Deeper sparsely nets are size-optimal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beiu, V.; Makaruk, H.E.

1997-12-01

The starting points of this paper are two size-optimal solutions: (i) one for implementing arbitrary Boolean functions (Horne, 1994); and (ii) another one for implementing certain sub-classes of Boolean functions (Red`kin, 1970). Because VLSI implementations do not cope well with highly interconnected nets--the area of a chip grows with the cube of the fan-in (Hammerstrom, 1988)--this paper will analyze the influence of limited fan-in on the size optimality for the two solutions mentioned. First, the authors will extend a result from Horne and Hush (1994) valid for fan-in {Delta} = 2 to arbitrary fan-in. Second, they will prove that size-optimalmore » solutions are obtained for small constant fan-in for both constructions, while relative minimum size solutions can be obtained for fan-ins strictly lower than linear. These results are in agreement with similar ones proving that for small constant fan-ins ({Delta} = 6...9) there exist VLSI-optimal (i.e. minimizing AT{sup 2}) solutions (Beiu, 1997a), while there are similar small constants relating to the capacity of processing information (Miller 1956).« less

Adaptation and survivors in a random Boolean network.

PubMed

Nakamura, Ikuo

2002-04-01

We introduce the competitive agent with imitation strategy in a random Boolean network, in which the agent plays a competitive game that rewards those in minority. After a long time interval, the worst performer changes its strategy to the one of the best and the process is repeated. The network, initially in a chaotic state, evolves to an intermittent state and finally reaches a frozen state. Time series of survived species (whose strategies are imitated by other agents) in the system depend on the connectivity of each agent. In a system with various connectivity groups, the low connectivity groups win the minority game over the high connectivity groups. We also compared the result with mutation strategy system.

Modeling and implementation of concurrent logic controllers with use of Petri nets, LSMs, and sequent calculus

NASA Astrophysics Data System (ADS)

Tkacz, J.; Bukowiec, A.; Doligalski, M.

2017-08-01

The paper presentes the method of modeling and implementation of concurrent controllers. Concurrent controllers are specified by Petri nets. Then Petri nets are decomposed using symbolic deduction method of analysis. Formal methods like sequent calculus system with considered elements of Thelen's algorithm have been used here. As a result, linked state machines (LSMs) are received. Each FSM is implemented using methods of structural decomposition during process of logic synthesis. The method of multiple encoding of microinstruction has been applied. It leads to decreased number of Boolean function realized by combinational part of FSM. The additional decoder could be implemented with the use of memory blocks.

Random Boolean networks for autoassociative memory: Optimization and sequential learning

NASA Astrophysics Data System (ADS)

Sherrington, D.; Wong, K. Y. M.

Conventional neural networks are based on synaptic storage of information, even when the neural states are discrete and bounded. In general, the set of potential local operations is much greater. Here we discuss some aspects of the properties of networks of binary neurons with more general Boolean functions controlling the local dynamics. Two specific aspects are emphasised; (i) optimization in the presence of noise and (ii) a simple model for short-term memory exhibiting primacy and recency in the recall of sequentially taught patterns.

Fisher information at the edge of chaos in random Boolean networks.

PubMed

Wang, X Rosalind; Lizier, Joseph T; Prokopenko, Mikhail

2011-01-01

We study the order-chaos phase transition in random Boolean networks (RBNs), which have been used as models of gene regulatory networks. In particular we seek to characterize the phase diagram in information-theoretic terms, focusing on the effect of the control parameters (activity level and connectivity). Fisher information, which measures how much system dynamics can reveal about the control parameters, offers a natural interpretation of the phase diagram in RBNs. We report that this measure is maximized near the order-chaos phase transitions in RBNs, since this is the region where the system is most sensitive to its parameters. Furthermore, we use this study of RBNs to clarify the relationship between Shannon and Fisher information measures.

Investigating Cell Criticality

NASA Astrophysics Data System (ADS)

Serra, R.; Villani, M.; Damiani, C.; Graudenzi, A.; Ingrami, P.; Colacci, A.

Random Boolean networks provide a way to give a precise meaning to the notion that living beings are in a critical state. Some phenomena which are observed in real biological systems (distribution of "avalanches" in gene knock-out experiments) can be modeled using random Boolean networks, and the results can be analytically proven to depend upon the Derrida parameter, which also determines whether the network is critical. By comparing observed and simulated data one can then draw inferences about the criticality of biological cells, although with some care because of the limited number of experimental observations. The relationship between the criticality of a single network and that of a set of interacting networks, which simulate a tissue or a bacterial colony, is also analyzed by computer simulations.

The computational core and fixed point organization in Boolean networks

NASA Astrophysics Data System (ADS)

Correale, L.; Leone, M.; Pagnani, A.; Weigt, M.; Zecchina, R.

2006-03-01

In this paper, we analyse large random Boolean networks in terms of a constraint satisfaction problem. We first develop an algorithmic scheme which allows us to prune simple logical cascades and underdetermined variables, returning thereby the computational core of the network. Second, we apply the cavity method to analyse the number and organization of fixed points. We find in particular a phase transition between an easy and a complex regulatory phase, the latter being characterized by the existence of an exponential number of macroscopically separated fixed point clusters. The different techniques developed are reinterpreted as algorithms for the analysis of single Boolean networks, and they are applied in the analysis of and in silico experiments on the gene regulatory networks of baker's yeast (Saccharomyces cerevisiae) and the segment-polarity genes of the fruitfly Drosophila melanogaster.

Understanding genetic regulatory networks

NASA Astrophysics Data System (ADS)

Kauffman, Stuart

2003-04-01

Random Boolean networks (RBM) were introduced about 35 years ago as first crude models of genetic regulatory networks. RBNs are comprised of N on-off genes, connected by a randomly assigned regulatory wiring diagram where each gene has K inputs, and each gene is controlled by a randomly assigned Boolean function. This procedure samples at random from the ensemble of all possible NK Boolean networks. The central ideas are to study the typical, or generic properties of this ensemble, and see 1) whether characteristic differences appear as K and biases in Boolean functions are introducted, and 2) whether a subclass of this ensemble has properties matching real cells. Such networks behave in an ordered or a chaotic regime, with a phase transition, "the edge of chaos" between the two regimes. Networks with continuous variables exhibit the same two regimes. Substantial evidence suggests that real cells are in the ordered regime. A key concept is that of an attractor. This is a reentrant trajectory of states of the network, called a state cycle. The central biological interpretation is that cell types are attractors. A number of properties differentiate the ordered and chaotic regimes. These include the size and number of attractors, the existence in the ordered regime of a percolating "sea" of genes frozen in the on or off state, with a remainder of isolated twinkling islands of genes, a power law distribution of avalanches of gene activity changes following perturbation to a single gene in the ordered regime versus a similar power law distribution plus a spike of enormous avalanches of gene changes in the chaotic regime, and the existence of branching pathway of "differentiation" between attractors induced by perturbations in the ordered regime. Noise is serious issue, since noise disrupts attractors. But numerical evidence suggests that attractors can be made very stable to noise, and meanwhile, metaplasias may be a biological manifestation of noise. As we learn more about the wiring diagram and constraints on rules controlling real genes, we can build refined ensembles reflecting these properties, study the generic properties of the refined ensembles, and hope to gain insight into the dynamics of real cells.

The value of less connected agents in Boolean networks

NASA Astrophysics Data System (ADS)

Epstein, Daniel; Bazzan, Ana L. C.

2013-11-01

In multiagent systems, agents often face binary decisions where one seeks to take either the minority or the majority side. Examples are minority and congestion games in general, i.e., situations that require coordination among the agents in order to depict efficient decisions. In minority games such as the El Farol Bar Problem, previous works have shown that agents may reach appropriate levels of coordination, mostly by looking at the history of past decisions. Not many works consider any kind of structure of the social network, i.e., how agents are connected. Moreover, when structure is indeed considered, it assumes some kind of random network with a given, fixed connectivity degree. The present paper departs from the conventional approach in some ways. First, it considers more realistic network topologies, based on preferential attachments. This is especially useful in social networks. Second, the formalism of random Boolean networks is used to help agents to make decisions given their attachments (for example acquaintances). This is coupled with a reinforcement learning mechanism that allows agents to select strategies that are locally and globally efficient. Third, we use agent-based modeling and simulation, a microscopic approach, which allows us to draw conclusions about individuals and/or classes of individuals. Finally, for the sake of illustration we use two different scenarios, namely the El Farol Bar Problem and a binary route choice scenario. With this approach we target systems that adapt dynamically to changes in the environment, including other adaptive decision-makers. Our results using preferential attachments and random Boolean networks are threefold. First we show that an efficient equilibrium can be achieved, provided agents do experimentation. Second, microscopic analysis show that influential agents tend to consider few inputs in their Boolean functions. Third, we have also conducted measurements related to network clustering and centrality that help to see how agents are organized.

Tracking perturbations in Boolean networks with spectral methods

NASA Astrophysics Data System (ADS)

Kesseli, Juha; Rämö, Pauli; Yli-Harja, Olli

2005-08-01

In this paper we present a method for predicting the spread of perturbations in Boolean networks. The method is applicable to networks that have no regular topology. The prediction of perturbations can be performed easily by using a presented result which enables the efficient computation of the required iterative formulas. This result is based on abstract Fourier transform of the functions in the network. In this paper the method is applied to show the spread of perturbations in networks containing a distribution of functions found from biological data. The advances in the study of the spread of perturbations can directly be applied to enable ways of quantifying chaos in Boolean networks. Derrida plots over an arbitrary number of time steps can be computed and thus distributions of functions compared with each other with respect to the amount of order they create in random networks.

The Event Based Language and Its Multiple Processor Implementations.

DTIC Science & Technology

1980-01-01

10 6.1 "Recursive" Linear Fibonacci ................................................ 105 6.2 The Readers Writers Problem...kinds. Examples of such systems are: C.mmp [Wu-72], Pluribus [He-73], Data Flow [ De -75], the boolean n-cube parallel machine [Su-77], and the MuNet [Wa...concurrency within programs; therefore, we hate concentrated on two types of systems which seem suitable: a processor network, and a data flow processor [ De -77

A versatile petri net based architecture for modeling and simulation of complex biological processes.

PubMed

Nagasaki, Masao; Doi, Atsushi; Matsuno, Hiroshi; Miyano, Satoru

2004-01-01

The research on modeling and simulation of complex biological systems is getting more important in Systems Biology. In this respect, we have developed Hybrid Function Petri net (HFPN) that was newly developed from existing Petri net because of their intuitive graphical representation and their capabilities for mathematical analyses. However, in the process of modeling metabolic, gene regulatory or signal transduction pathways with the architecture, we have realized three extensions of HFPN, (i) an entity should be extended to contain more than one value, (ii) an entity should be extended to handle other primitive types, e.g. boolean, string, (iii) an entity should be extended to handle more advanced type called object that consists of variables and methods, are necessary for modeling biological systems with Petri net based architecture. To deal with it, we define a new enhanced Petri net called hybrid functional Petri net with extension (HFPNe). To demonstrate the effectiveness of the enhancements, we model and simulate with HFPNe four biological processes that are diffcult to represent with the previous architecture HFPN.

Nonvolatile reconfigurable sequential logic in a HfO2 resistive random access memory array.

PubMed

Zhou, Ya-Xiong; Li, Yi; Su, Yu-Ting; Wang, Zhuo-Rui; Shih, Ling-Yi; Chang, Ting-Chang; Chang, Kuan-Chang; Long, Shi-Bing; Sze, Simon M; Miao, Xiang-Shui

2017-05-25

Resistive random access memory (RRAM) based reconfigurable logic provides a temporal programmable dimension to realize Boolean logic functions and is regarded as a promising route to build non-von Neumann computing architecture. In this work, a reconfigurable operation method is proposed to perform nonvolatile sequential logic in a HfO 2 -based RRAM array. Eight kinds of Boolean logic functions can be implemented within the same hardware fabrics. During the logic computing processes, the RRAM devices in an array are flexibly configured in a bipolar or complementary structure. The validity was demonstrated by experimentally implemented NAND and XOR logic functions and a theoretically designed 1-bit full adder. With the trade-off between temporal and spatial computing complexity, our method makes better use of limited computing resources, thus provides an attractive scheme for the construction of logic-in-memory systems.

Prescribed burning impact on forest soil properties--a Fuzzy Boolean Nets approach.

PubMed

Castro, Ana C Meira; Paulo Carvalho, Joao; Ribeiro, S

2011-02-01

The Portuguese northern forests are often and severely affected by wildfires during the Summer season. These occurrences significantly affect and negatively impact all ecosystems, namely soil, fauna and flora. In order to reduce the occurrences of natural wildfires, some measures to control the availability of fuel mass are regularly implemented. Those preventive actions concern mainly prescribed burnings and vegetation pruning. This work reports on the impact of a prescribed burning on several forest soil properties, namely pH, soil moisture, organic matter content and iron content, by monitoring the soil self-recovery capabilities during a one year span. The experiments were carried out in soil cover over a natural site of Andaluzitic schist, in Gramelas, Caminha, Portugal, which was kept intact from prescribed burnings during a period of four years. Soil samples were collected from five plots at three different layers (0-3, 3-6 and 6-18) 1 day before prescribed fire and at regular intervals after the prescribed fire. This paper presents an approach where Fuzzy Boolean Nets (FBN) and Fuzzy reasoning are used to extract qualitative knowledge regarding the effect of prescribed fire burning on soil properties. FBN were chosen due to the scarcity on available quantitative data. The results showed that soil properties were affected by prescribed burning practice and were unable to recover their initial values after one year. Copyright © 2010 Elsevier Inc. All rights reserved.

Information processing in dendrites I. Input pattern generalisation.

PubMed

Gurney, K N

2001-10-01

In this paper and its companion, we address the question as to whether there are any general principles underlying information processing in the dendritic trees of biological neurons. In order to address this question, we make two assumptions. First, the key architectural feature of dendrites responsible for many of their information processing abilities is the existence of independent sub-units performing local non-linear processing. Second, any general functional principles operate at a level of abstraction in which neurons are modelled by Boolean functions. To accommodate these assumptions, we therefore define a Boolean model neuron-the multi-cube unit (MCU)-which instantiates the notion of the discrete functional sub-unit. We then use this model unit to explore two aspects of neural functionality: generalisation (in this paper) and processing complexity (in its companion). Generalisation is dealt with from a geometric viewpoint and is quantified using a new metric-the set of order parameters. These parameters are computed for threshold logic units (TLUs), a class of random Boolean functions, and MCUs. Our interpretation of the order parameters is consistent with our knowledge of generalisation in TLUs and with the lack of generalisation in randomly chosen functions. Crucially, the order parameters for MCUs imply that these functions possess a range of generalisation behaviour. We argue that this supports the general thesis that dendrites facilitate input pattern generalisation despite any local non-linear processing within functionally isolated sub-units.

Damage spreading in spatial and small-world random Boolean networks

NASA Astrophysics Data System (ADS)

Lu, Qiming; Teuscher, Christof

2014-02-01

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 as 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 nonrandom 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 Hamming distance at very low connectivities (K¯≪1) and that the critical connectivity of stability Ks changes compared to random networks. At higher K¯, this scaling remains unchanged. We also show that the Hamming distance 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 arguments for small-world networks are obtained with respect to the system sizes and strength of spatially local connections. 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.

Small fan-in is beautiful

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beiu, V.; Makaruk, H.E.

1997-09-01

The starting points of this paper are two size-optimal solutions: (1) one for implementing arbitrary Boolean functions; and (2) another one for implementing certain subclasses of Boolean functions. Because VLSI implementations do not cope well with highly interconnected nets -- the area of a chip grows with the cube of the fan-in -- this paper will analyze the influence of limited fan-in on the size optimality for the two solutions mentioned. First, the authors will extend a result from Horne and Hush valid for fan-in {Delta} = 2 to arbitrary fan-in. Second, they will prove that size-optimal solutions are obtainedmore » for small constant fan-ins for both constructions, while relative minimum size solutions can be obtained for fan-ins strictly lower that linear. These results are in agreement with similar ones proving that for small constant fan-ins ({Delta} = 6...9) there exist VLSI-optimal (i.e., minimizing AT{sup 2}) solutions, while there are similar small constants relating to the capacity of processing information.« less

Network dynamics and systems biology

NASA Astrophysics Data System (ADS)

Norrell, Johannes A.

The physics of complex systems has grown considerably as a field in recent decades, largely due to improved computational technology and increased availability of systems level data. One area in which physics is of growing relevance is molecular biology. A new field, systems biology, investigates features of biological systems as a whole, a strategy of particular importance for understanding emergent properties that result from a complex network of interactions. Due to the complicated nature of the systems under study, the physics of complex systems has a significant role to play in elucidating the collective behavior. In this dissertation, we explore three problems in the physics of complex systems, motivated in part by systems biology. The first of these concerns the applicability of Boolean models as an approximation of continuous systems. Studies of gene regulatory networks have employed both continuous and Boolean models to analyze the system dynamics, and the two have been found produce similar results in the cases analyzed. We ask whether or not Boolean models can generically reproduce the qualitative attractor dynamics of networks of continuously valued elements. Using a combination of analytical techniques and numerical simulations, we find that continuous networks exhibit two effects---an asymmetry between on and off states, and a decaying memory of events in each element's inputs---that are absent from synchronously updated Boolean models. We show that in simple loops these effects produce exactly the attractors that one would predict with an analysis of the stability of Boolean attractors, but in slightly more complicated topologies, they can destabilize solutions that are stable in the Boolean approximation, and can stabilize new attractors. Second, we investigate ensembles of large, random networks. Of particular interest is the transition between ordered and disordered dynamics, which is well characterized in Boolean systems. Networks at the transition point, called critical, exhibit many of the features of regulatory networks, and recent studies suggest that some specific regulatory networks are indeed near-critical. We ask whether certain statistical measures of the ensemble behavior of large continuous networks are reproduced by Boolean models. We find that, in spite of the lack of correspondence between attractors observed in smaller systems, the statistical characterization given by the continuous and Boolean models show close agreement, and the transition between order and disorder known in Boolean systems can occur in continuous systems as well. One effect that is not present in Boolean systems, the failure of information to propagate down chains of elements of arbitrary length, is present in a class of continuous networks. In these systems, a modified Boolean theory that takes into account the collective effect of propagation failure on chains throughout the network gives a good description of the observed behavior. We find that propagation failure pushes the system toward greater order, resulting in a partial or complete suppression of the disordered phase. Finally, we explore a dynamical process of direct biological relevance: asymmetric cell division in A. thaliana. The long term goal is to develop a model for the process that accurately accounts for both wild type and mutant behavior. To contribute to this endeavor, we use confocal microscopy to image roots in a SHORT-ROOT inducible mutant. We compute correlation functions between the locations of asymmetrically divided cells, and we construct stochastic models based on a few simple assumptions that accurately predict the non-zero correlations. Our result shows that intracellular processes alone cannot be responsible for the observed divisions, and that an intercell signaling mechanism could account for the measured correlations.

Using Common Table Expressions to Build a Scalable Boolean Query Generator for Clinical Data Warehouses

PubMed Central

Harris, Daniel R.; Henderson, Darren W.; Kavuluru, Ramakanth; Stromberg, Arnold J.; Johnson, Todd R.

2015-01-01

We present a custom, Boolean query generator utilizing common-table expressions (CTEs) that is capable of scaling with big datasets. The generator maps user-defined Boolean queries, such as those interactively created in clinical-research and general-purpose healthcare tools, into SQL. We demonstrate the effectiveness of this generator by integrating our work into the Informatics for Integrating Biology and the Bedside (i2b2) query tool and show that it is capable of scaling. Our custom generator replaces and outperforms the default query generator found within the Clinical Research Chart (CRC) cell of i2b2. In our experiments, sixteen different types of i2b2 queries were identified by varying four constraints: date, frequency, exclusion criteria, and whether selected concepts occurred in the same encounter. We generated non-trivial, random Boolean queries based on these 16 types; the corresponding SQL queries produced by both generators were compared by execution times. The CTE-based solution significantly outperformed the default query generator and provided a much more consistent response time across all query types (M=2.03, SD=6.64 vs. M=75.82, SD=238.88 seconds). Without costly hardware upgrades, we provide a scalable solution based on CTEs with very promising empirical results centered on performance gains. The evaluation methodology used for this provides a means of profiling clinical data warehouse performance. PMID:25192572

Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological Level

NASA Astrophysics Data System (ADS)

Thakar, Juilee; Albert, Réka

The following sections are included: * Introduction * Boolean Network Concepts and History * Extensions of the Classical Boolean Framework * Boolean Inference Methods and Examples in Biology * Dynamic Boolean Models: Examples in Plant Biology, Developmental Biology and Immunology * Conclusions * References

A Hypermedia Computer-Aided Parasitology Tutoring System.

ERIC Educational Resources Information Center

Theodoropoulos, Georgios; Loumos, Vassili

A hypermedia tutoring system for teaching parasitology to college students was developed using an object oriented software development tool, Knowledge Pro. The program was designed to meet four objectives: knowledge incorporation, tutoring, indexing of key words for Boolean search, and random generation of quiz questions with instant scoring. The…

State feedback control design for Boolean networks.

PubMed

Liu, Rongjie; Qian, Chunjiang; Liu, Shuqian; Jin, Yu-Fang

2016-08-26

Driving Boolean networks to desired states is of paramount significance toward our ultimate goal of controlling the progression of biological pathways and regulatory networks. Despite recent computational development of controllability of general complex networks and structural controllability of Boolean networks, there is still a lack of bridging the mathematical condition on controllability to real boolean operations in a network. Further, no realtime control strategy has been proposed to drive a Boolean network. In this study, we applied semi-tensor product to represent boolean functions in a network and explored controllability of a boolean network based on the transition matrix and time transition diagram. We determined the necessary and sufficient condition for a controllable Boolean network and mapped this requirement in transition matrix to real boolean functions and structure property of a network. An efficient tool is offered to assess controllability of an arbitrary Boolean network and to determine all reachable and non-reachable states. We found six simplest forms of controllable 2-node Boolean networks and explored the consistency of transition matrices while extending these six forms to controllable networks with more nodes. Importantly, we proposed the first state feedback control strategy to drive the network based on the status of all nodes in the network. Finally, we applied our reachability condition to the major switch of P53 pathway to predict the progression of the pathway and validate the prediction with published experimental results. This control strategy allowed us to apply realtime control to drive Boolean networks, which could not be achieved by the current control strategy for Boolean networks. Our results enabled a more comprehensive understanding of the evolution of Boolean networks and might be extended to output feedback control design.

The Boolean Is Dead, Long Live the Boolean! Natural Language versus Boolean Searching in Introductory Undergraduate Instruction

ERIC Educational Resources Information Center

Lowe, M. Sara; Maxson, Bronwen K.; Stone, Sean M.; Miller, Willie; Snajdr, Eric; Hanna, Kathleen

2018-01-01

Boolean logic can be a difficult concept for first-year, introductory students to grasp. This paper compares the results of Boolean and natural language searching across several databases with searches created from student research questions. Performance differences between databases varied. Overall, natural search language is at least as good as…

Stability of Boolean multilevel networks.

PubMed

Cozzo, Emanuele; Arenas, Alex; Moreno, Yamir

2012-09-01

The study of the interplay between the structure and dynamics of complex multilevel systems is a pressing challenge nowadays. In this paper, we use a semiannealed approximation to study the stability properties of random Boolean networks in multiplex (multilayered) graphs. Our main finding is that the multilevel structure provides a mechanism for the stabilization of the dynamics of the whole system even when individual layers work on the chaotic regime, therefore identifying new ways of feedback between the structure and the dynamics of these systems. Our results point out the need for a conceptual transition from the physics of single-layered networks to the physics of multiplex networks. Finally, the fact that the coupling modifies the phase diagram and the critical conditions of the isolated layers suggests that interdependency can be used as a control mechanism.

A comparison of Boolean-based retrieval to the WAIS system for retrieval of aeronautical information

NASA Technical Reports Server (NTRS)

Marchionini, Gary; Barlow, Diane

1994-01-01

An evaluation of an information retrieval system using a Boolean-based retrieval engine and inverted file architecture and WAIS, which uses a vector-based engine, was conducted. Four research questions in aeronautical engineering were used to retrieve sets of citations from the NASA Aerospace Database which was mounted on a WAIS server and available through Dialog File 108 which served as the Boolean-based system (BBS). High recall and high precision searches were done in the BBS and terse and verbose queries were used in the WAIS condition. Precision values for the WAIS searches were consistently above the precision values for high recall BBS searches and consistently below the precision values for high precision BBS searches. Terse WAIS queries gave somewhat better precision performance than verbose WAIS queries. In every case, a small number of relevant documents retrieved by one system were not retrieved by the other, indicating the incomplete nature of the results from either retrieval system. Relevant documents in the WAIS searches were found to be randomly distributed in the retrieved sets rather than distributed by ranks. Advantages and limitations of both types of systems are discussed.

Feedback topology and XOR-dynamics in Boolean networks with varying input structure

NASA Astrophysics Data System (ADS)

Ciandrini, L.; Maffi, C.; Motta, A.; Bassetti, B.; Cosentino Lagomarsino, M.

2009-08-01

We analyze a model of fixed in-degree random Boolean networks in which the fraction of input-receiving nodes is controlled by the parameter γ . We investigate analytically and numerically the dynamics of graphs under a parallel XOR updating scheme. This scheme is interesting because it is accessible analytically and its phenomenology is at the same time under control and as rich as the one of general Boolean networks. We give analytical formulas for the dynamics on general graphs, showing that with a XOR-type evolution rule, dynamic features are direct consequences of the topological feedback structure, in analogy with the role of relevant components in Kauffman networks. Considering graphs with fixed in-degree, we characterize analytically and numerically the feedback regions using graph decimation algorithms (Leaf Removal). With varying γ , this graph ensemble shows a phase transition that separates a treelike graph region from one in which feedback components emerge. Networks near the transition point have feedback components made of disjoint loops, in which each node has exactly one incoming and one outgoing link. Using this fact, we provide analytical estimates of the maximum period starting from topological considerations.

Feedback topology and XOR-dynamics in Boolean networks with varying input structure.

PubMed

Ciandrini, L; Maffi, C; Motta, A; Bassetti, B; Cosentino Lagomarsino, M

2009-08-01

We analyze a model of fixed in-degree random Boolean networks in which the fraction of input-receiving nodes is controlled by the parameter gamma. We investigate analytically and numerically the dynamics of graphs under a parallel XOR updating scheme. This scheme is interesting because it is accessible analytically and its phenomenology is at the same time under control and as rich as the one of general Boolean networks. We give analytical formulas for the dynamics on general graphs, showing that with a XOR-type evolution rule, dynamic features are direct consequences of the topological feedback structure, in analogy with the role of relevant components in Kauffman networks. Considering graphs with fixed in-degree, we characterize analytically and numerically the feedback regions using graph decimation algorithms (Leaf Removal). With varying gamma , this graph ensemble shows a phase transition that separates a treelike graph region from one in which feedback components emerge. Networks near the transition point have feedback components made of disjoint loops, in which each node has exactly one incoming and one outgoing link. Using this fact, we provide analytical estimates of the maximum period starting from topological considerations.

Counting and classifying attractors in high dimensional dynamical systems.

PubMed

Bagley, R J; Glass, L

1996-12-07

Randomly connected Boolean networks have been used as mathematical models of neural, genetic, and immune systems. A key quantity of such networks is the number of basins of attraction in the state space. The number of basins of attraction changes as a function of the size of the network, its connectivity and its transition rules. In discrete networks, a simple count of the number of attractors does not reveal the combinatorial structure of the attractors. These points are illustrated in a reexamination of dynamics in a class of random Boolean networks considered previously by Kauffman. We also consider comparisons between dynamics in discrete networks and continuous analogues. A continuous analogue of a discrete network may have a different number of attractors for many different reasons. Some attractors in discrete networks may be associated with unstable dynamics, and several different attractors in a discrete network may be associated with a single attractor in the continuous case. Special problems in determining attractors in continuous systems arise when there is aperiodic dynamics associated with quasiperiodicity of deterministic chaos.

Computational complexity of Boolean functions

NASA Astrophysics Data System (ADS)

Korshunov, Aleksei D.

2012-02-01

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.

Evolutionary Algorithms for Boolean Functions in Diverse Domains of Cryptography.

PubMed

Picek, Stjepan; Carlet, Claude; Guilley, Sylvain; Miller, Julian F; Jakobovic, Domagoj

2016-01-01

The role of Boolean functions is prominent in several areas including cryptography, sequences, and coding theory. Therefore, various methods for the construction of Boolean functions with desired properties are of direct interest. New motivations on the role of Boolean functions in cryptography with attendant new properties have emerged over the years. There are still many combinations of design criteria left unexplored and in this matter evolutionary computation can play a distinct role. This article concentrates on two scenarios for the use of Boolean functions in cryptography. The first uses Boolean functions as the source of the nonlinearity in filter and combiner generators. Although relatively well explored using evolutionary algorithms, it still presents an interesting goal in terms of the practical sizes of Boolean functions. The second scenario appeared rather recently where the objective is to find Boolean functions that have various orders of the correlation immunity and minimal Hamming weight. In both these scenarios we see that evolutionary algorithms are able to find high-quality solutions where genetic programming performs the best.

A Simple Blueprint for Automatic Boolean Query Processing.

ERIC Educational Resources Information Center

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)…

Optimal stabilization of Boolean networks through collective influence

NASA Astrophysics Data System (ADS)

Wang, Jiannan; Pei, Sen; Wei, Wei; Feng, Xiangnan; Zheng, Zhiming

2018-03-01

Boolean networks have attracted much attention due to their wide applications in describing dynamics of biological systems. During past decades, much effort has been invested in unveiling how network structure and update rules affect the stability of Boolean networks. In this paper, we aim to identify and control a minimal set of influential nodes that is capable of stabilizing an unstable Boolean network. For locally treelike Boolean networks with biased truth tables, we propose a greedy algorithm to identify influential nodes in Boolean networks by minimizing the largest eigenvalue of a modified nonbacktracking matrix. We test the performance of the proposed collective influence algorithm on four different networks. Results show that the collective influence algorithm can stabilize each network with a smaller set of nodes compared with other heuristic algorithms. Our work provides a new insight into the mechanism that determines the stability of Boolean networks, which may find applications in identifying virulence genes that lead to serious diseases.

Effect of memory in non-Markovian Boolean networks illustrated with a case study: A cell cycling process

NASA Astrophysics Data System (ADS)

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.

On the Computation of Comprehensive Boolean Gröbner Bases

NASA Astrophysics Data System (ADS)

Inoue, Shutaro

We show that a comprehensive Boolean Gröbner basis of an ideal I in a Boolean polynomial ring B (bar A,bar X) with main variables bar X and parameters bar A can be obtained by simply computing a usual Boolean Gröbner basis of I regarding both bar X and bar A as variables with a certain block term order such that bar X ≫ bar A. The result together with a fact that a finite Boolean ring is isomorphic to a direct product of the Galois field mathbb{GF}_2 enables us to compute a comprehensive Boolean Gröbner basis by only computing corresponding Gröbner bases in a polynomial ring over mathbb{GF}_2. Our implementation in a computer algebra system Risa/Asir shows that our method is extremely efficient comparing with existing computation algorithms of comprehensive Boolean Gröbner bases.

Phase transition of Boolean networks with partially nested canalizing functions

NASA Astrophysics Data System (ADS)

Jansen, Kayse; Matache, Mihaela Teodora

2013-07-01

We generate the critical condition for the phase transition of a Boolean network governed by partially nested canalizing functions for which a fraction of the inputs are canalizing, while the remaining non-canalizing inputs obey a complementary threshold Boolean function. Past studies have considered the stability of fully or partially nested canalizing functions paired with random choices of the complementary function. In some of those studies conflicting results were found with regard to the presence of chaotic behavior. Moreover, those studies focus mostly on ergodic networks in which initial states are assumed equally likely. We relax that assumption and find the critical condition for the sensitivity of the network under a non-ergodic scenario. We use the proposed mathematical model to determine parameter values for which phase transitions from order to chaos occur. We generate Derrida plots to show that the mathematical model matches the actual network dynamics. The phase transition diagrams indicate that both order and chaos can occur, and that certain parameters induce a larger range of values leading to order versus chaos. The edge-of-chaos curves are identified analytically and numerically. It is shown that the depth of canalization does not cause major dynamical changes once certain thresholds are reached; these thresholds are fairly small in comparison to the connectivity of the nodes.

Synchronization of coupled large-scale Boolean networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Fangfei, E-mail: li-fangfei@163.com

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.

Calculating the bidirectional reflectance of natural vegetation covers using Boolean models and geometric optics

NASA Technical Reports Server (NTRS)

Strahler, Alan H.; Li, Xiao-Wen; Jupp, David L. B.

1991-01-01

The bidirectional radiance or reflectance of a forest or woodland can be modeled using principles of geometric optics and Boolean models for random sets in a three dimensional space. This model may be defined at two levels, the scene includes four components; sunlight and shadowed canopy, and sunlit and shadowed background. The reflectance of the scene is modeled as the sum of the reflectances of the individual components as weighted by their areal proportions in the field of view. At the leaf level, the canopy envelope is an assemblage of leaves, and thus the reflectance is a function of the areal proportions of sunlit and shadowed leaf, and sunlit and shadowed background. Because the proportions of scene components are dependent upon the directions of irradiance and exitance, the model accounts for the hotspot that is well known in leaf and tree canopies.

State feedback controller design for the synchronization of Boolean networks with time delays

NASA Astrophysics Data System (ADS)

Li, Fangfei; Li, Jianning; Shen, Lijuan

2018-01-01

State feedback control design to make the response Boolean network synchronize with the drive Boolean network is far from being solved in the literature. Motivated by this, this paper studies the feedback control design for the complete synchronization of two coupled Boolean networks with time delays. A necessary condition for the existence of a state feedback controller is derived first. Then the feedback control design procedure for the complete synchronization of two coupled Boolean networks is provided based on the necessary condition. Finally, an example is given to illustrate the proposed design procedure.

The mathematics of a quantum Hamiltonian computing half adder Boolean logic gate.

PubMed

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.

Development of Boolean calculus and its application

NASA Technical Reports Server (NTRS)

Tapia, M. A.

1979-01-01

Formal procedures for synthesis of asynchronous sequential system using commercially available edge-sensitive flip-flops are developed. Boolean differential is defined. The exact number of compatible integrals of a Boolean differential were calculated.

Boolean integral calculus

NASA Technical Reports Server (NTRS)

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.

Modeling the Normal and Neoplastic Cell Cycle with 'Realistic Boolean Genetic Networks': Their Application for Understanding Carcinogenesis and Assessing Therapeutic Strategies

NASA Technical Reports Server (NTRS)

Szallasi, Zoltan; Liang, Shoudan

2000-01-01

In this paper we show how Boolean genetic networks could be used to address complex problems in cancer biology. First, we describe a general strategy to generate Boolean genetic networks that incorporate all relevant biochemical and physiological parameters and cover all of their regulatory interactions in a deterministic manner. Second, we introduce 'realistic Boolean genetic networks' that produce time series measurements very similar to those detected in actual biological systems. Third, we outline a series of essential questions related to cancer biology and cancer therapy that could be addressed by the use of 'realistic Boolean genetic network' modeling.

Automatic query formulations in information retrieval.

PubMed

Salton, G; Buckley, C; Fox, E A

1983-07-01

Modern information retrieval systems are designed to supply relevant information in response to requests received from the user population. In most retrieval environments the search requests consist of keywords, or index terms, interrelated by appropriate Boolean operators. Since it is difficult for untrained users to generate effective Boolean search requests, trained search intermediaries are normally used to translate original statements of user need into useful Boolean search formulations. Methods are introduced in this study which reduce the role of the search intermediaries by making it possible to generate Boolean search formulations completely automatically from natural language statements provided by the system patrons. Frequency considerations are used automatically to generate appropriate term combinations as well as Boolean connectives relating the terms. Methods are covered to produce automatic query formulations both in a standard Boolean logic system, as well as in an extended Boolean system in which the strict interpretation of the connectives is relaxed. Experimental results are supplied to evaluate the effectiveness of the automatic query formulation process, and methods are described for applying the automatic query formulation process in practice.

An Attractor-Based Complexity Measurement for Boolean Recurrent Neural Networks

PubMed Central

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 -automata, and then translating the most refined classification of -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. PMID:24727866

Proposed method to construct Boolean functions with maximum possible annihilator immunity

NASA Astrophysics Data System (ADS)

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.

