Local Correction of Boolean Functions
Alon, Noga
2011-01-01
A Boolean function f over n variables is said to be q-locally correctable if, given a black-box access to a function g which is "close" to an isomorphism f_sigma of f, we can compute f_sigma(x) for any x in Z_2^n with good probability using q queries to g. We observe that any k-junta, that is, any function which depends only on k of its input variables, is O(2^k)-locally correctable. Moreover, we show that there are examples where this is essentially best possible, and locally correcting some k-juntas requires a number of queries which is exponential in k. These examples, however, are far from being typical, and indeed we prove that for almost every k-junta, O(k log k) queries suffice.
Structure-Based Local Search Heuristics for Circuit-Level Boolean Satisfiability
Belov, Anton
2011-01-01
This work focuses on improving state-of-the-art in stochastic local search (SLS) for solving Boolean satisfiability (SAT) instances arising from real-world industrial SAT application domains. The recently introduced SLS method CRSat has been shown to noticeably improve on previously suggested SLS techniques in solving such real-world instances by combining justification-based local search with limited Boolean constraint propagation on the non-clausal formula representation form of Boolean circuits. In this work, we study possibilities of further improving the performance of CRSat by exploiting circuit-level structural knowledge for developing new search heuristics for CRSat. To this end, we introduce and experimentally evaluate a variety of search heuristics, many of which are motivated by circuit-level heuristics originally developed in completely different contexts, e.g., for electronic design automation applications. To the best of our knowledge, most of the heuristics are novel in the context of SLS for S...
Measurement As Spontaneous Symmetry Breaking, Non-locality and Non-Boolean Holism
Ghose, Partha
2010-01-01
It is shown that having degenerate ground states over the domain of the wavefunction of a system is a sufficient condition for a quantum system to act as a measuring apparatus for the system. Measurements are then instances of spontaneous symmetry breaking to one of these ground states, induced by environmental perturbations. Together with non-Boolean holism this constitutes an optimal formulation of quantum mechanics that does not imply non-locality.
Adaptive Local Information Transfer in Random Boolean Networks.
Haruna, Taichi
2017-01-01
Living systems such as gene regulatory networks and neuronal networks have been supposed to work close to dynamical criticality, where their information-processing ability is optimal at the whole-system level. We investigate how this global information-processing optimality is related to the local information transfer at each individual-unit level. In particular, we introduce an internal adjustment process of the local information transfer and examine whether the former can emerge from the latter. We propose an adaptive random Boolean network model in which each unit rewires its incoming arcs from other units to balance stability of its information processing based on the measurement of the local information transfer pattern. First, we show numerically that random Boolean networks can self-organize toward near dynamical criticality in our model. Second, the proposed model is analyzed by a mean-field theory. We recognize that the rewiring rule has a bootstrapping feature. The stationary indegree distribution is calculated semi-analytically and is shown to be close to dynamical criticality in a broad range of model parameter values.
Local digital estimators of intrinsic volumes for Boolean models and in the design based setting
Svane, Anne Marie
In order to estimate the specific intrinsic volumes of a planar Boolean model from a binary image, we consider local digital algorithms based on weigted sums of 2×2 configuration counts. For Boolean models with balls as grains, explicit formulas for the bias of such algorithms are derived...... for the bias obtained for Boolean models are applied to existing algorithms in order to compare their accuracy....
Quantum walks outside of boolean domain as a gate for one, two, or three qubits
Cavin, Thomas; Solenov, Dmitry
Quantum computing needs entangling quantum gates to perform computation and error correction. We will discuss a novel way to implement quantum gates, such as CNOT, using quantum walks that are directed through a network of states outside of the boolean domain. In such implementations it is important to investigate walks on networks of different connectivities. Specifically, we will discuss solutions to non-symmetric linear chain networks and demonstrate how solutions to more complex networks that have branching, such as cubes, can be expressed in terms of linear chain solutions. We then show examples of implementing single qubit and two-qubit entangling gates.
Complete Boolean Satisfiability Solving Algorithms Based on Local Search
Wen-Sheng Guo; Guo-Wu Yang; William N.N.Hung; Xiaoyu Song
2013-01-01
Boolean satisfiability (SAT) is a well-known problem in computer science,artificial intelligence,and operations research.This paper focuses on the satisfiability problem of Model RB structure that is similar to graph coloring problems and others.We propose a translation method and three effective complete SAT solving algorithms based on the characterization of Model RB structure.We translate clauses into a graph with exclusive sets and relative sets.In order to reduce search depth,we determine search order using vertex weights and clique in the graph.The results show that our algorithms are much more effective than the best SAT solvers in numerous Model RB benchmarks,especially in those large benchmark instances.
On Validating Boolean Optimizers
Morgado, Antonio
2011-01-01
Boolean optimization finds a wide range of application domains, that motivated a number of different organizations of Boolean optimizers since the mid 90s. Some of the most successful approaches are based on iterative calls to an NP oracle, using either linear search, binary search or the identification of unsatisfiable sub-formulas. The increasing use of Boolean optimizers in practical settings raises the question of confidence in computed results. For example, the issue of confidence is paramount in safety critical settings. One way of increasing the confidence of the results computed by Boolean optimizers is to develop techniques for validating the results. Recent work studied the validation of Boolean optimizers based on branch-and-bound search. This paper complements existing work, and develops methods for validating Boolean optimizers that are based on iterative calls to an NP oracle. This entails implementing solutions for validating both satisfiable and unsatisfiable answers from the NP oracle. The wo...
Dynamical domain wall and localization
Yuta Toyozato
2016-03-01
Full Text Available Based on the previous works (Toyozato et al., 2013 [24]; Higuchi and Nojiri, 2014 [25], we investigate the localization of the fields on the dynamical domain wall, where the four-dimensional FRW universe is realized on the domain wall in the five-dimensional space–time. Especially we show that the chiral spinor can localize on the domain wall, which has not been succeeded in the past works as the seminal work in George et al. (2009 [23].
Boolean complexes and boolean numbers
Tenner, Bridget Eileen
2017-01-01
International audience; The Bruhat order gives a poset structure to any Coxeter group. The ideal of elements in this poset having boolean principal order ideals forms a simplicial poset. This simplicial poset defines the boolean complex for the group. In a Coxeter system of rank n, we show that the boolean complex is homotopy equivalent to a wedge of (n-1)-dimensional spheres. The number of these spheres is the boolean number, which can be computed inductively from the unlabeled Coxeter syste...
Boolean Inner product Spaces and Boolean Matrices
Gudder, Stan; Latremoliere, Frederic
2009-01-01
This article discusses the concept of Boolean spaces endowed with a Boolean valued inner product and their matrices. A natural inner product structure for the space of Boolean n-tuples is introduced. Stochastic boolean vectors and stochastic and unitary Boolean matrices are studied. A dimension theorem for orthonormal bases of a Boolean space is proven. We characterize the invariant stochastic Boolean vectors for a Boolean stochastic matrix and show that they can be used to reduce a unitary m...
闵应骅; 李忠诚; 赵著行
1997-01-01
Boolean algebra successfully describes the logical behavior of a digital circuit, and has been widely used in electronic circuit design and test With the development of high speed VLSIs it is a drawback for Boolean algebra to be unable to describe circuit timing behavior. Therefore a Boolean process is defined as a family of Boolean van ables relevant to the time parameter t. A real-valued sample of a Boolean process is a waveform. Waveform functions can be manipulated formally by using mathematical tools. The distance, difference and limit of a waveform polynomial are defined, and a sufficient and necessary condition of the limit existence is presented. Based on this, the concept of sensitization is redefined precisely to demonstrate the potential and wide application possibility The new definition is very different from the traditional one, and has an impact on determining the sensitizable paths with maximum or minimum length, and false paths, and then designing and testing high performance circuits
Goodstein, R L
2007-01-01
This elementary treatment by a distinguished mathematician employs Boolean algebra as a simple medium for introducing important concepts of modern algebra. Numerous examples appear throughout the text, plus full solutions.
Zhang, Rui; Cavalcante, Hugo L. D. de S.; Gao, Zheng; Gauthier, Daniel J.; Socolar, Joshua E. S.; Adams, Matthew M.; Lathrop, Daniel P.
2009-01-01
We observe deterministic chaos in a simple network of electronic logic gates that are not regulated by a clocking signal. The resulting power spectrum is ultra-wide-band, extending from dc to beyond 2 GHz. The observed behavior is reproduced qualitatively using an autonomously updating Boolean model with signal propagation times that depend on the recent history of the gates and filtering of pulses of short duration, whose presence is confirmed experimentally. Electronic Boolean chaos may fin...
Polynomial threshold functions and Boolean threshold circuits
Hansen, Kristoffer Arnsfelt; Podolskii, Vladimir V.
2013-01-01
We study the complexity of computing Boolean functions on general Boolean domains by polynomial threshold functions (PTFs). A typical example of a general Boolean domain is 12n . We are mainly interested in the length (the number of monomials) of PTFs, with their degree and weight being...... of secondary interest. We show that PTFs on general Boolean domains are tightly connected to depth two threshold circuits. Our main results in regard to this connection are: PTFs of polynomial length and polynomial degree compute exactly the functions computed by THRMAJ circuits. An exponential length lower...
Adjunctions between Boolean spaces and skew Boolean algebras
Kudryavtseva, Ganna
2011-01-01
We apply the representation theory of left-handed skew Boolean algebras by sections of their dual \\'{e}tale spaces, given in \\cite{K}, to construct a series of dual adjunctions between the categories of locally compact Boolean spaces and left-handed skew Boolean algebras by means of extensions of certain enriched $\\Hom$-set functors induced by objects sitting in two categories. The constructed adjunctions are "deformations" of Stone duality obtained by the replacement in the latter of the category of Boolean algebras by the category of left-handed skew Boolean algebras. The constructions provide natural settings for the $\\omega$-functor constructed in \\cite{LS} and its left adjoint functor.
Boolean universes above Boolean models
Wehrung, Friedrich
1993-01-01
We establish several first- or second-order properties of models of first-order theories by considering their elements as atoms of a new universe of set theory, and by extending naturally any structure of Boolean model on the atoms to the whole universe. For example, complete f-rings are ``boundedly algebraically compact" in the language $( + , - , . , \\wedge , \\vee , \\leq )$, and the positive cone of a complete l-group with infinity adjoined is algebraically compact in the language $( + , \\v...
DÍaz, R.; Rivas, M.
2010-01-01
In order to study Boolean algebras in the category of vector spaces we introduce a prop whose algebras in set are Boolean algebras. A probabilistic logical interpretation for linear Boolean algebras is provided. An advantage of defining Boolean algebras in the linear category is that we are able to study its symmetric powers. We give explicit formulae for products in symmetric and cyclic Boolean algebras of various dimensions and formulate symmetric forms of the inclusion-exclusion principle.
Arizmendi, Octavio
2012-01-01
We determine which Boolean stable law is freely infinitely divisible and which is not. Some positive Boolean stable laws and a mixture of them have completely monotonic densities and they are both freely and classically infinitely divisible. Freely infinitely divisible Boolean stable laws and the corresponding free stable laws are non trivial examples whose free divisibility indicators are infinity.
Free Boolean Topological Groups
Ol’ga Sipacheva
2015-11-01
Full Text Available Known and new results on free Boolean topological groups are collected. An account of the properties that these groups share with free or free Abelian topological groups and properties specific to free Boolean groups is given. Special emphasis is placed on the application of set-theoretic methods to the study of Boolean topological groups.
Boolean reasoning the logic of boolean equations
Brown, Frank Markham
2012-01-01
A systematic treatment of Boolean reasoning, this concise, newly revised edition combines the works of early logicians with recent investigations, including previously unpublished research results. Brown begins with an overview of elementary mathematical concepts and outlines the theory of Boolean algebras. Two concluding chapters deal with applications. 1990 edition.
Solomon, Alan D
2012-01-01
REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Boolean Algebra includes set theory, sentential calculus, fundamental ideas of Boolean algebras, lattices, rings and Boolean algebras, the structure of a Boolean algebra, and Boolean
Boolean metric spaces and Boolean algebraic varieties
Avilés, Antonio
2009-01-01
The concepts of Boolean metric space and convex combination are used to characterize polynomial maps in a class of commutative Von Neumann regular rings including Boolean rings and p-rings, that we have called CFG-rings. In those rings, the study of the category of algebraic varieties (i.e. sets of solutions to a finite number of polynomial equations with polynomial maps as morphisms) is equivalent to the study of a class of Boolean metric spaces, that we call here CFG-spaces.
Korshunov, A D [S.L. Sobolev Institute for Mathematics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (Russian Federation)
2003-10-31
Monotone Boolean functions are an important object in discrete mathematics and mathematical cybernetics. Topics related to these functions have been actively studied for several decades. Many results have been obtained, and many papers published. However, until now there has been no sufficiently complete monograph or survey of results of investigations concerning monotone Boolean functions. The object of this survey is to present the main results on monotone Boolean functions obtained during the last 50 years.
Gardy, Danièle
2005-01-01
International audience; We examine how we can define several probability distributions on the set of Boolean functions on a fixed number of variables, starting from a representation of Boolean expressions by trees. Analytic tools give us a systematic way to prove the existence of probability distributions, the main challenge being the actual computation of the distributions. We finally consider the relations between the probability of a Boolean function and its complexity.
Tucker, Jerry H.; Tapia, Moiez A.; Bennett, A. Wayne
1988-01-01
The concept of Boolean integration is developed, and different Boolean integral operators are introduced. Given the changes in a desired function in terms of the changes in its arguments, the ways of 'integrating' (i.e. realizing) such a function, if it exists, are presented. The necessary and sufficient conditions for integrating, in different senses, the expression specifying the changes are obtained. Boolean calculus has applications in the design of logic circuits and in fault analysis.
Tucker, Jerry H.; Tapia, Moiez A.; Bennett, A. Wayne
1988-01-01
The concept of Boolean integration is developed, and different Boolean integral operators are introduced. Given the changes in a desired function in terms of the changes in its arguments, the ways of 'integrating' (i.e. realizing) such a function, if it exists, are presented. The necessary and sufficient conditions for integrating, in different senses, the expression specifying the changes are obtained. Boolean calculus has applications in the design of logic circuits and in fault analysis.
Localization of Laplacian eigenfunctions in circular, spherical and elliptical domains
Nguyen, Binh-Thanh
2012-01-01
We consider Laplacian eigenfunctions in circular, spherical and elliptical domains in order to discuss three kinds of high-frequency localization: whispering gallery modes, bouncing ball modes, and focusing modes. Although the existence of these modes was known for a class of convex domains, the separation of variables for above domains helps to better understand the "mechanism" of localization, i.e. how an eigenfunction is getting distributed in a small region of the domain, and decays rapidly outside this region. Using the properties of Bessel and Mathieu functions, we derive the inequalities which imply and clearly illustrate localization. Moreover, we provide an example of a non-convex domain (an elliptical annulus) for which the high-frequency localized modes are still present. At the same time, we show that there is no localization in most of rectangle-like domains. This observation leads us to formulating an open problem of localization in polygonal domains and, more generally, in piecewise smooth conv...
Testing Booleanity and the Uncertainty Principle
Gur, Tom
2012-01-01
Let f:{-1,1}^n -> R be a real function on the hypercube, given by its discrete Fourier expansion, or, equivalently, represented as a multilinear polynomial. We say that it is Boolean if its image is in {-1,1}. We show that every function on the hypercube with a sparse Fourier expansion must either be Boolean or far from Boolean. In particular, we show that a multilinear polynomial with at most k terms must either be Boolean, or output values different than -1 or 1 for a fraction of at least 2/(k+2)^2 of its domain. It follows that given black box access to f, together with the guarantee that its representation as a multilinear polynomial has at most k terms, one can test Booleanity using O(k^2) queries. We show an Omega(k) queries lower bound for this problem. We also consider the problem of deciding if a function is Boolean, given its explicit representation as a k term multilinear polynomial. The naive approach of evaluating it at every input has O(kn2^n) time complexity. For large k (i.e, exponential) we p...
刘叙华; 邓安生
1994-01-01
A new approach of operator fuzzy logic, Boolean operator fuzzy logic (BOFL) based on Boolean algebra, is presented. The resolution principle is also introduced into BOFL. BOFL is a natural generalization of classical logic and can be applied to the qualitative description of fuzzy knowledge.
Andersen, Henrik Reif; Hulgaard, Henrik
2002-01-01
This paper presents a new data structure called boolean expression diagrams (BEDs) for representing and manipulating Boolean functions. BEDs are a generalization of binary decision diagrams (BDDs) which can represent any Boolean circuit in linear space. Two algorithms are described for transforming...... a BED into a reduced ordered BDD. One is a generalized version of the BDD apply-operator while the other can exploit the structural information of the Boolean expression. This ability is demonstrated by verifying that two different circuit implementations of a 16-bit multiplier implement the same...... Boolean function. Using BEDs, this verification problem is solved efficiently, while using standard BDD techniques this problem is infeasible. Generally, BEDs are useful in applications, for example tautology checking, where the end-result as a reduced ordered BDD is small. Moreover, using operators...
Andersen, Henrik Reif; Hulgaard, Henrik
1997-01-01
This paper presents a new data structure called Boolean Expression Diagrams (BEDs) for representing and manipulating Boolean functions. BEDs are a generalization of Binary Decision Diagrams (BDDs) which can represent any Boolean circuit in linear space and still maintain many of the desirable...... properties of BDDs. Two algorithms are described for transforming a BED into a reduced ordered BDD. One closely mimics the BDD apply-operator while the other can exploit the structural information of the Boolean expression. The efficacy of the BED representation is demonstrated by verifying...... that the redundant and non-redundant versions of the ISCAS 85 benchmark circuits are identical. In particular, it is verified that the two 16-bit multiplication circuits (c6288 and c6288nr) implement the same Boolean functions. Using BEDs, this verification problem is solved in less than a second, while using...
Constructive version of Boolean algebra
Ciraulo, Francesco; Toto, Paola
2012-01-01
The notion of overlap algebra introduced by G. Sambin provides a constructive version of complete Boolean algebra. Here we first show some properties concerning overlap algebras: we prove that the notion of overlap morphism corresponds classically to that of map preserving arbitrary joins; we provide a description of atomic set-based overlap algebras in the language of formal topology, thus giving a predicative characterization of discrete locales; we show that the power-collection of a set is the free overlap algebra join-generated from the set. Then, we generalize the concept of overlap algebra and overlap morphism in various ways to provide constructive versions of the category of Boolean algebras with maps preserving arbitrary existing joins.
广义Boolean-like环%Generalized Boolean-like Rings
秦蕊
2013-01-01
广义Boolean-like环是Boolean-like环的一个推广,文章主要介绍了广义Boolean-like环的构建,从而列举了若干广义Boolean-like环的相关例子及基本性质.并且,考虑了广义Boolean-like环的部分扩张,如上三角矩阵环.
Leont'ev, V. K.
2015-11-01
A pseudo-Boolean function is an arbitrary mapping of the set of binary n-tuples to the real line. Such functions are a natural generalization of classical Boolean functions and find numerous applications in various applied studies. Specifically, the Fourier transform of a Boolean function is a pseudo-Boolean function. A number of facts associated with pseudo-Boolean polynomials are presented, and their applications to well-known discrete optimization problems are described.
Monotone Boolean approximation
Hulme, B.L.
1982-12-01
This report presents a theory of approximation of arbitrary Boolean functions by simpler, monotone functions. Monotone increasing functions can be expressed without the use of complements. Nonconstant monotone increasing functions are important in their own right since they model a special class of systems known as coherent systems. It is shown here that when Boolean expressions for noncoherent systems become too large to treat exactly, then monotone approximations are easily defined. The algorithms proposed here not only provide simpler formulas but also produce best possible upper and lower monotone bounds for any Boolean function. This theory has practical application for the analysis of noncoherent fault trees and event tree sequences.
Boolean differential equations
Steinbach, Bernd
2013-01-01
The Boolean Differential Calculus (BDC) is a very powerful theory that extends the structure of a Boolean Algebra significantly. Based on a small number of definitions, many theorems have been proven. The available operations have been efficiently implemented in several software packages. There is a very wide field of applications. While a Boolean Algebra is focused on values of logic functions, the BDC allows the evaluation of changes of function values. Such changes can be explored for pairs of function values as well as for whole subspaces. Due to the same basic data structures, the BDC can
EXACT SIMULATION OF A BOOLEAN MODEL
Christian Lantuéjoul
2013-06-01
Full Text Available A Boolean model is a union of independent objects (compact random subsets located at Poisson points. Two algorithms are proposed for simulating a Boolean model in a bounded domain. The first one applies only to stationary models. It generates the objects prior to their Poisson locations. Two examples illustrate its applicability. The second algorithm applies to stationary and non-stationary models. It generates the Poisson points prior to the objects. Its practical difficulties of implementation are discussed. Both algorithms are based on importance sampling techniques, and the generated objects are weighted.
Bossé, Michael J.; Adu-Gyamfi, Kwaku; Chandler, Kayla; Lynch-Davis, Kathleen
2016-01-01
Dynamic mathematical environments allow users to reify mathematical concepts through multiple representations, transform mathematical relations and organically explore mathematical properties, investigate integrated mathematics, and develop conceptual understanding. Herein, we integrate Boolean algebra, the functionalities of a dynamic…
Metzler, S; Miettinen, P
2015-01-01
Tensor factorizations are computationally hard problems, and in particular, are often significantly harder than their matrix counterparts. In case of Boolean tensor factorizations -- where the input tensor and all the factors are required to be binary and we use Boolean algebra -- much of that hardness comes from the possibility of overlapping components. Yet, in many applications we are perfectly happy to partition at least one of the modes. In this paper we investigate what consequences doe...
Canteaut, Anne; Videau, Marion
2005-01-01
http://www.ieee.org/; We present an extensive study of symmetric Boolean functions, especially of their cryptographic properties. Our main result establishes the link between the periodicity of the simplified value vector of a symmetric Boolean function and its degree. Besides the reduction of the amount of memory required for representing a symmetric function, this property has some consequences from a cryptographic point of view. For instance, it leads to a new general bound on the order of...
Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains
Ren, X.Y.; Stiekema, W.J.; Nap, J.P.H.
2007-01-01
Chromosomal coexpression domains are found in a number of different genomes under various developmental conditions. The size of these domains and the number of genes they contain vary. Here, we define local coexpression domains as adjacent genes where all possible pair-wise correlations of
Nearly projective Boolean algebras
Heindorf, Lutz; Shapiro, Leonid B
1994-01-01
The book is a fairly complete and up-to-date survey of projectivity and its generalizations in the class of Boolean algebras. Although algebra adds its own methods and questions, many of the results presented were first proved by topologists in the more general setting of (not necessarily zero-dimensional) compact spaces. An appendix demonstrates the application of advanced set-theoretic methods to the field. The intended readers are Boolean and universal algebraists. The book will also be useful for general topologists wanting to learn about kappa-metrizable spaces and related classes. The text is practically self-contained but assumes experience with the basic concepts and techniques of Boolean algebras.
The Boolean Isomorphism problem
Agrawal, M. [Indian Institute of Technology, Kanpur (India); Thierauf, T. [Universitaet Ulm (Germany)
1996-12-31
We investigate the computational complexity of the Boolean Isomorphism problem (BI): on input of two Boolean formulas F and G decide whether there exists a permutation of the variables of G such that F and G become equivalent. Our main result is a one-round interactive proof for BI, where the verifier has access to an NP oracle. To obtain this, we use a recent result from learning theory by Bshouty et.al. that Boolean formulas can be learned probabilistically with equivalence queries and access to an NP oracle. As a consequence, BI cannot be {sigma}{sup p}{sub 2} complete unless the Polynomial Hierarchy collapses. This solves an open problem posed in [BRS95]. Further properties of BI are shown: BI has And- and Or-functions, the counting version, No. BI, can be computed in polynomial time relative to BI, and BI is self-reducible.
Berg, van den, Aad; Meester, R.; White, Damien
1997-01-01
Consider an ordinary Boolean model, that is, a homogeneous Poisson point process in Rd, where the points are all centres of random balls with i.i.d. radii. Now let these points move around according to i.i.d. stochastic processes. It is not hard to show that at each xed time t we again have a Boolean model with the original distribution. Hence if the original model is supercritical then, for any t, the probability of having an unbounded occupied component at time t equals 1. We show that unde...
Quantum Boolean image denoising
Mastriani, Mario
2015-05-01
A quantum Boolean image processing methodology is presented in this work, with special emphasis in image denoising. A new approach for internal image representation is outlined together with two new interfaces: classical to quantum and quantum to classical. The new quantum Boolean image denoising called quantum Boolean mean filter works with computational basis states (CBS), exclusively. To achieve this, we first decompose the image into its three color components, i.e., red, green and blue. Then, we get the bitplanes for each color, e.g., 8 bits per pixel, i.e., 8 bitplanes per color. From now on, we will work with the bitplane corresponding to the most significant bit (MSB) of each color, exclusive manner. After a classical-to-quantum interface (which includes a classical inverter), we have a quantum Boolean version of the image within the quantum machine. This methodology allows us to avoid the problem of quantum measurement, which alters the results of the measured except in the case of CBS. Said so far is extended to quantum algorithms outside image processing too. After filtering of the inverted version of MSB (inside quantum machine), the result passes through a quantum-classical interface (which involves another classical inverter) and then proceeds to reassemble each color component and finally the ending filtered image. Finally, we discuss the more appropriate metrics for image denoising in a set of experimental results.
Algebraic partial Boolean algebras
Smith, Derek [Math Department, Lafayette College, Easton, PA 18042 (United States)
2003-04-04
Partial Boolean algebras, first studied by Kochen and Specker in the 1960s, provide the structure for Bell-Kochen-Specker theorems which deny the existence of non-contextual hidden variable theories. In this paper, we study partial Boolean algebras which are 'algebraic' in the sense that their elements have coordinates in an algebraic number field. Several of these algebras have been discussed recently in a debate on the validity of Bell-Kochen-Specker theorems in the context of finite precision measurements. The main result of this paper is that every algebraic finitely-generated partial Boolean algebra B(T) is finite when the underlying space H is three-dimensional, answering a question of Kochen and showing that Conway and Kochen's infinite algebraic partial Boolean algebra has minimum dimension. This result contrasts the existence of an infinite (non-algebraic) B(T) generated by eight elements in an abstract orthomodular lattice of height 3. We then initiate a study of higher-dimensional algebraic partial Boolean algebras. First, we describe a restriction on the determinants of the elements of B(T) that are generated by a given set T. We then show that when the generating set T consists of the rays spanning the minimal vectors in a real irreducible root lattice, B(T) is infinite just if that root lattice has an A{sub 5} sublattice. Finally, we characterize the rays of B(T) when T consists of the rays spanning the minimal vectors of the root lattice E{sub 8}.
Sequences determining the cytoplasmic localization of a chemoreceptor domain.
Seligman, L; Bailey, J; Manoil, C
1995-01-01
The Escherichia coli serine chemoreceptor (Tsr) is a protein with a simple topology consisting of two membrane-spanning sequences (TM1 and TM2) separating a large periplasmic domain from N-terminal and C-terminal cytoplasmic regions. We analyzed the contributions of several sequence elements to the cytoplasmic localization of the C-terminal domain by using chemoreceptor-alkaline phosphatase gene fusions. The principal findings were as follows. (i) The cytoplasmic localization of the C-terminal domain depended on TM2 but was quite tolerant of mutations partially deleting or introducing charged residues into the sequence. (ii) The basal level of C-terminal domain export was significantly higher in proteins with the wild-type periplasmic domain than in derivatives with a shortened periplasmic domain, suggesting that the large size of the wild-type domain promotes partial membrane misinsertion. (iii) The membrane insertion of deletion derivatives with a single spanning segment (TM1 or TM2) could be controlled by either an adjacent positively charged sequence or an adjacent amphipathic sequence. The results provide evidence that the generation of the Tsr membrane topology is an overdetermined process directed by an interplay of sequences promoting and opposing establishment of the normal structure. PMID:7730259
Localization of vector field on dynamical domain wall
Masafumi Higuchi
2017-03-01
Full Text Available In the previous works (arXiv:1202.5375 and arXiv:1402.1346, the dynamical domain wall, where the four dimensional FRW universe is embedded in the five dimensional space–time, has been realized by using two scalar fields. In this paper, we consider the localization of vector field in three formulations. The first formulation was investigated in the previous paper (arXiv:1510.01099 for the U(1 gauge field. In the second formulation, we investigate the Dvali–Shifman mechanism (arXiv:hep-th/9612128, where the non-abelian gauge field is confined in the bulk but the gauge symmetry is spontaneously broken on the domain wall. In the third formulation, we investigate the Kaluza–Klein modes coming from the five dimensional graviton. In the Randall–Sundrum model, the graviton was localized on the brane. We show that the (5,μ components (μ=0,1,2,3 of the graviton are also localized on the domain wall and can be regarded as the vector field on the domain wall. There are, however, some corrections coming from the bulk extra dimension if the domain wall universe is expanding.
Domain-Size Pooling in Local Descriptors: DSP-SIFT
Dong, Jingming; Soatto, Stefano
2014-01-01
We introduce a simple modification of local image descriptors, such as SIFT, based on pooling gradient orientations across different domain sizes, in addition to spatial locations. The resulting descriptor, which we call DSP-SIFT, outperforms other methods in wide-baseline matching benchmarks, including those based on convolutional neural networks, despite having the same dimension of SIFT and requiring no training.
Computational complexity of Boolean functions
Korshunov, Aleksei D [Sobolev Institute of Mathematics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (Russian Federation)
2012-02-28
Boolean functions are among the fundamental objects of discrete mathematics, especially in those of its subdisciplines which fall under mathematical logic and mathematical cybernetics. The language of Boolean functions is convenient for describing the operation of many discrete systems such as contact networks, Boolean circuits, branching programs, and some others. An important parameter of discrete systems of this kind is their complexity. This characteristic has been actively investigated starting from Shannon's works. There is a large body of scientific literature presenting many fundamental results. The purpose of this survey is to give an account of the main results over the last sixty years related to the complexity of computation (realization) of Boolean functions by contact networks, Boolean circuits, and Boolean circuits without branching. Bibliography: 165 titles.
Local control of antiferromagnetic domains in Cr2O3
Adenwalla, S.; Singh, Uday; Echtenkamp, W.; Binek, Ch.
2015-03-01
We have used a Cr2O3/Pd/(Co/Pd)3 exchange biased heterostructure to measure the spatial distribution of anti-ferromagnetic (AFM) domains in magnetoelectric AFM Cr2O3.TheAFMCr2O3 possesses a residual roughness insensitive surface magnetization below its Néel temperature (TN 307K) This surface magnetization couples to the ferromagnetic material (Co/Pd) and results in exchange bias. Cooling the Cr2O3 from above its Néel temperature in different magnetization states of the ferromagnet results in the formation of AFM domains in Cr2O3. The AFM domains in the Cr2O3 were mapped by a spatial map of the exchange bias of the ferromagnet for the sample cooled in various remnant conditions of Co/Pd and at different temperatures. Local control of AFM domains was achieved by first, controlling the magnetization of Co/Pd multilayers and cooling below the Neel temperature, resulting in a single AFM domain, and then, subsequently writing a reversed AFM domain using the heat from a 6 mW focused laser beam. Scanning the laser beam allows for the writing of any domain pattern with a spatial resolution of 5 μm, limited only by the focusing optics. This work is supported by NSF Grant No. 1409622 and MRSEC DMR-0820521.
Antonio AIZPURU; Antonio GUTI(E)RREZ-D(A)VILA
2004-01-01
In this paper we will study some families and subalgebras ( ) of ( )(N) that let us characterize the unconditional convergence of series through the weak convergence of subseries ∑i∈A xi, A ∈ ( ).As a consequence, we obtain a new version of the Orlicz-Pettis theorem, for Banach spaces. We also study some relationships between algebraic properties of Boolean algebras and topological properties of the corresponding Stone spaces.
Fault Tolerant Boolean Satisfiability
Roy, A
2011-01-01
A delta-model is a satisfying assignment of a Boolean formula for which any small alteration, such as a single bit flip, can be repaired by flips to some small number of other bits, yielding a new satisfying assignment. These satisfying assignments represent robust solutions to optimization problems (e.g., scheduling) where it is possible to recover from unforeseen events (e.g., a resource becoming unavailable). The concept of delta-models was introduced by Ginsberg, Parkes and Roy (AAAI 1998), where it was proved that finding delta-models for general Boolean formulas is NP-complete. In this paper, we extend that result by studying the complexity of finding delta-models for classes of Boolean formulas which are known to have polynomial time satisfiability solvers. In particular, we examine 2-SAT, Horn-SAT, Affine-SAT, dual-Horn-SAT, 0-valid and 1-valid SAT. We see a wide variation in the complexity of finding delta-models, e.g., while 2-SAT and Affine-SAT have polynomial time tests for delta-models, testing w...
Localization of Vector Field on Dynamical Domain Wall
Higuchi, Masafumi
2016-01-01
In the previous works (arXiv:1202.5375 and 1402.1346), the dynamical domain wall, where the four dimensional FRW universe is embedded in the five imensional space-time, has been realized by using two scalar fields. In this paper, we consider the localization of vector field in three formulations. The first formulation was investigated in the previous paper (arXiv:1510.01099) for the $U(1)$ gauge field. In the second formulation, we investigate the Dvali-Shifman mechanism (hep-th/9612128), where the non-abelian gauge field is confined in the bulk but the gauge symmetry is spontaneously broken on the domain wall. In the third formulation, we investigate the Kaluza-Klein modes coming from the five dimensional graviton. In the Randall-Sundrum model, the graviton was localized on the brane. We show that the $(5,\\mu)$ components $\\left(\\mu=0,1,2,3\\right)$ of the graviton are also localized on the domain wall and can be regarded as the vector field on the domain wall. There are, however, some corrections coming from...
J-Boolean like环%J-Boolean Like Ring
秦蕊
2013-01-01
本文首先引进了Boolean-like环的一类新的扩张J-Boolean like环,即对任意环R中元素a,b都有(a-a2)(b-b2)∈J(R),这里J(R)为环R的Jacobson根,则环R称为J-Boolean like环.证明了两个定理分别为(1)设D是一个环,C是D的一个子环,R[D,C]是一个J-Boolean like环(=)(a)C,D是J-Boolean like环,(b)J2(C)(∈)J(D).(2)如果B/J(B)是Boolean环,并且B[i]={a+bi| i2=ui+η,a,b,u,η∈B},那么B[i]是J-Booleanlike环当且仅当uη∈J(B).
Structural eigenfrequency optimization based on local sub-domain "frequencies"
Pedersen, Pauli; Pedersen, Niels Leergaard
2013-01-01
The engineering approach of fully stressed design is a practical tool with a theoretical foundation. The analog approach to structural eigenfrequency optimization is presented here with its theoretical foundation. A numerical redesign procedure is proposed and illustrated with examples.......For the ideal case, an optimality criterion is fulfilled if the design have the same sub-domain ”frequency” (local Rayleigh quotient). Sensitivity analysis shows an important relation between squared system eigenfrequency and squared local sub-domain frequency for a given eigenmode. Higher order...... eigenfrequencies may also be controlled in this manner.The presented examples are based on 2D finite element models with the use of subspace iteration for analysis and a recursive design procedure based on the derived optimality condition. The design that maximize a frequency depend on the total amount...
Approximate Reasoning with Fuzzy Booleans
Broek, van den P.M.; Noppen, J.A.R.
2004-01-01
This paper introduces, in analogy to the concept of fuzzy numbers, the concept of fuzzy booleans, and examines approximate reasoning with the compositional rule of inference using fuzzy booleans. It is shown that each set of fuzzy rules is equivalent to a set of fuzzy rules with singleton crisp ante
Cardinal invariants on Boolean algebras
Monk, J Donald
2014-01-01
This book is concerned with cardinal number valued functions defined for any Boolean algebra. Examples of such functions are independence, which assigns to each Boolean algebra the supremum of the cardinalities of its free subalgebras, and cellularity, which gives the supremum of cardinalities of sets of pairwise disjoint elements. Twenty-one such functions are studied in detail, and many more in passing. The questions considered are the behaviour of these functions under algebraic operations such as products, free products, ultraproducts, and their relationships to one another. Assuming familiarity with only the basics of Boolean algebras and set theory, through simple infinite combinatorics and forcing, the book reviews current knowledge about these functions, giving complete proofs for most facts. A special feature of the book is the attention given to open problems, of which 185 are formulated. Based on Cardinal Functions on Boolean Algebras (1990) and Cardinal Invariants on Boolean Algebras (1996) by the...
Cryptographic Boolean functions and applications
Cusick, Thomas W
2009-01-01
Boolean functions are the building blocks of symmetric cryptographic systems. Symmetrical cryptographic algorithms are fundamental tools in the design of all types of digital security systems (i.e. communications, financial and e-commerce).Cryptographic Boolean Functions and Applications is a concise reference that shows how Boolean functions are used in cryptography. Currently, practitioners who need to apply Boolean functions in the design of cryptographic algorithms and protocols need to patch together needed information from a variety of resources (books, journal articles and other sources). This book compiles the key essential information in one easy to use, step-by-step reference. Beginning with the basics of the necessary theory the book goes on to examine more technical topics, some of which are at the frontier of current research.-Serves as a complete resource for the successful design or implementation of cryptographic algorithms or protocols using Boolean functions -Provides engineers and scient...
optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks
Trairatphisan, Panuwat; Mizera, Andrzej; Pang, Jun; Tantar, Alexandru Adrian; Sauter, Thomas
2014-01-01
Background There exist several computational tools which allow for the optimisation and inference of biological networks using a Boolean formalism. Nevertheless, the results from such tools yield only limited quantitative insights into the complexity of biological systems because of the inherited qualitative nature of Boolean networks. Results We introduce optPBN, a Matlab-based toolbox for the optimisation of probabilistic Boolean networks (PBN) which operates under the framework of the BN/PBN toolbox. optPBN offers an easy generation of probabilistic Boolean networks from rule-based Boolean model specification and it allows for flexible measurement data integration from multiple experiments. Subsequently, optPBN generates integrated optimisation problems which can be solved by various optimisers. In term of functionalities, optPBN allows for the construction of a probabilistic Boolean network from a given set of potential constitutive Boolean networks by optimising the selection probabilities for these networks so that the resulting PBN fits experimental data. Furthermore, the optPBN pipeline can also be operated on large-scale computational platforms to solve complex optimisation problems. Apart from exemplary case studies which we correctly inferred the original network, we also successfully applied optPBN to study a large-scale Boolean model of apoptosis where it allows identifying the inverse correlation between UVB irradiation, NFκB and Caspase 3 activations, and apoptosis in primary hepatocytes quantitatively. Also, the results from optPBN help elucidating the relevancy of crosstalk interactions in the apoptotic network. Summary The optPBN toolbox provides a simple yet comprehensive pipeline for integrated optimisation problem generation in the PBN formalism that can readily be solved by various optimisers on local or grid-based computational platforms. optPBN can be further applied to various biological studies such as the inference of gene regulatory
Boolean network robotics: a proof of concept
Roli, Andrea; Pinciroli, Carlo; Birattari, Mauro
2011-01-01
Dynamical systems theory and complexity science provide powerful tools for analysing artificial agents and robots. Furthermore, they have been recently proposed also as a source of design principles and guidelines. Boolean networks are a prominent example of complex dynamical systems and they have been shown to effectively capture important phenomena in gene regulation. From an engineering perspective, these models are very compelling, because they can exhibit rich and complex behaviours, in spite of the compactness of their description. In this paper, we propose the use of Boolean networks for controlling robots' behaviour. The network is designed by means of an automatic procedure based on stochastic local search techniques. We show that this approach makes it possible to design a network which enables the robot to accomplish a task that requires the capability of navigating the space using a light stimulus, as well as the formation and use of an internal memory.
Quantum algorithms for testing Boolean functions
Erika Andersson; Floess, Dominik F.; Mark Hillery
2010-01-01
We discuss quantum algorithms, based on the Bernstein-Vazirani algorithm, for finding which variables a Boolean function depends on. There are 2^n possible linear Boolean functions of n variables; given a linear Boolean function, the Bernstein-Vazirani quantum algorithm can deterministically identify which one of these Boolean functions we are given using just one single function query. The same quantum algorithm can also be used to learn which input variables other types of Boolean functions...
Unlimited multistability and Boolean logic in microbial signalling
Kothamachu, Varun B; Feliu, Elisenda; Cardelli, Luca;
2015-01-01
further prove that sharing of downstream components allows a system with n multi-domain hybrid HKs to attain 3n steady states. We find that such systems, when sensing distinct signals, can readily implement Boolean logic functions on these signals. Using two experimentally studied examples of two...
Combinatorial optimization with Boolean constraints
Hulme, B.L.; Worrell, R.B.
1983-02-01
This report shows how Boolean algebraic formula manipulation can be used to solve certain kinds of optimization problems. If the problem can be formulated in terms of 0 to 1 variables and if the feasible solutions can be described by a Boolean equation, then the method of this report can be used. The method generates feasible solutions algebraically as terms of a disjunctive normal form of a Boolean function. Many small sample problems are solved to illustrate the method and the practical situations in which these optimization problems arise.
Computing preimages of Boolean networks
2013-01-01
In this paper we present an algorithm based on the sum-product algorithm that finds elements in the preimage of a feed-forward Boolean networks given an output of the network. Our probabilistic method runs in linear time with respect to the number of nodes in the network. We evaluate our algorithm for randomly constructed Boolean networks and a regulatory network of Escherichia coli and found that it gives a valid solution in most cases. PMID:24267277
Boolean Searches--A Life Skill.
Ala, Judy; Cerabona, Kathy
1992-01-01
Discusses the importance of Boolean searching as a skill that students will need in the future. Methods for teaching Boolean searching are described, and the value of truncation as an online searching aid is considered. (MES)
Boolean networks with multiexpressions and parameters.
Zou, Yi Ming
2013-01-01
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean models, both synchronous and asynchronous, have been proposed in the literature. However, analytical study of these more general Boolean networks models is lagging. This paper aims to develop a concise theory for these different Boolean logic-based modeling methods. Boolean models for networks where each node can have more than two levels of expression and Boolean models with parameters are defined algebraically with examples provided. Certain classes of random asynchronous Boolean networks and deterministic moduli asynchronous Boolean networks are investigated in detail using the setting introduced in this paper. The derived theorems provide a clear picture for the attractor structures of these asynchronous Boolean networks.
Generalized periodic and generalized Boolean rings
Howard E. Bell
2001-01-01
Full Text Available We prove that a generalized periodic, as well as a generalized Boolean, ring is either commutative or periodic. We also prove that a generalized Boolean ring with central idempotents must be nil or commutative. We further consider conditions which imply the commutativity of a generalized periodic, or a generalized Boolean, ring.
Boolean Operations on Conic Polygons
Yong-Xi Gong; Yu Liu; Lun Wu; Yu-Bo Xie
2009-01-01
An algorithm for Boolean operations on conic polygons is proposed. Conic polygons are polygons consisting of conic segments or bounded conics with directions. Preliminaries of Boolean operations on general polygons are presented. In our algorithm, the intersection points and the topological relationships between two conic polygons are computed. Boundaries are obtained by tracking path and selecting uncrossed boundaries following rule tables to build resulting conic polygons.We define a set of rules for the intersection, union, and subtraction operations on conic polygons. The algorithm considers degeneration cases such as homology, complement, interior, and exterior. The algorithm is also evaluated and implemented.
Sublogarithmic uniform Boolean proof nets
Aubert, Clément
2012-01-01
Using a proofs-as-programs correspondence, Terui was able to compare two models of parallel computation: Boolean circuits and proof nets for multiplicative linear logic. Mogbil et. al. gave a logspace translation allowing us to compare their computational power as uniform complexity classes. This paper presents a novel translation in AC0 and focuses on a simpler restricted notion of uniform Boolean proof nets. We can then encode constant-depth circuits and compare complexity classes below logspace, which were out of reach with the previous translations.
Geometric Operators on Boolean Functions
Frisvad, Jeppe Revall; Falster, Peter
function. With this image of a Boolean function corresponding to a propositional formula, we prove that the orthogonal projection operator leads to a theorem describing all rules of inference in propositional reasoning. In other words, we can capture all kinds of inference in propositional logic by means...... independent of representation such that we no longer need to be much concerned with the form of the Boolean functions. Knowing that the operators can easily be implemented (as they have been in array-based logic), shows the advantage they give with respect to automated reasoning....
Partial stability and stabilisation of Boolean networks
Chen, Hong-Wei; Sun, Liang-Jie; Liu, Yang
2016-07-01
In this paper, we investigate the stability of Boolean networks and the stabilisation of Boolean control networks with respect to part of the system's states. First, an algebraic expression of the Boolean (control) network is derived by the semi-tensor product of matrices. Then, some necessary and sufficient conditions for partial stability of Boolean networks are given. Finally, the stabilisation of Boolean control networks by a free control sequence and a state-feedback control is investigated and the respective necessary and sufficient conditions are obtained. Examples are provided to illustrate the efficiency of the obtained results.
Synchronization of Asynchronous Switched Boolean Network.
Zhang, Hao; Wang, Xingyuan; Lin, Xiaohui
2015-01-01
In this paper, the complete synchronizations for asynchronous switched Boolean network with free Boolean sequence controllers and close-loop controllers are studied. First, the basic asynchronous switched Boolean network model is provided. With the method of semi-tensor product, the Boolean dynamics is translated into linear representation. Second, necessary and sufficient conditions for ASBN synchronization with free Boolean sequence control and close-loop control are derived, respectively. Third, some illustrative examples are provided to show the efficiency of the proposed methods.
Evolutionary Design of Boolean Functions
WANG Zhang-yi; ZHANG Huan-guo; QIN Zhong-ping; MENG Qing-shu
2005-01-01
We use evolutionary computing to synthesize Boolean functions randomly. By using specific crossover and mutation operator in evolving process and modifying search space and fitness function, we get some high non-linearity functions which have other good cryptography characteristics such as autocorrelation etc. Comparing to other heuristic search techniques, evolutionary computing approach is more effective because of global search strategy and implicit parallelism.
Mental Models of Boolean Concepts
Goodwin, Geoffrey P.; Johnson-Laird, P. N.
2011-01-01
Negation, conjunction, and disjunction are major building blocks in the formation of concepts. This article presents a new model-based theory of these Boolean components. It predicts that individuals simplify the models of instances of concepts. Evidence corroborates the theory and challenges alternative accounts, such as those based on minimal…
Construction of optimized Boolean functions
CHEN Wei; YANG Yi-xian; NIU Xin-xin
2006-01-01
Considering connections of characteristics,this paper is aimed at the construction of optimized Boolean functions.A new method based on the Bent function,discrete Walsh spectrum and characteristics matrices are presented by concatenating,breaking,and revising output sequences conditionally.This new construction can be used to construct different kinds of functions satisfying different design criteria.
Modular Decomposition of Boolean Functions
J.C. Bioch (Cor)
2002-01-01
textabstractModular decomposition is a thoroughly investigated topic in many areas such as switching theory, reliability theory, game theory and graph theory. Most appli- cations can be formulated in the framework of Boolean functions. In this paper we give a uni_ed treatment of modular decompositio
Modular Decomposition of Boolean Functions
J.C. Bioch (Cor)
2002-01-01
textabstractModular decomposition is a thoroughly investigated topic in many areas such as switching theory, reliability theory, game theory and graph theory. Most appli- cations can be formulated in the framework of Boolean functions. In this paper we give a uni_ed treatment of modular
Mental Models of Boolean Concepts
Goodwin, Geoffrey P.; Johnson-Laird, P. N.
2011-01-01
Negation, conjunction, and disjunction are major building blocks in the formation of concepts. This article presents a new model-based theory of these Boolean components. It predicts that individuals simplify the models of instances of concepts. Evidence corroborates the theory and challenges alternative accounts, such as those based on minimal…
Polynomial threshold functions and Boolean threshold circuits
Hansen, Kristoffer Arnsfelt; Podolskii, Vladimir V.
2013-01-01
of secondary interest. We show that PTFs on general Boolean domains are tightly connected to depth two threshold circuits. Our main results in regard to this connection are: PTFs of polynomial length and polynomial degree compute exactly the functions computed by THRMAJ circuits. An exponential length lower...... bound for PTFs that holds regardless of degree, thereby extending known lower bounds for THRMAJ circuits. We generalize two-party unbounded error communication complexity to the multi-party number-on-the-forehead setting, and show that communication lower bounds for 3-player protocols would yield size...... lower bounds for THRTHR circuits. We obtain several other results about PTFs. These include relationships between weight and degree of PTFs, and a degree lower bound for PTFs of constant length. We also consider a variant of PTFs over the max-plus algebra. We show that they are connected to PTFs over...
Local Palmitoylation Cycles and Specialized Membrane Domain Organization
Fukata, Yuko; Murakami, Tatsuro; Yokoi, Norihiko
2016-01-01
Palmitoylation is an evolutionally conserved lipid modification of proteins. Dynamic and reversible palmitoylation controls a wide range of molecular and cellular properties of proteins including the protein trafficking, protein function, protein stability, and specialized membrane domain organiz...
Homotopy formulas and ■-equation on local q- convex domains in Stein manifolds
钟同德
1997-01-01
The homotopy formulas of (r,s) differential forms and the solution of equation of type (r,s) on local q-convex domains in Stein manifolds are obtained.The homotopy formulas on local q-convex domains have important applications in uniform estimates of equation and holomorphic extension of CR-manifolds.
Boolean logic in artificial intelligence and Turing degrees of Boolean-valued sets
Cai, Maohua.
