, i.e. interplay between heterotypic strains, and analysis this kind using control theory are not addressed significantly. Therefore, paper, we theoretically analyze model microbial with non-participating strains (coexisting public goods producers non-producers) context evolutionary game nonlinear...

Dynamic biological systems can be modelled to an equivalent modular structure using Boolean networks (BNs) due their simple construction and relative ease of integration. The chemotaxis network the bacterium Escherichia coli (E. ) is one most investigated systems. In this study, authors developed a multi-bit approach model drifting behaviour E. system. Their approach, which slightly different than conventional BNs, designed provide finer resolution mimic high-level functional behaviour....

The problem of $\mathcal{L}_2$ stabilization a state feedback stochastic control loop is investigated under different constraints. discrete time linear invariant (LTI) open plant chosen to be unstable. additive white Gaussian noise assumed stationary. link between the and controller finite capacity stationary channel, which puts constraint on bit rate transmission. Moreover, observed only intermittently keeping some time. In this manuscript both scalar vector plants Bernoulli Markov...

Probabilistic Boolean Networks (PBNs) have been recently introduced as a paradigm for modeling genetic regulatory networks. One of the objectives PBN is to use network design and analysis intervention strategies aimed at moving out undesirable states, such those associated with disease, into desirable ones. To date, number proposed in context PBNs. However, most these techniques assume perfect knowledge transition probability matrix PBN. Such an assumption cannot be satisfied practice, may...

Bacteria such as Escherichia coli (E. coli) exhibit biased motion if kept in a spatially non-uniform chemical environment. Here, we bring out unique time-dependent characteristics of bacterial chemotaxis, response to diffusing spatial step ligand profile. The experimentally obtained temporal the drift velocity are compared with theoretical and Monte-Carlo simulation based estimates, excellent agreements can be obtained. These results new insights on time-responsive facets drift, bearing far...