Exploiting Data Missingness in Bayesian Network Modeling

NASA Astrophysics Data System (ADS)

Rodrigues de Morais, Sérgio; Aussem, Alex

This paper proposes a framework built on the use of Bayesian networks (BN) for representing statistical dependencies between the existing random variables and additional dummy boolean variables, which represent the presence/absence of the respective random variable value. We show how augmenting the BN with these additional variables helps pinpoint the mechanism through which missing data contributes to the classification task. The missing data mechanism is thus explicitly taken into account to predict the class variable using the data at hand. Extensive experiments on synthetic and real-world incomplete data sets reveals that the missingness information improves classification accuracy.

To Boolean or Not To Boolean.

ERIC Educational Resources Information Center

Hildreth, Charles R.

1983-01-01

This editorial addresses the issue of whether or not to provide free-text, keyword/boolean search capabilities in the information retrieval mechanisms of online public access catalogs and discusses online catalogs developed prior to 1980--keyword searching, phrase searching, and precoordination and postcoordination. (EJS)

Minimum energy control and optimal-satisfactory control of Boolean control network

NASA Astrophysics Data System (ADS)

Li, Fangfei; Lu, Xiwen

2013-12-01

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.

Identifying a Probabilistic Boolean Threshold Network From Samples.

PubMed

Melkman, Avraham A; Cheng, Xiaoqing; Ching, Wai-Ki; Akutsu, Tatsuya

2018-04-01

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 -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.

Griffin: A Tool for Symbolic Inference of Synchronous Boolean Molecular Networks.

PubMed

Muñoz, Stalin; Carrillo, Miguel; Azpeitia, Eugenio; Rosenblueth, David A

2018-01-01

Boolean networks are important models of biochemical systems, located at the high end of the abstraction spectrum. A number of Boolean gene networks have been inferred following essentially the same method. Such a method first considers experimental data for a typically underdetermined "regulation" graph. Next, Boolean networks are inferred by using biological constraints to narrow the search space, such as a desired set of (fixed-point or cyclic) attractors. We describe Griffin , a computer tool enhancing this method. Griffin incorporates a number of well-established algorithms, such as Dubrova and Teslenko's algorithm for finding attractors in synchronous Boolean networks. In addition, a formal definition of regulation allows Griffin to employ "symbolic" techniques, able to represent both large sets of network states and Boolean constraints. We observe that when the set of attractors is required to be an exact set, prohibiting additional attractors, a naive Boolean coding of this constraint may be unfeasible. Such cases may be intractable even with symbolic methods, as the number of Boolean constraints may be astronomically large. To overcome this problem, we employ an Artificial Intelligence technique known as "clause learning" considerably increasing Griffin 's scalability. Without clause learning only toy examples prohibiting additional attractors are solvable: only one out of seven queries reported here is answered. With clause learning, by contrast, all seven queries are answered. We illustrate Griffin with three case studies drawn from the Arabidopsis thaliana literature. Griffin is available at: http://turing.iimas.unam.mx/griffin.

On the Run-Time Optimization of the Boolean Logic of a Program.

ERIC Educational Resources Information Center

Cadolino, C.; Guazzo, M.

1982-01-01

Considers problem of optimal scheduling of Boolean expression (each Boolean variable represents binary outcome of program module) on single-processor system. Optimization discussed consists of finding operand arrangement that minimizes average execution costs representing consumption of resources (elapsed time, main memory, number of…

Boolean integral calculus for digital systems

NASA Technical Reports Server (NTRS)

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.

A Comparison of Two Methods for Boolean Query Relevancy Feedback.

ERIC Educational Resources Information Center

Salton, G.; And Others

1984-01-01

Evaluates and compares two recently proposed automatic methods for relevance feedback of Boolean queries (Dillon method, which uses probabilistic approach as basis, and disjunctive normal form method). Conclusions are drawn concerning the use of effective feedback methods in a Boolean query environment. Nineteen references are included. (EJS)

Realisation of all 16 Boolean logic functions in a single magnetoresistance memory cell.

PubMed

Gao, Shuang; Yang, Guang; Cui, Bin; Wang, Shouguo; Zeng, Fei; Song, Cheng; Pan, Feng

2016-07-07

Stateful logic circuits based on next-generation nonvolatile memories, such as magnetoresistance random access memory (MRAM), promise to break the long-standing von Neumann bottleneck in state-of-the-art data processing devices. For the successful commercialisation of stateful logic circuits, a critical step is realizing the best use of a single memory cell to perform logic functions. In this work, we propose a method for implementing all 16 Boolean logic functions in a single MRAM cell, namely a magnetoresistance (MR) unit. Based on our experimental results, we conclude that this method is applicable to any MR unit with a double-hump-like hysteresis loop, especially pseudo-spin-valve magnetic tunnel junctions with a high MR ratio. Moreover, after simply reversing the correspondence between voltage signals and output logic values, this method could also be applicable to any MR unit with a double-pit-like hysteresis loop. These results may provide a helpful solution for the final commercialisation of MRAM-based stateful logic circuits in the near future.

Boolean Classes and Qualitative Inquiry. WCER Working Paper No. 2006-3

ERIC Educational Resources Information Center

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…

Algebraic model checking for Boolean gene regulatory networks.

PubMed

Tran, Quoc-Nam

2011-01-01

We present a computational method in which modular and Groebner bases (GB) computation in Boolean rings are used for solving problems in Boolean gene regulatory networks (BN). In contrast to other known algebraic approaches, the degree of intermediate polynomials during the calculation of Groebner bases using our method will never grow resulting in a significant improvement in running time and memory space consumption. We also show how calculation in temporal logic for model checking can be done by means of our direct and efficient Groebner basis computation in Boolean rings. We present our experimental results in finding attractors and control strategies of Boolean networks to illustrate our theoretical arguments. The results are promising. Our algebraic approach is more efficient than the state-of-the-art model checker NuSMV on BNs. More importantly, our approach finds all solutions for the BN problems.

E-Referencer: Transforming Boolean OPACs to Web Search Engines.

ERIC Educational Resources Information Center

Khoo, Christopher S. G.; Poo, Danny C. C.; Toh, Teck-Kang; Hong, Glenn

E-Referencer is an expert intermediary system for searching library online public access catalogs (OPACs) on the World Wide Web. It is implemented as a proxy server that mediates the interaction between the user and Boolean OPACs. It transforms a Boolean OPAC into a retrieval system with many of the search capabilities of Web search engines.…

BEAT: A Web-Based Boolean Expression Fault-Based Test Case Generation Tool

ERIC Educational Resources Information Center

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…

Expected Number of Fixed Points in Boolean Networks with Arbitrary Topology.

PubMed

Mori, Fumito; Mochizuki, Atsushi

2017-07-14

Boolean network models describe genetic, neural, and social dynamics in complex networks, where the dynamics depend generally on network topology. Fixed points in a genetic regulatory network are typically considered to correspond to cell types in an organism. We prove that the expected number of fixed points in a Boolean network, with Boolean functions drawn from probability distributions that are not required to be uniform or identical, is one, and is independent of network topology if only a feedback arc set satisfies a stochastic neutrality condition. We also demonstrate that the expected number is increased by the predominance of positive feedback in a cycle.

SETS. Set Equation Transformation System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Worrell, R.B.

1992-01-13

SETS is used for symbolic manipulation of Boolean equations, particularly the reduction of equations by the application of Boolean identities. It is a flexible and efficient tool for performing probabilistic risk analysis (PRA), vital area analysis, and common cause analysis. The equation manipulation capabilities of SETS can also be used to analyze noncoherent fault trees and determine prime implicants of Boolean functions, to verify circuit design implementation, to determine minimum cost fire protection requirements for nuclear reactor plants, to obtain solutions to combinatorial optimization problems with Boolean constraints, and to determine the susceptibility of a facility to unauthorized access throughmore » nullification of sensors in its protection system.« less

Monotone Boolean approximation

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 formore » the analysis of noncoherent fault trees and event tree sequences.« less

Automatic Screening for Perturbations in Boolean Networks.

PubMed

Schwab, Julian D; Kestler, Hans A

2018-01-01

A common approach to address biological questions in systems biology is to simulate regulatory mechanisms using dynamic models. Among others, Boolean networks can be used to model the dynamics of regulatory processes in biology. Boolean network models allow simulating the qualitative behavior of the modeled processes. A central objective in the simulation of Boolean networks is the computation of their long-term behavior-so-called attractors. These attractors are of special interest as they can often be linked to biologically relevant behaviors. Changing internal and external conditions can influence the long-term behavior of the Boolean network model. Perturbation of a Boolean network by stripping a component of the system or simulating a surplus of another element can lead to different attractors. Apparently, the number of possible perturbations and combinations of perturbations increases exponentially with the size of the network. Manually screening a set of possible components for combinations that have a desired effect on the long-term behavior can be very time consuming if not impossible. We developed a method to automatically screen for perturbations that lead to a user-specified change in the network's functioning. This method is implemented in the visual simulation framework ViSiBool utilizing satisfiability (SAT) solvers for fast exhaustive attractor search.

Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures

NASA Technical Reports Server (NTRS)

Liang, Shoudan; Fuhrman, Stefanie; Somogyi, Roland

1998-01-01

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(exp 15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

Boolean Minimization and Algebraic Factorization Procedures for Fully Testable Sequential Machines

DTIC Science & Technology

1989-09-01

Boolean Minimization and Algebraic Factorization Procedures for Fully Testable Sequential Machines Srinivas Devadas and Kurt Keutzer F ( Abstract In this...Projects Agency under contract number N00014-87-K-0825. Author Information Devadas : Department of Electrical Engineering and Computer Science, Room 36...MA 02139; (617) 253-0292. 0 * Boolean Minimization and Algebraic Factorization Procedures for Fully Testable Sequential Machines Siivas Devadas

On the robustness of complex heterogeneous gene expression networks.

PubMed

Gómez-Gardeñes, Jesús; Moreno, Yamir; Floría, Luis M

2005-04-01

We analyze a continuous gene expression model on the underlying topology of a complex heterogeneous network. Numerical simulations aimed at studying the chaotic and periodic dynamics of the model are performed. The results clearly indicate that there is a region in which the dynamical and structural complexity of the system avoid chaotic attractors. However, contrary to what has been reported for Random Boolean Networks, the chaotic phase cannot be completely suppressed, which has important bearings on network robustness and gene expression modeling.

Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets.

PubMed

Park, Inho; Lee, Kwang H; Lee, Doheon

2010-06-15

Gene set analysis has become an important tool for the functional interpretation of high-throughput gene expression datasets. Moreover, pattern analyses based on inferred gene set activities of individual samples have shown the ability to identify more robust disease signatures than individual gene-based pattern analyses. Although a number of approaches have been proposed for gene set-based pattern analysis, the combinatorial influence of deregulated gene sets on disease phenotype classification has not been studied sufficiently. We propose a new approach for inferring combinatorial Boolean rules of gene sets for a better understanding of cancer transcriptome and cancer classification. To reduce the search space of the possible Boolean rules, we identify small groups of gene sets that synergistically contribute to the classification of samples into their corresponding phenotypic groups (such as normal and cancer). We then measure the significance of the candidate Boolean rules derived from each group of gene sets; the level of significance is based on the class entropy of the samples selected in accordance with the rules. By applying the present approach to publicly available prostate cancer datasets, we identified 72 significant Boolean rules. Finally, we discuss several identified Boolean rules, such as the rule of glutathione metabolism (down) and prostaglandin synthesis regulation (down), which are consistent with known prostate cancer biology. Scripts written in Python and R are available at http://biosoft.kaist.ac.kr/~ihpark/. The refined gene sets and the full list of the identified Boolean rules are provided in the Supplementary Material. Supplementary data are available at Bioinformatics online.

Realisation of all 16 Boolean logic functions in a single magnetoresistance memory cell

NASA Astrophysics Data System (ADS)

Gao, Shuang; Yang, Guang; Cui, Bin; Wang, Shouguo; Zeng, Fei; Song, Cheng; Pan, Feng

2016-06-01

Stateful logic circuits based on next-generation nonvolatile memories, such as magnetoresistance random access memory (MRAM), promise to break the long-standing von Neumann bottleneck in state-of-the-art data processing devices. For the successful commercialisation of stateful logic circuits, a critical step is realizing the best use of a single memory cell to perform logic functions. In this work, we propose a method for implementing all 16 Boolean logic functions in a single MRAM cell, namely a magnetoresistance (MR) unit. Based on our experimental results, we conclude that this method is applicable to any MR unit with a double-hump-like hysteresis loop, especially pseudo-spin-valve magnetic tunnel junctions with a high MR ratio. Moreover, after simply reversing the correspondence between voltage signals and output logic values, this method could also be applicable to any MR unit with a double-pit-like hysteresis loop. These results may provide a helpful solution for the final commercialisation of MRAM-based stateful logic circuits in the near future.Stateful logic circuits based on next-generation nonvolatile memories, such as magnetoresistance random access memory (MRAM), promise to break the long-standing von Neumann bottleneck in state-of-the-art data processing devices. For the successful commercialisation of stateful logic circuits, a critical step is realizing the best use of a single memory cell to perform logic functions. In this work, we propose a method for implementing all 16 Boolean logic functions in a single MRAM cell, namely a magnetoresistance (MR) unit. Based on our experimental results, we conclude that this method is applicable to any MR unit with a double-hump-like hysteresis loop, especially pseudo-spin-valve magnetic tunnel junctions with a high MR ratio. Moreover, after simply reversing the correspondence between voltage signals and output logic values, this method could also be applicable to any MR unit with a double-pit-like hysteresis loop. These results may provide a helpful solution for the final commercialisation of MRAM-based stateful logic circuits in the near future. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr03169b

A Boolean Consistent Fuzzy Inference System for Diagnosing Diseases and Its Application for Determining Peritonitis Likelihood

PubMed Central

Dragović, Ivana; Turajlić, Nina; Pilčević, Dejan; Petrović, Bratislav; Radojević, Dragan

2015-01-01

Fuzzy inference systems (FIS) enable automated assessment and reasoning in a logically consistent manner akin to the way in which humans reason. However, since no conventional fuzzy set theory is in the Boolean frame, it is proposed that Boolean consistent fuzzy logic should be used in the evaluation of rules. The main distinction of this approach is that it requires the execution of a set of structural transformations before the actual values can be introduced, which can, in certain cases, lead to different results. While a Boolean consistent FIS could be used for establishing the diagnostic criteria for any given disease, in this paper it is applied for determining the likelihood of peritonitis, as the leading complication of peritoneal dialysis (PD). Given that patients could be located far away from healthcare institutions (as peritoneal dialysis is a form of home dialysis) the proposed Boolean consistent FIS would enable patients to easily estimate the likelihood of them having peritonitis (where a high likelihood would suggest that prompt treatment is indicated), when medical experts are not close at hand. PMID:27069500

The informational architecture of the cell.

PubMed

Walker, Sara Imari; Kim, Hyunju; Davies, Paul C W

2016-03-13

We compare the informational architecture of biological and random networks to identify informational features that may distinguish biological networks from random. The study presented here focuses on the Boolean network model for regulation of the cell cycle of the fission yeast Schizosaccharomyces pombe. We compare calculated values of local and global information measures for the fission yeast cell cycle to the same measures as applied to two different classes of random networks: Erdös-Rényi and scale-free. We report patterns in local information processing and storage that do indeed distinguish biological from random, associated with control nodes that regulate the function of the fission yeast cell-cycle network. Conversely, we find that integrated information, which serves as a global measure of 'emergent' information processing, does not differ from random for the case presented. We discuss implications for our understanding of the informational architecture of the fission yeast cell-cycle network in particular, and more generally for illuminating any distinctive physics that may be operative in life. © 2016 The Author(s).

Modeling formalisms in Systems Biology

PubMed Central

2011-01-01

Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future. PMID:22141422

"Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis

PubMed Central

2011-01-01

Background In Thomas' formalism for modeling gene regulatory networks (GRNs), branching time, where a state can have more than one possible future, plays a prominent role. By representing a certain degree of unpredictability, branching time can model several important phenomena, such as (a) asynchrony, (b) incompletely specified behavior, and (c) interaction with the environment. Introducing more than one possible future for a state, however, creates a difficulty for ordinary simulators, because infinitely many paths may appear, limiting ordinary simulators to statistical conclusions. Model checkers for branching time, by contrast, are able to prove properties in the presence of infinitely many paths. Results We have developed Antelope ("Analysis of Networks through TEmporal-LOgic sPEcifications", http://turing.iimas.unam.mx:8080/AntelopeWEB/), a model checker for analyzing and constructing Boolean GRNs. Currently, software systems for Boolean GRNs use branching time almost exclusively for asynchrony. Antelope, by contrast, also uses branching time for incompletely specified behavior and environment interaction. We show the usefulness of modeling these two phenomena in the development of a Boolean GRN of the Arabidopsis thaliana root stem cell niche. There are two obstacles to a direct approach when applying model checking to Boolean GRN analysis. First, ordinary model checkers normally only verify whether or not a given set of model states has a given property. In comparison, a model checker for Boolean GRNs is preferable if it reports the set of states having a desired property. Second, for efficiency, the expressiveness of many model checkers is limited, resulting in the inability to express some interesting properties of Boolean GRNs. Antelope tries to overcome these two drawbacks: Apart from reporting the set of all states having a given property, our model checker can express, at the expense of efficiency, some properties that ordinary model checkers (e.g., NuSMV) cannot. This additional expressiveness is achieved by employing a logic extending the standard Computation-Tree Logic (CTL) with hybrid-logic operators. Conclusions We illustrate the advantages of Antelope when (a) modeling incomplete networks and environment interaction, (b) exhibiting the set of all states having a given property, and (c) representing Boolean GRN properties with hybrid CTL. PMID:22192526

Adaptiveness in monotone pseudo-Boolean optimization and stochastic neural computation.

PubMed

Grossi, Giuliano

2009-08-01

Hopfield neural network (HNN) is a nonlinear computational model successfully applied in finding near-optimal solutions of several difficult combinatorial problems. In many cases, the network energy function is obtained through a learning procedure so that its minima are states falling into a proper subspace (feasible region) of the search space. However, because of the network nonlinearity, a number of undesirable local energy minima emerge from the learning procedure, significantly effecting the network performance. In the neural model analyzed here, we combine both a penalty and a stochastic process in order to enhance the performance of a binary HNN. The penalty strategy allows us to gradually lead the search towards states representing feasible solutions, so avoiding oscillatory behaviors or asymptotically instable convergence. Presence of stochastic dynamics potentially prevents the network to fall into shallow local minima of the energy function, i.e., quite far from global optimum. Hence, for a given fixed network topology, the desired final distribution on the states can be reached by carefully modulating such process. The model uses pseudo-Boolean functions both to express problem constraints and cost function; a combination of these two functions is then interpreted as energy of the neural network. A wide variety of NP-hard problems fall in the class of problems that can be solved by the model at hand, particularly those having a monotonic quadratic pseudo-Boolean function as constraint function. That is, functions easily derived by closed algebraic expressions representing the constraint structure and easy (polynomial time) to maximize. We show the asymptotic convergence properties of this model characterizing its state space distribution at thermal equilibrium in terms of Markov chain and give evidence of its ability to find high quality solutions on benchmarks and randomly generated instances of two specific problems taken from the computational graph theory.

Theory and calculus of cubical complexes

NASA Technical Reports Server (NTRS)

Perlman, M.

1973-01-01

Combination switching networks with multiple outputs may be represented by Boolean functions. Report has been prepared which describes derivation and use of extraction algorithm that may be adapted to simplification of such simultaneous Boolean functions.

Dynamic Boolean Mathematics

ERIC Educational Resources Information Center

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…

Total Parenteral Nutrition

MedlinePlus

... Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean bFromProxy) at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess ...

Discrete Dynamics Lab

NASA Astrophysics Data System (ADS)

Wuensche, Andrew

DDLab is interactive graphics software for creating, visualizing, and analyzing many aspects of Cellular Automata, Random Boolean Networks, and Discrete Dynamical Networks in general and studying their behavior, both from the time-series perspective — space-time patterns, and from the state-space perspective — attractor basins. DDLab is relevant to research, applications, and education in the fields of complexity, self-organization, emergent phenomena, chaos, collision-based computing, neural networks, content addressable memory, genetic regulatory networks, dynamical encryption, generative art and music, and the study of the abstract mathematical/physical/dynamical phenomena in their own right.

A genetic code Boolean structure. II. The genetic information system as a Boolean information system.

PubMed

Sanchez, Robersy; Grau, Ricardo

2005-09-01

A Boolean structure of the genetic code where Boolean deductions have biological and physicochemical meanings was discussed in a previous paper. Now, from these Boolean deductions we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory. In this proposal, the value of amino acid information is proportional to the molecular weight of amino acids with a proportional constant of about 1.96 x 10(25) bits per kg. In addition to this, for the experimental estimations of the minimum energy dissipation in genetic logic operations, we present two postulates: (1) the energy Ei (i=1,2,...,20) of amino acids in the messages conveyed by proteins is proportional to the value of information, and (2) amino acids are distributed according to their energy Ei so the amino acid population in proteins follows a Boltzmann distribution. Specifically, in the genetic message carried by the DNA from the genomes of living organisms, we found that the minimum energy dissipation in genetic logic operations was close to kTLn(2) joules per bit.

Ordinary differential equations and Boolean networks in application to modelling of 6-mercaptopurine metabolism.

PubMed

Lavrova, Anastasia I; Postnikov, Eugene B; Zyubin, Andrey Yu; Babak, Svetlana V

2017-04-01

We consider two approaches to modelling the cell metabolism of 6-mercaptopurine, one of the important chemotherapy drugs used for treating acute lymphocytic leukaemia: kinetic ordinary differential equations, and Boolean networks supplied with one controlling node, which takes continual values. We analyse their interplay with respect to taking into account ATP concentration as a key parameter of switching between different pathways. It is shown that the Boolean networks, which allow avoiding the complexity of general kinetic modelling, preserve the possibility of reproducing the principal switching mechanism.

Improving the quantum cost of reversible Boolean functions using reorder algorithm

NASA Astrophysics Data System (ADS)

Ahmed, Taghreed; Younes, Ahmed; Elsayed, Ashraf

2018-05-01

This paper introduces a novel algorithm to synthesize a low-cost reversible circuits for any Boolean function with n inputs represented as a Positive Polarity Reed-Muller expansion. The proposed algorithm applies a predefined rules to reorder the terms in the function to minimize the multi-calculation of common parts of the Boolean function to decrease the quantum cost of the reversible circuit. The paper achieves a decrease in the quantum cost and/or the circuit length, on average, when compared with relevant work in the literature.

Volumetric T-spline Construction Using Boolean Operations

DTIC Science & Technology

2013-07-01

SUBTITLE Volumetric T-spline Construction Using Boolean Operations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d...Acknowledgements The work of L. Liu and Y. Zhang was supported by ONR-YIP award N00014- 10-1-0698 and an ONR Grant N00014-08-1-0653. T. J.R. Hughes was sup- 16...T-spline Construction Using Boolean Operations 17 ported by ONR Grant N00014-08-1-0992, NSF GOALI CMI-0700807/0700204, NSF CMMI-1101007 and a SINTEF

Dynamic Network-Based Epistasis Analysis: Boolean Examples

PubMed Central

Azpeitia, Eugenio; Benítez, Mariana; Padilla-Longoria, Pablo; Espinosa-Soto, Carlos; Alvarez-Buylla, Elena R.

2011-01-01

In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. 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, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). 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 inference of gene interaction topologies is 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 article complements previous accounts, not only by focusing on the implications of the hierarchical and single-path assumption, but also by demonstrating the importance of considering temporal dynamics, and specifically introducing the usefulness of Boolean network models and also reviewing some key properties of network approaches. PMID:22645556

Phased-mission system analysis using Boolean algebraic methods

NASA Technical Reports Server (NTRS)

Somani, Arun K.; Trivedi, Kishor S.

1993-01-01

Most reliability analysis techniques and tools assume that a system is used for a mission consisting of a single phase. However, multiple phases are natural in many missions. The failure rates of components, system configuration, and success criteria may vary from phase to phase. In addition, the duration of a phase may be deterministic or random. Recently, several researchers have addressed the problem of reliability analysis of such systems using a variety of methods. A new technique for phased-mission system reliability analysis based on Boolean algebraic methods is described. Our technique is computationally efficient and is applicable to a large class of systems for which the failure criterion in each phase can be expressed as a fault tree (or an equivalent representation). Our technique avoids state space explosion that commonly plague Markov chain-based analysis. A phase algebra to account for the effects of variable configurations and success criteria from phase to phase was developed. Our technique yields exact (as opposed to approximate) results. The use of our technique was demonstrated by means of an example and present numerical results to show the effects of mission phases on the system reliability.

Comparison of stationary and oscillatory dynamics described by differential equations and Boolean maps in transcriptional regulatory circuits

NASA Astrophysics Data System (ADS)

Ye, Weiming; Li, Pengfei; Huang, Xuhui; Xia, Qinzhi; Mi, Yuanyuan; Chen, Runsheng; Hu, Gang

2010-10-01

Exploring the principle and relationship of gene transcriptional regulations (TR) has been becoming a generally researched issue. So far, two major mathematical methods, ordinary differential equation (ODE) method and Boolean map (BM) method have been widely used for these purposes. It is commonly believed that simplified BMs are reasonable approximations of more realistic ODEs, and both methods may reveal qualitatively the same essential features though the dynamical details of both systems may show some differences. In this Letter we exhaustively enumerated all the 3-gene networks and many autonomous randomly constructed TR networks with more genes by using both the ODE and BM methods. In comparison we found that both methods provide practically identical results in most of cases of steady solutions. However, to our great surprise, most of network structures showing periodic cycles with the BM method possess only stationary states in ODE descriptions. These observations strongly suggest that many periodic oscillations and other complicated oscillatory states revealed by the BM rule may be related to the computational errors of variable and time discretizations and rarely have correspondence in realistic biology transcriptional regulatory circuits.

Acoustic logic gates and Boolean operation based on self-collimating acoustic beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Ting; Xu, Jian-yi; Cheng, Ying, E-mail: chengying@nju.edu.cn

2015-03-16

The reveal of self-collimation effect in two-dimensional (2D) photonic or acoustic crystals has opened up possibilities for signal manipulation. In this paper, we have proposed acoustic logic gates based on the linear interference of self-collimated beams in 2D sonic crystals (SCs) with line-defects. The line defects on the diagonal of the 2D square SCs are actually functioning as a 3 dB splitter. By adjusting the phase difference between two input signals, the basic Boolean logic functions such as XOR, OR, AND, and NOT are achieved both theoretically and experimentally. Due to the non-diffracting property of self-collimation beams, more complex Boolean logicmore » and algorithms such as NAND, NOR, and XNOR can be realized by cascading the basic logic gates. The achievement of acoustic logic gates and Boolean operation provides a promising approach for acoustic signal computing and manipulations.« less

Boolean networks with veto functions

NASA Astrophysics Data System (ADS)

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.

Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors.

PubMed

Sun, Mengyang; Cheng, Xianrui; Socolar, Joshua E S

2013-06-01

A common approach to the modeling of gene regulatory networks is to represent activating or repressing interactions using ordinary differential equations for target gene concentrations that include Hill function dependences on regulator gene concentrations. An alternative formulation represents the same interactions using Boolean logic with time delays associated with each network link. We consider the attractors that emerge from the two types of models in the case of a simple but nontrivial network: a figure-8 network with one positive and one negative feedback loop. We show that the different modeling approaches give rise to the same qualitative set of attractors with the exception of a possible fixed point in the ordinary differential equation model in which concentrations sit at intermediate values. The properties of the attractors are most easily understood from the Boolean perspective, suggesting that time-delay Boolean modeling is a useful tool for understanding the logic of regulatory networks.

A transition calculus for Boolean functions. [logic circuit analysis

NASA Technical Reports Server (NTRS)

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.

Inferring Boolean network states from partial information

PubMed Central

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

Quantum algorithms on Walsh transform and Hamming distance for Boolean functions

NASA Astrophysics Data System (ADS)

Xie, Zhengwei; Qiu, Daowen; Cai, Guangya

2018-06-01

Walsh spectrum or Walsh transform is an alternative description of Boolean functions. In this paper, we explore quantum algorithms to approximate the absolute value of Walsh transform W_f at a single point z0 (i.e., |W_f(z0)|) for n-variable Boolean functions with probability at least 8/π 2 using the number of O(1/|W_f(z_{0)|ɛ }) queries, promised that the accuracy is ɛ , while the best known classical algorithm requires O(2n) queries. The Hamming distance between Boolean functions is used to study the linearity testing and other important problems. We take advantage of Walsh transform to calculate the Hamming distance between two n-variable Boolean functions f and g using O(1) queries in some cases. Then, we exploit another quantum algorithm which converts computing Hamming distance between two Boolean functions to quantum amplitude estimation (i.e., approximate counting). If Ham(f,g)=t≠0, we can approximately compute Ham( f, g) with probability at least 2/3 by combining our algorithm and {Approx-Count(f,ɛ ) algorithm} using the expected number of Θ( √{N/(\\lfloor ɛ t\\rfloor +1)}+√{t(N-t)}/\\lfloor ɛ t\\rfloor +1) queries, promised that the accuracy is ɛ . Moreover, our algorithm is optimal, while the exact query complexity for the above problem is Θ(N) and the query complexity with the accuracy ɛ is O(1/ɛ 2N/(t+1)) in classical algorithm, where N=2n. Finally, we present three exact quantum query algorithms for two promise problems on Hamming distance using O(1) queries, while any classical deterministic algorithm solving the problem uses Ω(2n) queries.

Development of Boolean calculus and its applications. [digital systems design

NASA Technical Reports Server (NTRS)

Tapia, M. A.

1980-01-01

The development of Boolean calculus for its application to developing digital system design methodologies that would reduce system complexity, size, cost, speed, power requirements, etc., is discussed. Synthesis procedures for logic circuits are examined particularly asynchronous circuits using clock triggered flip flops.

Advanced Feedback Methods in Information Retrieval.

ERIC Educational Resources Information Center

Salton, G.; And Others

1985-01-01

In this study, automatic feedback techniques are applied to Boolean query statements in online information retrieval to generate improved query statements based on information contained in previously retrieved documents. Feedback operations are carried out using conventional Boolean logic and extended logic. Experimental output is included to…

Compact universal logic gates realized using quantization of current in nanodevices.

PubMed

Zhang, Wancheng; Wu, Nan-Jian; Yang, Fuhua

2007-12-12

This paper proposes novel universal logic gates using the current quantization characteristics of nanodevices. In nanodevices like the electron waveguide (EW) and single-electron (SE) turnstile, the channel current is a staircase quantized function of its control voltage. We use this unique characteristic to compactly realize Boolean functions. First we present the concept of the periodic-threshold threshold logic gate (PTTG), and we build a compact PTTG using EW and SE turnstiles. We show that an arbitrary three-input Boolean function can be realized with a single PTTG, and an arbitrary four-input Boolean function can be realized by using two PTTGs. We then use one PTTG to build a universal programmable two-input logic gate which can be used to realize all two-input Boolean functions. We also build a programmable three-input logic gate by using one PTTG. Compared with linear threshold logic gates, with the PTTG one can build digital circuits more compactly. The proposed PTTGs are promising for future smart nanoscale digital system use.

Phase transition in NK-Kauffman networks and its correction for Boolean irreducibility

NASA Astrophysics Data System (ADS)

Zertuche, Federico

2014-05-01

In a series of articles published in 1986, Derrida and his colleagues studied two mean field treatments (the quenched and the annealed) for NK-Kauffman networks. Their main results lead to a phase transition curve Kc 2 pc(1-pc)=1 (0

Controllability and observability of Boolean networks arising from biology

NASA Astrophysics Data System (ADS)

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.

Solving a discrete model of the lac operon using Z3

NASA Astrophysics Data System (ADS)

Gutierrez, Natalia A.

2014-05-01

A discrete model for the Lcac Operon is solved using the SMT-solver Z3. Traditionally the Lac Operon is formulated in a continuous math model. This model is a system of ordinary differential equations. Here, it was considerated as a discrete model, based on a Boolean red. The biological problem of Lac Operon is enunciated as a problem of Boolean satisfiability, and it is solved using an STM-solver named Z3. Z3 is a powerful solver that allows understanding the basic dynamic of the Lac Operon in an easier and more efficient way. The multi-stability of the Lac Operon can be easily computed with Z3. The code that solves the Boolean red can be written in Python language or SMT-Lib language. Both languages were used in local version of the program as online version of Z3. For future investigations it is proposed to solve the Boolean red of Lac Operon using others SMT-solvers as cvc4, alt-ergo, mathsat and yices.

Multilayer neural networks with extensively many hidden units.

PubMed

Rosen-Zvi, M; Engel, A; Kanter, I

2001-08-13

The information processing abilities of a multilayer neural network with a number of hidden units scaling as the input dimension are studied using statistical mechanics methods. The mapping from the input layer to the hidden units is performed by general symmetric Boolean functions, whereas the hidden layer is connected to the output by either discrete or continuous couplings. Introducing an overlap in the space of Boolean functions as order parameter, the storage capacity is found to scale with the logarithm of the number of implementable Boolean functions. The generalization behavior is smooth for continuous couplings and shows a discontinuous transition to perfect generalization for discrete ones.

Toxicological Tipping Points: Learning Boolean Networks from High-Content Imaging Data. (BOSC meeting)

EPA Science Inventory

The objective of this work is to elucidate biological networks underlying cellular tipping points using time-course data. We discretized the high-content imaging (HCI) data and inferred Boolean networks (BNs) that could accurately predict dynamic cellular trajectories. We found t...

Boolean linear differential operators on elementary cellular automata

NASA Astrophysics Data System (ADS)

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.

Describing the What and Why of Students' Difficulties in Boolean Logic

ERIC Educational Resources Information Center

Herman, Geoffrey L.; Loui, Michael C.; Kaczmarczyk, Lisa; Zilles, Craig

2012-01-01

The ability to reason with formal logic is a foundational skill for computer scientists and computer engineers that scaffolds the abilities to design, debug, and optimize. By interviewing students about their understanding of propositional logic and their ability to translate from English specifications to Boolean expressions, we characterized…

Evolution of canalizing Boolean networks

NASA Astrophysics Data System (ADS)

Szejka, A.; Drossel, B.

2007-04-01

Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive walk, which allows us to explore the fitness landscape. Mutations change the connections and the functions of the nodes. Our fitness criterion is the robustness of the dynamical attractors against small perturbations. We find that with this fitness criterion the global maximum is always reached and that there is a huge neutral space of 100% fitness. Furthermore, in spite of having such a high degree of robustness, the evolved networks still share many features with “chaotic” networks.

Using Synchronous Boolean Networks to Model Several Phenomena of Collective Behavior

PubMed Central

Kochemazov, Stepan; Semenov, Alexander

2014-01-01

In this paper, we propose an approach for modeling and analysis of a number of phenomena of collective behavior. By collectives we mean multi-agent systems that transition from one state to another at discrete moments of time. The behavior of a member of a collective (agent) is called conforming if the opinion of this agent at current time moment conforms to the opinion of some other agents at the previous time moment. We presume that at each moment of time every agent makes a decision by choosing from the set (where 1-decision corresponds to action and 0-decision corresponds to inaction). In our approach we model collective behavior with synchronous Boolean networks. We presume that in a network there can be agents that act at every moment of time. Such agents are called instigators. Also there can be agents that never act. Such agents are called loyalists. Agents that are neither instigators nor loyalists are called simple agents. We study two combinatorial problems. The first problem is to find a disposition of instigators that in several time moments transforms a network from a state where the majority of simple agents are inactive to a state with the majority of active agents. The second problem is to find a disposition of loyalists that returns the network to a state with the majority of inactive agents. Similar problems are studied for networks in which simple agents demonstrate the contrary to conforming behavior that we call anticonforming. We obtained several theoretical results regarding the behavior of collectives of agents with conforming or anticonforming behavior. In computational experiments we solved the described problems for randomly generated networks with several hundred vertices. We reduced corresponding combinatorial problems to the Boolean satisfiability problem (SAT) and used modern SAT solvers to solve the instances obtained. PMID:25526612

TemperSAT: A new efficient fair-sampling random k-SAT solver

NASA Astrophysics Data System (ADS)

Fang, Chao; Zhu, Zheng; Katzgraber, Helmut G.