1989-01-01
Over the years a number of generalizations of recursion theory have been introduced and studied. In this dissertation the author presents yet another such generalization. Based on the concept of a weakly recursively presented Boolean algebra, he defines Boolean-valued sets, Boolean-valued recursive sets, and Boolean-valued recursively enumerable sets and discuss the basic relationships between a Boolean-valued set, its principal part, and its support. Then he generalizes many elementary concepts and results about recursive and recursively enumerable sets such as the s-m-n theorem, the recursion theorem, and the projection theorem, etc. to Boolean valued sets. By using finite and infinite injury arguments, he generalizes the Friedberg-Muchnik theorem, the theorem about nonrecursive low r.e. sets, the minimal pair theorem, and other results. Finally, he discusses the possible application of Boolean-valued logic in artificial intelligence, and gives an implementation of a parser for the four-valued Boolean logic.
Synchronization of Boolean Networks with Different Update Schemes.
Zhang, Hao; Wang, Xingyuan; Lin, Xiaohui
2014-01-01
In this paper, the synchronizations of Boolean networks with different update schemes (synchronized Boolean networks and asynchronous Boolean networks) are investigated. All nodes in Boolean network are represented in terms of semi-tensor product. First, we give the concept of inner synchronization and observe that all nodes in a Boolean network are synchronized with each other. Second, we investigate the outer synchronization between a driving Boolean network and a corresponding response Boolean network. We provide not only the concept of traditional complete synchronization, but also the anti-synchronization and get the anti-synchronization in simulation. Third, we extend the outer synchronization to asynchronous Boolean network and get the complete synchronization between an asynchronous Boolean network and a response Boolean network. Consequently, theorems for synchronization of Boolean networks and asynchronous Boolean networks are derived. Examples are provided to show the correctness of our theorems.
Quantum algorithms for testing Boolean functions
Erika Andersson
2010-06-01
Full Text Available We discuss quantum algorithms, based on the Bernstein-Vazirani algorithm, for finding which variables a Boolean function depends on. There are 2^n possible linear Boolean functions of n variables; given a linear Boolean function, the Bernstein-Vazirani quantum algorithm can deterministically identify which one of these Boolean functions we are given using just one single function query. The same quantum algorithm can also be used to learn which input variables other types of Boolean functions depend on, with a success probability that depends on the form of the Boolean function that is tested, but does not depend on the total number of input variables. We also outline a procedure to futher amplify the success probability, based on another quantum algorithm, the Grover search.
Generalizing Boolean Satisfiability III: Implementation
Dixon, H E; Hofer, D; Luks, E M; Parkes, A J; 10.1613/jair.1656
2011-01-01
This is the third of three papers describing ZAP, a satisfiability engine that substantially generalizes existing tools while retaining the performance characteristics of modern high-performance solvers. The fundamental idea underlying ZAP is that many problems passed to such engines contain rich internal structure that is obscured by the Boolean representation used; our goal has been to define a representation in which this structure is apparent and can be exploited to improve computational performance. The first paper surveyed existing work that (knowingly or not) exploited problem structure to improve the performance of satisfiability engines, and the second paper showed that this structure could be understood in terms of groups of permutations acting on individual clauses in any particular Boolean theory. We conclude the series by discussing the techniques needed to implement our ideas, and by reporting on their performance on a variety of problem instances.
Reconstructing Boolean Models of Signaling
Karp, Richard M.
2013-01-01
Abstract Since the first emergence of protein–protein interaction networks more than a decade ago, they have been viewed as static scaffolds of the signaling–regulatory events taking place in cells, and their analysis has been mainly confined to topological aspects. Recently, functional models of these networks have been suggested, ranging from Boolean to constraint-based methods. However, learning such models from large-scale data remains a formidable task, and most modeling approaches rely on extensive human curation. Here we provide a generic approach to learning Boolean models automatically from data. We apply our approach to growth and inflammatory signaling systems in humans and show how the learning phase can improve the fit of the model to experimental data, remove spurious interactions, and lead to better understanding of the system at hand. PMID:23286509
Boolean Factor Congruences and Property (*)
Terraf, Pedro Sánchez
2008-01-01
A variety V has Boolean factor congruences (BFC) if the set of factor congruences of every algebra in V is a distributive sublattice of its congruence lattice; this property holds in rings with unit and in every variety which has a semilattice operation. BFC has a prominent role in the study of uniqueness of direct product representations of algebras, since it is a strengthening of the refinement property. We provide an explicit Mal'cev condition for BFC. With the aid of this condition, it is shown that BFC is equivalent to a variant of the definability property (*), an open problem in R. Willard's work ("Varieties Having Boolean Factor Congruences," J. Algebra, 132 (1990)).
Single axioms for Boolean algebra.
McCune, W.
2000-06-30
Explicit single axioms are presented for Boolean algebra in terms of (1) the Sheffer stroke; (2) disjunction and negation; (3) disjunction, conjunction, and negation; and (4) disjunction, conjunction, negation, 0, and 1. It was previously known that single axioms exist for these systems, but the procedures to generate them are exponential, producing huge equations. Automated deduction techniques were applied to find axioms of lengths 105, 131, 111, and 127, respectively, each with six variables.
Supersaturation in the Boolean lattice
Dove, A.P.; Griggs, J.R.; Kang, Ross; Sereni, Jean-Sébastien
2014-01-01
We seek families of subsets of an n-set of given size that contain the fewest k-chains. We prove a “supersaturation-type” extension of both Sperner’s Theorem (1928) and its generalization by Erd˝os (1945). Erd˝os showed that a largest k-chain free family in the Boolean lattice is formed by taking
Rational Verification in Iterated Electric Boolean Games
Youssouf Oualhadj
2016-07-01
Full Text Available Electric boolean games are compact representations of games where the players have qualitative objectives described by LTL formulae and have limited resources. We study the complexity of several decision problems related to the analysis of rationality in electric boolean games with LTL objectives. In particular, we report that the problem of deciding whether a profile is a Nash equilibrium in an iterated electric boolean game is no harder than in iterated boolean games without resource bounds. We show that it is a PSPACE-complete problem. As a corollary, we obtain that both rational elimination and rational construction of Nash equilibria by a supervising authority are PSPACE-complete problems.
Progress in Applications of Boolean Functions
Sasao, Tsutomu
2010-01-01
This book brings together five topics on the application of Boolean functions. They are 1. Equivalence classes of Boolean functions: The number of n-variable functions is large, even for values as small as n = 6, and there has been much research on classifying functions. There are many classifications, each with their own distinct merit. 2. Boolean functions for cryptography: The process of encrypting/decrypting plain text messages often depends on Boolean functions with specific properties. For example, highly nonlinear functions are valued because they are less susceptible to linear attacks.
Boolean networks with veto functions
Ebadi, Haleh; Klemm, Konstantin
2014-08-01
Boolean networks are discrete dynamical systems for modeling regulation and signaling in living cells. We investigate a particular class of Boolean functions with inhibiting inputs exerting a veto (forced zero) on the output. We give analytical expressions for the sensitivity of these functions and provide evidence for their role in natural systems. In an intracellular signal transduction network [Helikar et al., Proc. Natl. Acad. Sci. USA 105, 1913 (2008), 10.1073/pnas.0705088105], the functions with veto are over-represented by a factor exceeding the over-representation of threshold functions and canalyzing functions in the same system. In Boolean networks for control of the yeast cell cycle [Li et al., Proc. Natl. Acad. Sci. USA 101, 4781 (2004), 10.1073/pnas.0305937101; Davidich et al., PLoS ONE 3, e1672 (2008), 10.1371/journal.pone.0001672], no or minimal changes to the wiring diagrams are necessary to formulate their dynamics in terms of the veto functions introduced here.
Coletti, Cristian F.; Miranda, Daniel; Mussini, Filipe
2016-02-01
In this work we study the Poisson Boolean model of percolation in locally compact Polish metric spaces and we prove the invariance of subcritical and supercritical phases under mm-quasi-isometries. More precisely, we prove that if a metric space M is mm-quasi-isometric to another metric space N and the Poisson Boolean model in M exhibits any of the following: (a) a subcritical phase; (b) a supercritical phase; or (c) a phase transition, then respectively so does the Poisson Boolean model of percolation in N. Then we use these results in order to understand the phase transition phenomenon in a large family of metric spaces. Indeed, we study the Poisson Boolean model of percolation in the context of Riemannian manifolds, in a large family of nilpotent Lie groups and in Cayley graphs. Also, we prove the existence of a subcritical phase in Gromov spaces with bounded growth at some scale.
Boolean Operations with Prism Algebraic Patches
Bajaj, Chandrajit; Paoluzzi, Alberto; Portuesi, Simone; Lei, Na; Zhao, Wenqi
2009-01-01
In this paper we discuss a symbolic-numeric algorithm for Boolean operations, closed in the algebra of curved polyhedra whose boundary is triangulated with algebraic patches (A-patches). This approach uses a linear polyhedron as a first approximation of both the arguments and the result. On each triangle of a boundary representation of such linear approximation, a piecewise cubic algebraic interpolant is built, using a C1-continuous prism algebraic patch (prism A-patch) that interpolates the three triangle vertices, with given normal vectors. The boundary representation only stores the vertices of the initial triangulation and their external vertex normals. In order to represent also flat and/or sharp local features, the corresponding normal-per-face and/or normal-per-edge may be also given, respectively. The topology is described by storing, for each curved triangle, the two triples of pointers to incident vertices and to adjacent triangles. For each triangle, a scaffolding prism is built, produced by its extreme vertices and normals, which provides a containment volume for the curved interpolating A-patch. When looking for the result of a regularized Boolean operation, the 0-set of a tri-variate polynomial within each such prism is generated, and intersected with the analogous 0-sets of the other curved polyhedron, when two prisms have non-empty intersection. The intersection curves of the boundaries are traced and used to decompose each boundary into the 3 standard classes of subpatches, denoted in, out and on. While tracing the intersection curves, the locally refined triangulation of intersecting patches is produced, and added to the boundary representation. PMID:21516262
Wu Zhi-jian; Tang Zhi-long; Kang Li-shan
2003-01-01
This paper presents a parallel two level evolutionary algorithm based on domain decomposition for solving function optimization problem containing multiple solutions.By combining the characteristics of the global search and local search in each sub-domain, the former enables individual to draw closer to each optirma and keeps the diversity of individuals, while the latter selects local optimal solutions known as latent solutions in sub-domain. In the end, by selecting the global optimal solutions from latent solutions in each sub-domain, we can discover all the optimal solutions easily and quickly.
Localization of the c-ets-2 transactivation domain.
Chumakov, A M; Chen, D L; Chumakova, E A; Koeffler, H P
1993-01-01
The human ets-2 proto-oncogene is one of the homologs of the v-ets gene, found in avian acutely transforming retrovirus E26 (D. Leprince, A. Gegonne, J. Call, C. de Taisne, A. Schneeberger, C. Lagrou, and D. Stehelin, Nature [London] 306:395-397, 1983; M. F. Nunn, P. H. Seeburg, C. Moscovici, and P. H. Duesberg, Nature [London] 306:391-395, 1983), which causes leukemia in chickens. We used the DNA-binding domain of yeast transcriptional activator GAL4 to locate the transactivation region of human ets-2. The transactivation domain of ets-2 was found in the N-terminal part of the protein, which is homologous to ets-1, and can be disrupted by deletion of a stretch of acidic amino acid residues. A transactivation-deficient mutant of ets-2 failed to transform Rat-1 cells and suppressed the transforming activity of coexpressed wild-type ets-2. A mutation in the putative DNA-binding region of ets-2 abolished transforming activity. We show that the motif crucial for ets-2 transactivation capability is necessary for transforming activity in Rat-1 cells. Mutant ets-2 protein that lacks the transactivation domain has a dominant negative effect on transformation by wild-type ets-2. We were unable to detect ets-2-dependent transcriptional regulation of several enhancers containing ets-binding motifs. Images PMID:8445738
THE INVERSE PROBLEM FOR BOOLEAN EQUATIONS
Hussain Mobarak Albarakati
2012-01-01
Full Text Available The Forward Problem (FB of Boolean equations consists of finding solutions of a system of Boolean equations, or equivalently, a single Boolean equation of the form f(X = 0 where f(X: Bn â B and B is an arbitrary Boolean algebra. By contrast, the Inverse Problem (IB of Boolean equations aims to reconstruct the equation f (X = 0 given the set of solutions and hence to verify the correctness of this set. This study derives methods that handle this inverse problem for the main types of solutions of Boolean equations. These include: (a Subsumptive general solutions, in which each of the variables is expressed as an interval by deriving successive conjunctive or disjunctive eliminants of the original function, (b Parametric general solutions, in which each of the variables is expressed via arbitrary parameters which are freely chosen elements of the underlying Boolean algebra and (c Particular solutions, each of which is an assignment from the underlying Boolean algebra to every pertinent variable that makes the Boolean equation an identity. The reconstructed function f(X in every case is set in a canonical form, such as the complete-sum form, to facilitate proving its equivalence to the original function. The methods presented herein are demonstrated with carefully-chosen illustrative examples over big Boolean algebras of various sizes. Among the methods utilized in handling the inverse problem for Boolean equations, the ones utilizing the variable-entered Karnaugh map offered pictorial insight and exhibited an efficient divide-and-conquer strategy.
Localized lipid packing of transmembrane domains impedes integrin clustering.
Mehrdad Mehrbod
Full Text Available Integrin clustering plays a pivotal role in a host of cell functions. Hetero-dimeric integrin adhesion receptors regulate cell migration, survival, and differentiation by communicating signals bidirectionally across the plasma membrane. Thus far, crystallographic structures of integrin components are solved only separately, and for some integrin types. Also, the sequence of interactions that leads to signal transduction remains ambiguous. Particularly, it remains controversial whether the homo-dimerization of integrin transmembrane domains occurs following the integrin activation (i.e. when integrin ectodomain is stretched out or if it regulates integrin clustering. This study employs molecular dynamics modeling approaches to address these questions in molecular details and sheds light on the crucial effect of the plasma membrane. Conducting a normal mode analysis of the intact αllbβ3 integrin, it is demonstrated that the ectodomain and transmembrane-cytoplasmic domains are connected via a membrane-proximal hinge region, thus merely transmembrane-cytoplasmic domains are modeled. By measuring the free energy change and force required to form integrin homo-oligomers, this study suggests that the β-subunit homo-oligomerization potentially regulates integrin clustering, as opposed to α-subunit, which appears to be a poor regulator for the clustering process. If α-subunits are to regulate the clustering they should overcome a high-energy barrier formed by a stable lipid pack around them. Finally, an outside-in activation-clustering scenario is speculated, explaining how further loading the already-active integrin affects its homo-oligomerization so that focal adhesions grow in size.
Boolean integral calculus for digital systems
Tucker, J. H.; Tapia, M. A.; Bennett, A. W.
1985-01-01
The concept of Boolean integration is introduced and developed. When the changes in a desired function are specified in terms of changes in its arguments, then ways of 'integrating' (i.e., realizing) the function, if it exists, are presented. Boolean integral calculus has applications in design of logic circuits.
Kazhdan-Lusztig polynomials of boolean elements
Mongelli, Pietro
2011-01-01
We give closed combinatorial product formulas for Kazhdan-Lusztig poynomials and their parabolic analogue of type q in the case of boolean elements, introduced in [M. Marietti, Boolean elements in Kazhdan-Lusztig theory, J. Algebra 295 (2006)], in Coxeter groups whose Coxeter graph is a tree.
Boolean analysis of addition and multiplication
Faltin, F. (Cornell Univ., Ithaca, NY); Metropolis, N.; Ross, B.; Rota, G.-C.
1977-01-01
The notions of binary string and binary symmetric function are introduced, and basic results presented. Boolean algorithms are given for binary addition and multiplication. An analysis of the redundancies involved is straightforward. The examination of carry propagation which arises in the Boolean analysis of functions may lead to a new interpretation of the notion of computational complexity.
Boolean Search: Current State and Perspectives.
Frants, Valery I.; Shapiro, Jacob; Taksa, Isak; Voiskunskii, Vladimir G.
1999-01-01
Discusses the use of Boolean logic in information-retrieval systems and analyzes existing criticisms of operational systems. Considers users' ability to use and understand Boolean operators, ranking, the quality of query formulations, and negative effects of criticism; and concludes that criticism is directed at the methodology employed in…
Delay synchronization of temporal Boolean networks
Wei, Qiang; Xie, Cheng-jun; Liang, Yi; Niu, Yu-jun; Lin, Da
2016-01-01
This paper investigates the delay synchronization between two temporal Boolean networks base on semi-tensor product method, which improve complete synchronization. Necessary and sufficient conditions for delay synchronization are drawn base on algebraic expression of temporal Boolean networks. A example is presented to show the effectiveness of theoretical analysis.
A Note on Boolean Stochastic Processes
Fidaleo, Francesco
2015-03-01
For the quantum stochastic processes generated by the Boolean commutation relations, we prove the following version of De Finetti Theorem: each of such Boolean processes is exchangeable if and only if it is independent and identically distributed with respect to the tail algebra.
Version Spaces and Generalized Monotone Boolean Functions
J.C. Bioch (Cor); T. Ibaraki
2002-01-01
textabstractWe consider generalized monotone functions f: X --> {0,1} defined for an arbitrary binary relation <= on X by the property x <= y implies f(x) <= f(y). These include the standard monotone (or positive) Boolean functions, regular Boolean functions and other interesting functions as speci
Version Spaces and Generalized Monotone Boolean Functions
J.C. Bioch (Cor); T. Ibaraki
2002-01-01
textabstractWe consider generalized monotone functions f: X --> {0,1} defined for an arbitrary binary relation <= on X by the property x <= y implies f(x) <= f(y). These include the standard monotone (or positive) Boolean functions, regular Boolean functions and other interesting functions as
The dissipative quantum model of brain how do memory localize in correlated neuronal domains
Alfinito, E
2000-01-01
The mechanism of memory localization in extended domains is described in the framework of the parametric dissipative quantum model of brain. The size of the domains and the capability in memorizing depend on the number of links the system is able to establish with the external world.
Efficient stopping of current-driven domain wall using a local Rashba field
Tatara, Gen; Saarikoski, Henri; Mitsumata, Chiharu
2016-10-01
We show theoretically that a locally embedded Rashba interaction acts as a strong pinning center for current-driven domain walls and demonstrate efficient capturing and depinning of the wall using a weak Rashba interaction of the order of 0.01 eV Å. Our discovery is expected to be useful for highly reliable control of domain walls in racetrack memories.
Experimental design schemes for learning Boolean network models
Atias, Nir; Gershenzon, Michal; Labazin, Katia; Sharan, Roded
2014-01-01
Motivation: A holy grail of biological research is a working model of the cell. Current modeling frameworks, especially in the protein–protein interaction domain, are mostly topological in nature, calling for stronger and more expressive network models. One promising alternative is logic-based or Boolean network modeling, which was successfully applied to model signaling regulatory circuits in human. Learning such models requires observing the system under a sufficient number of different conditions. To date, the amount of measured data is the main bottleneck in learning informative Boolean models, underscoring the need for efficient experimental design strategies. Results: We developed novel design approaches that greedily select an experiment to be performed so as to maximize the difference or the entropy in the results it induces with respect to current best-fit models. Unique to our maximum difference approach is the ability to account for all (possibly exponential number of) Boolean models displaying high fit to the available data. We applied both approaches to simulated and real data from the EFGR and IL1 signaling systems in human. We demonstrate the utility of the developed strategies in substantially improving on a random selection approach. Our design schemes highlight the redundancy in these datasets, leading up to 11-fold savings in the number of experiments to be performed. Availability and implementation: Source code will be made available upon acceptance of the manuscript. Contact: roded@post.tau.ac.il PMID:25161232
Boolean networks as modelling framework
Florian eGreil
2012-08-01
Full Text Available In a network, the components of a given system are represented as nodes, the interactions are abstracted as links between the nodes. Boolean networks refer to a class of dynamics on networks, in fact it is the simplest possible dynamics where each node has a value 0 or 1. This allows to investigate extensively the dynamics both analytically and by numerical experiments. The present article focuses on the theoretical concept of relevant components and the immediate application in plant biology, references for more in-depths treatment of the mathematical details are also given.
LOCAL DEVELOPMENT IN NORTHEST REGION THROUGH ACTIVITIES IN ITC DOMAIN
Daniela\tENACHESCU
2015-06-01
Full Text Available Economic areas with high technology are key drivers in sustainable regional development, including unemployment and consequently decreasing population migration in the region. Northeast Region is the largest development region of Romania in terms of number of inhabitants and the owned area. On 01/01/2014, according to balance employment, labor resources of the region were numbered 2,428,700, which represent 49.6% of employed population. The registered unemployment rate at 31 August 2014 was 6.5%, with 82 thousand unemployed registered. In terms of participation in the main economic activities, civilian employment in agriculture, forestry and fishing is predominant (40.1% while in service, civilian employment is 37.1%, while industry and construction is 22.8%. The paper aims to analyze the situation that the potential employment and development opportunities for the Northeast region through activities in the field of ITC domain. Unfortunately, this area was the worst in most indicators, the use of computers and the internet to the turnover of companies and investments in the IT & C and unfortunately in terms of employment population that is under 50%
Boolean-Lie algebras and the Leibniz rule
Bazso, Fueloep [KFKI Research Institute for Particle and Nuclear Physics of the Hungarian Academy of Sciences, PO Box 49, H-1525 Budapest (Hungary); Labos, Elemer [Neurobiology Research Group, United Research Organization of the Hungarian Academy of Sciences and Semmelweis University, H-1450 Budapest, PO Box 95 (Hungary)
2006-06-02
Using internal negations acting on Boolean functions, the notion of Boolean-Lie algebra is introduced. The underlying Lie product is the Boolean analogue of the Poisson bracket. The structure of a Boolean-Lie algebra is determined; it turns out to be solvable, but not nilpotent. We prove that the adjoint representation of an element of the Boolean-Lie algebra acts as a derivative operator on the space of Boolean functions. The adjoint representation is related to the previously known concept of the sensitivity function. Using the notion of adjoint representation we give the definition of a temporal derivative applicable to iterative dynamics of Boolean mappings.
Enhancement of Local Photovoltaic Current at Ferroelectric Domain Walls in BiFeO3
Yang, Ming-Min; Bhatnagar, Akash; Luo, Zheng-Dong; Alexe, Marin
2017-02-01
Domain walls, which are intrinsically two dimensional nano-objects exhibiting nontrivial electronic and magnetic behaviours, have been proven to play a crucial role in photovoltaic properties of ferroelectrics. Despite this recognition, the electronic properties of domain walls under illumination until now have been accessible only to macroscopic studies and their effects upon the conduction of photovoltaic current still remain elusive. The lack of understanding hinders the developing of nanoscale devices based on ferroelectric domain walls. Here, we directly characterize the local photovoltaic and photoconductive properties of 71° domain walls on BiFeO3 thin films with a nanoscale resolution. Local photovoltaic current, proven to be driven by the bulk photovoltaic effect, has been probed over the whole illuminated surface by using a specially designed photoelectric atomic force microscopy and found to be significantly enhanced at domain walls. Additionally, spatially resolved photoconductive current distribution reveals a higher density of excited carriers at domain walls in comparison with domains. Our measurements demonstrate that domain wall enhanced photovoltaic current originates from its high conduction rather than the internal electric field. This photoconduction facilitated local photovoltaic current is likely to be a universal property of topological defects in ferroelectric semiconductors.
Boolean gates on actin filaments
Siccardi, Stefano; Tuszynski, Jack A.; Adamatzky, Andrew
2016-01-01
Actin is a globular protein which forms long polar filaments in the eukaryotic cytoskeleton. Actin networks play a key role in cell mechanics and cell motility. They have also been implicated in information transmission and processing, memory and learning in neuronal cells. The actin filaments have been shown to support propagation of voltage pulses. Here we apply a coupled nonlinear transmission line model of actin filaments to study interactions between voltage pulses. To represent digital information we assign a logical TRUTH value to the presence of a voltage pulse in a given location of the actin filament, and FALSE to the pulse's absence, so that information flows along the filament with pulse transmission. When two pulses, representing Boolean values of input variables, interact, then they can facilitate or inhibit further propagation of each other. We explore this phenomenon to construct Boolean logical gates and a one-bit half-adder with interacting voltage pulses. We discuss implications of these findings on cellular process and technological applications.
Evolving sensitivity balances Boolean Networks.
Jamie X Luo
Full Text Available We investigate the sensitivity of Boolean Networks (BNs to mutations. We are interested in Boolean Networks as a model of Gene Regulatory Networks (GRNs. We adopt Ribeiro and Kauffman's Ergodic Set and use it to study the long term dynamics of a BN. We define the sensitivity of a BN to be the mean change in its Ergodic Set structure under all possible loss of interaction mutations. In silico experiments were used to selectively evolve BNs for sensitivity to losing interactions. We find that maximum sensitivity was often achievable and resulted in the BNs becoming topologically balanced, i.e. they evolve towards network structures in which they have a similar number of inhibitory and excitatory interactions. In terms of the dynamics, the dominant sensitivity strategy that evolved was to build BNs with Ergodic Sets dominated by a single long limit cycle which is easily destabilised by mutations. We discuss the relevance of our findings in the context of Stem Cell Differentiation and propose a relationship between pluripotent stem cells and our evolved sensitive networks.
Local discrete cosine transformation domain Volterra prediction of chaotic time series
张家树; 李恒超; 肖先赐
2005-01-01
In this paper a local discrete cosine transformation (DCT) domain Volterra prediction method is proposed to predict chaotic time series, where the DCT is used to lessen the complexity of solving the coefficient matrix. Numerical simulation results show that the proposed prediction method can effectively predict chaotic time series and improve the prediction accuracy compared with the traditional local linear prediction methods.
Mining TCGA Data Using Boolean Implications
Sinha, Subarna; Tsang, Emily K.; Zeng, Haoyang; Meister, Michela; Dill, David L.
2014-01-01
Boolean implications (if-then rules) provide a conceptually simple, uniform and highly scalable way to find associations between pairs of random variables. In this paper, we propose to use Boolean implications to find relationships between variables of different data types (mutation, copy number alteration, DNA methylation and gene expression) from the glioblastoma (GBM) and ovarian serous cystadenoma (OV) data sets from The Cancer Genome Atlas (TCGA). We find hundreds of thousands of Boolean implications from these data sets. A direct comparison of the relationships found by Boolean implications and those found by commonly used methods for mining associations show that existing methods would miss relationships found by Boolean implications. Furthermore, many relationships exposed by Boolean implications reflect important aspects of cancer biology. Examples of our findings include cis relationships between copy number alteration, DNA methylation and expression of genes, a new hierarchy of mutations and recurrent copy number alterations, loss-of-heterozygosity of well-known tumor suppressors, and the hypermethylation phenotype associated with IDH1 mutations in GBM. The Boolean implication results used in the paper can be accessed at http://crookneck.stanford.edu/microarray/TCGANetworks/. PMID:25054200
Mining TCGA data using Boolean implications.
Sinha, Subarna; Tsang, Emily K; Zeng, Haoyang; Meister, Michela; Dill, David L
2014-01-01
Boolean implications (if-then rules) provide a conceptually simple, uniform and highly scalable way to find associations between pairs of random variables. In this paper, we propose to use Boolean implications to find relationships between variables of different data types (mutation, copy number alteration, DNA methylation and gene expression) from the glioblastoma (GBM) and ovarian serous cystadenoma (OV) data sets from The Cancer Genome Atlas (TCGA). We find hundreds of thousands of Boolean implications from these data sets. A direct comparison of the relationships found by Boolean implications and those found by commonly used methods for mining associations show that existing methods would miss relationships found by Boolean implications. Furthermore, many relationships exposed by Boolean implications reflect important aspects of cancer biology. Examples of our findings include cis relationships between copy number alteration, DNA methylation and expression of genes, a new hierarchy of mutations and recurrent copy number alterations, loss-of-heterozygosity of well-known tumor suppressors, and the hypermethylation phenotype associated with IDH1 mutations in GBM. The Boolean implication results used in the paper can be accessed at http://crookneck.stanford.edu/microarray/TCGANetworks/.
Model Checking of Boolean Process Models
Schneider, Christoph
2011-01-01
In the field of Business Process Management formal models for the control flow of business processes have been designed since more than 15 years. Which methods are best suited to verify the bulk of these models? The first step is to select a formal language which fixes the semantics of the models. We adopt the language of Boolean systems as reference language for Boolean process models. Boolean systems form a simple subclass of coloured Petri nets. Their characteristics are low tokens to model explicitly states with a subsequent skipping of activations and arbitrary logical rules of type AND, XOR, OR etc. to model the split and join of the control flow. We apply model checking as a verification method for the safeness and liveness of Boolean systems. Model checking of Boolean systems uses the elementary theory of propositional logic, no modal operators are needed. Our verification builds on a finite complete prefix of a certain T-system attached to the Boolean system. It splits the processes of the Boolean sy...
Mining TCGA data using Boolean implications.
Subarna Sinha
Full Text Available Boolean implications (if-then rules provide a conceptually simple, uniform and highly scalable way to find associations between pairs of random variables. In this paper, we propose to use Boolean implications to find relationships between variables of different data types (mutation, copy number alteration, DNA methylation and gene expression from the glioblastoma (GBM and ovarian serous cystadenoma (OV data sets from The Cancer Genome Atlas (TCGA. We find hundreds of thousands of Boolean implications from these data sets. A direct comparison of the relationships found by Boolean implications and those found by commonly used methods for mining associations show that existing methods would miss relationships found by Boolean implications. Furthermore, many relationships exposed by Boolean implications reflect important aspects of cancer biology. Examples of our findings include cis relationships between copy number alteration, DNA methylation and expression of genes, a new hierarchy of mutations and recurrent copy number alterations, loss-of-heterozygosity of well-known tumor suppressors, and the hypermethylation phenotype associated with IDH1 mutations in GBM. The Boolean implication results used in the paper can be accessed at http://crookneck.stanford.edu/microarray/TCGANetworks/.
Baculovirus FP25K Localization: Role of the Coiled-Coil Domain.
Garretson, Tyler A; McCoy, Jason C; Cheng, Xiao-Wen
2016-11-01
Two types of viruses are produced during the baculovirus life cycle: budded virus (BV) and occlusion-derived virus (ODV). A particular baculovirus protein, FP25K, is involved in the switch from BV to ODV production. Previously, FP25K from the model alphabaculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) was shown to traffic ODV envelope proteins. However, FP25K localization and the domains involved are inconclusive. Here we used a quantitative approach to study FP25K subcellular localization during infection using an AcMNPV bacmid virus that produces a functional AcMNPV FP25K-green fluorescent protein (GFP) fusion protein. During cell infection, FP25K-GFP localized primarily to the cytoplasm, particularly amorphous structures, with a small fraction being localized in the nucleus. To investigate the sequences involved in FP25K localization, an alignment of baculovirus FP25K sequences revealed that the N-terminal putative coiled-coil domain is present in all alphabaculoviruses but absent in betabaculoviruses. Structural prediction indicated a strong relatedness of AcMNPV FP25K to long interspersed element 1 (LINE-1) open reading frame 1 protein (ORF1p), which contains an N-terminal coiled-coil domain responsible for cytoplasmic retention. Point mutations and deletions of this domain lead to a change in AcMNPV FP25K localization from cytoplasmic to nuclear. The coiled-coil and C-terminal deletion viruses increased BV production. Furthermore, a betabaculovirus FP25K protein lacking this N-terminal coiled-coil domain localized predominantly to the nucleus and exhibited increased BV production. These data suggest that the acquisition of this N-terminal coiled-coil domain in FP25K is important for the evolution of alphabaculoviruses. Moreover, with the divergence of preocclusion nuclear membrane breakdown in betabaculoviruses and membrane integrity in alphabaculoviruses, this domain represents an alphabaculovirus adaptation for nuclear trafficking
G.C. Rao
2012-11-01
Full Text Available A C- algebra is the algebraic form of the 3-valued conditional logic, which was introduced by F. Guzman and C. C. Squier in 1990. In this paper, some equivalent conditions for a C- algebra to become a boolean algebra in terms of congruences are given. It is proved that the set of all central elements B(A is isomorphic to the Boolean algebra of all C-algebras Sa, where a B(A. It is also proved that B(A is isomorphic to the Boolean algebra of all C-algebras Aa, where a B(A.
Robust Reachability of Boolean Control Networks.
Li, Fangfei; Tang, Yang
2016-04-20
Boolean networks serve a powerful tool in analysis of genetic regulatory networks since it emphasizes the fundamental principles and establishes a nature framework for capturing the dynamics of regulation of cellular states. In this paper, the robust reachability of Boolean control networks is investigated by means of semi-tensor product. Necessary and sufficient conditions for the robust reachability of Boolean control networks are provided, in which control inputs relying on disturbances or not are considered, respectively. Besides, the corresponding control algorithms are developed for these two cases. A reduced model of the lac operon in the Escherichia coli is presented to show the effectiveness of the presented results.
Flexible method for Boolean information retrieval
Salton, G.; Wu, H.
1983-01-01
A new flexible retrieval system is described which makes it possible to relax the strict conditions of Boolean query logic thereby retrieving useful items that are rejected in a conventional retrieval situation. The query structure inherent in the Boolean system is preserved, while at the same time weighted terms may be incorporated into both queries and stored documents; the retrieved output can also be ranked in strict similarity order with the user queries. A conventional retrieval system can be modified to make use of the flexible metric system. Laboratory tests indicate that the extended system produces better retrieval output than either the Boolean or the vector processing systems. 11 references.
Stability of Boolean Multiplex Networks
Cozzo, Emanuele; Moreno, Yamir
2012-01-01
We extend the formalism of Random Boolean Networks with canalizing rules to multilevel complex networks. The formalism allows to model genetic networks in which each gene might take part in more than one signaling pathway. We use a semi-annealed approach to study the stability of this class of models when coupled in a multiplex network and show that the analytical results are in good agreement with numerical simulations. Our main finding is that the multiplex structure provides a mechanism for the stabilization of the system and of chaotic regimes of individual layers. Our results help understanding why some genetic networks that are theoretically expected to operate in the chaotic regime can actually display dynamical stability.
Generalizing Boolean Satisfiability II: Theory
Dixon, H E; Luks, E M; Parkes, A J; 10.1613/jair.1555
2011-01-01
This is the second of three planned papers describing ZAP, a satisfiability engine that substantially generalizes existing tools while retaining the performance characteristics of modern high performance solvers. The fundamental idea underlying ZAP is that many problems passed to such engines contain rich internal structure that is obscured by the Boolean representation used; our goal is to define a representation in which this structure is apparent and can easily be exploited to improve computational performance. This paper presents the theoretical basis for the ideas underlying ZAP, arguing that existing ideas in this area exploit a single, recurring structure in that multiple database axioms can be obtained by operating on a single axiom using a subgroup of the group of permutations on the literals in the problem. We argue that the group structure precisely captures the general structure at which earlier approaches hinted, and give numerous examples of its use. We go on to extend the Davis-Putnam-Logemann-...
Boolean networks with reliable dynamics
Peixoto, Tiago P
2009-01-01
We investigated the properties of Boolean networks that follow a given reliable trajectory in state space. A reliable trajectory is defined as a sequence of states which is independent of the order in which the nodes are updated. We explored numerically the topology, the update functions, and the state space structure of these networks, which we constructed using a minimum number of links and the simplest update functions. We found that the clustering coefficient is larger than in random networks, and that the probability distribution of three-node motifs is similar to that found in gene regulation networks. Among the update functions, only a subset of all possible functions occur, and they can be classified according to their probability. More homogeneous functions occur more often, leading to a dominance of canalyzing functions. Finally, we studied the entire state space of the networks. We observed that with increasing systems size, fixed points become more dominant, moving the networks close to the frozen...
Adiabatic quantum gates and Boolean functions
Andrecut, M; Ali, M K [Department of Physics, University of Lethbridge, Lethbridge, AB, T1K 3M4 (Canada)
2004-06-25
We discuss the logical implementation of quantum gates and Boolean functions in the framework of quantum adiabatic method, which uses the language of ground states, spectral gaps and Hamiltonians instead of the standard unitary transformation language. (letter to the editor)
Boolean computation of optimum hitting sets
Hulme, B.L.; Baca, L.S.; Shiver, A.W.; Worrell, R.B.
1984-04-01
This report presents the results of computational experience in solving weighted hitting set problems by Boolean algebraic methods. The feasible solutions are obtained by Boolean formula manipulations, and the optimum solutions are obtained by comparing the weight sums of the feasible solutions. Both the algebra and the optimization can be accomplished using the SETS language. One application is to physical protection problems. 8 references, 2 tables.
Non-Boolean probabilities and quantum measurement
Niestegge, Gerd
2001-08-03
A non-Boolean extension of the classical probability model is proposed. The non-Boolean probabilities reproduce typical quantum phenomena. The proposed model is more general and more abstract, but easier to interpret, than the quantum mechanical Hilbert space formalism and exhibits a particular phenomenon (state-independent conditional probabilities) which may provide new opportunities for an understanding of the quantum measurement process. Examples of the proposed model are provided, using Jordan operator algebras. (author)
On Boolean matrices with full factor rank
Shitov, Ya [National Research University " Higher School of Economics" , Moscow (Russian Federation)
2013-11-30
It is demonstrated that every (0,1)-matrix of size n×m having Boolean rank n contains a column with at least √n/2−1 zero entries. This bound is shown to be asymptotically optimal. As a corollary, it is established that the size of a full-rank Boolean matrix is bounded from above by a function of its tropical and determinantal ranks. Bibliography: 16 titles.
Stochastic coupling of two random Boolean networks
Ho, M.-C. [Department of Physics, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)]. E-mail: t1603@nknucc.nknu.edu.tw; Hung, Y.-C. [Department of Physics, National Sun Yat-sen University, Kaohsiung, Taiwan (China)]. E-mail: d9123801@student.nsysu.edu.tw; Jiang, I-M. [Department of Physics, National Sun Yat-sen University, Kaohsiung, Taiwan (China)
2005-08-29
We study the dynamics of two coupled random Boolean networks. Based on the Boolean model studied by Andrecut and Ali [Int. J. Mod. Phys. B 15 (2001) 17] and the stochastic coupling techniques, the density evolution of networks is precisely described by two deterministic coupled polynomial maps. The iteration results of the model match the real networks well. By using MSE and the maximal Lyapunov exponents, the synchronization phenomena of coupled networks is also under our discussion.
Local absorbing boundary conditions for nonlinear wave equation on unbounded domain.
Li, Hongwei; Wu, Xiaonan; Zhang, Jiwei
2011-09-01
The numerical solution of the nonlinear wave equation on unbounded spatial domain is considered. The artificial boundary method is introduced to reduce the nonlinear problem on unbounded spatial domain to an initial boundary value problem on a bounded domain. Using the unified approach, which is based on the operator splitting method, we construct the efficient nonlinear local absorbing boundary conditions for the nonlinear wave equation, and give the stability analysis of the resulting boundary conditions. Finally, several numerical examples are given to demonstrate the effectiveness of our method.
Selective domain wall depinning by localized Oersted fields and Joule heating
Ilgaz, Dennis; Kläui, Mathias; Heyne, Lutz; Boulle, Olivier; Zinser, Fabian; Krzyk, Stephen; Fonin, Mikhail; Rüdiger, Ulrich; Backes, Dirk; Heyderman, Laura J.
2008-09-01
Using low temperature magnetoresistance measurements, the possibility to selectively move a domain wall locally by applying current pulses through a Au nanowire adjacent to a permalloy element is studied. We find that the domain wall depinning field is drastically modified with increasing current density due to the Joule heating and the Oersted field of the current, and controlled motion due to the Oersted field without any externally applied fields is achieved. By placing the domain wall at various distances from the Au wire, we determine the range of the Joule heating and the Oersted field and both effects can be separated.
Symmetry in critical random Boolean network dynamics
Hossein, Shabnam; Reichl, Matthew D.; Bassler, Kevin E.
2014-04-01
Using Boolean networks as prototypical examples, the role of symmetry in the dynamics of heterogeneous complex systems is explored. We show that symmetry of the dynamics, especially in critical states, is a controlling feature that can be used both to greatly simplify analysis and to characterize different types of dynamics. Symmetry in Boolean networks is found by determining the frequency at which the various Boolean output functions occur. There are classes of functions that consist of Boolean functions that behave similarly. These classes are orbits of the controlling symmetry group. We find that the symmetry that controls the critical random Boolean networks is expressed through the frequency by which output functions are utilized by nodes that remain active on dynamical attractors. This symmetry preserves canalization, a form of network robustness. We compare it to a different symmetry known to control the dynamics of an evolutionary process that allows Boolean networks to organize into a critical state. Our results demonstrate the usefulness and power of using the symmetry of the behavior of the nodes to characterize complex network dynamics, and introduce an alternative approach to the analysis of heterogeneous complex systems.
Symmetry in critical random Boolean network dynamics.
Hossein, Shabnam; Reichl, Matthew D; Bassler, Kevin E
2014-04-01
Using Boolean networks as prototypical examples, the role of symmetry in the dynamics of heterogeneous complex systems is explored. We show that symmetry of the dynamics, especially in critical states, is a controlling feature that can be used both to greatly simplify analysis and to characterize different types of dynamics. Symmetry in Boolean networks is found by determining the frequency at which the various Boolean output functions occur. There are classes of functions that consist of Boolean functions that behave similarly. These classes are orbits of the controlling symmetry group. We find that the symmetry that controls the critical random Boolean networks is expressed through the frequency by which output functions are utilized by nodes that remain active on dynamical attractors. This symmetry preserves canalization, a form of network robustness. We compare it to a different symmetry known to control the dynamics of an evolutionary process that allows Boolean networks to organize into a critical state. Our results demonstrate the usefulness and power of using the symmetry of the behavior of the nodes to characterize complex network dynamics, and introduce an alternative approach to the analysis of heterogeneous complex systems.
Robust method for infrared small-target detection based on Boolean map visual theory.
Qi, Shengxiang; Ming, Delie; Ma, Jie; Sun, Xiao; Tian, Jinwen
2014-06-20
In this paper, we present an infrared small target detection method based on Boolean map visual theory. The scheme is inspired by the phenomenon that small targets can often attract human attention due to two characteristics: brightness and Gaussian-like shape in the local context area. Motivated by this observation, we perform the task under a visual attention framework with Boolean map theory, which reveals that an observer's visual awareness corresponds to one Boolean map via a selected feature at any given instant. Formally, the infrared image is separated into two feature channels, including a color channel with the original gray intensity map and an orientation channel with the orientation texture maps produced by a designed second order directional derivative filter. For each feature map, Boolean maps delineating targets are computed from hierarchical segmentations. Small targets are then extracted from the target enhanced map, which is obtained by fusing the weighted Boolean maps of the two channels. In experiments, a set of real infrared images covering typical backgrounds with sky, sea, and ground clutters are tested to verify the effectiveness of our method. The results demonstrate that it outperforms the state-of-the-art methods with good performance.
Immune evolutionary algorithms with domain knowledge for simultaneous localization and mapping
LI Mei-yi; CAI Zi-xing
2006-01-01
Immune evolutionary algorithms with domain knowledge were presented to solve the problem of simultaneous localization and mapping for a mobile robot in unknown environments. Two operators with domain knowledge were designed in algorithms, where the feature of parallel line segments without the problem of data association was used to construct a vaccination operator, and the characters of convex vertices in polygonal obstacle were extended to develop a pulling operator of key point grid. The experimental results of a real mobile robot show that the computational expensiveness of algorithms designed is less than other evolutionary algorithms for simultaneous localization and mapping and the maps obtained are very accurate. Because immune evolutionary algorithms with domain knowledge have some advantages, the convergence rate of designed algorithms is about 44 % higher than those of other algorithms.
A20 Functional Domains Regulate Subcellular Localization and NF-Kappa B Activation
2013-08-15
coined the term POLKADOTS or punctate and oligomeric killing or activating domains transducing signals to describe these structures (92...signalsome: Three decades of discovery. Cell Cycle 2011;10:2485-96. 94. Rudner DZ, Losick R. Protein Subcellular localization in bacteria . Cold
On the average sensitivity of laced Boolean functions
jiyou, Li
2011-01-01
In this paper we obtain the average sensitivity of the laced Boolean functions. This confirms a conjecture of Shparlinski. We also compute the weights of the laced Boolean functions and show that they are almost balanced.
Boolean Networks with Multi-Expressions and Parameters.
Zou, Yi Ming
2013-07-01
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean models, both synchronous and asynchronous, have been proposed in the literature. However, analytical study of these more general Boolean networks models is lagging. This paper aims to develop a concise theory for these different Boolean logic based modeling methods. Boolean models for networks where each node can have more than two levels of expression and Boolean models with parameters are defined algebraically with examples provided. Certain classes of random asynchronous Boolean networks and deterministic moduli asynchronous Boolean networks are investigated in detail using the setting introduced in this paper. The derived theorems provide a clear picture for the attractor structures of these asynchronous Boolean networks.
Using domain walls to perform non-local measurements with high spin signal amplitudes
Savero Torres, W.; Pham, V.-T.; Zahnd, G.; Laczkowski, P.; Nguyen, V.-D.; Beigné, C.; Notin, L.; Jamet, M.; Marty, A.; Vila, L.; Attané, J.-P.
2016-07-01
Standard non-local measurements require lateral spin-valves with two different ferromagnetic electrodes, to create and to detect the spin accumulation. Here we show that non-local measurements can also be performed in a cross-shaped nanostructure, made of a single ferromagnetic wire connected to an orthogonal non-magnetic wire. A magnetic domain wall located underneath the ferromagnetic/non-magnetic interface is used to control the magnetizations of the injection and detection zones. As these zones can be very close, our results display spin signals possessing amplitudes larger than those obtained in conventional non-local measurements. We also show that this method can be used as a domain wall detection technique.
Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates.
Elia, Andrew E H; Cantley, Lewis C; Yaffe, Michael B
2003-02-21
We have developed a proteomic approach for identifying phosphopeptide binding domains that modulate kinase-dependent signaling pathways. An immobilized library of partially degenerate phosphopeptides biased toward a particular protein kinase phosphorylation motif is used to isolate phospho-binding domains that bind to proteins phosphorylated by that kinase. Applying this approach to cyclin-dependent kinases (Cdks), we identified the polo-box domain (PBD) of the mitotic kinase polo-like kinase 1 (Plk1) as a specific phosphoserine (pSer) or phosphothreonine (pThr) binding domain and determined its optimal binding motif. This motif is present in known Plk1 substrates such as Cdc25, and an optimal phosphopeptide containing the motif disrupted PBD-substrate binding and localization of the PBD to centrosomes. This finding reveals how Plk1 can localize to specific sites within cells in response to Cdk phosphorylation at those sites and provides a structural mechanism for targeting the Plk1 kinase domain to its substrates.
Symmetry in Critical Random Boolean Networks Dynamics
Bassler, Kevin E.; Hossein, Shabnam
2014-03-01
Using Boolean networks as prototypical examples, the role of symmetry in the dynamics of heterogeneous complex systems is explored. We show that symmetry of the dynamics, especially in critical states, is a controlling feature that can be used to both greatly simplify analysis and to characterize different types of dynamics. Symmetry in Boolean networks is found by determining the frequency at which the various Boolean output functions occur. Classes of functions occur at the same frequency. These classes are orbits of the controlling symmetry group. We find the nature of the symmetry that controls the dynamics of critical random Boolean networks by determining the frequency of output functions utilized by nodes that remain active on dynamical attractors. This symmetry preserves canalization, a form of network robustness. We compare it to a different symmetry known to control the dynamics of an evolutionary process that allows Boolean networks to organize into a critical state. Our results demonstrate the usefulness and power of using symmetry to characterize complex network dynamics, and introduce a novel approach to the analysis of heterogeneous complex systems. This work was supported by the NSF through grants DMR-0908286 and DMR-1206839, and by the AFSOR and DARPA through grant FA9550-12-1-0405.
Simulating Boolean circuits on a DNA computer
Ogihara, Mitsunori; Ray, A. [Univ. of Rochester, NY (United States)
1997-12-01
We demonstrate that DNA computers can simulate Boolean circuits with a small overhead. Boolean circuits embody the notion of massively parallel signal processing and are frequently encountered in many parallel algorithms. Many important problems such as sorting, integer arithmetic, and matrix multiplication are known to be computable by small size Boolean circuits much faster than by ordinary sequential digital computers. This paper shows that DNA chemistry allows one to simulate large semi-unbounded fan-in Boolean circuits with a logarithmic slowdown in computation time. Also, for the class NC{sup 1}, the slowdown can be reduced to a constant. In this algorithm we have encoded the inputs, the Boolean AND gates, and the OR gates to DNA oligonucleotide sequences. We operate on the gates and the inputs by standard molecular techniques of sequence-specific annealing, ligation, separation by size, amplification, sequence-specific cleavage, and detection by size. Additional steps of amplification are not necessary for NC{sup 1} circuits. Preliminary biochemical experiments on a small test circuit have produced encouraging results. Further confirmatory experiments are in progress. 19 refs., 3 figs., 1 tab.
Complex network analysis of state spaces for random Boolean networks
Shreim, Amer [Complexity Science Group, Department of Physics and Astronomy, University of Calgary, Calgary, AB, T2N 1N4 (Canada); Berdahl, Andrew [Complexity Science Group, Department of Physics and Astronomy, University of Calgary, Calgary, AB, T2N 1N4 (Canada); Sood, Vishal [Complexity Science Group, Department of Physics and Astronomy, University of Calgary, Calgary, AB, T2N 1N4 (Canada); Grassberger, Peter [Complexity Science Group, Department of Physics and Astronomy, University of Calgary, Calgary, AB, T2N 1N4 (Canada); Paczuski, Maya [Complexity Science Group, Department of Physics and Astronomy, University of Calgary, Calgary, AB, T2N 1N4 (Canada)
2008-01-15
We apply complex network analysis to the state spaces of random Boolean networks (RBNs). An RBN contains N Boolean elements each with K inputs. A directed state space network (SSN) is constructed by linking each dynamical state, represented as a node, to its temporal successor. We study the heterogeneity of these SSNs at both local and global scales, as well as sample to-sample fluctuations within an ensemble of SSNs. We use in-degrees of nodes as a local topological measure, and the path diversity (Shreim A et al 2007 Phys. Rev. Lett. 98 198701) of an SSN as a global topological measure. RBNs with 2 {<=} K {<=} 5 exhibit non-trivial fluctuations at both local and global scales, while K = 2 exhibits the largest sample-to-sample (possibly non-self-averaging) fluctuations. We interpret the observed 'multi scale' fluctuations in the SSNs as indicative of the criticality and complexity of K = 2 RBNs. 'Garden of Eden' (GoE) states are nodes on an SSN that have in-degree zero. While in-degrees of non-GoE nodes for K > 1 SSNs can assume any integer value between 0 and 2{sup N}, for K = 1 all the non-GoE nodes in a given SSN have the same in-degree which is always a power of two.
Synchronization of coupled large-scale Boolean networks
Li, Fangfei, E-mail: li-fangfei@163.com [Department of Mathematics, East China University of Science and Technology, No. 130, Meilong Road, Shanghai, Shanghai 200237 (China)
2014-03-15
This paper investigates the complete synchronization and partial synchronization of two large-scale Boolean networks. First, the aggregation algorithm towards large-scale Boolean network is reviewed. Second, the aggregation algorithm is applied to study the complete synchronization and partial synchronization of large-scale Boolean networks. Finally, an illustrative example is presented to show the efficiency of the proposed results.
Synchronization of coupled large-scale Boolean networks
Li, Fangfei
2014-03-01
This paper investigates the complete synchronization and partial synchronization of two large-scale Boolean networks. First, the aggregation algorithm towards large-scale Boolean network is reviewed. Second, the aggregation algorithm is applied to study the complete synchronization and partial synchronization of large-scale Boolean networks. Finally, an illustrative example is presented to show the efficiency of the proposed results.
A Simple Blueprint for Automatic Boolean Query Processing.
Salton, G.
1988-01-01
Describes a new Boolean retrieval environment in which an extended soft Boolean logic is used to automatically construct queries from original natural language formulations provided by users. Experimental results that compare the retrieval effectiveness of this method to conventional Boolean and vector processing are discussed. (27 references)…
Duality theories for Boolean algebras with operators
Givant, Steven
2014-01-01
In this new text, Steven Givant—the author of several acclaimed books, including works co-authored with Paul Halmos and Alfred Tarski—develops three theories of duality for Boolean algebras with operators. Givant addresses the two most recognized dualities (one algebraic and the other topological) and introduces a third duality, best understood as a hybrid of the first two. This text will be of interest to graduate students and researchers in the fields of mathematics, computer science, logic, and philosophy who are interested in exploring special or general classes of Boolean algebras with operators. Readers should be familiar with the basic arithmetic and theory of Boolean algebras, as well as the fundamentals of point-set topology.
Forced synchronization of autonomous dynamical Boolean networks
Rivera-Durón, R. R., E-mail: roberto.rivera@ipicyt.edu.mx; Campos-Cantón, E., E-mail: eric.campos@ipicyt.edu.mx [División de Matemáticas Aplicadas, Instituto Potosino de Investigación Científica y Tecnológica A. C., Camino a la Presa San José 2055, Col. Lomas 4 Sección, C.P. 78216, San Luis Potosí, S.L.P. (Mexico); Campos-Cantón, I. [Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, C.P. 78000, San Luis Potosí, S.L.P. (Mexico); Gauthier, Daniel J. [Department of Physics and Center for Nonlinear and Complex Systems, Duke University, Box 90305, Durham, North Carolina 27708 (United States)
2015-08-15
We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enable future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics.
Forced synchronization of autonomous dynamical Boolean networks.
Rivera-Durón, R R; Campos-Cantón, E; Campos-Cantón, I; Gauthier, Daniel J
2015-08-01
We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enable future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics.
Boolean nested canalizing functions: a comprehensive analysis
Li, Yuan; Murrugarra, David; Aguilar, Boris; Laubenbacher, Reinhard
2012-01-01
Boolean network models of molecular regulatory networks have been used successfully in computational systems biology. The Boolean functions that appear in published models tend to have special properties, in particular the property of being nested canalizing, a property inspired by the concept of canalization in evolutionary biology. It has been shown that networks comprised of nested canalizing functions have dynamic properties that make them suitable for modeling molecular regulatory networks, namely a small number of (large) attractors, as well as relatively short limit cycles. This paper contains a detailed analysis of this class of functions, based on a novel normal form as polynomial functions over the Boolean field. The concept of layer is introduced that stratifies variables into different classes depending on their level of dominance. Using this layer concept a closed form formula is derived for the number of nested canalizing functions with a given number of variables. Additional metrics analyzed in...
Coherent spaces, Boolean rings and quantum gates
Vourdas, A.
2016-10-01
Coherent spaces spanned by a finite number of coherent states, are introduced. Their coherence properties are studied, using the Dirac contour representation. It is shown that the corresponding projectors resolve the identity, and that they transform into projectors of the same type, under displacement transformations, and also under time evolution. The set of these spaces, with the logical OR and AND operations is a distributive lattice, and with the logical XOR and AND operations is a Boolean ring (Stone's formalism). Applications of this Boolean ring into classical CNOT gates with n-ary variables, and also quantum CNOT gates with coherent states, are discussed.
Inferring Boolean network states from partial information
2013-01-01
Networks of molecular interactions regulate key processes in living cells. Therefore, understanding their functionality is a high priority in advancing biological knowledge. Boolean networks are often used to describe cellular networks mathematically and are fitted to experimental datasets. The fitting often results in ambiguities since the interpretation of the measurements is not straightforward and since the data contain noise. In order to facilitate a more reliable mapping between datasets and Boolean networks, we develop an algorithm that infers network trajectories from a dataset distorted by noise. We analyze our algorithm theoretically and demonstrate its accuracy using simulation and microarray expression data. PMID:24006954
Information encryption systems based on Boolean functions
Aureliu Zgureanu
2011-02-01
Full Text Available An information encryption system based on Boolean functions is proposed. Information processing is done using multidimensional matrices, performing logical operations with these matrices. At the basis of ensuring high level security of the system the complexity of solving the problem of building systems of Boolean functions that depend on many variables (tens and hundreds is set. Such systems represent the private key. It varies both during the encryption and decryption of information, and during the transition from one message to another.
Analysis of affinely equivalent Boolean functions
MENG QingShu; ZHANG HuanGuo; YANG Min; WANG ZhangYi
2007-01-01
By some basic transforms and invariant theory, we give two results: 1) an algorithm,which can be used to judge if two Boolean functions are affinely equivalent and to obtain the equivalence relationship if they are equivalent. This is useful in studying Boolean functions and in engineering. For example, we classify all 8-variable homogeneous bent functions of degree 3 into two classes; 2) Reed-Muller codes R(4,6)/R(1,6), R(3,7)/R(1,7) are classified efficiently.
Boolean differentiation and integration using Karnaugh maps
Tucker, J. H.; Tapia, M. A.; Bennett, A. W.
1977-01-01
Algorithms are presented for differentiation and integration of Boolean functions by means of Karnaugh maps. The algorithms are considered simple when the number of variables is six or less; in this case Boolean differentiation and integration is said to be as easy as the Karnaugh map method of simplifying switching functions. It is suggested that the algorithms would be useful in the analysis of faults in combinational systems and in the synthesis of asynchronous sequential systems which utilize edge-sensitive flip-flops.
Localization and chiral symmetry in 2+1 flavor domain wall QCD
Antonio, David J; Boyle, Peter A; Christ, Norman H; Clark, Michael A; Cohen, Saul D; Dawson, Chris; Hart, Alistair; Joó, Balint; Jung, Chulwoo; Kenway, Richard D; Li, Shu; Lin, Meifeng; Mawhinney, Robert D; Maynard, Christopher M; Ohta, Shigemi; Tweedie, Robert J; Yamaguchi, Azusa
2007-01-01
We present results for the dependence of the residual mass of domain wall fermions (DWF) on the size of the fifth dimension and its relation to the density and localization properties of low-lying eigenvectors of the corresponding hermitian Wilson Dirac operator for 2+1 flavor domain wall QCD. Using the DBW2 and Iwasaki gauge actions, we generate ensembles of configurations with a $16^3\\times 32$ space-time volume and an extent of 8 in the fifth dimension for the sea quarks. We demonstrate the existence of a regime where the degree of locality, the size of chiral symmetry breaking and the rate of topology change can be acceptable for inverse lattice spacings $a^{-1} \\ge 1.6$ GeV.
Localization and chiral symmetry in 2+1 flavor domain wall QCD
David J. Antonio; Kenneth C. Bowler; Peter A. Boyle; Norman H. Christ; Michael A. Clark; Saul D. Cohen; Chris Dawson; Alistair Hart; Balint Joó; Chulwoo Jung; Richard D. Kenway; Shu Li; Meifeng Lin; Robert D. Mawhinney; Christopher M. Maynard; Shigemi Ohta; Robert J. Tweedie; Azusa Yamaguchi
2008-01-01
We present results for the dependence of the residual mass of domain wall fermions (DWF) on the size of the fifth dimension and its relation to the density and localization properties of low-lying eigenvectors of the corresponding hermitian Wilson Dirac operator relevant to simulations of 2+1 flavor domain wall QCD. Using the DBW2 and Iwasaki gauge actions, we generate ensembles of configurations with a $16^3\\times 32$ space-time volume and an extent of 8 in the fifth dimension for the sea quarks. We demonstrate the existence of a regime where the degree of locality, the size of chiral symmetry breaking and the rate of topology change can be acceptable for inverse lattice spacings $a^{-1} \\ge 1.6$ GeV.
Domain selection for the varying coefficient model via local polynomial regression.
Kong, Dehan; Bondell, Howard; Wu, Yichao
2015-03-01
In this article, we consider the varying coefficient model, which allows the relationship between the predictors and response to vary across the domain of interest, such as time. In applications, it is possible that certain predictors only affect the response in particular regions and not everywhere. This corresponds to identifying the domain where the varying coefficient is nonzero. Towards this goal, local polynomial smoothing and penalized regression are incorporated into one framework. Asymptotic properties of our penalized estimators are provided. Specifically, the estimators enjoy the oracle properties in the sense that they have the same bias and asymptotic variance as the local polynomial estimators as if the sparsity is known as a priori. The choice of appropriate bandwidth and computational algorithms are discussed. The proposed method is examined via simulations and a real data example.
Single domain wall manipulation in curved nanowires using a mobile, local, circular field
Shortt, Madeline; Bickel, Jessica; Khan, Mina; Tuominen, Mark; Aidala, Katherine
2014-03-01
Ferromagnetic nanostructures present exciting physics with a range of potential applications in data storage devices, such as magnetoresistive random access memory (MRAM). These proposals require precise control and understanding of domain wall (DW) movement and interactions. We developed a technique that generates a local circular Oersted field at a precise location by applying current through the tip of the atomic force microscope (AFM). We previously used this technique to control DW motion in nanorings. We extend this method to control individual DW movement in curved nanowires by placing the tip near a 180 DW at the vertex of a curved wire and generating a local field. In this way, we can examine the motion of domain walls through regions with different curvature and the effects of pinning. This work was supported in part by NSF DMR-1207924 and the UMass Center for Hierarchical Manufacturing, NSF CMMI-1025020.
A RF time domain approach for electric arcs detection and localization systems
Deacu, Daniela; Tamas, Razvan; Petrescu, Teodor; Paun, Mirel; Anchidin, Liliana; Algiu, Madalina
2016-12-01
In this paper we propose a new method for detection and localization of electric arcs by using two ultra-wide band (UWB) antennas together with data processing in the time-domain. The source of electric arcs is localized by computing an average on the inter-correlation functions of the signals received on two channels. By calculating the path length difference to the antennas, the direction of the electric arcs is then found. The novelty of the method consists in the spatial averaging in order to reduce the incertitude caused by the finite sampling rate.
Local Exponential Methods: a domain decomposition approach to exponential time integration of PDEs
Bonaventura, Luca
2015-01-01
A local approach to the time integration of PDEs by exponential methods is proposed, motivated by theoretical estimates by A.Iserles on the decay of off-diagonal terms in the exponentials of sparse matrices. An overlapping domain decomposition technique is outlined, that allows to replace the computation of a global exponential matrix by a number of independent and easily parallelizable local problems. Advantages and potential problems of the proposed technique are discussed. Numerical experiments on simple, yet relevant model problems show that the resulting method allows to increase computational efficiency with respect to standard implementations of exponential methods.
刘卫锋
2013-01-01
将软集理论应用到布尔代数中，提出了软布尔代数、软布尔子代数、软布尔代数的软理想、软理想布尔代数等概念，研究了它们的相关性质，并初步讨论了软布尔代数与几类布尔代数的模糊子代数的关系。%The soft set theory is applied to the Boolean algebra.The concepts of soft Boolean algebra, soft Boolean sub-algebra, soft ideal of soft Boolean algebra and idealistic soft Boolean algebra are presented and some related algebraic properties are discussed.The relations between soft Boolean algebra and several kinds of fuzzy subalgebras of Boolean algebra are preliminarily investigated.
Subcellular localization and functional analyses of structural domains of COP1 in transgenic tobacco
无
2002-01-01
Plants have evolved an extremely exquisite light signal regulatory network to adapt to the changing ambient light conditions, in which COP1 plays a critical roleof the light signal transduction. Based on the cloned pea COP1 cDNA sequence and its protein structure, four indi-vidual gene fragments encoding different structural domains of the COP1 were designed to fuse to the GFP gene. The plant expression vectors containing these fusion genes as well as the COP1GFP fusion gene were constructed and used to transform tobacco by Agribacterium as confirmed by South-]ern analyses. Antibodies were raised against the recombi-nant GFP-COP1 overproduced in Escherichia coli. Im-munoblotting results demonstrated that all of the fusion genes were constitutively expressed in transgenic tobacco plants. We systematically investigated the different subcell- ular localization of these fusion proteins and the resulting phenotypic characteristics of these transgenic plants under light and dark conditions. Our data show that (1) the mo-lecular mass of the tobacco endogenous COP1 protein is 76 kD. It is constitutively expressed in all of the tested tissues and the total cellular content of COP1 protein is not noticea-bly affected by light conditions. (2) The nuclear localization signal of COP1 plays a critical role in regulation of its nu-clear-cytoplasmic partitioning. The subcellular localization of the COP1 protein containing nuclear localization signal is regulated by light in the epidermal cells of leaves, but, it is located in nucleus constitutively in root cells. (3) The coiled-coil domain is very critical to the function of COP1 protein, while the zinc binding RING finger domain only plays a supportive role. (4) The WD-40 repeats domain is essential to the COP1 function, but this domain alone does not affect photomorphogenesis. (5) Overexpression of COP1 protein not only inhibits the photomorphogenesis of the stems and leaves of the transgenic tobacco, but also results in the
Conserved roles of the prion protein domains on subcellular localization and cell-cell adhesion.
Gonzalo P Solis
Full Text Available Analyses of cultured cells and transgenic mice expressing prion protein (PrP deletion mutants have revealed that some properties of PrP -such as its ability to misfold, aggregate and trigger neurotoxicity- are controlled by discrete molecular determinants within its protein domains. Although the contributions of these determinants to PrP biosynthesis and turnover are relatively well characterized, it is still unclear how they modulate cellular functions of PrP. To address this question, we used two defined activities of PrP as functional readouts: 1 the recruitment of PrP to cell-cell contacts in Drosophila S2 and human MCF-7 epithelial cells, and 2 the induction of PrP embryonic loss- and gain-of-function phenotypes in zebrafish. Our results show that homologous mutations in mouse and zebrafish PrPs similarly affect their subcellular localization patterns as well as their in vitro and in vivo activities. Among PrP's essential features, the N-terminal leader peptide was sufficient to drive targeting of our constructs to cell contact sites, whereas lack of GPI-anchoring and N-glycosylation rendered them inactive by blocking their cell surface expression. Importantly, our data suggest that the ability of PrP to homophilically trans-interact and elicit intracellular signaling is primarily encoded in its globular domain, and modulated by its repetitive domain. Thus, while the latter induces the local accumulation of PrPs at discrete punctae along cell contacts, the former counteracts this effect by promoting the continuous distribution of PrP. In early zebrafish embryos, deletion of either domain significantly impaired PrP's ability to modulate E-cadherin cell adhesion. Altogether, these experiments relate structural features of PrP to its subcellular distribution and in vivo activity. Furthermore, they show that despite their large evolutionary history, the roles of PrP domains and posttranslational modifications are conserved between mouse and
Short single axioms for boolean algebra.
McCune, W.; Veroff, R.; Fitelson, B.; Harris, K.; Feist, A.; Wos, L.; Mathematics and Computer Science; Univ. of New Mexico; Univ. of Wisconsin at Madison; Duke Univ.
2002-01-01
We present short single equational axioms for Boolean algebra in terms of disjunction and negation and in terms of the Sheffer stroke. Previously known single axioms for these theories are much longer than the ones we present. We show that there is no shorter axiom in terms of the Sheffer stroke. Automated deduction techniques were used in several parts of the work.
A Short Sheffer axiom for Boolean algebra.
Veroff, R.; McCune, W.
2000-06-30
A short Sheffer stroke identity is shown to be a single axiom for Boolean algebra. The axiom has length 15 and 3 variables. The proof shows that it is equivalent to Sheffer's original 3-basis for the theory. Automated deduction techniques were used to find the proof. The shortest single axiom previously known to us has length 105 and 6 variables.
Demonstrating Boolean Logic Using Simple Electrical Circuits
McElhaney, Kevin W.
2004-01-01
While exploring the subject of geometric proofs, boolean logic operators AND and OR can be used to allow students to visualize their true-or-false patterns. An activity in the form of constructing electrical circuits is illustrated to explain the concept.
A Boolean Map Theory of Visual Attention
Huang, Liqiang; Pashler, Harold
2007-01-01
A theory is presented that attempts to answer two questions. What visual contents can an observer consciously access at one moment? Answer: only one feature value (e.g., green) per dimension, but those feature values can be associated (as a group) with multiple spatially precise locations (comprising a single labeled Boolean map). How can an…
Competitive learning of monotone Boolean functions
2014-01-01
We apply competitive analysis onto the problem of minimizing the number of queries to an oracle to completely reconstruct a given monotone Boolean function. Besides lower and upper bounds on the competitivity we determine optimal deterministic online algorithms for the smallest problem instances.
A complexity theory based on Boolean algebra
Skyum, Sven; Valiant, Leslie
1985-01-01
A projection of a Boolean function is a function obtained by substituting for each of its variables a variable, the negation of a variable, or a constant. Reducibilities among computational problems under this relation of projection are considered. It is shown that much of what is of everyday rel...
A. E. Ershov; A. P. Gavrilyuk; S. V. Karpov; P. N. Semina
2015-01-01
Interactions of pulsed laser radiation with resonance domains of multiparticle colloidal aggregates having an increas-ingly complex local environment are studied via an optodynamic model. The model is applied to the simplest configurations, such as single particles, dimers, and trimers consisting of mono-and polydisperse Ag nanoparticles. We analyze how the local environment and the associated local field enhancement by surrounding particles affect the optodynamic processes in domains, including their photomodification and optical properties.
Evolution of a designless nanoparticle network into reconfigurable Boolean logic
Bose, S. K.; Lawrence, C. P.; Liu, Z.; Makarenko, K. S.; van Damme, R. M. J.; Broersma, H. J.; van der Wiel, W. G.
2015-12-01
Natural computers exploit the emergent properties and massive parallelism of interconnected networks of locally active components. Evolution has resulted in systems that compute quickly and that use energy efficiently, utilizing whatever physical properties are exploitable. Man-made computers, on the other hand, are based on circuits of functional units that follow given design rules. Hence, potentially exploitable physical processes, such as capacitive crosstalk, to solve a problem are left out. Until now, designless nanoscale networks of inanimate matter that exhibit robust computational functionality had not been realized. Here we artificially evolve the electrical properties of a disordered nanomaterials system (by optimizing the values of control voltages using a genetic algorithm) to perform computational tasks reconfigurably. We exploit the rich behaviour that emerges from interconnected metal nanoparticles, which act as strongly nonlinear single-electron transistors, and find that this nanoscale architecture can be configured in situ into any Boolean logic gate. This universal, reconfigurable gate would require about ten transistors in a conventional circuit. Our system meets the criteria for the physical realization of (cellular) neural networks: universality (arbitrary Boolean functions), compactness, robustness and evolvability, which implies scalability to perform more advanced tasks. Our evolutionary approach works around device-to-device variations and the accompanying uncertainties in performance. Moreover, it bears a great potential for more energy-efficient computation, and for solving problems that are very hard to tackle in conventional architectures.
Grabowski, Krzysztof; Gawronski, Mateusz; Baran, Ireneusz; Spychalski, Wojciech; Staszewski, Wieslaw J; Uhl, Tadeusz; Kundu, Tribikram; Packo, Pawel
2016-05-01
Acoustic Emission used in Non-Destructive Testing is focused on analysis of elastic waves propagating in mechanical structures. Then any information carried by generated acoustic waves, further recorded by a set of transducers, allow to determine integrity of these structures. It is clear that material properties and geometry strongly impacts the result. In this paper a method for Acoustic Emission source localization in thin plates is presented. The approach is based on the Time-Distance Domain Transform, that is a wavenumber-frequency mapping technique for precise event localization. The major advantage of the technique is dispersion compensation through a phase-shifting of investigated waveforms in order to acquire the most accurate output, allowing for source-sensor distance estimation using a single transducer. The accuracy and robustness of the above process are also investigated. This includes the study of Young's modulus value and numerical parameters influence on damage detection. By merging the Time-Distance Domain Transform with an optimal distance selection technique, an identification-localization algorithm is achieved. The method is investigated analytically, numerically and experimentally. The latter involves both laboratory and large scale industrial tests.
Vacuum Domain Walls in D-dimensions Local and Global Space-Time Structure
Cvetic, M; Cvetic, Mirjam; Wang, Jing
2000-01-01
We study local and global gravitational effects of (D-2)-brane configurations (domain-walls) in the vacuum of D-dimensional space-time. We focus on infinitely thin vacuum domain walls with arbitrary cosmological constants on either side of the wall. In the comoving frame of the wall we derive a general metric Ansatz, consistent with the homogeneity and isotropy of the space-time intrinsic to the wall, and employ Israel's matching conditions at the wall. The space-time, intrinsic to the wall, is that of (D-1)-dimensional Freedman-Lemaitre-Robertson-Walker universe (with k=-1,0,1) which has a (local) description as either anti-deSitter, Minkowski or deSitter space-time. For each of these geometries, we provide a systematic classification of the local and global space-time structure transverse to the walls, for those with both positive and negative tension; they fall into different classes according to the values of their energy density relative to that of the extreme (superysmmetric) configurations. We find tha...
Dambreville, Frederic
2011-01-01
This work contributes to the domains of Boolean algebra and of Bayesian probability, by proposing an algebraic extension of Boolean algebras, which implements an operator for the Bayesian conditional inference and is closed under this operator. It is known since the work of Lewis (Lewis' triviality) that it is not possible to construct such conditional operator within the space of events. Nevertheless, this work proposes an answer which complements Lewis' triviality, by the construction of a conditional operator outside the space of events, thus resulting in an algebraic extension. In particular, it is proved that any probability defined on a Boolean algebra may be extended to its algebraic extension in compliance with the multiplicative definition of the conditional probability. In the last part of this paper, a new \\emph{bivalent} logic is introduced on the basis of this algebraic extension, and basic properties are derived.
Effect of memory in non-Markovian Boolean networks
Ebadi, Haleh; Ausloos, Marcel; Jafari, GholamReza
2016-01-01
One successful model of interacting biological systems is the Boolean network. The dynamics of a Boolean network, controlled with Boolean functions, is usually considered to be a Markovian (memory-less) process. However, both self organizing features of biological phenomena and their intelligent nature should raise some doubt about ignoring the history of their time evolution. Here, we extend the Boolean network Markovian approach: we involve the effect of memory on the dynamics. This can be explored by modifying Boolean functions into non-Markovian functions, for example, by investigating the usual non-Markovian threshold function, - one of the most applied Boolean functions. By applying the non-Markovian threshold function on the dynamical process of a cell cycle network, we discover a power law memory with a more robust dynamics than the Markovian dynamics.
The effectivenes of science domain-based science learning integrated with local potency
Kurniawati, Arifah Putri; Prasetyo, Zuhdan Kun; Wilujeng, Insih; Suryadarma, I. Gusti Putu
2017-08-01
This research aimed to determine the significant effect of science domain-based science learning integrated with local potency toward science process skills. The research method used was a quasi-experimental design with nonequivalent control group design. The population of this research was all students of class VII SMP Negeri 1 Muntilan. The sample of this research was selected through cluster random sampling, namely class VII B as an experiment class (24 students) and class VII C as a control class (24 students). This research used a test instrument that was adapted from Agus Dwianto's research. The aspect of science process skills in this research was observation, classification, interpretation and communication. The analysis of data used the one factor anova at 0,05 significance level and normalized gain score. The significance level result of science process skills with one factor anova is 0,000. It shows that the significance level science domain-based science learning integrated with local potency toward science learning process skills. The results of analysis show that the normalized gain score are 0,29 (low category) in control class and 0,67 (medium category) in experiment class.
Exact and heuristic methods for solving Boolean games
DE CLERCQ, Sofie; Bauters, Kim; Schockaert, Steven; Mihaylov, Mihail; Nowé, Ann; De Cock, Martine
2015-01-01
Boolean games are a framework for reasoning about the rational behavior of agents whose goals are formalized using propositional formulas. Compared to normal form games, a well-studied and related game framework, Boolean games allow for an intuitive and more compact representation of the agents’ goals. So far, Boolean games have been mainly studied in the literature from the Knowledge Representation perspective, and less attention has been paid on the algorithmic issues underlying the computa...
Rotation Symmetric Bent Boolean Functions for n = 2p
Cusick, T. W.; Sanger, E. M.
2017-01-01
It has been conjectured that there are no homogeneous rotation symmetric bent Boolean functions of degree greater than two. In this paper we begin by proving that sums of short-cycle rotation symmetric bent Boolean functions must contain a specific degree two monomial rotation symmetric Boolean function. We then prove most cases of the conjecture in n=2p, p>2 prime, variables and extend this work to the nonhomogeneous case.
Energy and criticality in random Boolean networks
Andrecut, M. [Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4 (Canada)], E-mail: mandrecu@ucalgary.ca; Kauffman, S.A. [Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4 (Canada)
2008-06-30
The central issue of the research on the Random Boolean Networks (RBNs) model is the characterization of the critical transition between ordered and chaotic phases. Here, we discuss an approach based on the 'energy' associated with the unsatisfiability of the Boolean functions in the RBNs model, which provides an upper bound estimation for the energy used in computation. We show that in the ordered phase the RBNs are in a 'dissipative' regime, performing mostly 'downhill' moves on the 'energy' landscape. Also, we show that in the disordered phase the RBNs have to 'hillclimb' on the 'energy' landscape in order to perform computation. The analytical results, obtained using Derrida's approximation method, are in complete agreement with numerical simulations.
Fast Vertical Mining Using Boolean Algebra
Hosny M. Ibrahim
2015-01-01
Full Text Available The vertical association rules mining algorithm is an efficient mining method, which makes use of support sets of frequent itemsets to calculate the support of candidate itemsets. It overcomes the disadvantage of scanning database many times like Apriori algorithm. In vertical mining, frequent itemsets can be represented as a set of bit vectors in memory, which enables for fast computation. The sizes of bit vectors for itemsets are the main space expense of the algorithm that restricts its expansibility. Therefore, in this paper, a proposed algorithm that compresses the bit vectors of frequent itemsets will be presented. The new bit vector schema presented here depends on Boolean algebra rules to compute the intersection of two compressed bit vectors without making any costly decompression operation. The experimental results show that the proposed algorithm, Vertical Boolean Mining (VBM algorithm is better than both Apriori algorithm and the classical vertical association rule mining algorithm in the mining time and the memory usage.
Non-monotony and Boolean automata networks
Noual, Mathilde; Sené, Sylvain
2011-01-01
This paper aims at setting the keystone of a prospective theoretical study on the role of non-monotone interactions in biological regulation networks. Focusing on discrete models of these networks, namely, Boolean automata networks, we propose to analyse the contribution of non-monotony to the diversity and complexity in their dynamical behaviours. More precisely, in this paper, we start by detailing some motivations, both mathematical and biological, for our interest in non-monotony, and we discuss how it may account for phenomena that cannot be produced by monotony only. Then, to build some understanding in this direction, we propose some preliminary results on the dynamical behaviour of some specific non-monotone Boolean automata networks called XOR circulant networks.
Classical Boolean logic gates with quantum systems
Renaud, N; Joachim, C, E-mail: n-renaud@northwestern.edu [Nanoscience Group and MANA Satellite CEMES/CNRS, 29 rue J Marvig, BP 94347, 31055 Toulouse Cedex (France)
2011-04-15
An analytical method is proposed to implement any classical Boolean function in a small quantum system by taking the advantage of its electronic transport properties. The logical input, {alpha} = {l_brace}{alpha}{sub 1}, ..., {alpha}{sub N}{r_brace}, is used to control well-identified parameters of the Hamiltonian of the system noted H{sub 0}({alpha}). The logical output is encoded in the tunneling current intensity passing through the quantum system when connected to conducting electrodes. It is demonstrated how to implement the six symmetric two-input/one-output Boolean functions in a quantum system. This system can be switched from one logic function to another by changing its structural parameters. The stability of the logic gates is discussed, perturbing the Hamiltonian with noise sources and studying the effect of decoherence.
Boolean representations of simplicial complexes and matroids
Rhodes, John
2015-01-01
This self-contained monograph explores a new theory centered around boolean representations of simplicial complexes leading to a new class of complexes featuring matroids as central to the theory. The book illustrates these new tools to study the classical theory of matroids as well as their important geometric connections. Moreover, many geometric and topological features of the theory of matroids find their counterparts in this extended context. Graduate students and researchers working in the areas of combinatorics, geometry, topology, algebra and lattice theory will find this monograph appealing due to the wide range of new problems raised by the theory. Combinatorialists will find this extension of the theory of matroids useful as it opens new lines of research within and beyond matroids. The geometric features and geometric/topological applications will appeal to geometers. Topologists who desire to perform algebraic topology computations will appreciate the algorithmic potential of boolean represent...
Totally optimal decision trees for Boolean functions
Chikalov, Igor
2016-07-28
We study decision trees which are totally optimal relative to different sets of complexity parameters for Boolean functions. A totally optimal tree is an optimal tree relative to each parameter from the set simultaneously. We consider the parameters characterizing both time (in the worst- and average-case) and space complexity of decision trees, i.e., depth, total path length (average depth), and number of nodes. We have created tools based on extensions of dynamic programming to study totally optimal trees. These tools are applicable to both exact and approximate decision trees, and allow us to make multi-stage optimization of decision trees relative to different parameters and to count the number of optimal trees. Based on the experimental results we have formulated the following hypotheses (and subsequently proved): for almost all Boolean functions there exist totally optimal decision trees (i) relative to the depth and number of nodes, and (ii) relative to the depth and average depth.
Observability of Boolean multiplex control networks
Wu, Yuhu; Xu, Jingxue; Sun, Xi-Ming; Wang, Wei
2017-04-01
Boolean multiplex (multilevel) networks (BMNs) are currently receiving considerable attention as theoretical arguments for modeling of biological systems and system level analysis. Studying control-related problems in BMNs may not only provide new views into the intrinsic control in complex biological systems, but also enable us to develop a method for manipulating biological systems using exogenous inputs. In this article, the observability of the Boolean multiplex control networks (BMCNs) are studied. First, the dynamical model and structure of BMCNs with control inputs and outputs are constructed. By using of Semi-Tensor Product (STP) approach, the logical dynamics of BMCNs is converted into an equivalent algebraic representation. Then, the observability of the BMCNs with two different kinds of control inputs is investigated by giving necessary and sufficient conditions. Finally, examples are given to illustrate the efficiency of the obtained theoretical results.
Mate Suzanne E
2012-09-01
Full Text Available Abstract Background Recycling of endosomes is important for trafficking and maintenance of proteins at the neuromuscular junction (NMJ. We have previously shown high expression of the endocytic recycling regulator Eps15 homology domain-containing (EHD1 proteinin the Torpedo californica electric organ, a model tissue for investigating a cholinergic synapse. In this study, we investigated the localization of EHD1 and its paralogs EHD2, EHD3, and EHD4 in mouse skeletal muscle, and assessed the morphological changes in EHD1−/− NMJs. Methods Localization of the candidate NMJ protein EHD1 was assessed by confocal microscopy analysis of whole-mount mouse skeletal muscle fibers after direct gene transfer and immunolabeling. The potential function of EHD1 was assessed by specific force measurement and α-bungarotoxin-based endplate morphology mapping in EHD1−/− mouse skeletal muscle. Results Endogenous EHD1 localized to primary synaptic clefts of murine NMJ, and this localization was confirmed by expression of recombinant green fluorescent protein labeled-EHD1 in murine skeletal muscle in vivo. EHD1−/− mouse skeletal muscle had normal histology and NMJ morphology, and normal specific force generation during muscle contraction. The EHD 1–4 proteins showed differential localization in skeletal muscle: EHD2 to muscle vasculature, EHD3 to perisynaptic regions, and EHD4 to perinuclear regions and to primary synaptic clefts, but at lower levels than EHD1. Additionally, specific antibodies raised against mammalian EHD1-4 recognized proteins of the expected mass in the T. californica electric organ. Finally, we found that EHD4 expression was more abundant in EHD1−/− mouse skeletal muscle than in wild-type skeletal muscle. Conclusion EHD1 and EHD4 localize to the primary synaptic clefts of the NMJ. Lack of obvious defects in NMJ structure and muscle function in EHD1−/− muscle may be due to functional compensation by other EHD paralogs.
Improved Time Complexities for Learning Boolean Networks
Chee Keong Kwoh
2013-09-01
Full Text Available Existing algorithms for learning Boolean networks (BNs have time complexities of at least O(N · n0:7(k+1, where n is the number of variables, N is the number of samples and k is the number of inputs in Boolean functions. Some recent studies propose more efficient methods with O(N · n2 time complexities. However, these methods can only be used to learn monotonic BNs, and their performances are not satisfactory when the sample size is small. In this paper, we mathematically prove that OR/AND BNs, where the variables are related with logical OR/AND operations, can be found with the time complexity of O(k·(N+ logn·n2, if there are enough noiseless training samples randomly generated from a uniform distribution. We also demonstrate that our method can successfully learn most BNs, whose variables are not related with exclusive OR and Boolean equality operations, with the same order of time complexity for learning OR/AND BNs, indicating our method has good efficiency for learning general BNs other than monotonic BNs. When the datasets are noisy, our method can still successfully identify most BNs with the same efficiency. When compared with two existing methods with the same settings, our method achieves a better comprehensive performance than both of them, especially for small training sample sizes. More importantly, our method can be used to learn all BNs. However, of the two methods that are compared, one can only be used to learn monotonic BNs, and the other one has a much worse time complexity than our method. In conclusion, our results demonstrate that Boolean networks can be learned with improved time complexities.
Boolean methods of optimization over independence systems
Hulme, B.L.
1983-01-01
This paper presents both a direct and an iterative method of solving the combinatorial optimization problem associated with any independence system. The methods use Boolean algebraic computations to produce solutions. In addition, the iterative method employs a version of the greedy algorithm both to compute upper bounds on the optimum value and to produce the additional circuits needed at every stage. The methods are extensions of those used to solve a problem of fire protection at nuclear reactor power plants.
Boolean approach to common event analysis
Worrell, R.B.; Stack, D.W.
1980-01-01
Although different phenomena may be involved, the problem that must be solved for each kind of common event analysis is essentially the same: to determine the effect of common events on the behavior of a system. A Boolean approach to the problem is set forth. Because of the large equations that arise, processing must be done by computers. Vital location analysis is a particular kind of common event analysis that is used to study ways to prevent the sabotage of nuclear reactors. (RWR)
Estimation for the simple linear Boolean model
2006-01-01
We consider the simple linear Boolean model, a fundamental coverage process also known as the Markov/General/infinity queue. In the model, line segments of independent and identically distributed length are located at the points of a Poisson process. The segments may overlap, resulting in a pattern of "clumps"-regions of the line that are covered by one or more segments-alternating with uncovered regions or "spacings". Study and application of the model have been impeded by the difficult...
Combinational Logic-Level Verification using Boolean Expression Diagrams
Hulgaard, Henrik; Williams, Poul Frederick; Andersen, Henrik Reif
1997-01-01
Boolean Expression Diagrams (BEDs) is a new data structure for representing and manipulating Boolean functions. BEDs are a generalization of Binary Decision Diagrams (BDDs) that are capable of representing any Boolean circuit in linear space and still maintain many of the desirable properties...... of BDDs. This paper demonstrates that BEDs are well suited for solving the combinational logic-level verification problem which is, given two combinational circuits, to determine whether they implement the same Boolean functions. Based on all combinational circuits in the ISCAS 85 and LGSynth 91...
The Number of Monotone and Self-Dual Boolean Functions
Haviarova L.
2014-12-01
Full Text Available In the present paper we study properties of pre-complete class of Boolean functions - monotone Boolean functions. We discuss interval graph, the abbreviated d.n.f., a minimal d.n.f. and a shortest d.n.f. of this function. Then we present a d.n.f. with the highest number of conjunctionsand we determinate the exact number of them. We count the number of monotone Boolean functions with some special properties. In the end we estimate the number of Boolean functionthat are monotone and self-dual at the same time.
Boolean Differentiation Equations Applicable in Reconfigurable Computational Medium
Shidlovskiy Stanislav
2016-01-01
Full Text Available High performance computing environment synthesis with parallel architecture reconstructing throughout the process itself is described. Synthesized computational medium involving Boolean differential equation calculations so as to function in real-time image processing. Automaton imaging was illustrated involving the rearrangement of every processing medium element to calculate the partial differentials of n-th order in respect to Boolean function variables. The method of obtaining setting codes for each element was also described. An example in calculating 2nd -order Boolean derivative to two differentials in respect to Boolean functions, depending on three arguments within the reconstructible computational medium of 8×8 processing elements was given.
Random Boolean network models and the yeast transcriptional network
Kauffman, Stuart; Peterson, Carsten; Samuelsson, Björn; Troein, Carl
2003-12-01
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean networks. We find that for ensembles of generated models, those with canalyzing Boolean rules are remarkably stable, whereas those with random Boolean rules are only marginally stable. Furthermore, substantial parts of the generated networks are frozen, in the sense that they reach the same state regardless of initial state. Thus, our ensemble approach suggests that the yeast network shows highly ordered dynamics.
A Generalization of J-Boolean Like Rings%J-Boolean like 环的扩张
秦蕊
2014-01-01
对 J-Boolean like环进行了扩张，并且将 J-Boolean like环与广义矩阵环和Morita Context环联系起来，进而探索了部分环为 J-Boolean like环时应具备的条件，且给出若干相关例子。%The paper mainly explored the generalization of J-Boolean like rings ,and connected J-Boolean like rings with generalized matrix rings and Morita Context rings ,then studied the conditions when a part of other rings became J-Boolean like rings ,and listed some examples .
Reaction-contingency based bipartite Boolean modelling
2013-01-01
Background Intracellular signalling systems are highly complex, rendering mathematical modelling of large signalling networks infeasible or impractical. Boolean modelling provides one feasible approach to whole-network modelling, but at the cost of dequantification and decontextualisation of activation. That is, these models cannot distinguish between different downstream roles played by the same component activated in different contexts. Results Here, we address this with a bipartite Boolean modelling approach. Briefly, we use a state oriented approach with separate update rules based on reactions and contingencies. This approach retains contextual activation information and distinguishes distinct signals passing through a single component. Furthermore, we integrate this approach in the rxncon framework to support automatic model generation and iterative model definition and validation. We benchmark this method with the previously mapped MAP kinase network in yeast, showing that minor adjustments suffice to produce a functional network description. Conclusions Taken together, we (i) present a bipartite Boolean modelling approach that retains contextual activation information, (ii) provide software support for automatic model generation, visualisation and simulation, and (iii) demonstrate its use for iterative model generation and validation. PMID:23835289
Discrete interference modeling via boolean algebra.
Beckhoff, Gerhard
2011-01-01
Two types of boolean functions are considered, the locus function of n variables, and the interval function of ν = n - 1 variables. A 1-1 mapping is given that takes elements (cells) of the interval function to antidual pairs of elements in the locus function, and vice versa. A set of ν binary codewords representing the intervals are defined and used to generate the codewords of all genomic regions. Next a diallelic three-point system is reviewed in the light of boolean functions, which leads to redefining complete interference by a logic function. Together with the upper bound of noninterference already defined by a boolean function, it confines the region of interference. Extensions of these two functions to any finite number of ν are straightforward, but have been also made in terms of variables taken from the inclusion-exclusion principle (expressing "at least" and "exactly equal to" a decimal integer). Two coefficients of coincidence for systems with more than three loci are defined and discussed, one using the average of several individual coefficients and the other taking as coefficient a real number between zero and one. Finally, by way of a malfunction of the mod-2 addition, it is shown that a four-point system may produce two different functions, one of which exhibiting loss of a class of odd recombinants.
Miyamoto, S; Miura, T; Watanabe, S; Nagase, K; Hirayama, Y
2016-03-09
We present fractional quantum Hall domain walls confined in a gate-defined wire structure. Our experiments utilize spatial oscillation of domain walls driven by radio frequency electric fields to cause nuclear magnetic resonance. The resulting spectra are discussed in terms of both large quadrupole fields created around the wire and hyperfine fields associated with the oscillating domain walls. This provides the experimental fact that the domain walls survive near the confined geometry despite of potential deformation, by which a localized magnetic resonance is allowed in electrical means.
Control of random Boolean networks via average sensitivity of Boolean functions
Chen Shi-Jian; Hong Yi-Guang
2011-01-01
In this paper, we discuss how to transform the disordered phase into an ordered phase in random Boolean networks. To increase the effectiveness, a control scheme is proposed, which periodically freezes a fraction of the network based on the average sensitivity of Boolean functions of the nodes. Theoretical analysis is carried out to estimate the expected critical value of the fraction, and shows that the critical value is reduced using this scheme compared to that of randomly freezing a fraction of the nodes. Finally, the simulation is given for illustrating the effectiveness of the proposed method.
Donghoon M Lee
Full Text Available The recruitment of GDP/GTP exchange factors (GEFs to specific subcellular sites dictates where they activate small G proteins for the regulation of various cellular processes. Cytohesins are a conserved family of plasma membrane GEFs for Arf small G proteins that regulate endocytosis. Analyses of mammalian cytohesins have identified a number of recruitment mechanisms for these multi-domain proteins, but the conservation and developmental roles for these mechanisms are unclear. Here, we report how the pleckstrin homology (PH domain of the Drosophila cytohesin Steppke affects its localization and activity at cleavage furrows of the early embryo. We found that the PH domain is necessary for Steppke furrow localization, and for it to regulate furrow structure. However, the PH domain was not sufficient for the localization. Next, we examined the role of conserved PH domain amino acid residues that are required for mammalian cytohesins to bind PIP3 or GTP-bound Arf G proteins. We confirmed that the Steppke PH domain preferentially binds PIP3 in vitro through a conserved mechanism. However, disruption of residues for PIP3 binding had no apparent effect on GFP-Steppke localization and effects. Rather, residues for binding to GTP-bound Arf G proteins made major contributions to this Steppke localization and activity. By analyzing GFP-tagged Arf and Arf-like small G proteins, we found that Arf1-GFP, Arf6-GFP and Arl4-GFP, but not Arf4-GFP, localized to furrows. However, analyses of embryos depleted of Arf1, Arf6 or Arl4 revealed either earlier defects than occur in embryos depleted of Steppke, or no detectable furrow defects, possibly because of redundancies, and thus it was difficult to assess how individual Arf small G proteins affect Steppke. Nonetheless, our data show that the Steppke PH domain and its conserved residues for binding to GTP-bound Arf G proteins have substantial effects on Steppke localization and activity in early Drosophila embryos.
Lee, Donghoon M; Rodrigues, Francisco F; Yu, Cao Guo; Swan, Michael; Harris, Tony J C
2015-01-01
The recruitment of GDP/GTP exchange factors (GEFs) to specific subcellular sites dictates where they activate small G proteins for the regulation of various cellular processes. Cytohesins are a conserved family of plasma membrane GEFs for Arf small G proteins that regulate endocytosis. Analyses of mammalian cytohesins have identified a number of recruitment mechanisms for these multi-domain proteins, but the conservation and developmental roles for these mechanisms are unclear. Here, we report how the pleckstrin homology (PH) domain of the Drosophila cytohesin Steppke affects its localization and activity at cleavage furrows of the early embryo. We found that the PH domain is necessary for Steppke furrow localization, and for it to regulate furrow structure. However, the PH domain was not sufficient for the localization. Next, we examined the role of conserved PH domain amino acid residues that are required for mammalian cytohesins to bind PIP3 or GTP-bound Arf G proteins. We confirmed that the Steppke PH domain preferentially binds PIP3 in vitro through a conserved mechanism. However, disruption of residues for PIP3 binding had no apparent effect on GFP-Steppke localization and effects. Rather, residues for binding to GTP-bound Arf G proteins made major contributions to this Steppke localization and activity. By analyzing GFP-tagged Arf and Arf-like small G proteins, we found that Arf1-GFP, Arf6-GFP and Arl4-GFP, but not Arf4-GFP, localized to furrows. However, analyses of embryos depleted of Arf1, Arf6 or Arl4 revealed either earlier defects than occur in embryos depleted of Steppke, or no detectable furrow defects, possibly because of redundancies, and thus it was difficult to assess how individual Arf small G proteins affect Steppke. Nonetheless, our data show that the Steppke PH domain and its conserved residues for binding to GTP-bound Arf G proteins have substantial effects on Steppke localization and activity in early Drosophila embryos.
Lubineau, Gilles
2015-03-01
We propose a domain decomposition formalism specifically designed for the identification of local elastic parameters based on full-field measurements. This technique is made possible by a multi-scale implementation of the constitutive compatibility method. Contrary to classical approaches, the constitutive compatibility method resolves first some eigenmodes of the stress field over the structure rather than directly trying to recover the material properties. A two steps micro/macro reconstruction of the stress field is performed: a Dirichlet identification problem is solved first over every subdomain, the macroscopic equilibrium is then ensured between the subdomains in a second step. We apply the method to large linear elastic 2D identification problems to efficiently produce estimates of the material properties at a much lower computational cost than classical approaches.
Mason, Frank M; Tworoger, Michael; Martin, Adam C
2013-08-01
Apical constriction promotes epithelia folding, which changes tissue architecture. During Drosophila gastrulation, mesoderm cells exhibit repeated contractile pulses that are stabilized such that cells apically constrict like a ratchet. The transcription factor Twist is required to stabilize cell shape. However, it is unknown how Twist spatially coordinates downstream signals to prevent cell relaxation. We find that during constriction, Rho-associated kinase (Rok) is polarized to the middle of the apical domain (medioapical cortex), separate from adherens junctions. Rok recruits or stabilizes medioapical myosin II (Myo-II), which contracts dynamic medioapical actin cables. The formin Diaphanous mediates apical actin assembly to suppress medioapical E-cadherin localization and form stable connections between the medioapical contractile network and adherens junctions. Twist is not required for apical Rok recruitment, but instead polarizes Rok medioapically. Therefore, Twist establishes radial cell polarity of Rok/Myo-II and E-cadherin and promotes medioapical actin assembly in mesoderm cells to stabilize cell shape fluctuations.
Pedersen, Pauli; Pedersen, Niels Leergaard
2014-01-01
result has many applications. It is therefore presented before specific use in optimization examples. The engineering approach of fully stressed design is a practical tool with a theoretical foundation. The analog approach to structural eigenfrequency optimization is presented here with its theoretical...... foundation. A numerical heuristic redesign procedure is proposed and illustrated with examples. For the ideal case, an optimality criterion is fulfilled if the design have the same sub-domain frequency (local Rayleigh quotient). Sensitivity analysis shows an important relation between squared system...... on the derived optimality condition. The design that maximize a frequency depend on the total amount of available material and on a necessary interpolation as illustrated by different design cases.In this note we have assumed a linear and conservative eigenvalue problem without multiple eigenvalues. The presence...
An innovative application of time-domain spectroscopy on localized surface plasmon resonance sensing
Li, Meng-Chi; Chang, Ying-Feng; Wang, Huai-Yi; Lin, Yu-Xen; Kuo, Chien-Cheng; Annie Ho, Ja-An; Lee, Cheng-Chung; Su, Li-Chen
2017-03-01
White-light scanning interferometry (WLSI) is often used to study the surface profiles and properties of thin films because the strength of the technique lies in its ability to provide fast and high resolution measurements. An innovative attempt is made in this paper to apply WLSI as a time-domain spectroscopic system for localized surface plasmon resonance (LSPR) sensing. A WLSI-based spectrometer is constructed with a breadboard of WLSI in combination with a spectral centroid algorithm for noise reduction and performance improvement. Experimentally, the WLSI-based spectrometer exhibits a limit of detection (LOD) of 1.2 × 10-3 refractive index units (RIU), which is better than that obtained with a conventional UV-Vis spectrometer, by resolving the LSPR peak shift. Finally, the bio-applicability of the proposed spectrometer was investigated using the rs242557 tau gene, an Alzheimer’s and Parkinson’s disease biomarker. The LOD was calculated as 15 pM. These results demonstrate that the proposed WLSI-based spectrometer could become a sensitive time-domain spectroscopic biosensing platform.