The set membership problem is of great importance to many applications and, in particular, database searches for target groups. Recently, an approach to speed up set membership searches based on the NP-hard constraint-satisfaction problem (random k-SAT) has been developed. However, the bottleneck of the approach lies in finding the solution to a large SAT formula efficiently and, in particular, a large number of independent solutions is needed to reduce the probability of false positives. Unfortunately, traditional random k-SAT solvers such as WalkSAT are biased when seeking solutions to the Boolean formulas. By porting parallel tempering Monte Carlo to the sampling of binary optimization problems, we introduce a new algorithm (TemperSAT) whose performance is comparable to current state-of-the-art SAT solvers for large k with the added benefit that theoretically it can find many independent solutions quickly. We illustrate our results by comparing to the currently fastest implementation of WalkSAT, WalkSATlm.

Effects of topology on network evolution

NASA Astrophysics Data System (ADS)

Oikonomou, Panos; Cluzel, Philippe

2006-08-01

The ubiquity of scale-free topology in nature raises the question of whether this particular network design confers an evolutionary advantage. A series of studies has identified key principles controlling the growth and the dynamics of scale-free networks. Here, we use neuron-based networks of boolean components as a framework for modelling a large class of dynamical behaviours in both natural and artificial systems. Applying a training algorithm, we characterize how networks with distinct topologies evolve towards a pre-established target function through a process of random mutations and selection. We find that homogeneous random networks and scale-free networks exhibit drastically different evolutionary paths. Whereas homogeneous random networks accumulate neutral mutations and evolve by sparse punctuated steps, scale-free networks evolve rapidly and continuously. Remarkably, this latter property is robust to variations of the degree exponent. In contrast, homogeneous random networks require a specific tuning of their connectivity to optimize their ability to evolve. These results highlight an organizing principle that governs the evolution of complex networks and that can improve the design of engineered systems.

Circulant Matrices and Affine Equivalence of Monomial Rotation Symmetric Boolean Functions

DTIC Science & Technology

2015-01-01

definitions , including monomial rotation symmetric (MRS) Boolean functions and affine equivalence, and a known result for such quadratic functions...degree of the MRS is, we have a similar result as [40, Theorem 1.1] for n = 4p (p prime), or squarefree integers n, which along with our Theorem 5.2

User Practices in Keyword and Boolean Searching on an Online Public Access Catalog.

ERIC Educational Resources Information Center

Ensor, Pat

1992-01-01

Discussion of keyword and Boolean searching techniques in online public access catalogs (OPACs) focuses on a study conducted at Indiana State University that examined users' attitudes toward searching on NOTIS (Northwestern Online Total Integrated System). Relevant literature is reviewed, and implications for library instruction are suggested. (17…

Using Vector and Extended Boolean Matching in an Expert System for Selecting Foster Homes.

ERIC Educational Resources Information Center

Fox, Edward A.; Winett, Sheila G.

1990-01-01

Describes FOCES (Foster Care Expert System), a prototype expert system for choosing foster care placements for children which integrates information retrieval techniques with artificial intelligence. The use of prototypes and queries in Prolog routines, extended Boolean matching, and vector correlation are explained, as well as evaluation by…

A Construction of Boolean Functions with Good Cryptographic Properties

DTIC Science & Technology

2014-01-01

be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. 1. REPORT...2008, LNCS 5350, Springer–Verlag, 2008, pp. 425–440. [10] C. Carlet and K. Feng, “An Infinite Class of Balanced Vectorial Boolean Functions with Optimum

Using computer algebra and SMT solvers in algebraic biology

NASA Astrophysics Data System (ADS)

Pineda Osorio, Mateo

2014-05-01

Biologic processes are represented as Boolean networks, in a discrete time. The dynamics within these networks are approached with the help of SMT Solvers and the use of computer algebra. Software such as Maple and Z3 was used in this case. The number of stationary states for each network was calculated. The network studied here corresponds to the immune system under the effects of drastic mood changes. Mood is considered as a Boolean variable that affects the entire dynamics of the immune system, changing the Boolean satisfiability and the number of stationary states of the immune network. Results obtained show Z3's great potential as a SMT Solver. Some of these results were verified in Maple, even though it showed not to be as suitable for the problem approach. The solving code was constructed using Z3-Python and Z3-SMT-LiB. Results obtained are important in biology systems and are expected to help in the design of immune therapies. As a future line of research, more complex Boolean network representations of the immune system as well as the whole psychological apparatus are suggested.

Therapeutic target discovery using Boolean network attractors: improvements of kali

PubMed Central

Guziolowski, Carito

2018-01-01

In a previous article, an algorithm for identifying therapeutic targets in Boolean networks modelling pathological mechanisms was introduced. In the present article, the improvements made on this algorithm, named kali, are described. These improvements are (i) the possibility to work on asynchronous Boolean networks, (ii) a finer assessment of therapeutic targets and (iii) the possibility to use multivalued logic. kali assumes that the attractors of a dynamical system, such as a Boolean network, are associated with the phenotypes of the modelled biological system. Given a logic-based model of pathological mechanisms, kali searches for therapeutic targets able to reduce the reachability of the attractors associated with pathological phenotypes, thus reducing their likeliness. kali is illustrated on an example network and used on a biological case study. The case study is a published logic-based model of bladder tumorigenesis from which kali returns consistent results. However, like any computational tool, kali can predict but cannot replace human expertise: it is a supporting tool for coping with the complexity of biological systems in the field of drug discovery. PMID:29515890

3D Boolean operations in virtual surgical planning.

PubMed

Charton, Jerome; Laurentjoye, Mathieu; Kim, Youngjun

2017-10-01

Boolean operations in computer-aided design or computer graphics are a set of operations (e.g. intersection, union, subtraction) between two objects (e.g. a patient model and an implant model) that are important in performing accurate and reproducible virtual surgical planning. This requires accurate and robust techniques that can handle various types of data, such as a surface extracted from volumetric data, synthetic models, and 3D scan data. This article compares the performance of the proposed method (Boolean operations by a robust, exact, and simple method between two colliding shells (BORES)) and an existing method based on the Visualization Toolkit (VTK). In all tests presented in this article, BORES could handle complex configurations as well as report impossible configurations of the input. In contrast, the VTK implementations were unstable, do not deal with singular edges and coplanar collisions, and have created several defects. The proposed method of Boolean operations, BORES, is efficient and appropriate for virtual surgical planning. Moreover, it is simple and easy to implement. In future work, we will extend the proposed method to handle non-colliding components.

Generalization and capacity of extensively large two-layered perceptrons.

PubMed

Rosen-Zvi, Michal; Engel, Andreas; Kanter, Ido

2002-09-01

The generalization ability and storage capacity of a treelike two-layered neural network with a number of hidden units scaling as the input dimension is examined. The mapping from the input to the hidden layer is via Boolean functions; the mapping from the hidden layer to the output is done by a perceptron. The analysis is within the replica framework where an order parameter characterizing the overlap between two networks in the combined space of Boolean functions and hidden-to-output couplings is introduced. The maximal capacity of such networks is found to scale linearly with the logarithm of the number of Boolean functions per hidden unit. The generalization process exhibits a first-order phase transition from poor to perfect learning for the case of discrete hidden-to-output couplings. The critical number of examples per input dimension, alpha(c), at which the transition occurs, again scales linearly with the logarithm of the number of Boolean functions. In the case of continuous hidden-to-output couplings, the generalization error decreases according to the same power law as for the perceptron, with the prefactor being different.

Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming.

PubMed

Ostrowski, M; Paulevé, L; Schaub, T; Siegel, A; Guziolowski, C

2016-11-01

Boolean networks (and more general logic models) are useful frameworks to study signal transduction across multiple pathways. Logic models can be learned from a prior knowledge network structure and multiplex phosphoproteomics data. However, most efficient and scalable training methods focus on the comparison of two time-points and assume that the system has reached an early steady state. In this paper, we generalize such a learning procedure to take into account the time series traces of phosphoproteomics data in order to discriminate Boolean networks according to their transient dynamics. To that end, we identify a necessary condition that must be satisfied by the dynamics of a Boolean network to be consistent with a discretized time series trace. Based on this condition, we use Answer Set Programming to compute an over-approximation of the set of Boolean networks which fit best with experimental data and provide the corresponding encodings. Combined with model-checking approaches, we end up with a global learning algorithm. Our approach is able to learn logic models with a true positive rate higher than 78% in two case studies of mammalian signaling networks; for a larger case study, our method provides optimal answers after 7min of computation. We quantified the gain in our method predictions precision compared to learning approaches based on static data. Finally, as an application, our method proposes erroneous time-points in the time series data with respect to the optimal learned logic models. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation.

PubMed

Polak, Marta E; Ung, Chuin Ying; Masapust, Joanna; Freeman, Tom C; Ardern-Jones, Michael R

2017-04-06

Langerhans cells (LCs) are able to orchestrate adaptive immune responses in the skin by interpreting the microenvironmental context in which they encounter foreign substances, but the regulatory basis for this has not been established. Utilising systems immunology approaches combining in silico modelling of a reconstructed gene regulatory network (GRN) with in vitro validation of the predictions, we sought to determine the mechanisms of regulation of immune responses in human primary LCs. The key role of Interferon regulatory factors (IRFs) as controllers of the human Langerhans cell response to epidermal cytokines was revealed by whole transcriptome analysis. Applying Boolean logic we assembled a Petri net-based model of the IRF-GRN which provides molecular pathway predictions for the induction of different transcriptional programmes in LCs. In silico simulations performed after model parameterisation with transcription factor expression values predicted that human LC activation of antigen-specific CD8 T cells would be differentially regulated by epidermal cytokine induction of specific IRF-controlled pathways. This was confirmed by in vitro measurement of IFN-γ production by activated T cells. As a proof of concept, this approach shows that stochastic modelling of a specific immune networks renders transcriptome data valuable for the prediction of functional outcomes of immune responses.

Steady state analysis of Boolean molecular network models via model reduction and computational algebra.

PubMed

Veliz-Cuba, Alan; Aguilar, Boris; Hinkelmann, Franziska; Laubenbacher, Reinhard

2014-06-26

A key problem in the analysis of mathematical models of molecular networks is the determination of their steady states. The present paper addresses this problem for Boolean network models, an increasingly popular modeling paradigm for networks lacking detailed kinetic information. For small models, the problem can be solved by exhaustive enumeration of all state transitions. But for larger models this is not feasible, since the size of the phase space grows exponentially with the dimension of the network. The dimension of published models is growing to over 100, so that efficient methods for steady state determination are essential. Several methods have been proposed for large networks, some of them heuristic. While these methods represent a substantial improvement in scalability over exhaustive enumeration, the problem for large networks is still unsolved in general. This paper presents an algorithm that consists of two main parts. The first is a graph theoretic reduction of the wiring diagram of the network, while preserving all information about steady states. The second part formulates the determination of all steady states of a Boolean network as a problem of finding all solutions to a system of polynomial equations over the finite number system with two elements. This problem can be solved with existing computer algebra software. This algorithm compares favorably with several existing algorithms for steady state determination. One advantage is that it is not heuristic or reliant on sampling, but rather determines algorithmically and exactly all steady states of a Boolean network. The code for the algorithm, as well as the test suite of benchmark networks, is available upon request from the corresponding author. The algorithm presented in this paper reliably determines all steady states of sparse Boolean networks with up to 1000 nodes. The algorithm is effective at analyzing virtually all published models even those of moderate connectivity. The problem for large Boolean networks with high average connectivity remains an open problem.

Steady state analysis of Boolean molecular network models via model reduction and computational algebra

PubMed Central

2014-01-01

Background A key problem in the analysis of mathematical models of molecular networks is the determination of their steady states. The present paper addresses this problem for Boolean network models, an increasingly popular modeling paradigm for networks lacking detailed kinetic information. For small models, the problem can be solved by exhaustive enumeration of all state transitions. But for larger models this is not feasible, since the size of the phase space grows exponentially with the dimension of the network. The dimension of published models is growing to over 100, so that efficient methods for steady state determination are essential. Several methods have been proposed for large networks, some of them heuristic. While these methods represent a substantial improvement in scalability over exhaustive enumeration, the problem for large networks is still unsolved in general. Results This paper presents an algorithm that consists of two main parts. The first is a graph theoretic reduction of the wiring diagram of the network, while preserving all information about steady states. The second part formulates the determination of all steady states of a Boolean network as a problem of finding all solutions to a system of polynomial equations over the finite number system with two elements. This problem can be solved with existing computer algebra software. This algorithm compares favorably with several existing algorithms for steady state determination. One advantage is that it is not heuristic or reliant on sampling, but rather determines algorithmically and exactly all steady states of a Boolean network. The code for the algorithm, as well as the test suite of benchmark networks, is available upon request from the corresponding author. Conclusions The algorithm presented in this paper reliably determines all steady states of sparse Boolean networks with up to 1000 nodes. The algorithm is effective at analyzing virtually all published models even those of moderate connectivity. The problem for large Boolean networks with high average connectivity remains an open problem. PMID:24965213

Identification of Boolean Network Models From Time Series Data Incorporating Prior Knowledge.

PubMed

Leifeld, Thomas; Zhang, Zhihua; Zhang, Ping

2018-01-01

Motivation: Mathematical models take an important place in science and engineering. A model can help scientists to explain dynamic behavior of a system and to understand the functionality of system components. Since length of a time series and number of replicates is limited by the cost of experiments, Boolean networks as a structurally simple and parameter-free logical model for gene regulatory networks have attracted interests of many scientists. In order to fit into the biological contexts and to lower the data requirements, biological prior knowledge is taken into consideration during the inference procedure. In the literature, the existing identification approaches can only deal with a subset of possible types of prior knowledge. Results: We propose a new approach to identify Boolean networks from time series data incorporating prior knowledge, such as partial network structure, canalizing property, positive and negative unateness. Using vector form of Boolean variables and applying a generalized matrix multiplication called the semi-tensor product (STP), each Boolean function can be equivalently converted into a matrix expression. Based on this, the identification problem is reformulated as an integer linear programming problem to reveal the system matrix of Boolean model in a computationally efficient way, whose dynamics are consistent with the important dynamics captured in the data. By using prior knowledge the number of candidate functions can be reduced during the inference. Hence, identification incorporating prior knowledge is especially suitable for the case of small size time series data and data without sufficient stimuli. The proposed approach is illustrated with the help of a biological model of the network of oxidative stress response. Conclusions: The combination of efficient reformulation of the identification problem with the possibility to incorporate various types of prior knowledge enables the application of computational model inference to systems with limited amount of time series data. The general applicability of this methodological approach makes it suitable for a variety of biological systems and of general interest for biological and medical research.

Modeling integrated cellular machinery using hybrid Petri-Boolean networks.

PubMed

Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay

2013-01-01

The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more detailed mathematical models.

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

PubMed Central

Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay

2013-01-01

The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more detailed mathematical models. PMID:24244124

featsel: A framework for benchmarking of feature selection algorithms and cost functions

NASA Astrophysics Data System (ADS)

Reis, Marcelo S.; Estrela, Gustavo; Ferreira, Carlos Eduardo; Barrera, Junior

In this paper, we introduce featsel, a framework for benchmarking of feature selection algorithms and cost functions. This framework allows the user to deal with the search space as a Boolean lattice and has its core coded in C++ for computational efficiency purposes. Moreover, featsel includes Perl scripts to add new algorithms and/or cost functions, generate random instances, plot graphs and organize results into tables. Besides, this framework already comes with dozens of algorithms and cost functions for benchmarking experiments. We also provide illustrative examples, in which featsel outperforms the popular Weka workbench in feature selection procedures on data sets from the UCI Machine Learning Repository.

Interpolation of the Extended Boolean Retrieval Model.

ERIC Educational Resources Information Center

Zanger, Daniel Z.

2002-01-01

Presents an interpolation theorem for an extended Boolean information retrieval model. Results show that whenever two or more documents are similarly ranked at any two points for a query containing exactly two terms, then they are similarly ranked at all points in between; and that results can fail for queries with more than two terms. (Author/LRW)

The Concept of the "Imploded Boolean Search": A Case Study with Undergraduate Chemistry Students

ERIC Educational Resources Information Center

Tomaszewski, Robert

2016-01-01

Critical thinking and analytical problem-solving skills in research involves using different search strategies. A proposed concept for an "Imploded Boolean Search" combines three unique identifiable field types to perform a search: keyword(s), numerical value(s), and a chemical structure or reaction. The object of this type of search is…

Optical programmable Boolean logic unit.

PubMed

Chattopadhyay, Tanay

2011-11-10

Logic units are the building blocks of many important computational operations likes arithmetic, multiplexer-demultiplexer, radix conversion, parity checker cum generator, etc. Multifunctional logic operation is very much essential in this respect. Here a programmable Boolean logic unit is proposed that can perform 16 Boolean logical operations from a single optical input according to the programming input without changing the circuit design. This circuit has two outputs. One output is complementary to the other. Hence no loss of data can occur. The circuit is basically designed by a 2×2 polarization independent optical cross bar switch. Performance of the proposed circuit has been achieved by doing numerical simulations. The binary logical states (0,1) are represented by the absence of light (null) and presence of light, respectively.

Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction.

PubMed

Velderraín, José Dávila; Martínez-García, Juan Carlos; Álvarez-Buylla, Elena R

2017-01-01

Mathematical models based on dynamical systems theory are well-suited tools for the integration of available molecular experimental data into coherent frameworks in order to propose hypotheses about the cooperative regulatory mechanisms driving developmental processes. Computational analysis of the proposed models using well-established methods enables testing the hypotheses by contrasting predictions with observations. Within such framework, Boolean gene regulatory network dynamical models have been extensively used in modeling plant development. Boolean models are simple and intuitively appealing, ideal tools for collaborative efforts between theorists and experimentalists. In this chapter we present protocols used in our group for the study of diverse plant developmental processes. We focus on conceptual clarity and practical implementation, providing directions to the corresponding technical literature.

A different Deutsch-Jozsa

NASA Astrophysics Data System (ADS)

Bera, Debajyoti

2015-06-01

One of the early achievements of quantum computing was demonstrated by Deutsch and Jozsa (Proc R Soc Lond A Math Phys Sci 439(1907):553, 1992) regarding classification of a particular type of Boolean functions. Their solution demonstrated an exponential speedup compared to classical approaches to the same problem; however, their solution was the only known quantum algorithm for that specific problem so far. This paper demonstrates another quantum algorithm for the same problem, with the same exponential advantage compared to classical algorithms. The novelty of this algorithm is the use of quantum amplitude amplification, a technique that is the key component of another celebrated quantum algorithm developed by Grover (Proceedings of the twenty-eighth annual ACM symposium on theory of computing, ACM Press, New York, 1996). A lower bound for randomized (classical) algorithms is also presented which establishes a sound gap between the effectiveness of our quantum algorithm and that of any randomized algorithm with similar efficiency.

Multiscale volatility duration characteristics on financial multi-continuum percolation dynamics

NASA Astrophysics Data System (ADS)

Wang, Min; Wang, Jun

A random stock price model based on the multi-continuum percolation system is developed to investigate the nonlinear dynamics of stock price volatility duration, in an attempt to explain various statistical facts found in financial data, and have a deeper understanding of mechanisms in the financial market. The continuum percolation system is usually referred to be a random coverage process or a Boolean model, it is a member of a class of statistical physics systems. In this paper, the multi-continuum percolation (with different values of radius) is employed to model and reproduce the dispersal of information among the investors. To testify the rationality of the proposed model, the nonlinear analyses of return volatility duration series are preformed by multifractal detrending moving average analysis and Zipf analysis. The comparison empirical results indicate the similar nonlinear behaviors for the proposed model and the actual Chinese stock market.

Designing Networks that are Capable of Self-Healing and Adapting

DTIC Science & Technology

2017-04-01

from statistical mechanics, combinatorics, boolean networks, and numerical simulations, and inspired by design principles from biological networks, we... principles for self-healing networks, and applications, and construct an all-possible-paths model for network adaptation. 2015-11-16 UNIT CONVERSION...combinatorics, boolean networks, and numerical simulations, and inspired by design principles from biological networks, we will undertake the fol

Equilibrium and nonequilibrium properties of Boolean decision problems on scale-free graphs with competing interactions with external biases

NASA Astrophysics Data System (ADS)

Zhu, Zheng; Andresen, Juan Carlos; Janzen, Katharina; Katzgraber, Helmut G.

2013-03-01

We study the equilibrium and nonequilibrium properties of Boolean decision problems with competing interactions on scale-free graphs in a magnetic field. Previous studies at zero field have shown a remarkable equilibrium stability of Boolean variables (Ising spins) with competing interactions (spin glasses) on scale-free networks. When the exponent that describes the power-law decay of the connectivity of the network is strictly larger than 3, the system undergoes a spin-glass transition. However, when the exponent is equal to or less than 3, the glass phase is stable for all temperatures. First we perform finite-temperature Monte Carlo simulations in a field to test the robustness of the spin-glass phase and show, in agreement with analytical calculations, that the system exhibits a de Almeida-Thouless line. Furthermore, we study avalanches in the system at zero temperature to see if the system displays self-organized criticality. This would suggest that damage (avalanches) can spread across the whole system with nonzero probability, i.e., that Boolean decision problems on scale-free networks with competing interactions are fragile when not in thermal equilibrium.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivera-Durón, R. R., E-mail: roberto.rivera@ipicyt.edu.mx; Campos-Cantón, E., E-mail: eric.campos@ipicyt.edu.mx; Campos-Cantón, I.

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 enablemore » 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.« less

Stabilizing Motifs in Autonomous Boolean Networks and the Yeast Cell Cycle Oscillator

NASA Astrophysics Data System (ADS)

Sevim, Volkan; Gong, Xinwei; Socolar, Joshua

2009-03-01

Synchronously updated Boolean networks are widely used to model gene regulation. Some properties of these model networks are known to be artifacts of the clocking in the update scheme. Autonomous updating is a less artificial scheme that allows one to introduce small timing perturbations and study stability of the attractors. We argue that the stabilization of a limit cycle in an autonomous Boolean network requires a combination of motifs such as feed-forward loops and auto-repressive links that can correct small fluctuations in the timing of switching events. A recently published model of the transcriptional cell-cycle oscillator in yeast contains the motifs necessary for stability under autonomous updating [1]. [1] D. A. Orlando, et al. Nature (London), 4530 (7197):0 944--947, 2008.

Towards Symbolic Model Checking for Multi-Agent Systems via OBDDs

NASA Technical Reports Server (NTRS)

Raimondi, Franco; Lomunscio, Alessio

2004-01-01

We present an algorithm for model checking temporal-epistemic properties of multi-agent systems, expressed in the formalism of interpreted systems. We first introduce a technique for the translation of interpreted systems into boolean formulae, and then present a model-checking algorithm based on this translation. The algorithm is based on OBDD's, as they offer a compact and efficient representation for boolean formulae.

Feedback Controller Design for the Synchronization of Boolean Control Networks.

PubMed

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.

Computer Aided Instruction for a Course in Boolean Algebra and Logic Design. Final Report (Revised).

ERIC Educational Resources Information Center

Roy, Rob

The use of computers to prepare deficient college and graduate students for courses that build upon previously acquired information would solve the growing problem of professors who must spend up to one third of their class time in review of material. But examination of students who were taught Boolean Algebra and Logic Design by means of Computer…

Deriving Laws from Ordering Relations

NASA Technical Reports Server (NTRS)

Knuth, Kevin H.

2003-01-01

It took much effort in the early days of non-Euclidean geometry to break away from the mindset that all spaces are flat and that two distinct parallel lines do not cross. Up to that point, all that was known was Euclidean geometry, and it was difficult to imagine anything else. We have suffered a similar handicap brought on by the enormous relevance of Boolean algebra to the problems of our age-logic and set theory. Previously, I demonstrated that the algebra of questions is not Boolean, but rather is described by the free distributive algebra. To get to this stage took much effort, as many obstacles-most self-placed-had to be overcome. As Boolean algebras were all I had ever known, it was almost impossible for me to imagine working with an algebra where elements do not have complements. With this realization, it became very clear that the sum and product rules of probability theory at the most basic level had absolutely nothing to do with the Boolean algebra of logical statements. Instead, a measure of degree of inclusion can be invented for many different partially ordered sets, and the sum and product rules fall out of the associativity and distributivity of the algebra. To reinforce this very important idea, this paper will go over how these constructions are made, while focusing on the underlying assumptions. I will derive the sum and product rules for a distributive lattice in general and demonstrate how this leads to probability theory on the Boolean lattice and is related to the calculus of quantum mechanical amplitudes on the partially ordered set of experimental setups. I will also discuss the rules that can be derived from modular lattices and their relevance to the cross-ratio of projective geometry.

Identification of control targets in Boolean molecular network models via computational algebra.

PubMed

Murrugarra, David; Veliz-Cuba, Alan; Aguilar, Boris; Laubenbacher, Reinhard

2016-09-23

Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The potential control targets can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. This paper presents a method for the identification of potential intervention targets in Boolean molecular network models using algebraic techniques. The approach exploits an algebraic representation of Boolean networks to encode the control candidates in the network wiring diagram as the solutions of a system of polynomials equations, and then uses computational algebra techniques to find such controllers. The control methods in this paper are validated through the identification of combinatorial interventions in the signaling pathways of previously reported control targets in two well studied systems, a p53-mdm2 network and a blood T cell lymphocyte granular leukemia survival signaling network. Supplementary data is available online and our code in Macaulay2 and Matlab are available via http://www.ms.uky.edu/~dmu228/ControlAlg . This paper presents a novel method for the identification of intervention targets in Boolean network models. The results in this paper show that the proposed methods are useful and efficient for moderately large networks.

Observability of Boolean multiplex control networks

NASA Astrophysics Data System (ADS)

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.

Boolean network representation of contagion dynamics during a financial crisis

NASA Astrophysics Data System (ADS)

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.

Collective dynamics in heterogeneous networks of neuronal cellular automata

NASA Astrophysics Data System (ADS)

Manchanda, Kaustubh; Bose, Amitabha; Ramaswamy, Ramakrishna

2017-12-01

We examine the collective dynamics of heterogeneous random networks of model neuronal cellular automata. Each automaton has b active states, a single silent state and r - b - 1 refractory states, and can show 'spiking' or 'bursting' behavior, depending on the values of b. We show that phase transitions that occur in the dynamical activity can be related to phase transitions in the structure of Erdõs-Rényi graphs as a function of edge probability. Different forms of heterogeneity allow distinct structural phase transitions to become relevant. We also show that the dynamics on the network can be described by a semi-annealed process and, as a result, can be related to the Boolean Lyapunov exponent.

Modeling stochasticity and robustness in gene regulatory networks.

PubMed

Garg, Abhishek; Mohanram, Kartik; Di Cara, Alessandro; De Micheli, Giovanni; Xenarios, Ioannis

2009-06-15

Understanding gene regulation in biological processes and modeling the robustness of underlying regulatory networks is an important problem that is currently being addressed by computational systems biologists. Lately, there has been a renewed interest in Boolean modeling techniques for gene regulatory networks (GRNs). However, due to their deterministic nature, it is often difficult to identify whether these modeling approaches are robust to the addition of stochastic noise that is widespread in gene regulatory processes. Stochasticity in Boolean models of GRNs has been addressed relatively sparingly in the past, mainly by flipping the expression of genes between different expression levels with a predefined probability. This stochasticity in nodes (SIN) model leads to over representation of noise in GRNs and hence non-correspondence with biological observations. In this article, we introduce the stochasticity in functions (SIF) model for simulating stochasticity in Boolean models of GRNs. By providing biological motivation behind the use of the SIF model and applying it to the T-helper and T-cell activation networks, we show that the SIF model provides more biologically robust results than the existing SIN model of stochasticity in GRNs. Algorithms are made available under our Boolean modeling toolbox, GenYsis. The software binaries can be downloaded from http://si2.epfl.ch/ approximately garg/genysis.html.

Discrete interference modeling via boolean algebra.

PubMed

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.

Boolean decision problems with competing interactions on scale-free networks: Equilibrium and nonequilibrium behavior in an external bias

NASA Astrophysics Data System (ADS)

Zhu, Zheng; Andresen, Juan Carlos; Moore, M. A.; Katzgraber, Helmut G.

2014-02-01

We study the equilibrium and nonequilibrium properties of Boolean decision problems with competing interactions on scale-free networks in an external bias (magnetic field). Previous studies at zero field have shown a remarkable equilibrium stability of Boolean variables (Ising spins) with competing interactions (spin glasses) on scale-free networks. When the exponent that describes the power-law decay of the connectivity of the network is strictly larger than 3, the system undergoes a spin-glass transition. However, when the exponent is equal to or less than 3, the glass phase is stable for all temperatures. First, we perform finite-temperature Monte Carlo simulations in a field to test the robustness of the spin-glass phase and show that the system has a spin-glass phase in a field, i.e., exhibits a de Almeida-Thouless line. Furthermore, we study avalanche distributions when the system is driven by a field at zero temperature to test if the system displays self-organized criticality. Numerical results suggest that avalanches (damage) can spread across the whole system with nonzero probability when the decay exponent of the interaction degree is less than or equal to 2, i.e., that Boolean decision problems on scale-free networks with competing interactions can be fragile when not in thermal equilibrium.

Exact Algorithms for Output Encoding, State Assignment and Four-Level Boolean Minimization

DTIC Science & Technology

1989-10-01

APPROVED FOR PUBLIC DISTRIBUTION • DTIC MASSACHUSETTS INTITUTE OF TECHNOLOGY M VLSI PUBLICATIONSJAN 17 1990 VLSI Memo No. 89-569 JN. 9October 1989...nunijize large funclions exacly within reasonable amocunt. of CPt targeting twro-level logic imnplemientations involve finding ap- time. However, thle ,, m ...0(NV!) m ~iimizations . n5 10 The inptut encoding problemt can be exactly solved using mrultiple-valued Boolean nimuization. We present an exact (a) (b

Boolean logic tree of graphene-based chemical system for molecular computation and intelligent molecular search query.

PubMed

Huang, Wei Tao; Luo, Hong Qun; Li, Nian Bing

2014-05-06

The most serious, and yet unsolved, problem of constructing molecular computing devices consists in connecting all of these molecular events into a usable device. This report demonstrates the use of Boolean logic tree for analyzing the chemical event network based on graphene, organic dye, thrombin aptamer, and Fenton reaction, organizing and connecting these basic chemical events. And this chemical event network can be utilized to implement fluorescent combinatorial logic (including basic logic gates and complex integrated logic circuits) and fuzzy logic computing. On the basis of the Boolean logic tree analysis and logic computing, these basic chemical events can be considered as programmable "words" and chemical interactions as "syntax" logic rules to construct molecular search engine for performing intelligent molecular search query. Our approach is helpful in developing the advanced logic program based on molecules for application in biosensing, nanotechnology, and drug delivery.

A single-layer platform for Boolean logic and arithmetic through DNA excision in mammalian cells

PubMed Central

Weinberg, Benjamin H.; Hang Pham, N. T.; Caraballo, Leidy D.; Lozanoski, Thomas; Engel, Adrien; Bhatia, Swapnil; Wong, Wilson W.

2017-01-01

Genetic circuits engineered for mammalian cells often require extensive fine-tuning to perform their intended functions. To overcome this problem, we present a generalizable biocomputing platform that can engineer genetic circuits which function in human cells with minimal optimization. We used our Boolean Logic and Arithmetic through DNA Excision (BLADE) platform to build more than 100 multi-input-multi-output circuits. We devised a quantitative metric to evaluate the performance of the circuits in human embryonic kidney and Jurkat T cells. Of 113 circuits analysed, 109 functioned (96.5%) with the correct specified behavior without any optimization. We used our platform to build a three-input, two-output Full Adder and six-input, one-output Boolean Logic Look Up Table. We also used BLADE to design circuits with temporal small molecule-mediated inducible control and circuits that incorporate CRISPR/Cas9 to regulate endogenous mammalian genes. PMID:28346402

An Automated Design Framework for Multicellular Recombinase Logic.

PubMed

Guiziou, Sarah; Ulliana, Federico; Moreau, Violaine; Leclere, Michel; Bonnet, Jerome

2018-05-18

Tools to systematically reprogram cellular behavior are crucial to address pressing challenges in manufacturing, environment, or healthcare. Recombinases can very efficiently encode Boolean and history-dependent logic in many species, yet current designs are performed on a case-by-case basis, limiting their scalability and requiring time-consuming optimization. Here we present an automated workflow for designing recombinase logic devices executing Boolean functions. Our theoretical framework uses a reduced library of computational devices distributed into different cellular subpopulations, which are then composed in various manners to implement all desired logic functions at the multicellular level. Our design platform called CALIN (Composable Asynchronous Logic using Integrase Networks) is broadly accessible via a web server, taking truth tables as inputs and providing corresponding DNA designs and sequences as outputs (available at http://synbio.cbs.cnrs.fr/calin ). We anticipate that this automated design workflow will streamline the implementation of Boolean functions in many organisms and for various applications.

The effect of small solar powered 'Bͻkͻͻ' net fans on mosquito net use: results from a randomized controlled cross-over trial in southern Ghana.

PubMed

Briët, Olivier J T; Yukich, Joshua O; Pfeiffer, Constanze; Miller, William; Jaeger, Mulako S; Khanna, Nitin; Oppong, Samuel; Nardini, Peter; Ahorlu, Collins K; Keating, Joseph

2017-01-03

Long-lasting insecticidal nets (LLINs) are ineffective malaria transmission prevention tools if they are unused. Discomfort due to heat is the most commonly reported reason for not using nets, but this problem is largely unaddressed. With increasing rural electrification and the dropping price of solar power, fans could improve comfort inside nets and be affordable to populations in malaria endemic areas. Here, results are presented from a pilot randomized controlled cross-over study testing the effect of fans on LLIN use. Eighty-three households from two rural communities in Greater Accra, Ghana, randomized into three groups, participated in a 10-month cross-over trial. After a screening survey to identify eligible households, all households received new LLINs. Bͻkͻͻ net fan systems (one fan per member) were given to households in Group 1 and water filters were given to households in Group 2. At mid-point, Group 1 and 2 crossed over interventions. Households in Group 1 and 2 participated in fortnightly surveys on households' practices related to nets, fans and water filters, while households in Group 3 were surveyed only at screening, mid-point and study end. Entomological and weather data were collected throughout the study. Analysis took both 'per protocol' (PP) and 'intention to treat' (ITT) approaches. The mid- and end-point survey data from Group 1 and 2 were analysed using Firth logistic regressions. Fortnightly survey data from all groups were analysed using logistic regressions with random effects. Provision of fans to households appeared to increase net use in this study. Although the increase in net use explained by fans was not significant in the primary analyses (ITT odds ratio 3.24, p > 0.01; PP odds ratio = 1.17, p > 0.01), it was significant in secondary PP analysis (odds ratio = 1.95, p < 0.01). Net use was high at screening and even higher after provision of new LLINs and with follow up. Fan use was 90-100% depending on the fortnightly visit. This pilot study could not provide definitive evidence that fans increase net use. A larger study with additional statistical power is needed to assess this association across communities with diverse environmental and socio-demographic characteristics.

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.

PubMed

Adalsteinsson, David; McMillen, David; Elston, Timothy C

2004-03-08

Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solves the appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

Emergence of diversity in homogeneous coupled Boolean networks

NASA Astrophysics Data System (ADS)

Kang, Chris; Aguilar, Boris; Shmulevich, Ilya

2018-05-01

The origin of multicellularity in metazoa is one of the fundamental questions of evolutionary biology. We have modeled the generic behaviors of gene regulatory networks in isogenic cells as stochastic nonlinear dynamical systems—coupled Boolean networks with perturbation. Model simulations under a variety of dynamical regimes suggest that the central characteristic of multicellularity, permanent spatial differentiation (diversification), indeed can arise. Additionally, we observe that diversification is more likely to occur near the critical regime of Lyapunov stability.

Adaptive Neuro-Fuzzy Determination of the Effect of Experimental Parameters on Vehicle Agent Speed Relative to Vehicle Intruder.

PubMed

Shamshirband, Shahaboddin; Banjanovic-Mehmedovic, Lejla; Bosankic, Ivan; Kasapovic, Suad; Abdul Wahab, Ainuddin Wahid Bin

2016-01-01

Intelligent Transportation Systems rely on understanding, predicting and affecting the interactions between vehicles. The goal of this paper is to choose a small subset from the larger set so that the resulting regression model is simple, yet have good predictive ability for Vehicle agent speed relative to Vehicle intruder. The method of ANFIS (adaptive neuro fuzzy inference system) was applied to the data resulting from these measurements. The ANFIS process for variable selection was implemented in order to detect the predominant variables affecting the prediction of agent speed relative to intruder. This process includes several ways to discover a subset of the total set of recorded parameters, showing good predictive capability. The ANFIS network was used to perform a variable search. Then, it was used to determine how 9 parameters (Intruder Front sensors active (boolean), Intruder Rear sensors active (boolean), Agent Front sensors active (boolean), Agent Rear sensors active (boolean), RSSI signal intensity/strength (integer), Elapsed time (in seconds), Distance between Agent and Intruder (m), Angle of Agent relative to Intruder (angle between vehicles °), Altitude difference between Agent and Intruder (m)) influence prediction of agent speed relative to intruder. The results indicated that distance between Vehicle agent and Vehicle intruder (m) and angle of Vehicle agent relative to Vehicle Intruder (angle between vehicles °) is the most influential parameters to Vehicle agent speed relative to Vehicle intruder.

Boolean Modeling of Neural Systems with Point-Process Inputs and Outputs. Part I: Theory and Simulations

PubMed Central

Marmarelis, Vasilis Z.; Zanos, Theodoros P.; Berger, Theodore W.

2010-01-01

This paper presents a new modeling approach for neural systems with point-process (spike) inputs and outputs that utilizes Boolean operators (i.e. modulo 2 multiplication and addition that correspond to the logical AND and OR operations respectively, as well as the AND_NOT logical operation representing inhibitory effects). The form of the employed mathematical models is akin to a “Boolean-Volterra” model that contains the product terms of all relevant input lags in a hierarchical order, where terms of order higher than first represent nonlinear interactions among the various lagged values of each input point-process or among lagged values of various inputs (if multiple inputs exist) as they reflect on the output. The coefficients of this Boolean-Volterra model are also binary variables that indicate the presence or absence of the respective term in each specific model/system. Simulations are used to explore the properties of such models and the feasibility of their accurate estimation from short data-records in the presence of noise (i.e. spurious spikes). The results demonstrate the feasibility of obtaining reliable estimates of such models, with excitatory and inhibitory terms, in the presence of considerable noise (spurious spikes) in the outputs and/or the inputs in a computationally efficient manner. A pilot application of this approach to an actual neural system is presented in the companion paper (Part II). PMID:19517238

Inferring Toxicological Responses of HepG2 Cells from ...

EPA Pesticide Factsheets

Understanding the dynamic perturbation of cell states by chemicals can aid in for predicting their adverse effects. High-content imaging (HCI) was used to measure the state of HepG2 cells over three time points (1, 24, and 72 h) in response to 976 ToxCast chemicals for 10 different concentrations (0.39-200µM). Cell state was characterized by p53 activation (p53), c-Jun activation (SK), phospho-Histone H2A.x (OS), phospho-Histone H3 (MA), alpha tubulin (Mt), mitochondrial membrane potential (MMP), mitochondrial mass (MM), cell cycle arrest (CCA), nuclear size (NS) and cell number (CN). Dynamic cell state perturbations due to each chemical concentration were utilized to infer coarse-grained dependencies between cellular functions as Boolean networks (BNs). BNs were inferred from data in two steps. First, the data for each state variable were discretized into changed/active (> 1 standard deviation), and unchanged/inactive values. Second, the discretized data were used to learn Boolean relationships between variables. In our case, a BN is a wiring diagram between nodes that represent 10 previously described observable phenotypes. Functional relationships between nodes were represented as Boolean functions. We found that inferred BN show that HepG2 cell response is chemical and concentration specific. We observed presence of both point and cycle BN attractors. In addition, there are instances where Boolean functions were not found. We believe that this may be either

Finding the Optimal Nets for Self-Folding Kirigami

NASA Astrophysics Data System (ADS)

Araújo, N. A. M.; da Costa, R. A.; Dorogovtsev, S. N.; Mendes, J. F. F.

2018-05-01

Three-dimensional shells can be synthesized from the spontaneous self-folding of two-dimensional templates of interconnected panels, called nets. However, some nets are more likely to self-fold into the desired shell under random movements. The optimal nets are the ones that maximize the number of vertex connections, i.e., vertices that have only two of its faces cut away from each other in the net. Previous methods for finding such nets are based on random search, and thus, they do not guarantee the optimal solution. Here, we propose a deterministic procedure. We map the connectivity of the shell into a shell graph, where the nodes and links of the graph represent the vertices and edges of the shell, respectively. Identifying the nets that maximize the number of vertex connections corresponds to finding the set of maximum leaf spanning trees of the shell graph. This method allows us not only to design the self-assembly of much larger shell structures but also to apply additional design criteria, as a complete catalog of the maximum leaf spanning trees is obtained.

American College of Rheumatology/European League Against Rheumatism remission criteria for rheumatoid arthritis maintain reliable performance when evaluated in 44 joints.

PubMed

Kaneko, Yuko; Kondo, Harumi; Takeuchi, Tsutomu

2013-08-01

To investigate the performance of the new remission criteria for rheumatoid arthritis (RA) in daily clinical practice and the effect of possible misclassification of remission when 44 joints are assessed. Disease activity and remission rate were calculated according to the Disease Activity Score (DAS28), Simplified Disease Activity Index (SDAI), Clinical Disease Activity Index (CDAI), and a Boolean-based definition for 1402 patients with RA in Keio University Hospital. Characteristics of patients in remission were investigated, and the number of misclassified patients was determined--those classified as being in remission based on 28-joint count but as nonremission based on a 44-joint count for each definition criterion. Of all patients analyzed, 46.6%, 45.9%, 41.0%, and 31.5% were classified as in remission in the DAS28, SDAI, CDAI, and Boolean definitions, respectively. Patients classified into remission based only on the DAS28 showed relatively low erythrocyte sedimentation rates but greater swollen joint counts than those classified into remission based on the other definitions. In patients classified into remission based only on the Boolean criteria, the mean physician global assessment was greater than the mean patient global assessment. Although 119 patients had ≤ 1 involved joint in the 28-joint count but > 1 in the 44-joint count, only 34 of these 119 (2.4% of all subjects) were found to have been misclassified into remission. In practice, about half of patients with RA can achieve clinical remission within the DAS28, SDAI, and CDAI; and one-third according to the Boolean-based definition. Patients classified in remission based on a 28-joint count may have pain and swelling in the feet, but misclassification of remission was relatively rare and was seen in only 2.4% of patients under a Boolean definition. The 28-joint count can be sufficient for assessing clinical remission based on the new remission criteria.

Security analysis of boolean algebra based on Zhang-Wang digital signature scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Jinbin, E-mail: jbzheng518@163.com

2014-10-06

In 2005, Zhang and Wang proposed an improvement signature scheme without using one-way hash function and message redundancy. In this paper, we show that this scheme exits potential safety concerns through the analysis of boolean algebra, such as bitwise exclusive-or, and point out that mapping is not one to one between assembly instructions and machine code actually by means of the analysis of the result of the assembly program segment, and which possibly causes safety problems unknown to the software.

Realization of a quantum Hamiltonian Boolean logic gate on the Si(001):H surface.

PubMed

Kolmer, Marek; Zuzak, Rafal; Dridi, Ghassen; Godlewski, Szymon; Joachim, Christian; Szymonski, Marek

2015-08-07

The design and construction of the first prototypical QHC (Quantum Hamiltonian Computing) atomic scale Boolean logic gate is reported using scanning tunnelling microscope (STM) tip-induced atom manipulation on an Si(001):H surface. The NOR/OR gate truth table was confirmed by dI/dU STS (Scanning Tunnelling Spectroscopy) tracking how the surface states of the QHC quantum circuit on the Si(001):H surface are shifted according to the input logical status.

Boolean gates on actin filaments

NASA Astrophysics Data System (ADS)

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.

Discrete dynamic modeling of cellular signaling networks.

PubMed

Albert, Réka; Wang, Rui-Sheng

2009-01-01

Understanding signal transduction in cellular systems is a central issue in systems biology. Numerous experiments from different laboratories generate an abundance of individual components and causal interactions mediating environmental and developmental signals. However, for many signal transduction systems there is insufficient information on the overall structure and the molecular mechanisms involved in the signaling network. Moreover, lack of kinetic and temporal information makes it difficult to construct quantitative models of signal transduction pathways. Discrete dynamic modeling, combined with network analysis, provides an effective way to integrate fragmentary knowledge of regulatory interactions into a predictive mathematical model which is able to describe the time evolution of the system without the requirement for kinetic parameters. This chapter introduces the fundamental concepts of discrete dynamic modeling, particularly focusing on Boolean dynamic models. We describe this method step-by-step in the context of cellular signaling networks. Several variants of Boolean dynamic models including threshold Boolean networks and piecewise linear systems are also covered, followed by two examples of successful application of discrete dynamic modeling in cell biology.

Origins of Chaos in Autonomous Boolean Networks

NASA Astrophysics Data System (ADS)

Socolar, Joshua; Cavalcante, Hugo; Gauthier, Daniel; Zhang, Rui

2010-03-01

Networks with nodes consisting of ideal Boolean logic gates are known to display either steady states, periodic behavior, or an ultraviolet catastrophe where the number of logic-transition events circulating in the network per unit time grows as a power-law. In an experiment, non-ideal behavior of the logic gates prevents the ultraviolet catastrophe and may lead to deterministic chaos. We identify certain non-ideal features of real logic gates that enable chaos in experimental networks. We find that short-pulse rejection and the asymmetry between the logic states tends to engender periodic behavior. On the other hand, a memory effect termed ``degradation'' can generate chaos. Our results strongly suggest that deterministic chaos can be expected in a large class of experimental Boolean-like networks. Such devices may find application in a variety of technologies requiring fast complex waveforms or flat power spectra. The non-ideal effects identified here also have implications for the statistics of attractors in large complex networks.

Phase diagram of restricted Boltzmann machines and generalized Hopfield networks with arbitrary priors.

PubMed

Barra, Adriano; Genovese, Giuseppe; Sollich, Peter; Tantari, Daniele

2018-02-01

Restricted Boltzmann machines are described by the Gibbs measure of a bipartite spin glass, which in turn can be seen as a generalized Hopfield network. This equivalence allows us to characterize the state of these systems in terms of their retrieval capabilities, both at low and high load, of pure states. We study the paramagnetic-spin glass and the spin glass-retrieval phase transitions, as the pattern (i.e., weight) distribution and spin (i.e., unit) priors vary smoothly from Gaussian real variables to Boolean discrete variables. Our analysis shows that the presence of a retrieval phase is robust and not peculiar to the standard Hopfield model with Boolean patterns. The retrieval region becomes larger when the pattern entries and retrieval units get more peaked and, conversely, when the hidden units acquire a broader prior and therefore have a stronger response to high fields. Moreover, at low load retrieval always exists below some critical temperature, for every pattern distribution ranging from the Boolean to the Gaussian case.

Experimental Clocking of Nanomagnets with Strain for Ultralow Power Boolean Logic.

PubMed

D'Souza, Noel; Salehi Fashami, Mohammad; Bandyopadhyay, Supriyo; Atulasimha, Jayasimha

2016-02-10

Nanomagnetic implementations of Boolean logic have attracted attention because of their nonvolatility and the potential for unprecedented overall energy-efficiency. Unfortunately, the large dissipative losses that occur when nanomagnets are switched with a magnetic field or spin-transfer-torque severely compromise the energy-efficiency. Recently, there have been experimental reports of utilizing the Spin Hall effect for switching magnets, and theoretical proposals for strain induced switching of single-domain magnetostrictive nanomagnets, that might reduce the dissipative losses significantly. Here, we experimentally demonstrate, for the first time that strain-induced switching of single-domain magnetostrictive nanomagnets of lateral dimensions ∼200 nm fabricated on a piezoelectric substrate can implement a nanomagnetic Boolean NOT gate and steer bit information unidirectionally in dipole-coupled nanomagnet chains. On the basis of the experimental results with bulk PMN-PT substrates, we estimate that the energy dissipation for logic operations in a reasonably scaled system using thin films will be a mere ∼1 aJ/bit.

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

PubMed Central

Lähdesmäki, Harri; Hautaniemi, Sampsa; Shmulevich, Ilya; Yli-Harja, Olli

2006-01-01

A significant amount of attention has recently been focused on modeling of gene regulatory networks. Two frequently used large-scale modeling frameworks are Bayesian networks (BNs) and Boolean networks, the latter one being a special case of its recent stochastic extension, probabilistic Boolean networks (PBNs). PBN is a promising model class that generalizes the standard rule-based interactions of Boolean networks into the stochastic setting. Dynamic Bayesian networks (DBNs) is a general and versatile model class that is able to represent complex temporal stochastic processes and has also been proposed as a model for gene regulatory systems. In this paper, we concentrate on these two model classes and demonstrate that PBNs and a certain subclass of DBNs can represent the same joint probability distribution over their common variables. The major benefit of introducing the relationships between the models is that it opens up the possibility of applying the standard tools of DBNs to PBNs and vice versa. Hence, the standard learning tools of DBNs can be applied in the context of PBNs, and the inference methods give a natural way of handling the missing values in PBNs which are often present in gene expression measurements. Conversely, the tools for controlling the stationary behavior of the networks, tools for projecting networks onto sub-networks, and efficient learning schemes can be used for DBNs. In other words, the introduced relationships between the models extend the collection of analysis tools for both model classes. PMID:17415411

Antitumor Effects of Somatostatin Analogs in Neuroendocrine Tumors

PubMed Central

Dubé, Pierre; Rinke, Anja

2012-01-01

Background. For decades, somatostatin analogs (including octreotide and lanreotide) have been indicated for relief of the symptoms of flushing, diarrhea, and wheezing associated with secretory neuroendocrine tumors (NETs). Recently, it has been suggested that somatostatin analogs may provide direct and indirect antitumor effects in secretory and nonsecretory NETs in addition to symptom control in secretory NETs. Methods. A systematic review of MEDLINE was conducted to identify studies that investigated the antitumor effects of octreotide or lanreotide for patients with NETs. Additional studies not published in the peer-reviewed literature were identified by searching online abstracts. Results. In all, 17 octreotide trials and 11 lanreotide trials that included antitumor effects were identified. Partial response rates were between 0% and 31%, and stable disease rates were between 15% and 89%. Octreotide was the only somatostatin analog for which results of a phase III, randomized, placebo-controlled clinical trial that investigated antitumor effects were published. After 6 months of treatment in this randomized phase III trial, stable disease was observed in 67% of patients (hazard ratio for time to disease progression: 0.34; 95% confidence interval: 0.20–0.59; p = .000072). Conclusions. In addition to symptom control for NETs, the data support an antitumor effect of somatostatin analogs and suggest that they may slow tumor growth. Long-acting repeatable octreotide has been shown to have an antitumor effect in a randomized phase III trial in midgut NETs, whereas results are pending in a corresponding controlled trial with lanreotide for patients with intestinal and pancreatic primary NETs. PMID:22628056

BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.

PubMed

Shi, Xu; Barnes, Robert O; Chen, Li; Shajahan-Haq, Ayesha N; Hilakivi-Clarke, Leena; Clarke, Robert; Wang, Yue; Xuan, Jianhua

2015-07-15

Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and C++, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein-protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic user interface is developed as a Cytoscape plugin for the BMRF-Net software to deal with the input/output interface. The detailed structure of the identified networks can be visualized in Cytoscape conveniently. The BMRF-Net package has been applied to breast cancer data to identify significant subnetworks related to breast cancer recurrence. The BMRF-Net package is available at http://sourceforge.net/projects/bmrfcjava/. The package is tested under Ubuntu 12.04 (64-bit), Java 7, glibc 2.15 and Cytoscape 3.1.0. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Ad Hoc Information Extraction for Clinical Data Warehouses.

PubMed

Dietrich, Georg; Krebs, Jonathan; Fette, Georg; Ertl, Maximilian; Kaspar, Mathias; Störk, Stefan; Puppe, Frank

2018-05-01

Clinical Data Warehouses (CDW) reuse Electronic health records (EHR) to make their data retrievable for research purposes or patient recruitment for clinical trials. However, much information are hidden in unstructured data like discharge letters. They can be preprocessed and converted to structured data via information extraction (IE), which is unfortunately a laborious task and therefore usually not available for most of the text data in CDW. The goal of our work is to provide an ad hoc IE service that allows users to query text data ad hoc in a manner similar to querying structured data in a CDW. While search engines just return text snippets, our systems also returns frequencies (e.g. how many patients exist with "heart failure" including textual synonyms or how many patients have an LVEF < 45) based on the content of discharge letters or textual reports for special investigations like heart echo. Three subtasks are addressed: (1) To recognize and to exclude negations and their scopes, (2) to extract concepts, i.e. Boolean values and (3) to extract numerical values. We implemented an extended version of the NegEx-algorithm for German texts that detects negations and determines their scope. Furthermore, our document oriented CDW PaDaWaN was extended with query functions, e.g. context sensitive queries and regex queries, and an extraction mode for computing the frequencies for Boolean and numerical values. Evaluations in chest X-ray reports and in discharge letters showed high F1-scores for the three subtasks: Detection of negated concepts in chest X-ray reports with an F1-score of 0.99 and in discharge letters with 0.97; of Boolean values in chest X-ray reports about 0.99, and of numerical values in chest X-ray reports and discharge letters also around 0.99 with the exception of the concept age. The advantages of an ad hoc IE over a standard IE are the low development effort (just entering the concept with its variants), the promptness of the results and the adaptability by the user to his or her particular question. Disadvantage are usually lower accuracy and confidence.This ad hoc information extraction approach is novel and exceeds existing systems: Roogle [1] extracts predefined concepts from texts at preprocessing and makes them retrievable at runtime. Dr. Warehouse [2] applies negation detection and indexes the produced subtexts which include affirmed findings. Our approach combines negation detection and the extraction of concepts. But the extraction does not take place during preprocessing, but at runtime. That provides an ad hoc, dynamic, interactive and adjustable information extraction of random concepts and even their values on the fly at runtime. We developed an ad hoc information extraction query feature for Boolean and numerical values within a CDW with high recall and precision based on a pipeline that detects and removes negations and their scope in clinical texts. Schattauer GmbH.

Symbolic Boolean Manipulation with Ordered Binary Decision Diagrams

DTIC Science & Technology

1992-07-01

memories , where careful attention has been given to programming the memory management routines [Brace et al 19901. To extract maximum performance, it...OBDDs) represent Boolean functions as directed acyclic graphs. They form a canonical representation, making testing of functional properties such as...indicated 3 X X2 X3 f 000 0 0 01 0X22 0 10 0 0 11 1 d 1 0 0 0 X3 X 3X 1 01 1 1 10 0 - i"o11 10o 1 1 Figure 1: Truth Table and Decison Tree Repremmtatios

Generating probabilistic Boolean networks from a prescribed transition probability matrix.

PubMed

Ching, W-K; Chen, X; Tsing, N-K

2009-11-01

Probabilistic Boolean networks (PBNs) have received much attention in modeling genetic regulatory networks. A PBN can be regarded as a Markov chain process and is characterised by a transition probability matrix. In this study, the authors propose efficient algorithms for constructing a PBN when its transition probability matrix is given. The complexities of the algorithms are also analysed. This is an interesting inverse problem in network inference using steady-state data. The problem is important as most microarray data sets are assumed to be obtained from sampling the steady-state.

Consistent Correlations for Parameterised Boolean Equation Systems with Applications in Correctness Proofs for Manipulations

NASA Astrophysics Data System (ADS)

Willemse, Tim A. C.

We introduce the concept of consistent correlations for parameterised Boolean equation systems (PBESs), motivated largely by the laborious proofs of correctness required for most manipulations in this setting. Consistent correlations focus on relating the equations that occur in PBESs, rather than their solutions. For a fragment of PBESs, consistent correlations are shown to coincide with a recently introduced form of bisimulation. Finally, we show that bisimilarity on processes induces consistent correlations on PBESs encoding model checking problems. We apply our theory to two example manipulations from the literature.

A Parallel Approach in Computing Correlation Immunity up to Six Variables

DTIC Science & Technology

2015-03-10

their nonlinearity is divisible by 4. Let CI(n, k) (respectively, BCI (n, k)) be the number of exact order k correlation im- mune, (respectively...further balanced) n-variable Boolean functions. The notations CI(n, k, d), BCI (n, k, d) restricts the previous count to degree d Boolean functions...Theorem 3. The following are true: (i) BCI (n, n, 0) = 0, CI(n, n, 0) = 2, CI(n, k, 1) = BCI (n, k, 1) = 2 ( n k+1 ) , 0 ≤ k ≤ n− 1. (ii) BCI (n, n− 2) = 2

On Weak and Strong 2k- bent Boolean Functions

DTIC Science & Technology

2016-01-01

U.S.A. Email: pstanica@nps.edu Abstract—In this paper we introduce a sequence of discrete Fourier transforms and define new versions of bent...denotes the complex conjugate of z. An important tool in our analysis is the discrete Fourier transform , known in Boolean functions literature, as Walsh...Hadamard, or Walsh–Hadamard transform , which is the func- tion Wf : Fn2 → C, defined by Wf (u) = 2− n 2 ∑ x∈Vn (−1)f(x)⊕u·x. Any f ∈ Bn can be

Qubits and quantum Hamiltonian computing performances for operating a digital Boolean 1/2-adder

NASA Astrophysics Data System (ADS)

Dridi, Ghassen; Faizy Namarvar, Omid; Joachim, Christian

2018-04-01

Quantum Boolean (1 + 1) digits 1/2-adders are designed with 3 qubits for the quantum computing (Qubits) and 4 quantum states for the quantum Hamiltonian computing (QHC) approaches. Detailed analytical solutions are provided to analyse the time operation of those different 1/2-adder gates. QHC is more robust to noise than Qubits and requires about the same amount of energy for running its 1/2-adder logical operations. QHC is faster in time than Qubits but its logical output measurement takes longer.

Freeze-out conditions from net-proton and net-charge fluctuations at RHIC

DOE PAGES

Alba, Paolo; Alberico, Wanda; Bellwied, Rene; ...

2014-09-26

We calculate ratios of higher-order susceptibilities quantifying fluctuations in the number of net-protons and in the net-electric charge using the Hadron Resonance Gas (HRG) model. We take into account the effect of resonance decays, the kinematic acceptance cuts in rapidity, pseudo-rapidity and transverse momentum used in the experimental analysis, as well as a randomization of the isospin of nucleons in the hadronic phase. By comparing these results to the latest experimental data from the STAR Collaboration, we determine the freeze-out conditions from net-electric charge and net-proton distributions and discuss their consistency.

Research on user behavior authentication model based on stochastic Petri nets

NASA Astrophysics Data System (ADS)

Zhang, Chengyuan; Xu, Haishui

2017-08-01

A behavioural authentication model based on stochastic Petri net is proposed to meet the randomness, uncertainty and concurrency characteristics of user behaviour. The use of random models in the location, changes, arc and logo to describe the characteristics of a variety of authentication and game relationships, so as to effectively implement the graphical user behaviour authentication model analysis method, according to the corresponding proof to verify the model is valuable.

The importance of imagination (or lack thereof) in artificial, human and quantum decision making.

PubMed

Gustafson, Karl

2016-01-13

Enlarging upon experiments and analysis that I did jointly some years ago, in which artificial (symbolic, neural-net and pattern) learning and generalization were compared with that of humans, I will emphasize the role of imagination (or lack thereof) in artificial, human and quantum cognition and decision-making processes. Then I will look in more detail at some of the 'engineering details' of its implementation (or lack thereof) in each of these settings. In other words, the question posed is: What is actually happening? For example, we previously found that humans overwhelmingly seek, create or imagine context in order to provide meaning when presented with abstract, apparently incomplete, contradictory or otherwise untenable decision-making situations. Humans are intolerant of contradiction and will greatly simplify to avoid it. They can partially correlate but do not average. Human learning is not Boolean. These and other human reasoning properties will then be taken to critique how well artificial intelligence methods and quantum mechanical modelling might compete with them in decision-making tasks within psychology and economics. © 2015 The Author(s).

Logic circuits from zero forcing.

PubMed

Burgarth, Daniel; Giovannetti, Vittorio; Hogben, Leslie; Severini, Simone; Young, Michael

We design logic circuits based on the notion of zero forcing on graphs; each gate of the circuits is a gadget in which zero forcing is performed. We show that such circuits can evaluate every monotone Boolean function. By using two vertices to encode each logical bit, we obtain universal computation. We also highlight a phenomenon of "back forcing" as a property of each function. Such a phenomenon occurs in a circuit when the input of gates which have been already used at a given time step is further modified by a computation actually performed at a later stage. Finally, we show that zero forcing can be also used to implement reversible computation. The model introduced here provides a potentially new tool in the analysis of Boolean functions, with particular attention to monotonicity. Moreover, in the light of applications of zero forcing in quantum mechanics, the link with Boolean functions may suggest a new directions in quantum control theory and in the study of engineered quantum spin systems. It is an open technical problem to verify whether there is a link between zero forcing and computation with contact circuits.

Boolean dynamics of genetic regulatory networks inferred from microarray time series data

DOE PAGES

Martin, Shawn; Zhang, Zhaoduo; Martino, Anthony; ...

2007-01-31

Methods available for the inference of genetic regulatory networks strive to produce a single network, usually by optimizing some quantity to fit the experimental observations. In this paper we investigate the possibility that multiple networks can be inferred, all resulting in similar dynamics. This idea is motivated by theoretical work which suggests that biological networks are robust and adaptable to change, and that the overall behavior of a genetic regulatory network might be captured in terms of dynamical basins of attraction. We have developed and implemented a method for inferring genetic regulatory networks for time series microarray data. Our methodmore » first clusters and discretizes the gene expression data using k-means and support vector regression. We then enumerate Boolean activation–inhibition networks to match the discretized data. In conclusion, the dynamics of the Boolean networks are examined. We have tested our method on two immunology microarray datasets: an IL-2-stimulated T cell response dataset and a LPS-stimulated macrophage response dataset. In both cases, we discovered that many networks matched the data, and that most of these networks had similar dynamics.« less

Synchronization Analysis of Master-Slave Probabilistic Boolean Networks.

PubMed

Lu, Jianquan; Zhong, Jie; Li, Lulu; Ho, Daniel W C; Cao, Jinde

2015-08-28

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.

Verification and Optimal Control of Context-Sensitive Probabilistic Boolean Networks Using Model Checking and Polynomial Optimization

PubMed Central

Hiraishi, Kunihiko

2014-01-01

One of the significant topics in systems biology is to develop control theory of gene regulatory networks (GRNs). In typical control of GRNs, expression of some genes is inhibited (activated) by manipulating external stimuli and expression of other genes. It is expected to apply control theory of GRNs to gene therapy technologies in the future. In this paper, a control method using a Boolean network (BN) is studied. A BN is widely used as a model of GRNs, and gene expression is expressed by a binary value (ON or OFF). In particular, a context-sensitive probabilistic Boolean network (CS-PBN), which is one of the extended models of BNs, is used. For CS-PBNs, the verification problem and the optimal control problem are considered. For the verification problem, a solution method using the probabilistic model checker PRISM is proposed. For the optimal control problem, a solution method using polynomial optimization is proposed. Finally, a numerical example on the WNT5A network, which is related to melanoma, is presented. The proposed methods provide us useful tools in control theory of GRNs. PMID:24587766

Synchronization Analysis of Master-Slave Probabilistic Boolean Networks

PubMed Central

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

Toward a Principled Sampling Theory for Quasi-Orders

PubMed Central

Ünlü, Ali; Schrepp, Martin

2016-01-01

Quasi-orders, that is, reflexive and transitive binary relations, have numerous applications. In educational theories, the dependencies of mastery among the problems of a test can be modeled by quasi-orders. Methods such as item tree or Boolean analysis that mine for quasi-orders in empirical data are sensitive to the underlying quasi-order structure. These data mining techniques have to be compared based on extensive simulation studies, with unbiased samples of randomly generated quasi-orders at their basis. In this paper, we develop techniques that can provide the required quasi-order samples. We introduce a discrete doubly inductive procedure for incrementally constructing the set of all quasi-orders on a finite item set. A randomization of this deterministic procedure allows us to generate representative samples of random quasi-orders. With an outer level inductive algorithm, we consider the uniform random extensions of the trace quasi-orders to higher dimension. This is combined with an inner level inductive algorithm to correct the extensions that violate the transitivity property. The inner level correction step entails sampling biases. We propose three algorithms for bias correction and investigate them in simulation. It is evident that, on even up to 50 items, the new algorithms create close to representative quasi-order samples within acceptable computing time. Hence, the principled approach is a significant improvement to existing methods that are used to draw quasi-orders uniformly at random but cannot cope with reasonably large item sets. PMID:27965601

Toward a Principled Sampling Theory for Quasi-Orders.

PubMed

Ünlü, Ali; Schrepp, Martin

2016-01-01

Quasi-orders, that is, reflexive and transitive binary relations, have numerous applications. In educational theories, the dependencies of mastery among the problems of a test can be modeled by quasi-orders. Methods such as item tree or Boolean analysis that mine for quasi-orders in empirical data are sensitive to the underlying quasi-order structure. These data mining techniques have to be compared based on extensive simulation studies, with unbiased samples of randomly generated quasi-orders at their basis. In this paper, we develop techniques that can provide the required quasi-order samples. We introduce a discrete doubly inductive procedure for incrementally constructing the set of all quasi-orders on a finite item set. A randomization of this deterministic procedure allows us to generate representative samples of random quasi-orders. With an outer level inductive algorithm, we consider the uniform random extensions of the trace quasi-orders to higher dimension. This is combined with an inner level inductive algorithm to correct the extensions that violate the transitivity property. The inner level correction step entails sampling biases. We propose three algorithms for bias correction and investigate them in simulation. It is evident that, on even up to 50 items, the new algorithms create close to representative quasi-order samples within acceptable computing time. Hence, the principled approach is a significant improvement to existing methods that are used to draw quasi-orders uniformly at random but cannot cope with reasonably large item sets.

Changing Community Health Behaviors with a Health Promotion Computer Network: Preliminary Findings from Stanford Health-Net

PubMed Central

Robinson, Thomas N.; Walters, Paul A.

1987-01-01

Computer-based health education has been employed in many settings. However, data on resultant behavior change are lacking. A randomized, controlled, prospective study was performed to test the efficacy of Stanford Health-Net in changing community health behaviors. Graduate and undergraduate students (N=1003) were randomly assigned to treatment and control conditions. The treatment group received access to Health-Net, a health promotion computer network emphasizing specific self-care and preventive strategies. Over a four month intervention period, 26% of the treatment group used Health-Net an average of 6.4 times each (range 1 to 97). Users rated Health-Net favorably. The mean number of ambulatory medical visits decreesed 22.5% more in the treatment group than in the control group (P<.05), while hospitalizations did not differ significantly between groups. In addition, perceived self-efficacy for preventing the acquisition of a STD and herpes increased 577% (P<.05) and 261% (P<.01) more, respectively, in the treatment group than in the control group. These findings suggest that access to Stanford Health-Net can result in significant health behavior change. The advantages of the network approach make it a potential model for other communities.

Criticality in finite dynamical networks

NASA Astrophysics Data System (ADS)

Rohlf, Thimo; Gulbahce, Natali; Teuscher, Christof

2007-03-01

It has been shown analytically and experimentally that both random boolean and random threshold networks show a transition from ordered to chaotic dynamics at a critical average connectivity Kc in the thermodynamical limit [1]. By looking at the statistical distributions of damage spreading (damage sizes), we go beyond this extensively studied mean-field approximation. We study the scaling properties of damage size distributions as a function of system size N and initial perturbation size d(t=0). We present numerical evidence that another characteristic point, Kd exists for finite system sizes, where the expectation value of damage spreading in the network is independent of the system size N. Further, the probability to obtain critical networks is investigated for a given system size and average connectivity k. Our results suggest that, for finite size dynamical networks, phase space structure is very complex and may not exhibit a sharp order-disorder transition. Finally, we discuss the implications of our findings for evolutionary processes and learning applied to networks which solve specific computational tasks. [1] Derrida, B. and Pomeau, Y. (1986), Europhys. Lett., 1, 45-49

Modeling stock price dynamics by continuum percolation system and relevant complex systems analysis

NASA Astrophysics Data System (ADS)

Xiao, Di; Wang, Jun

2012-10-01

The continuum percolation system is developed to model a random stock price process in this work. Recent empirical research has demonstrated various statistical features of stock price changes, the financial model aiming at understanding price fluctuations needs to define a mechanism for the formation of the price, in an attempt to reproduce and explain this set of empirical facts. The continuum percolation model is usually referred to as a random coverage process or a Boolean model, the local interaction or influence among traders is constructed by the continuum percolation, and a cluster of continuum percolation is applied to define the cluster of traders sharing the same opinion about the market. We investigate and analyze the statistical behaviors of normalized returns of the price model by some analysis methods, including power-law tail distribution analysis, chaotic behavior analysis and Zipf analysis. Moreover, we consider the daily returns of Shanghai Stock Exchange Composite Index from January 1997 to July 2011, and the comparisons of return behaviors between the actual data and the simulation data are exhibited.

Bell-Boole Inequality: Nonlocality or Probabilistic Incompatibility of Random Variables?

NASA Astrophysics Data System (ADS)

Khrennikov, Andrei

2008-06-01

The main aim of this report is to inform the quantum information community about investigations on the problem of probabilistic compatibility of a family of random variables: a possibility to realize such a family on the basis of a single probability measure (to construct a single Kolmogorov probability space). These investigations were started hundred of years ago by J. Boole (who invented Boolean algebras). The complete solution of the problem was obtained by Soviet mathematician Vorobjev in 60th. Surprisingly probabilists and statisticians obtained inequalities for probabilities and correlations among which one can find the famous Bell’s inequality and its generalizations. Such inequalities appeared simply as constraints for probabilistic compatibility. In this framework one can not see a priori any link to such problems as nonlocality and “death of reality” which are typically linked to Bell’s type inequalities in physical literature. We analyze the difference between positions of mathematicians and quantum physicists. In particular, we found that one of the most reasonable explanations of probabilistic incompatibility is mixing in Bell’s type inequalities statistical data from a number of experiments performed under different experimental contexts.

A survey of SAT solver

NASA Astrophysics Data System (ADS)

Gong, Weiwei; Zhou, Xu

2017-06-01

In Computer Science, the Boolean Satisfiability Problem(SAT) is the problem of determining if there exists an interpretation that satisfies a given Boolean formula. SAT is one of the first problems that was proven to be NP-complete, which is also fundamental to artificial intelligence, algorithm and hardware design. This paper reviews the main algorithms of the SAT solver in recent years, including serial SAT algorithms, parallel SAT algorithms, SAT algorithms based on GPU, and SAT algorithms based on FPGA. The development of SAT is analyzed comprehensively in this paper. Finally, several possible directions for the development of the SAT problem are proposed.

Modeling bidirectional reflectance of forests and woodlands using Boolean models and geometric optics

NASA Technical Reports Server (NTRS)

Strahler, Alan H.; Jupp, David L. B.

1990-01-01

Geometric-optical discrete-element mathematical models for forest canopies have been developed using the Boolean logic and models of Serra. The geometric-optical approach is considered to be particularly well suited to describing the bidirectional reflectance of forest woodland canopies, where the concentration of leaf material within crowns and the resulting between-tree gaps make plane-parallel, radiative-transfer models inappropriate. The approach leads to invertible formulations, in which the spatial and directional variance provides the means for remote estimation of tree crown size, shape, and total cover from remotedly sensed imagery.

A Parallel Approach in Computing Correlation Immunity up to Six Variables

DTIC Science & Technology

2015-07-24

nonlinearity is divisible by 4. Let CI(n, k) (respectively, BCI (n, k)) be the number of exact order k corre- lation immune, (respectively, further...balanced) n-variable Boolean functions. The notations CI(n, k, d), BCI (n, k, d) restricts the previous count to degree d Boolean functions. Theorem 3...The following are true: (i) BCI (n, n, 0) = 0, CI(n, n, 0) = 2, CI(n, k, 1) = BCI (n, k, 1) = 2 ( n k+1 ) , 0 ≤ k ≤ n− 1. (ii) BCI (n, n− 2) = 2 ( n n−1

High speed all optical logic gates based on quantum dot semiconductor optical amplifiers.