Fatigue damage localization using time-domain features extracted from nonlinear Lamb waves
Hong, Ming; Su, Zhongqing; Lu, Ye; Cheng, Li
2014-03-01
Nonlinear guided waves are sensitive to small-scale fatigue damage that may hardly be identified by traditional techniques. A characterization method for fatigue damage is established based on nonlinear Lamb waves in conjunction with the use of a piezoelectric sensor network. Theories on nonlinear Lamb waves for damage detection are first introduced briefly. Then, the ineffectiveness of using pure frequency-domain information of nonlinear wave signals for locating damage is discussed. With a revisit to traditional gross-damage localization techniques based on the time of flight, the idea of using temporal signal features of nonlinear Lamb waves to locate fatigue damage is introduced. This process involves a time-frequency analysis that enables the damage-induced nonlinear signal features, which are either undiscernible in the original time history or uninformative in the frequency spectrum, to be revealed. Subsequently, a finite element modeling technique is employed, accounting for various sources of nonlinearities in a fatigued medium. A piezoelectric sensor network is configured to actively generate and acquire probing Lamb waves that involve damageinduced nonlinear features. A probability-based diagnostic imaging algorithm is further proposed, presenting results in diagnostic images intuitively. The approach is experimentally verified on a fatigue-damaged aluminum plate, showing reasonably good accuracy. Compared to existing nonlinear ultrasonics-based inspection techniques, this approach uses a permanently attached sensor network that well accommodates automated online health monitoring; more significantly, it utilizes time-domain information of higher-order harmonics from time-frequency analysis, and demonstrates a great potential for quantitative characterization of small-scale damage with improved localization accuracy.
Some aspects of the local theory of generalized Dhombres functional equations in the complex domain
Tomaschek Jörg
2012-08-01
Full Text Available We study the generalized Dhombres functional equation f(zf(z = ϕ(f(z in the complex domain. The function ϕ is given and we are looking for solutions f with f(0 = w0 and w0 is a primitive root of unity of order l ≥ 2. All formal solutions for this case are described in this work, for the situation where ϕ can be transformed into a function which is linearizable and local analytic in a neighbourhood of zero we also show that we obtain local analytic solutions. We also discuss an example where it is possible to use other methods than we use in the general case. Nous étudions la fonctionnelle de Dhombres f(zf(z = ϕ(f(z dans le plan complexe. La fonction ϕ est donnée et nous cherchons les solutions f avec f(0 = w0 où w0 est une racine primitive de l’unité d’ordre l ≥ 2. Nous décrivons dans ce travail toutes les solutions formelles dans ce cas, et lorsque ϕ peut être transformée en une fonction linéarisable et localement analytique au voisinage de zéro nous montrons également comment obtenir des solutions analytiques locales. Nous discutons enfin un exemple où il est possible d’utiliser des méthodes différentes de celles que nous mettons en œuvre dans le cas général.
Noise as a Boolean algebra of sigma-fields
Tsirelson, Boris
2011-01-01
The black noise of two-dimensional percolation, disclosed recently by O. Schramm, S. Smirnov and C. Garban, exceeds the limits of the existing framework based on one-dimensional intervals. A remake of the theory of noises, provided here, treats them as Boolean algebras of sigma-fields. Completeness of the Boolean algebra implies classicality, which answers an old question of J. Feldman.
Boolean Queries and Term Dependencies in Probabilistic Retrieval Models.
Croft, W. Bruce
1986-01-01
Proposes approach to integrating Boolean and statistical systems where Boolean queries are interpreted as a means of specifying term dependencies in relevant set of documents. Highlights include series of retrieval experiments designed to test retrieval strategy based on term dependence model and relation of results to other work. (18 references)…
Spectra of Tukey types of ultrafilters on Boolean algebras
Brown, Jennifer A.; Dobrinen, Natasha
2014-01-01
Extending recent investigations on the structure of Tukey types of ultrafilters on $\\mathcal{P}(\\omega)$ to Boolean algebras in general, we classify the spectra of Tukey types of ultrafilters for several classes of Boolean algebras, including interval algebras, tree algebras, and pseudo-tree algebras.
Constructions of vector output Boolean functions with high generalized nonlinearity
KE Pin-hui; ZHANG Sheng-yuan
2008-01-01
Carlet et al. recently introduced generalized nonlinearity to measure the ability to resist the improved correlation attack of a vector output Boolean function. This article presents a construction of vector output Boolean functions with high generalized nonlinearity using the sample space. The relation between the resilient order and generalized nonlinearity is also discussed.
Standard Plane Localization in Fetal Ultrasound via Domain Transferred Deep Neural Networks.
Chen, Hao; Ni, Dong; Qin, Jing; Li, Shengli; Yang, Xin; Wang, Tianfu; Heng, Pheng Ann
2015-09-01
Automatic localization of the standard plane containing complicated anatomical structures in ultrasound (US) videos remains a challenging problem. In this paper, we present a learning-based approach to locate the fetal abdominal standard plane (FASP) in US videos by constructing a domain transferred deep convolutional neural network (CNN). Compared with previous works based on low-level features, our approach is able to represent the complicated appearance of the FASP and hence achieve better classification performance. More importantly, in order to reduce the overfitting problem caused by the small amount of training samples, we propose a transfer learning strategy, which transfers the knowledge in the low layers of a base CNN trained from a large database of natural images to our task-specific CNN. Extensive experiments demonstrate that our approach outperforms the state-of-the-art method for the FASP localization as well as the CNN only trained on the limited US training samples. The proposed approach can be easily extended to other similar medical image computing problems, which often suffer from the insufficient training samples when exploiting the deep CNN to represent high-level features.
On diamond-free subposets of the Boolean lattice
Kramer, Lucas; Young, Michael
2012-01-01
The Boolean lattice of dimension two, also known as the diamond, consists of four distinct elements with the following property: $A\\subset B,C\\subset D$. A diamond-free family in the $n$-dimensional Boolean lattice is a subposet such that no four elements form a diamond. Note that elements $B$ and $C$ may or may not be related. There is a diamond-free family in the $n$-dimensional Boolean lattice of size $(2-o(1)){n\\choose\\lfloor n/2\\rfloor}$. In this paper, we prove that any diamond-free family in the $n$-dimensional Boolean lattice has size at most $(2.25+o(1)){n\\choose\\lfloor n/2\\rfloor}$. Furthermore, we show that the so-called Lubell function of a diamond-free family in the $n$-dimensional Boolean lattice is at most $2.25+o(1)$, which is asympotically best possible.
Stratification and enumeration of Boolean functions by canalizing depth
He, Qijun; Macauley, Matthew
2016-01-01
Boolean network models have gained popularity in computational systems biology over the last dozen years. Many of these networks use canalizing Boolean functions, which has led to increased interest in the study of these functions. The canalizing depth of a function describes how many canalizing variables can be recursively "picked off", until a non-canalizing function remains. In this paper, we show how every Boolean function has a unique algebraic form involving extended monomial layers and a well-defined core polynomial. This generalizes recent work on the algebraic structure of nested canalizing functions, and it yields a stratification of all Boolean functions by their canalizing depth. As a result, we obtain closed formulas for the number of n-variable Boolean functions with depth k, which simultaneously generalizes enumeration formulas for canalizing, and nested canalizing functions.
Stratification and enumeration of Boolean functions by canalizing depth
He, Qijun
2015-01-01
Boolean network models have gained popularity in computational systems biology over the last dozen years. Many of these networks use canalizing Boolean functions, which has led to increased interest in the study of these functions. The canalizing depth of a function describes how many canalizing variables can be recursively picked off, until a non-canalizing function remains. In this paper, we show how every Boolean function has a unique algebraic form involving extended monomial layers and a well-defined core polynomial. This generalizes recent work on the algebraic structure of nested canalizing functions, and it yields a stratification of all Boolean functions by their canalizing depth. As a result, we obtain closed formulas for the number of n-variable Boolean functions with depth k, which simultaneously generalizes enumeration formulas for canalizing, and nested canalizing functions.
Boolean algebraic analysis of fire protection
Hulme, B.L.; Shiver, A.W.; Slater, P.J.
1982-01-01
This paper describes a computational procedure which can be used to find minimum cost ways to protect the critical combinations of equipment from a single-source fire by protecting certain areas and strengthening certain barriers against fire. The procedure yields a complete set of optimum solutions by iteratively computing upper and lower bounds on the minimum cost. The fire protection sets evolve from Boolean algebraic computations which obtain minimum cost blocking sets associated with the lower bounds while the upper bounds are producd by maxflow-mincut calculations in a network.
Towards Boolean operations with thermal photons
Ben-Abdallah, Philippe; Biehs, Svend-Age
2016-12-01
The Boolean algebra is the natural theoretical framework for a classical information treatment. The basic logical operations are usually performed using logic gates. In this Rapid Communication we demonstrate that not, or, and and gates can be realized exploiting the near-field radiative interaction in N -body systems with phase change materials. With the recent development of a photon thermal transistor and thermal memory, this result paves the way for a full information treatment and smart solutions for active thermal management at nanoscale with photons.
On the robustness of random Boolean formulae
Mozeika, Alexander; Saad, David [Non-linearity and Complexity Research Group, Aston University, Birmingham B4 7ET (United Kingdom); Raymond, Jack, E-mail: a.s.mozeika@aston.ac.u, E-mail: d.saad@aston.ac.u [Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay (Hong Kong)
2010-06-01
Random Boolean formulae, generated by a growth process of noisy logical gates are analyzed using the generating functional methodology of statistical physics. We study the type of functions generated for different input distributions, their robustness for a given level of gate error and its dependence on the formulae depth and complexity and the gates used. Bounds on their performance, derived in the information theory literature for specific gates, are straightforwardly retrieved, generalized and identified as the corresponding typical-case phase transitions. Results for error-rates, function-depth and sensitivity of the generated functions are obtained for various gate-type and noise models.
The Boolean algebra and central Galois algebras
George Szeto
2001-01-01
Full Text Available Let B be a Galois algebra with Galois group G, Jg={b∈B∣bx=g(xb for all x∈B} for g∈G, and BJg=Beg for a central idempotent eg. Then a relation is given between the set of elements in the Boolean algebra (Ba,≤ generated by {0,eg∣g∈G} and a set of subgroups of G, and a central Galois algebra Be with a Galois subgroup of G is characterized for an e∈Ba.
Partial Synchronization of Interconnected Boolean Networks.
Chen, Hongwei; Liang, Jinling; Lu, Jianquan
2017-01-01
This paper addresses the partial synchronization problem for the interconnected Boolean networks (BNs) via the semi-tensor product (STP) of matrices. First, based on an algebraic state space representation of BNs, a necessary and sufficient criterion is presented to ensure the partial synchronization of the interconnected BNs. Second, by defining an induced digraph of the partial synchronized states set, an equivalent graphical description for the partial synchronization of the interconnected BNs is established. Consequently, the second partial synchronization criterion is derived in terms of adjacency matrix of the induced digraph. Finally, two examples (including an epigenetic model) are provided to illustrate the efficiency of the obtained results.
Reasoning formalism in Boolean operator fuzzy logic
邓安生; 刘叙华
1995-01-01
Based on the newly introduced concepts of true-level and false-level, the formal structure of reasoning in Boolean operator fuzzy logic is presented. As a generalization of the theory of epistemic process in open logic, a formalism is also proposed to describe human reasoning with uncertain, inconsistent and insufficient knowledge, which can characterize the knowledge increment and revision, as well as the epistemic evolution. The formalism provides an explanation to the dynamic properties of human reasoning, i. e. continuous revision and combination of beliefs.
Towards boolean operations with thermal photons
Ben-Abdallah, Philippe
2016-01-01
The Boolean algebra is the natural theoretical framework for a classical information treatment. The basic logical operations are usually performed using logic gates. In this Letter we demonstrate that NOT, OR and AND gates can be realized exploiting the near-field radiative interaction in N-body systems with phase change materials. With the recent development of a photon thermal transistor and thermal memory, this result paves the way for a full information treatment and smart solutions for active thermal management at nanoscale with photons.
Boolean Algebra. Geometry Module for Use in a Mathematics Laboratory Setting.
Brotherton, Sheila; And Others
This module is recommended as an honors unit to follow a unit on logic. There are four basic parts: (1) What is a Boolean Algebra; (2) Using Boolean Algebra to Prove Theorems; (3) Using Boolean Algebra to Simplify Logical Statements; and (4) Circuit Problems with Logic and Boolean Algebra. Of these, sections 1, 2, and 3 are primarily written…
Site-specific genomic (SSG and random domain-localized (RDL mutagenesis in yeast
Honigberg Saul M
2004-04-01
Full Text Available Abstract Background A valuable weapon in the arsenal available to yeast geneticists is the ability to introduce specific mutations into yeast genome. In particular, methods have been developed to introduce deletions into the yeast genome using PCR fragments. These methods are highly efficient because they do not require cloning in plasmids. Results We have modified the existing method for introducing deletions in the yeast (S. cerevisiae genome using PCR fragments in order to target point mutations to this genome. We describe two PCR-based methods for directing point mutations into the yeast genome such that the final product contains no other disruptions. In the first method, site-specific genomic (SSG mutagenesis, a specific point mutation is targeted into the genome. In the second method, random domain-localized (RDL mutagenesis, a mutation is introduced at random within a specific domain of a gene. Both methods require two sequential transformations, the first transformation integrates the URA3 marker into the targeted locus, and the second transformation replaces URA3 with a PCR fragment containing one or a few mutations. This PCR fragment is synthesized using a primer containing a mutation (SSG mutagenesis or is synthesized by error-prone PCR (RDL mutagenesis. In SSG mutagenesis, mutations that are proximal to the URA3 site are incorporated at higher frequencies than distal mutations, however mutations can be introduced efficiently at distances of at least 500 bp from the URA3 insertion. In RDL mutagenesis, to ensure that incorporation of mutations occurs at approximately equal frequencies throughout the targeted region, this region is deleted at the same time URA3 is integrated. Conclusion SSG and RDL mutagenesis allow point mutations to be easily and efficiently incorporated into the yeast genome without disrupting the native locus.
Priya, Shashank [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Viehland, Dwight [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
2014-12-14
Three year program entitled “Correlation of bulk dielectric and piezoelectric properties to the local scale phase transformations, domain morphology, and crystal structure in modified lead-free grain-textured ceramics and single crystals” was supported by the Department of Energy. This was a joint research program between D. Viehland and S. Priya at Virginia Tech. Single crystal and textured ceramics have been synthesized and characterized. Our goals have been (i) to conduct investigations of lead-free piezoelectric systems to establish the local structural and domain morphologies that result in enhanced properties, and (ii) to synthesize polycrystalline and grain oriented ceramics for understanding the role of composition, microstructure, and anisotropy
Hydrograph structure informed calibration in the frequency domain with time localization
Kumarasamy, K.; Belmont, P.
2015-12-01
Complex models with large number of parameters are commonly used to estimate sediment yields and predict changes in sediment loads as a result of changes in management or conservation practice at large watershed (>2000 km2) scales. As sediment yield is a strongly non-linear function that responds to channel (peak or mean) velocity or flow depth, it is critical to accurately represent flows. The process of calibration in such models (e.g., SWAT) generally involves the adjustment of several parameters to obtain better estimates of goodness of fit metrics such as Nash Sutcliff Efficiency (NSE). However, such indicators only provide a global view of model performance, potentially obscuring accuracy of the timing or magnitude of specific flows of interest. We describe an approach for streamflow calibration that will greatly reduce the black-box nature of calibration, when response from a parameter adjustment is not clearly known. Fourier Transform or the Short Term Fourier Transform could be used to characterize model performance in the frequency domain as well, however, the ambiguity of a Fourier transform with regards to time localization renders its implementation in a model calibration setting rather useless. Brief and sudden changes (e.g. stream flow peaks) in signals carry the most interesting information from parameter adjustments, which are completely lost in the transform without time localization. Wavelet transform captures the frequency component in the signal without compromising time and is applied to contrast changes in signal response to parameter adjustments. Here we employ the mother wavelet called the Mexican hat wavelet and apply a Continuous Wavelet Transform to understand the signal in the frequency domain. Further, with the use of the cross-wavelet spectrum we examine the relationship between the two signals (prior or post parameter adjustment) in the time-scale plane (e.g., lower scales correspond to higher frequencies). The non-stationarity of
Membrane localization is critical for activation of the PICK1 BAR domain
Madsen, Kenneth L; Eriksen, Jacob; Milan-Lobo, Laura
2008-01-01
The PSD-95/Discs-large/ZO-1 homology (PDZ) domain protein, protein interacting with C kinase 1 (PICK1) contains a C-terminal Bin/amphiphysin/Rvs (BAR) domain mediating recognition of curved membranes; however, the molecular mechanisms controlling the activity of this domain are poorly understood....... In agreement with negative regulation of the BAR domain by the N-terminal PDZ domain, PICK1 distributed evenly in the cytoplasm, whereas truncation of the PDZ domain caused BAR domain-dependent redistribution to clusters colocalizing with markers of recycling endosomal compartments. A similar clustering...... was observed both upon truncation of a short putative alpha-helical segment in the linker between the PDZ and the BAR domains and upon coexpression of PICK1 with a transmembrane PDZ ligand, including the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor GluR2 subunit, the GluR2 C...
Synchronization of coupled Boolean phase oscillators
Rosin, David P.; Rontani, Damien; Gauthier, Daniel J.
2014-04-01
We design, characterize, and couple Boolean phase oscillators that include state-dependent feedback delay. The state-dependent delay allows us to realize an adjustable coupling strength, even though only Boolean signals are exchanged. Specifically, increasing the coupling strength via the range of state-dependent delay leads to larger locking ranges in uni- and bidirectional coupling of oscillators in both experiment and numerical simulation with a piecewise switching model. In the unidirectional coupling scheme, we unveil asymmetric triangular-shaped locking regions (Arnold tongues) that appear at multiples of the natural frequency of the oscillators. This extends observations of a single locking region reported in previous studies. In the bidirectional coupling scheme, we map out a symmetric locking region in the parameter space of frequency detuning and coupling strength. Because of the large scalability of our setup, our observations constitute a first step towards realizing large-scale networks of coupled oscillators to address fundamental questions on the dynamical properties of networks in a new experimental setting.
Controllability of asynchronous Boolean multiplex control networks.
Luo, Chao; Wang, Xingyuan; Liu, Hong
2014-09-01
In this article, the controllability of asynchronous Boolean multiplex control networks (ABMCNs) is studied. First, the model of Boolean multiplex control networks under Harvey' asynchronous update is presented. By means of semi-tensor product approach, the logical dynamics is converted into linear representation, and a generalized formula of control-depending network transition matrices is achieved. Second, a necessary and sufficient condition is proposed to verify that only control-depending fixed points of ABMCNs can be controlled with probability one. Third, using two types of controls, the controllability of system is studied and formulae are given to show: (a) when an initial state is given, the reachable set at time s under a group of specified controls; (b) the reachable set at time s under arbitrary controls; (c) the specific probability values from a given initial state to destination states. Based on the above formulae, an algorithm to calculate overall reachable states from a specified initial state is presented. Moreover, we also discuss an approach to find the particular control sequence which steers the system between two states with maximum probability. Examples are shown to illustrate the feasibility of the proposed scheme.
Controllability of asynchronous Boolean multiplex control networks
Luo, Chao; Wang, Xingyuan; Liu, Hong
2014-09-01
In this article, the controllability of asynchronous Boolean multiplex control networks (ABMCNs) is studied. First, the model of Boolean multiplex control networks under Harvey' asynchronous update is presented. By means of semi-tensor product approach, the logical dynamics is converted into linear representation, and a generalized formula of control-depending network transition matrices is achieved. Second, a necessary and sufficient condition is proposed to verify that only control-depending fixed points of ABMCNs can be controlled with probability one. Third, using two types of controls, the controllability of system is studied and formulae are given to show: (a) when an initial state is given, the reachable set at time s under a group of specified controls; (b) the reachable set at time s under arbitrary controls; (c) the specific probability values from a given initial state to destination states. Based on the above formulae, an algorithm to calculate overall reachable states from a specified initial state is presented. Moreover, we also discuss an approach to find the particular control sequence which steers the system between two states with maximum probability. Examples are shown to illustrate the feasibility of the proposed scheme.
Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited
Babak Faryabi
2009-01-01
Full Text Available An approximate representation for the state space of a context-sensitive probabilistic Boolean network has previously been proposed and utilized to devise therapeutic intervention strategies. Whereas the full state of a context-sensitive probabilistic Boolean network is specified by an ordered pair composed of a network context and a gene-activity profile, this approximate representation collapses the state space onto the gene-activity profiles alone. This reduction yields an approximate transition probability matrix, absent of context, for the Markov chain associated with the context-sensitive probabilistic Boolean network. As with many approximation methods, a price must be paid for using a reduced model representation, namely, some loss of optimality relative to using the full state space. This paper examines the effects on intervention performance caused by the reduction with respect to various values of the model parameters. This task is performed using a new derivation for the transition probability matrix of the context-sensitive probabilistic Boolean network. This expression of transition probability distributions is in concert with the original definition of context-sensitive probabilistic Boolean network. The performance of optimal and approximate therapeutic strategies is compared for both synthetic networks and a real case study. It is observed that the approximate representation describes the dynamics of the context-sensitive probabilistic Boolean network through the instantaneously random probabilistic Boolean network with similar parameters.
Formalization of Human Categorization Process Using Interpolative Boolean Algebra
Vladimir Dobrić
2015-01-01
Full Text Available Since the ancient times, it has been assumed that categorization has the basic form of classical sets. This implies that the categorization process rests on the Boolean laws. In the second half of the twentieth century, the classical theory has been challenged in cognitive science. According to the prototype theory, objects belong to categories with intensities, while humans categorize objects by comparing them to prototypes of relevant categories. Such categorization process is governed by the principles of perceived world structure and cognitive economy. Approaching the prototype theory by using truth-functional fuzzy logic has been harshly criticized due to not satisfying the complementation laws. In this paper, the prototype theory is approached by using structure-functional fuzzy logic, the interpolative Boolean algebra. The proposed formalism is within the Boolean frame. Categories are represented as fuzzy sets of objects, while comparisons between objects and prototypes are formalized by using Boolean consistent fuzzy relations. Such relations are directly constructed from a Boolean consistent fuzzy partial order relation, which is treated by Boolean implication. The introduced formalism secures the principles of categorization showing that Boolean laws are fundamental in the categorization process. For illustration purposes, the artificial cognitive system which mimics human categorization activity is proposed.
Time domain localization technique with sparsity constraint for imaging acoustic sources
Padois, Thomas; Doutres, Olivier; Sgard, Franck; Berry, Alain
2017-09-01
This paper addresses source localization technique in time domain for broadband acoustic sources. The objective is to accurately and quickly detect the position and amplitude of noise sources in workplaces in order to propose adequate noise control options and prevent workers hearing loss or safety risk. First, the generalized cross correlation associated with a spherical microphone array is used to generate an initial noise source map. Then a linear inverse problem is defined to improve this initial map. Commonly, the linear inverse problem is solved with an l2 -regularization. In this study, two sparsity constraints are used to solve the inverse problem, the orthogonal matching pursuit and the truncated Newton interior-point method. Synthetic data are used to highlight the performances of the technique. High resolution imaging is achieved for various acoustic sources configurations. Moreover, the amplitudes of the acoustic sources are correctly estimated. A comparison of computation times shows that the technique is compatible with quasi real-time generation of noise source maps. Finally, the technique is tested with real data.
Couchman, J R; Ljubimov, A V; Sthanam, M;
1995-01-01
Perlecan is the best-characterized basement membrane heparan sulfate proteoglycan. It has a large (approximately 400 KD) core protein consisting of five distinct domains. Domain III, a centrally located domain, contains three globular domains separated by cysteine-rich epidermal growth factor (EGF...... blotting showed that six of the nine MAbs recognized Domain III of perlecan, three of them mapping to globular Subdomain IIIc, and the other three recognized epitopes within the cysteine-rich regions. All six MAbs stained every basement membrane of several mouse organs as well as some connective tissues...
Boolean approach to zero-one linear programming
Hulme, B.L.; Baca, L.S.
1984-07-01
Problems of minimizing or maximizing a linear objective function in zero-one variables subject to linear constraints can be solved by Boolean algebraic methods. This report gives both a general procedure for stating such problems in Boolean form and a solution procedure that has been implemented by a SETS user program. The program uses the Boolean algebraic formula manipulation techniques of the SETS language. Sample problems illustrate how to make optimum choices in the contexts of physical protection, packing knapsacks, designing manufacturing processes and making assignments.
Li, Qiaoli; Li, Mangmang; Jiang, Lubin; Zhang, Qingqi; Song, Rentao; Xu, Zhengkai
2006-05-10
With regard to the effects of various foreign peptides fused to the coat protein subunits on the infectivity of corresponding TMV recombinants, some of TMV recombinants were found to induce necrotic local lesions on the inoculated leaves of susceptible tobacco. This paper reported that there existed a group of TMV recombinants in which the fused foreign peptides contained a transmembrane domain according to the predictions by three programs of SOSUI, TMpred and DAS. Further studies showed for the first time that a foreign transmembrane domain in a fused peptide of the corresponding TMV recombinant would result in the local lesions on the susceptible tobacco leaves. In addition, it was concluded that none of the TMV recombinants that systematically infected susceptible tobacco contained a transmembrane domain in the coat protein subunits.
Distinct domains in Bub1 localize RZZ and BubR1 to kinetochores to regulate the checkpoint
Zhang, Gang; Lischetti, Tiziana; Hayward, Daniel G;
2015-01-01
, we show that a distinct region in Bub1 mediates kinetochore localization of BubR1 through direct binding, but surprisingly removal of this region increases checkpoint strength. Our work thus uncovers how Bub1 coordinates checkpoint signalling by distinct domains for RZZ and BubR1 recruitment...
布尔代数的软商布尔代数%Soft quotient Boolean algebra of Boolean algebra
刘卫锋
2015-01-01
The concepts of soft congruence relation,soft quotient algebra and soft quotient Boolean algebra of Boolean algebra are defined,and it is proved that soft congruence relation and soft ideal of Boolean algebra can be determined by each other.Then soft quotient Boolean algebra of Boolean algebra is obtained from soft proper ideal of Boolean algebra. Finally,the nature of preserving soft congruence relation of soft homomorphism of Boolean algebras is proved.%定义了布尔代数的软合同关系、软商代数和软商布尔代数等概念，证明了布尔代数的软合同关系与软理想相互确定，进而由布尔代数的软真理想得到布尔代数的软商布尔代数。最后，证明了布尔代数的软同态具有保软合同性。
Robbins algebra : conditions that make a near-Boolean algebra Boolean.
Winker, S.; Mathematics and Computer Science
1990-01-01
Some problems posed years ago remain challenging today. In particular, the Robbins problem, which is still open and which is the focus of attention in this paper, offers interesting challenges for attack with the assistance of an automated reasoning program; for the study presented here, we used the program OTTER. For example, when one submits this problem, which asks for a proof that every Robbins algebra is a Boolean algebra, a large number of deduced clauses results. One must, therefore, consider the possibility that there exists a Robbins algebra that is not Boolean; such an algebra would have to be infinite. One can instead search for properties that, if adjoined to those of a Robbins algebra, guarantee that the algebra is Boolean. Here we present a number of such properties, and we show how an automated reasoning program was used to obtain the corresponding proofs. Additional properties have been identified, and we include here examples of using such a program to check that the corresponding hand-proofs are correct. We present the appropriate input for many of the examples and also include the resulting proofs in clause notation.
A Boolean action of C(M,U(1)) without a spatial model
Moore, Justin Tatch
2012-01-01
We will demonstrate that if M is an uncountable compact metric space, then there is an action of the Polish group of all continuous functions from M to U(1) on a separable probability algebra which preserves the measure and yet does not admit a point realization (in a standard probability space) in the sense of Mackey. This contrasts Mackey's point realization theorem for locally compact, second countable groups which asserts that any measure preserving Boolean action of a locally compact, second countable group on a separable probability algebra can be realized as an action on the points of a standard probability space.
Stability of Boolean networks: The joint effects of topology and update rules
Squires, Shane; Girvan, Michelle; Ott, Edward
2013-01-01
We study the stability of orbits in large Boolean networks with given complex topology. We impose no restrictions on the form of the update rules, which may be correlated with local topological properties of the network. While recent past work has addressed the separate effects of nontrivial network topology and certain special classes of update rules on stability, only crude results exist about how these effects interact. We present a widely applicable solution to this problem. Numerical experiments confirm our theory and show that local correlations between topology and update rules can have profound effects on the qualitative behavior of these systems.
Stability of Boolean networks: The joint effects of topology and update rules
Squires, Shane; Pomerance, Andrew; Girvan, Michelle; Ott, Edward
2014-08-01
We study the stability of orbits in large Boolean networks. We treat the case in which the network has a given complex topology, and we do not assume a specific form for the update rules, which may be correlated with local topological properties of the network. While recent past work has addressed the separate effects of complex network topology and certain classes of update rules on stability, only crude results exist about how these effects interact. We present a widely applicable solution to this problem. Numerical simulations confirm our theory and show that local correlations between topology and update rules can have profound effects on the qualitative behavior of these systems.
The impact of a carbon nanotube on the cholesterol domain localized on a protein surface
Gburski, Zygmunt; Raczynski, Przemyslaw; 10.1016/j.ssc.2009.12.005
2011-01-01
The influence of a single walled carbon nanotube on the structure of a cholesterol cluster (domain) developed over the surface of the endothelial protein 1LQV has been investigated using the classical molecular dynamics (MD) simulation technique. We have observed a substantial impact of carbon nanotube on the arrangement of the cholesterol domain. The carbon nanotube can drag out cholesterol molecules, remarkable reducing the volume of the domain settled down on the protein.
Fokicheva, V V [M. V. Lomonosov Moscow State University, Faculty of Mechanics and Mathematics, Moscow (Russian Federation)
2015-10-31
A new class of integrable billiard systems, called generalized billiards, is discovered. These are billiards in domains formed by gluing classical billiard domains along pieces of their boundaries. (A classical billiard domain is a part of the plane bounded by arcs of confocal quadrics.) On the basis of the Fomenko-Zieschang theory of invariants of integrable systems, a full topological classification of generalized billiards is obtained, up to Liouville equivalence. Bibliography: 18 titles.
Li Long; Zhang Yu; Liang Changhong
2004-01-01
An Improved Locally Conformal Finite-Difference Time-Domain (ILC-FDTD) method is presented in this paper, which is used to analyze the edge inclined slots penetrating adjacent broadwalls of a finite wall thickness waveguide. ILC-FDTD not only removes the instability of the original locally conformal FDTD algorithm, but also improves the computational accuracy by locally modifying magnetic field update equations and the virtual iterative electric fields according to the complexity of the slot fringe fields. The mutual coupling between two edge inclined slots can also be analyzed by ILC-FDTD effectively.
Multipath Detection Using Boolean Satisfiability Techniques
Fadi A. Aloul
2011-01-01
Full Text Available A new technique for multipath detection in wideband mobile radio systems is presented. The proposed scheme is based on an intelligent search algorithm using Boolean Satisfiability (SAT techniques to search through the uncertainty region of the multipath delays. The SAT-based scheme utilizes the known structure of the transmitted wideband signal, for example, pseudo-random (PN code, to effectively search through the entire space by eliminating subspaces that do not contain a possible solution. The paper presents a framework for modeling the multipath detection problem as a SAT application. It also provides simulation results that demonstrate the effectiveness of the proposed scheme in detecting the multipath components in frequency-selective Rayleigh fading channels.
Boolean networks with robust and reliable trajectories
Schmal, Christoph; Peixoto, Tiago P; Drossel, Barbara, E-mail: schmal@physik.uni-bielefeld.d, E-mail: tiago@fkp.tu-darmstadt.d, E-mail: drossel@fkp.tu-darmstadt.d [Institut fuer Festkoerperphysik, TU Darmstadt, Hochschulstrasse 6, 64289 Darmstadt (Germany)
2010-11-15
We construct and investigate Boolean networks that follow a given reliable trajectory in state space, which is insensitive to fluctuations in the updating schedule and which is also robust against noise. Robustness is quantified as the probability that the dynamics return to the reliable trajectory after a perturbation of the state of a single node. In order to achieve high robustness, we navigate through the space of possible update functions by using an evolutionary algorithm. We constrain the networks to those having the minimum number of connections required to obtain the reliable trajectory. Surprisingly, we find that robustness always reaches values close to 100% during the evolutionary optimization process. The set of update functions can be evolved such that it differs only slightly from that of networks that were not optimized with respect to robustness. The state space of the optimized networks is dominated by the basin of attraction of the reliable trajectory.
Message passing for quantified Boolean formulas
Zhang, Pan; Zdeborová, Lenka; Zecchina, Riccardo
2012-01-01
We introduce two types of message passing algorithms for quantified Boolean formulas (QBF). The first type is a message passing based heuristics that can prove unsatisfiability of the QBF by assigning the universal variables in such a way that the remaining formula is unsatisfiable. In the second type, we use message passing to guide branching heuristics of a Davis-Putnam Logemann-Loveland (DPLL) complete solver. Numerical experiments show that on random QBFs our branching heuristics gives robust exponential efficiency gain with respect to the state-of-art solvers. We also manage to solve some previously unsolved benchmarks from the QBFLIB library. Apart from this our study sheds light on using message passing in small systems and as subroutines in complete solvers.
Reduction Mappings between Probabilistic Boolean Networks
Ivan Ivanov
2004-01-01
Full Text Available Probabilistic Boolean networks (PBNs comprise a model describing a directed graph with rule-based dependences between its nodes. The rules are selected, based on a given probability distribution which provides a flexibility when dealing with the uncertainty which is typical for genetic regulatory networks. Given the computational complexity of the model, the characterization of mappings reducing the size of a given PBN becomes a critical issue. Mappings between PBNs are important also from a theoretical point of view. They provide means for developing a better understanding about the dynamics of PBNs. This paper considers two kinds of mappings reduction and projection and their effect on the original probability structure of a given PBN.
Robust Boolean Operation for Sculptured Models
无
2000-01-01
To enhance the ability of current modeling system, an uniformed representation is designed to represent wire-frame, solid, surface models. We present an algorithm for Boolean operation between the models under this representation. Accuracy, efficiency and robustness are the main consideration. The geometric information is represented with trimmed parametric patches and trimmed parametric splines. The topological information is represented with an extended half-edge data structure. In the process of intersection calculation, hierarchy intersection method is applied for unified classification. Tracing the intersection curve to overcome degenerate cases that occur frequently in practice. The algorithm has been implemented as the modeling kernel of a feature based modeling system named GS-CAD98, which was developed on Windows/NT platform.
Synchronization of Arbitrarily Switched Boolean Networks.
Chen, Hongwei; Liang, Jinling; Huang, Tingwen; Cao, Jinde
2017-03-01
This paper investigates the complete synchronization problem for the drive-response switched Boolean networks (SBNs) under arbitrary switching signals, where the switching signals of the response SBN follow those generated by the drive SBN at each time instant. First, the definition of complete synchronization is introduced for the drive-response SBNs under arbitrary switching signals. Second, the concept of switching reachable set starting from a given initial state set is put forward. Based on it, a necessary and sufficient condition is derived for the complete synchronization of the drive-response SBNs. Last, we give a simple algebraic expression for the switching reachable set in a given number of time steps, and two computable algebraic criteria are obtained for the complete synchronization of the SBNs. A biological example is given to demonstrate the effectiveness of the obtained main results.
Synthesizing biomolecule-based Boolean logic gates.
Miyamoto, Takafumi; Razavi, Shiva; DeRose, Robert; Inoue, Takanari
2013-02-15
One fascinating recent avenue of study in the field of synthetic biology is the creation of biomolecule-based computers. The main components of a computing device consist of an arithmetic logic unit, the control unit, memory, and the input and output devices. Boolean logic gates are at the core of the operational machinery of these parts, and hence to make biocomputers a reality, biomolecular logic gates become a necessity. Indeed, with the advent of more sophisticated biological tools, both nucleic acid- and protein-based logic systems have been generated. These devices function in the context of either test tubes or living cells and yield highly specific outputs given a set of inputs. In this review, we discuss various types of biomolecular logic gates that have been synthesized, with particular emphasis on recent developments that promise increased complexity of logic gate circuitry, improved computational speed, and potential clinical applications.
Representing Boolean Functions by Decision Trees
Chikalov, Igor
2011-01-01
A Boolean or discrete function can be represented by a decision tree. A compact form of decision tree named binary decision diagram or branching program is widely known in logic design [2, 40]. This representation is equivalent to other forms, and in some cases it is more compact than values table or even the formula [44]. Representing a function in the form of decision tree allows applying graph algorithms for various transformations [10]. Decision trees and branching programs are used for effective hardware [15] and software [5] implementation of functions. For the implementation to be effective, the function representation should have minimal time and space complexity. The average depth of decision tree characterizes the expected computing time, and the number of nodes in branching program characterizes the number of functional elements required for implementation. Often these two criteria are incompatible, i.e. there is no solution that is optimal on both time and space complexity. © Springer-Verlag Berlin Heidelberg 2011.
The Boolean algebra of Galois algebras
Lianyong Xue
2003-02-01
Full Text Available Let B be a Galois algebra with Galois group G, Jg={bÃ¢ÂˆÂˆB|bx=g(xbÃ¢Â€Â‰for allÃ¢Â€Â‰xÃ¢ÂˆÂˆB} for each gÃ¢ÂˆÂˆG, and BJg=Beg for a central idempotent eg, Ba the Boolean algebra generated by {0,eg|gÃ¢ÂˆÂˆG}, e a nonzero element in Ba, and He={gÃ¢ÂˆÂˆG|eeg=e}. Then, a monomial e is characterized, and the Galois extension Be, generated by e with Galois group He, is investigated.
Boolean function applied to Mimosa pudica movements.
De Luccia, Thiago Paes de Barros; Friedman, Pedro
2011-09-01
Seismonastic or thigmonastic movements of Mimosa pudica L. is mostly because of the fast loss of water from swollen motor cells, resulting in temporary collapse of cells and quick curvature in the parts where these cells are located. Because of this, the plant has been much studied since the 18th century, leading us to think about the classical binomial stimulus-response (action-reaction) when compared to animals. Mechanic and electrical stimuli were used to investigate the analogy of mimosa branch with an artificial neuron model and to observe the action potential propagation through the mimosa branch. Boolean function applied to the mimosa branch in analogy with an artificial neuron model is one of the peculiarities of our hypothesis.
Kruse, Janis; Meier, Doreen; Zenk, Fides; Rehders, Maren; Nellen, Wolfgang; Hammann, Christian
2016-10-02
The maturation pathways of microRNAs (miRNAs) have been delineated for plants and several animals, belonging to the evolutionary supergroups of Archaeplastida and Opisthokonta, respectively. Recently, we reported the discovery of the microprocessor complex in Dictyostelium discoideum of the Amoebozoa supergroup. The complex is composed of the Dicer DrnB and the dsRBD (double-stranded RNA binding domain) containing protein RbdB. Both proteins localize at nucleoli, where they physically interact, and both are required for miRNA maturation. Here we show that the miRNA phenotype of a ΔdrnB gene deletion strain can be rescued by ectopic expression of a series of DrnB GFP fusion proteins, which consistently showed punctate perinucleolar localization in fluorescence microscopy. These punctate foci appear surprisingly stable, as they persist both disintegration of nucleoli and degradation of cellular nucleic acids. We observed that DrnB expression levels influence the number of microprocessor foci and alter RbdB accumulation. An investigation of DrnB variants revealed that its newly identified nuclear localization signal is necessary, but not sufficient for the perinucleolar localization. Biogenesis of miRNAs, which are RNA Pol II transcripts, is correlated with that localization. Besides its bidentate RNase III domains, DrnB contains only a dsRBD, which surprisingly is dispensable for miRNA maturation. This dsRBD can, however, functionally replace the homologous domain in RbdB. Based on the unique setup of the Dictyostelium microprocessor with a subcellular localization similar to plants, but a protein domain composition similar to animals, we propose a model for the evolutionary origin of RNase III proteins acting in miRNA maturation.
A transition calculus for Boolean functions. [logic circuit analysis
Tucker, J. H.; Bennett, A. W.
1974-01-01
A transition calculus is presented for analyzing the effect of input changes on the output of logic circuits. The method is closely related to the Boolean difference, but it is more powerful. Both differentiation and integration are considered.
A Full Bayesian Approach for Boolean Genetic Network Inference
Han, Shengtong; Wong, Raymond K. W.; Lee, Thomas C. M.; Shen, Linghao; Li, Shuo-Yen R.; Fan, Xiaodan
2014-01-01
Boolean networks are a simple but efficient model for describing gene regulatory systems. A number of algorithms have been proposed to infer Boolean networks. However, these methods do not take full consideration of the effects of noise and model uncertainty. In this paper, we propose a full Bayesian approach to infer Boolean genetic networks. Markov chain Monte Carlo algorithms are used to obtain the posterior samples of both the network structure and the related parameters. In addition to regular link addition and removal moves, which can guarantee the irreducibility of the Markov chain for traversing the whole network space, carefully constructed mixture proposals are used to improve the Markov chain Monte Carlo convergence. Both simulations and a real application on cell-cycle data show that our method is more powerful than existing methods for the inference of both the topology and logic relations of the Boolean network from observed data. PMID:25551820
QBF-Based Boolean Function Bi-Decomposition
Chen, Huan; Marques-Silva, Joao
2011-01-01
Boolean function bi-decomposition is ubiquitous in logic synthesis. It entails the decomposition of a Boolean function using two-input simple logic gates. Existing solutions for bi-decomposition are often based on BDDs and, more recently, on Boolean Satisfiability. In addition, the partition of the input set of variables is either assumed, or heuristic solutions are considered for finding good partitions. In contrast to earlier work, this paper proposes the use of Quantified Boolean Formulas (QBF) for computing bi- decompositions. These bi-decompositions are optimal in terms of the achieved disjointness and balancedness of the input set of variables. Experimental results, obtained on representative benchmarks, demonstrate clear improvements in the quality of computed decompositions, but also the practical feasibility of QBF-based bi-decomposition.
A fast quantum algorithm for the affine Boolean function identification
Younes, Ahmed
2015-02-01
Bernstein-Vazirani algorithm (the one-query algorithm) can identify a completely specified linear Boolean function using a single query to the oracle with certainty. The first aim of the paper is to show that if the provided Boolean function is affine, then one more query to the oracle (the two-query algorithm) is required to identify the affinity of the function with certainty. The second aim of the paper is to show that if the provided Boolean function is incompletely defined, then the one-query and the two-query algorithms can be used as bounded-error quantum polynomial algorithms to identify certain classes of incompletely defined linear and affine Boolean functions respectively with probability of success at least 2/3.
Construction and enumeration of Boolean functions with maximum algebraic immunity
ZHANG WenYing; WU ChuanKun; LIU XiangZhong
2009-01-01
Algebraic immunity is a new cryptographic criterion proposed against algebraic attacks. In order to resist algebraic attacks, Boolean functions used in many stream ciphers should possess high algebraic immunity. This paper presents two main results to find balanced Boolean functions with maximum algebraic immunity. Through swapping the values of two bits, and then generalizing the result to swap some pairs of bits of the symmetric Boolean function constructed by Dalai, a new class of Boolean functions with maximum algebraic immunity are constructed. Enumeration of such functions is also given. For a given function p(x) with deg(p(x)) < [n/2], we give a method to construct functions in the form p(x)+q(x) which achieve the maximum algebraic immunity, where every term with nonzero coefficient in the ANF of q(x) has degree no less than [n/2].
A full bayesian approach for boolean genetic network inference.
Shengtong Han
Full Text Available Boolean networks are a simple but efficient model for describing gene regulatory systems. A number of algorithms have been proposed to infer Boolean networks. However, these methods do not take full consideration of the effects of noise and model uncertainty. In this paper, we propose a full Bayesian approach to infer Boolean genetic networks. Markov chain Monte Carlo algorithms are used to obtain the posterior samples of both the network structure and the related parameters. In addition to regular link addition and removal moves, which can guarantee the irreducibility of the Markov chain for traversing the whole network space, carefully constructed mixture proposals are used to improve the Markov chain Monte Carlo convergence. Both simulations and a real application on cell-cycle data show that our method is more powerful than existing methods for the inference of both the topology and logic relations of the Boolean network from observed data.
Boolean Burritos: How the Faculty Ate Up Keyword Searching.
York, Sherry
1999-01-01
Describes an activity that librarians can use to acquaint teachers with keyword searching and Boolean operators to more successfully use the library's online catalog. Uses food ingredients to represent various possible combinations. (LRW)
A Construction of Boolean Functions with Good Cryptographic Properties
2014-01-01
using Binary Decision Diagram ( BDD ). Later research [19, 33] showed the effectiveness of BDD -based attacks on stream ciphers (albeit, they generally...require a large amount of memory). Krause notes that one of the effective ways to disrupt BDD -based attacks is for the Boolean function combiner of the...stream cipher is to have a robust BDD . There are many constructions of Boolean functions with high algebraic immu- nity [1, 7, 9, 10, 14, 15, 20, 21
An Amphiphysin-Like Domain in Fus2p Is Required for Rvs161p Interaction and Cortical Localization
Richard A. Stein
2016-02-01
Full Text Available Cell–cell fusion fulfils essential roles in fertilization, development and tissue repair. In the budding yeast, Saccharomyces cerevisiae, fusion between two haploid cells of opposite mating type generates the diploid zygote. Fus2p is a pheromone-induced protein that regulates cell wall removal during mating. Fus2p shuttles from the nucleus to localize at the shmoo tip, bound to Rvs161p, an amphiphysin. However, Rvs161p independently binds a second amphiphysin, Rvs167p, playing an essential role in endocytosis. To understand the basis of the Fus2p–Rvs161p interaction, we analyzed Fus2p structural domains. A previously described N-terminal domain (NTD is necessary and sufficient to regulate nuclear/cytoplasmic trafficking of Fus2p. The Dbl homology domain (DBH binds GTP-bound Cdc42p; binding is required for cell fusion, but not localization. We identified an approximately 200 amino acid region of Fus2p that is both necessary and sufficient for Rvs161p binding. The Rvs161p binding domain (RBD contains three predicted alpha-helices; structural modeling suggests that the RBD adopts an amphiphysin-like structure. The RBD contains a 13-amino-acid region, conserved with Rvs161p and other amphiphysins, which is essential for binding. Mutations in the RBD, predicted to affect membrane binding, abolish cell fusion without affecting Rvs161p binding. We propose that Fus2p/Rvs161p form a novel heterodimeric amphiphysin required for cell fusion. Rvs161p binding is required but not sufficient for Fus2p localization. Mutations in the C-terminal domain (CTD of Fus2p block localization, but not Rvs161p binding, causing a significant defect in cell fusion. We conclude that the Fus2p CTD mediates an additional, Rvs161p-independent interaction at the shmoo tip.
Boolean network model predicts knockout mutant phenotypes of fission yeast.
Maria I Davidich
Full Text Available BOOLEAN NETWORKS (OR: networks of switches are extremely simple mathematical models of biochemical signaling networks. Under certain circumstances, Boolean networks, despite their simplicity, are capable of predicting dynamical activation patterns of gene regulatory networks in living cells. For example, the temporal sequence of cell cycle activation patterns in yeasts S. pombe and S. cerevisiae are faithfully reproduced by Boolean network models. An interesting question is whether this simple model class could also predict a more complex cellular phenomenology as, for example, the cell cycle dynamics under various knockout mutants instead of the wild type dynamics, only. Here we show that a Boolean network model for the cell cycle control network of yeast S. pombe correctly predicts viability of a large number of known mutants. So far this had been left to the more detailed differential equation models of the biochemical kinetics of the yeast cell cycle network and was commonly thought to be out of reach for models as simplistic as Boolean networks. The new results support our vision that Boolean networks may complement other mathematical models in systems biology to a larger extent than expected so far, and may fill a gap where simplicity of the model and a preference for an overall dynamical blueprint of cellular regulation, instead of biochemical details, are in the focus.
Boolean Network Model Predicts Knockout Mutant Phenotypes of Fission Yeast
Davidich, Maria I.; Bornholdt, Stefan
2013-01-01
Boolean networks (or: networks of switches) are extremely simple mathematical models of biochemical signaling networks. Under certain circumstances, Boolean networks, despite their simplicity, are capable of predicting dynamical activation patterns of gene regulatory networks in living cells. For example, the temporal sequence of cell cycle activation patterns in yeasts S. pombe and S. cerevisiae are faithfully reproduced by Boolean network models. An interesting question is whether this simple model class could also predict a more complex cellular phenomenology as, for example, the cell cycle dynamics under various knockout mutants instead of the wild type dynamics, only. Here we show that a Boolean network model for the cell cycle control network of yeast S. pombe correctly predicts viability of a large number of known mutants. So far this had been left to the more detailed differential equation models of the biochemical kinetics of the yeast cell cycle network and was commonly thought to be out of reach for models as simplistic as Boolean networks. The new results support our vision that Boolean networks may complement other mathematical models in systems biology to a larger extent than expected so far, and may fill a gap where simplicity of the model and a preference for an overall dynamical blueprint of cellular regulation, instead of biochemical details, are in the focus. PMID:24069138
Synchronization in an array of coupled Boolean networks
Li, Rui, E-mail: rui.li@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, College of Engineering, Peking University, Beijing 100871 (China); Chu, Tianguang, E-mail: chutg@pku.edu.cn [State Key Laboratory for Turbulence and Complex Systems, College of Engineering, Peking University, Beijing 100871 (China)
2012-10-01
This Letter presents an analytical study of synchronization in an array of coupled deterministic Boolean networks. A necessary and sufficient criterion for synchronization is established based on algebraic representations of logical dynamics in terms of the semi-tensor product of matrices. Some basic properties of a synchronized array of Boolean networks are then derived for the existence of transient states and the upper bound of the number of fixed points. Particularly, an interesting consequence indicates that a “large” mismatch between two coupled Boolean networks in the array may result in loss of synchrony in the entire system. Examples, including the Boolean model of coupled oscillations in the cell cycle, are given to illustrate the present results. -- Highlights: ► We analytically study synchronization in an array of coupled Boolean networks. ► The study is based on the algebraic representations of logical dynamics. ► A necessary and sufficient algebraic criterion for synchronization is established. ► It reveals some basic properties of a synchronized array of Boolean networks. ► A large mismatch between two coupled networks may result in the loss of synchrony.