PubMed

Ma, Shaozhen; Chen, Zhe; Sun, Hongzhi; Dutta, Niloy K

2010-03-29

A scheme to realize all-optical Boolean logic functions AND, XOR and NOT using semiconductor optical amplifiers with quantum-dot active layers is studied. nonlinear dynamics including carrier heating and spectral hole-burning are taken into account together with the rate equations scheme. Results show with QD excited state and wetting layer serving as dual-reservoir of carriers, as well as the ultra fast carrier relaxation of the QD device, this scheme is suitable for high speed Boolean logic operations. Logic operation can be carried out up to speed of 250 Gb/s.

Improving Unipolar Resistive Switching Uniformity with Cone-Shaped Conducting Filaments and Its Logic-In-Memory Application.

PubMed

Gao, Shuang; Liu, Gang; Chen, Qilai; Xue, Wuhong; Yang, Huali; Shang, Jie; Chen, Bin; Zeng, Fei; Song, Cheng; Pan, Feng; Li, Run-Wei

2018-02-21

Resistive random access memory (RRAM) with inherent logic-in-memory capability exhibits great potential to construct beyond von-Neumann computers. Particularly, unipolar RRAM is more promising because its single polarity operation enables large-scale crossbar logic-in-memory circuits with the highest integration density and simpler peripheral control circuits. However, unipolar RRAM usually exhibits poor switching uniformity because of random activation of conducting filaments and consequently cannot meet the strict uniformity requirement for logic-in-memory application. In this contribution, a new methodology that constructs cone-shaped conducting filaments by using chemically a active metal cathode is proposed to improve unipolar switching uniformity. Such a peculiar metal cathode will react spontaneously with the oxide switching layer to form an interfacial layer, which together with the metal cathode itself can act as a load resistor to prevent the overgrowth of conducting filaments and thus make them more cone-like. In this way, the rupture of conducting filaments can be strictly limited to the tip region, making their residual parts favorable locations for subsequent filament growth and thus suppressing their random regeneration. As such, a novel "one switch + one unipolar RRAM cell" hybrid structure is capable to realize all 16 Boolean logic functions for large-scale logic-in-memory circuits.

Fishing with bed nets on Lake Tanganyika: a randomized survey.

PubMed

McLean, Kate A; Byanaku, Aisha; Kubikonse, Augustine; Tshowe, Vincent; Katensi, Said; Lehman, Amy G

2014-10-07

Malaria is among the most common causes of death along Lake Tanganyika, a problem which many aid organizations have attempted to combat through the distribution of free mosquito bed nets to high-risk communities. The Lake Tanganyika Floating Health Clinic (LTFHC), a health-based non-governmental organization (NGO), has observed residents of the Lake Tanganyika basin using bed nets to fish small fry near the shoreline, despite a series of laws that prohibit bed net use and other fine-gauge nets for fishing, implemented to protect the near-shore fish ecology. The LTFHC sought to quantify the sources of bed nets and whether they were being used for fishing. The LTFHC conducted a survey of seven lakeside villages in Lagosa Ward, Tanzania. The government has divided each village into two to six pre-existing geographic sub-villages depending on population size. Seven households per sub-village were chosen at random for survey administration. The survey consisted of 23 questions regarding mosquito bed net practices, including the use of bed nets for fishing, as well as questions pertaining to any perceived changes to the fish supply. A total of 196 surveys were administered over a four-week period with a 100% response rate. Over 87% of households surveyed have used a mosquito bed net for fishing at some point. The majority of respondents reported receiving their bed net for free (96.4%), observing "many" residents of their village using bed nets for fishing (97.4%), and noticing a subjective decrease in the fish supply over time (64.9%). The findings of this study raise concerns that the use of free malaria bed nets for fishing is widespread along Lake Tanganyika, and that this dynamic will have an adverse effect on fish ecology. Further studies are indicated to fully define the scope of bed net misuse and the effects of alternative vector control strategies in water-based communities.

ADAM: analysis of discrete models of biological systems using computer algebra.

PubMed

Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard

2011-07-20

Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web-based tool for several different input formats, and it makes analysis of complex models accessible to a larger community, as it is platform independent as a web-service and does not require understanding of the underlying mathematics.

Effect of remission definition on healthcare cost savings estimates for patients with rheumatoid arthritis treated with biologic therapies.

PubMed

Barnabe, Cheryl; Thanh, Nguyen Xuan; Ohinmaa, Arto; Homik, Joanne; Barr, Susan G; Martin, Liam; Maksymowych, Walter P

2014-08-01

Sustained remission in rheumatoid arthritis (RA) results in healthcare utilization cost savings. We evaluated the variation in estimates of savings when different definitions of remission [2011 American College of Rheumatology/European League Against Rheumatism Boolean Definition, Simplified Disease Activity Index (SDAI) ≤ 3.3, Clinical Disease Activity Index (CDAI) ≤ 2.8, and Disease Activity Score-28 (DAS28) ≤ 2.6] are applied. The annual mean healthcare service utilization costs were estimated from provincial physician billing claims, outpatient visits, and hospitalizations, with linkage to clinical data from the Alberta Biologics Pharmacosurveillance Program (ABioPharm). Cost savings in patients who had a 1-year continuous period of remission were compared to those who did not, using 4 definitions of remission. In 1086 patients, sustained remission rates were 16.1% for DAS28, 8.8% for Boolean, 5.5% for CDAI, and 4.2% for SDAI. The estimated mean annual healthcare cost savings per patient achieving remission (relative to not) were SDAI $1928 (95% CI 592, 3264), DAS28 $1676 (95% CI 987, 2365), and Boolean $1259 (95% CI 417, 2100). The annual savings by CDAI remission per patient were not significant at $423 (95% CI -1757, 2602). For patients in DAS28, Boolean, and SDAI remission, savings were seen both in costs directly related to RA and its comorbidities, and in costs for non-RA-related conditions. The magnitude of the healthcare cost savings varies according to the remission definition used in classifying patient disease status. The highest point estimate for cost savings was observed in patients attaining SDAI remission and the least with the CDAI; confidence intervals for these estimates do overlap. Future pharmacoeconomic analyses should employ all response definitions in assessing the influence of treatment.

Modeling and controlling the two-phase dynamics of the p53 network: a Boolean network approach

NASA Astrophysics Data System (ADS)

Lin, Guo-Qiang; Ao, Bin; Chen, Jia-Wei; Wang, Wen-Xu; Di, Zeng-Ru

2014-12-01

Although much empirical evidence has demonstrated that p53 plays a key role in tumor suppression, the dynamics and function of the regulatory network centered on p53 have not yet been fully understood. Here, we develop a Boolean network model to reproduce the two-phase dynamics of the p53 network in response to DNA damage. In particular, we map the fates of cells into two types of Boolean attractors, and we find that the apoptosis attractor does not exist for minor DNA damage, reflecting that the cell is reparable. As the amount of DNA damage increases, the basin of the repair attractor shrinks, accompanied by the rising of the apoptosis attractor and the expansion of its basin, indicating that the cell becomes more irreparable with more DNA damage. For severe DNA damage, the repair attractor vanishes, and the apoptosis attractor dominates the state space, accounting for the exclusive fate of death. Based on the Boolean network model, we explore the significance of links, in terms of the sensitivity of the two-phase dynamics, to perturbing the weights of links and removing them. We find that the links are either critical or ordinary, rather than redundant. This implies that the p53 network is irreducible, but tolerant of small mutations at some ordinary links, and this can be interpreted with evolutionary theory. We further devised practical control schemes for steering the system into the apoptosis attractor in the presence of DNA damage by pinning the state of a single node or perturbing the weight of a single link. Our approach offers insights into understanding and controlling the p53 network, which is of paramount importance for medical treatment and genetic engineering.

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

PubMed Central

Wittmann, Dominik M; Krumsiek, Jan; Saez-Rodriguez, Julio; Lauffenburger, Douglas A; Klamt, Steffen; Theis, Fabian J

2009-01-01

Background The understanding of regulatory and signaling networks has long been a core objective in Systems Biology. Knowledge about these networks is mainly of qualitative nature, which allows the construction of Boolean models, where the state of a component is either 'off' or 'on'. While often able to capture the essential behavior of a network, these models can never reproduce detailed time courses of concentration levels. Nowadays however, experiments yield more and more quantitative data. An obvious question therefore is how qualitative models can be used to explain and predict the outcome of these experiments. Results In this contribution we present a canonical way of transforming Boolean into continuous models, where the use of multivariate polynomial interpolation allows transformation of logic operations into a system of ordinary differential equations (ODE). The method is standardized and can readily be applied to large networks. Other, more limited approaches to this task are briefly reviewed and compared. Moreover, we discuss and generalize existing theoretical results on the relation between Boolean and continuous models. As a test case a logical model is transformed into an extensive continuous ODE model describing the activation of T-cells. We discuss how parameters for this model can be determined such that quantitative experimental results are explained and predicted, including time-courses for multiple ligand concentrations and binding affinities of different ligands. This shows that from the continuous model we may obtain biological insights not evident from the discrete one. Conclusion The presented approach will facilitate the interaction between modeling and experiments. Moreover, it provides a straightforward way to apply quantitative analysis methods to qualitatively described systems. PMID:19785753

The DAS28-ESR cutoff value necessary to achieve remission under the new Boolean-based remission criteria in patients receiving tocilizumab.

PubMed

Hirabayashi, Yasuhiko; Ishii, Tomonori

2013-01-01

To seek the cutoff value of the 28-joint disease activity score using erythrocyte sedimentation rate (DAS28-ESR) that is necessary to achieve remission under the new Boolean-based criteria, we analyzed the data for 285 patients with rheumatoid arthritis registered between May 2008 and November 2009 by the Michinoku Tocilizumab Study Group and observed for 1 year after receiving tocilizumab (TCZ) in real clinical practice. Remission rates under the DAS28-ESR criteria and the Boolean criteria were assessed every 6 months after the first TCZ dose. The DAS28-ESR cutoff value necessary to achieve remission under the new criteria was analyzed by receiver operating characteristic (ROC) analysis. Data were analyzed using last observation carried forward. After 12 months of TCZ use, remission was achieved in 164 patients (57.5 %) by DAS28-ESR and 71 patients (24.9 %) under the new criteria for clinical trials. CRP levels scarcely affected remission rates, and the difference between remission rates defined by DAS28-ESR and by the new criteria was mainly due to patient global assessment (PGA). Improvement of PGA was inversely related to disease duration. ROC analysis revealed that the DAS28-ESR cutoff value necessary to predict remission under the new criteria for clinical trials was 1.54, with a sensitivity of 88.7 %, specificity of 85.5 %, positive predictive value of 67.0 %, and negative predictive value of 95.8 %. A DAS28-ESR cutoff value of 1.54 may be reasonable to predict achievement of remission under the new Boolean-based criteria for clinical trials in patients receiving TCZ.

Brief narrative exposure therapy for posttraumatic stress in Iraqi refugees: a preliminary randomized clinical trial.

PubMed

Hijazi, Alaa M; Lumley, Mark A; Ziadni, Maisa S; Haddad, Luay; Rapport, Lisa J; Arnetz, Bengt B

2014-06-01

Many Iraqi refugees suffer from posttraumatic stress. Efficient, culturally sensitive interventions are needed, and so we adapted narrative exposure therapy into a brief version (brief NET) and tested its effects in a sample of traumatized Iraqi refugees. Iraqi refugees in the United States reporting elevated posttraumatic stress (N = 63) were randomized to brief NET or waitlist control conditions in a 2:1 ratio; brief NET was 3 sessions, conducted individually, in Arabic. Positive indicators (posttraumatic growth and well-being) and symptoms (posttraumatic stress, depressive, and somatic) were assessed at baseline and 2- and 4-month follow-up. Treatment participation (95.1% completion) and study retention (98.4% provided follow-up data) were very high. Significant condition by time interactions showed that those receiving brief NET had greater posttraumatic growth (d = 0.83) and well-being (d = 0.54) through 4 months than controls. Brief NET reduced symptoms of posttraumatic stress (d = -0.48) and depression (d = -0.46) more, but only at 2 months; symptoms of controls also decreased from 2 to 4 months, eliminating condition differences at 4 months. Three sessions of brief NET increased growth and well-being and led to symptom reduction in highly traumatized Iraqi refugees. This preliminary study suggests that brief NET is both acceptable and potentially efficacious in traumatized Iraqi refugees. Copyright © 2014 International Society for Traumatic Stress Studies.

Boolean network inference from time series data incorporating prior biological knowledge.

PubMed

Haider, Saad; Pal, Ranadip

2012-01-01

Numerous approaches exist for modeling of genetic regulatory networks (GRNs) but the low sampling rates often employed in biological studies prevents the inference of detailed models from experimental data. In this paper, we analyze the issues involved in estimating a model of a GRN from single cell line time series data with limited time points. We present an inference approach for a Boolean Network (BN) model of a GRN from limited transcriptomic or proteomic time series data based on prior biological knowledge of connectivity, constraints on attractor structure and robust design. We applied our inference approach to 6 time point transcriptomic data on Human Mammary Epithelial Cell line (HMEC) after application of Epidermal Growth Factor (EGF) and generated a BN with a plausible biological structure satisfying the data. We further defined and applied a similarity measure to compare synthetic BNs and BNs generated through the proposed approach constructed from transitions of various paths of the synthetic BNs. We have also compared the performance of our algorithm with two existing BN inference algorithms. Through theoretical analysis and simulations, we showed the rarity of arriving at a BN from limited time series data with plausible biological structure using random connectivity and absence of structure in data. The framework when applied to experimental data and data generated from synthetic BNs were able to estimate BNs with high similarity scores. Comparison with existing BN inference algorithms showed the better performance of our proposed algorithm for limited time series data. The proposed framework can also be applied to optimize the connectivity of a GRN from experimental data when the prior biological knowledge on regulators is limited or not unique.

Markovian robots: Minimal navigation strategies for active particles

NASA Astrophysics Data System (ADS)

Nava, Luis Gómez; Großmann, Robert; Peruani, Fernando

2018-04-01

We explore minimal navigation strategies for active particles in complex, dynamical, external fields, introducing a class of autonomous, self-propelled particles which we call Markovian robots (MR). These machines are equipped with a navigation control system (NCS) that triggers random changes in the direction of self-propulsion of the robots. The internal state of the NCS is described by a Boolean variable that adopts two values. The temporal dynamics of this Boolean variable is dictated by a closed Markov chain—ensuring the absence of fixed points in the dynamics—with transition rates that may depend exclusively on the instantaneous, local value of the external field. Importantly, the NCS does not store past measurements of this value in continuous, internal variables. We show that despite the strong constraints, it is possible to conceive closed Markov chain motifs that lead to nontrivial motility behaviors of the MR in one, two, and three dimensions. By analytically reducing the complexity of the NCS dynamics, we obtain an effective description of the long-time motility behavior of the MR that allows us to identify the minimum requirements in the design of NCS motifs and transition rates to perform complex navigation tasks such as adaptive gradient following, detection of minima or maxima, or selection of a desired value in a dynamical, external field. We put these ideas in practice by assembling a robot that operates by the proposed minimalistic NCS to evaluate the robustness of MR, providing a proof of concept that is possible to navigate through complex information landscapes with such a simple NCS whose internal state can be stored in one bit. These ideas may prove useful for the engineering of miniaturized robots.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miyadera, Takayuki; Imai, Hideki; Graduate School of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551

This paper discusses the no-cloning theorem in a logicoalgebraic approach. In this approach, an orthoalgebra is considered as a general structure for propositions in a physical theory. We proved that an orthoalgebra admits cloning operation if and only if it is a Boolean algebra. That is, only classical theory admits the cloning of states. If unsharp propositions are to be included in the theory, then a notion of effect algebra is considered. We proved that an atomic Archimedean effect algebra admitting cloning operation is a Boolean algebra. This paper also presents a partial result, indicating a relation between the cloningmore » on effect algebras and hidden variables.« less

Diagnostic reasoning techniques for selective monitoring

NASA Technical Reports Server (NTRS)

Homem-De-mello, L. S.; Doyle, R. J.

1991-01-01

An architecture for using diagnostic reasoning techniques in selective monitoring is presented. Given the sensor readings and a model of the physical system, a number of assertions are generated and expressed as Boolean equations. The resulting system of Boolean equations is solved symbolically. Using a priori probabilities of component failure and Bayes' rule, revised probabilities of failure can be computed. These will indicate what components have failed or are the most likely to have failed. This approach is suitable for systems that are well understood and for which the correctness of the assertions can be guaranteed. Also, the system must be such that changes are slow enough to allow the computation.

Computer Program Development Specification for Ada Integrated Environment. Ada Compiler Phases B5-AIE (1). COMP (1).

DTIC Science & Technology

1982-11-05

routines required by the Back End. 3.3 Detailed Functional Requirements 3.3.1 Front End 3.3.1.1 DRIVER The DRIVER is the primary user interface to the...Main 2. Exam ple" !.i ,, , ,vari able • id -: go for B Boolean Ai ’ A" ’ I type d 1 I , for Boolean I (from Standard) i I - - for A function i fuction ...TN in. If a TN cannot be allocated to the primary area of storage it needs(such as a register) it is allocated to the spill area reserved in the local

Concept locator: a client-server application for retrieval of UMLS metathesaurus concepts through complex boolean query.

PubMed

Nadkarni, P M

1997-08-01

Concept Locator (CL) is a client-server application that accesses a Sybase relational database server containing a subset of the UMLS Metathesaurus for the purpose of retrieval of concepts corresponding to one or more query expressions supplied to it. CL's query grammar permits complex Boolean expressions, wildcard patterns, and parenthesized (nested) subexpressions. CL translates the query expressions supplied to it into one or more SQL statements that actually perform the retrieval. The generated SQL is optimized by the client to take advantage of the strengths of the server's query optimizer, and sidesteps its weaknesses, so that execution is reasonably efficient.

Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks

NASA Astrophysics Data System (ADS)

Villegas, Pablo; Ruiz-Franco, José; Hidalgo, Jorge; Muñoz, Miguel A.

2016-10-01

Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline between their ordered and disordered phases. Critical networks have been argued to lead to a number of functional advantages such as maximal dynamical range, maximal sensitivity to environmental changes, as well as to an excellent tradeoff between stability and flexibility. Here, we study the effect of noise within the context of Boolean networks trained to learn complex tasks under supervision. We verify that quasi-critical networks are the ones learning in the fastest possible way -even for asynchronous updating rules- and that the larger the task complexity the smaller the distance to criticality. On the other hand, when additional sources of intrinsic noise in the network states and/or in its wiring pattern are introduced, the optimally performing networks become clearly subcritical. These results suggest that in order to compensate for inherent stochasticity, regulatory and other type of biological networks might become subcritical rather than being critical, all the most if the task to be performed has limited complexity.

On the number of different dynamics in Boolean networks with deterministic update schedules.

PubMed

Aracena, J; Demongeot, J; Fanchon, E; Montalva, M

2013-04-01

Deterministic Boolean networks are a type of discrete dynamical systems widely used in the modeling of genetic networks. The dynamics of such systems is characterized by the local activation functions and the update schedule, i.e., the order in which the nodes are updated. In this paper, we address the problem of knowing the different dynamics of a Boolean network when the update schedule is changed. We begin by proving that the problem of the existence of a pair of update schedules with different dynamics is NP-complete. However, we show that certain structural properties of the interaction diagraph are sufficient for guaranteeing distinct dynamics of a network. In [1] the authors define equivalence classes which have the property that all the update schedules of a given class yield the same dynamics. In order to determine the dynamics associated to a network, we develop an algorithm to efficiently enumerate the above equivalence classes by selecting a representative update schedule for each class with a minimum number of blocks. Finally, we run this algorithm on the well known Arabidopsis thaliana network to determine the full spectrum of its different dynamics. Copyright © 2013 Elsevier Inc. All rights reserved.

Boolean logic analysis for flow regime recognition of gas-liquid horizontal flow

NASA Astrophysics Data System (ADS)

Ramskill, Nicholas P.; Wang, Mi

2011-10-01

In order to develop a flowmeter for the accurate measurement of multiphase flows, it is of the utmost importance to correctly identify the flow regime present to enable the selection of the optimal method for metering. In this study, the horizontal flow of air and water in a pipeline was studied under a multitude of conditions using electrical resistance tomography but the flow regimes that are presented in this paper have been limited to plug and bubble air-water flows. This study proposes a novel method for recognition of the prevalent flow regime using only a fraction of the data, thus rendering the analysis more efficient. By considering the average conductivity of five zones along the central axis of the tomogram, key features can be identified, thus enabling the recognition of the prevalent flow regime. Boolean logic and frequency spectrum analysis has been applied for flow regime recognition. Visualization of the flow using the reconstructed images provides a qualitative comparison between different flow regimes. Application of the Boolean logic scheme enables a quantitative comparison of the flow patterns, thus reducing the subjectivity in the identification of the prevalent flow regime.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alba, Paolo; Alberico, Wanda; Bellwied, Rene

We calculate ratios of higher-order susceptibilities quantifying fluctuations in the number of net-protons and in the net-electric charge using the Hadron Resonance Gas (HRG) model. We take into account the effect of resonance decays, the kinematic acceptance cuts in rapidity, pseudo-rapidity and transverse momentum used in the experimental analysis, as well as a randomization of the isospin of nucleons in the hadronic phase. By comparing these results to the latest experimental data from the STAR Collaboration, we determine the freeze-out conditions from net-electric charge and net-proton distributions and discuss their consistency.

[SOPHO-NET - a research network on psychotherapy for social phobia].

PubMed

Leichsenring, Falk; Salzer, Simone; Beutel, Manfred E; von Consbruch, Katrin; Herpertz, Stephan; Hiller, Wolfgang; Hoyer, Jürgen; Hüsing, Johannes; Irle, Eva; Joraschky, Peter; Konnopka, Alexander; König, Hans-Helmut; de Liz, Therese; Nolting, Björn; Pöhlmann, Karin; Ruhleder, Mirjana; Schauenburg, Henning; Stangier, Ulrich; Strauss, Bernhard; Subic-Wrana, Claudia; Vormfelde, Stefan V; Weniger, Godehard; Willutzki, Ulrike; Wiltink, Jörg; Leibing, Eric

2009-01-01

This paper presents the Social Phobia Psychotherapy Research Network (SOPHO-NET). SOPHO-NET is among the five research networks on psychotherapy funded by "Bundesministerium für Bildung und Forschung". The research program encompasses a coordinated group of studies of social phobia. In the central project (Study A), a multi-center randomized controlled trial, refined models of manualized cognitive-behavioral therapy (CBT) and manualized short-term psychodynamic psychotherapy (STPP) are compared in the treatment of social phobia. A sample of n=512 outpatients will be randomized to either CBT, STPP or wait list. For quality assurance and treatment integrity, a specific project has been established (Project Q). Study A is complemented by four interrelated projects focusing on attachment style (Study B1), cost-effectiveness (Study B2), polymorphisms in the serotonin transporter gene (Study C1) and on structural and functional deviations of hippocampus and amygdala (Study C2). Thus, the SOPHO-NET program allows for a highly interdisciplinary research of psychotherapy in social phobia.

An algebra-based method for inferring gene regulatory networks.

PubMed

Vera-Licona, Paola; Jarrah, Abdul; Garcia-Puente, Luis David; McGee, John; Laubenbacher, Reinhard

2014-03-26

The inference of gene regulatory networks (GRNs) from experimental observations is at the heart of systems biology. This includes the inference of both the network topology and its dynamics. While there are many algorithms available to infer the network topology from experimental data, less emphasis has been placed on methods that infer network dynamics. Furthermore, since the network inference problem is typically underdetermined, it is essential to have the option of incorporating into the inference process, prior knowledge about the network, along with an effective description of the search space of dynamic models. Finally, it is also important to have an understanding of how a given inference method is affected by experimental and other noise in the data used. This paper contains a novel inference algorithm using the algebraic framework of Boolean polynomial dynamical systems (BPDS), meeting all these requirements. The algorithm takes as input time series data, including those from network perturbations, such as knock-out mutant strains and RNAi experiments. It allows for the incorporation of prior biological knowledge while being robust to significant levels of noise in the data used for inference. It uses an evolutionary algorithm for local optimization with an encoding of the mathematical models as BPDS. The BPDS framework allows an effective representation of the search space for algebraic dynamic models that improves computational performance. The algorithm is validated with both simulated and experimental microarray expression profile data. Robustness to noise is tested using a published mathematical model of the segment polarity gene network in Drosophila melanogaster. Benchmarking of the algorithm is done by comparison with a spectrum of state-of-the-art network inference methods on data from the synthetic IRMA network to demonstrate that our method has good precision and recall for the network reconstruction task, while also predicting several of the dynamic patterns present in the network. Boolean polynomial dynamical systems provide a powerful modeling framework for the reverse engineering of gene regulatory networks, that enables a rich mathematical structure on the model search space. A C++ implementation of the method, distributed under LPGL license, is available, together with the source code, at http://www.paola-vera-licona.net/Software/EARevEng/REACT.html.

The Effect of Single or Repeated Home Visits on the Hanging and Use of Insecticide-Treated Mosquito Nets following a Mass Distribution Campaign - A Cluster Randomized, Controlled Trial

PubMed Central

Kilian, Albert; Balayo, Connie; Feldman, Mitra; Koenker, Hannah; Lokko, Kojo; Ashton, Ruth A.; Bruce, Jane; Lynch, Matthew; Boulay, Marc

2015-01-01

Background Study objective was to evaluate the effectiveness of commonly used post-campaign hang-up visits on the hanging and use of campaign nets. Methods A cluster-randomized trial was carried out in Uganda following an ITN distribution campaign. Five clusters (parishes, consisting of ∼11 villages each) were randomly selected for each of the three study arms with between 7,534 and 9,401 households per arm. Arm 1 received one hang-up visit, while Arm 2 received two visits by volunteers four and seven months after the campaign. Visits consisted of assistance hanging the net and education on net use. The control arm was only exposed to messages during the campaign itself. Three cross-sectional surveys with a two-stage cluster sampling design, representative of the study populations, were carried out to capture the two key outcome variables of net hanging and ITN use. Sample size was calculated to detect at least a 15 percentage-points change in net use, and was 1811 at endline. The analysis used an intention-to-treat approach. Findings Both hanging and use of ITN increased during follow-up in a similar way in all three study arms. The proportion of the population using an ITN the previous night was 64.0% (95% CI 60.8, 67.2), for one additional visit, 68.2% (63.8, 72.2) for two visits and 64.0% (59.4, 68.5) for the control. The proportion of households with all campaign nets hanging increased from 55.7% to 72.5% at endline (p<0.0005 for trend), with no difference between study arms. Financial cost per household visited was estimated as USD 2.33 for the first visit and USD 2.24 for the second. Conclusions Behavior change communication provided during the campaign or through other channels was sufficient to induce high levels of net hanging and use and additional “hang-up” activities were not cost-effective. PMID:25774676

New scaling relation for information transfer in biological networks

PubMed Central

Kim, Hyunju; Davies, Paul; Walker, Sara Imari

2015-01-01

We quantify characteristics of the informational architecture of two representative biological networks: the Boolean network model for the cell-cycle regulatory network of the fission yeast Schizosaccharomyces pombe (Davidich et al. 2008 PLoS ONE 3, e1672 (doi:10.1371/journal.pone.0001672)) and that of the budding yeast Saccharomyces cerevisiae (Li et al. 2004 Proc. Natl Acad. Sci. USA 101, 4781–4786 (doi:10.1073/pnas.0305937101)). We compare our results for these biological networks with the same analysis performed on ensembles of two different types of random networks: Erdös–Rényi and scale-free. We show that both biological networks share features in common that are not shared by either random network ensemble. In particular, the biological networks in our study process more information than the random networks on average. Both biological networks also exhibit a scaling relation in information transferred between nodes that distinguishes them from random, where the biological networks stand out as distinct even when compared with random networks that share important topological properties, such as degree distribution, with the biological network. We show that the most biologically distinct regime of this scaling relation is associated with a subset of control nodes that regulate the dynamics and function of each respective biological network. Information processing in biological networks is therefore interpreted as an emergent property of topology (causal structure) and dynamics (function). Our results demonstrate quantitatively how the informational architecture of biologically evolved networks can distinguish them from other classes of network architecture that do not share the same informational properties. PMID:26701883

A stitch in time: a cross-sectional survey looking at long lasting insecticide-treated bed net ownership, utilization and attrition in SNNPR, Ethiopia.

PubMed

Batisso, Esey; Habte, Tedila; Tesfaye, Gezahegn; Getachew, Dawit; Tekalegne, Agonafer; Kilian, Albert; Mpeka, Betty; Lynch, Caroline

2012-06-07

Since 2002/03, an estimated 4.7 million nets have been distributed in the Southern Nations, Nationalities and Peoples Region (SNNPR) among an at risk population of approximately 10 million people. Evidence from the region suggests that large-scale net ownership rapidly increased over a relatively short period of time. However, little is known about how coverage is being maintained given that the last mass distribution was in 2006/2007. This study sought to determine the status of current net ownership, utilization and rate of long lasting insecticide-treated nets (LLIN) loss in the previous three years in the context of planning for future net distribution to try to achieve sustainable universal coverage. A total of 750 household respondents were interviewed across malarious, rural kebeles of SNNPR. Households were randomly selected following a two-stage cluster sampling design where kebeles were defined as clusters. Kebeles were chosen using proportional population sampling (PPS), and 25 households within 30 kebeles randomly chosen. Approximately 67.5% (95%CI: 64.1-70.8) of households currently owned at least one net. An estimated 31.0% (95%CI 27.9-34.4) of all nets owned in the previous three years had been discarded by owners, the majority of whom considered the nets too torn, old or dirty (79.9%: 95%CI 75.8-84.0). Households reported that one-third of nets (33.7%) were less than one year old when they were discarded. The majority (58.8%) of currently owned nets had 'good' structural integrity according to a proportionate Hole Index. Nearly two-thirds of households (60.6%) reported using their nets the previous night. The overriding reason for not using nets was that they were too torn (45.7%, 95% CI 39.1-50.7). Yet, few households are making repairs to their nets (3.7%, 95% CI: 2.4-5.1). Results suggest that the life span of nets may be shorter than previously thought, with little maintenance by their owners. With the global move towards malaria elimination it makes sense to aim for sustained high coverage of LLINs. However, in the current economic climate, it also makes sense to hark back to simple tools and messages on the importance of careful net maintenance, which could increase their lifespans.

Spatial Rule-Based Modeling: A Method and Its Application to the Human Mitotic Kinetochore

PubMed Central

Ibrahim, Bashar; Henze, Richard; Gruenert, Gerd; Egbert, Matthew; Huwald, Jan; Dittrich, Peter

2013-01-01

A common problem in the analysis of biological systems is the combinatorial explosion that emerges from the complexity of multi-protein assemblies. Conventional formalisms, like differential equations, Boolean networks and Bayesian networks, are unsuitable for dealing with the combinatorial explosion, because they are designed for a restricted state space with fixed dimensionality. To overcome this problem, the rule-based modeling language, BioNetGen, and the spatial extension, SRSim, have been developed. Here, we describe how to apply rule-based modeling to integrate experimental data from different sources into a single spatial simulation model and how to analyze the output of that model. The starting point for this approach can be a combination of molecular interaction data, reaction network data, proximities, binding and diffusion kinetics and molecular geometries at different levels of detail. We describe the technique and then use it to construct a model of the human mitotic inner and outer kinetochore, including the spindle assembly checkpoint signaling pathway. This allows us to demonstrate the utility of the procedure, show how a novel perspective for understanding such complex systems becomes accessible and elaborate on challenges that arise in the formulation, simulation and analysis of spatial rule-based models. PMID:24709796

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

PubMed

Chaouiya, Claudine; Keating, Sarah M; Berenguier, Duncan; Naldi, Aurélien; Thieffry, Denis; van Iersel, Martijn P; Le Novère, Nicolas; Helikar, Tomáš

2015-09-04

Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as, for example, gene expression data coming from functional genomic experiments. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding qualitative models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Qualitative Models package for SBML Level 3 adds features so that qualitative models can be directly and explicitly encoded. The approach taken in this package is essentially based on the definition of regulatory or influence graphs. The SBML Qualitative Models package defines the structure and syntax necessary to describe qualitative models that associate discrete levels of activities with entity pools and the transitions between states that describe the processes involved. This is particularly suited to logical models (Boolean or multi-valued) and some classes of Petri net models can be encoded with the approach.

Random walk-percolation-based modeling of two-phase flow in porous media: Breakthrough time and net to gross ratio estimation

NASA Astrophysics Data System (ADS)

Ganjeh-Ghazvini, Mostafa; Masihi, Mohsen; Ghaedi, Mojtaba

2014-07-01

Fluid flow modeling in porous media has many applications in waste treatment, hydrology and petroleum engineering. In any geological model, flow behavior is controlled by multiple properties. These properties must be known in advance of common flow simulations. When uncertainties are present, deterministic modeling often produces poor results. Percolation and Random Walk (RW) methods have recently been used in flow modeling. Their stochastic basis is useful in dealing with uncertainty problems. They are also useful in finding the relationship between porous media descriptions and flow behavior. This paper employs a simple methodology based on random walk and percolation techniques. The method is applied to a well-defined model reservoir in which the breakthrough time distributions are estimated. The results of this method and the conventional simulation are then compared. The effect of the net to gross ratio on the breakthrough time distribution is studied in terms of Shannon entropy. Use of the entropy plot allows one to assign the appropriate net to gross ratio to any porous medium.

Boolean function applied to Mimosa pudica movements.

PubMed

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.

Nonvolatile “AND,” “OR,” and “NOT” Boolean logic gates based on phase-change memory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Y.; Zhong, Y. P.; Deng, Y. F.

2013-12-21

Electronic devices or circuits that can implement both logic and memory functions are regarded as the building blocks for future massive parallel computing beyond von Neumann architecture. Here we proposed phase-change memory (PCM)-based nonvolatile logic gates capable of AND, OR, and NOT Boolean logic operations verified in SPICE simulations and circuit experiments. The logic operations are parallel computing and results can be stored directly in the states of the logic gates, facilitating the combination of computing and memory in the same circuit. These results are encouraging for ultralow-power and high-speed nonvolatile logic circuit design based on novel memory devices.

Reservoir computing with a single time-delay autonomous Boolean node

NASA Astrophysics Data System (ADS)

Haynes, Nicholas D.; Soriano, Miguel C.; Rosin, David P.; Fischer, Ingo; Gauthier, Daniel J.

2015-02-01

We demonstrate reservoir computing with a physical system using a single autonomous Boolean logic element with time-delay feedback. The system generates a chaotic transient with a window of consistency lasting between 30 and 300 ns, which we show is sufficient for reservoir computing. We then characterize the dependence of computational performance on system parameters to find the best operating point of the reservoir. When the best parameters are chosen, the reservoir is able to classify short input patterns with performance that decreases over time. In particular, we show that four distinct input patterns can be classified for 70 ns, even though the inputs are only provided to the reservoir for 7.5 ns.

Questions Revisited: A Close Examination of Calculus of Inference and Inquiry

NASA Technical Reports Server (NTRS)

Knuth, Kevin H.; Koga, Dennis (Technical Monitor)

2003-01-01

In this paper I examine more closely the way in which probability theory, the calculus of inference, is derived from the Boolean lattice structure of logical assertions ordered by implication. I demonstrate how the duality between the logical conjunction and disjunction in Boolean algebra is lost when deriving the probability calculus. In addition, I look more closely at the other lattice identities to verify that they are satisfied by the probability calculus. Last, I look towards developing the calculus of inquiry demonstrating that there is a sum and product rule for the relevance measure as well as a Bayes theorem. Current difficulties in deriving the complete inquiry calculus will also be discussed.

Optical reversible programmable Boolean logic unit.

PubMed

Chattopadhyay, Tanay

2012-07-20

Computing with reversibility is the only way to avoid dissipation of energy associated with bit erase. So, a reversible microprocessor is required for future computing. In this paper, a design of a simple all-optical reversible programmable processor is proposed using a polarizing beam splitter, liquid crystal-phase spatial light modulators, a half-wave plate, and plane mirrors. This circuit can perform 16 logical operations according to three programming inputs. Also, inputs can be easily recovered from the outputs. It is named the "reversible programmable Boolean logic unit (RPBLU)." The logic unit is the basic building block of many complex computational operations. Hence the design is important in sense. Two orthogonally polarized lights are defined here as two logical states, respectively.

A sparse matrix algorithm on the Boolean vector machine

NASA Technical Reports Server (NTRS)

Wagner, Robert A.; Patrick, Merrell L.

1988-01-01

VLSI technology is being used to implement a prototype Boolean Vector Machine (BVM), which is a large network of very small processors with equally small memories that operate in SIMD mode; these use bit-serial arithmetic, and communicate via cube-connected cycles network. The BVM's bit-serial arithmetic and the small memories of individual processors are noted to compromise the system's effectiveness in large numerical problem applications. Attention is presently given to the implementation of a basic matrix-vector iteration algorithm for space matrices of the BVM, in order to generate over 1 billion useful floating-point operations/sec for this iteration algorithm. The algorithm is expressed in a novel language designated 'BVM'.

Extending Clause Learning of SAT Solvers with Boolean Gröbner Bases

NASA Astrophysics Data System (ADS)

Zengler, Christoph; Küchlin, Wolfgang

We extend clause learning as performed by most modern SAT Solvers by integrating the computation of Boolean Gröbner bases into the conflict learning process. Instead of learning only one clause per conflict, we compute and learn additional binary clauses from a Gröbner basis of the current conflict. We used the Gröbner basis engine of the logic package Redlog contained in the computer algebra system Reduce to extend the SAT solver MiniSAT with Gröbner basis learning. Our approach shows a significant reduction of conflicts and a reduction of restarts and computation time on many hard problems from the SAT 2009 competition.

MPIGeneNet: Parallel Calculation of Gene Co-Expression Networks on Multicore Clusters.

PubMed

Gonzalez-Dominguez, Jorge; Martin, Maria J

2017-10-10

In this work we present MPIGeneNet, a parallel tool that applies Pearson's correlation and Random Matrix Theory to construct gene co-expression networks. It is based on the state-of-the-art sequential tool RMTGeneNet, which provides networks with high robustness and sensitivity at the expenses of relatively long runtimes for large scale input datasets. MPIGeneNet returns the same results as RMTGeneNet but improves the memory management, reduces the I/O cost, and accelerates the two most computationally demanding steps of co-expression network construction by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on two different systems using three typical input datasets shows that MPIGeneNet is significantly faster than RMTGeneNet. As an example, our tool is up to 175.41 times faster on a cluster with eight nodes, each one containing two 12-core Intel Haswell processors. Source code of MPIGeneNet, as well as a reference manual, are available at https://sourceforge.net/projects/mpigenenet/.

Evolution of regulatory networks towards adaptability and stability in a changing environment

NASA Astrophysics Data System (ADS)

Lee, Deok-Sun

2014-11-01

Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which evolve by selectively rewiring links towards enhancing adaptability to a changing environment and stability against dynamical perturbations. We find that sparse and heterogeneous connectivity patterns emerge, which show qualitative agreement with real transcriptional regulatory networks and metabolic networks. The characteristic scaling behavior of stability reflects the balance between robustness and flexibility. The scaling of fluctuation in the perturbation spread shows a dynamic crossover, which is analyzed by investigating separately the stochasticity of internal dynamics and the network structure differences depending on the evolution pathways. Our study delineates how the ambivalent pressure of evolution shapes biological networks, which can be helpful for studying general complex systems interacting with environments.

The fuzzy cube and causal efficacy: representation of concomitant mechanisms in stroke.

PubMed

Jobe, Thomas H.; Helgason, Cathy M.

1998-04-01

Twentieth century medical science has embraced nineteenth century Boolean probability theory based upon two-valued Aristotelian logic. With the later addition of bit-based, von Neumann structured computational architectures, an epistemology based on randomness has led to a bivalent epidemiological methodology that dominates medical decision making. In contrast, fuzzy logic, based on twentieth century multi-valued logic, and computational structures that are content addressed and adaptively modified, has advanced a new scientific paradigm for the twenty-first century. Diseases such as stroke involve multiple concomitant causal factors that are difficult to represent using conventional statistical methods. We tested which paradigm best represented this complex multi-causal clinical phenomenon-stroke. We show that the fuzzy logic paradigm better represented clinical complexity in cerebrovascular disease than current probability theory based methodology. We believe this finding is generalizable to all of clinical science since multiple concomitant causal factors are involved in nearly all known pathological processes.

When Gravity Fails: Local Search Topology

NASA Technical Reports Server (NTRS)

Frank, Jeremy; Cheeseman, Peter; Stutz, John; Lau, Sonie (Technical Monitor)

1997-01-01

Local search algorithms for combinatorial search problems frequently encounter a sequence of states in which it is impossible to improve the value of the objective function; moves through these regions, called {\\em plateau moves), dominate the time spent in local search. We analyze and characterize {\\em plateaus) for three different classes of randomly generated Boolean Satisfiability problems. We identify several interesting features of plateaus that impact the performance of local search algorithms. We show that local minima tend to be small but occasionally may be very large. We also show that local minima can be escaped without unsatisfying a large number of clauses, but that systematically searching for an escape route may be computationally expensive if the local minimum is large. We show that plateaus with exits, called benches, tend to be much larger than minima, and that some benches have very few exit states which local search can use to escape. We show that the solutions (i.e. global minima) of randomly generated problem instances form clusters, which behave similarly to local minima. We revisit several enhancements of local search algorithms and explain their performance in light of our results. Finally we discuss strategies for creating the next generation of local search algorithms.

Osteoporosis and bone fractures in alcoholic liver disease: a meta-analysis.

PubMed

Bang, Chang Seok; Shin, In Soo; Lee, Sung Wha; Kim, Jin Bong; Baik, Gwang Ho; Suk, Ki Tae; Yoon, Jai Hoon; Kim, Yeon Soo; Kim, Dong Joon

2015-04-07

To evaluate the association between alcoholic liver disease (ALD) and bone fractures or osteoporosis. Non-randomized studies were identified from databases (PubMed, EMBASE, and the Cochrane Library). The search was conducted using Boolean operators and keywords, which included "alcoholic liver diseases", "osteoporosis", or "bone fractures". The prevalence of any fractures or osteoporosis, and bone mineral density (BMD) were extracted and analyzed using risk ratios and standardized mean difference (SMD). A random effects model was applied. In total, 15 studies were identified and analyzed. Overall, ALD demonstrated a RR of 1.944 (95%CI: 1.354-2.791) for the development of bone fractures. However, ALD showed a RR of 0.849 (95%CI: 0.523-1.380) for the development of osteoporosis. BMD was not significantly different between the ALD and control groups, although there was a trend toward lower BMD in patients with ALD (SMD in femur-BMD: -0.172, 95%CI: -0.453-0.110; SMD in spine-BMD: -0.169, 95%CI: -0.476-0.138). Sensitivity analyses showed consistent results. Current publications indicate significant associations between bone fractures and ALD, independent of BMD or the presence of osteoporosis.

Therapeutic efficacy of self-ligating brackets: A systematic review.

PubMed

Dehbi, Hasnaa; Azaroual, Mohamed Faouzi; Zaoui, Fatima; Halimi, Abdelali; Benyahia, Hicham

2017-09-01

Over the last few years, the use of self-ligating brackets in orthodontics has progressed considerably. These systems have been the subject of numerous studies with good levels of evidence making it possible to evaluate their efficacy and efficiency compared to conventional brackets. The aim of this study was to evaluate the therapeutic efficacy of self-ligating brackets by means of a systematic review of the scientific literature. A systematic study was undertaken in the form of a recent search of the electronic Pubmed database, oriented by the use of several keywords combined by Boolean operators relating to the therapeutic efficacy of self-ligating brackets through the study of tooth alignment, space closure, expansion, treatment duration and degree of discomfort. The search was limited to randomized controlled studies, and two independent readers identified studies corresponding to the selection criteria. The chosen articles comprised 20 randomized controlled trials. The studies analyzed revealed the absence of significant differences between the two types of system on the basis of the clinical criteria adopted, thereby refuting the hypothesis of the superiority of self-ligating brackets over conventional systems. Copyright © 2017 CEO. Published by Elsevier Masson SAS. All rights reserved.

Osteoporosis and bone fractures in alcoholic liver disease: A meta-analysis

PubMed Central

Bang, Chang Seok; Shin, In Soo; Lee, Sung Wha; Kim, Jin Bong; Baik, Gwang Ho; Suk, Ki Tae; Yoon, Jai Hoon; Kim, Yeon Soo; Kim, Dong Joon

2015-01-01

AIM: To evaluate the association between alcoholic liver disease (ALD) and bone fractures or osteoporosis. METHODS: Non-randomized studies were identified from databases (PubMed, EMBASE, and the Cochrane Library). The search was conducted using Boolean operators and keywords, which included “alcoholic liver diseases”, “osteoporosis”, or “bone fractures”. The prevalence of any fractures or osteoporosis, and bone mineral density (BMD) were extracted and analyzed using risk ratios and standardized mean difference (SMD). A random effects model was applied. RESULTS: In total, 15 studies were identified and analyzed. Overall, ALD demonstrated a RR of 1.944 (95%CI: 1.354-2.791) for the development of bone fractures. However, ALD showed a RR of 0.849 (95%CI: 0.523-1.380) for the development of osteoporosis. BMD was not significantly different between the ALD and control groups, although there was a trend toward lower BMD in patients with ALD (SMD in femur-BMD: -0.172, 95%CI: -0.453-0.110; SMD in spine-BMD: -0.169, 95%CI: -0.476-0.138). Sensitivity analyses showed consistent results. CONCLUSION: Current publications indicate significant associations between bone fractures and ALD, independent of BMD or the presence of osteoporosis. PMID:25852292

Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters

PubMed Central

Liu, Fei; Heiner, Monika; Yang, Ming

2016-01-01

Stochastic Petri nets (SPNs) have been widely used to model randomness which is an inherent feature of biological systems. However, for many biological systems, some kinetic parameters may be uncertain due to incomplete, vague or missing kinetic data (often called fuzzy uncertainty), or naturally vary, e.g., between different individuals, experimental conditions, etc. (often called variability), which has prevented a wider application of SPNs that require accurate parameters. Considering the strength of fuzzy sets to deal with uncertain information, we apply a specific type of stochastic Petri nets, fuzzy stochastic Petri nets (FSPNs), to model and analyze biological systems with uncertain kinetic parameters. FSPNs combine SPNs and fuzzy sets, thereby taking into account both randomness and fuzziness of biological systems. For a biological system, SPNs model the randomness, while fuzzy sets model kinetic parameters with fuzzy uncertainty or variability by associating each parameter with a fuzzy number instead of a crisp real value. We introduce a simulation-based analysis method for FSPNs to explore the uncertainties of outputs resulting from the uncertainties associated with input parameters, which works equally well for bounded and unbounded models. We illustrate our approach using a yeast polarization model having an infinite state space, which shows the appropriateness of FSPNs in combination with simulation-based analysis for modeling and analyzing biological systems with uncertain information. PMID:26910830

Development of a computer-aided design software for dental splint in orthognathic surgery

NASA Astrophysics Data System (ADS)

Chen, Xiaojun; Li, Xing; Xu, Lu; Sun, Yi; Politis, Constantinus; Egger, Jan

2016-12-01

In the orthognathic surgery, dental splints are important and necessary to help the surgeon reposition the maxilla or mandible. However, the traditional methods of manual design of dental splints are difficult and time-consuming. The research on computer-aided design software for dental splints is rarely reported. Our purpose is to develop a novel special software named EasySplint to design the dental splints conveniently and efficiently. The design can be divided into two steps, which are the generation of initial splint base and the Boolean operation between it and the maxilla-mandibular model. The initial splint base is formed by ruled surfaces reconstructed using the manually picked points. Then, a method to accomplish Boolean operation based on the distance filed of two meshes is proposed. The interference elimination can be conducted on the basis of marching cubes algorithm and Boolean operation. The accuracy of the dental splint can be guaranteed since the original mesh is utilized to form the result surface. Using EasySplint, the dental splints can be designed in about 10 minutes and saved as a stereo lithography (STL) file for 3D printing in clinical applications. Three phantom experiments were conducted and the efficiency of our method was demonstrated.

Toward using games to teach fundamental computer science concepts

NASA Astrophysics Data System (ADS)

Edgington, Jeffrey Michael

Video and computer games have become an important area of study in the field of education. Games have been designed to teach mathematics, physics, raise social awareness, teach history and geography, and train soldiers in the military. Recent work has created computer games for teaching computer programming and understanding basic algorithms. We present an investigation where computer games are used to teach two fundamental computer science concepts: boolean expressions and recursion. The games are intended to teach the concepts and not how to implement them in a programming language. For this investigation, two computer games were created. One is designed to teach basic boolean expressions and operators and the other to teach fundamental concepts of recursion. We describe the design and implementation of both games. We evaluate the effectiveness of these games using before and after surveys. The surveys were designed to ascertain basic understanding, attitudes and beliefs regarding the concepts. The boolean game was evaluated with local high school students and students in a college level introductory computer science course. The recursion game was evaluated with students in a college level introductory computer science course. We present the analysis of the collected survey information for both games. This analysis shows a significant positive change in student attitude towards recursion and modest gains in student learning outcomes for both topics.

Development of a computer-aided design software for dental splint in orthognathic surgery

PubMed Central

Chen, Xiaojun; Li, Xing; Xu, Lu; Sun, Yi; Politis, Constantinus; Egger, Jan

2016-01-01

In the orthognathic surgery, dental splints are important and necessary to help the surgeon reposition the maxilla or mandible. However, the traditional methods of manual design of dental splints are difficult and time-consuming. The research on computer-aided design software for dental splints is rarely reported. Our purpose is to develop a novel special software named EasySplint to design the dental splints conveniently and efficiently. The design can be divided into two steps, which are the generation of initial splint base and the Boolean operation between it and the maxilla-mandibular model. The initial splint base is formed by ruled surfaces reconstructed using the manually picked points. Then, a method to accomplish Boolean operation based on the distance filed of two meshes is proposed. The interference elimination can be conducted on the basis of marching cubes algorithm and Boolean operation. The accuracy of the dental splint can be guaranteed since the original mesh is utilized to form the result surface. Using EasySplint, the dental splints can be designed in about 10 minutes and saved as a stereo lithography (STL) file for 3D printing in clinical applications. Three phantom experiments were conducted and the efficiency of our method was demonstrated. PMID:27966601

Development of a computer-aided design software for dental splint in orthognathic surgery.

PubMed

Chen, Xiaojun; Li, Xing; Xu, Lu; Sun, Yi; Politis, Constantinus; Egger, Jan

2016-12-14

In the orthognathic surgery, dental splints are important and necessary to help the surgeon reposition the maxilla or mandible. However, the traditional methods of manual design of dental splints are difficult and time-consuming. The research on computer-aided design software for dental splints is rarely reported. Our purpose is to develop a novel special software named EasySplint to design the dental splints conveniently and efficiently. The design can be divided into two steps, which are the generation of initial splint base and the Boolean operation between it and the maxilla-mandibular model. The initial splint base is formed by ruled surfaces reconstructed using the manually picked points. Then, a method to accomplish Boolean operation based on the distance filed of two meshes is proposed. The interference elimination can be conducted on the basis of marching cubes algorithm and Boolean operation. The accuracy of the dental splint can be guaranteed since the original mesh is utilized to form the result surface. Using EasySplint, the dental splints can be designed in about 10 minutes and saved as a stereo lithography (STL) file for 3D printing in clinical applications. Three phantom experiments were conducted and the efficiency of our method was demonstrated.

Bounds on the number of hidden neurons in three-layer binary neural networks.

PubMed

Zhang, Zhaozhi; Ma, Xiaomin; Yang, Yixian

2003-09-01

This paper investigates an important problem concerning the complexity of three-layer binary neural networks (BNNs) with one hidden layer. The neuron in the studied BNNs employs a hard limiter activation function with only integer weights and an integer threshold. The studies are focused on implementations of arbitrary Boolean functions which map from [0, 1]n into [0, 1]. A deterministic algorithm called set covering algorithm (SCA) is proposed for the construction of a three-layer BNN to implement an arbitrary Boolean function. The SCA is based on a unit sphere covering (USC) of the Hamming space (HS) which is chosen in advance. It is proved that for the implementation of an arbitrary Boolean function of n-variables (n > or = 3) by using SCA, [3L/2] hidden neurons are necessary and sufficient, where L is the number of unit spheres contained in the chosen USC of the n-dimensional HS. It is shown that by using SCA, the number of hidden neurons required is much less than that by using a two-parallel hyperplane method. In order to indicate the potential ability of three-layer BNNs, a lower bound on the required number of hidden neurons which is derived by using the method of estimating the Vapnik-Chervonenkis (VC) dimension is also given.

Cellular Automata

NASA Astrophysics Data System (ADS)

Gutowitz, Howard

1991-08-01

Cellular automata, dynamic systems in which space and time are discrete, are yielding interesting applications in both the physical and natural sciences. The thirty four contributions in this book cover many aspects of contemporary studies on cellular automata and include reviews, research reports, and guides to recent literature and available software. Chapters cover mathematical analysis, the structure of the space of cellular automata, learning rules with specified properties: cellular automata in biology, physics, chemistry, and computation theory; and generalizations of cellular automata in neural nets, Boolean nets, and coupled map lattices. Current work on cellular automata may be viewed as revolving around two central and closely related problems: the forward problem and the inverse problem. The forward problem concerns the description of properties of given cellular automata. Properties considered include reversibility, invariants, criticality, fractal dimension, and computational power. The role of cellular automata in computation theory is seen as a particularly exciting venue for exploring parallel computers as theoretical and practical tools in mathematical physics. The inverse problem, an area of study gaining prominence particularly in the natural sciences, involves designing rules that possess specified properties or perform specified task. A long-term goal is to develop a set of techniques that can find a rule or set of rules that can reproduce quantitative observations of a physical system. Studies of the inverse problem take up the organization and structure of the set of automata, in particular the parameterization of the space of cellular automata. Optimization and learning techniques, like the genetic algorithm and adaptive stochastic cellular automata are applied to find cellular automaton rules that model such physical phenomena as crystal growth or perform such adaptive-learning tasks as balancing an inverted pole. Howard Gutowitz is Collaborateur in the Service de Physique du Solide et Résonance Magnetique, Commissariat a I'Energie Atomique, Saclay, France.

Finding Mount Everest and handling voids.

PubMed

Storch, Tobias

2011-01-01

Evolutionary algorithms (EAs) are randomized search heuristics that solve problems successfully in many cases. Their behavior is often described in terms of strategies to find a high location on Earth's surface. Unfortunately, many digital elevation models describing it contain void elements. These are elements not assigned an elevation. Therefore, we design and analyze simple EAs with different strategies to handle such partially defined functions. They are experimentally investigated on a dataset describing the elevation of Earth's surface. The largest value found by an EA within a certain runtime is measured, and the median over a few runs is computed and compared for the different EAs. For the dataset, the distribution of void elements seems to be neither random nor adversarial. They are so-called semirandomly distributed. To deepen our understanding of the behavior of the different EAs, they are theoretically considered on well-known pseudo-Boolean functions transferred to partially defined ones. These modifications are also performed in a semirandom way. The typical runtime until an optimum is found by an EA is analyzed, namely bounded from above and below, and compared for the different EAs. We figure out that for the random model it is a good strategy to assume that a void element has a worse function value than all previous elements. Whereas for the adversary model it is a good strategy to assume that a void element has the best function value of all previous elements.

Disparity between ultrasound and clinical findings in psoriatic arthritis.

PubMed

Husic, Rusmir; Gretler, Judith; Felber, Anja; Graninger, Winfried B; Duftner, Christina; Hermann, Josef; Dejaco, Christian

2014-08-01

To investigate the association between psoriatic arthritis (PsA)-specific clinical composite scores and ultrasound-verified pathology as well as comparison of clinical and ultrasound definitions of remission. We performed a prospective study on 70 consecutive PsA patients. Clinical assessments included components of Disease Activity Index for Psoriatic Arthritis (DAPSA) and the Composite Psoriatic Disease Activity Index (CPDAI). Minimal disease activity (MDA) and the following remission criteria were applied: CPDAI joint, entheses and dactylitis domains (CPDAI-JED)=0, DAPSA≤3.3, Boolean's remission definition and physician-judged remission (rem-phys). B-mode and power Doppler (PD-) ultrasound findings were semiquantitatively scored at 68 joints (evaluating synovia, peritendinous tissue, tendons and bony changes) and 14 entheses. Ultrasound remission and minimal ultrasound disease activity (MUDA) were defined as PD-score=0 and PD-score ≤1, respectively, at joints, peritendinous tissue, tendons and entheses. DAPSA but not CPDAI correlated with B-mode and PD-synovitis. Ultrasound signs of enthesitis, dactylitis, tenosynovitis and perisynovitis were not linked with clinical composites. Clinical remission or MDA was observed in 15.7% to 47.1% of PsA patients. Ultrasound remission and MUDA were present in 4.3% and 20.0% of patients, respectively. Joint and tendon-related PD-scores were higher in patients with active versus inactive disease according to CPDAI-JED, DAPSA, Boolean's and rem-phys, whereas no difference was observed regarding enthesitis and perisynovitis. DAPSA≤3.3 (OR 3.9, p=0.049) and Boolean's definition (OR 4.6, p=0.03) were more useful to predict MUDA than other remission criteria. PsA-specific composite scores partially reflect ultrasound findings. DAPSA and Boolean's remission definitions better identify MUDA patients than other clinical criteria. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm.

PubMed

Stoll, Gautier; Viara, Eric; Barillot, Emmanuel; Calzone, Laurence

2012-08-29

Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the effect of perturbations. This article presents an algorithm for modeling biological networks in a discrete framework with continuous time. There exist two major types of mathematical modeling approaches: (1) quantitative modeling, representing various chemical species concentrations by real numbers, mainly based on differential equations and chemical kinetics formalism; (2) and qualitative modeling, representing chemical species concentrations or activities by a finite set of discrete values. Both approaches answer particular (and often different) biological questions. Qualitative modeling approach permits a simple and less detailed description of the biological systems, efficiently describes stable state identification but remains inconvenient in describing the transient kinetics leading to these states. In this context, time is represented by discrete steps. Quantitative modeling, on the other hand, can describe more accurately the dynamical behavior of biological processes as it follows the evolution of concentration or activities of chemical species as a function of time, but requires an important amount of information on the parameters difficult to find in the literature. Here, we propose a modeling framework based on a qualitative approach that is intrinsically continuous in time. The algorithm presented in this article fills the gap between qualitative and quantitative modeling. It is based on continuous time Markov process applied on a Boolean state space. In order to describe the temporal evolution of the biological process we wish to model, we explicitly specify the transition rates for each node. For that purpose, we built a language that can be seen as a generalization of Boolean equations. Mathematically, this approach can be translated in a set of ordinary differential equations on probability distributions. We developed a C++ software, MaBoSS, that is able to simulate such a system by applying Kinetic Monte-Carlo (or Gillespie algorithm) on the Boolean state space. This software, parallelized and optimized, computes the temporal evolution of probability distributions and estimates stationary distributions. Applications of the Boolean Kinetic Monte-Carlo are demonstrated for three qualitative models: a toy model, a published model of p53/Mdm2 interaction and a published model of the mammalian cell cycle. Our approach allows to describe kinetic phenomena which were difficult to handle in the original models. In particular, transient effects are represented by time dependent probability distributions, interpretable in terms of cell populations.

Changing health behaviors to improve health outcomes after angioplasty: a randomized trial of net present value versus future value risk communication.

PubMed

Charlson, M E; Peterson, J C; Boutin-Foster, C; Briggs, W M; Ogedegbe, G G; McCulloch, C E; Hollenberg, J; Wong, C; Allegrante, J P

2008-10-01

Patients who have undergone angioplasty experience difficulty modifying at-risk behaviors for subsequent cardiac events. The purpose of this study was to test whether an innovative approach to framing of risk, based on 'net present value' economic theory, would be more effective in behavioral intervention than the standard 'future value approach' in reducing cardiovascular morbidity and mortality following angioplasty. At baseline, all patients completed a health assessment, received an individualized risk profile and selected risk factors for modification. The intervention randomized patients into two varying methods for illustrating positive effects of behavior change. For the experimental group, each selected risk factor was assigned a numeric biologic age (the net present value) that approximated the relative potential to improve current health status and quality of life when modifying that risk factor. In the control group, risk reduction was framed as the value of preventing future health problems. Ninety-four percent of patients completed 2-year follow-up. There was no difference between the rates of death, stroke, myocardial infarction, Class II-IV angina or severe ischemia (on non-invasive testing) between the net present value group and the future value group. Our results show that a net present risk communication intervention did not result in significant differences in health outcomes.

Boolean function applied to Mimosa pudica movements

PubMed Central

Friedman, Pedro

2011-01-01

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. PMID:21847029

Programming Cell Adhesion for On-Chip Sequential Boolean Logic Functions.

PubMed

Qu, Xiangmeng; Wang, Shaopeng; Ge, Zhilei; Wang, Jianbang; Yao, Guangbao; Li, Jiang; Zuo, Xiaolei; Shi, Jiye; Song, Shiping; Wang, Lihua; Li, Li; Pei, Hao; Fan, Chunhai

2017-08-02

Programmable remodelling of cell surfaces enables high-precision regulation of cell behavior. In this work, we developed in vitro constructed DNA-based chemical reaction networks (CRNs) to program on-chip cell adhesion. We found that the RGD-functionalized DNA CRNs are entirely noninvasive when interfaced with the fluidic mosaic membrane of living cells. DNA toehold with different lengths could tunably alter the release kinetics of cells, which shows rapid release in minutes with the use of a 6-base toehold. We further demonstrated the realization of Boolean logic functions by using DNA strand displacement reactions, which include multi-input and sequential cell logic gates (AND, OR, XOR, and AND-OR). This study provides a highly generic tool for self-organization of biological systems.

Reliable computation from contextual correlations

NASA Astrophysics Data System (ADS)

Oestereich, André L.; Galvão, Ernesto F.

2017-12-01

An operational approach to the study of computation based on correlations considers black boxes with one-bit inputs and outputs, controlled by a limited classical computer capable only of performing sums modulo-two. In this setting, it was shown that noncontextual correlations do not provide any extra computational power, while contextual correlations were found to be necessary for the deterministic evaluation of nonlinear Boolean functions. Here we investigate the requirements for reliable computation in this setting; that is, the evaluation of any Boolean function with success probability bounded away from 1 /2 . We show that bipartite CHSH quantum correlations suffice for reliable computation. We also prove that an arbitrarily small violation of a multipartite Greenberger-Horne-Zeilinger noncontextuality inequality also suffices for reliable computation.

The pseudo-Boolean optimization approach to form the N-version software structure

NASA Astrophysics Data System (ADS)

Kovalev, I. V.; Kovalev, D. I.; Zelenkov, P. V.; Voroshilova, A. A.

2015-10-01

The problem of developing an optimal structure of N-version software system presents a kind of very complex optimization problem. This causes the use of deterministic optimization methods inappropriate for solving the stated problem. In this view, exploiting heuristic strategies looks more rational. In the field of pseudo-Boolean optimization theory, the so called method of varied probabilities (MVP) has been developed to solve problems with a large dimensionality. Some additional modifications of MVP have been made to solve the problem of N-version systems design. Those algorithms take into account the discovered specific features of the objective function. The practical experiments have shown the advantage of using these algorithm modifications because of reducing a search space.

A procedure concept for local reflex control of grasping

NASA Technical Reports Server (NTRS)

Fiorini, Paolo; Chang, Jeffrey

1989-01-01

An architecture is proposed for the control of robotic devices, and in particular of anthropomorphic hands, characterized by a hierarchical structure in which every level of the architecture contains data and control function with varying degree of abstraction. Bottom levels of the hierarchy interface directly with sensors and actuators, and process raw data and motor commands. Higher levels perform more symbolic types of tasks, such as application of boolean rules and general planning operations. Layers implementation has to be consistent with the type of operation and its requirements for real time control. It is proposed to implement the rule level with a Boolean Artificial Neural Network characterized by a response time sufficient for producing reflex corrective action at the actuator level.

Rapid Increase in Ownership and Use of Long-Lasting Insecticidal Nets and Decrease in Prevalence of Malaria in Three Regional States of Ethiopia (2006-2007)

PubMed Central

Shargie, Estifanos Biru; Ngondi, Jeremiah; Graves, Patricia M.; Getachew, Asefaw; Hwang, Jimee; Gebre, Teshome; Mosher, Aryc W.; Ceccato, Pietro; Endeshaw, Tekola; Jima, Daddi; Tadesse, Zerihun; Tenaw, Eskindir; Reithinger, Richard; Emerson, Paul M.; Richards, Frank O.; Ghebreyesus, Tedros Adhanom

2010-01-01

Following recent large scale-up of malaria control interventions in Ethiopia, this study aimed to compare ownership and use of long-lasting insecticidal nets (LLIN), and the change in malaria prevalence using two population-based household surveys in three regions of the country. Each survey used multistage cluster random sampling with 25 households per cluster. Household net ownership tripled from 19.6% in 2006 to 68.4% in 2007, with mean LLIN per household increasing from 0.3 to 1.2. Net use overall more than doubled from 15.3% to 34.5%, but in households owning LLIN, use declined from 71.7% to 48.3%. Parasitemia declined from 4.1% to 0.4%. Large scale-up of net ownership over a short period of time was possible. However, a large increase in net ownership was not necessarily mirrored directly by increased net use. Better targeting of nets to malaria-risk areas and sustained behavioural change communication are needed to increase and maintain net use. PMID:20936103

Impact of eLearning course on nurses' professional competence in seclusion and restraint practices: 9-month follow-up results of a randomized controlled study (ISRCTN32869544).

PubMed

Kontio, R; Hätönen, H; Joffe, G; Pitkänen, A; Lahti, M; Välimäki, M

2013-04-01

eLearning may facilitate continuing vocational education, but data on the long-term effects of an eLearning course are lacking. The aim of this study was to explore the long-term impact of an eLearning course entitled ePsychNurse.Net on psychiatric nurses' professional competence in practicing seclusion and restraint and on their job satisfaction and general self-efficacy at 9-month follow-up. In a randomized controlled study, 12 wards were randomly assigned to the ePsychNurse.Net (intervention) or training as usual (control). Baseline and 9-month follow-up data on nurses' knowledge of coercion-related legislation, physical restraint and seclusion, their attitudes towards physical restraint and seclusion, job satisfaction and general self-efficacy were analysed for 137 completers (those who participated in the 9-month follow-up assessment). No between-group differences were found on any variable, with the exception of a change in attitude to seclusion in favour of the control group. The findings of the long-term effects did not differ from the immediate outcomes (3-month follow-up) and the improved level of knowledge acquired and further consolidation of that knowledge did not take place in the 6-month period after the 3-month ePsychNurse.Net course. The ePsychNurse.Net should be further developed and its future modifications will require additional studies, probably with some new outcome measures. © 2012 Blackwell Publishing.

Laparoscopic resection of gastrointestinal neuroendocrine tumors with special contribution of radionuclide imaging

PubMed Central

Shamiyeh, Andreas; Gabriel, Michael

2014-01-01

The surgical treatment of neuroendocrine tumors (NETs) draws on experience and guidelines more than on prospective randomized trials. The incidence of NET is increasing in all parts of the gastrointestinal tract. A variety of classifications introduced over the last decade may have led to difficulties in judging clinical relevance and determining the right surgical strategy. The North American Neuroendocrine Tumor Society and the European Neuroendocrine Tumor Society have developed usable guidelines from the available literature. For more than 20 years laparoscopy has developed as the gold standard for various surgical indications. Nevertheless, few trials have compared open and laparoscopic surgery with regard to NET. This review summarizes the recent literature on surgery for NET and incorporates the evidence on laparoscopy for cancer which might be also applied for NET. PMID:25400444

Inequalities in purchase of mosquito nets and willingness to pay for insecticide-treated nets in Nigeria: Challenges for malaria control interventions

PubMed Central

Onwujekwe, Obinna; Hanson, Kara; Fox-Rushby, Julia

2004-01-01

Objective To explore the equity implications of insecticide-treated nets (ITN) distribution programmes that are based on user charges. Methods A questionnaire was used to collect information on previous purchase of untreated nets and hypothetical willingness to pay (WTP) for ITNs from a random sample of householders. A second survey was conducted one month later to collect information on actual purchases of ITNs. An economic status index was used for characterizing inequity. Major findings The lower economic status quintiles were less likely to have previously purchased untreated nets and also had a lower hypothetical and actual WTP for ITNs. Conclusion ITN distribution programmes need to take account of the diversity in WTP for ITNs if they are to ensure equity in access to the nets. This could form part of the overall poverty reduction strategy. PMID:15023234

Accounting for between-study variation in incremental net benefit in value of information methodology.

PubMed

Willan, Andrew R; Eckermann, Simon

2012-10-01

Previous applications of value of information methods for determining optimal sample size in randomized clinical trials have assumed no between-study variation in mean incremental net benefit. By adopting a hierarchical model, we provide a solution for determining optimal sample size with this assumption relaxed. The solution is illustrated with two examples from the literature. Expected net gain increases with increasing between-study variation, reflecting the increased uncertainty in incremental net benefit and reduced extent to which data are borrowed from previous evidence. Hence, a trial can become optimal where current evidence is sufficient assuming no between-study variation. However, despite the expected net gain increasing, the optimal sample size in the illustrated examples is relatively insensitive to the amount of between-study variation. Further percentage losses in expected net gain were small even when choosing sample sizes that reflected widely different between-study variation. Copyright © 2011 John Wiley & Sons, Ltd.

Protein cross-linking by chlorinated polyamines and transglutamylation stabilizes neutrophil extracellular traps.

PubMed

Csomós, Krisztián; Kristóf, Endre; Jakob, Bernadett; Csomós, István; Kovács, György; Rotem, Omri; Hodrea, Judit; Bagoly, Zsuzsa; Muszbek, Laszlo; Balajthy, Zoltán; Csősz, Éva; Fésüs, László

2016-08-11

Neutrophil extracellular trap (NET) ejected from activated dying neutrophils is a highly ordered structure of DNA and selected proteins capable to eliminate pathogenic microorganisms. Biochemical determinants of the non-randomly formed stable NETs have not been revealed so far. Studying the formation of human NETs we have observed that polyamines were incorporated into the NET. Inhibition of myeloperoxidase, which is essential for NET formation and can generate reactive chlorinated polyamines through hypochlorous acid, decreased polyamine incorporation. Addition of exogenous primary amines that similarly to polyamines inhibit reactions catalyzed by the protein cross-linker transglutaminases (TGases) has similar effect. Proteomic analysis of the highly reproducible pattern of NET components revealed cross-linking of NET proteins through chlorinated polyamines and ɛ(γ-glutamyl)lysine as well as bis-γ-glutamyl polyamine bonds catalyzed by the TGases detected in neutrophils. Competitive inhibition of protein cross-linking by monoamines disturbed the cross-linking pattern of NET proteins, which resulted in the loss of the ordered structure of the NET and significantly reduced capacity to trap bacteria. Our findings provide explanation of how NETs are formed in a reproducible and ordered manner to efficiently neutralize microorganisms at the first defense line of the innate immune system.

Protein cross-linking by chlorinated polyamines and transglutamylation stabilizes neutrophil extracellular traps

PubMed Central

Csomós, Krisztián; Kristóf, Endre; Jakob, Bernadett; Csomós, István; Kovács, György; Rotem, Omri; Hodrea, Judit; Bagoly, Zsuzsa; Muszbek, Laszlo; Balajthy, Zoltán; Csősz, Éva; Fésüs, László

2016-01-01

Neutrophil extracellular trap (NET) ejected from activated dying neutrophils is a highly ordered structure of DNA and selected proteins capable to eliminate pathogenic microorganisms. Biochemical determinants of the non-randomly formed stable NETs have not been revealed so far. Studying the formation of human NETs we have observed that polyamines were incorporated into the NET. Inhibition of myeloperoxidase, which is essential for NET formation and can generate reactive chlorinated polyamines through hypochlorous acid, decreased polyamine incorporation. Addition of exogenous primary amines that similarly to polyamines inhibit reactions catalyzed by the protein cross-linker transglutaminases (TGases) has similar effect. Proteomic analysis of the highly reproducible pattern of NET components revealed cross-linking of NET proteins through chlorinated polyamines and ɛ(γ-glutamyl)lysine as well as bis-γ-glutamyl polyamine bonds catalyzed by the TGases detected in neutrophils. Competitive inhibition of protein cross-linking by monoamines disturbed the cross-linking pattern of NET proteins, which resulted in the loss of the ordered structure of the NET and significantly reduced capacity to trap bacteria. Our findings provide explanation of how NETs are formed in a reproducible and ordered manner to efficiently neutralize microorganisms at the first defense line of the innate immune system. PMID:27512953

Combining deep residual neural network features with supervised machine learning algorithms to classify diverse food image datasets.