Unlimited multistability and Boolean logic in microbial signalling
Kothamachu, Varun B.; Feliu, Elisenda; Cardelli, Luca; Soyer, Orkun S.
2015-01-01
The ability to map environmental signals onto distinct internal physiological states or programmes is critical for single-celled microbes. A crucial systems dynamics feature underpinning such ability is multistability. While unlimited multistability is known to arise from multi-site phosphorylation seen in the signalling networks of eukaryotic cells, a similarly universal mechanism has not been identified in microbial signalling systems. These systems are generally known as two-component systems comprising histidine kinase (HK) receptors and response regulator proteins engaging in phosphotransfer reactions. We develop a mathematical framework for analysing microbial systems with multi-domain HK receptors known as hybrid and unorthodox HKs. We show that these systems embed a simple core network that exhibits multistability, thereby unveiling a novel biochemical mechanism for multistability. We further prove that sharing of downstream components allows a system with n multi-domain hybrid HKs to attain 3n steady states. We find that such systems, when sensing distinct signals, can readily implement Boolean logic functions on these signals. Using two experimentally studied examples of two-component systems implementing hybrid HKs, we show that bistability and implementation of logic functions are possible under biologically feasible reaction rates. Furthermore, we show that all sequenced microbial genomes contain significant numbers of hybrid and unorthodox HKs, and some genomes have a larger fraction of these proteins compared with regular HKs. Microbial cells are thus theoretically unbounded in mapping distinct environmental signals onto distinct physiological states and perform complex computations on them. These findings facilitate the understanding of natural two-component systems and allow their engineering through synthetic biology. PMID:26040599
Unlimited multistability and Boolean logic in microbial signalling.
Kothamachu, Varun B; Feliu, Elisenda; Cardelli, Luca; Soyer, Orkun S
2015-07-01
The ability to map environmental signals onto distinct internal physiological states or programmes is critical for single-celled microbes. A crucial systems dynamics feature underpinning such ability is multistability. While unlimited multistability is known to arise from multi-site phosphorylation seen in the signalling networks of eukaryotic cells, a similarly universal mechanism has not been identified in microbial signalling systems. These systems are generally known as two-component systems comprising histidine kinase (HK) receptors and response regulator proteins engaging in phosphotransfer reactions. We develop a mathematical framework for analysing microbial systems with multi-domain HK receptors known as hybrid and unorthodox HKs. We show that these systems embed a simple core network that exhibits multistability, thereby unveiling a novel biochemical mechanism for multistability. We further prove that sharing of downstream components allows a system with n multi-domain hybrid HKs to attain 3n steady states. We find that such systems, when sensing distinct signals, can readily implement Boolean logic functions on these signals. Using two experimentally studied examples of two-component systems implementing hybrid HKs, we show that bistability and implementation of logic functions are possible under biologically feasible reaction rates. Furthermore, we show that all sequenced microbial genomes contain significant numbers of hybrid and unorthodox HKs, and some genomes have a larger fraction of these proteins compared with regular HKs. Microbial cells are thus theoretically unbounded in mapping distinct environmental signals onto distinct physiological states and perform complex computations on them. These findings facilitate the understanding of natural two-component systems and allow their engineering through synthetic biology.
Lavinia Sheets
Full Text Available Synaptic ribbons are presynaptic structures formed by the self-association of RIBEYE-the main structural component of ribbon synapses. RIBEYE consists of two domains: a unique N-terminal A-domain and a C-terminal B-domain that is identical to the transcription co-repressor C-terminal binding protein 2 (CtBP2. Previous studies in cell lines have shown that RIBEYE A-domain alone is sufficient to form ribbon-like aggregates and that both A- and B- domains form homo-and heterotypic interactions. As these interactions are likely the basis for synaptic-ribbon assembly and structural plasticity, we wanted to examine how zebrafish Ribeye A- and B- domains interact with synaptic ribbons in vivo. To that end, we characterized the localization of exogenously expressed Ribeye A- and B- domains and the closely related protein, CtBP1, in the hair cells of transgenic zebrafish larvae. Unexpectedly, exogenously expressed Ribeye A-domain showed variable patterns of localization in hair cells; one zebrafish paralog of A-domain failed to self-associate or localize to synaptic ribbons, while the other self-assembled but sometimes failed to localize to synaptic ribbons. By contrast, Ribeye B-domain/CtBP2 was robustly localized to synaptic ribbons. Moreover, both exogenously expressed B-domain/CtBP2 and CtBP1 were preferentially localized to the basal end of ribbons adjacent to the postsynaptic density. Overexpression of B-domain/CtBP2 also appeared to affect synaptic-ribbon composition; endogenous levels of ribbon-localized Ribeye were significantly reduced as hair cells matured in B-domain/CtBP2 transgenic larvae compared to wild-type. These results reveal how exogenously expressed Ribeye domains interact with synaptic ribbons, and suggest a potential organization of elements within the ribbon body.
Hisao, Grant S; Brothers, Michael C; Ho, Mengfei; Wilson, Brenda A; Rienstra, Chad M
2017-03-01
Membrane localization domain (MLD) was first proposed for a 4-helix-bundle motif in the crystal structure of the C1 domain of Pasteurella multocida toxin (PMT). This structure motif is also found in the crystal structures of several clostridial glycosylating toxins (TcdA, TcdB, TcsL, and TcnA). The Ras/Rap1-specific endopeptidase (RRSP) module of the multifunctional autoprocessing repeats-in-toxins (MARTX) toxin produced by Vibrio vulnificus has sequence homology to the C1-C2 domains of PMT, including a putative MLD. We have determined the solution structure for the MLDs in PMT and in RRSP using solution state NMR. We conclude that the MLDs in these two toxins assume a 4-helix-bundle structure in solution. © 2016 The Protein Society.
Laser induced local modification of magnetic domain in Co/Pt multilayer
Talapatra, A.; Mohanty, J.
2016-11-01
Manipulation of magnetic system by the use of laser has drawn the attention of contemporary research. We demonstrate here the modification of magnetic domain in perpendicularly magnetized Co/Pt multilayer by using ultrashort laser pulse. The as-prepared sample shows an out-of-plane saturation magnetic field of 803.4 mT and almost zero remanence with a labyrinth-like domain pattern at room temperature. Atomistic simulation showed that interaction with femto-second laser results in demagnetization of the material in 200 fs followed by a slower recovery. As it indicates a net loss in magnetization, so magnetic force microscopy is carried out to investigate the equilibrium state after the system is relaxed. Demagnetized random domains appeared at the centre of the laser spot with having a rim at the boundary which signifies a deterministic switching with respect to the neighbouring area. Rotation of domains at the central area with the application of small transverse field (100 mT) proves the region to be magnetically weaker. Systematic 3D micromagnetic simulation has been performed to model the laser induced change by selective reduction of anisotropy which is discussed in detail. This shows shrinking of domains to a near circular pattern to minimize the magnetostatic energy. 50% reduction in anisotropy energy is observed with increasing the total energy of the system and a sharp increase in demagnetization energy also takes place simultaneously. This also satisfies the anisotropy in domain rotation with the application of transverse field.
Learning Techniques for Automatic Test Pattern Generation using Boolean Satisfiability
Liu Xin
2013-07-01
Full Text Available Automatic Test Pattern Generation (ATPG is one of the core problems in testing of digital circuits. ATPG algorithms based on Boolean Satisfiability (SAT turned out to be very powerful, due to great advances in the performance of satisfiability solvers for propositional logic in the last two decades. SAT-based ATPG clearly outperforms classical approaches especially for hard-to-detect faults. But its inaccessibility of structural information and don’t care, there exists the over-specification problem of input patterns. In this paper we present techniques to delve into an additional layer to make use of structural properties of the circuit and value justification relations to a generic SAT algorithm. It joins binary decision graphs (BDD and SAT techniques to improve the efficiency of ATPG. It makes a study of inexpensive reconvergent fanout analysis of circuit to gather information on the local signal correlation by using BDD learning, then uses the above learned information to restrict and focus the overall search space of SAT-based ATPG. The learning technique is effective and lightweight. Experimental results show the effectiveness of the approach.
Bai, Mingsian R; Yao, Yueh Hua; Lai, Chang-Sheng; Lo, Yi-Yang
2016-03-01
In this paper, four delay-and-sum (DAS) beamformers formulated in the modal domain and the space domain for open and solid spherical apertures are examined through numerical simulations. The resulting beampatterns reveal that the mainlobe of the solid spherical DAS array is only slightly narrower than that of the open array, whereas the sidelobes of the modal domain array are more significant than those of the space domain array due to the discrete approximation of continuous spherical Fourier transformation. To verify the theory experimentally, a three-dimensionally printed spherical array on which 32 micro-electro-mechanical system microphones are mounted is utilized for localization and separation of sound sources. To overcome the basis mismatch problem in signal separation, source localization is first carried out using minimum variance distortionless response beamformer. Next, Tikhonov regularization (TIKR) and compressive sensing (CS) are employed to extract the source signal amplitudes. Simulations and experiments are conducted to validate the proposed spherical array system. Objective perceptual evaluation of speech quality test and a subjective listening test are undertaken in performance evaluation. The experimental results demonstrate better separation quality achieved by the CS approach than by the TIKR approach at the cost of computational complexity.
Rotary and unidirectional metal shadowing of VAT: localization of the substrate-binding domain.
Rockel, B; Guckenberger, R; Gross, H; Tittmann, P; Baumeister, W
2000-11-01
AAA-ATPases have important roles in manifold cellular processes. VAT (valosine-containing protein-like ATPase of Thermoplasma acidophilum), a hexameric archaeal member of this family, has the tripartite domain structure N-D1-D2 that is characteristic of many members of this family. N, the N-terminal domain of 20.5 kDa, has been implicated in substrate binding. We have applied rotary and unidirectional shadowing to VAT and an N-terminally deleted mutant, VAT(Delta N), in order to map the location of this domain. For the analysis of data derived from unidirectionally shadowed samples we used a new approach combining eigenvector analysis with surface relief reconstruction. Averages of rotary shadowed particles as well as relief reconstructions map the N-terminal domains to the periphery of the hexameric complex and reveal their bipartite structure. Thus, this method appears to be well suited to study the conformational changes that occur during the functional cycle of the protein.
Boolean Satisfiability using Noise Based Logic
Lin, Pey-Chang Kent; Khatri, Sunil P
2011-01-01
In this paper, we present a novel algorithm to solve the Boolean Satisfiability (SAT) problem, using noise-based logic (NBL). Contrary to what the name may suggest, NBL is not a random/fuzzy logic system. In fact, it is a completely deterministic logic system. A key property of NBL is that it allows us to apply a superposition of many input vectors to a SAT instance at the same time, circumventing a key restriction and assumption in the traditional approach to solving SAT. By exploiting the superposition property of NBL, our NBL-based SAT algorithm can determine whether an instance is SAT or not in a single operation. A satisfying solution can be found by iteratively performing SAT check operations up to n times, where n is the number of variables in the SAT instance. Although this paper does not focus on the realization of an NBL-based SAT engine, such an engine can be conceived using analog circuits (wide-band amplifiers, adders and multipliers), FPGAs or ASICs. Additionally, we also discus scalability of o...
Efficient Analog Circuits for Boolean Satisfiability
Yin, Xunzhao; Varga, Melinda; Ercsey-Ravasz, Maria; Toroczkai, Zoltan; Hu, Xiaobo Sharon
2016-01-01
Efficient solutions to NP-complete problems would significantly benefit both science and industry. However, such problems are intractable on digital computers based on the von Neumann architecture, thus creating the need for alternative solutions to tackle such problems. Recently, a deterministic, continuous-time dynamical system (CTDS) was proposed (Nature Physics, 7(12), 966 (2011)) to solve a representative NP-complete problem, Boolean Satisfiability (SAT). This solver shows polynomial analog time-complexity on even the hardest benchmark $k$-SAT ($k \\geq 3$) formulas, but at an energy cost through exponentially driven auxiliary variables. With some modifications to the CTDS equations, here we present a novel analog hardware SAT solver, AC-SAT, implementing the CTDS. AC-SAT is intended to be used as a co-processor, and with its modular design can be readily extended to different problem sizes. The circuit is designed and simulated based on a 32nm CMOS technology. SPICE simulation results show speedup factor...
Klatt, Michael A; Schröder-Turk, Gerd E; Mecke, Klaus
2017-07-01
Structure-property relations, which relate the shape of the microstructure to physical properties such as transport or mechanical properties, need sensitive measures of structure. What are suitable fabric tensors that quantify the shape of anisotropic heterogeneous materials? The mean intercept length is among the most commonly used characteristics of anisotropy in porous media, for example, of trabecular bone in medical physics. We analyze the orientation-biased Boolean model, a versatile stochastic model that represents microstructures as overlapping grains with an orientation bias towards a preferred direction. This model is an extension of the isotropic Boolean model, which has been shown to truthfully reproduce multi-functional properties of isotropic porous media. We explain the close relationship between the concept of intersections with test lines to the elaborate mathematical theory of queues, and how explicit results from the latter can be directly applied to characterize microstructures. In this series of two papers, we provide analytic formulas for the anisotropic Boolean model and demonstrate often overlooked conceptual shortcomings of this approach. Queuing theory is used to derive simple and illustrative formulas for the mean intercept length. It separates into an intensity-dependent and an orientation-dependent factor. The global average of the mean intercept length can be expressed by local characteristics of a single grain alone. We thus identify which shape information about the random process the mean intercept length contains. The connection between global and local quantities helps to interpret observations and provides insights into the possibilities and limitations of the analysis. In the second paper of this series, we discuss, based on the findings in this paper, short-comings of the mean intercept analysis for (bone-)microstructure characterization. We will suggest alternative and better defined sensitive anisotropy measures from integral
Identifying a Probabilistic Boolean Threshold Network From Samples.
Melkman, Avraham A; Cheng, Xiaoqing; Ching, Wai-Ki; Akutsu, Tatsuya
2017-01-25
This paper studies the problem of exactly identifying the structure of a probabilistic Boolean network (PBN) from a given set of samples, where PBNs are probabilistic extensions of Boolean networks. Cheng et al. studied the problem while focusing on PBNs consisting of pairs of AND/OR functions. This paper considers PBNs consisting of Boolean threshold functions while focusing on those threshold functions that have unit coefficients. The treatment of Boolean threshold functions, and triplets and n-tuplets of such functions, necessitates a deepening of the theoretical analyses. It is shown that wide classes of PBNs with such threshold functions can be exactly identified from samples under reasonable constraints, which include: 1) PBNs in which any number of threshold functions can be assigned provided that all have the same number of input variables and 2) PBNs consisting of pairs of threshold functions with different numbers of input variables. It is also shown that the problem of deciding the equivalence of two Boolean threshold functions is solvable in pseudopolynomial time but remains co-NP complete.
Masayuki Ozawa
2015-11-01
Full Text Available Myoblast fusion is a highly regulated process that is essential for skeletal muscle formation during muscle development and regeneration in mammals. Much remains to be elucidated about the molecular mechanism of myoblast fusion although cadherins, which are Ca2+-dependent cell–cell adhesion molecules, are thought to play a critical role in this process. Mouse myoblasts lacking either N-cadherin or M-cadherin can still fuse to form myotubes, indicating that they have no specific function in this process and may be functionally replaced by either M-cadherin or N-cadherin, respectively. In this study, we show that expressing the E-cadherin cytoplasmic domain ectopically in C2C12 myoblasts inhibits cell surface localization of endogenous M-cadherin and N-cadherin, as well as cell–cell fusion. This domain, however, does not inhibit myoblast differentiation according to microarray-based gene expression analysis. In contrast, expressing a dominant-negative β-catenin mutant ectopically, which suppresses Wnt/β-catenin signaling, did not inhibit cell–cell fusion. Therefore, the E-cadherin cytoplasmic domain inhibits cell–cell fusion by inhibiting cell surface localization of endogenous cadherins and not by inhibiting Wnt/β-catenin signaling.
Noise as a Boolean algebra of sigma-fields. II. Classicality, blackness, spectrum
Tsirelson, Boris
2011-01-01
Similarly to noises, Boolean algebras of sigma-fields can be black. A noise may be treated as a homomorphism from a Boolean algebra of regular open sets to a Boolean algebra of sigma-fields. Spectral sets are useful also in this framework.
Boolean Logic: An Aid for Searching Computer Databases in Special Education and Rehabilitation.
Summers, Edward G.
1989-01-01
The article discusses using Boolean logic as a tool for searching computerized information retrieval systems in special education and rehabilitation technology. It includes discussion of the Boolean search operators AND, OR, and NOT; Venn diagrams; and disambiguating parentheses. Six suggestions are offered for development of good Boolean logic…
Mikhailov, SE
2006-01-01
Copyright @ 2006 Tech Science Press A quasi-static mixed boundary value problem of elastic damage mechanics for a continuously inhomogeneous body is considered. Using the two-operator Green-Betti formula and the fundamental solution of an auxiliary homogeneous linear elasticity with frozen initial, secant or tangent elastic coe±cients, a boundary-domain integro-differential formulation of the elasto-plastic problem with respect to the displacement rates and their gradients is derived. Usin...
A more robust Boolean model describing inhibitor binding
Zhaoqian Steven XIE; Chao TANG
2008-01-01
From the first application of the Boolean model to the cell cycle regulation network of budding yeast, new regulative pathways have been discovered, par-ticularly in the G1/S transition circuit. This discovery called for finer modeling to study the essential biology, and the resulting outcomes are first introduced in the ar-ticle. A traditional Boolean network model set up for the new G1/S transition circuit shows that it cannot correctly simulate real biology unless the model parameters are fine tuned. The deficiency is caused by an overly coarse-grained description of the inhibitor binding process, which shall be overcome by a two-vector model proposed whose robustness is surveyed using random perturba-tions. Simulations show that the proposed two-vector model is much more robust in describing inhibitor binding processes within the Boolean framework.
Exploiting Surroundedness for Saliency Detection: A Boolean Map Approach.
Zhang, Jianming; Sclaroff, Stan
2016-05-01
We demonstrate the usefulness of surroundedness for eye fixation prediction by proposing a Boolean Map based Saliency model (BMS). In our formulation, an image is characterized by a set of binary images, which are generated by randomly thresholding the image's feature maps in a whitened feature space. Based on a Gestalt principle of figure-ground segregation, BMS computes a saliency map by discovering surrounded regions via topological analysis of Boolean maps. Furthermore, we draw a connection between BMS and the Minimum Barrier Distance to provide insight into why and how BMS can properly captures the surroundedness cue via Boolean maps. The strength of BMS is verified by its simplicity, efficiency and superior performance compared with 10 state-of-the-art methods on seven eye tracking benchmark datasets.
Control of Large-Scale Boolean Networks via Network Aggregation.
Zhao, Yin; Ghosh, Bijoy K; Cheng, Daizhan
2016-07-01
A major challenge to solve problems in control of Boolean networks is that the computational cost increases exponentially when the number of nodes in the network increases. We consider the problem of controllability and stabilizability of Boolean control networks, address the increasing cost problem by partitioning the network graph into several subnetworks, and analyze the subnetworks separately. Easily verifiable necessary conditions for controllability and stabilizability are proposed for a general aggregation structure. For acyclic aggregation, we develop a sufficient condition for stabilizability. It dramatically reduces the computational complexity if the number of nodes in each block of the acyclic aggregation is small enough compared with the number of nodes in the entire Boolean network.
Constant-overhead secure computation of Boolean circuits using preprocessing
Damgård, Ivan Bjerre; Zakarias, S.
2013-01-01
We present a protocol for securely computing a Boolean circuit C in presence of a dishonest and malicious majority. The protocol is unconditionally secure, assuming a preprocessing functionality that is not given the inputs. For a large number of players the work for each player is the same...... as computing the circuit in the clear, up to a constant factor. Our protocol is the first to obtain these properties for Boolean circuits. On the technical side, we develop new homomorphic authentication schemes based on asymptotically good codes with an additional multiplication property. We also show a new...... algorithm for verifying the product of Boolean matrices in quadratic time with exponentially small error probability, where previous methods only achieved constant error....
Piecewise linear and Boolean models of chemical reaction networks
Veliz-Cuba, Alan; Kumar, Ajit; Josić, Krešimir
2014-01-01
Models of biochemical networks are frequently complex and high-dimensional. Reduction methods that preserve important dynamical properties are therefore essential for their study. Interactions in biochemical networks are frequently modeled using Hill functions (xn/(Jn + xn)). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent n is large. However, while the case of small constant J appears in practice, it is not well understood. We provide a mathematical analysis of this limit, and show that a reduction to a set of piecewise linear ODEs and Boolean networks can be mathematically justified. The piecewise linear systems have closed form solutions that closely track those of the fully nonlinear model. The simpler, Boolean network can be used to study the qualitative behavior of the original system. We justify the reduction using geometric singular perturbation theory and compact convergence, and illustrate the results in network models of a toggle switch and an oscillator. PMID:25412739
Synchronization in output-coupled temporal Boolean networks
Lu, Jianquan; Zhong, Jie; Tang, Yang; Huang, Tingwen; Cao, Jinde; Kurths, Jürgen
2014-09-01
This paper presents an analytical study of synchronization in an array of output-coupled temporal Boolean networks. A temporal Boolean network (TBN) is a logical dynamic system developed to model Boolean networks with regulatory delays. Both state delay and output delay are considered, and these two delays are assumed to be different. By referring to the algebraic representations of logical dynamics and using the semi-tensor product of matrices, the output-coupled TBNs are firstly converted into a discrete-time algebraic evolution system, and then the relationship between the states of coupled TBNs and the initial state sequence is obtained. Then, some necessary and sufficient conditions are derived for the synchronization of an array of TBNs with an arbitrary given initial state sequence. Two numerical examples including one epigenetic model are finally given to illustrate the obtained results.
Constant-Overhead Secure Computation of Boolean Circuits using Preprocessing
Damgård, Ivan Bjerre; Zakarias, Sarah Nouhad Haddad
We present a protocol for securely computing a Boolean circuit $C$ in presence of a dishonest and malicious majority. The protocol is unconditionally secure, assuming access to a preprocessing functionality that is not given the inputs to compute on. For a large number of players the work done...... by each player is the same as the work needed to compute the circuit in the clear, up to a constant factor. Our protocol is the first to obtain these properties for Boolean circuits. On the technical side, we develop new homomorphic authentication schemes based on asymptotically good codes...... with an additional multiplication property. We also show a new algorithm for verifying the product of Boolean matrices in quadratic time with exponentially small error probability, where previous methods would only give a constant error....
The Influence of Canalization on the Robustness of Boolean Networks
Kadelka, Claus; Laubenbacher, Reinhard
2016-01-01
Time- and state-discrete dynamical systems are frequently used to model molecular networks. This paper provides a collection of mathematical and computational tools for the study of robustness in Boolean network models. The focus is on networks governed by $k$-canalizing functions, a recently introduced class of Boolean functions that contains the well-studied class of nested canalizing functions. The activities and sensitivity of a function quantify the impact of input changes on the function output. This paper generalizes the latter concept to $c$-sensitivity and provides formulas for the activities and $c$-sensitivity of general $k$-canalizing functions as well as canalizing functions with more precisely defined structure. A popular measure for the robustness of a network, the Derrida value, can be expressed as a weighted sum of the $c$-sensitivities of the governing canalizing functions, and can also be calculated for a stochastic extension of Boolean networks. These findings provide a computationally eff...
Piecewise linear and Boolean models of chemical reaction networks.
Veliz-Cuba, Alan; Kumar, Ajit; Josić, Krešimir
2014-12-01
Models of biochemical networks are frequently complex and high-dimensional. Reduction methods that preserve important dynamical properties are therefore essential for their study. Interactions in biochemical networks are frequently modeled using Hill functions ([Formula: see text]). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent [Formula: see text] is large. However, while the case of small constant [Formula: see text] appears in practice, it is not well understood. We provide a mathematical analysis of this limit and show that a reduction to a set of piecewise linear ODEs and Boolean networks can be mathematically justified. The piecewise linear systems have closed-form solutions that closely track those of the fully nonlinear model. The simpler, Boolean network can be used to study the qualitative behavior of the original system. We justify the reduction using geometric singular perturbation theory and compact convergence, and illustrate the results in network models of a toggle switch and an oscillator.
Equivalence Checking of Combinational Circuits using Boolean Expression Diagrams
Hulgaard, Henrik; Williams, Poul Frederick; Andersen, Henrik Reif
1999-01-01
The combinational logic-level equivalence problem is to determine whether two given combinational circuits implement the same Boolean function. This problem arises in a number of CAD applications, for example when checking the correctness of incremental design changes (performed either manually...... similarities between the two circuits that are compared. These properties make BEDs suitable for verifying the equivalence of combinational circuits. BEDs can be seen as an intermediate representation between circuits (which are compact) and OBDDs (which are canonical).Based on a large number of combinational...... or by a design automation tool).This paper introduces a data structure called Boolean Expression Diagrams (BEDs) and two algorithms for transforming a BED into a Reduced Ordered Binary Decision Diagram (OBDD). BEDs are capable of representing any Boolean circuit in linear space and can exploit structural...
A comparison of hypertext and Boolean access to biomedical information.
Friedman, C P; Wildemuth, B M; Muriuki, M; Gant, S P; Downs, S M; Twarog, R G; de Bliek, R
1996-01-01
This study explored which of two modes of access to a biomedical database better supported problem solving in bacteriology. Boolean access, which allowed subjects to frame their queries as combinations of keywords, was compared to hypertext access, which allowed subjects to navigate from one database node to another. The accessible biomedical data were identical across systems. Data were collected from 42 first year medical students, each randomized to the Boolean or hypertext system, before and after their bacteriology course. Subjects worked eight clinical case problems, first using only their personal knowledge and, subsequently, with aid from the database. Database retrievals enabled students to answer questions they could not answer based on personal knowledge only. This effect was greater when personal knowledge of bacteriology was lower. The results also suggest that hypertext was superior to Boolean access in helping subjects identify possible infectious agents in these clinical case problems.
Nishino, Tasuku; Matsunaga, Ryota; Konishi, Hiroaki, E-mail: hkonishi@pu-hiroshima.ac.jp
2015-08-21
GAREM1 (Grb2-associated regulator of Erk/MAPK1) is an adaptor protein that is involved in the epidermal growth factor (EGF) pathway. The nuclear localization of GAREM1 depends on the nuclear localization sequence (NLS), which is located at the N-terminal CABIT (cysteine-containing, all in Themis) domain. Here, we identified 14-3-3ε as a GAREM-binding protein, and its binding site is closely located to the NLS. This 14-3-3 binding site was of the atypical type and independent of GAREM phosphorylation. Moreover, the binding of 14-3-3 had an effect on the nuclear localization of GAREM1. Unexpectedly, we observed that the CABIT domain had intramolecular association with the C-terminal SAM (sterile alpha motif) domain. This association might be inhibited by binding of 14-3-3 at the CABIT domain. Our results demonstrate that the mechanism underlying the nuclear localization of GAREM1 depends on its NLS in the CABIT domain, which is controlled by the binding of 14-3-3 and the C-terminal SAM domain. We suggest that the interplay between 14-3-3, SAM domain and CABIT domain might be responsible for the distribution of GAREM1 in mammalian cells. - Highlights: • 14-3-3ε regulated the nuclear localization of GAREM1 as its binding partner. • The atypical 14-3-3 binding site of GAREM1 is located near the NLS in CABIT domain. • The CABIT domain had intramolecular association with the SAM domain in GAREM1. • Subcellular localization of GAREM1 is affected with its CABIT-SAM interaction.
Adelsberger, Helmuth; Zainos, Antonio; Alvarez, Manuel; Romo, Ranulfo; Konnerth, Arthur
2014-01-01
Brain mapping experiments involving electrical microstimulation indicate that the primary motor cortex (M1) directly regulates muscle contraction and thereby controls specific movements. Possibly, M1 contains a small circuit “map” of the body that is formed by discrete local networks that code for specific movements. Alternatively, movements may be controlled by distributed, larger-scale overlapping circuits. Because of technical limitations, it remained unclear how movement-determining circuits are organized in M1. Here we introduce a method that allows the functional mapping of small local neuronal circuits in awake behaving nonhuman primates. For this purpose, we combined optic-fiber–based calcium recordings of neuronal activity and cortical microstimulation. The method requires targeted bulk loading of synthetic calcium indicators (e.g., OGB-1 AM) for the staining of neuronal microdomains. The tip of a thin (200 µm) optical fiber can detect the coherent activity of a small cluster of neurons, but is insensitive to the asynchronous activity of individual cells. By combining such optical recordings with microstimulation at two well-separated sites of M1, we demonstrate that local cortical activity was tightly associated with distinct and stereotypical simple movements. Increasing stimulation intensity increased both the amplitude of the movements and the level of neuronal activity. Importantly, the activity remained local, without invading the recording domain of the second optical fiber. Furthermore, there was clear response specificity at the two recording sites in a trained behavioral task. Thus, the results provide support for movement control in M1 by local neuronal clusters that are organized in discrete cortical domains. PMID:24344287
Boolean versus ranked querying for biomedical systematic reviews
Cavedon Lawrence
2010-10-01
Full Text Available Abstract Background The process of constructing a systematic review, a document that compiles the published evidence pertaining to a specified medical topic, is intensely time-consuming, often taking a team of researchers over a year, with the identification of relevant published research comprising a substantial portion of the effort. The standard paradigm for this information-seeking task is to use Boolean search; however, this leaves the user(s the requirement of examining every returned result. Further, our experience is that effective Boolean queries for this specific task are extremely difficult to formulate and typically require multiple iterations of refinement before being finalized. Methods We explore the effectiveness of using ranked retrieval as compared to Boolean querying for the purpose of constructing a systematic review. We conduct a series of experiments involving ranked retrieval, using queries defined methodologically, in an effort to understand the practicalities of incorporating ranked retrieval into the systematic search task. Results Our results show that ranked retrieval by itself is not viable for this search task requiring high recall. However, we describe a refinement of the standard Boolean search process and show that ranking within a Boolean result set can improve the overall search performance by providing early indication of the quality of the results, thereby speeding up the iterative query-refinement process. Conclusions Outcomes of experiments suggest that an interactive query-development process using a hybrid ranked and Boolean retrieval system has the potential for significant time-savings over the current search process in the systematic reviewing.
Periodic pattern detection in sparse boolean sequences
Hérisson Joan
2010-09-01
Full Text Available Abstract Background The specific position of functionally related genes along the DNA has been shown to reflect the interplay between chromosome structure and genetic regulation. By investigating the statistical properties of the distances separating such genes, several studies have highlighted various periodic trends. In many cases, however, groups built up from co-functional or co-regulated genes are small and contain wrong information (data contamination so that the statistics is poorly exploitable. In addition, gene positions are not expected to satisfy a perfectly ordered pattern along the DNA. Within this scope, we present an algorithm that aims to highlight periodic patterns in sparse boolean sequences, i.e. sequences of the type 010011011010... where the ratio of the number of 1's (denoting here the transcription start of a gene to 0's is small. Results The algorithm is particularly robust with respect to strong signal distortions such as the addition of 1's at arbitrary positions (contaminated data, the deletion of existing 1's in the sequence (missing data and the presence of disorder in the position of the 1's (noise. This robustness property stems from an appropriate exploitation of the remarkable alignment properties of periodic points in solenoidal coordinates. Conclusions The efficiency of the algorithm is demonstrated in situations where standard Fourier-based spectral methods are poorly adapted. We also show how the proposed framework allows to identify the 1's that participate in the periodic trends, i.e. how the framework allows to allocate a positional score to genes, in the same spirit of the sequence score. The software is available for public use at http://www.issb.genopole.fr/MEGA/Softwares/iSSB_SolenoidalApplication.zip.
A Boolean Approach to Airline Business Model Innovation
Hvass, Kristian Anders
Research in business model innovation has identified its significance in creating a sustainable competitive advantage for a firm, yet there are few empirical studies identifying which combination of business model activities lead to success and therefore deserve innovative attention. This study...... innovation, introduce Boolean minimization methods to the field, and propose alternative business model activities to North American carriers striving for positive operating results....... analyzes the business models of North America low-cost carriers from 2001 to 2010 using a Boolean minimization algorithm to identify which combinations of business model activities lead to operational profitability. The research aim is threefold: complement airline literature in the realm of business model...
Perturbation propagation in random and evolved Boolean networks
Fretter, Christoph [Instistut fuer Informatik, Martin-Luther-Universitaet Halle-Wittenberg, Von-Seckendorffplatz 1, 06120 Halle (Germany); Szejka, Agnes; Drossel, Barbara [Institut fuer Festkoerperphysik, Technische Universitaet Darmstadt, Hochschulstrasse 6, 64289 Darmstadt (Germany)], E-mail: Christoph.Fretter@informatik.uni-halle.de
2009-03-15
In this paper, we investigate the propagation of perturbations in Boolean networks by evaluating the Derrida plot and its modifications. We show that even small random Boolean networks agree well with the predictions of the annealed approximation, but nonrandom networks show a very different behaviour. We focus on networks that were evolved for high dynamical robustness. The most important conclusion is that the simple distinction between frozen, critical and chaotic networks is no longer useful, since such evolved networks can display the properties of all three types of networks. Furthermore, we evaluate a simplified empirical network and show how its specific state space properties are reflected in the modified Derrida plots.
Optimization-Based Approaches to Control of Probabilistic Boolean Networks
Koichi Kobayashi
2017-02-01
Full Text Available Control of gene regulatory networks is one of the fundamental topics in systems biology. In the last decade, control theory of Boolean networks (BNs, which is well known as a model of gene regulatory networks, has been widely studied. In this review paper, our previously proposed methods on optimal control of probabilistic Boolean networks (PBNs are introduced. First, the outline of PBNs is explained. Next, an optimal control method using polynomial optimization is explained. The finite-time optimal control problem is reduced to a polynomial optimization problem. Furthermore, another finite-time optimal control problem, which can be reduced to an integer programming problem, is also explained.
Analysis of Boolean Equation Systems through Structure Graphs
Reniers, Michel A; 10.4204/EPTCS.18.7
2010-01-01
We analyse the problem of solving Boolean equation systems through the use of structure graphs. The latter are obtained through an elegant set of Plotkin-style deduction rules. Our main contribution is that we show that equation systems with bisimilar structure graphs have the same solution. We show that our work conservatively extends earlier work, conducted by Keiren and Willemse, in which dependency graphs were used to analyse a subclass of Boolean equation systems, viz., equation systems in standard recursive form. We illustrate our approach by a small example, demonstrating the effect of simplifying an equation system through minimisation of its structure graph.
On Kolmogorov's superpositions and Boolean functions
Beiu, V.
1998-12-31
The paper overviews results dealing with the approximation capabilities of neural networks, as well as bounds on the size of threshold gate circuits. Based on an explicit numerical (i.e., constructive) algorithm for Kolmogorov's superpositions they will show that for obtaining minimum size neutral networks for implementing any Boolean function, the activation function of the neurons is the identity function. Because classical AND-OR implementations, as well as threshold gate implementations require exponential size (in the worst case), it will follow that size-optimal solutions for implementing arbitrary Boolean functions require analog circuitry. Conclusions and several comments on the required precision are ending the paper.
Refinement monoids, equidecomposability types, and boolean inverse semigroups
Wehrung, Friedrich
2017-01-01
Adopting a new universal algebraic approach, this book explores and consolidates the link between Tarski's classical theory of equidecomposability types monoids, abstract measure theory (in the spirit of Hans Dobbertin's work on monoid-valued measures on Boolean algebras) and the nonstable K-theory of rings. This is done via the study of a monoid invariant, defined on Boolean inverse semigroups, called the type monoid. The new techniques contrast with the currently available topological approaches. Many positive results, but also many counterexamples, are provided.
Localization and distribution of fibrinogen C domain containing 1 (FIBCD1) in human tissues
von Huth, Sebastian; Møller, Jesper Bonnet; Schlosser, Anders
in an immunohistochemistry-based analysis and demonstrate that FIBCD1 protein is highly expressed at the apical surfaces of the epithelium throughout the gastrointestinal tract, in the uterus, testis, bladder, gallbladder and the salivary glands. To a lesser extent, FIBCD1 is expressed in the pancreas, the spleen......Introduction: We have previously identified and characterized fibrinogen C domain-containing 1 (FIBCD1) as a homotetrameric type II transmembrane protein. FIBCD1 is a member of the fibrinogen- related protein (FReP) family, and is thought to play a crucial role in the innate immune system...
E Chamorro; M Duque; C Cárdenas; J Santos; W Tiznado; P Fuentealba
2005-09-01
Use of regions of space defined by topological analysis of electron localization function (ELF) as reactivity descriptors is explored. By starting from the fact that the ELF presents high values in the regions where it is most probable to find an electron pair and that the square of the HOMO is a good measure of the reactivity of a molecule, it is proposed that the integration of the square of the HOMO over the volumes defined by the ELF should be a local index for predicting the most nucleophilic site of a molecule. We present here some computational results on simple systems in order to get some insights about this possibility.
Joglekar, D. M.; Mitra, Mira
2017-02-01
The nonlinear interaction of a dual frequency flexural wave with a breathing crack generates a peculiar frequency mixing phenomena, which is manifested in form of the side bands or peaks at combinations frequencies in frequency spectrum of the response. Although these peaks have been proven useful in ascertaining the presence of crack, they barely carry any information about the crack location. In this regards, the present article analyzes the time domain representation of the response obtained by employing a wavelet spectral finite element method. The study reveals that the combination tones generated at the crack location travel with dissimilar speeds along the waveguide, owing to its dispersive nature. The separation between the lobes corresponding to these combination tones therefore, depends on the distance that they have travelled. This observation is then used to formulate a method to predict the crack location with respect to the sensor. A brief parametric study shows marginal errors in predicting the crack location, which ascertains the validity of the method. This article also studies the frequency spectrum of the response. The peaks at combination tones are quantified in terms of a modulate parameter which depends on the severity of the crack. The inferences drawn from the time and the frequency domain study can be instrumental in designing a robust strategy for detecting location and severity of the crack.
Characterization of Linearly Separable Boolean Functions: A Graph-Theoretic Perspective.
Rao, Yanyi; Zhang, Xianda
2016-04-05
In this paper, we present a novel approach for studying Boolean function in a graph-theoretic perspective. In particular, we first transform a Boolean function f of n variables into an induced subgraph Hf of the n-dimensional hypercube, and then, we show the properties of linearly separable Boolean functions on the basis of the analysis of the structure of Hf. We define a new class of graphs, called hyperstar, and prove that the induced subgraph Hf of any linearly separable Boolean function f is a hyperstar. The proposal of hyperstar helps us uncover a number of fundamental properties of linearly separable Boolean functions in this paper.
Mohammad Tavakolizadeh-Ravari
2015-02-01
Conclusion: Based on this metric, the tendency toward the use of national publications in the social science domain is constant despite the number of scientific productions is growing in Iran. This means that the Iranian social science domain not only doesn’t tend to the science localization but its use of foreign science is growing in the span of time as well.
Guo Shuixia
2010-06-01
Full Text Available Abstract Background Reverse-engineering approaches such as Bayesian network inference, ordinary differential equations (ODEs and information theory are widely applied to deriving causal relationships among different elements such as genes, proteins, metabolites, neurons, brain areas and so on, based upon multi-dimensional spatial and temporal data. There are several well-established reverse-engineering approaches to explore causal relationships in a dynamic network, such as ordinary differential equations (ODE, Bayesian networks, information theory and Granger Causality. Results Here we focused on Granger causality both in the time and frequency domain and in local and global networks, and applied our approach to experimental data (genes and proteins. For a small gene network, Granger causality outperformed all the other three approaches mentioned above. A global protein network of 812 proteins was reconstructed, using a novel approach. The obtained results fitted well with known experimental findings and predicted many experimentally testable results. In addition to interactions in the time domain, interactions in the frequency domain were also recovered. Conclusions The results on the proteomic data and gene data confirm that Granger causality is a simple and accurate approach to recover the network structure. Our approach is general and can be easily applied to other types of temporal data.
Carrington, David Bradley [Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Monayem, A. K. M. [Univ. of New Mexico, Albuquerque, NM (United States); Mazumder, H. [Univ. of New Mexico, Albuquerque, NM (United States); Heinrich, Juan C. [Univ. of New Mexico, Albuquerque, NM (United States)
2015-03-05
A three-dimensional finite element method for the numerical simulations of fluid flow in domains containing moving rigid objects or boundaries is developed. The method falls into the general category of Arbitrary Lagrangian Eulerian methods; it is based on a fixed mesh that is locally adapted in the immediate vicinity of the moving interfaces and reverts to its original shape once the moving interfaces go past the elements. The moving interfaces are defined by separate sets of marker points so that the global mesh is independent of interface movement and the possibility of mesh entanglement is eliminated. The results is a fully robust formulation capable of calculating on domains of complex geometry with moving boundaries or devises that can also have a complex geometry without danger of the mesh becoming unsuitable due to its continuous deformation thus eliminating the need for repeated re-meshing and interpolation. Moreover, the boundary conditions on the interfaces are imposed exactly. This work is intended to support the internal combustion engines simulator KIVA developed at Los Alamos National Laboratories. The model's capabilities are illustrated through application to incompressible flows in different geometrical settings that show the robustness and flexibility of the technique to perform simulations involving moving boundaries in a three-dimensional domain.
Abe, Shunnosuke; Sakai, Masako; Yagi, Kosaku; Hagino, Takehiko; Ochi, Katsumasa; Shibata, Koichi; Davies, Eric
2003-03-01
A major high molecular weight protein (HMP) in the cytoskeletal fraction from pea has been purified. A combination of chromatographic techniques and protease fragment analysis also facilitated the isolation of the encoding cDNA, disclosing the sequence of the complete open reading frame. The protein possesses four complete N-terminal Staphylococcal nuclease (SNc) domains, a central Tudor domain and a partial SNc domain at the C-terminus, which may act as a coiled-coil cytoskeleton interaction motif. Cell fractionation studies showed that the protein was abundant in the cytoskeleton fraction in dark-grown pea seedlings, but essentially was absent from the nucleus. Gel filtration column chromatography indicated that the native protein exists as a dimer, while isoelectric focusing suggested that there were at least four HMP isotypes. The protein co-eluted with ribosomes from a heparin affinity column in vitro, consistent with ribosome/polysome interactions in vivo. Significantly, sequence analysis of the C-terminal SNc motif may accurately predict nuclear versus cytoplasmic localization resulting in potentially very different functional roles for this protein family in different organisms. An antibody to HMP from peas was also raised and an HMP with a similar molecular mass was detected in the cytoskeleton fractions and to a lesser extent in the nuclear fraction (250 g pellet) from rice and wheat seedlings.
Jeong Ja Bae
2012-01-01
In this article,we consider the global existence and decay rates of solutions for the transmission problem of Kirchhoff type wave equations consisting of two physically different types of materials,one component is a Kirchhoff type wave equation with nonlinear time dependent localized dissipation which is effective only on a neighborhood of certain part of the boundary,while the other is a Kirchhoff type wave equation with nonlinear memory.
Anatomical-functional image fusion by information of interest in local Laplacian filtering domain.
Du, Jiao; Li, Weisheng; Xiao, Bin
2017-08-25
A novel method for performing anatomical (MRI)-functional (PET or SPECT) image fusion is presented. The method merges specific feature information from input image signals of a single or multiple medical imaging modalities into a single fused image while preserving more information and generating less distortion. The proposed method uses a local Laplacian filtering based technique realized through a novel multi-scale system architecture. Firstly, the input images are generated in a multi-scale image representation and are processed using local Laplacian filtering. Secondly, at each scale, the decomposed images are combined to produce fused approximate images using a local energy maximum scheme and produce the fused residual images using an information of interest-based scheme. Finally, a fused image is obtained using a reconstruction process that is analogous to that of conventional Laplacian pyramid transform. Experimental results computed using individual multi-scale analysis-based decomposition schemes or fusion rules clearly demonstrate the superiority of the proposed method through subjective observation as well as objective metrics. Furthermore, the proposed method can obtain better performance, compared to the state-of-the-art fusion methods.
Linear Strategy for Boolean Ring Based Theorem Proving
WU Jinzhao; LIU Zhuojun
2000-01-01
Two inference rules are discussed in boolean ring based theorem proving, and linear strategy is developed. It is shown that both of them are complete for linear strategy. Moreover, by introducing a partial ordering on atoms, pseudo O-linear and O-linear strategies are presented. The former is complete, the latter, however, is complete for clausal theorem proving.
Feedback Controller Design for the Synchronization of Boolean Control Networks.
Liu, Yang; Sun, Liangjie; Lu, Jianquan; Liang, Jinling
2016-09-01
This brief investigates the partial and complete synchronization of two Boolean control networks (BCNs). Necessary and sufficient conditions for partial and complete synchronization are established by the algebraic representations of logical dynamics. An algorithm is obtained to construct the feedback controller that guarantees the synchronization of master and slave BCNs. Two biological examples are provided to illustrate the effectiveness of the obtained results.
Boolean linear differential operators on elementary cellular automata
Martín Del Rey, Ángel
2014-12-01
In this paper, the notion of boolean linear differential operator (BLDO) on elementary cellular automata (ECA) is introduced and some of their more important properties are studied. Special attention is paid to those differential operators whose coefficients are the ECA with rule numbers 90 and 150.
New Considerations for Spectral Classification of Boolean Switching Functions
J. E. Rice
2011-01-01
Full Text Available This paper presents some new considerations for spectral techniques for classification of Boolean functions. These considerations incorporate discussions of the feasibility of extending this classification technique beyond n=5. A new implementation is presented along with a basic analysis of the complexity of the problem. We also note a correction to results in this area that were reported in previous work.
Pointwise Approximation for the Iterated Boolean Sums of Bernstein Operators
HUO Xiao-yan; LI Cui-xiang; YAO Qiu-mei
2013-01-01
In this paper,with the help of modulus of smoothness ω2r(4)(f,t),we discuss the pointwise approximation properties for the iterated Boolean sums of Bernstein operator Bnn and obtain direct and inverse theorems when 1-1/r ≤ λ ≤ 1,r ∈ N.
Learning restricted Boolean network model by time-series data
2014-01-01
Restricted Boolean networks are simplified Boolean networks that are required for either negative or positive regulations between genes. Higa et al. (BMC Proc 5:S5, 2011) proposed a three-rule algorithm to infer a restricted Boolean network from time-series data. However, the algorithm suffers from a major drawback, namely, it is very sensitive to noise. In this paper, we systematically analyze the regulatory relationships between genes based on the state switch of the target gene and propose an algorithm with which restricted Boolean networks may be inferred from time-series data. We compare the proposed algorithm with the three-rule algorithm and the best-fit algorithm based on both synthetic networks and a well-studied budding yeast cell cycle network. The performance of the algorithms is evaluated by three distance metrics: the normalized-edge Hamming distance μhame, the normalized Hamming distance of state transition μhamst, and the steady-state distribution distance μssd. Results show that the proposed algorithm outperforms the others according to both μhame and μhamst, whereas its performance according to μssd is intermediate between best-fit and the three-rule algorithms. Thus, our new algorithm is more appropriate for inferring interactions between genes from time-series data. PMID:25093019
Complexity of Identification and Dualization of Positive Boolean Functions
J.C. Bioch (Cor); T. Ibaraki
1995-01-01
textabstractWe consider in this paper the problem of identifying min T(f{hook}) and max F(f{hook}) of a positive (i.e., monotone) Boolean function f{hook}, by using membership queries only, where min T(f{hook}) (max F(f{hook})) denotes the set of minimal true vectors (maximal false vectors) of f{hoo
Boolean approaches to graph embeddings related to VLSI
刘彦佩
2001-01-01
This paper discusses the development of Boolean methods in some topics on graph em-beddings which are related to VLSI. They are mainly the general theory of graph embeddability, the orientabilities of a graph and the rectilinear layout of an electronic circuit.
Learning restricted Boolean network model by time-series data.
Ouyang, Hongjia; Fang, Jie; Shen, Liangzhong; Dougherty, Edward R; Liu, Wenbin
2014-01-01
Restricted Boolean networks are simplified Boolean networks that are required for either negative or positive regulations between genes. Higa et al. (BMC Proc 5:S5, 2011) proposed a three-rule algorithm to infer a restricted Boolean network from time-series data. However, the algorithm suffers from a major drawback, namely, it is very sensitive to noise. In this paper, we systematically analyze the regulatory relationships between genes based on the state switch of the target gene and propose an algorithm with which restricted Boolean networks may be inferred from time-series data. We compare the proposed algorithm with the three-rule algorithm and the best-fit algorithm based on both synthetic networks and a well-studied budding yeast cell cycle network. The performance of the algorithms is evaluated by three distance metrics: the normalized-edge Hamming distance [Formula: see text], the normalized Hamming distance of state transition [Formula: see text], and the steady-state distribution distance μ (ssd). Results show that the proposed algorithm outperforms the others according to both [Formula: see text] and [Formula: see text], whereas its performance according to μ (ssd) is intermediate between best-fit and the three-rule algorithms. Thus, our new algorithm is more appropriate for inferring interactions between genes from time-series data.
Profiling of genetic switches using boolean implications in expression data.
Çakır, Mehmet Volkan; Binder, Hans; Wirth, Henry
2014-01-01
Correlation analysis assuming coexpression of the genes is a widely used method for gene expression analysis in molecular biology. Yet growing extent, quality and dimensionality of the molecular biological data permits emerging, more sophisticated approaches like Boolean implications. We present an approach which is a combination of the SOM (self organizing maps) machine learning method and Boolean implication analysis to identify relations between genes, metagenes and similarly behaving metagene groups (spots). Our method provides a way to assign Boolean states to genes/metagenes/spots and offers a functional view over significantly variant elements of gene expression data on these three different levels. While being able to cover relations between weakly correlated entities Boolean implication method also decomposes these relations into six implication classes. Our method allows one to validate or identify potential relationships between genes and functional modules of interest and to assess their switching behaviour. Furthermore the output of the method renders it possible to construct and study the network of genes. By providing logical implications as updating rules for the network it can also serve to aid modelling approaches.