PubMed

McAllister, Patrick; Zheng, Huiru; Bond, Raymond; Moorhead, Anne

2018-04-01

Obesity is increasing worldwide and can cause many chronic conditions such as type-2 diabetes, heart disease, sleep apnea, and some cancers. Monitoring dietary intake through food logging is a key method to maintain a healthy lifestyle to prevent and manage obesity. Computer vision methods have been applied to food logging to automate image classification for monitoring dietary intake. In this work we applied pretrained ResNet-152 and GoogleNet convolutional neural networks (CNNs), initially trained using ImageNet Large Scale Visual Recognition Challenge (ILSVRC) dataset with MatConvNet package, to extract features from food image datasets; Food 5K, Food-11, RawFooT-DB, and Food-101. Deep features were extracted from CNNs and used to train machine learning classifiers including artificial neural network (ANN), support vector machine (SVM), Random Forest, and Naive Bayes. Results show that using ResNet-152 deep features with SVM with RBF kernel can accurately detect food items with 99.4% accuracy using Food-5K validation food image dataset and 98.8% with Food-5K evaluation dataset using ANN, SVM-RBF, and Random Forest classifiers. Trained with ResNet-152 features, ANN can achieve 91.34%, 99.28% when applied to Food-11 and RawFooT-DB food image datasets respectively and SVM with RBF kernel can achieve 64.98% with Food-101 image dataset. From this research it is clear that using deep CNN features can be used efficiently for diverse food item image classification. The work presented in this research shows that pretrained ResNet-152 features provide sufficient generalisation power when applied to a range of food image classification tasks. Copyright © 2018 Elsevier Ltd. All rights reserved.

Attractor-Based Obstructions to Growth in Homogeneous Cyclic Boolean Automata.

PubMed

Khan, Bilal; Cantor, Yuri; Dombrowski, Kirk

2015-11-01

We consider a synchronous Boolean organism consisting of N cells arranged in a circle, where each cell initially takes on an independently chosen Boolean value. During the lifetime of the organism, each cell updates its own value by responding to the presence (or absence) of diversity amongst its two neighbours' values. We show that if all cells eventually take a value of 0 (irrespective of their initial values) then the organism necessarily has a cell count that is a power of 2. In addition, the converse is also proved: if the number of cells in the organism is a proper power of 2, then no matter what the initial values of the cells are, eventually all cells take on a value of 0 and then cease to change further. We argue that such an absence of structure in the dynamical properties of the organism implies a lack of adaptiveness, and so is evolutionarily disadvantageous. It follows that as the organism doubles in size (say from m to 2m) it will necessarily encounter an intermediate size that is a proper power of 2, and suffers from low adaptiveness. Finally we show, through computational experiments, that one way an organism can grow to more than twice its size and still avoid passing through intermediate sizes that lack structural dynamics, is for the organism to depart from assumptions of homogeneity at the cellular level.

Evolution of a designless nanoparticle network into reconfigurable Boolean logic

NASA Astrophysics Data System (ADS)

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.

Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis.

PubMed

Bandyopadhyay, Sanghamitra; Mallik, Saurav

2018-01-01

Identification of combinatorial markers from multiple data sources is a challenging task in bioinformatics. Here, we propose a novel computational framework for identifying significant combinatorial markers ( s) using both gene expression and methylation data. The gene expression and methylation data are integrated into a single continuous data as well as a (post-discretized) boolean data based on their intrinsic (i.e., inverse) relationship. A novel combined score of methylation and expression data (viz., ) is introduced which is computed on the integrated continuous data for identifying initial non-redundant set of genes. Thereafter, (maximal) frequent closed homogeneous genesets are identified using a well-known biclustering algorithm applied on the integrated boolean data of the determined non-redundant set of genes. A novel sample-based weighted support ( ) is then proposed that is consecutively calculated on the integrated boolean data of the determined non-redundant set of genes in order to identify the non-redundant significant genesets. The top few resulting genesets are identified as potential s. Since our proposed method generates a smaller number of significant non-redundant genesets than those by other popular methods, the method is much faster than the others. Application of the proposed technique on an expression and a methylation data for Uterine tumor or Prostate Carcinoma produces a set of significant combination of markers. We expect that such a combination of markers will produce lower false positives than individual markers.

Predictive computation of genomic logic processing functions in embryonic development

PubMed Central

Peter, Isabelle S.; Faure, Emmanuel; Davidson, Eric H.

2012-01-01

Gene regulatory networks (GRNs) control the dynamic spatial patterns of regulatory gene expression in development. Thus, in principle, GRN models may provide system-level, causal explanations of developmental process. To test this assertion, we have transformed a relatively well-established GRN model into a predictive, dynamic Boolean computational model. This Boolean model computes spatial and temporal gene expression according to the regulatory logic and gene interactions specified in a GRN model for embryonic development in the sea urchin. Additional information input into the model included the progressive embryonic geometry and gene expression kinetics. The resulting model predicted gene expression patterns for a large number of individual regulatory genes each hour up to gastrulation (30 h) in four different spatial domains of the embryo. Direct comparison with experimental observations showed that the model predictively computed these patterns with remarkable spatial and temporal accuracy. In addition, we used this model to carry out in silico perturbations of regulatory functions and of embryonic spatial organization. The model computationally reproduced the altered developmental functions observed experimentally. Two major conclusions are that the starting GRN model contains sufficiently complete regulatory information to permit explanation of a complex developmental process of gene expression solely in terms of genomic regulatory code, and that the Boolean model provides a tool with which to test in silico regulatory circuitry and developmental perturbations. PMID:22927416

Attractor-Based Obstructions to Growth in Homogeneous Cyclic Boolean Automata

PubMed Central

Khan, Bilal; Cantor, Yuri; Dombrowski, Kirk

2016-01-01

We consider a synchronous Boolean organism consisting of N cells arranged in a circle, where each cell initially takes on an independently chosen Boolean value. During the lifetime of the organism, each cell updates its own value by responding to the presence (or absence) of diversity amongst its two neighbours’ values. We show that if all cells eventually take a value of 0 (irrespective of their initial values) then the organism necessarily has a cell count that is a power of 2. In addition, the converse is also proved: if the number of cells in the organism is a proper power of 2, then no matter what the initial values of the cells are, eventually all cells take on a value of 0 and then cease to change further. We argue that such an absence of structure in the dynamical properties of the organism implies a lack of adaptiveness, and so is evolutionarily disadvantageous. It follows that as the organism doubles in size (say from m to 2m) it will necessarily encounter an intermediate size that is a proper power of 2, and suffers from low adaptiveness. Finally we show, through computational experiments, that one way an organism can grow to more than twice its size and still avoid passing through intermediate sizes that lack structural dynamics, is for the organism to depart from assumptions of homogeneity at the cellular level. PMID:27660398

Semi-supervised word polarity identification in resource-lean languages.

PubMed

Dehdarbehbahani, Iman; Shakery, Azadeh; Faili, Heshaam

2014-10-01

Sentiment words, as fundamental constitutive parts of subjective sentences, have a substantial effect on analysis of opinions, emotions and beliefs. Most of the proposed methods for identifying the semantic orientations of words exploit rich linguistic resources such as WordNet, subjectivity corpora, or polarity tagged words. Shortage of such linguistic resources in resource-lean languages affects the performance of word polarity identification in these languages. In this paper, we present a method which exploits a language with rich subjectivity analysis resources (English) to identify the polarity of words in a resource-lean foreign language. The English WordNet and a sparse foreign WordNet infrastructure are used to create a heterogeneous, multilingual and weighted semantic network. To identify the semantic orientation of foreign words, a random walk based method is applied to the semantic network along with a set of automatically weighted English positive and negative seeds. In a post-processing phase, synonym and antonym relations in the foreign WordNet are used to filter the random walk results. Our experiments on English and Persian languages show that the proposed method can outperform state-of-the-art word polarity identification methods in both languages. Copyright © 2014 Elsevier Ltd. All rights reserved.

Net mineral requirements of dairy goats during pregnancy.

PubMed

Härter, C J; Lima, L D; Castagnino, D S; Silva, H O; Figueiredo, F O M; St-Pierre, N R; Resende, K T; Teixeira, I A M A

2017-09-01

Mineral requirements of pregnant dairy goats are still not well defined; therefore, we investigated the net Ca, P, Mg, Na and K requirements for pregnancy and for maintenance during pregnancy in two separate experiments. Experiment 1 was performed to estimate the net Ca, P, Mg, Na and K requirements in goats carrying single or twin fetuses from 50 to 140 days of pregnancy (DOP). The net mineral requirements for pregnancy were determined by measuring mineral deposition in gravid uterus and mammary gland after comparative slaughter. In total, 57 dairy goats of two breeds (Oberhasli or Saanen), in their third or fourth parturition, were randomly assigned to groups based on litter size (single or twin) and day of slaughter (50, 80, 110 and 140 DOP) in a fully factorial design. Net mineral accretion for pregnancy did not differ by goat breed. The total daily Ca, P, Mg, Na and K requirements for pregnancy were greatest in goats carrying twins (P<0.05), and the requirements increased as pregnancy progressed. Experiment 2 was performed to estimate net Ca, P, Mg, Na and K requirements for dairy goat maintenance during pregnancy. In total, 58 dairy goats (Oberhasli and Saanen) carrying twin fetuses were assigned to groups based on slaughter day (80, 110 and 140 DOP) and feed restriction (ad libitum, 20% and 40% feed restriction) in a randomized block design. The net Ca, P and Mg requirements for maintenance did not vary by breed or over the course of pregnancy. The daily net requirements of Ca, P and Mg for maintenance were 60.4, 31.1 and 2.42 mg/kg live BW (LBW), respectively. The daily net Na requirement for maintenance was greater in Saanen goats (11.8 mg/kg LBW) than in Oberhasli goats (8.96 mg/kg LBW; P<0.05). Daily net K requirements increased as pregnancy progressed from 8.73 to 15.4 mg/kg LBW (P<0.01). The findings of this study will guide design of diets with adequate mineral content for pregnant goats throughout their pregnancy.

Design of a Nanoscale, CMOS-Integrable, Thermal-Guiding Structure for Boolean-Logic and Neuromorphic Computation.

PubMed

Loke, Desmond; Skelton, Jonathan M; Chong, Tow-Chong; Elliott, Stephen R

2016-12-21

One of the requirements for achieving faster CMOS electronics is to mitigate the unacceptably large chip areas required to steer heat away from or, more recently, toward the critical nodes of state-of-the-art devices. Thermal-guiding (TG) structures can efficiently direct heat by "meta-materials" engineering; however, some key aspects of the behavior of these systems are not fully understood. Here, we demonstrate control of the thermal-diffusion properties of TG structures by using nanometer-scale, CMOS-integrable, graphene-on-silica stacked materials through finite-element-methods simulations. It has been shown that it is possible to implement novel, controllable, thermally based Boolean-logic and spike-timing-dependent plasticity operations for advanced (neuromorphic) computing applications using such thermal-guide architectures.

Modeling gene regulatory networks: A network simplification algorithm

NASA Astrophysics Data System (ADS)

Ferreira, Luiz Henrique O.; de Castro, Maria Clicia S.; da Silva, Fabricio A. B.

2016-12-01

Boolean networks have been used for some time to model Gene Regulatory Networks (GRNs), which describe cell functions. Those models can help biologists to make predictions, prognosis and even specialized treatment when some disturb on the GRN lead to a sick condition. However, the amount of information related to a GRN can be huge, making the task of inferring its boolean network representation quite a challenge. The method shown here takes into account information about the interactome to build a network, where each node represents a protein, and uses the entropy of each node as a key to reduce the size of the network, allowing the further inferring process to focus only on the main protein hubs, the ones with most potential to interfere in overall network behavior.

Reward and uncertainty in exploration programs

NASA Technical Reports Server (NTRS)

Kaufman, G. M.; Bradley, P. G.

1971-01-01

A set of variables which are crucial to the economic outcome of petroleum exploration are discussed. These are treated as random variables; the values they assume indicate the number of successes that occur in a drilling program and determine, for a particular discovery, the unit production cost and net economic return if that reservoir is developed. In specifying the joint probability law for those variables, extreme and probably unrealistic assumptions are made. In particular, the different random variables are assumed to be independently distributed. Using postulated probability functions and specified parameters, values are generated for selected random variables, such as reservoir size. From this set of values the economic magnitudes of interest, net return and unit production cost are computed. This constitutes a single trial, and the procedure is repeated many times. The resulting histograms approximate the probability density functions of the variables which describe the economic outcomes of an exploratory drilling program.

Health and agricultural productivity: Evidence from Zambia.

PubMed

Fink, Günther; Masiye, Felix

2015-07-01

We evaluate the productivity effects of investment in preventive health technology through a randomized controlled trial in rural Zambia. In the experiment, access to subsidized bed nets was randomly assigned at the community level; 516 farmers were followed over a one-year farming period. We find large positive effects of preventative health investment on productivity: among farmers provided with access to free nets, harvest value increased by US$ 76, corresponding to about 14.7% of the average output value. While only limited information was collected on farming inputs, shifts in the extensive and the intensive margins of labor supply appear to be the most likely mechanism underlying the productivity improvements observed. Copyright © 2015 Elsevier B.V. All rights reserved.

An algebra-based method for inferring gene regulatory networks

PubMed Central

2014-01-01

Background The inference of gene regulatory networks (GRNs) from experimental observations is at the heart of systems biology. This includes the inference of both the network topology and its dynamics. While there are many algorithms available to infer the network topology from experimental data, less emphasis has been placed on methods that infer network dynamics. Furthermore, since the network inference problem is typically underdetermined, it is essential to have the option of incorporating into the inference process, prior knowledge about the network, along with an effective description of the search space of dynamic models. Finally, it is also important to have an understanding of how a given inference method is affected by experimental and other noise in the data used. Results This paper contains a novel inference algorithm using the algebraic framework of Boolean polynomial dynamical systems (BPDS), meeting all these requirements. The algorithm takes as input time series data, including those from network perturbations, such as knock-out mutant strains and RNAi experiments. It allows for the incorporation of prior biological knowledge while being robust to significant levels of noise in the data used for inference. It uses an evolutionary algorithm for local optimization with an encoding of the mathematical models as BPDS. The BPDS framework allows an effective representation of the search space for algebraic dynamic models that improves computational performance. The algorithm is validated with both simulated and experimental microarray expression profile data. Robustness to noise is tested using a published mathematical model of the segment polarity gene network in Drosophila melanogaster. Benchmarking of the algorithm is done by comparison with a spectrum of state-of-the-art network inference methods on data from the synthetic IRMA network to demonstrate that our method has good precision and recall for the network reconstruction task, while also predicting several of the dynamic patterns present in the network. Conclusions Boolean polynomial dynamical systems provide a powerful modeling framework for the reverse engineering of gene regulatory networks, that enables a rich mathematical structure on the model search space. A C++ implementation of the method, distributed under LPGL license, is available, together with the source code, at http://www.paola-vera-licona.net/Software/EARevEng/REACT.html. PMID:24669835

Changing Health Behaviors to Improve Health Outcomes after Angioplasty: A Randomized Trial of Net Present Value versus Future Value Risk Communication

ERIC Educational Resources Information Center

Charlson, M. E.; Peterson, J. C.; Boutin-Foster, C.; Briggs, W. M.; Ogedegbe, G. G.; McCulloch, C. E.; Hollenberg, J.; Wong, C.; Allegrante, J. P.

2008-01-01

Patients who have undergone angioplasty experience difficulty modifying at-risk behaviors for subsequent cardiac events. The purpose of this study was to test whether an innovative approach to framing of risk, based on "net present value" economic theory, would be more effective in behavioral intervention than the standard "future value approach"…

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

PubMed Central

2011-01-01

Background Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. Results We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Conclusions Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web-based tool for several different input formats, and it makes analysis of complex models accessible to a larger community, as it is platform independent as a web-service and does not require understanding of the underlying mathematics. PMID:21774817

Impact of resonance regeneration and decay on the net proton fluctuations in a hadron resonance gas

DOE PAGES

Nahrgang, Marlene; Bluhm, Marcus; Alba, Paolo; ...

2015-12-01

We investigate net proton fluctuations as important observables measured in heavy-ion collisions within the hadron resonance gas (HRG) model. Special emphasis is given to effects which are a priori not inherent in a thermally and chemically equilibrated HRG approach. In particular, we point out the importance of taking into account the successive regeneration and decay of resonances after the chemical freeze-out, which lead to a randomization of the isospin of nucleons and thus to additional fluctuations in the net proton number. In conclusion, we find good agreement between our model results and the recent STAR measurements of the higher-order momentsmore » of the net proton distribution.« less

Neural networks for structural design - An integrated system implementation

NASA Technical Reports Server (NTRS)

Berke, Laszlo; Hafez, Wassim; Pao, Yoh-Han

1992-01-01

The development of powerful automated procedures to aid the creative designer is becoming increasingly critical for complex design tasks. In the work described here Artificial Neural Nets are applied to acquire structural analysis and optimization domain expertise. Based on initial instructions from the user an automated procedure generates random instances of structural analysis and/or optimization 'experiences' that cover a desired domain. It extracts training patterns from the created instances, constructs and trains an appropriate network architecture and checks the accuracy of net predictions. The final product is a trained neural net that can estimate analysis and/or optimization results instantaneously.

Symbolic Computation Using Cellular Automata-Based Hyperdimensional Computing.

PubMed

Yilmaz, Ozgur

2015-12-01

This letter introduces a novel framework of reservoir computing that is capable of both connectionist machine intelligence and symbolic computation. A cellular automaton is used as the reservoir of dynamical systems. Input is randomly projected onto the initial conditions of automaton cells, and nonlinear computation is performed on the input via application of a rule in the automaton for a period of time. The evolution of the automaton creates a space-time volume of the automaton state space, and it is used as the reservoir. The proposed framework is shown to be capable of long-term memory, and it requires orders of magnitude less computation compared to echo state networks. As the focus of the letter, we suggest that binary reservoir feature vectors can be combined using Boolean operations as in hyperdimensional computing, paving a direct way for concept building and symbolic processing. To demonstrate the capability of the proposed system, we make analogies directly on image data by asking, What is the automobile of air?

Extremal Optimization for Quadratic Unconstrained Binary Problems

NASA Astrophysics Data System (ADS)

Boettcher, S.

We present an implementation of τ-EO for quadratic unconstrained binary optimization (QUBO) problems. To this end, we transform modify QUBO from its conventional Boolean presentation into a spin glass with a random external field on each site. These fields tend to be rather large compared to the typical coupling, presenting EO with a challenging two-scale problem, exploring smaller differences in couplings effectively while sufficiently aligning with those strong external fields. However, we also find a simple solution to that problem that indicates that those external fields apparently tilt the energy landscape to a such a degree such that global minima become more easy to find than those of spin glasses without (or very small) fields. We explore the impact of the weight distribution of the QUBO formulation in the operations research literature and analyze their meaning in a spin-glass language. This is significant because QUBO problems are considered among the main contenders for NP-hard problems that could be solved efficiently on a quantum computer such as D-Wave.

A linear programming approach to max-sum problem: a review.

PubMed

Werner, Tomás

2007-07-01

The max-sum labeling problem, defined as maximizing a sum of binary (i.e., pairwise) functions of discrete variables, is a general NP-hard optimization problem with many applications, such as computing the MAP configuration of a Markov random field. We review a not widely known approach to the problem, developed by Ukrainian researchers Schlesinger et al. in 1976, and show how it contributes to recent results, most importantly, those on the convex combination of trees and tree-reweighted max-product. In particular, we review Schlesinger et al.'s upper bound on the max-sum criterion, its minimization by equivalent transformations, its relation to the constraint satisfaction problem, the fact that this minimization is dual to a linear programming relaxation of the original problem, and the three kinds of consistency necessary for optimality of the upper bound. We revisit problems with Boolean variables and supermodular problems. We describe two algorithms for decreasing the upper bound. We present an example application for structural image analysis.

Multistate Memristive Tantalum Oxide Devices for Ternary Arithmetic

PubMed Central

Kim, Wonjoo; Chattopadhyay, Anupam; Siemon, Anne; Linn, Eike; Waser, Rainer; Rana, Vikas

2016-01-01

Redox-based resistive switching random access memory (ReRAM) offers excellent properties to implement future non-volatile memory arrays. Recently, the capability of two-state ReRAMs to implement Boolean logic functionality gained wide interest. Here, we report on seven-states Tantalum Oxide Devices, which enable the realization of an intrinsic modular arithmetic using a ternary number system. Modular arithmetic, a fundamental system for operating on numbers within the limit of a modulus, is known to mathematicians since the days of Euclid and finds applications in diverse areas ranging from e-commerce to musical notations. We demonstrate that multistate devices not only reduce the storage area consumption drastically, but also enable novel in-memory operations, such as computing using high-radix number systems, which could not be implemented using two-state devices. The use of high radix number system reduces the computational complexity by reducing the number of needed digits. Thus the number of calculation operations in an addition and the number of logic devices can be reduced. PMID:27834352

Multistate Memristive Tantalum Oxide Devices for Ternary Arithmetic.

PubMed

Kim, Wonjoo; Chattopadhyay, Anupam; Siemon, Anne; Linn, Eike; Waser, Rainer; Rana, Vikas

2016-11-11

Redox-based resistive switching random access memory (ReRAM) offers excellent properties to implement future non-volatile memory arrays. Recently, the capability of two-state ReRAMs to implement Boolean logic functionality gained wide interest. Here, we report on seven-states Tantalum Oxide Devices, which enable the realization of an intrinsic modular arithmetic using a ternary number system. Modular arithmetic, a fundamental system for operating on numbers within the limit of a modulus, is known to mathematicians since the days of Euclid and finds applications in diverse areas ranging from e-commerce to musical notations. We demonstrate that multistate devices not only reduce the storage area consumption drastically, but also enable novel in-memory operations, such as computing using high-radix number systems, which could not be implemented using two-state devices. The use of high radix number system reduces the computational complexity by reducing the number of needed digits. Thus the number of calculation operations in an addition and the number of logic devices can be reduced.

Quantum one-way permutation over the finite field of two elements

NASA Astrophysics Data System (ADS)

de Castro, Alexandre

2017-06-01

In quantum cryptography, a one-way permutation is a bounded unitary operator U:{H} → {H} on a Hilbert space {H} that is easy to compute on every input, but hard to invert given the image of a random input. Levin (Probl Inf Transm 39(1):92-103, 2003) has conjectured that the unitary transformation g(a,x)=(a,f(x)+ax), where f is any length-preserving function and a,x \\in {GF}_{{2}^{\\Vert x\\Vert }}, is an information-theoretically secure operator within a polynomial factor. Here, we show that Levin's one-way permutation is provably secure because its output values are four maximally entangled two-qubit states, and whose probability of factoring them approaches zero faster than the multiplicative inverse of any positive polynomial poly( x) over the Boolean ring of all subsets of x. Our results demonstrate through well-known theorems that existence of classical one-way functions implies existence of a universal quantum one-way permutation that cannot be inverted in subexponential time in the worst case.

Multistate Memristive Tantalum Oxide Devices for Ternary Arithmetic

NASA Astrophysics Data System (ADS)

Kim, Wonjoo; Chattopadhyay, Anupam; Siemon, Anne; Linn, Eike; Waser, Rainer; Rana, Vikas

2016-11-01

Redox-based resistive switching random access memory (ReRAM) offers excellent properties to implement future non-volatile memory arrays. Recently, the capability of two-state ReRAMs to implement Boolean logic functionality gained wide interest. Here, we report on seven-states Tantalum Oxide Devices, which enable the realization of an intrinsic modular arithmetic using a ternary number system. Modular arithmetic, a fundamental system for operating on numbers within the limit of a modulus, is known to mathematicians since the days of Euclid and finds applications in diverse areas ranging from e-commerce to musical notations. We demonstrate that multistate devices not only reduce the storage area consumption drastically, but also enable novel in-memory operations, such as computing using high-radix number systems, which could not be implemented using two-state devices. The use of high radix number system reduces the computational complexity by reducing the number of needed digits. Thus the number of calculation operations in an addition and the number of logic devices can be reduced.

Electrical Circuits in the Mathematics/Computer Science Classroom.

ERIC Educational Resources Information Center

McMillan, Robert D.

1988-01-01

Shows how, with little or no electrical background, students can apply Boolean algebra concepts to design and build integrated electrical circuits in the classroom that will reinforce important ideas in mathematics. (PK)

Topological Aspects of Information Retrieval.

ERIC Educational Resources Information Center

Egghe, Leo; Rousseau, Ronald

1998-01-01

Discusses topological aspects of theoretical information retrieval, including retrieval topology; similarity topology; pseudo-metric topology; document spaces as topological spaces; Boolean information retrieval as a subsystem of any topological system; and proofs of theorems. (LRW)

Combinatorial optimization in foundry practice

NASA Astrophysics Data System (ADS)

Antamoshkin, A. N.; Masich, I. S.

2016-04-01

The multicriteria mathematical model of foundry production capacity planning is suggested in the paper. The model is produced in terms of pseudo-Boolean optimization theory. Different search optimization methods were used to solve the obtained problem.

Defining of the BDX930 Assembly Language

NASA Technical Reports Server (NTRS)

Boyer, R. S.; Moore, J. S.

1983-01-01

A definition of the BDX930 assembly language is presented. Various definition problems and suggested solutions are included. A class of defined recognizers based on boolean valued nowrecursive functions is employed in preprocessing.

Optoelectronic analogs of self-programming neural nets - Architecture and methodologies for implementing fast stochastic learning by simulated annealing

NASA Technical Reports Server (NTRS)

Farhat, Nabil H.

1987-01-01

Self-organization and learning is a distinctive feature of neural nets and processors that sets them apart from conventional approaches to signal processing. It leads to self-programmability which alleviates the problem of programming complexity in artificial neural nets. In this paper architectures for partitioning an optoelectronic analog of a neural net into distinct layers with prescribed interconnectivity pattern to enable stochastic learning by simulated annealing in the context of a Boltzmann machine are presented. Stochastic learning is of interest because of its relevance to the role of noise in biological neural nets. Practical considerations and methodologies for appreciably accelerating stochastic learning in such a multilayered net are described. These include the use of parallel optical computing of the global energy of the net, the use of fast nonvolatile programmable spatial light modulators to realize fast plasticity, optical generation of random number arrays, and an adaptive noisy thresholding scheme that also makes stochastic learning more biologically plausible. The findings reported predict optoelectronic chips that can be used in the realization of optical learning machines.

Application of a Discrete Nonlinear Spectral Model to Ideal Cases of Wind Wave Generation.

DTIC Science & Technology

1982-04-01

WRITE (6965)) bBD ODRM4T (IHII C SKI ’> 3 LINS i AND WRITE PLOT TITLE (IDOCHAR S PER LINE t 10 LINES AXI4CH-,(NClkR*9) /10 dRJTE (660) (TJL..EfI),I-I...A*CaGE.D.)JPP-J>P 𔃻 I F ( 8 D Do)) jpp-j P?+2 MiFPPeE)’i)&O TO 44 73 40JT-NPr(NIN,JPP) ;o TD (72, 14,7b,7BhNOUT 44 IF(A*3)q46q4b47 46 JPP-2 ;0 TO 73...EXTEZNAL FJNrI3N LAND IJS 13 THE BOOLEAN I.EoLDGICAL$ AND 01’ Td C FULLWORD INTEGCRS. C EXTEtNAL FJN:TION LOR, I,JS 1)7 THE BOOLEAN OR OF TWO FULLWORD

Analog Approach to Constraint Satisfaction Enabled by Spin Orbit Torque Magnetic Tunnel Junctions.

PubMed

Wijesinghe, Parami; Liyanagedera, Chamika; Roy, Kaushik

2018-05-02

Boolean satisfiability (k-SAT) is an NP-complete (k ≥ 3) problem that constitute one of the hardest classes of constraint satisfaction problems. In this work, we provide a proof of concept hardware based analog k-SAT solver, that is built using Magnetic Tunnel Junctions (MTJs). The inherent physics of MTJs, enhanced by device level modifications, is harnessed here to emulate the intricate dynamics of an analog satisfiability (SAT) solver. In the presence of thermal noise, the MTJ based system can successfully solve Boolean satisfiability problems. Most importantly, our results exhibit that, the proposed MTJ based hardware SAT solver is capable of finding a solution to a significant fraction (at least 85%) of hard 3-SAT problems, within a time that has a polynomial relationship with the number of variables(<50).

A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks

PubMed Central

Kerkhofs, Johan; Geris, Liesbet

2015-01-01

Boolean models have been instrumental in predicting general features of gene networks and more recently also as explorative tools in specific biological applications. In this study we introduce a basic quantitative and a limited time resolution to a discrete (Boolean) framework. Quantitative resolution is improved through the employ of normalized variables in unison with an additive approach. Increased time resolution stems from the introduction of two distinct priority classes. Through the implementation of a previously published chondrocyte network and T helper cell network, we show that this addition of quantitative and time resolution broadens the scope of biological behaviour that can be captured by the models. Specifically, the quantitative resolution readily allows models to discern qualitative differences in dosage response to growth factors. The limited time resolution, in turn, can influence the reachability of attractors, delineating the likely long term system behaviour. Importantly, the information required for implementation of these features, such as the nature of an interaction, is typically obtainable from the literature. Nonetheless, a trade-off is always present between additional computational cost of this approach and the likelihood of extending the model’s scope. Indeed, in some cases the inclusion of these features does not yield additional insight. This framework, incorporating increased and readily available time and semi-quantitative resolution, can help in substantiating the litmus test of dynamics for gene networks, firstly by excluding unlikely dynamics and secondly by refining falsifiable predictions on qualitative behaviour. PMID:26067297

Remission of rheumatoid arthritis and potential determinants: a national multi-center cross-sectional survey.

PubMed

Wang, Guan-Ying; Zhang, Sa-Li; Wang, Xiu-Ru; Feng, Min; Li, Chun; An, Yuan; Li, Xiao-Feng; Wang, Li-Zhi; Wang, Cai-Hong; Wang, Yong-Fu; Yang, Rong; Yan, Hui-Ming; Wang, Guo-Chun; Lu, Xin; Liu, Xia; Zhu, Ping; Chen, Li-Na; Jin, Hong-Tao; Liu, Jin-Ting; Guo, Hui-Fang; Chen, Hai-Ying; Xie, Jian-Li; Wei, Ping; Wang, Jun-Xiang; Liu, Xiang-Yuan; Sun, Lin; Cui, Liu-Fu; Shu, Rong; Liu, Bai-Lu; Yu, Ping; Zhang, Zhuo-Li; Li, Guang-Tao; Li, Zhen-Bin; Yang, Jing; Li, Jun-Fang; Jia, Bin; Zhang, Feng-Xiao; Tao, Jie-Mei; Lin, Jin-Ying; Wei, Mei-Qiu; Liu, Xiao-Min; Ke, Dan; Hu, Shao-Xian; Ye, Cong; Han, Shu-Ling; Yang, Xiu-Yan; Li, Hao; Huang, Ci-Bo; Gao, Ming; Lai, Bei; Cheng, Yong-Jing; Li, Xing-Fu; Song, Li-Jun; Yu, Xiao-Xia; Wang, Ai-Xue; Wu, Li-Jun; Wang, Yan-Hua; He, Lan; Sun, Wen-Wen; Gong, Lu; Wang, Xiao-Yuan; Wang, Yi; Zhao, Yi; Li, Xiao-Xia; Wang, Yan; Zhang, Yan; Su, Yin; Zhang, Chun-Fang; Mu, Rong; Li, Zhan-Guo

2015-02-01

The aim of this study is to investigate the remission rate of rheumatoid arthritis (RA) in China and identify its potential determinants. A multi-center cross-sectional study was conducted from July 2009 to January 2012. Data were collected by face-to-face interviews of the rheumatology outpatients in 28 tertiary hospitals in China. The remission rates were calculated in 486 RA patients according to different definitions of remission: the Disease Activity Score in 28 joints (DAS28), the Simplified Disease Activity Index (SDAI), the Clinical Disease Activity Index (CDAI), and the American College of Rheumatology/European League Against Rheumatism (ACR/EULAR) Boolean definition. Potential determinants of RA remission were assessed by univariate and multivariate analyses. The remission rates of RA from this multi-center cohort were 8.6% (DAS28), 8.4% (SDAI), 8.2% (CDAI), and 6.8% (Boolean), respectively. Favorable factors associated with remission were: low Health Assessment Questionnaire (HAQ) score, absence of rheumatoid factor (RF) and anti-cyclic citrullinated peptide (anti-CCP), and treatment of methotrexate (MTX) and hydroxychloroquine (HCQ). Younger age was also predictive for the DAS28 and the Boolean remission. Multivariate analyses revealed a low HAQ score, the absence of anti-CCP, and the treatment with HCQ as independent determinants of remission. The clinical remission rate of RA patients was low in China. A low HAQ score, the absence of anti-CCP, and HCQ were significant independent determinants for RA remission.

Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space.

PubMed

Ahnert, S E; Fink, T M A

2016-07-01

Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the 'function' of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature. © 2016 The Authors.

Psychological state is related to the remission of the Boolean-based definition of patient global assessment in patients with rheumatoid arthritis.

PubMed

Fusama, Mie; Miura, Yasushi; Yukioka, Kumiko; Kuroiwa, Takanori; Yukioka, Chikako; Inoue, Miyako; Nakanishi, Tae; Murata, Norikazu; Takai, Noriko; Higashi, Kayoko; Kuritani, Taro; Maeda, Keiji; Sano, Hajime; Yukioka, Masao; Nakahara, Hideko

2015-09-01

To evaluate whether the psychological state is related to the Boolean-based definition of patient global assessment (PGA) remission in patients with rheumatoid arthritis (RA). Patients with RA who met the criteria of swollen joint count (SJC) ≤ 1, tender joint count (TJC) ≤ 1 and C-reactive protein (CRP) ≤ 1 were divided into two groups, PGA remission group (PGA ≤ 1 cm) and non-remission group (PGA > 1 cm). Anxiety was evaluated utilizing the Hospital Anxiety and Depression Scale-Anxiety (HADS-A), while depression was evaluated with HADS-Depression (HADS-D) and the Center for Epidemiologic Studies Depression Scale (CES-D). Comparison analyses were done between the PGA remission and non-remission groups in HADS-A, HADS-D and CES-D. Seventy-eight patients met the criteria for SJC ≤ 1, TJC ≤ 1 and CRP ≤ 1. There were no significant differences between the PGA remission group (n = 45) and the non-remission group (n = 33) in age, sex, disease duration and Steinbrocker's class and stage. HADS-A, HADS-D and CES-D scores were significantly lower in the PGA remission group. Patients with RA who did not meet the PGA remission criteria despite good disease condition were in a poorer psychological state than those who satisfied the Boolean-based definition of clinical remission. Psychological support might be effective for improvement of PGA, resulting in the attainment of true remission.

76 FR 74076 - Notice of Random Assignment Study To Evaluate the YouthBuild Program; Final Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-30

... Evaluate the YouthBuild Program; Final Notice AGENCY: Employment and Training Administration (ETA), Labor... rigorous, nationally-representative estimates of the net impacts of the YouthBuild program. The Department... study. In the sites randomly selected to participate in this evaluation, all applicants for YouthBuild...

Effectiveness of Intraoral Chlorhexidine Protocols in the Prevention of Ventilator-Associated Pneumonia: Meta-Analysis and Systematic Review.