Graphical interpretation of Boolean operators for protein NMR assignments
Verdegem, Dries; Dijkstra, Klaas; Hanoulle, Xavier; Lippens, Guy
We have developed a graphics based algorithm for semi-automated protein NMR assignments. Using the basic sequential triple resonance assignment strategy, the method is inspired by the Boolean operators as it applies "AND"-, "OR"- and "NOT"-like operations on planes pulled out of the classical
Superatomic Boolean algebras constructed from strongly unbounded functions
Martinez, Juan Carlos
2010-01-01
Using Koszmider's strongly unbounded functions, we show the following consistency result: Suppose that $\\kappa,\\lambda$ are infinite cardinals such that $\\kappa^{+++} \\leq \\lambda$, $\\kappa^{_{{\\omega}_1}\\concatenation \\$ and $\\_{{\\omega}_2}\\concatenation \\$ can be cardinal sequences of superatomic Boolean algebras.
State complexity of catenation combined with boolean operations
Caron, Pascal; Luque, Jean-Gabriel; Patrou, Bruno
2017-01-01
We exhaustively investigate possible combinations of a boolean operation together with a catenation. In many cases we prove and improve some conjectures by Brzozowski. For each family of operation, we endeavour to provide a common witness with a small size alphabet.
Complexity of Identification and Dualization of Positive Boolean Functions
J.C. Bioch (Cor); T. Ibaraki
1995-01-01
textabstractWe consider in this paper the problem of identifying min T(f{hook}) and max F(f{hook}) of a positive (i.e., monotone) Boolean function f{hook}, by using membership queries only, where min T(f{hook}) (max F(f{hook})) denotes the set of minimal true vectors (maximal false vectors) of
Local pH domains regulate NHE3-mediated Na+ reabsorption in the renal proximal tubule
Burford, James L.; McDonough, Alicia A.; Holstein-Rathlou, Niels-Henrik; Peti-Peterdi, Janos
2014-01-01
The proximal tubule Na+/H+ exchanger 3 (NHE3), located in the apical dense microvilli (brush border), plays a major role in the reabsorption of NaCl and water in the renal proximal tubule. In response to a rise in blood pressure NHE3 redistributes in the plane of the plasma membrane to the base of the brush border, where NHE3 activity is reduced. This NHE3 redistribution is assumed to provoke pressure natriuresis; however, it is unclear how NHE3 redistribution per se reduces NHE3 activity. To investigate if the distribution of NHE3 in the brush border can change the reabsorption rate, we constructed a spatiotemporal mathematical model of NHE3-mediated Na+ reabsorption across a proximal tubule cell and compared the model results with in vivo experiments in rats. The model predicts that when NHE3 is localized exclusively at the base of the brush border, it creates local pH microdomains that reduce NHE3 activity by >30%. We tested the model's prediction experimentally: the rat kidney cortex was loaded with the pH-sensitive fluorescent dye BCECF, and cells of the proximal tubule were imaged in vivo using confocal fluorescence microscopy before and after an increase of blood pressure by ∼50 mmHg. The experimental results supported the model by demonstrating that a rise of blood pressure induces the development of pH microdomains near the bottom of the brush border. These local changes in pH reduce NHE3 activity, which may explain the pressure natriuresis response to NHE3 redistribution. PMID:25298526
Krizia Tuand
Full Text Available Neurobeachin (NBEA is an autism spectrum disorders (ASD candidate gene. NBEA deficiency affects regulated secretion, receptor trafficking, synaptic architecture and protein kinase A (PKA-mediated phosphorylation. NBEA is a large multidomain scaffolding protein. From N- to C-terminus, NBEA has a concanavalin A-like lectin domain flanked by armadillo repeats (ACA, an A-kinase anchoring protein domain that can bind to PKA, a domain of unknown function (DUF1088 and a BEACH domain, preceded by a pleckstrin homology-like domain and followed by WD40 repeats (PBW. Although most of these domains mediate protein-protein interactions, no interaction screen has yet been performed.Yeast two-hybrid screens with the ACA and PBW domain modules of NBEA gave a list of interaction partners, which were analyzed for Gene Ontology (GO enrichment. Neuro-2a cells were used for confocal microscopy and nuclear extraction analysis. NOTCH-mediated transcription was studied with luciferase reporter assays and qRT-PCR, combined with NBEA knockdown or overexpression.Both domain modules showed a GO enrichment for the nucleus. PBW almost exclusively interacted with transcription regulators, while ACA interacted with a number of PKA substrates. NBEA was partially localized in the nucleus of Neuro-2a cells, albeit much less than in the cytoplasm. A nuclear localization signal was found in the DUF1088 domain, which was shown to contribute to the nuclear localization of an EGFP-DPBW fusion protein. Yeast two-hybrid identified the Notch1 intracellular domain as a physical interactor of the PBW domain and a role for NBEA as a negative regulator in Notch-mediated transcription was demonstrated.Defining novel interaction partners of conserved NBEA domain modules identified a role for NBEA as transcriptional regulator in the nucleus. The physical interaction of NBEA with NOTCH1 is most relevant for ASD pathogenesis because NOTCH signaling is essential for neural development.
Piezo2 channel conductance and localization domains in Merkel cells of rat whisker hair follicles.
Ikeda, Ryo; Gu, Jianguo G
2014-11-07
We have recently shown that Merkel cells transduce tactile stimuli via Piezo2 channels to initiate the sense of touch. Here we performed patch-clamp recordings to assess single channel activity on the membranes of Merkel cells in whisker hair follicles. Under the cell-attached configuration, most Merkel cell membrane patches showed large outward unitary currents with single channel conductance being ∼200pS. The outward unitary currents were not affected by negative pressures up to 150mmHg when applied to the membrane patches. The application of negative pressures up to 190mmHg also could not directly elicit any inward unitary current in the membrane patches. However, after establishing the whole-cell configuration, mechanically activated currents (MA) that resembled Piezo2 currents could be elicited by membrane displacements in every Merkel cell tested. While the MA current decayed rapidly, a small steady-state current component with significant channel noise could be observed. Applications of stationary and non-stationary fluctuation analyses to the MA currents yielded single channel conductance of 32.5±3.8 and 54.0±5.3pS, respectively. The lack of mechanical responses under the cell-attached configuration and the existence of Piezo2 MA currents under the whole-cell configuration raised a possibility that Piezo2 channels are preferentially located on Merkel cell processes, the membrane domains inaccessible by recording electrodes. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
Pirbhoy, Patricia Salgado; Farris, Shannon; Steward, Oswald
2016-06-01
Previous studies have shown that induction of long-term potentiation (LTP) induces phosphorylation of ribosomal protein S6 (rpS6) in postsynaptic neurons, but the functional significance of rpS6 phosphorylation is poorly understood. Here, we show that synaptic stimulation that induces perforant path LTP triggers phosphorylation of rpS6 (p-rpS6) locally near active synapses. Using antibodies specific for phosphorylation at different sites (ser235/236 versus ser240/244), we show that strong synaptic activation led to dramatic increases in immunostaining throughout postsynaptic neurons with selectively higher staining for p-ser235/236 in the activated dendritic lamina. Following LTP induction, phosphorylation at ser235/236 was detectable by 5 min, peaked at 30 min, and was maintained for hours. Phosphorylation at both sites was completely blocked by local infusion of the NMDA receptor antagonist, APV. Despite robust induction of p-rpS6 following high frequency stimulation, assessment of protein synthesis by autoradiography revealed no detectable increases. Exploration of a novel environment led to increases in the number of p-rpS6-positive neurons throughout the forebrain in a pattern reminiscent of immediate early gene induction and many individual neurons that were p-rpS6-positive coexpressed Arc protein. Our results constrain hypotheses about the possible role of rpS6 phosphorylation in regulating postsynaptic protein synthesis during induction of synaptic plasticity.
Hu, Yi, E-mail: yihooyi@gmail.com; Ericsson, Ida, E-mail: ida.ericsson@ntnu.no; Doseth, Berit, E-mail: berit.doseth@ntnu.no; Liabakk, Nina B., E-mail: nina.beate.liabakk@ntnu.no; Krokan, Hans E., E-mail: hans.krokan@ntnu.no; Kavli, Bodil, E-mail: bodil.kavli@ntnu.no
2014-03-10
Activation-induced cytidine deaminase (AID) is the mutator enzyme in adaptive immunity. AID initiates the antibody diversification processes in activated B cells by deaminating cytosine to uracil in immunoglobulin genes. To some extent other genes are also targeted, which may lead to genome instability and B cell malignancy. Thus, it is crucial to understand its targeting and regulation mechanisms. AID is regulated at several levels including subcellular compartmentalization. However, the complex nuclear distribution and trafficking of AID has not been studied in detail previously. In this work, we examined the subnuclear localization of AID and its interaction partner CTNNBL1 and found that they associate with spliceosome-associated structures including Cajal bodies and nuclear speckles. Moreover, protein kinase A (PKA), which activates AID by phosphorylation at Ser38, is present together with AID in nuclear speckles. Importantly, we demonstrate that AID physically associates with the major spliceosome subunits (small nuclear ribonucleoproteins, snRNPs), as well as other essential splicing components, in addition to the transcription machinery. Based on our findings and the literature, we suggest a transcription-coupled splicing-associated model for AID targeting and activation. - Highlights: • AID and its interaction partner CTNNBL1 localize to Cajal bodies and nuclear speckles. • AID associates with its activating kinase PKA in nuclear speckles. • AID is linked to the splicing machinery in switching B-cells. • Our findings suggest a transcription-coupled splicing associated mechanism for AID targeting and activation.
Dynamic network-based epistasis analysis: Boolean examples
Eugenio eAzpeitia
2011-12-01
Full Text Available In this review we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the topologies of gene interactions infered. This has been acknowledged in several previous papers and reviews, but here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson (herein, classical epistasis, defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus. Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct gene interaction topologies are hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis. We also use examples from the literature to show how a Boolean network-based approach has resolved ambiguities and guided epistasis analysis. Our review complements previous accounts, not
Gomà A
2014-12-01
Full Text Available Alba Gomà,1,* Roser Mir,1–3,* Fina Martínez-Soler,1,4 Avelina Tortosa,4 August Vidal,5,6 Enric Condom,5,6 Ricardo Pérez–Tomás,6 Pepita Giménez-Bonafé1 1Departament de Ciències Fisiològiques II, Faculty of Medicine, Campus of Health Sciences of Bellvitge, Universitat de Barcelona, IDIBELL, Barcelona, Spain; 2División de Investigación Básica, Instituto Nacional de Cancerología, México DF, Mexico; 3Instituto de Física, Universidad Nacional Autónoma de México (UNAM, México DF, Mexico; 4Department of Basic Nursing, School of Nursing of the Health Campus of Bellvitge, Universitat de Barcelona, 5Department of Pathology, Hospital Universitari de Bellvitge, 6Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, IDIBELL, Barcelona, Spain*These authors contributed equally to this work Background: One of the problems in prostate cancer (CaP treatment is the appearance of the multidrug resistance phenotype, in which ATP-binding cassette transporters such as multidrug resistance protein 1 (MRP1 play a role. Different localizations of the transporter have been reported, some of them related to the chemoresistant phenotype.Aim: This study aimed to compare the localization of MRP1 in three prostate cell lines (normal, androgen-sensitive, and androgen-independent in order to understand its possible role in CaP chemoresistance.Methods: MRP1 and caveolae protein markers were detected using confocal microscopy, performing colocalization techniques. Lipid raft isolation made it possible to detect these proteins by Western blot analysis. Caveolae and prostasomes were identified by electron microscopy.Results: We show that MRP1 is found in lipid raft fractions of tumor cells and that the number of caveolae increases with malignancy acquisition. MRP1 is found not only in the plasma membrane associated with lipid rafts but also in cytoplasmic accumulations colocalizing with the prostasome markers Caveolin-1 and CD59
Decisional Processes with Boolean Neural Network: the Emergence of Mental Schemes
Barnabei, Graziano; Conversano, Ciro; Lensi, Elena
2010-01-01
Human decisional processes result from the employment of selected quantities of relevant information, generally synthesized from environmental incoming data and stored memories. Their main goal is the production of an appropriate and adaptive response to a cognitive or behavioral task. Different strategies of response production can be adopted, among which haphazard trials, formation of mental schemes and heuristics. In this paper, we propose a model of Boolean neural network that incorporates these strategies by recurring to global optimization strategies during the learning session. The model characterizes as well the passage from an unstructured/chaotic attractor neural network typical of data-driven processes to a faster one, forward-only and representative of schema-driven processes. Moreover, a simplified version of the Iowa Gambling Task (IGT) is introduced in order to test the model. Our results match with experimental data and point out some relevant knowledge coming from psychological domain.
Localization and distribution of fibrinogen C domain containing 1 (FIBCD1) in human tissues
von Huth, Sebastian; Møller, Jesper Bonnet; Schlosser, Anders
have previously shown that FIBCD1 is present at mucosal surfaces in the lung and large intestine. Aim: The present study investigates the distribution and localization of FIBCD1 in various healthy human tissues. Results: We used a monoclonal antibody directed towards the FIBCD1 ectodomain...... in an immunohistochemistry-based analysis and demonstrate that FIBCD1 protein is highly expressed at the apical surfaces of the epithelium throughout the gastrointestinal tract, in the uterus, testis, bladder, gallbladder and the salivary glands. To a lesser extent, FIBCD1 is expressed in the pancreas, the spleen...... and the tonsils. Moreover, using quantitative real-time PCR we demonstrate that FIBCD1 mRNA is highly expressed in the gastrointestinal tract, the lung, the adrenal gland and the testis, which is in coherence with our immunohistochemical findings. Conclusion: FIBCD1 is present at the apical epithelial surfaces...
从布尔代数到布尔微积分%From Boolean algebra to Boolean calculus
程代展; 赵寅; 徐相如
2011-01-01
布尔函数作为最简单的有限值函数具有特殊的重要性．它在包括信息、控制等许多领域有着广泛的应用．本文综合介绍有关布尔函数的理论基础．包括从布尔代数到布尔微积分的主要理论结果，它们在信息与控制中的一些重要应用，以及其前沿动态与新进展．介绍的一个重点是矩阵半张量积在这些领域的应用．%Boolean functions are of special importance, though they are the simplest class of finite-valued functions. It is widely applied to many fields, including information, control and so on. The theoretical foundation of Boolean functions is introduced in this paper, involving some main results from Boolean algebra to Boolean Calculus, applications in information and control and some recent frontiers and developments. The semi-tensor product approach to these fields is introduced emohaticallv.
Hossein Rabbani
2013-01-01
Full Text Available In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR.
General Services Administration — This dataset offers the list of all .gov domains, including state, local, and tribal .gov domains. It does not include .mil domains, or other federal domains outside...
Cao, Shancheng; Ouyang, Huajiang
2017-01-01
The structural characteristic deflection shapes (CDS’s) such as mode shapes and operational deflection shapes are highly sensitive to structural damage in beam- or plate-type structures. Nevertheless, they are vulnerable to measurement noise and could result in unacceptable identification errors. In order to increase the accuracy and noise robustness of damage identification based on CDS’s using vibration responses of random excitation, joint approximate diagonalization (JAD) technique and gapped smoothing method (GSM) are combined to form a sensitive and robust damage index (DI), which can simultaneously detect the existence of damage and localize its position. In addition, it is possible to apply this approach to damage identification of structures under ambient excitation. First, JAD method which is an essential technique of blind source separation is investigated to simultaneously diagonalize a set of power spectral density matrices corresponding to frequencies near a certain natural frequency to estimate a joint unitary diagonalizer. The columns of this joint diagonalizer contain dominant CDS’s. With the identified dominant CDS’s around different natural frequencies, GSM is used to extract damage features and a robust damage identification index is then proposed. Numerical and experimental examples of beams with cracks are used to verify the validity and noise robustness of JAD based CDS estimation and the proposed DI. Furthermore, damage identification using dominant CDS’s estimated by JAD method is demonstrated to be more accurate and noise robust than by the commonly used singular value decomposition method.
Medical Image Fusion Algorithm based on Local Average Energy-Motivated PCNN in NSCT Domain
Huda Ahmed
2016-10-01
Full Text Available Medical Image Fusion (MIF can improve the performance of medical diagnosis, treatment planning and image-guided surgery significantly through providing high-quality and rich-information medical images. Traditional MIF techniques suffer from common drawbacks such as: contrast reduction, edge blurring and image degradation. Pulse-coupled Neural Network (PCNN based MIF techniques outperform the traditional methods in providing high-quality fused images due to its global coupling and pulse synchronization property; however, the selection of significant features that motivate the PCNN is still an open problem and plays a major role in measuring the contribution of each source image into the fused image. In this paper, a medical image fusion algorithm is proposed based on the Non-subsampled Contourlet Transform (NSCT and the Pulse-Coupled Neural Network (PCNN to fuse images from different modalities. Local Average Energy is used to motivate the PCNN due to its ability to capture salient features of the image such as edges, contours and textures. The proposed approach produces a high quality fused image with high contrast and improved content in comparison with other image fusion techniques without loss of significant details on both levels: the visual and the quantitative.
Valeriano, Márcio de Morisson; Rossetti, Dilce de Fátima
2017-03-01
regionalization process improved the potential of local geomorphometric data for updating and revision of geological maps and for guiding future surveys in the sedimentary domain of Amazônia.
An efficient approach of attractor calculation for large-scale Boolean gene regulatory networks.
He, Qinbin; Xia, Zhile; Lin, Bin
2016-11-07
Boolean network models provide an efficient way for studying gene regulatory networks. The main dynamics of a Boolean network is determined by its attractors. Attractor calculation plays a key role for analyzing Boolean gene regulatory networks. An approach of attractor calculation was proposed in this study, which improved the predecessor-based approach. Furthermore, the proposed approach combined with the identification of constant nodes and simplified Boolean networks to accelerate attractor calculation. The proposed algorithm is effective to calculate all attractors for large-scale Boolean gene regulatory networks. If the average degree of the network is not too large, the algorithm can get all attractors of a Boolean network with dozens or even hundreds of nodes.
Boolean Ring and Its Spectrum%布尔环及其素谱
曲伟
2012-01-01
利用交换代数、拓扑等相关知识，讨论了布尔代数、布尔格、布尔环三者之间的对应关系，给出了布尔环及其素谱的一些性质并证明了由布尔环诱导出的布尔格与布尔环上素谱的既开又闲的子集构成的格同构．%In this paper,we show that Boolean rings,Boolean lattices and Boolean algebra are essentially the same. Moreover, every Boolean lattice induced by Boolean ring is isomorphic to the lattice of open and closed subsets of the Boolean ring's spectrum.
Interval soft Boolean algebras%区间软布尔代数
刘卫锋; 杜迎雪; 许宏伟
2014-01-01
将区间软集应用于布尔代数之中，定义了区间软布尔代数、区间软布尔子代数、区间理想软布尔代数和区间软布尔代数的区间软同态等概念，并研究了它们的相关性质。推广了软布尔代数及其相关结论。%The interval soft set is applied to the Boolean algebras.The concepts of interval soft Boolean algebras, inter-val soft Boolean subalgebras, interval idealistic soft Boolean algebras and interval soft homomorphism between interval soft Boolean algebras are defined and some related properties are discussed.Soft Boolean algebras and related results are generalized.
An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data.
Berestovsky, Natalie; Nakhleh, Luay
2013-01-01
Regulatory networks play a central role in cellular behavior and decision making. Learning these regulatory networks is a major task in biology, and devising computational methods and mathematical models for this task is a major endeavor in bioinformatics. Boolean networks have been used extensively for modeling regulatory networks. In this model, the state of each gene can be either 'on' or 'off' and that next-state of a gene is updated, synchronously or asynchronously, according to a Boolean rule that is applied to the current-state of the entire system. Inferring a Boolean network from a set of experimental data entails two main steps: first, the experimental time-series data are discretized into Boolean trajectories, and then, a Boolean network is learned from these Boolean trajectories. In this paper, we consider three methods for data discretization, including a new one we propose, and three methods for learning Boolean networks, and study the performance of all possible nine combinations on four regulatory systems of varying dynamics complexities. We find that employing the right combination of methods for data discretization and network learning results in Boolean networks that capture the dynamics well and provide predictive power. Our findings are in contrast to a recent survey that placed Boolean networks on the low end of the "faithfulness to biological reality" and "ability to model dynamics" spectra. Further, contrary to the common argument in favor of Boolean networks, we find that a relatively large number of time points in the time-series data is required to learn good Boolean networks for certain data sets. Last but not least, while methods have been proposed for inferring Boolean networks, as discussed above, missing still are publicly available implementations thereof. Here, we make our implementation of the methods available publicly in open source at http://bioinfo.cs.rice.edu/.
Boolean network representation of contagion dynamics during a financial crisis
Caetano, Marco Antonio Leonel; Yoneyama, Takashi
2015-01-01
This work presents a network model for representation of the evolution of certain patterns of economic behavior. More specifically, after representing the agents as points in a space in which each dimension associated to a relevant economic variable, their relative "motions" that can be either stationary or discordant, are coded into a boolean network. Patterns with stationary averages indicate the maintenance of status quo, whereas discordant patterns represent aggregation of new agent into the cluster or departure from the former policies. The changing patterns can be embedded into a network representation, particularly using the concept of autocatalytic boolean networks. As a case study, the economic tendencies of the BRIC countries + Argentina were studied. Although Argentina is not included in the cluster formed by BRIC countries, it tends to follow the BRIC members because of strong commercial ties.
The Nonlinearity of Sum and Product for Boolean Functions
Huang Jinglian
2016-01-01
Full Text Available In this paper, we study the relationship between the nonlinearity of Boolean function and the nonlinearity of the sum and product of Boolean function, while derivative and e-derivative are used to study the problem further. We obtain that the sum of two functions’ nonlinearity is not less than the nonlinearity of the sum of two functions. The relationship between the nonlinearity of function and the nonlinearity of the sum and product of two functions are also obtained. Furthermore, we also get the relationship between the nonlinearity of the product of functions, and the derivative and e-derivative of function. Moreover, we also deduced some important applications on the basis of the above work.
Algorithms for Finding Small Attractors in Boolean Networks
Hayashida Morihiro
2007-01-01
Full Text Available A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to identify singleton attractors and small attractors in Boolean networks. We analyze the average case time complexities of some of the proposed algorithms. For instance, it is shown that the outdegree-based ordering algorithm for finding singleton attractors works in time for , which is much faster than the naive time algorithm, where is the number of genes and is the maximum indegree. We performed extensive computational experiments on these algorithms, which resulted in good agreement with theoretical results. In contrast, we give a simple and complete proof for showing that finding an attractor with the shortest period is NP-hard.
Improved Decomposition for a System of Completely Specified Boolean Functions
Saeid Taghavi Afshord
2013-12-01
Full Text Available Functional decomposition is an important and powerful technique in the logic synthesis. The ternary matrix cover approach is one of the existing methods of this type. This method is also used in decomposition of a system of completely specified Boolean functions. Before constructing the desired superposition, it needs to encode a table. There is a trivial encoding method. But to find a better solution, it is important to use a special approach, because the result of the encoding has a direct influence on the obtained functions. In this paper, an efficient algorithm to encode this table is presented. It uses the approach connected with the assembling Boolean hyper cube method. The proposed algorithm is explained in details with an example. The benefits and impacts of the suggested technique are also discussed.
Canalization and symmetry in Boolean models for genetic regulatory networks
Reichhardt, C J Olson [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Bassler, Kevin E [Department of Physics, University of Houston, Houston, TX 77204-5005 (United States)
2007-04-20
Canalization of genetic regulatory networks has been argued to be favoured by evolutionary processes due to the stability that it can confer to phenotype expression. We explore whether a significant amount of canalization and partial canalization can arise in purely random networks in the absence of evolutionary pressures. We use a mapping of the Boolean functions in the Kauffman N-K model for genetic regulatory networks onto a k-dimensional Ising hypercube (where k = K) to show that the functions can be divided into different classes strictly due to geometrical constraints. The classes can be counted and their properties determined using results from group theory and isomer chemistry. We demonstrate that partially canalizing functions completely dominate all possible Boolean functions, particularly for higher k. This indicates that partial canalization is extremely common, even in randomly chosen networks, and has implications for how much information can be obtained in experiments on native state genetic regulatory networks.
On K-wise Independent Distributions and Boolean Functions
Benjamini, Itai; Peled, Ron
2012-01-01
We pursue a systematic study of the following problem. Let f:{0,1}^n -> {0,1} be a (usually monotone) Boolean function whose behaviour is well understood when the input bits are identically independently distributed. What can be said about the behaviour of the function when the input bits are not completely independent, but only k-wise independent, i.e. every subset of k bits is independent? more precisely, how high should k be so that any k-wise independent distribution "fools" the function, i.e. causes it to behave nearly the same as when the bits are completely independent? We analyze several well known Boolean functions (including AND, Majority, Tribes and Percolation among others), some of which turn out to have surprising properties. In some of our results we use tools from the theory of the classical moment problem, seemingly for the first time in this subject, to shed light on these questions.
Kramers-Wannier duality applied to the boolean satifiability problem
Mitchell, Joe; Hsu, Benjamin; Galitski, Victor
2014-03-01
Kramers-Wannier duality, first considered in 1941, is an exact technique used in statistical mechanics to relate two models together through an order-disorder transformation, and thereby study their structure and critical phenomena. The boolean satisfiability problem is one of the most important problems in computer science, specifically complexity theory; it is the first proven NP-complete problem. Using a mapping to a multi-spin Ising model in the limit of zero temperature, we present an application of Kramers-Wannier duality to this problem. This results in a novel relationship between solving the boolean satisfiability counting problem and a different computational problem: listing the non-negative solutions to a particular system of linear integer equations. This mapping relates the complexity of the two problems. We discuss the generality of Kramers-Wannier duality and its possible application to other computational problems. This research was supported by NSF-CAREER award No. DMR-0847224 and Simons Foundation.
Stability of biological networks as represented in Random Boolean Nets.
Slepoy, Alexander; Thompson, Marshall
2004-09-01
We explore stability of Random Boolean Networks as a model of biological interaction networks. We introduce surface-to-volume ratio as a measure of stability of the network. Surface is defined as the set of states within a basin of attraction that maps outside the basin by a bit-flip operation. Volume is defined as the total number of states in the basin. We report development of an object-oriented Boolean network analysis code (Attract) to investigate the structure of stable vs. unstable networks. We find two distinct types of stable networks. The first type is the nearly trivial stable network with a few basins of attraction. The second type contains many basins. We conclude that second type stable networks are extremely rare.
Properties of Boolean networks and methods for their tests
2013-01-01
Transcriptional regulation networks are often modeled as Boolean networks. We discuss certain properties of Boolean functions (BFs), which are considered as important in such networks, namely, membership to the classes of unate or canalizing functions. Of further interest is the average sensitivity (AS) of functions. In this article, we discuss several algorithms to test the properties of interest. To test canalizing properties of functions, we apply spectral techniques, which can also be used to characterize the AS of functions as well as the influences of variables in unate BFs. Further, we provide and review upper and lower bounds on the AS of unate BFs based on the spectral representation. Finally, we apply these methods to a transcriptional regulation network of Escherichia coli, which controls central parts of the E. coli metabolism. We find that all functions are unate. Also the analysis of the AS of the network reveals an exceptional robustness against transient fluctuations of the binary variables.a PMID:23311536
Effects of a silenced gene in Boolean network models
Emir Haliki
2017-03-01
Full Text Available Gene regulation and their regulatory networks are one of the most challenging research problems of computational biology and complexity sciences. Gene regulation is formed by indirect interaction between DNA segments which are protein coding genes to configure the expression level of one another. Prevention of expression of any genes in gene regulation at the levels of transcription or translation indicates the gene silencing event. The present study examined what types of results in gene silencing would bring about in the dynamics of Boolean genetic regulatory mechanisms. The analytical study was performed in gene expression variations of Boolean dynamics first, then the related numerical analysis was simulated in real networks in the literature.
Fault Based Techniques for Testing Boolean Expressions: A Survey
Badhera, Usha; Taruna, S
2012-01-01
Boolean expressions are major focus of specifications and they are very much prone to introduction of faults, this survey presents various fault based testing techniques. It identifies that the techniques differ in their fault detection capabilities and generation of test suite. The various techniques like Cause effect graph, meaningful impact strategy, Branch Operator Strategy (BOR), BOR+MI, MUMCUT, Modified Condition/ Decision Coverage (MCDC) has been considered. This survey describes the basic algorithms and fault categories used by these strategies for evaluating their performance. Finally, it contains short summaries of the papers that use Boolean expressions used to specify the requirements for detecting faults. These techniques have been empirically evaluated by various researchers on a simplified safety related real time control system.
Estimation of delays in generalized asynchronous Boolean networks.
Das, Haimabati; Layek, Ritwik Kumar
2016-10-20
A new generalized asynchronous Boolean network (GABN) model has been proposed in this paper. This continuous-time discrete-state model captures the biological reality of cellular dynamics without compromising the computational efficiency of the Boolean framework. The GABN synthesis procedure is based on the prior knowledge of the logical structure of the regulatory network, and the experimental transcriptional parameters. The novelty of the proposed methodology lies in considering different delays associated with the activation and deactivation of a particular protein (especially the transcription factors). A few illustrative examples of some well-studied network motifs have been provided to explore the scope of using the GABN model for larger networks. The GABN model of the p53-signaling pathway in response to γ-irradiation has also been simulated in the current paper to provide an indirect validation of the proposed schema.
Autonomous Boolean modelling of developmental gene regulatory networks
Cheng, Xianrui; Sun, Mengyang; Socolar, Joshua E. S.
2013-01-01
During early embryonic development, a network of regulatory interactions among genes dynamically determines a pattern of differentiated tissues. We show that important timing information associated with the interactions can be faithfully represented in autonomous Boolean models in which binary variables representing expression levels are updated in continuous time, and that such models can provide a direct insight into features that are difficult to extract from ordinary differential equation (ODE) models. As an application, we model the experimentally well-studied network controlling fly body segmentation. The Boolean model successfully generates the patterns formed in normal and genetically perturbed fly embryos, permits the derivation of constraints on the time delay parameters, clarifies the logic associated with different ODE parameter sets and provides a platform for studying connectivity and robustness in parameter space. By elucidating the role of regulatory time delays in pattern formation, the results suggest new types of experimental measurements in early embryonic development. PMID:23034351
Inference of asynchronous Boolean network from biological pathways.
Das, Haimabati; Layek, Ritwik Kumar
2015-01-01
Gene regulation is a complex process with multiple levels of interactions. In order to describe this complex dynamical system with tractable parameterization, the choice of the dynamical system model is of paramount importance. The right abstraction of the modeling scheme can reduce the complexity in the inference and intervention design, both computationally and experimentally. This article proposes an asynchronous Boolean network framework to capture the transcriptional regulation as well as the protein-protein interactions in a genetic regulatory system. The inference of asynchronous Boolean network from biological pathways information and experimental evidence are explained using an algorithm. The suitability of this paradigm for the variability of several reaction rates is also discussed. This methodology and model selection open up new research challenges in understanding gene-protein interactive system in a coherent way and can be beneficial for designing effective therapeutic intervention strategy.
Complexity of Propositional Abduction for Restricted Sets of Boolean Functions
Creignou, Nadia; Thomas, Michael
2009-01-01
Abduction is a fundamental and important form of non-monotonic reasoning. Given a knowledge base explaining how the world behaves it aims at finding an explanation for some observed manifestation. In this paper we focus on propositional abduction, where the knowledge base and the manifestation are represented by propositional formulae. The problem of deciding whether there exists an explanation has been shown to be SigmaP2-complete in general. We consider variants obtained by restricting the allowed connectives in the formulae to certain sets of Boolean functions. We give a complete classification of the complexity for all considerable sets of Boolean functions. In this way, we identify easier cases, namely NP-complete and polynomial cases; and we highlight sources of intractability. Further, we address the problem of counting the explanations and draw a complete picture for the counting complexity.
Mapping knowledge to boolean dynamic systems in Bateson's epistemology.
Malloy, Thomas E; Jensen, Gary C; Song, Timothy
2005-01-01
Gregory Bateson (1972, 1979) established an epistemology that integrates mind and nature as a necessary unity, a unity in which learning and evolution share fundamental principles and in which criteria for mental process are explicitly specified. E42 is a suite of freely available Java applets that constitute an online research lab for creating and interacting with simulations of the Boolean systems developed by Kauffman (1993) in his study of evolution where he proposed that self-organization and natural selection are co-principles "weaving the tapestry of life." This paper maps Boolean systems, developed in the study of evolution, onto Bateson's epistemology in general and onto his criteria of mental process in particular.
On designated-weight Boolean functions with highest algebraic immunity
无
2010-01-01
Algebraic immunity has been considered as one of cryptographically significant properties for Boolean functions. In this paper, we study ∑d-1 i=0 (ni)-weight Boolean functions with algebraic immunity achiev-ing the minimum of d and n - d + 1, which is highest for the functions. We present a simpler sufficient and necessary condition for these functions to achieve highest algebraic immunity. In addition, we prove that their algebraic degrees are not less than the maximum of d and n - d + 1, and for d = n1 +2 their nonlinearities equalthe minimum of ∑d-1 i=0 (ni) and ∑ d-1 i=0 (ni). Lastly, we identify two classes of such functions, one having algebraic degree of n or n-1.
High Quality Test Pattern Generation and Boolean Satisfiability
Eggersglüß, Stephan
2012-01-01
This book provides an overview of automatic test pattern generation (ATPG) and introduces novel techniques to complement classical ATPG, based on Boolean Satisfiability (SAT). A fast and highly fault efficient SAT-based ATPG framework is presented which is also able to generate high-quality delay tests such as robust path delay tests, as well as tests with long propagation paths to detect small delay defects. The aim of the techniques and methodologies presented in this book is to improve SAT-based ATPG, in order to make it applicable in industrial practice. Readers will learn to improve the performance and robustness of the overall test generation process, so that the ATPG algorithm reliably will generate test patterns for most targeted faults in acceptable run time to meet the high fault coverage demands of industry. The techniques and improvements presented in this book provide the following advantages: Provides a comprehensive introduction to test generation and Boolean Satisfiability (SAT); Describes a...
borealis - A generalized global update algorithm for Boolean optimization problems
Zhu, Zheng; Katzgraber, Helmut G
2016-01-01
Optimization problems with Boolean variables that fall into the nondeterministic polynomial (NP) class are of fundamental importance in computer science, mathematics, physics and industrial applications. Most notably, solving constraint-satisfaction problems, which are related to spin-glass-like Hamiltonians in physics, remains a difficult numerical task. As such, there has been great interest in designing efficient heuristics to solve these computationally difficult problems. Inspired by parallel tempering Monte Carlo in conjunction with the rejection-free isoenergetic cluster algorithm developed for Ising spin glasses, we present a generalized global update optimization heuristic that can be applied to different NP-complete problems with Boolean variables. The global cluster updates allow for a wide-spread sampling of phase space, thus considerably speeding up optimization. By carefully tuning the pseudo-temperature (needed to randomize the configurations) of the problem, we show that the method can efficie...
Rita, Giuliano; Zbigniew, S. Szewczak
2014-01-01
In the present paper we obtain a new correlation inequality and use it for the purpose of extending the theory of the Almost Sure Local Limit Theorem to the case of lattice random sequences in the domain of attraction of a stable law. In particular, we prove ASLLT in the case of the normal domain of attraction of $\\alpha$--stable law, $\\alpha\\in(1,2)$.
Problems in modeling a weighted Boolean retrieval system
Kraft, D.H.; Waller, W.G.
1979-01-01
The use of weights to denote a query representation and/or the indexing of a document is analyzed as a generalization of a Boolean retrieval system. Criteria are given for the functions used to evaluate the relevance of the records to a specific query. Various mechanisms for evaluating the relevance of records with regard to a given query are tested and found to be less than satisfactory. A new approach is suggested to avoid some of the perils.
Selection of probability based weighting models for Boolean retrieval system
Ebinuma, Y. (Japan Atomic Energy Research Inst., Tokai, Ibaraki. Tokai Research Establishment)
1981-09-01
Automatic weighting models based on probability theory were studied if they can be applied to boolean search logics including logical sum. The INIS detabase was used for searching of one particular search formula. Among sixteen models three with good ranking performance were selected. These three models were further applied to searching of nine search formulas in the same database. It was found that two models among them show slightly better average ranking performance while the other model, the simplest one, seems also practical.
On the parity complexity measures of Boolean functions
Zhang,Zhiqiang; Shi, Yaoyun
2010-01-01
The parity decision tree model extends the decision tree model by allowing the computation of a parity function in one step. We prove that the deterministic parity decision tree complexity of any Boolean function is polynomially related to the non-deterministic complexity of the function or its complement. We also show that they are polynomially related to an analogue of the block sensitivity. We further study parity decision trees in their relations with an intermediate variant of the decisi...
J-rings of characteristic two that are boolean
D. J. Hansen
1994-01-01
Full Text Available This paper is concerned with determining all integers n, with n≥2, such that if R is a ring having the property that xn=x and 2x=0 for each x∈R, then R is boolean. The solution to the above problem extends previous results obtained by Shiue and Chao in [5] and that of MacHale in [4].
The mathematics of a quantum Hamiltonian computing half adder Boolean logic gate.
Dridi, G; Julien, R; Hliwa, M; Joachim, C
2015-08-28
The mathematics behind the quantum Hamiltonian computing (QHC) approach of designing Boolean logic gates with a quantum system are given. Using the quantum eigenvalue repulsion effect, the QHC AND, NAND, OR, NOR, XOR, and NXOR Hamiltonian Boolean matrices are constructed. This is applied to the construction of a QHC half adder Hamiltonian matrix requiring only six quantum states to fullfil a half Boolean logical truth table. The QHC design rules open a nano-architectronic way of constructing Boolean logic gates inside a single molecule or atom by atom at the surface of a passivated semi-conductor.
On Third-Order Nonlinearity of Biquadratic Monomial Boolean Functions
Brajesh Kumar Singh
2014-01-01
Full Text Available The rth-order nonlinearity of Boolean function plays a central role against several known attacks on stream and block ciphers. Because of the fact that its maximum equals the covering radius of the rth-order Reed-Muller code, it also plays an important role in coding theory. The computation of exact value or high lower bound on the rth-order nonlinearity of a Boolean function is very complicated problem, especially when r>1. This paper is concerned with the computation of the lower bounds for third-order nonlinearities of two classes of Boolean functions of the form Tr1nλxd for all x∈2n, λ∈2n*, where a d=2i+2j+2k+1, where i, j, and k are integers such that i>j>k≥1 and n>2i, and b d=23ℓ+22ℓ+2ℓ+1, where ℓ is a positive integer such that gcdℓ,=1 and n>6.
Global Avalanche Characteristics of Boolean Functions by Concatenation
Mingsheng Ren
2016-01-01
In order to measure the correlation propeties of two Boolean functions, the global avalanche characteristics of Boolean functions constructed by concatenation are discussed, i.e., f1‖f2 and f1‖f2‖f3‖f4. Firstly, for the function f = f1‖f2 , the cross⁃correlation function of f1 , f2 in the special condition are studied. In this case, f, f1 , f2 must be in desired form. By computing their sum⁃of⁃squares indicators, the cross⁃correlation function between f1 , f2 is obtained. Secondly, for the function g = f1‖f2‖f3‖f4 , by analyzing the relation among their auto⁃correlation functions, their sum⁃of⁃squares indicators are investigated. Based on them, the sum⁃of⁃squares indicators of functions obtained by Canteaut et al. are investigated. The results show that the correlation property of g is good when the correlation properties of Boolean functions f1 , f2 , f3 , f4 are good.
MILES FORMULAE FOR BOOLEAN MODELS OBSERVED ON LATTICES
Joachim Ohser
2011-05-01
Full Text Available The densities of the intrinsic volumes – in 3D the volume density, surface density, the density of the integral of the mean curvature and the density of the Euler number – are a very useful collection of geometric characteristics of random sets. Combining integral and digital geometry we develop a method for efficient and simultaneous calculation of the intrinsic volumes of random sets observed in binary images in arbitrary dimensions. We consider isotropic and reflection invariant Boolean models sampled on homogeneous lattices and compute the expectations of the estimators of the intrinsic volumes. It turns out that the estimator for the surface density is proved to be asymptotically unbiased and thusmultigrid convergent for Boolean models with convex grains. The asymptotic bias of the estimators for the densities of the integral of the mean curvature and of the Euler number is assessed for Boolean models of balls of random diameters. Miles formulae with corresponding correction terms are derived for the 3D case.
Detecting Emergent Behaviors with Semi-Boolean Algebra
Haglich, Peter [Lockheed Martin Corporation; Rouff, Christopher [Lockheed Martin Corporation; Pullum, Laura L [ORNL
2010-01-01
As systems continue to be interconnected, their collective behavior becomes increasingly difficult to predict. The emergent properties of systems of systems make them powerful, but at the same time make them more difficult to design, assure proper behaviors emerge, operate correctly, and have no new security holes. Learning and adaptation cause additional concerns because emergent behavior patterns simply cannot be fully predicted through the use of traditional system development methods, such as testing and model checking. In addition, self-organization can occur as the individual systems optimize to address inefficiencies in the larger system. Designing for and detecting emergent behavior is something that has not been addressed in current systems development methodologies. This paper gives background on approaches for modeling and verifying emergent behavior and then discusses the use of semi-Boolean algebra as a means for detecting emergence in combined behaviors. Semi-Boolean algebra is a generalization of the Boolean algebra concept obtained by weakening the requirement that any two elements have a common upper bound. An example is given and several ways are described that allow emergent behavior to be detected with this technique.
Boolean Models of Biological Processes Explain Cascade-Like Behavior.
Chen, Hao; Wang, Guanyu; Simha, Rahul; Du, Chenghang; Zeng, Chen
2016-01-29
Biological networks play a key role in determining biological function and therefore, an understanding of their structure and dynamics is of central interest in systems biology. In Boolean models of such networks, the status of each molecule is either "on" or "off" and along with the molecules interact with each other, their individual status changes from "on" to "off" or vice-versa and the system of molecules in the network collectively go through a sequence of changes in state. This sequence of changes is termed a biological process. In this paper, we examine the common perception that events in biomolecular networks occur sequentially, in a cascade-like manner, and ask whether this is likely to be an inherent property. In further investigations of the budding and fission yeast cell-cycle, we identify two generic dynamical rules. A Boolean system that complies with these rules will automatically have a certain robustness. By considering the biological requirements in robustness and designability, we show that those Boolean dynamical systems, compared to an arbitrary dynamical system, statistically present the characteristics of cascadeness and sequentiality, as observed in the budding and fission yeast cell- cycle. These results suggest that cascade-like behavior might be an intrinsic property of biological processes.
Approximating Attractors of Boolean Networks by Iterative CTL Model Checking.
Klarner, Hannes; Siebert, Heike
2015-01-01
This paper introduces the notion of approximating asynchronous attractors of Boolean networks by minimal trap spaces. We define three criteria for determining the quality of an approximation: "faithfulness" which requires that the oscillating variables of all attractors in a trap space correspond to their dimensions, "univocality" which requires that there is a unique attractor in each trap space, and "completeness" which requires that there are no attractors outside of a given set of trap spaces. Each is a reachability property for which we give equivalent model checking queries. Whereas faithfulness and univocality can be decided by model checking the corresponding subnetworks, the naive query for completeness must be evaluated on the full state space. Our main result is an alternative approach which is based on the iterative refinement of an initially poor approximation. The algorithm detects so-called autonomous sets in the interaction graph, variables that contain all their regulators, and considers their intersection and extension in order to perform model checking on the smallest possible state spaces. A benchmark, in which we apply the algorithm to 18 published Boolean networks, is given. In each case, the minimal trap spaces are faithful, univocal, and complete, which suggests that they are in general good approximations for the asymptotics of Boolean networks.
Controllability and observability of Boolean networks arising from biology.
Li, Rui; Yang, Meng; Chu, Tianguang
2015-02-01
Boolean networks are currently receiving considerable attention as a computational scheme for system level analysis and modeling of biological systems. Studying control-related problems in Boolean networks may reveal new insights into the intrinsic control in complex biological systems and enable us to develop strategies for manipulating biological systems using exogenous inputs. This paper considers controllability and observability of Boolean biological networks. We propose a new approach, which draws from the rich theory of symbolic computation, to solve the problems. Consequently, simple necessary and sufficient conditions for reachability, controllability, and observability are obtained, and algorithmic tests for controllability and observability which are based on the Gröbner basis method are presented. As practical applications, we apply the proposed approach to several different biological systems, namely, the mammalian cell-cycle network, the T-cell activation network, the large granular lymphocyte survival signaling network, and the Drosophila segment polarity network, gaining novel insights into the control and/or monitoring of the specific biological systems.
Williams, Kyle B; Yahashiri, Atsushi; Arends, S J Ryan; Popham, David L; Fowler, C Andrew; Weiss, David S
2013-01-29
SPOR domains are present in thousands of bacterial proteins and probably bind septal peptidoglycan (PG), but the details of the SPOR-PG interaction have yet to be elucidated. Here we characterize the structure and function of the SPOR domain for an Escherichia coli division protein named DamX. Nuclear magnetic resonance revealed the domain comprises a four-stranded antiparallel β-sheet buttressed on one side by two α-helices. A third helix, designated α3, associates with the other face of the β-sheet, but this helix is relatively mobile. Site-directed mutagenesis revealed the face of the β-sheet that interacts with α3 is important for septal localization and binding to PG sacculi. The position and mobility of α3 suggest it might regulate PG binding, but although α3 deletion mutants still localized to the septal ring, they were too unstable to use in a PG binding assay. Finally, to assess the importance of the SPOR domain in DamX function, we constructed and characterized E. coli mutants that produced DamX proteins with SPOR domain point mutations or SPOR domain deletions. These studies revealed the SPOR domain is important for multiple activities associated with DamX: targeting the protein to the division site, conferring full resistance to the bile salt deoxycholate, improving the efficiency of cell division when DamX is produced at normal levels, and inhibiting cell division when DamX is overproduced.
2014-01-01
A negating functionality is fundamental to information processing of logic circuits within cells and computers. Aiming to adapt unutilized electronic concepts to the interrogation of signaling circuits in cells, we first took a bottom-up strategy whereby we created protein-based devices that perform negating Boolean logic operations such as NOT, NOR, NAND, and N-IMPLY. These devices function in living cells within a minute by precisely commanding the localization of an activator molecule among three subcellular spaces. We networked these synthetic gates to an endogenous signaling circuit and devised a physiological output. In search of logic functions in signal transduction, we next took a top–down approach and computationally screened 108 signaling pathways to identify commonalities and differences between these biological pathways and electronic circuits. This combination of synthetic and systems approaches will guide us in developing foundations for deconstruction of intricate cell signaling, as well as construction of biomolecular computers. PMID:25000210
Nijenhuis, Wilco; von Castelmur, Eleonore; Littler, Dene; De Marco, Valeria; Tromer, Eelco; Vleugel, Mathijs; van Osch, Maria H J; Snel, Berend; Perrakis, Anastassis; Kops, Geert J P L
2013-04-15
The mitotic checkpoint ensures correct chromosome segregation by delaying cell cycle progression until all kinetochores have attached to the mitotic spindle. In this paper, we show that the mitotic checkpoint kinase MPS1 contains an N-terminal localization module, organized in an N-terminal extension (NTE) and a tetratricopeptide repeat (TPR) domain, for which we have determined the crystal structure. Although the module was necessary for kinetochore localization of MPS1 and essential for the mitotic checkpoint, the predominant kinetochore binding activity resided within the NTE. MPS1 localization further required HEC1 and Aurora B activity. We show that MPS1 localization to kinetochores depended on the calponin homology domain of HEC1 but not on Aurora B-dependent phosphorylation of the HEC1 tail. Rather, the TPR domain was the critical mediator of Aurora B control over MPS1 localization, as its deletion rendered MPS1 localization insensitive to Aurora B inhibition. These data are consistent with a model in which Aurora B activity relieves a TPR-dependent inhibitory constraint on MPS1 localization.
Lim, Ssang-Taek; Longley, Robert L; Couchman, John R
2003-01-01
Syndecan-4 is a transmembrane heparan sulfate proteoglycan that acts as a coreceptor with integrins in focal adhesion formation. The central region of syndecan-4 cytoplasmic domain (4V; LGKKPIYKK) binds phosphatidylinositol 4,5-bisphosphate, and together they regulate protein kinase C alpha (PKC...... alpha) activity. Syndecan 4V peptide directly potentiates PKC alpha activity, leading to "superactivation" of the enzyme, apparently through an interaction with its catalytic domain. We now have performed yeast two-hybrid and in vitro binding assays to determine the interaction sites between 4V and PKC...... alpha. Full-length PKC alpha weakly interacted with 4V by yeast two-hybrid assays, but PKC alpha constructs that lack the pseudosubstrate region or constructs of the whole catalytic domain interacted more strongly. A mutated 4V sequence (4V(YF): LGKKPIFKK) did not interact with PKC alpha, indicating...
Briggs, Martin A.; Day-Lewis, Frederick D.; Ong, John B.; Curtis, Gary P.; Lane, Jr., John W.
2013-01-01
Anomalous solute transport, modeled as rate-limited mass transfer, has an observable geoelectrical signature that can be exploited to infer the controlling parameters. Previous experiments indicate the combination of time-lapse geoelectrical and fluid conductivity measurements collected during ionic tracer experiments provides valuable insight into the exchange of solute between mobile and immobile porosity. Here, we use geoelectrical measurements to monitor tracer experiments at a former uranium mill tailings site in Naturita, Colorado. We use nonlinear regression to calibrate dual-domain mass transfer solute-transport models to field data. This method differs from previous approaches by calibrating the model simultaneously to observed fluid conductivity and geoelectrical tracer signals using two parameter scales: effective parameters for the flow path upgradient of the monitoring point and the parameters local to the monitoring point. We use regression statistics to rigorously evaluate the information content and sensitivity of fluid conductivity and geophysical data, demonstrating multiple scales of mass transfer parameters can simultaneously be estimated. Our results show, for the first time, field-scale spatial variability of mass transfer parameters (i.e., exchange-rate coefficient, porosity) between local and upgradient effective parameters; hence our approach provides insight into spatial variability and scaling behavior. Additional synthetic modeling is used to evaluate the scope of applicability of our approach, indicating greater range than earlier work using temporal moments and a Lagrangian-based Damköhler number. The introduced Eulerian-based Damköhler is useful for estimating tracer injection duration needed to evaluate mass transfer exchange rates that range over several orders of magnitude.
Freeman, N L; Lila, T; Mintzer, K A; Chen, Z; Pahk, A J; Ren, R; Drubin, D G; Field, J
1996-02-01
Saccharomyces cerevisiae cyclase-associated protein (CAP or Srv2p) is multifunctional. The N-terminal third of CAP binds to adenylyl cyclase and has been implicated in adenylyl cyclase activation in vivo. The widely conserved C-terminal domain of CAP binds to monomeric actin and serves an important cytoskeletal regulatory function in vivo. In addition, all CAP homologs contain a centrally located proline-rich region which has no previously identified function. Recently, SH3 (Src homology 3) domains were shown to bind to proline-rich regions of proteins. Here we report that the proline-rich region of CAP is recognized by the SH3 domains of several proteins, including the yeast actin-associated protein Abp1p. Immunolocalization experiments demonstrate that CAP colocalizes with cortical actin-containing structures in vivo and that a region of CAP containing the SH3 domain binding site is required for this localization. We also demonstrate that the SH3 domain of yeast Abp1p and that of the yeast RAS protein guanine nucleotide exchange factor Cdc25p complex with adenylyl cyclase in vitro. Interestingly, the binding of the Cdc25p SH3 domain is not mediated by CAP and therefore may involve direct binding to adenylyl cyclase or to an unidentified protein which complexes with adenylyl cyclase. We also found that CAP homologous from Schizosaccharomyces pombe and humans bind SH3 domains. The human protein binds most strongly to the SH3 domain from the abl proto-oncogene. These observations identify CAP as an SH3 domain-binding protein and suggest that CAP mediates interactions between SH3 domain proteins and monomeric actin.
Leidy, C.; Linderoth, L.; Andresen, T.L.
2006-01-01
, we show that local enrichment of anionic lipids into fluid domains triggers PLA(2)-IIA activity. In addition, the compositional range of enzyme activity is shown to be related to the underlying lipid phase diagram. A comparison is done between PLA(2)-IIA and snake venom PLA(2), which in contrast...
Mushtaq Mir
2011-07-01
Full Text Available The Mycobacterium tuberculosis Ser/Thr kinase PknB has been implicated in the regulation of cell growth and morphology in this organism. The extracytoplasmic domain of this membrane protein comprises four penicillin binding protein and Ser/Thr kinase associated (PASTA domains, which are predicted to bind stem peptides of peptidoglycan. Using a comprehensive library of synthetic muropeptides, we demonstrate that the extracytoplasmic domain of PknB binds muropeptides in a manner dependent on the presence of specific amino acids at the second and third positions of the stem peptide, and on the presence of the sugar moiety N-acetylmuramic acid linked to the peptide. We further show that PknB localizes strongly to the mid-cell and also to the cell poles, and that the extracytoplasmic domain is required for PknB localization. In contrast to strong growth stimulation by conditioned medium, we observe no growth stimulation of M. tuberculosis by a synthetic muropeptide with high affinity for the PknB PASTAs. We do find a moderate effect of a high affinity peptide on resuscitation of dormant cells. While the PASTA domains of PknB may play a role in stimulating growth by binding exogenous peptidoglycan fragments, our data indicate that a major function of these domains is for proper PknB localization, likely through binding of peptidoglycan fragments produced locally at the mid-cell and the cell poles. These data suggest a model in which PknB is targeted to the sites of peptidoglycan turnover to regulate cell growth and cell division.
On Boolean algebras which have the Vitali-Hahn-Saks property
Dimitru Popa
1997-05-01
Full Text Available Given a boolean algebra A, we say when A verifies the Drewnowski condition. In thepaper we prove that if a boolean algebra verifies the Drewnowski condition then A has the Vitali-Hahn-Saks property. Also other related questions are investigated.
Three New Construction Methods of the Highly Nonlinear Balanced Boolean Function
TANXinglie; SHEKun; JIQingbing; ZHOUMingtian; SHENChangxiang
2003-01-01
Nonlinearity is a nonlinear criterion of Boolean function. In this paper, some useful definitions and theorems are introduced, and then three new ways to construct the highly nonlinear balanced boolean function are given by ways of concatenating, dividing, modifying and alternating, which are proven to be very effective.
On the 2m-variable symmetric Boolean functions with maximum algebraic immunity
QU LongJiang; LI Chao
2008-01-01
The properties of the 2m-variable symmetric Boolean functions with maximum al-gebraic immunity are studied in this paper. Their value vectors, algebraic normal forms, and algebraic degrees and weights are all obtained. At last, some necessary conditions for a symmetric Boolean function on even number variables to have maximum algebraic immunity are introduced.
Comparing Boolean and Probabilistic Information Retrieval Systems Across Queries and Disciplines.
Losee, Robert M.
1997-01-01
Suggests a method that allows searchers to analytically compare the Boolean and probabilistic information retrieval approaches. Sample performance figures are provided for queries using the Boolean strategy, and for probabilistic systems. The variation of performance across sublanguages and queries is examined, as well as the performance of models…
Boolean Operators and the Naive End-User: Moving to AND.
Proctor, Edward
2002-01-01
Discusses the confusion among end users in using Boolean operators when searching electronic resources. Highlights include search engines; site-specific search engines; the counterintuitive nature of Boolean logic; hidden defaults; the problem of conceptualization; reprogramming defaults; and a lack of user education. (LRW)
Freestyle Vs. Boolean: A Comparison of Partial and Exact Match Retrieval Systems.
Paris, Lee Anne H.; Tibbo, Helen R.
1998-01-01
Compares results of traditional Boolean searching with those of Freestyle, LEXIS/NEXIS's natural language application. Study found that though the Boolean searches had better results more often, neither method demonstrated superior performance for every query, suggesting that different queries demand different techniques. Concludes that further…
Boolean Classes and Qualitative Inquiry. WCER Working Paper No. 2006-3
Nathan, Mitchell J.; Jackson, Kristi
2006-01-01
The prominent role of Boolean classes in qualitative data analysis software is viewed by some as an encroachment of logical positivism on qualitative research methodology. The authors articulate an embodiment perspective, in which Boolean classes are viewed as conceptual metaphors for apprehending and manipulating data, concepts, and categories in…
BEAT: A Web-Based Boolean Expression Fault-Based Test Case Generation Tool
Chen, T. Y.; Grant, D. D.; Lau, M. F.; Ng, S. P.; Vasa, V. R.
2006-01-01
BEAT is a Web-based system that generates fault-based test cases from Boolean expressions. It is based on the integration of our several fault-based test case selection strategies. The generated test cases are considered to be fault-based, because they are aiming at the detection of particular faults. For example, when the Boolean expression is in…
Richter, Kornel; Krone, Andrea; Mawass, Mohamad-Assaad; Krüger, Benjamin; Weigand, Markus; Stoll, Hermann; Schütz, Gisela; Kläui, Mathias
2016-07-01
We report time-resolved observations of field-induced domain wall nucleation in asymmetric ferromagnetic rings using single direction field pulses and rotating fields. We show that the asymmetric geometry of a ring allows for controlling the position of nucleation events, when a domain wall is nucleated by a rotating magnetic field. Direct observation by scanning transmission x-ray microscopy (STXM) reveals that the nucleation of domain walls occurs through the creation of transient ripplelike structures. This magnetization state is found to exhibit a surprisingly high reproducibility even at room temperature and we determine the combinations of field strengths and field directions that allow for reliable nucleation of domain walls and directly quantify the stability of the magnetic states. Our analysis of the processes occurring during field induced domain wall nucleation shows how the effective fields determine the nucleation location reproducibly, which is a key prerequisite toward using domain walls for spintronic devices.
Computer-aided design of modular protein devices: Boolean AND gene activation
Salis, H.; Kaznessis, Y. N.
2006-12-01
Many potentially useful synthetic gene networks require the expression of an engineered gene if and only if two different DNA-binding proteins exist in sufficient concentration. While some natural and engineered systems activate gene expression according to a logical AND-like behavior, they often utilize allosteric or cooperative protein-protein interactions, rendering their components unsuitable for a toolbox of modular parts for use in multiple applications. Here, we develop a quantitative model to demonstrate that a small system of interacting fusion proteins, called a protein device, can activate an engineered gene according to the Boolean AND behavior while using only modular protein domains and DNA sites. The fusion proteins are created from transactivating, DNA-binding, non-DNA binding, and protein-protein interaction domains along with the corresponding peptide ligands. Using a combined kinetic and thermodynamic model, we identify the characteristics of the molecular components and their rates of constitutive production that maximize the fidelity of AND behavior. These AND protein devices facilitate the creation of complex genetic programs and may be used to create gene therapies, biosensors and other biomedical and biotechnological applications that turn on gene expression only when multiple DNA-binding proteins are simultaneously present.
On the construction of cryptographically strong Boolean functions with desirable trade-off
REN Kui; PARK Jaemin; KIM Kwangjo
2005-01-01
This paper proposes a practical algorithm for systematically generating strong Boolean functions (f:GF(2)n→GF(2))with cryptographic meaning. This algorithm takes bent function as input and directly outputs the resulted Boolean function in terms of truth table sequence. This algorithm was used to develop two classes of balanced Boolean functions, one of which has very good cryptographic properties: nl(f)=22k-1-2k+2k-2 (n=2k), with the sum-of-squares avalanche characteristic off satisfying σf=24k+23k+2+23k+23k-2 and the absolute avalanche characteristic of △f satisfying △f=2k+1. This is the best result up to now compared to existing ones. Instead of bent sequences, starting from random Boolean functions was also tested in the algorithm. Experimental results showed that starting from bent sequences is highly superior to starting from random Boolean functions.
Proposed method to construct Boolean functions with maximum possible annihilator immunity
Goyal, Rajni; Panigrahi, Anupama; Bansal, Rohit
2017-07-01
Nonlinearity and Algebraic(annihilator) immunity are two core properties of a Boolean function because optimum values of Annihilator Immunity and nonlinearity are required to resist fast algebraic attack and differential cryptanalysis respectively. For a secure cypher system, Boolean function(S-Boxes) should resist maximum number of attacks. It is possible if a Boolean function has optimal trade-off among its properties. Before constructing Boolean functions, we fixed the criteria of our constructions based on its properties. In present work, our construction is based on annihilator immunity and nonlinearity. While keeping above facts in mind,, we have developed a multi-objective evolutionary approach based on NSGA-II and got the optimum value of annihilator immunity with good bound of nonlinearity. We have constructed balanced Boolean functions having the best trade-off among balancedness, Annihilator immunity and nonlinearity for 5, 6 and 7 variables by the proposed method.
Goossens, Bart; Aelterman, Jan; Luong, Hiep; Pizurica, Aleksandra; Philips, Wilfried
2013-02-01
In digital cameras and mobile phones, there is an ongoing trend to increase the image resolution, decrease the sensor size and to use lower exposure times. Because smaller sensors inherently lead to more noise and a worse spatial resolution, digital post-processing techniques are required to resolve many of the artifacts. Color filter arrays (CFAs), which use alternating patterns of color filters, are very popular because of price and power consumption reasons. However, color filter arrays require the use of a post-processing technique such as demosaicing to recover full resolution RGB images. Recently, there has been some interest in techniques that jointly perform the demosaicing and denoising. This has the advantage that the demosaicing and denoising can be performed optimally (e.g. in the MSE sense) for the considered noise model, while avoiding artifacts introduced when using demosaicing and denoising sequentially. In this paper, we will continue the research line of the wavelet-based demosaicing techniques. These approaches are computationally simple and very suited for combination with denoising. Therefore, we will derive Bayesian Minimum Squared Error (MMSE) joint demosaicing and denoising rules in the complex wavelet packet domain, taking local adaptivity into account. As an image model, we will use Gaussian Scale Mixtures, thereby taking advantage of the directionality of the complex wavelets. Our results show that this technique is well capable of reconstructing fine details in the image, while removing all of the noise, at a relatively low computational cost. In particular, the complete reconstruction (including color correction, white balancing etc) of a 12 megapixel RAW image takes 3.5 sec on a recent mid-range GPU.
Digital clocks: simple Boolean models can quantitatively describe circadian systems.
Akman, Ozgur E; Watterson, Steven; Parton, Andrew; Binns, Nigel; Millar, Andrew J; Ghazal, Peter
2012-09-07
The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. The clock functions by generating endogenous rhythms that can be entrained to the external 24-h day-night cycle, enabling organisms to optimally time biochemical processes relative to dawn and dusk. In recent years, computational models based on differential equations have become useful tools for dissecting and quantifying the complex regulatory relationships underlying the clock's oscillatory dynamics. However, optimizing the large parameter sets characteristic of these models places intense demands on both computational and experimental resources, limiting the scope of in silico studies. Here, we develop an approach based on Boolean logic that dramatically reduces the parametrization, making the state and parameter spaces finite and tractable. We introduce efficient methods for fitting Boolean models to molecular data, successfully demonstrating their application to synthetic time courses generated by a number of established clock models, as well as experimental expression levels measured using luciferase imaging. Our results indicate that despite their relative simplicity, logic models can (i) simulate circadian oscillations with the correct, experimentally observed phase relationships among genes and (ii) flexibly entrain to light stimuli, reproducing the complex responses to variations in daylength generated by more detailed differential equation formulations. Our work also demonstrates that logic models have sufficient predictive power to identify optimal regulatory structures from experimental data. By presenting the first Boolean models of circadian circuits together with general techniques for their optimization, we hope to establish a new framework for the systematic modelling of more complex clocks, as well as other circuits with different qualitative dynamics. In particular, we anticipate
Stabilization of perturbed Boolean network attractors through compensatory interactions
2014-01-01
Background Understanding and ameliorating the effects of network damage are of significant interest, due in part to the variety of applications in which network damage is relevant. For example, the effects of genetic mutations can cascade through within-cell signaling and regulatory networks and alter the behavior of cells, possibly leading to a wide variety of diseases. The typical approach to mitigating network perturbations is to consider the compensatory activation or deactivation of system components. Here, we propose a complementary approach wherein interactions are instead modified to alter key regulatory functions and prevent the network damage from triggering a deregulatory cascade. Results We implement this approach in a Boolean dynamic framework, which has been shown to effectively model the behavior of biological regulatory and signaling networks. We show that the method can stabilize any single state (e.g., fixed point attractors or time-averaged representations of multi-state attractors) to be an attractor of the repaired network. We show that the approach is minimalistic in that few modifications are required to provide stability to a chosen attractor and specific in that interventions do not have undesired effects on the attractor. We apply the approach to random Boolean networks, and further show that the method can in some cases successfully repair synchronous limit cycles. We also apply the methodology to case studies from drought-induced signaling in plants and T-LGL leukemia and find that it is successful in both stabilizing desired behavior and in eliminating undesired outcomes. Code is made freely available through the software package BooleanNet. Conclusions The methodology introduced in this report offers a complementary way to manipulating node expression levels. A comprehensive approach to evaluating network manipulation should take an "all of the above" perspective; we anticipate that theoretical studies of interaction modification
Evolution and Controllability of Cancer Networks: A Boolean Perspective.
Srihari, Sriganesh; Raman, Venkatesh; Leong, Hon Wai; Ragan, Mark A
2014-01-01
Cancer forms a robust system capable of maintaining stable functioning (cell sustenance and proliferation) despite perturbations. Cancer progresses as stages over time typically with increasing aggressiveness and worsening prognosis. Characterizing these stages and identifying the genes driving transitions between them is critical to understand cancer progression and to develop effective anti-cancer therapies. In this work, we propose a novel model for the `cancer system' as a Boolean state space in which a Boolean network, built from protein-interaction and gene-expression data from different stages of cancer, transits between Boolean satisfiability states by "editing" interactions and "flipping" genes. Edits reflect rewiring of the PPI network while flipping of genes reflect activation or silencing of genes between stages. We formulate a minimization problem min flip to identify these genes driving the transitions. The application of our model (called BoolSpace) on three case studies-pancreatic and breast tumours in human and post spinal-cord injury (SCI) in rats-reveals valuable insights into the phenomenon of cancer progression: (i) interactions involved in core cell-cycle and DNA-damage repair pathways are significantly rewired in tumours, indicating significant impact to key genome-stabilizing mechanisms; (ii) several of the genes flipped are serine/threonine kinases which act as biological switches, reflecting cellular switching mechanisms between stages; and (iii) different sets of genes are flipped during the initial and final stages indicating a pattern to tumour progression. Based on these results, we hypothesize that robustness of cancer partly stems from "passing of the baton" between genes at different stages-genes from different biological processes and/or cellular components are involved in different stages of tumour progression thereby allowing tumour cells to evade targeted therapy, and therefore an effective therapy should target a "cover set" of
Damage spreading in spatial and small-world random boolean networks
Lu, Qiming [Los Alamos National Laboratory; Teuscher, Christof [Los Alamos National Laboratory
2008-01-01
Random Boolean Networks (RBNs) are often used as generic models for certain dynamics of complex systems, ranging from social networks, neural networks, to gene or protein interaction networks. Traditionally, RBNs are interconnected randomly and without considering any spatial arrangement of the links and nodes. However, most real-world networks are spatially extended and arranged with regular, small-world, or other non-random connections. Here we explore the RBN network topology between extreme local connections, random small-world, and random networks, and study the damage spreading with small perturbations. We find that spatially local connections change the scaling of the relevant component at very low connectivities ({bar K} << 1) and that the critical connectivity of stability K{sub s} changes compared to random networks. At higher {bar K}, this scaling remains unchanged. We also show that the relevant component of spatially local networks scales with a power-law as the system size N increases, but with a different exponent for local and small-world networks. The scaling behaviors are obtained by finite-size scaling. We further investigate the wiring cost of the networks. From an engineering perspective, our new findings provide the key trade-offs between damage spreading (robustness), the network wiring cost, and the network's communication characteristics.
Damage Spreading in Spatial and Small-world Random Boolean Networks
Lu, Qiming [Fermilab; Teuscher, Christof [Portland State U.
2014-02-18
The study of the response of complex dynamical social, biological, or technological networks to external perturbations has numerous applications. Random Boolean Networks (RBNs) are commonly used a simple generic model for certain dynamics of complex systems. Traditionally, RBNs are interconnected randomly and without considering any spatial extension and arrangement of the links and nodes. However, most real-world networks are spatially extended and arranged with regular, power-law, small-world, or other non-random connections. Here we explore the RBN network topology between extreme local connections, random small-world, and pure random networks, and study the damage spreading with small perturbations. We find that spatially local connections change the scaling of the relevant component at very low connectivities ($\\bar{K} \\ll 1$) and that the critical connectivity of stability $K_s$ changes compared to random networks. At higher $\\bar{K}$, this scaling remains unchanged. We also show that the relevant component of spatially local networks scales with a power-law as the system size N increases, but with a different exponent for local and small-world networks. The scaling behaviors are obtained by finite-size scaling. We further investigate the wiring cost of the networks. From an engineering perspective, our new findings provide the key design trade-offs between damage spreading (robustness), the network's wiring cost, and the network's communication characteristics.
Boolean Variables in Economic Models Solved by Linear Programming
Lixandroiu D.
2014-12-01
Full Text Available The article analyses the use of logical variables in economic models solved by linear programming. Focus is given to the presentation of the way logical constraints are obtained and of the definition rules based on predicate logic. Emphasis is also put on the possibility to use logical variables in constructing a linear objective function on intervals. Such functions are encountered when costs or unitary receipts are different on disjunct intervals of production volumes achieved or sold. Other uses of Boolean variables are connected to constraint systems with conditions and the case of a variable which takes values from a finite set of integers.
Graph-based algorithms for Boolean function manipulation
Bryant, R.E.
1986-08-01
In this paper the authors present a new data structure for representing Boolean functions and an associated set of manipulation algorithms. Although a function requires, in the worst case, a graph of size exponential in the number of arguments, many of the functions encountered in typical applications have a more reasonable representation. The algorithms have time complexity proportional to the sizes of the graphs being operated on, and hence are quite efficient as long as the graphs do not grow too large. The authors present experimental results from applying these algorithms to problems in logic design verification that demonstrate the practicality of the approach.
On orders of two transformation semigroups of the boolean
I. V. Livinsky
2014-12-01
Full Text Available We consider the semigroup $\\mathcal{O}(\\mathcal{B}_n$ of all order--preserving transformations $\\varphi : \\mathcal{B}_n \\rightarrow \\mathcal{B}_n$ of ordered by inclusion boolean $\\mathcal{B}_n$ of $n$-element set (i.e. such transformations that$A \\subseteq B$ implies $\\varphi(A \\subseteq \\varphi(B$ and its subsemigroup $\\mathcal{C}(\\mathcal{B}_n$ of those transformations for which $\\varphi(A \\subseteq A$ for all $A \\in \\mathcal{B}_n$. Orders of these semigroups are calculated.
From Exact Learning to Computing Boolean Functions and Back Again
Goschin, Sergiu
2012-01-01
The goal of the paper is to relate complexity measures associated with the evaluation of Boolean functions (certificate complexity, decision tree complexity) and learning dimensions used to characterize exact learning (teaching dimension, extended teaching dimension). The high level motivation is to discover non-trivial relations between exact learning of an unknown concept and testing whether an unknown concept is part of a concept class or not. Concretely, the goal is to provide lower and upper bounds of complexity measures for one problem type in terms of the other.
Seismic imaging and evaluation of channels modeled by boolean approach
Spinola, M.; Aggio, A. [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas
1999-07-01
The seismic method attempt to image the subsurface architecture and has been able to significantly contribute to detect areal and vertical changes in rock properties. This work presents a seismic imaging study of channel objects generated using the boolean technique. Three channels having different thicknesses were simulated, using the same width, sinuosity and direction. A velocity model was constructed in order to allow seismic contrasts between the interior of channels and the embedding rock. To examine the seismic response for different channel thicknesses, a 3D ray tracing with a normal incident point survey was performed. The three channels were resolved and the way the seismic could image them was studied. (author)
Boolean approaches to graph embeddings related to VLSI
LIU; Yanpei(
2001-01-01
［1］Hu, T. C., Kuh, S. E., Theory and concepts of circuit layout, in VLSI Circuit Layout: Theory and Design, New York:IEEE Press, 1985, 3-18.［2］Liu Yanpei, Embeddability in Graphs, Boston-Beijing: Kluwer Science, 1995.［3］Liu Yanpei, Some combinatorial optimization problems arising from VLSI circuit design, Applied Math. -JCU, 1993, 38:218-235.［4］Liu Yanpei, Marchioro, P. , Petreschi, R., At most single bend embeddings of cubic graphs, Applied Math. -CJU, 1994,39: 127-142.［5］Liu Yanpei, Marchioro, P. , Petreschi, R. et al. , Theoretical results on at most 1-bend embeddability of graphs, Acta Math.Appl. Sinica, 1992, 8: 188-192.［6］Liu Yanpei, Morgana, A., Simeone, B., General theoretical results on rectilinear embeddability of graphs, Acta Math. Ap- pl. Simca, 1991, 7: 187-192.［7］Calamoneri, T., Petreschi, R., Liu Yanpei, Optimally Extending Bistandard Graphs on the Orthogonal Grid, ASCM2000 Symposium, Tailand, Dec.17-21, 2000.［8］Liu Yanpei, Morgana, A., Simeone, B., A graph partition problem, Acta Math. Appl. Sinica, 1996, 12: 393-400.［9］Liu Yanpei, Morgana, A. , Simeone, B. , A linear algorithm for 2-bend embeddings of planar graphs in the two dimensional grid, Discrete Appl. Math., 1998, 81: 69-91.［10］Liu Yanpei, Boolean approach to planar embeddings of a graph, Acta Math. Sinica, New Series, 1989, 5: 64-79.［11］Hammer, P. L., Liu Yanpei, Simeone, B., Boolean approaches to combinatorial optimization, J. Math. Res. Expos.,1990, 10: 300-312, 455-468, 619-628.［12］Liu Yanpei, Boolean planarity characterization of graphs, Acta Math. Sinica, New Series, 1988, 4: 316-329.［13］Liu Yanpei, Boolean characterizations of planarity and planar embeddings of graphs, Ann. O. R., 1990, 24: 165-174.
On the parity complexity measures of Boolean functions
Zhang, Zhiqiang; 10.1016/j.tcs.2010.03.027
2010-01-01
The parity decision tree model extends the decision tree model by allowing the computation of a parity function in one step. We prove that the deterministic parity decision tree complexity of any Boolean function is polynomially related to the non-deterministic complexity of the function or its complement. We also show that they are polynomially related to an analogue of the block sensitivity. We further study parity decision trees in their relations with an intermediate variant of the decision trees, as well as with communication complexity.
Bebop to the Boolean boogie an unconventional guide to electronics
Maxfield, Clive
2003-01-01
From reviews of the first edition:""If you want to be reminded of the joy of electronics, take a look at Clive (Max) Maxfield's book Bebop to the Boolean Boogie.""--Computer Design ""Lives up to its title as a useful and entertaining technical guide....well-suited for students, technical writers, technicians, and sales and marketing people.""--Electronic Design""Writing a book like this one takes audacity! ... Maxfield writes lucidly on a variety of complex topics without 'writing down' to his audience."" --EDN""A highly readable, well-illustrated guided tour
On Natural Genetic Engineering: Structural Dynamism in Random Boolean Networks
Bull, Larry
2012-01-01
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include changes in node connectivity based upon the current cell state, e.g., via transposable elements. The underlying behaviour of the resulting dynamical networks is investigated before their evolvability is explored using a version of the NK model of fitness landscapes. Structural dynamism is found to be selected for in non-stationary environments and subsequently shown capable of providing a mechanism for evolutionary innovation when such reorganizations are inherited.
An Association Rule Mining Algorithm Based on a Boolean Matrix
Hanbing Liu
2007-09-01
Full Text Available Association rule mining is a very important research topic in the field of data mining. Discovering frequent itemsets is the key process in association rule mining. Traditional association rule algorithms adopt an iterative method to discovery, which requires very large calculations and a complicated transaction process. Because of this, a new association rule algorithm called ABBM is proposed in this paper. This new algorithm adopts a Boolean vector "relational calculus" method to discovering frequent itemsets. Experimental results show that this algorithm can quickly discover frequent itemsets and effectively mine potential association rules.
Fujita, T. C.; Uchida, M., E-mail: uchida@ap.t.u-tokyo.ac.jp; Kozuka, Y.; Ogawa, S. [Department of Applied Physics and Quantum-Phase Electronics Center (QPEC), University of Tokyo, Tokyo 113-8656 (Japan); Tsukazaki, A. [Institute for Materials Research, Tohoku University, Sendai 980-8577 (Japan); PRESTO, Japan Science and Technology Agency (JST), Tokyo 102-0075 (Japan); Arima, T. [Department of Advanced Materials Science, University of Tokyo, Kashiwa 277-8561 (Japan); RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198 (Japan); Kawasaki, M. [Department of Applied Physics and Quantum-Phase Electronics Center (QPEC), University of Tokyo, Tokyo 113-8656 (Japan); RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198 (Japan)
2016-01-11
Pyrochlore iridates have attracted growing attention because of a theoretical prediction of a possible topological semimetal phase originating from all-in-all-out spin ordering. Related to the topological band structure, recent findings of the magnetic domain wall conduction have stimulated investigations of magnetic domain distribution in this system. Here, we investigate the size of magnetic domains in Eu{sub 2}Ir{sub 2}O{sub 7} single crystalline thin films by magnetoresistance (MR) using microscale Hall bars. Two distinct magnetic domains of the all-in-all-out spin structure are known to exhibit linear MR but with opposite signs, which enables us to estimate the ratio of the two domains in the patterned channel. The linear MR for 80 × 60 μm{sup 2} channel is nearly zero after zero-field cooling, suggesting random distribution of domains smaller than the channel size. In contrast, the wide distribution of the value of the linear MR is detected in 2 × 2 μm{sup 2} channel, reflecting the detectable domain size depending on each cooling-cycle. Compared to simulation results, we estimate the average size of a single all-in-all-out magnetic domain as 1–2 μm.
Oka, Tsutomu; Remue, Eline; Meerschaert, Kris; Vanloo, Berlinda; Boucherie, Ciska; Gfeller, David; Bader, Gary D; Sidhu, Sachdev S; Vandekerckhove, Joël; Gettemans, Jan; Sudol, Marius
2010-12-15
The Hippo pathway regulates the size of organs by controlling two opposing processes: proliferation and apoptosis. YAP2 (Yes kinase-associated protein 2), one of the three isoforms of YAP, is a WW domain-containing transcriptional co-activator that acts as the effector of the Hippo pathway in mammalian cells. In addition to WW domains, YAP2 has a PDZ-binding motif at its C-terminus. We reported previously that this motif was necessary for YAP2 localization in the nucleus and for promoting cell detachment and apoptosis. In the present study, we show that the tight junction protein ZO (zonula occludens)-2 uses its first PDZ domain to form a complex with YAP2. The endogenous ZO-2 and YAP2 proteins co-localize in the nucleus. We also found that ZO-2 facilitates the nuclear localization and pro-apoptotic function of YAP2, and that this activity of ZO-2 is PDZ-domain-dependent. The present paper is the first report on a PDZ-based nuclear translocation mechanism. Moreover, since the Hippo pathway acts as a tumour suppressor pathway, the YAP2-ZO-2 complex could represent a target for cancer therapy.
Al Abdallah, Qusai; Choe, Se-In; Campoli, Paolo; Baptista, Stefanie; Gravelat, Fabrice N.; Lee, Mark J.; Sheppard, Donald C.
2012-01-01
MedA is a developmental regulator that is conserved in the genome of most filamentous fungi. In the pathogenic fungus Aspergillus fumigatus MedA regulates conidiogenesis, adherence to host cells, and pathogenicity. The mechanism by which MedA governs these phenotypes remains unknown. Although the nuclear import of MedA orthologues has been reported in other fungi, no nuclear localization signal, DNA-binding domain or other conserved motifs have been identified within MedA. In this work, we performed a deletion analysis of MedA and identified a novel domain within the C-terminal region of the protein, designated MedA346–557, that is necessary and sufficient for nuclear localization of MedA. We further demonstrate that MedA nuclear localization is required for the function of MedA. Surprisingly, expression of the minimal nuclear localization fragment MedA346–557 alone was sufficient to restore conidogenesis, biofilm formation and virulence to the medA mutant strain. Collectively these results suggest that MedA functions in the regulation of transcription, and that the MedA346–557 domain is both necessary and sufficient to mediate MedA function. PMID:23185496
Boolean network models of cellular regulation: prospects and limitations.
Bornholdt, Stefan
2008-08-06
Computer models are valuable tools towards an understanding of the cell's biochemical regulatory machinery. Possible levels of description of such models range from modelling the underlying biochemical details to top-down approaches, using tools from the theory of complex networks. The latter, coarse-grained approach is taken where regulatory circuits are classified in graph-theoretical terms, with the elements of the regulatory networks being reduced to simply nodes and links, in order to obtain architectural information about the network. Further, considering dynamics on networks at such an abstract level seems rather unlikely to match dynamical regulatory activity of biological cells. Therefore, it came as a surprise when recently examples of discrete dynamical network models based on very simplistic dynamical elements emerged which in fact do match sequences of regulatory patterns of their biological counterparts. Here I will review such discrete dynamical network models, or Boolean networks, of biological regulatory networks. Further, we will take a look at such models extended with stochastic noise, which allow studying the role of network topology in providing robustness against noise. In the end, we will discuss the interesting question of why at all such simple models can describe aspects of biology despite their simplicity. Finally, prospects of Boolean models in exploratory dynamical models for biological circuits and their mutants will be discussed.
Chemical Visualization of Boolean Functions: A Simple Chemical Computer
Blittersdorf, R.; Müller, J.; Schneider, F. W.
1995-08-01
We present a chemical realization of the Boolean functions AND, OR, NAND, and NOR with a neutralization reaction carried out in three coupled continuous flow stirred tank reactors (CSTR). Two of these CSTR's are used as input reactors, the third reactor marks the output. The chemical reaction is the neutralization of hydrochloric acid (HCl) with sodium hydroxide (NaOH) in the presence of phenolphtalein as an indicator, which is red in alkaline solutions and colorless in acidic solutions representing the two binary states 1 and 0, respectively. The time required for a "chemical computation" is determined by the flow rate of reactant solutions into the reactors since the neutralization reaction itself is very fast. While the acid flow to all reactors is equal and constant, the flow rate of NaOH solution controls the states of the input reactors. The connectivities between the input and output reactors determine the flow rate of NaOH solution into the output reactor, according to the chosen Boolean function. Thus the state of the output reactor depends on the states of the input reactors.
Synchronization Analysis of Master-Slave Probabilistic Boolean Networks.
Lu, Jianquan; Zhong, Jie; Li, Lulu; Ho, Daniel W C; Cao, Jinde
2015-01-01
In this paper, we analyze the synchronization problem of master-slave probabilistic Boolean networks (PBNs). The master Boolean network (BN) is a deterministic BN, while the slave BN is determined by a series of possible logical functions with certain probability at each discrete time point. In this paper, we firstly define the synchronization of master-slave PBNs with probability one, and then we investigate synchronization with probability one. By resorting to new approach called semi-tensor product (STP), the master-slave PBNs are expressed in equivalent algebraic forms. Based on the algebraic form, some necessary and sufficient criteria are derived to guarantee synchronization with probability one. Further, we study the synchronization of master-slave PBNs in probability. Synchronization in probability implies that for any initial states, the master BN can be synchronized by the slave BN with certain probability, while synchronization with probability one implies that master BN can be synchronized by the slave BN with probability one. Based on the equivalent algebraic form, some efficient conditions are derived to guarantee synchronization in probability. Finally, several numerical examples are presented to show the effectiveness of the main results.
Boolean difference equations. I - Formulation and dynamic behavior
Dee, D.; Ghil, M.
1984-01-01
In many biological and physical systems, feedback mechanisms depend on a set of thresholds associated with the state variables. Each feedback has a characteristic time scale. It is suggested that delay-difference equations for Boolean-valued variables are an appropriate mathematical framework for such situations: the feedback thresholds result in the discrete, on-off character of the variables, and the interaction time scales of the feedbacks are expressed as delays. The initial-value problem for Boolean delay equations (B-Delta-Es) is formulated, and shown to have unique solutions for all times. Examples of periodic and aperiodic solutions are given. Aperiodic solutions have increasing complexity which depends on time t roughly as t to the l-1 power, l being the number of delays. Stability of solutions is defined, and some examples of stability analysis are given; additional stability questions are raised. The present formulation of (B-Delta-Es) is compared with related work and generalizations are suggested.
Direct relations between morphology and transport in Boolean models.
Scholz, Christian; Wirner, Frank; Klatt, Michael A; Hirneise, Daniel; Schröder-Turk, Gerd E; Mecke, Klaus; Bechinger, Clemens
2015-10-01
We study the relation of permeability and morphology for porous structures composed of randomly placed overlapping circular or elliptical grains, so-called Boolean models. Microfluidic experiments and lattice Boltzmann simulations allow us to evaluate a power-law relation between the Euler characteristic of the conducting phase and its permeability. Moreover, this relation is so far only directly applicable to structures composed of overlapping grains where the grain density is known a priori. We develop a generalization to arbitrary structures modeled by Boolean models and characterized by Minkowski functionals. This generalization works well for the permeability of the void phase in systems with overlapping grains, but systematic deviations are found if the grain phase is transporting the fluid. In the latter case our analysis reveals a significant dependence on the spatial discretization of the porous structure, in particular the occurrence of single isolated pixels. To link the results to percolation theory we performed Monte Carlo simulations of the Euler characteristic of the open cluster, which reveals different regimes of applicability for our permeability-morphology relations close to and far away from the percolation threshold.
Harmonic Analysis of Boolean Networks: Determinative Power and Perturbations
Heckel, Reinhard; Bossert, Martin
2011-01-01
Consider a large Boolean network with a feed forward structure. Given a probability distribution for the inputs, can one find-possibly small-collections of input nodes that determine the states of most other nodes in the network? To identify these nodes, a notion that quantifies the determinative power of an input over states in the network is needed. We argue that the mutual information (MI) between a subset of the inputs X = {X_1, ..., X_n} of node i and the function f_i(X)$ associated with node i quantifies the determinative power of this subset of inputs over node i. To study the relation of determinative power to sensitivity to perturbations, we relate the MI to measures of perturbations, such as the influence of a variable, in terms of inequalities. The result shows that, maybe surprisingly, an input that has large influence does not necessarily have large determinative power. The main tool for the analysis is Fourier analysis of Boolean functions. Whether a function is sensitive to perturbations or not...
Efficient Instantiation of Parameterised Boolean Equation Systems to Parity Games
Gijs Kant
2012-10-01
Full Text Available Parameterised Boolean Equation Systems (PBESs are sequences of Boolean fixed point equations with data variables, used for, e.g., verification of modal mu-calculus formulae for process algebraic specifications with data. Solving a PBES is usually done by instantiation to a Parity Game and then solving the game. Practical game solvers exist, but the instantiation step is the bottleneck. We enhance the instantiation in two steps. First, we transform the PBES to a Parameterised Parity Game (PPG, a PBES with each equation either conjunctive or disjunctive. Then we use LTSmin, that offers transition caching, efficient storage of states and both distributed and symbolic state space generation, for generating the game graph. To that end we define a language module for LTSmin, consisting of an encoding of variables with parameters into state vectors, a grouped transition relation and a dependency matrix to indicate the dependencies between parts of the state vector and transition groups. Benchmarks on some large case studies, show that the method speeds up the instantiation significantly and decreases memory usage drastically.
Testing Odd-Cycle-Freeness in Boolean Functions
Bhattacharyya, Arnab; Raghavendra, Prasad; Shapira, Asaf
2011-01-01
Call a function f : F_2^n -> {0,1} odd-cycle-free if there are no x_1, ..., x_k in F_2^n with k an odd integer such that f(x_1) = ... = f(x_k) = 1 and x_1 + ... + x_k = 0. We show that one can distinguish odd-cycle-free functions from those eps-far from being odd-cycle-free by making poly(1/eps) queries to an evaluation oracle. To obtain this result, we use connections between basic Fourier analysis and spectral graph theory to show that one can reduce testing odd-cycle-freeness of Boolean functions to testing bipartiteness of dense graphs. Our work forms part of a recent sequence of works that shows connections between testability of properties of Boolean functions and of graph properties. We also prove that there is a canonical tester for odd-cycle-freeness making poly(1/eps) queries, meaning that the testing algorithm operates by picking a random linear subspace of dimension O(log 1/eps) and then checking if the restriction of the function to the subspace is odd-cycle-free or not. The test is analyzed by s...
Synchronization Analysis of Master-Slave Probabilistic Boolean Networks
Lu, Jianquan; Zhong, Jie; Li, Lulu; Ho, Daniel W. C.; Cao, Jinde
2015-01-01
In this paper, we analyze the synchronization problem of master-slave probabilistic Boolean networks (PBNs). The master Boolean network (BN) is a deterministic BN, while the slave BN is determined by a series of possible logical functions with certain probability at each discrete time point. In this paper, we firstly define the synchronization of master-slave PBNs with probability one, and then we investigate synchronization with probability one. By resorting to new approach called semi-tensor product (STP), the master-slave PBNs are expressed in equivalent algebraic forms. Based on the algebraic form, some necessary and sufficient criteria are derived to guarantee synchronization with probability one. Further, we study the synchronization of master-slave PBNs in probability. Synchronization in probability implies that for any initial states, the master BN can be synchronized by the slave BN with certain probability, while synchronization with probability one implies that master BN can be synchronized by the slave BN with probability one. Based on the equivalent algebraic form, some efficient conditions are derived to guarantee synchronization in probability. Finally, several numerical examples are presented to show the effectiveness of the main results. PMID:26315380
Boolean models of biosurfactants production in Pseudomonas fluorescens.
Adrien Richard
Full Text Available Cyclolipopeptides (CLPs are biosurfactants produced by numerous Pseudomonas fluorescens strains. CLP production is known to be regulated at least by the GacA/GacS two-component pathway, but the full regulatory network is yet largely unknown. In the clinical strain MFN1032, CLP production is abolished by a mutation in the phospholipase C gene (plcC and not restored by plcC complementation. Their production is also subject to phenotypic variation. We used a modelling approach with Boolean networks, which takes into account all these observations concerning CLP production without any assumption on the topology of the considered network. Intensive computation yielded numerous models that satisfy these properties. All models minimizing the number of components point to a bistability in CLP production, which requires the presence of a yet unknown key self-inducible regulator. Furthermore, all suggest that a set of yet unexplained phenotypic variants might also be due to this epigenetic switch. The simplest of these Boolean networks was used to propose a biological regulatory network for CLP production. This modelling approach has allowed a possible regulation to be unravelled and an unusual behaviour of CLP production in P. fluorescens to be explained.
von Trotha, Jakob W; Campos-Ortega, José A; Reugels, Alexander M
2006-04-01
Neurulation in zebrafish (Danio rerio) embryos is characterized by oriented cell divisions and the progressive establishment of cellular polarity. Mitoses in the neural plate and neural tube are planar, but in the neural keel/rod stage, the mitotic spindle rotates by 90 degrees, causing cell divisions to occur perpendicular to the plane of the neuroepithelium. The mechanisms and molecules that establish cellular polarity and cause the stereotypic orientation of the mitotic spindle during neurulation are largely unknown. In Caenorhabditis elegans and Drosophila, the PAR/aPKC complex has been shown to be involved in both establishment of cellular polarity and spindle orientation. Here, we show that the conserved N-terminal oligomerization domain (CR1) and the PDZ domains of ASIP/PAR-3:EGFP are involved in its localization to the apical membrane in zebrafish neuroepithelial cells. We further show that the C-terminal part of ASIP/PAR-3 contributes to proper localization and that the apical localization signals in ASIP/PAR-3 prevent the basolateral localization of a Numb:PAR-3 fusion protein. The parallel orientation of the mitotic spindle in the neural tube, however, is only weakly impaired upon overexpression of various ASIP/PAR-3:EGFP constructs.
无
2009-01-01
The polarity-sensitive fluorescent probe, 3-(4-chloro-6-p-glyoxalphenoxy-1,3,5-triazinylamino)-7- (dimethylamino)-2-methylphenazine, was used to analyze the local structure of apo-α-lactalbumin by detecting the polarity and conformational changes of the arginine residue (Arg10) domain. The polarity of the Arg10 domain in both native and heat-denatured apo-α-lactalbumin was determined, which corresponds to a dielectric constant of 16, and the hydrophobic core near the Arg10 was found to be conservative for heating. Meanwhile, the effect of Ca2+ binding on the conformational changes of the Arg10 domain was studied, revealing that the hydrophobic core near the Arg10 is insensitive to the binding of Ca2+.
On the robustness of NK-Kauffman networks against changes in their connections and Boolean functions
Zertuche, Federico
2009-04-01
NK-Kauffman networks LKN are a subset of the Boolean functions on N Boolean variables to themselves, ΛN={ξ :Z2N→Z2N}. To each NK-Kauffman network it is possible to assign a unique Boolean function on N variables through the function Ψ :LKN→ΛN. The probability PK that Ψ(f )=Ψ(f'), when f' is obtained through f by a change in one of its K-Boolean functions (bK:Z2K→Z2), and/or connections, is calculated. The leading term of the asymptotic expansion of PK, for N ≫1, turns out to depend on the probability to extract the tautology and contradiction Boolean functions, and in the average value of the distribution of probability of the Boolean functions, the other terms decay as O(1/N). In order to accomplish this, a classification of the Boolean functions in terms of what I have called their irreducible degree of connectivity is established. The mathematical findings are discussed in the biological context, where Ψ is used to model the genotype-phenotype map.
Takada, Saeko; Collins, Eric R; Kurahashi, Kayo
2015-05-15
DNA damage responses, including mitotic centrosome inactivation, cell-cycle delay in mitosis, and nuclear dropping from embryo cortex, maintain genome integrity in syncytial Drosophila embryos. A conserved signaling kinase, Chk2, known as Mnk/Loki, is essential for the responses. Here we demonstrate that functional EGFP-Mnk expressed from a transgene localizes to the nucleus, centrosomes, interkinetochore/centromere region, midbody, and pseudocleavage furrows without DNA damage and in addition forms numerous foci/aggregates on mitotic chromosomes upon DNA damage. We expressed EGFP-tagged Mnk deletion or point mutation variants and investigated domain functions of Mnk in vivo. A triple mutation in the phosphopeptide-binding site of the forkhead-associated (FHA) domain disrupted normal Mnk localization except to the nucleus. The mutation also disrupted Mnk foci formation on chromosomes upon DNA damage. FHA mutations and deletion of the SQ/TQ-cluster domain (SCD) abolished Mnk transphosphorylations and autophosphorylations, indicative of kinase activation after DNA damage. A potent NLS was found at the C-terminus, which is required for normal Mnk function. We propose that the FHA domain in Mnk plays essential dual functions in mediating embryonic DNA damage responses by means of its phosphopeptide-binding ability: activating Mnk in the nucleus upon DNA damage and recruiting Mnk to multiple subcellular structures independently of DNA damage.
Extending XCS with Cyclic Graphs for Scalability on Complex Boolean Problems.
Iqbal, Muhammad; Browne, Will N; Zhang, Mengjie
2015-09-25
A main research direction in the field of evolutionary machine learning is to develop a scalable classifier system to solve high-dimensional problems. Recently work has begun on autonomously reusing learned building blocks of knowledge to scale from low-dimensional problems to high-dimensional ones. An XCS-based classifier system, known as XCSCFC, has been shown to be scalable, through the addition of expression tree-like code fragments, to a limit beyond standard learning classifier systems. XCSCFC is especially beneficial if the target problem can be divided into a hierarchy of subproblems and each of them is solvable in a bottom-up fashion. However, if the hierarchy of subproblems is too deep, then XCSCFC becomes impractical because of the needed computational time and thus eventually hits a limit in problem size. A limitation in this technique is the lack of a cyclic representation, which is inherent in finite state machines (FSMs). However, the evolution of FSMs is a hard task owing to the combinatorially large number of possible states, connections, and interaction. Usually this requires supervised learning to minimize inappropriate FSMs, which for high-dimensional problems necessitates subsampling or incremental testing. To avoid these constraints, this work introduces a state-machine-based encoding scheme into XCS for the first time, termed XCSSMA. The proposed system has been tested on six complex Boolean problem domains: multiplexer, majority-on, carry, even-parity, count ones, and digital design verification problems. The proposed approach outperforms XCSCFA (an XCS that computes actions) and XCSF (an XCS that computes predictions) in three of the six problem domains, while the performance in others is similar. In addition, XCSSMA evolved, for the first time, compact and human readable general classifiers (i.e., solving any n-bit problems) for the even-parity and carry problem domains, demonstrating its ability to produce scalable solutions using a
Denis Alikin; Anton Turygin; Andrei Kholkin; Vladimir Shur
2017-01-01
Recent advances in the development of novel methods for the local characterization of ferroelectric domains open up new opportunities not only to image, but also to control and to create desired domain configurations (domain engineering). The morphotropic and polymorphic phase boundaries that are frequently used to increase the electromechanical and dielectric performance of ferroelectric ceramics have a tremendous effect on the domain structure, which can serve as a signature of complex pola...
Feedback control design for the complete synchronisation of two coupled Boolean networks
Li, Fangfei
2016-09-01
In the literatures, to design state feedback controllers to make the response Boolean network synchronise with the drive Boolean network is rarely considered. Motivated by this, feedback control design for the complete synchronisation of two coupled Boolean networks is investigated in this paper. A necessary condition for the existence of a state feedback controller achieving the complete synchronisation is established first. Then, based on the necessary condition, the feedback control law is proposed. Finally, an example is worked out to illustrate the proposed design procedure.
Characterizing short-term stability for Boolean networks over any distribution of transfer functions
Seshadhri, C.; Smith, Andrew M.; Vorobeychik, Yevgeniy; Mayo, Jackson R.; Armstrong, Robert C.
2016-07-01
We present a characterization of short-term stability of Kauffman's N K (random) Boolean networks under arbitrary distributions of transfer functions. Given such a Boolean network where each transfer function is drawn from the same distribution, we present a formula that determines whether short-term chaos (damage spreading) will happen. Our main technical tool which enables the formal proof of this formula is the Fourier analysis of Boolean functions, which describes such functions as multilinear polynomials over the inputs. Numerical simulations on mixtures of threshold functions and nested canalyzing functions demonstrate the formula's correctness.
Minimum energy control and optimal-satisfactory control of Boolean control network
Li, Fangfei, E-mail: li_fangfei@163.com; Lu, Xiwen
2013-12-09
In the literatures, to transfer the Boolean control network from the initial state to the desired state, the expenditure of energy has been rarely considered. Motivated by this, this Letter investigates the minimum energy control and optimal-satisfactory control of Boolean control network. Based on the semi-tensor product of matrices and Floyd's algorithm, minimum energy, constrained minimum energy and optimal-satisfactory control design for Boolean control network are given respectively. A numerical example is presented to illustrate the efficiency of the obtained results.
Improving the User Query for the Boolean Model Using Genetic Algorithms
Nassar, Mohammad Othman; Mashagba, Eman Al
2011-01-01
The Use of genetic algorithms in the Information retrieval (IR) area, especially in optimizing a user query in Arabic data collections is presented in this paper. Very little research has been carried out on Arabic text collections. Boolean model have been used in this research. To optimize the query using GA we used different fitness functions, different mutation strategies to find which is the best strategy and fitness function that can be used with Boolean model when the data collection is the Arabic language. Our results show that the best GA strategy for the Boolean model is the GA (M2, Precision) method.
Vectorial Resilient PC(l) of Order k Boolean Functions from AG-Codes
Hao CHEN; Liang MA; Jianhua LI
2011-01-01
Propagation criteria and resiliency of vectorial Boolean functions are important for cryptographic purpose (see [1- 4, 7, 8, 10, 11, 16]). Kurosawa, Stoh [8] and Carlet [1]gave a construction of Boolean functions satisfying PC(l) of order k from binary linear or nonlinear codes. In this paper, the algebraic-geometric codes over GF(2m) are used to modify the Carlet and Kurosawa-Satoh's construction for giving vectorial resilient Boolean functions satisfying PC(l) of order k criterion. This new construction is compared with previously known results.
Boolean functions of an odd number of variables with maximum algebraic immunity
LI Na; QI WenFeng
2007-01-01
In this paper, we study Boolean functions of an odd number of variables with maximum algebraic immunity, We identify three classes of such functions, and give some necessary conditions of such functions, which help to examine whether a Boolean function of an odd number of variables has the maximum algebraic immunity. Further, some necessary conditions for such functions to have also higher nonlinearity are proposed, and a class of these functions are also obtained. Finally,we present a sufficient and necessary condition for Boolean functions of an odd number of variables to achieve maximum algebraic immunity and to be also 1-resilient.
Seshadhri, C; Smith, Andrew M; Vorobeychik, Yevgeniy; Mayo, Jackson R; Armstrong, Robert C
2016-07-01
We present a characterization of short-term stability of Kauffman's NK (random) Boolean networks under arbitrary distributions of transfer functions. Given such a Boolean network where each transfer function is drawn from the same distribution, we present a formula that determines whether short-term chaos (damage spreading) will happen. Our main technical tool which enables the formal proof of this formula is the Fourier analysis of Boolean functions, which describes such functions as multilinear polynomials over the inputs. Numerical simulations on mixtures of threshold functions and nested canalyzing functions demonstrate the formula's correctness.
Santos, L.O.E.; Philippi, P.C.; Fernandes, C.P. [Porous Media and Thermophysical Properties Laboratory LMPT, Mechanical Engineering Department, Federal University of Santa Catarina, 88040-900 , SC Florianopolis (Brazil); Damiani, M.C. [Engineering Simulation and Scientific Software ESSS, Parque Tecnologico de Florianopolis, Rodovia SC 401 km 001, 88030-000 , SC Florianopolis (Brazil)
2002-07-01
This paper presents a method for predicting the intrinsic permeability of porous media based on the integration of the local velocity field. Three-dimensional representations of the porous structure are reconstructed from two-dimensional binary images, after segmentation of digital images acquired from thin plates, commonly used in microscopy. Velocity field is calculated on these three-dimensional representations using a Boolean lattice gas method (LGA). Reconstruction is based on a Gaussian stochastic simulation. Mercury-intrusion results furnish auxiliary data that are used for the estimation of a critical percolation diameter and to establish a necessary condition for the binary source images to give accurate predictions of permeability, considering the intrinsic limitations of the reconstruction process. Reconstruction method and connection loss, resolution factor, adherence conditions and the effects of Boolean noise in the calculation of permeability are fully discussed. The method is used to simulate flows through several petroleum reservoir rocks, leading to intrinsic permeability prediction. Simulation is compared with experimental results. Considered as an intrinsic permeability prediction method based on the geometrical information that is possible to recovery from microscopy thin plates, three-dimensional reconstruction appears to be the most critical step in present simulation scheme.
Lu, Guangtao; Li, Yourong; Song, Gangbing
2016-09-01
The delay-and-sum (DAS) imaging algorithm usually sends an excitation signal at each piezoceramic transducer and obtains a defect image by using transmitter-sensor pair signals to draw ellipses or hyperbolas. A delay-and-Boolean-ADD (DABA) imaging algorithm is developed for defect detection of plate-like structures with a small number of piezoceramic transducers. This new method requires sending only one excitation signal for each detection, and obtains a better defect image by employing Boolean ADD operation instead of addition or multiplication operation in the DAS algorithm. A reflection coefficient is introduced in the new algorithm to attenuate the signals reflected from the boundary. The widely used envelop-detection method based on Hilbert-transformation is replaced by a new envelop-detection technique based on a local maximum value to increase the accuracy of locating. An additional time shift due to the excitation signal itself is also considered to decrease the location error. The results of the experiments conducted on an aluminum plate indicate that the proposed DABA imaging algorithm combining with the new techniques can detect a bonded mass defect accurately and efficiently.
Minimal Sign Representation of Boolean Functions: Algorithms and Exact Results for Low Dimensions.
Sezener, Can Eren; Oztop, Erhan
2015-08-01
Boolean functions (BFs) are central in many fields of engineering and mathematics, such as cryptography, circuit design, and combinatorics. Moreover, they provide a simple framework for studying neural computation mechanisms of the brain. Many representation schemes for BFs exist to satisfy the needs of the domain they are used in. In neural computation, it is of interest to know how many input lines a neuron would need to represent a given BF. A common BF representation to study this is the so-called polynomial sign representation where [Formula: see text] and 1 are associated with true and false, respectively. The polynomial is treated as a real-valued function and evaluated at its parameters, and the sign of the polynomial is then taken as the function value. The number of input lines for the modeled neuron is exactly the number of terms in the polynomial. This letter investigates the minimum number of terms, that is, the minimum threshold density, that is sufficient to represent a given BF and more generally aims to find the maximum over this quantity for all BFs in a given dimension. With this work, for the first time exact results for four- and five-variable BFs are obtained, and strong bounds for six-variable BFs are derived. In addition, some connections between the sign representation framework and bent functions are derived, which are generally studied for their desirable cryptographic properties.
Local Model Checking of Weighted CTL with Upper-Bound Constraints
Jensen, Jonas Finnemann; Larsen, Kim Guldstrand; Srba, Jiri
2013-01-01
graphs. We implement all algorithms in a publicly available tool prototype and evaluate them on several experiments. The principal conclusion is that our local algorithm is the most efficient one with an order of magnitude improvement for model checking problems with a high number of “witnesses”.......We present a symbolic extension of dependency graphs by Liu and Smolka in order to model-check weighted Kripke structures against the logic CTL with upper-bound weight constraints. Our extension introduces a new type of edges into dependency graphs and lifts the computation of fixed-points from...... boolean domain to nonnegative integers in order to cope with the weights. We present both global and local algorithms for the fixed-point computation on symbolic dependency graphs and argue for the advantages of our approach compared to the direct encoding of the model checking problem into dependency...
Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles
Shah Imran
2011-07-01
Full Text Available Abstract Background With increasing knowledge about the potential mechanisms underlying cellular functions, it is becoming feasible to predict the response of biological systems to genetic and environmental perturbations. Due to the lack of homogeneity in living tissues it is difficult to estimate the physiological effect of chemicals, including potential toxicity. Here we investigate a biologically motivated model for estimating tissue level responses by aggregating the behavior of a cell population. We assume that the molecular state of individual cells is independently governed by discrete non-deterministic signaling mechanisms. This results in noisy but highly reproducible aggregate level responses that are consistent with experimental data. Results We developed an asynchronous threshold Boolean network simulation algorithm to model signal transduction in a single cell, and then used an ensemble of these models to estimate the aggregate response across a cell population. Using published data, we derived a putative crosstalk network involving growth factors and cytokines - i.e., Epidermal Growth Factor, Insulin, Insulin like Growth Factor Type 1, and Tumor Necrosis Factor α - to describe early signaling events in cell proliferation signal transduction. Reproducibility of the modeling technique across ensembles of Boolean networks representing cell populations is investigated. Furthermore, we compare our simulation results to experimental observations of hepatocytes reported in the literature. Conclusion A systematic analysis of the results following differential stimulation of this model by growth factors and cytokines suggests that: (a using Boolean network ensembles with asynchronous updating provides biologically plausible noisy individual cellular responses with reproducible mean behavior for large cell populations, and (b with sufficient data our model can estimate the response to different concentrations of extracellular ligands. Our
The Properties of 2-Summable Boolean Function and 3-Summable Boolean Function%可求和布尔函数的性质
曾利全; 许道云
2016-01-01
可求和布尔函数是临界布尔函数判定理论中比较重要的内容之一。该类函数有一个参数k , k表示布尔函数存在k个成真点X1,X2,…Xk和k个成假点Y1,Y2,…Yk ,并且它们的和相等。本文主要研究了n元2-可求和布尔函数和n元3-可求和布尔函数的基本性质。%One of the most important theorem in recognition of threshold function is the k- asummable Boolean function for all k≥2, where k is the number of true point of the Boolean function, say X1,X2,…Xk , and the number of false point of the Boolean function, say, Y1,Y2,…Yk ,such that∑ki=1Xi =∑ki=1Yi . It is shown that the basic properties of 2-summable Boolean function and 3-summable Boolean function.
Nozari, Nazbanou; Trueswell, John C; Thompson-Schill, Sharon L
2016-12-01
During sentence comprehension, real-time identification of a referent is driven both by local, context-independent lexical information and by more global sentential information related to the meaning of the utterance as a whole. This paper investigates the cognitive factors that limit the consideration of referents that are supported by local lexical information but not supported by more global sentential information. In an eye-tracking paradigm, participants heard sentences like "She will eat the red pear" while viewing four black-and-white (colorless) line-drawings. In the experimental condition, the display contained a "local attractor" (e.g., a heart), which was locally compatible with the adjective but incompatible with the context ("eat"). In the control condition, the local attractor was replaced by a picture which was incompatible with the adjective (e.g., "igloo"). A second factor manipulated contextual constraint, by using either a constraining verb (e.g., "eat"), or a non-constraining one (e.g., "see"). Results showed consideration of the local attractor, the magnitude of which was modulated by verb constraint, but also by each subject's cognitive control abilities, as measured in a separate Flanker task run on the same subjects. The findings are compatible with a processing model in which the interplay between local attraction, context, and domain-general control mechanisms determines the consideration of possible referents.
Prince, Robin N.; Schreiter, Eric R.; Zou, Peng; Wiley, H. S.; Ting, Alice Y.; Lee, Richard T.; Lauffenburger, Douglas A.
2010-07-01
Heparin-binding EGF-like growth factor (HB-EGF) is a ligand for EGF receptor (EGFR) and possesses the ability to signal in juxtacrine, autocrine and/or paracrine mode, with these alternatives being governed by the degree of proteolytic release of the ligand. Although the spatial range of diffusion of released HB-EGF is restricted by binding heparan-sulfate proteoglycans (HSPGs) in the extracellular matrix and/or cellular glycocalyx, ascertaining mechanisms governing non-released HB-EGF localization is also important for understanding its effects. We have employed a new method for independently tracking the localization of the extracellular EGFlike domain of HB-EGF and the cytoplasmic C-terminus. A striking observation was the absence of the HB-EGF transmembrane proform from the leading edge of COS-7 cells in a wound-closure assay; instead, this protein localized in regions of cell-cell contact. A battery of detailed experiments found that this localization derives from a trans interaction between extracellular HSPGs and the HBEGF heparin-binding domain, and that disruption of this interaction leads to increased release of soluble ligand and a switch in cell phenotype from juxtacrine-induced growth inhibition to autocrine-induced proliferation. Our results indicate that extracellular HSPGs serve to sequester the transmembrane pro-form of HB-EGF at the point of cell-cell contact, and that this plays a role in governing the balance between juxtacrine versus autocrine and paracrine signaling.
基于布尔语义的Gentzen推导模型%Gentzen Deduction Model Based on Boolean Logic Semantics
陈博; 眭跃飞
2015-01-01
Deduction systems are important arts of searching technology. This paper gives a new correspondence between the propositional logic and Boolean algebra, where an inequation is corresponding to a Gentzen sequent, so that the inequation is true in every Boolean algebra if and only if the Gentzen sequent is provable. In information retrieval, the information inference can effectively turn into the operation on poset. Precisely, the logical language for the propositional logic contains operators Ø'Ù'Ú;the terms instead of formulas are defined (a|Øt|t1 Ù t2|t1 Ú t2 , where a is an element) and used to represent elements in Boolean algebra. This paper defines an assignment v using Boolean algebra as its domain, and assigns the terms to be the element in Boolean algebra. The sequence ΓÞΔ is satisfied if tv £tv. Finally, this paper gives a Gentzen system to prove the soundness and completeness theorem.%布尔模型是信息检索系统的一种基础模型。给出了命题逻辑和布尔代数间的一种新的对应关系，其中布尔代数中的不等式对应Gentzen系统中的矢列式，使得当一个不等式在任意布尔代数中为真，当且仅当它所对应的矢列式是可证的。并且使得在信息检索中，针对信息的推理可以有效地转为偏序集上的运算。讨论的命题逻辑语言的运算符为Ø、Ù、Ú；并且定义了项（a|Øt|t1Ù t2|t1Ú t2'其中a是一个元素）来替代原先的公式和表示布尔代数中的元素。此外，定义了以布尔代数为论域的赋值v，将命题逻辑中的项赋值为布尔代数中的元素，并且如果tv £t v ，则矢列式ΓÞ D为真。最后给出了Gentzen系统下的可靠性和完备性定理的证明。tÎΓtÎΔ
Reconfigurable Boolean Logic Using Magnetic Single-Electron Transistors
Gonzalez-Zalba, M. Fernando; Ciccarelli, Chiara; Zarbo, Liviu P.; Irvine, Andrew C.; Campion, Richard C.; Gallagher, Bryan L.; Jungwirth, Tomas; Ferguson, Andrew J.; Wunderlich, Joerg
2015-01-01
We propose a novel hybrid single-electron device for reprogrammable low-power logic operations, the magnetic single-electron transistor (MSET). The device consists of an aluminium single-electron transistor with a GaMnAs magnetic back-gate. Changing between different logic gate functions is realized by reorienting the magnetic moments of the magnetic layer, which induces a voltage shift on the Coulomb blockade oscillations of the MSET. We show that we can arbitrarily reprogram the function of the device from an n-type SET for in-plane magnetization of the GaMnAs layer to p-type SET for out-of-plane magnetization orientation. Moreover, we demonstrate a set of reprogrammable Boolean gates and its logical complement at the single device level. Finally, we propose two sets of reconfigurable binary gates using combinations of two MSETs in a pull-down network. PMID:25923789
Graphical interpretation of Boolean operators for protein NMR assignments
Verdegem, Dries [Universite des Sciences et Technologies de Lille, Unite de Glycobiologie Structurale et Fonctionelle, UMR 8576 CNRS, IFR 147 (France); Dijkstra, Klaas [University of Groningen, Department of Biophysical Chemistry (Netherlands); Hanoulle, Xavier; Lippens, Guy [Universite des Sciences et Technologies de Lille, Unite de Glycobiologie Structurale et Fonctionelle, UMR 8576 CNRS, IFR 147 (France)], E-mail: guy.lippens@univ-lille1.fr
2008-09-15
We have developed a graphics based algorithm for semi-automated protein NMR assignments. Using the basic sequential triple resonance assignment strategy, the method is inspired by the Boolean operators as it applies 'AND'-, 'OR'- and 'NOT'-like operations on planes pulled out of the classical three-dimensional spectra to obtain its functionality. The method's strength lies in the continuous graphical presentation of the spectra, allowing both a semi-automatic peaklist construction and sequential assignment. We demonstrate here its general use for the case of a folded protein with a well-dispersed spectrum, but equally for a natively unfolded protein where spectral resolution is minimal.
Sampled-Data State Feedback Stabilization of Boolean Control Networks.
Liu, Yang; Cao, Jinde; Sun, Liangjie; Lu, Jianquan
2016-04-01
In this letter, we investigate the sampled-data state feedback control (SDSFC) problem of Boolean control networks (BCNs). Some necessary and sufficient conditions are obtained for the global stabilization of BCNs by SDSFC. Different from conventional state feedback controls, new phenomena observed the study of SDSFC. Based on the controllability matrix, we derive some necessary and sufficient conditions under which the trajectories of BCNs can be stabilized to a fixed point by piecewise constant control (PCC). It is proved that the global stabilization of BCNs under SDSFC is equivalent to that by PCC. Moreover, algorithms are given to construct the sampled-data state feedback controllers. Numerical examples are given to illustrate the efficiency of the obtained results.
Synchronization for the Realization-Dependent Probabilistic Boolean Networks.
Chen, Hongwei; Liang, Jinling; Lu, Jianquan; Qiu, Jianlong
2017-01-24
This paper investigates the synchronization problem for the realization-dependent probabilistic Boolean networks (PBNs) coupled unidirectionally in the drive-response configuration. The realization of the response PBN is assumed to be uniquely determined by the realization signal generated by the drive PBN at each discrete time instant. First, the drive-response PBNs are expressed in their algebraic forms based on the semitensor product method, and then, a necessary and sufficient condition is presented for the synchronization of the PBNs. Second, by resorting to a newly defined matrix operator, the reachable set from any initial state is expressed by a column vector. Consequently, an easily computable algebraic criterion is derived assuring the synchronization of the drive-response PBNs. Finally, three illustrative examples are employed to demonstrate the applicability and usefulness of the developed theoretical results.
Broad edge of chaos in strongly heterogeneous Boolean networks
Lee, Deok-Sun [Center for Complex Network Research and Department of Physics, Northeastern University, Boston, MA 02115 (United States); Rieger, Heiko [Theoretische Physik, Universitaet des Saarlandes, 66041 Saarbruecken (Germany)
2008-10-17
The dynamic stability of the Boolean networks representing a model for the gene transcriptional regulation (Kauffman model) is studied by calculating analytically and numerically the Hamming distance between two evolving configurations. This turns out to behave in a universal way close to the phase boundary only for in-degree distributions with a finite second moment. In-degree distributions of the form P{sub d}(k) {approx} k{sup -{gamma}} with 2 < {gamma} < 3, thus having a diverging second moment, lead to a slower increase of the Hamming distance when moving towards the unstable phase and to a broadening of the phase boundary for finite N with decreasing {gamma}. We conclude that the heterogeneous regulatory network connectivity facilitates the balancing between robustness and evolvability in living organisms.
Chaos synchronization of two stochastically coupled random Boolean networks
Hung, Y.-C. [Department of Physics, National Sun Yat-sen University, Kaohsiung, Taiwan (China) and Nonlinear Science Group, Department of Physics, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)]. E-mail: d9123801@student.nsysu.edu.tw; Ho, M.-C. [Nonlinear Science Group, Department of Physics, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)]. E-mail: t1603@nknucc.nknu.edu.tw; Lih, J.-S. [Department of Physics and Geoscience, National Pingtung University of Education, Pingtung, Taiwan (China); Nonlinear Science Group, Department of Physics, National Kaohsiung Normal University, Kaohsiung, Taiwan (China); Jiang, I-M. [Department of Physics, National Sun Yat-sen University, Kaohsiung, Taiwan (China); Nonlinear Science Group, Department of Physics, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)
2006-07-24
In this Letter, we study the chaos synchronization of two stochastically coupled random Boolean networks (RBNs). Instead of using the 'site-by-site and all-to-all' coupling, the coupling mechanism we consider here is that: the nth cell in a network is linked by an arbitrarily chosen cell in the other network with probability {rho}, and it possesses no links with probability 1-{rho}. The mechanism is useful to investigate the coevolution of biological species via horizontal genetic exchange. We show that the density evolution of networks can be described by two deterministic coupled polynomial maps. The complete synchronization occurs when the coupling parameter exceeds a critical value. Moreover, the reverse bifurcations in inhomogeneous condition are observed and under our discussion.
Boolean Algebra Application in Analysis of Flight Accidents
Casandra Venera BALAN
2015-12-01
Full Text Available Fault tree analysis is a deductive approach for resolving an undesired event into its causes, identifying the causes of a failure and providing a framework for a qualitative and quantitative evaluation of the top event. An alternative approach to fault tree analysis methods calculus goes to logical expressions and it is based on a graphical representation of the data structure for a logic - based binary decision diagram representation. In this analysis, such sites will be reduced to a minimal size and arranged in the sense that the variables appear in the same order in each path. An event can be defined as a statement that can be true or false. Therefore, Boolean algebra rules allow restructuring of a Fault Tree into one equivalent to it, but simpler.
Realization of Functional Complete Stateful Boolean Logic in Memristive Crossbar.
Li, Yi; Zhou, Ya-Xiong; Xu, Lei; Lu, Ke; Wang, Zhuo-Rui; Duan, Nian; Jiang, Lei; Cheng, Long; Chang, Ting-Chang; Chang, Kuan-Chang; Sun, Hua-Jun; Xue, Kan-Hao; Miao, Xiang-Shui
2016-12-21
Nonvolatile stateful logic computing in memristors is a promising paradigm with which to realize the unity of information storage and processing in the same physical location that has shown great feasibility for breaking the von Neumann bottleneck in traditional computing architecture. How to reduce the computational complexity of memristor-based logic functions is a matter of concern. Here, based on a general logic expression, we proposed a method to implement the arbitrary logic of complete 16 Boolean logic in two steps with one memristor in the crossbar architecture. A representative functional complete NAND logic is successfully experimentally demonstrated in the filamentary Ag-AgGeTe-Ta memristors to prove the validity of our method. We believe our work may promote the development of the revolutionary logic in memory architectures.
Optimization, Randomized Approximability, and Boolean Constraint Satisfaction Problems
Yamakami, Tomoyuki
2011-01-01
We give a unified treatment to optimization problems that can be expressed in the form of nonnegative-real-weighted Boolean constraint satisfaction problems. Creignou, Khanna, Sudan, Trevisan, and Williamson studied the complexity of approximating their optimal solutions whose optimality is measured by the sums of outcomes of constraints. To explore a wider range of optimization constraint satisfaction problems, following an early work of Marchetti-Spaccamela and Romano, we study the case where the optimality is measured by products of constraints' outcomes. We completely classify those problems into three categories: PO problems, NPO-hard problems, and intermediate problems that lie between the former two categories. To prove this trichotomy theorem, we analyze characteristics of nonnegative-real-weighted constraints using a variant of the notion of T-constructibility developed earlier for complex-weighted counting constraint satisfaction problems.
Identification of Boolean Networks Using Premined Network Topology Information.
Zhang, Xiaohua; Han, Huaxiang; Zhang, Weidong
2017-02-01
This brief aims to reduce the data requirement for the identification of Boolean networks (BNs) by using the premined network topology information. First, a matching table is created and used for sifting the true from the false dependences among the nodes in the BNs. Then, a dynamic extension to matching table is developed to enable the dynamic locating of matching pairs to start as soon as possible. Next, based on the pseudocommutative property of the semitensor product, a position-transform mining is carried out to further improve data utilization. Combining the above, the topology of the BNs can be premined for the subsequent identification. Examples are given to illustrate the efficiency of reducing the data requirement. Some excellent features, such as the online and parallel processing ability, are also demonstrated.
Embedding meshes in Boolean cubes by graph decomposition
Ho, C.T. (IBM Almaden Research Center, San Jose, CA (US)); Johnsson, S.L. (Dept. of Computer Science and Electrical Engineering, Yale Univ., New Haven, CT (US))
1990-04-01
This paper explores the embeddings of multidimensional meshes into minimal Boolean cubes by graph decomposition. The graph decomposition technique can be used to improve the average dilation and average congestion. The graph decomposition technique combined with some particular two-dimensional embeddings allows for minimal-expansion, dilation-two, congestion-two embeddings of about 87% of all two-dimensional meshes, with a significantly lower average dilation and congestion than by modified line compression. For three-dimensional meshes the authors show that the graph decomposition technique, together with two three-dimensional mesh embeddings presented in this paper and modified line compression, yields dilation-two embeddings of more than 96% of all three dimensional meshes contained in a 512 {times} 512 {times} 512 mesh.
Degree two approximate Boolean #CSPs with variable weights
McQuillan, Colin
2012-01-01
A counting constraint satisfaction problem (#CSP) asks for the number of ways to satisfy a given list of constraints, drawn from a fixed constraint language \\Gamma. We study how hard it is to evaluate this number approximately. There is an interesting partial classification, due to Dyer, Goldberg, Jalsenius and Richerby, of Boolean constraint languages when the degree of instances is bounded by d>=3 - every variable appears in at most d constraints - under the assumption that "pinning" is allowed as part of the instance. We study the d=2 case under the stronger assumption that "variable weights" are allowed as part of the instance. We give a dichotomy: in each case, either the #CSP is tractable, or one of two important open problems, #BIS or #PM, reduces to the #CSP.
An optimal control approach to probabilistic Boolean networks
Liu, Qiuli
2012-12-01
External control of some genes in a genetic regulatory network is useful for avoiding undesirable states associated with some diseases. For this purpose, a number of stochastic optimal control approaches have been proposed. Probabilistic Boolean networks (PBNs) as powerful tools for modeling gene regulatory systems have attracted considerable attention in systems biology. In this paper, we deal with a problem of optimal intervention in a PBN with the help of the theory of discrete time Markov decision process. Specifically, we first formulate a control model for a PBN as a first passage model for discrete time Markov decision processes and then find, using a value iteration algorithm, optimal effective treatments with the minimal expected first passage time over the space of all possible treatments. In order to demonstrate the feasibility of our approach, an example is also displayed.
Logical Attractors: a Boolean Approach to the Dynamics of Psychosis
Kupper, Z.; Hoffmann, H.
A Boolean modeling approach to attractors in the dynamics of psychosis is presented: Kinetic Logic, originating from R. Thomas, describes systems on an intermediate level between a purely verbal, qualitative description and a description using nonlinear differential equations. With this method we may model impact, feedback and temporal evolution, as well as analyze the resulting attractors. In our previous research the method has been applied to general and more specific questions in the dynamics of psychotic disorders. In this paper a model is introduced that describes different dynamical patterns of chronic psychosis in the context of vocational rehabilitation. It also shows to be useful in formulating and exploring possible treatment strategies. Finally, some of the limitations and benefits of Kinetic Logic as a modeling tool for psychology and psychiatry are discussed.
Design Intent for CAD Modeling Features Using Boolean Operations
Sonawane, Chandrakant R.; Sujit, Ghadge
2017-05-01
The objective of this paper is to add one more enhancement to design intent by adding a rule to find the intersection edges created between Boolean features. Design Intent is a core module in CAD software which is used for smart design of referencing elements to create required features. In general, the particular design intent will form a particular rule which can be utilized for specified purpose. In this paper, a design intent rule for Edge Blend feature is designed. The rule is also implemented and integrated with CAD software. The major contributions of this paper is to create a new intent design rule which picks the edges of the feature Present design intent rule is intended to pick the intersection edges of the feature, in doing so; the intent will avoid referencing to topology over referencing to hierarchy objects for greater reliability
ZKBoo: Faster Zero-Knowledge for Boolean Circuits
Giacomelli, Irene; Madsen, Jesper; Orlandi, Claudio
2016-01-01
In this paper we describe ZKBoo, a proposal for practically efficient zero-knowledge arguments especially tailored for Boolean circuits and report on a proof-of- concept implementation. As an highlight, we can generate (resp. verify) a non-interactive proof for the SHA-1 circuit in approximately 13......ms (resp. 5ms), with a proof size of 444KB. Our techniques are based on the “MPC-in-the-head” approach to zero-knowledge of Ishai et al. (IKOS), which has been successfully used to achieve significant asymp- totic improvements. Our contributions include: ◦ A thorough analysis of the different...... such that y = φ (x)” (where φ is a circuit and y a public value); ◦ A case study, where we provide explicit protocols, implementations and benchmarking of zero-knowledge protocols for the SHA-1 and SHA-256 circuits....
Peña, James R.; Pinney, James; Ayala, Perla; Desai, Tejal; Goldspink, Paul H.
2015-01-01
The Insulin like growth factor-I isoform mechano-growth factor (MGF), is expressed in the heart following myocardial infarction and encodes a unique E-domain region. To examine E-domain function, we delivered a synthetic peptide corresponding to the unique E-domain region of the human MGF (IGF-1Ec) via peptide eluting polymeric microstructures to the heart. The microstructures were made of poly (ethylene glycol) dimethacrylate hydrogel and bioengineered to be the same size as an adult cardiac myocyte (100×15×15 μm) and with a stiffness of 20 kPa. Peptide eluting microrods and empty microrods were delivered via intramuscular injection following coronary artery ligation in mice. To examine the physiologic consequences, we assessed the impact of peptide delivery on cardiac function and cardiovascular hemodynamics using pressure-volume loops and gene expression by quantitative RT-PCR. A significant decline in both systolic and diastolic function accompanied by pathologic hypertrophy occurred by 2 weeks which decompensated further by 10 weeks post-infarct in the untreated groups. Delivery of the E-domain peptide eluting microrods decreased mortality, ameliorated the decline in hemodynamics, and delayed decompensation. This was associated with the inhibition of pathologic hypertrophy despite increasing vascular impedance. Delivery of the empty microrods had limited effects on hemodynamics and while pathologic hypertrophy persisted there was a decrease in ventricular stiffness. Our data show that cardiac restricted administration of the MGF E-domain peptide using polymeric microstructures may be used to prevent adverse remodeling of the heart and improve function following myocardial infarction. PMID:25678113
Abílio Amiguinho
2005-01-01
Full Text Available The process of socio-educational territorialisation in rural contexts is the topic of this text. The theme corresponds to a challenge to address it having as main axis of discussion either the problem of social exclusion or that of local development. The reasons to locate the discussion in this last field of analysis are discussed in the first part of the text. Theoretical and political reasons are there articulated because the question is about projects whose intentions and practices call for the political both in the theoretical debate and in the choices that anticipate intervention. From research conducted for several years, I use contributions that aim at discuss and enlighten how school can be a potential locus of local development. Its identification and recognition as local institution (either because of those that work and live in it or because of those that act in the surrounding context are crucial steps to progressively constitute school as a partner for development. The promotion of the local values and roots, the reconstruction of socio-personal and local identities, the production of sociabilities and the equation and solution of shared problems were the dimensions of a socio-educative intervention, markedly globalising. This scenario, as it is argued, was also, intentionally, one of transformation and of deliberate change of school and of the administration of the educative territoires.
Zimmermann, Ralf
2014-01-01
) in an offline stage. The claimed trajectory is obtained locally by interpolating the given local subspaces considered as sample points in the Grassmann manifold. It is shown that the manifold interpolation technique is subject to certain restrictions. Moreover, it turns out that the application of computing...... under a sinusoidal pitching motion....
Boolean and advanced searching for EDGAR data on www.sec.gov
Securities and Exchange Commission — This search allows users to enter complex boolean queries to access all but the most recent day's EDGAR filings on www.sec.gov. Filings are from 1994 to present.
Fengjuan CHAI; Xiao-Shan GAO; Chunming YUAN
2008-01-01
This paper presents a characteristic set method for solving Boolean equations, which is more efficient and has better properties than the general characteristic set method. In particular, the authors give a disjoint and monic zero decomposition algorithm for the zero set of a Boolean equation system and an explicit formula for the number of solutions of a Boolean equation system. The authors also prove that a characteristic set can be computed with a polynomial number of multiplications of Boolean polynomials in terms of the number of variables. As experiments, the proposed method is used to solve equations from cryptanalysis of a class of stream ciphers based on nonlinear filter generators. Extensive experiments show that the method is quite effective.
Design of Probabilistic Boolean Networks Based on Network Structure and Steady-State Probabilities.
Kobayashi, Koichi; Hiraishi, Kunihiko
2016-06-06
In this brief, we consider the problem of finding a probabilistic Boolean network (PBN) based on a network structure and desired steady-state properties. In systems biology and synthetic biology, such problems are important as an inverse problem. Using a matrix-based representation of PBNs, a solution method for this problem is proposed. The problem of finding a BN has been studied so far. In the problem of finding a PBN, we must calculate not only the Boolean functions, but also the probabilities of selecting a Boolean function and the number of candidates of the Boolean functions. Hence, the problem of finding a PBN is more difficult than that of finding a BN. The effectiveness of the proposed method is presented by numerical examples.
Automatic test pattern generation for logic circuits using the Boolean tree
Jeong Taegwon.
1991-01-01
The goal of this study was to develop an algorithm that can generate test patterns for combinational circuits and sequential logic circuits automatically. The new proposed algorithm generates a test pattern by using a special tree called a modified Boolean tree. In this algorithm, the construction of a modified Boolean tree is the most time-consuming step. Following the construction of a modified Boolean tree, a test pattern can be found by simply assigning a logic value 1 for even primary inputs and a logic value 0 for odd primary inputs of the constructed modified Boolean tree. The algorithm is applied to several benchmark circuits. The results showed the following: (1) for combinational circuits, the algorithm can generate test patterns 10-15% faster than the FAN algorithm, which is known as one of the most efficient algorithms to-date; (2) for sequential circuits, the algorithm shows more fault coverage than the nine valued algorithm.
Model construction from orthographic views as Pseudo Boolean constraint satisfaction problem
Itoh, Kiyoshi; Suzuki, Shigemich [Sophia Univ., Tokyo (Japan)
1996-12-31
A surface model representation of a solid can be constructed in straightforward fashion from a set of three orthographic views. The surface model may include ghost vertexes, ghost edges and ghost faces. The authors` project, called Sophia-Alsovig, treats the problem for obtaining valid combination of surfaces and edges as Pseudo Boolean constraint satisfaction problem (CSP). It can remove such ghosts. As CSP, Sophia-Alsovig adopts a set of units consisting of edges and surfaces, a set of Boolean labels, and a set of constraints with the formulation of a collection of topological/geometrical rules for edges and surfaces by Pseudo Boolean equations. Sophia-Alsovig obtains solutions by Pseudo Boolean Nonlinear Programming.
Sensitivity analysis of efficient solution in vector MINMAX boolean programming problem
Vladimir A. Emelichev
2002-11-01
Full Text Available We consider a multiple criterion Boolean programming problem with MINMAX partial criteria. The extreme level of independent perturbations of partial criteria parameters such that efficient (Pareto optimal solution preserves optimality was obtained.
A new approach for global controllability of higher order Boolean control network.
Chen, Hao; Sun, Jitao
2013-03-01
Using the semi-tensor product, the global control problem of the higher order Boolean control network with avoiding set is considered. First, the number of different control sequences that drive the higher order Boolean control network from the initial state to the destination state while avoiding undesirable set is provided. Then, the definition of global controllability of higher order Boolean control network is given. Third, by using the classical theory of nonnegative matrices, the necessary and sufficient condition for the global controllability of higher order Boolean control network with avoiding set is presented. Furthermore, a sufficient condition for k fixed-time global controllability of the system is also obtained. At last, an example is given to illustrate the main results.
A SAT-based algorithm for finding attractors in synchronous Boolean networks.
Dubrova, Elena; Teslenko, Maxim
2011-01-01
This paper addresses the problem of finding attractors in synchronous Boolean networks. The existing Boolean decision diagram-based algorithms have limited capacity due to the excessive memory requirements of decision diagrams. The simulation-based algorithms can be applied to larger networks, however, they are incomplete. We present an algorithm, which uses a SAT-based bounded model checking to find all attractors in a Boolean network. The efficiency of the presented algorithm is evaluated by analyzing seven networks models of real biological processes, as well as 150,000 randomly generated Boolean networks of sizes between 100 and 7,000. The results show that our approach has a potential to handle an order of magnitude larger models than currently possible.
Xu, Hua; Jiang, Xiaoshan; Shen, Ke; Fischer, Christopher C; Wedegaertner, Philip B
2014-07-01
The G protein-coupled receptor (GPCR) kinases (GRKs) phosphorylate activated GPCRs at the plasma membrane (PM). Here GRK5/GRK4 chimeras and point mutations in GRK5 identify a short sequence within the regulator of G protein signaling (RGS) domain in GRK5 that is critical for GRK5 PM localization. This region of the RGS domain of GRK5 coincides with a region of GRK6 and GRK1 shown to form a hydrophobic dimeric interface (HDI) in crystal structures. Coimmunoprecipitation (coIP) and acceptor photobleaching fluorescence resonance energy transfer assays show that expressed GRK5 self-associates in cells, whereas GRK5-M165E/F166E (GRK5-EE), containing hydrophilic mutations in the HDI region of the RGS domain, displays greatly decreased coIP interactions. Both forcing dimerization of GRK5-EE, via fusion to leucine zipper motifs, and appending an extra C-terminal membrane-binding region to GRK5-EE (GRK5-EE-CT) recover PM localization. In addition, GRK5-EE displays a decreased ability to inhibit PAR1-induced calcium release compared with GRK5 wild type (wt). In contrast, PM-localized GRK5-EE-CaaX (appending a C-terminal prenylation and polybasic motif from K-ras) or GRK5-EE-CT shows comparable ability to GRK5 wt to inhibit PAR1-induced calcium release. The results suggest a novel model in which GRK5 dimerization is important for its plasma membrane localization and function. © 2014 Xu, Jiang, et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).
On $2k$-Variable Symmetric Boolean Functions with Maximum Algebraic Immunity $k$
Wang, Hui; Li, Yuan; Kan, Haibin
2011-01-01
Given a positive even integer $n$, it is found that the weight distribution of any $n$-variable symmetric Boolean function with maximum algebraic immunity $\\frac{n}{2}$ is determined by the binary expansion of $n$. Based on that, all $n$-variable symmetric Boolean functions with maximum algebraic immunity are constructed. The amount is $(2\\wt(n)+1)2^{\\lfloor \\log_2 n \\rfloor}$.
Multiple fault analysis in synchronous sequential circuits by means of vector Boolean difference
Goldstein, L.H.
1977-01-01
The Boolean difference is an elegant mathematical concept which has found significant application in the study of single faults of a stuck-at nature in combinational logic circuits. Recently, several authors have extended this technique to the analysis of multiple faults in combinational circuits. The concept of vector Boolean difference is further extended to the analysis of multiple stuck-at faults in synchronous sequential circuits.
Interpolation of the discrete logarithm in a finite field of characteristic two by Boolean functions
Brandstaetter, Nina; Lange, Tanja; Winterhof, Arne
2005-01-01
We obtain bounds on degree, weight, and the maximal Fourier coefficient of Boolean functions interpolating the discrete logarithm in finite fields of characteristic two. These bounds complement earlier results for finite fields of odd characteristic.......We obtain bounds on degree, weight, and the maximal Fourier coefficient of Boolean functions interpolating the discrete logarithm in finite fields of characteristic two. These bounds complement earlier results for finite fields of odd characteristic....
Affine Equivalence of Quartic Monomial Rotation Symmetric Boolean Functions in Prime Power Dimension
2015-01-27
ANF. This representation of f (not unique, since one can choose any representative in Gn(x1xi2 . . . xil)) is called the short algebraic normal form ...Affine Equivalence of Quartic Monomial Rotation Symmetric Boolean Functions in Prime Power Dimension Pantelimon Stănică Naval Postgraduate School...Boolean functions, circulant matrices, affine equivalence , permutations, prime powers. Mathematics Subject Classification [2010]: 94A60, 94C10, 06E30 1
Feedback control and output feedback control for the stabilisation of switched Boolean networks
Li, Fangfei; Yu, Zhaoxu
2016-02-01
This paper presents the feedback control and output feedback control for the stabilisation of switched Boolean network. A necessary condition for the existence of a state feedback controller for the stabilisation of switched Boolean networks under arbitrary switching signal is derived first, and constructive procedures for feedback control and output feedback control design are provided. An example is introduced to show the effectiveness of this paper.
Totally Optimal Decision Trees for Monotone Boolean Functions with at Most Five Variables
Chikalov, Igor
2013-01-01
In this paper, we present the empirical results for relationships between time (depth) and space (number of nodes) complexity of decision trees computing monotone Boolean functions, with at most five variables. We use Dagger (a tool for optimization of decision trees and decision rules) to conduct experiments. We show that, for each monotone Boolean function with at most five variables, there exists a totally optimal decision tree which is optimal with respect to both depth and number of nodes.
CONSTRUCTION OF GENERAL SUBSUMPTIVE SOLUTIONS OF BOOLEAN EQUATIONS VIA COMPLETE-SUM DERIVATION
Ali Muhammad Ali Rushdi
2014-01-01
Full Text Available Boolean-equation solving permeates many diverse areas of modern science. To solve a system of Boolean equations, one usually combines them into an equivalent single Boolean equation whose set of solutions is exactly the same as that of the original system of equations. One of the general classes of solutions for Boolean equations is the subsumptive general solution, in which each variable is expressed as an interval decided by a double inequality in terms of the succeeding variables. The solution validity depends on the satisfaction of a required consistency condition. In this study, we introduce a novel method (henceforth called the CS method for producing subsumptive Boolean-equation solutions based on deriving the complete sum of the pertinent Boolean function . The complete sum is a disjunction of all prime implicants of and nothing else. It explicitly shows all information about in the most compact form. We demonstrate the proposed CS solutions in terms of four examples, covering Boolean algebras of different sizes and using two prominent methods for deriving . Occasionally, the consistency condition results in a collapse of the underlying Boolean algebra into a smaller subalgebra. We also illustrate how an expansion tree (typically reduced to an acyclic graph can be used to deduce a complete list of all particular solutions from the subsumptive solution. The present CS method yields correct solutions, since it fits into the frame of the most general subsumptive solution. Among competing subsumptive methods, the CS method strikes a reasonable tradeoff between the conflicting requirements of less computational cost and more compact form for the solution obtained. In fact, it is the second best known method from both criteria of efficiency and compactness of solution.
In silico design and in vivo implementation of yeast gene Boolean gates
2014-01-01
In our previous computational work, we showed that gene digital circuits can be automatically designed in an electronic fashion. This demands, first, a conversion of the truth table into Boolean formulas with the Karnaugh map method and, then, the translation of the Boolean formulas into circuit schemes organized into layers of Boolean gates and Pools of signal carriers. In our framework, gene digital circuits that take up to three different input signals (chemicals) arise from the composition of three kinds of basic Boolean gates, namely YES, NOT, and AND. Here we present a library of YES, NOT, and AND gates realized via plasmidic DNA integration into the yeast genome. Boolean behavior is reproduced via the transcriptional control of a synthetic bipartite promoter that contains sequences of the yeast VPH1 and minimal CYC1 promoters together with operator binding sites for bacterial (i.e. orthogonal) repressor proteins. Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required. Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits. As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library. PMID:24485181
In silico design and in vivo implementation of yeast gene Boolean gates.
Marchisio, Mario A
2014-01-01
In our previous computational work, we showed that gene digital circuits can be automatically designed in an electronic fashion. This demands, first, a conversion of the truth table into Boolean formulas with the Karnaugh map method and, then, the translation of the Boolean formulas into circuit schemes organized into layers of Boolean gates and Pools of signal carriers. In our framework, gene digital circuits that take up to three different input signals (chemicals) arise from the composition of three kinds of basic Boolean gates, namely YES, NOT, and AND. Here we present a library of YES, NOT, and AND gates realized via plasmidic DNA integration into the yeast genome. Boolean behavior is reproduced via the transcriptional control of a synthetic bipartite promoter that contains sequences of the yeast VPH1 and minimal CYC1 promoters together with operator binding sites for bacterial (i.e. orthogonal) repressor proteins. Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required. Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits. As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.
An attractor-based complexity measurement for Boolean recurrent neural networks.
Cabessa, Jérémie; Villa, Alessandro E P
2014-01-01
We provide a novel refined attractor-based complexity measurement for Boolean recurrent neural networks that represents an assessment of their computational power in terms of the significance of their attractor dynamics. This complexity measurement is achieved by first proving a computational equivalence between Boolean recurrent neural networks and some specific class of ω-automata, and then translating the most refined classification of ω-automata to the Boolean neural network context. As a result, a hierarchical classification of Boolean neural networks based on their attractive dynamics is obtained, thus providing a novel refined attractor-based complexity measurement for Boolean recurrent neural networks. These results provide new theoretical insights to the computational and dynamical capabilities of neural networks according to their attractive potentialities. An application of our findings is illustrated by the analysis of the dynamics of a simplified model of the basal ganglia-thalamocortical network simulated by a Boolean recurrent neural network. This example shows the significance of measuring network complexity, and how our results bear new founding elements for the understanding of the complexity of real brain circuits.
An attractor-based complexity measurement for Boolean recurrent neural networks.
Jérémie Cabessa
Full Text Available We provide a novel refined attractor-based complexity measurement for Boolean recurrent neural networks that represents an assessment of their computational power in terms of the significance of their attractor dynamics. This complexity measurement is achieved by first proving a computational equivalence between Boolean recurrent neural networks and some specific class of ω-automata, and then translating the most refined classification of ω-automata to the Boolean neural network context. As a result, a hierarchical classification of Boolean neural networks based on their attractive dynamics is obtained, thus providing a novel refined attractor-based complexity measurement for Boolean recurrent neural networks. These results provide new theoretical insights to the computational and dynamical capabilities of neural networks according to their attractive potentialities. An application of our findings is illustrated by the analysis of the dynamics of a simplified model of the basal ganglia-thalamocortical network simulated by a Boolean recurrent neural network. This example shows the significance of measuring network complexity, and how our results bear new founding elements for the understanding of the complexity of real brain circuits.
Komorowski, P
1999-01-01
Time Domain Reflectometry (TDR) is one of the most powerful methods used to analyze the integrity of the signal propagating in a transmission line. The method is based on the principle that the wave propagating in the line is reflected at the locations where the impedance of the line changes. The fault points, joints, branches, junctions, abrupt cross-section changes, etc., cause such reflections. The reflectometry technique involves the excitation of the circuit under test with either a fast edge step function or a well-defined impulse confined in time and frequency domains, and thereafter detection of the amplitude and time of the reflections. Both variants of the method were successfully applied to localize open circuit faults in the voltage tap connections, pressure transducers, and temperature sensing carbon gages circuits of the LHC String Dipole Magnet MB2 and Short Straight Section Quadrupole.
Ebadi, H.; Saeedian, M.; Ausloos, M.; Jafari, G. R.
2016-11-01
The Boolean network is one successful model to investigate discrete complex systems such as the gene interacting phenomenon. The dynamics of a Boolean network, controlled with Boolean functions, is usually considered to be a Markovian (memory-less) process. However, both self-organizing features of biological phenomena and their intelligent nature should raise some doubt about ignoring the history of their time evolution. Here, we extend the Boolean network Markovian approach: we involve the effect of memory on the dynamics. This can be explored by modifying Boolean functions into non-Markovian functions, for example, by investigating the usual non-Markovian threshold function —one of the most applied Boolean functions. By applying the non-Markovian threshold function on the dynamical process of the yeast cell cycle network, we discover a power-law-like memory with a more robust dynamics than the Markovian dynamics.
Metzger Kelsey J
2010-05-01
Full Text Available Abstract Background CC chemokine receptor proteins (CCR1 through CCR10 are seven-transmembrane G-protein coupled receptors whose signaling pathways are known for their important roles coordinating immune system responses through targeted trafficking of white blood cells. In addition, some of these receptors have been identified as fusion proteins for viral pathogens: for example, HIV-1 strains utilize CCR5, CCR2 and CCR3 proteins to obtain cellular entry in humans. The extracellular domains of these receptor proteins are involved in ligand-binding specificity as well as pathogen recognition interactions. In mammals, the majority of chemokine receptor genes are clustered together; in humans, seven of the ten genes are clustered in the 3p21-24 chromosome region. Gene conversion events, or exchange of DNA sequence between genes, have been reported in chemokine receptor paralogs in various mammalian lineages, especially between the cytogenetically closely located pairs CCR2/5 and CCR1/3. Datasets of mammalian orthologs for each gene were analyzed separately to minimize the potential confounding impact of analyzing highly similar sequences resulting from gene conversion events. Molecular evolution approaches and the software package Phylogenetic Analyses by Maximum Likelihood (PAML were utilized to investigate the signature of selection that has acted on the mammalian CC chemokine receptor (CCR gene family. The results of neutral vs. adaptive evolution (positive selection hypothesis testing using Site Models are reported. In general, positive selection is defined by a ratio of nonsynonymous/synonymous nucleotide changes (dN/dS, or ω >1. Results Of the ten mammalian CC motif chemokine receptor sequence datasets analyzed, only CCR2 and CCR3 contain amino acid codon sites that exhibit evidence of positive selection using site based hypothesis testing in PAML. Nineteen of the twenty codon sites putatively indentified as likely to be under positive
Poggio, Sebastian; Takacs, Constantin N; Vollmer, Waldemar; Jacobs-Wagner, Christine
2010-07-01
During division of Gram-negative bacteria, invagination of the cytoplasmic membrane and inward growth of the peptidoglycan (PG) are followed by the cleavage of connective septal PG to allow cell separation. This PG splitting process requires temporal and spatial regulation of cell wall hydrolases. In Escherichia coli, LytM factors play an important role in PG splitting. Here we identify and characterize a member of this family (DipM) in Caulobacter crescentus. Unlike its E. coli counterparts, DipM is essential for viability under fast-growth conditions. Under slow-growth conditions, the DeltadipM mutant displays severe defects in cell division and FtsZ constriction. Consistent with its function in division, DipM colocalizes with the FtsZ ring during the cell cycle. Mutagenesis suggests that the LytM domain of DipM is essential for protein function, despite being non-canonical. DipM also carries two tandems of the PG-binding LysM domain that are sufficient for FtsZ ring localization. Localization and fluorescence recovery after photobleaching microscopy experiments suggest that DipM localization is mediated, at least in part, by the ability of the LysM tandems to distinguish septal, multilayered PG from non-septal, monolayered PG.