PubMed

Villar, Cristina C; Pannuti, Claudio M; Nery, Danielle M; Morillo, Carlos M R; Carmona, Maria José C; Romito, Giuseppe A

2016-09-01

Ventilator-associated pneumonia (VAP) is common in critical patients and related with increased morbidity and mortality. We conducted a systematic review and meta-analysis, with intention-to-treat analysis, of randomized controlled clinical trials that assessed the effectiveness of different intraoral chlorhexidine protocols for the prevention of VAP. Search strategies were developed for the MEDLINE, EMBASE, and LILACS databases. MeSH terms were combined with Boolean operators and used to search the databases. Eligible studies were randomized controlled trials of mechanically ventilated subjects receiving oral care with chlorhexidine or standard oral care protocols consisting of or associated with the use of a placebo or no chemicals. Pooled estimates of the relative risk and corresponding 95% CIs were calculated with random effects models, and heterogeneity was assessed with the Cochran Q statistic and I(2). The 13 included studies provided data on 1,640 subjects that were randomly allocated to chlorhexidine (n = 834) or control (n = 806) treatments. A preliminary analysis revealed that oral application of chlorhexidine fails to promote a significant reduction in VAP incidence (relative risk 0.80, 95% CI 0.59-1.07, I(2) = 45%). However, subgroup analyses showed that chlorhexidine prevents VAP development when used at 2% concentration (relative risk 0.53, 95% CI 0.31-0.91, I(2) = 0%) or 4 times/d (relative risk 0.56, 95% CI 0.38-0.81, I(2) = 0%). We found that oral care with chlorhexidine is effective in reducing VAP incidence in the adult population if administered at 2% concentration or 4 times/d. Copyright © 2016 by Daedalus Enterprises.

Random Forest Algorithm for the Classification of Neuroimaging Data in Alzheimer's Disease: A Systematic Review.

PubMed

Sarica, Alessia; Cerasa, Antonio; Quattrone, Aldo

2017-01-01

Objective: Machine learning classification has been the most important computational development in the last years to satisfy the primary need of clinicians for automatic early diagnosis and prognosis. Nowadays, Random Forest (RF) algorithm has been successfully applied for reducing high dimensional and multi-source data in many scientific realms. Our aim was to explore the state of the art of the application of RF on single and multi-modal neuroimaging data for the prediction of Alzheimer's disease. Methods: A systematic review following PRISMA guidelines was conducted on this field of study. In particular, we constructed an advanced query using boolean operators as follows: ("random forest" OR "random forests") AND neuroimaging AND ("alzheimer's disease" OR alzheimer's OR alzheimer) AND (prediction OR classification) . The query was then searched in four well-known scientific databases: Pubmed, Scopus, Google Scholar and Web of Science. Results: Twelve articles-published between the 2007 and 2017-have been included in this systematic review after a quantitative and qualitative selection. The lesson learnt from these works suggest that when RF was applied on multi-modal data for prediction of Alzheimer's disease (AD) conversion from the Mild Cognitive Impairment (MCI), it produces one of the best accuracies to date. Moreover, the RF has important advantages in terms of robustness to overfitting, ability to handle highly non-linear data, stability in the presence of outliers and opportunity for efficient parallel processing mainly when applied on multi-modality neuroimaging data, such as, MRI morphometric, diffusion tensor imaging, and PET images. Conclusions: We discussed the strengths of RF, considering also possible limitations and by encouraging further studies on the comparisons of this algorithm with other commonly used classification approaches, particularly in the early prediction of the progression from MCI to AD.

Computer Modeling of Electrostatic Aggregation of Granular Materials in Planetary and Astrophysical Settings

NASA Technical Reports Server (NTRS)

Marshall, J.; Sauke, T.

1999-01-01

Electrostatic forces strongly influence the behavior of granular materials in both dispersed (cloud) systems and semi-packed systems. These forces can cause aggregation or dispersion of particles and are important in a variety of astrophysical and planetary settings. There are also many industrial and commercial settings where granular matter and electrostatics become partners for both good and bad. This partnership is important for human exploration on Mars where dust adheres to suits, machines, and habitats. Long-range Coulombic (electrostatic) forces, as opposed to contact-induced dipoles and van der Waals attractions, are generally regarded as resulting from net charge. We have proposed that in addition to net charge interactions, randomly distributed charge carriers on grains will result in a dipole moment regardless of any net charge. If grains are unconfined, or fluidized, they will rotate so that the dipole always induces attraction between grains. Aggregates are readily formed, and Coulombic polarity resulting from the dipole produces end-to-end stacking of grains to form filamentary aggregates. This has been demonstrated in USML experiments on Space Shuttle where microgravity facilitated the unmasking of static forces. It has also been demonstrated in a computer model using grains with charge carriers of both sign. Model results very closely resembled micro-g results with actual sand grains. Further computer modeling of the aggregation process has been conducted to improve our understanding of the aggregation process, and to provide a predictive tool for microgravity experiments slated for Space Station. These experiments will attempt to prove the dipole concept as outlined above. We have considerably enhanced the original computer model: refinements to the algorithm have improved the fidelity of grain behavior during grain contact, special attention has been paid to simulation time steps to enable establishment of a meaningful, quantitative time axis, and calibration of rounding accuracies have been conducted to test cumulative numerical influences in the model. The model has been run for larger grain populations, variable initial cloud densities, and we have introduced random net charging to individual grains, as well as a net charge to the cloud as a whole. The model uses 3 positive and 3 negative charges randomly distributed on each grain, with up to 160 grains contained within various size "boxes" that define the initial number densities in the clouds. Each charge represents localized charged region on a grain, but does not necessarily imply single quantized charge carriers. The Coulomb equations are then allowed to interact for each monopole: dipoles and any higher order charge coupling is a natural product of these "free" interactions over which the modeler exerts no influence. The charges are placed on surfaces of grains at random locations. A series of runs was conducted for neutral grains that had a perfect balance of negative and positive char carriers. Runs were also conducted with grains having additional fractional charges ranging between 0 and 1. By adding fractional charges of one sign, the model created grain populations in which all grains had excess charges the same sign, giving the cloud an overall net charge. This simulates clouds subjected to ionizing radiation (e. protoplanetary debris disk around a protosun), or any other process of charge biasing in a grain population (e.g., volcanic plumes). In another run series, random fractional charges of either sign were added to the grains so th some grains had a slight net positive charge while others had a slight net negative charge. This simulates triboelectrically-charged grain populations in which acquisition of an electron by one surface is at the expense creating a hole elsewhere. This dual sign charging was applied in two ways: in one case the cloud remained neutral by ensuring that all grain excess charges added to zero; in the other case, the cloud was permitted slight net char by not imposing a charge-balance condition. Additional information is contained in the original.

Automated Library System Specifications.

DTIC Science & Technology

1986-06-01

University), LIS (Georqetown Universitv Medical Center) 20 DiSTRI3UT!ON.. AVAILABILITY OF ABSTRACT 21 ABSTRACT SECURITY CLASSIFICATION :UNCLASSIFIED...Interface) acquisitions, patron access catalo. (Boolean search), authority Afiles, zana ~ezient reports. Serials control expected in 1985. INDIVIDUALIZATIOI

Using NetCloak to develop server-side Web-based experiments without writing CGI programs.

PubMed

Wolfe, Christopher R; Reyna, Valerie F

2002-05-01

Server-side experiments use the Web server, rather than the participant's browser, to handle tasks such as random assignment, eliminating inconsistencies with JAVA and other client-side applications. Heretofore, experimenters wishing to create server-side experiments have had to write programs to create common gateway interface (CGI) scripts in programming languages such as Perl and C++. NetCloak uses simple, HTML-like commands to create CGIs. We used NetCloak to implement an experiment on probability estimation. Measurements of time on task and participants' IP addresses assisted quality control. Without prior training, in less than 1 month, we were able to use NetCloak to design and create a Web-based experiment and to help graduate students create three Web-based experiments of their own.

Learning Petri net models of non-linear gene interactions.

PubMed

Mayo, Michael

2005-10-01

Understanding how an individual's genetic make-up influences their risk of disease is a problem of paramount importance. Although machine-learning techniques are able to uncover the relationships between genotype and disease, the problem of automatically building the best biochemical model or "explanation" of the relationship has received less attention. In this paper, I describe a method based on random hill climbing that automatically builds Petri net models of non-linear (or multi-factorial) disease-causing gene-gene interactions. Petri nets are a suitable formalism for this problem, because they are used to model concurrent, dynamic processes analogous to biochemical reaction networks. I show that this method is routinely able to identify perfect Petri net models for three disease-causing gene-gene interactions recently reported in the literature.

Use of the EpiNet database for observational study of status epilepticus in Auckland, New Zealand.

PubMed

Bergin, Peter; Jayabal, Jayaganth; Walker, Elizabeth; Davis, Suzanne; Jones, Peter; Dalziel, Stuart; Yates, Kim; Thornton, Vanessa; Bennett, Patricia; Wilson, Kaisa; Roberts, Lynair; Litchfield, Rhonda; Te Ao, Braden; Parmer, Priya; Feigin, Valery; Jost, Jeremy; Beghi, Ettore; Rossetti, Andrea O

2015-08-01

The EpiNet project has been established to facilitate investigator-initiated clinical research in epilepsy, to undertake epidemiological studies, and to simultaneously improve the care of patients who have records created within the EpiNet database. The EpiNet database has recently been adapted to collect detailed information regarding status epilepticus. An incidence study is now underway in Auckland, New Zealand in which the incidence of status epilepticus in the greater Auckland area (population: 1.5 million) will be calculated. The form that has been developed for this study can be used in the future to collect information for randomized controlled trials in status epilepticus. This article is part of a Special Issue entitled "Status Epilepticus". Copyright © 2015 Elsevier Inc. All rights reserved.

Autonomous Byte Stream Randomizer

NASA Technical Reports Server (NTRS)

Paloulian, George K.; Woo, Simon S.; Chow, Edward T.

2013-01-01

Net-centric networking environments are often faced with limited resources and must utilize bandwidth as efficiently as possible. In networking environments that span wide areas, the data transmission has to be efficient without any redundant or exuberant metadata. The Autonomous Byte Stream Randomizer software provides an extra level of security on top of existing data encryption methods. Randomizing the data s byte stream adds an extra layer to existing data protection methods, thus making it harder for an attacker to decrypt protected data. Based on a generated crypto-graphically secure random seed, a random sequence of numbers is used to intelligently and efficiently swap the organization of bytes in data using the unbiased and memory-efficient in-place Fisher-Yates shuffle method. Swapping bytes and reorganizing the crucial structure of the byte data renders the data file unreadable and leaves the data in a deconstructed state. This deconstruction adds an extra level of security requiring the byte stream to be reconstructed with the random seed in order to be readable. Once the data byte stream has been randomized, the software enables the data to be distributed to N nodes in an environment. Each piece of the data in randomized and distributed form is a separate entity unreadable on its own right, but when combined with all N pieces, is able to be reconstructed back to one. Reconstruction requires possession of the key used for randomizing the bytes, leading to the generation of the same cryptographically secure random sequence of numbers used to randomize the data. This software is a cornerstone capability possessing the ability to generate the same cryptographically secure sequence on different machines and time intervals, thus allowing this software to be used more heavily in net-centric environments where data transfer bandwidth is limited.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nahrgang, Marlene; Bluhm, Marcus; Alba, Paolo

We investigate net proton fluctuations as important observables measured in heavy-ion collisions within the hadron resonance gas (HRG) model. Special emphasis is given to effects which are a priori not inherent in a thermally and chemically equilibrated HRG approach. In particular, we point out the importance of taking into account the successive regeneration and decay of resonances after the chemical freeze-out, which lead to a randomization of the isospin of nucleons and thus to additional fluctuations in the net proton number. In conclusion, we find good agreement between our model results and the recent STAR measurements of the higher-order momentsmore » of the net proton distribution.« less

Vector control of wind turbine on the basis of the fuzzy selective neural net*

NASA Astrophysics Data System (ADS)

Engel, E. A.; Kovalev, I. V.; Engel, N. E.

2016-04-01

An article describes vector control of wind turbine based on fuzzy selective neural net. Based on the wind turbine system’s state, the fuzzy selective neural net tracks an maximum power point under random perturbations. Numerical simulations are accomplished to clarify the applicability and advantages of the proposed vector wind turbine’s control on the basis of the fuzzy selective neuronet. The simulation results show that the proposed intelligent control of wind turbine achieves real-time control speed and competitive performance, as compared to a classical control model with PID controllers based on traditional maximum torque control strategy.

An Interactive Computer Model for Improved Student Understanding of Random Particle Motion and Osmosis

ERIC Educational Resources Information Center

Kottonau, Johannes

2011-01-01

Effectively teaching the concepts of osmosis to college-level students is a major obstacle in biological education. Therefore, a novel computer model is presented that allows students to observe the random nature of particle motion simultaneously with the seemingly directed net flow of water across a semipermeable membrane during osmotic…

The Effect of Recent Tax Changes on Taxable Income: Evidence from a New Panel of Tax Returns

ERIC Educational Resources Information Center

Heim, Bradley T.

2009-01-01

This paper estimates the elasticity of taxable income to the net-of-tax share using a panel of tax returns that follows a random sample of taxpayers from 1999 to 2005, spanning the EGTRRA 2001 and JGTRRA 2003 tax changes. Results suggest that the elasticity of taxable income to the current year's net-of-tax share lies between 0.3 and 0.4 overall,…

The influence of broadcast tape-recorded calls on captures of fall migrant Northern Saw-whet Owls (Aegolius acadicus) and Long-eared Owls (Asio otus)

Treesearch

David L. Evans

1997-01-01

Nocturnal netting operations have been conducted at the Hawk Ridge Nature Reserve since 1972. From 1988 to 1992 a recording of human whistles simulating the calls of fall migrant Northern Saw-whet Owls (Aegolius acadicus) was broadcast on a random, on or off, half-night basis. Mist net captures of Saw-whet Owls increased about fourfold during the...

Synthesizing Biomolecule-based Boolean Logic Gates

PubMed Central

Miyamoto, Takafumi; Razavi, Shiva; DeRose, Robert; Inoue, Takanari

2012-01-01

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, 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. PMID:23526588

Interconnect-free parallel logic circuits in a single mechanical resonator

PubMed Central

Mahboob, I.; Flurin, E.; Nishiguchi, K.; Fujiwara, A.; Yamaguchi, H.

2011-01-01

In conventional computers, wiring between transistors is required to enable the execution of Boolean logic functions. This has resulted in processors in which billions of transistors are physically interconnected, which limits integration densities, gives rise to huge power consumption and restricts processing speeds. A method to eliminate wiring amongst transistors by condensing Boolean logic into a single active element is thus highly desirable. Here, we demonstrate a novel logic architecture using only a single electromechanical parametric resonator into which multiple channels of binary information are encoded as mechanical oscillations at different frequencies. The parametric resonator can mix these channels, resulting in new mechanical oscillation states that enable the construction of AND, OR and XOR logic gates as well as multibit logic circuits. Moreover, the mechanical logic gates and circuits can be executed simultaneously, giving rise to the prospect of a parallel logic processor in just a single mechanical resonator. PMID:21326230

Interconnect-free parallel logic circuits in a single mechanical resonator.

PubMed

Mahboob, I; Flurin, E; Nishiguchi, K; Fujiwara, A; Yamaguchi, H

2011-02-15

In conventional computers, wiring between transistors is required to enable the execution of Boolean logic functions. This has resulted in processors in which billions of transistors are physically interconnected, which limits integration densities, gives rise to huge power consumption and restricts processing speeds. A method to eliminate wiring amongst transistors by condensing Boolean logic into a single active element is thus highly desirable. Here, we demonstrate a novel logic architecture using only a single electromechanical parametric resonator into which multiple channels of binary information are encoded as mechanical oscillations at different frequencies. The parametric resonator can mix these channels, resulting in new mechanical oscillation states that enable the construction of AND, OR and XOR logic gates as well as multibit logic circuits. Moreover, the mechanical logic gates and circuits can be executed simultaneously, giving rise to the prospect of a parallel logic processor in just a single mechanical resonator.

Synthesizing biomolecule-based Boolean logic gates.

PubMed

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.

Simultaneous G-Quadruplex DNA Logic.

PubMed

Bader, Antoine; Cockroft, Scott L

2018-04-03

A fundamental principle of digital computer operation is Boolean logic, where inputs and outputs are described by binary integer voltages. Similarly, inputs and outputs may be processed on the molecular level as exemplified by synthetic circuits that exploit the programmability of DNA base-pairing. Unlike modern computers, which execute large numbers of logic gates in parallel, most implementations of molecular logic have been limited to single computing tasks, or sensing applications. This work reports three G-quadruplex-based logic gates that operate simultaneously in a single reaction vessel. The gates respond to unique Boolean DNA inputs by undergoing topological conversion from duplex to G-quadruplex states that were resolved using a thioflavin T dye and gel electrophoresis. The modular, addressable, and label-free approach could be incorporated into DNA-based sensors, or used for resolving and debugging parallel processes in DNA computing applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Satisfiability of logic programming based on radial basis function neural networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamadneh, Nawaf; Sathasivam, Saratha; Tilahun, Surafel Luleseged

2014-07-10

In this paper, we propose a new technique to test the Satisfiability of propositional logic programming and quantified Boolean formula problem in radial basis function neural networks. For this purpose, we built radial basis function neural networks to represent the proportional logic which has exactly three variables in each clause. We used the Prey-predator algorithm to calculate the output weights of the neural networks, while the K-means clustering algorithm is used to determine the hidden parameters (the centers and the widths). Mean of the sum squared error function is used to measure the activity of the two algorithms. We appliedmore » the developed technique with the recurrent radial basis function neural networks to represent the quantified Boolean formulas. The new technique can be applied to solve many applications such as electronic circuits and NP-complete problems.« less

Some Applications Of Semigroups And Computer Algebra In Discrete Structures

NASA Astrophysics Data System (ADS)

Bijev, G.

2009-11-01

An algebraic approach to the pseudoinverse generalization problem in Boolean vector spaces is used. A map (p) is defined, which is similar to an orthogonal projection in linear vector spaces. Some other important maps with properties similar to those of the generalized inverses (pseudoinverses) of linear transformations and matrices corresponding to them are also defined and investigated. Let Ax = b be an equation with matrix A and vectors x and b Boolean. Stochastic experiments for solving the equation, which involves the maps defined and use computer algebra methods, have been made. As a result, the Hamming distance between vectors Ax = p(b) and b is equal or close to the least possible. We also share our experience in using computer algebra systems for teaching discrete mathematics and linear algebra and research. Some examples for computations with binary relations using Maple are given.

Altered Micro-RNA Degradation Promotes Tumor Heterogeneity: A Result from Boolean Network Modeling.

PubMed

Wu, Yunyi; Krueger, Gerhard R F; Wang, Guanyu

2016-02-01

Cancer heterogeneity may reflect differential dynamical outcomes of the regulatory network encompassing biomolecules at both transcriptional and post-transcriptional levels. In other words, differential gene-expression profiles may correspond to different stable steady states of a mathematical model for simulation of biomolecular networks. To test this hypothesis, we simplified a regulatory network that is important for soft-tissue sarcoma metastasis and heterogeneity, comprising of transcription factors, micro-RNAs, and signaling components of the NOTCH pathway. We then used a Boolean network model to simulate the dynamics of this network, and particularly investigated the consequences of differential miRNA degradation modes. We found that efficient miRNA degradation is crucial for sustaining a homogenous and healthy phenotype, while defective miRNA degradation may lead to multiple stable steady states and ultimately to carcinogenesis and heterogeneity. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Lattice Theory, Measures and Probability

NASA Astrophysics Data System (ADS)

Knuth, Kevin H.

2007-11-01

In this tutorial, I will discuss the concepts behind generalizing ordering to measuring and apply these ideas to the derivation of probability theory. The fundamental concept is that anything that can be ordered can be measured. Since we are in the business of making statements about the world around us, we focus on ordering logical statements according to implication. This results in a Boolean lattice, which is related to the fact that the corresponding logical operations form a Boolean algebra. The concept of logical implication can be generalized to degrees of implication by generalizing the zeta function of the lattice. The rules of probability theory arise naturally as a set of constraint equations. Through this construction we are able to neatly connect the concepts of order, structure, algebra, and calculus. The meaning of probability is inherited from the meaning of the ordering relation, implication, rather than being imposed in an ad hoc manner at the start.

A solution to the surface intersection problem. [Boolean functions in geometric modeling

NASA Technical Reports Server (NTRS)

Timer, H. G.

1977-01-01

An application-independent geometric model within a data base framework should support the use of Boolean operators which allow the user to construct a complex model by appropriately combining a series of simple models. The use of these operators leads to the concept of implicitly and explicitly defined surfaces. With an explicitly defined model, the surface area may be computed by simply summing the surface areas of the bounding surfaces. For an implicitly defined model, the surface area computation must deal with active and inactive regions. Because the surface intersection problem involves four unknowns and its solution is a space curve, the parametric coordinates of each surface must be determined as a function of the arc length. Various subproblems involved in the general intersection problem are discussed, and the mathematical basis for their solution is presented along with a program written in FORTRAN IV for implementation on the IBM 370 TSO system.

Graphene-based non-Boolean logic circuits

NASA Astrophysics Data System (ADS)

Liu, Guanxiong; Ahsan, Sonia; Khitun, Alexander G.; Lake, Roger K.; Balandin, Alexander A.

2013-10-01

Graphene revealed a number of unique properties beneficial for electronics. However, graphene does not have an energy band-gap, which presents a serious hurdle for its applications in digital logic gates. The efforts to induce a band-gap in graphene via quantum confinement or surface functionalization have not resulted in a breakthrough. Here we show that the negative differential resistance experimentally observed in graphene field-effect transistors of "conventional" design allows for construction of viable non-Boolean computational architectures with the gapless graphene. The negative differential resistance—observed under certain biasing schemes—is an intrinsic property of graphene, resulting from its symmetric band structure. Our atomistic modeling shows that the negative differential resistance appears not only in the drift-diffusion regime but also in the ballistic regime at the nanometer-scale—although the physics changes. The obtained results present a conceptual change in graphene research and indicate an alternative route for graphene's applications in information processing.

Impact of eLearning course on nurses' professional competence in seclusion and restraint practices: a randomized controlled study (ISRCTN32869544).

PubMed

Kontio, R; Lahti, M; Pitkänen, A; Joffe, G; Putkonen, H; Hätönen, H; Katajisto, J; Välimäki, M

2011-11-01

Education on the care of aggressive and disturbed patients is fragmentary. eLearning could ensure the quality of such education, but data on its impact on professional competence in psychiatry are lacking. The aim of this study was to explore the impact of ePsychNurse.Net, an eLearning course, on psychiatric nurses' professional competence in seclusion and restraint and on their job satisfaction and general self-efficacy. In a randomized controlled study, 12 wards were randomly assigned to ePsychNurse.Net (intervention) or education as usual (control). Baseline and 3-month follow-up data on nurses' knowledge of coercion-related legislation, physical restraint and seclusion, their attitudes towards physical restraint and seclusion, job satisfaction and general self-efficacy were analysed for 158 completers. Knowledge (primary outcome) of coercion-related legislation improved in the intervention group, while knowledge of physical restraint improved and knowledge of seclusion remained unchanged in both groups. General self-efficacy improved in the intervention group also attitude to seclusion in the control group. In between-group comparison, attitudes to seclusion (one of secondary outcomes) favoured the control group. Although the ePsychNurse.Net demonstrated only slight advantages over conventional learning, it may be worth further development with, e.g. flexible time schedule and individualized content. © 2011 Blackwell Publishing.

Trace element concentrations and distributions in the main body tissues and the net requirements for maintenance and growth of Dorper × Hu lambs.

PubMed

Zhang, H; Nie, H T; Wang, Q; Wang, Z Y; Zhang, Y L; Guo, R H; Wang, F

2015-05-01

A comparative slaughter trial was conducted to estimate the trace element concentrations and distributions in the main body tissues and the net requirements for maintenance and growth of Dorper × Hu crossbred lambs. Thirty-five lambs of each gender (19.2 ± 0.36 kg initial BW) were used. Seven lambs of each gender were randomly chosen and slaughtered at approximately 20 kg BW as the baseline group for measuring initial body composition. Another 7 lambs of each gender were also randomly chosen and offered a pelleted mixed diet for ad libitum intake and slaughtered at approximately 28 kg BW. The remaining 21 sheep of each gender were randomly divided into 3 groups with 7 sheep each and assigned to ad libitum or 40 or 70% of ad libitum intake of a pelleted mixed diet (42:58 concentrate:roughage, DM basis). The 3 groups of each gender were slaughtered when the sheep fed ad libitum reached approximately 35 kg BW. Empty body (head + feet, hide, viscera + blood, and carcass) trace element contents were determined after slaughter. The results showed that the trace elements were mainly distributed in viscera (blood included), except for Zn, which was mainly distributed in the muscle and bone tissues. The net requirements were calculated using the comparative slaughter technique. For males and females, the daily net trace element requirements for maintenance were 356.1 and 164.1 μg Fe, 4.3 and 3.4 μg Mn, 42.0 and 29.8 μg Cu, and 83.5 and 102.0 μg Zn per kilogram empty body weight (EBW), respectively. Net requirements for growth decreased from 65.67 to 57.27 mg Fe, 0.35 to 0.25 mg Mn, and 3.45 to 2.82 mg Cu and increased from 26.36 to 26.65 mg Zn per kilogram EBW gain (EBWG) for males. Net requirements for growth decreased from 30.66 to 22.14 mg Fe, 0.43 to 0.32 mg Mn, 2.86 to 2.18 mg Cu, and 27.71 to 25.83 mg Zn per kilogram EBWG for females from 20 to 35 kg BW. This study indicated that the net trace element requirements for Dorper × Hu crossbred lambs may be different from those of purebred or other genotypes, and more data are needed for sheep in general.

Onion epidermis as a new model to study the control of growth anisotropy in higher plants.

PubMed

Suslov, Dmitry; Verbelen, Jean-Pierre; Vissenberg, Kris

2009-01-01

To elucidate the role of cellulose microfibrils in the control of growth anisotropy, a link between their net orientation, in vitro cell wall extensibility, and anisotropic cell expansion was studied during development of the adaxial epidermis of onion (Allium cepa) bulb scales using polarization confocal microscopy, creep tests, and light microscopy. During growth the net cellulose alignment across the whole thickness of the outer epidermal wall changed from transverse through random to longitudinal and back to transverse relative to the bulb axis. Cell wall extension in vitro was always higher transverse than parallel to the net cellulose alignment. The direction of growth anisotropy was perpendicular to the net microfibril orientation and changed during development from longitudinal to transverse to the bulb axis. The correlation between the degree of growth anisotropy and the net cellulose alignment was poor. Thus the net cellulose microfibril orientation across the whole thickness of the outer periclinal epidermis wall defines the direction but not the degree of growth anisotropy. Strips isolated from the epidermis in the directions perpendicular and transverse to a net cellulose orientation can be used as an extensiometric model to prove a protein involvement in the control of growth anisotropy.

Factors associated with sustained remission in patients with rheumatoid arthritis.

PubMed

Martire, María Victoria; Marino Claverie, Lucila; Duarte, Vanesa; Secco, Anastasia; Mammani, Marta

2015-01-01

To find out the factors that are associated with sustained remission measured by DAS28 and boolean ACR EULAR 2011 criteria at the time of diagnosis of rheumatoid arthritis. Medical records of patients with rheumatoid arthritis in sustained remission according to DAS28 were reviewed. They were compared with patients who did not achieved values of DAS28<2.6 in any visit during the first 3 years after diagnosis. We also evaluated if patients achieved the boolean ACR/EULAR criteria. Variables analyzed: sex, age, smoking, comorbidities, rheumatoid factor, anti-CCP, ESR, CRP, erosions, HAQ, DAS28, extra-articular manifestations, time to initiation of treatment, involvement of large joints, number of tender joints, number of swollen joints, pharmacological treatment. Forty five patients that achieved sustained remission were compared with 44 controls. The variables present at diagnosis that significantly were associated with remission by DAS28 were: lower values of DAS28, HAQ, ESR, NTJ, NSJ, negative CRP, absence of erosions, male sex and absence of involvement of large joints. Only 24.71% achieved the boolean criteria. The variables associated with sustained remission by these criteria were: lower values of DAS28, HAQ, ESR, number of tender joints and number of swollen joints, negative CRP and absence of erosions. The factors associated with sustained remission were the lower baseline disease activity, the low degree of functional disability and lower joint involvement. We consider it important to recognize these factors to optimize treatment. Copyright © 2014 Elsevier España, S.L.U. All rights reserved.

Jimena: efficient computing and system state identification for genetic regulatory networks.

PubMed

Karl, Stefan; Dandekar, Thomas

2013-10-11

Boolean networks capture switching behavior of many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states is necessary. The high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such as apoptosis or proliferation allows for the modeling of a wider range of node interactions than continuous activator-inhibitor models, but suffers from scaling problems for networks which contain nodes with more than ~10 inputs. Many GRNs from literature or new gene expression experiments exceed those limitations and a new approach was developed. (i) As a part of our new GRN simulation framework Jimena we introduce and setup Boolean-tree-based data structures; (ii) corresponding algorithms greatly expedite the calculation of the polynomial interpolation in almost all cases, thereby expanding the range of networks which can be simulated by this model in reasonable time. (iii) Stable states for discrete models are efficiently counted and identified using binary decision diagrams. As application example, we show how system states can now be sampled efficiently in small up to large scale hormone disease networks (Arabidopsis thaliana development and immunity, pathogen Pseudomonas syringae and modulation by cytokinins and plant hormones). Jimena simulates currently available GRNs about 10-100 times faster than the previous implementation of the polynomial interpolation model and even greater gains are achieved for large scale-free networks. This speed-up also facilitates a much more thorough sampling of continuous state spaces which may lead to the identification of new stable states. Mutants of large networks can be constructed and analyzed very quickly enabling new insights into network robustness and behavior.

Boolean Operations with Prism Algebraic Patches

PubMed Central

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

Computing smallest intervention strategies for multiple metabolic networks in a boolean model.

PubMed

Lu, Wei; Tamura, Takeyuki; Song, Jiangning; Akutsu, Tatsuya

2015-02-01

This article considers the problem whereby, given two metabolic networks N1 and N2, a set of source compounds, and a set of target compounds, we must find the minimum set of reactions whose removal (knockout) ensures that the target compounds are not producible in N1 but are producible in N2. Similar studies exist for the problem of finding the minimum knockout with the smallest side effect for a single network. However, if technologies of external perturbations are advanced in the near future, it may be important to develop methods of computing the minimum knockout for multiple networks (MKMN). Flux balance analysis (FBA) is efficient if a well-polished model is available. However, that is not always the case. Therefore, in this article, we study MKMN in Boolean models and an elementary mode (EM)-based model. Integer linear programming (ILP)-based methods are developed for these models, since MKMN is NP-complete for both the Boolean model and the EM-based model. Computer experiments are conducted with metabolic networks of clostridium perfringens SM101 and bifidobacterium longum DJO10A, respectively known as bad bacteria and good bacteria for the human intestine. The results show that larger networks are more likely to have MKMN solutions. However, solving for these larger networks takes a very long time, and often the computation cannot be completed. This is reasonable, because small networks do not have many alternative pathways, making it difficult to satisfy the MKMN condition, whereas in large networks the number of candidate solutions explodes. Our developed software minFvskO is available online.

Rationale for the Diabetic Retinopathy Clinical Research Network Treatment Protocol for Center-involved Diabetic Macular Edema

PubMed Central

Aiello, Lloyd Paul; Beck, Roy W; Bressler, Neil M.; Browning, David J.; Chalam, KV; Davis, Matthew; Ferris, Frederick L; Glassman, Adam; Maturi, Raj; Stockdale, Cynthia R.; Topping, Trexler

2011-01-01

Objective Describe the underlying principles used to develop a web-based algorithm that incorporated intravitreal anti-vascular endothelial growth factor (anti-VEGF) treatment for diabetic macular edema (DME) in a Diabetic Retinopathy Clinical Research Network (DRCR.net) randomized clinical trial. Design Discussion of treatment protocol for DME. Participants Subjects with vision loss from DME involving the center of the macula. Methods The DRCR.net created an algorithm incorporating anti-VEGF injections in a comparative effectiveness randomized clinical trial evaluating intravitreal ranibizumab with prompt or deferred (≥24 weeks) focal/grid laser in eyes with vision loss from center-involved DME. Results confirmed that intravitreal ranibizumab with prompt or deferred laser provides superior visual acuity outcomes, compared with prompt laser alone through at least 2 years. Duplication of this algorithm may not be practical for clinical practice. In order to share their opinion on how ophthalmologists might emulate the study protocol, participating DRCR.net investigators developed guidelines based on the algorithm's underlying rationale. Main Outcome Measures Clinical guidelines based on a DRCR.net protocol. Results The treatment protocol required real time feedback from a web-based data entry system for intravitreal injections, focal/grid laser, and follow-up intervals. Guidance from this system indicated whether treatment was required or given at investigator discretion and when follow-up should be scheduled. Clinical treatment guidelines, based on the underlying clinical rationale of the DRCR.net protocol, include repeating treatment monthly as long as there is improvement in edema compared with the previous month, or until the retina is no longer thickened. If thickening recurs or worsens after discontinuing treatment, treatment is resumed. Conclusions Duplication of the approach used in the DRCR.net randomized clinical trial to treat DME involving the center of the macula with intravitreal ranibizumab may not be practical in clinical practice, but likely can be emulated based on an understanding of the underlying rationale for the study protocol. Inherent differences between a web-based treatment algorithm and a clinical approach may lead to differences in outcomes that are impossible to predict. The closer the clinical approach is to the algorithm used in the study, the more likely the outcomes will be similar to those published. PMID:22136692

Rationale for the diabetic retinopathy clinical research network treatment protocol for center-involved diabetic macular edema.

PubMed

Aiello, Lloyd Paul; Beck, Roy W; Bressler, Neil M; Browning, David J; Chalam, K V; Davis, Matthew; Ferris, Frederick L; Glassman, Adam R; Maturi, Raj K; Stockdale, Cynthia R; Topping, Trexler M

2011-12-01

To describe the underlying principles used to develop a web-based algorithm that incorporated intravitreal anti-vascular endothelial growth factor (anti-VEGF) treatment for diabetic macular edema (DME) in a Diabetic Retinopathy Clinical Research Network (DRCR.net) randomized clinical trial. Discussion of treatment protocol for DME. Subjects with vision loss resulting from DME involving the center of the macula. The DRCR.net created an algorithm incorporating anti-VEGF injections in a comparative effectiveness randomized clinical trial evaluating intravitreal ranibizumab with prompt or deferred (≥24 weeks) focal/grid laser treatment in eyes with vision loss resulting from center-involved DME. Results confirmed that intravitreal ranibizumab with prompt or deferred laser provides superior visual acuity outcomes compared with prompt laser alone through at least 2 years. Duplication of this algorithm may not be practical for clinical practice. To share their opinion on how ophthalmologists might emulate the study protocol, participating DRCR.net investigators developed guidelines based on the algorithm's underlying rationale. Clinical guidelines based on a DRCR.net protocol. The treatment protocol required real-time feedback from a web-based data entry system for intravitreal injections, focal/grid laser treatment, and follow-up intervals. Guidance from this system indicated whether treatment was required or given at investigator discretion and when follow-up should be scheduled. Clinical treatment guidelines, based on the underlying clinical rationale of the DRCR.net protocol, include repeating treatment monthly as long as there is improvement in edema compared with the previous month or until the retina is no longer thickened. If thickening recurs or worsens after discontinuing treatment, treatment is resumed. Duplication of the approach used in the DRCR.net randomized clinical trial to treat DME involving the center of the macula with intravitreal ranibizumab may not be practical in clinical practice, but likely can be emulated based on an understanding of the underlying rationale for the study protocol. Inherent differences between a web-based treatment algorithm and a clinical approach may lead to differences in outcomes that are impossible to predict. The closer the clinical approach is to the algorithm used in the study, the more likely the outcomes will be similar to those published. Proprietary or commercial disclosure may be found after the references. Copyright © 2011 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

A Note about Information Science Research.

ERIC Educational Resources Information Center

Salton, Gerard

1985-01-01

Discusses the relationship between information science research and practice and briefly describes current research on 10 topics in information retrieval literature: vector processing retrieval strategy, probabilistic retrieval models, inverted file procedures, relevance feedback, Boolean query formulations, front-end procedures, citation…

Bibliographic Instruction in the 21st Century.

ERIC Educational Resources Information Center

Poirier, Gayle

2000-01-01

Discusses bibliographic instruction in libraries. Topics include a history of bibliographic instruction; the Internet and electronic searching; librarians' use of technology; defining information needs; locating and accessing information, including classification systems and Boolean searching; evaluating information; using and communication…

Which nets are being used: factors associated with mosquito net use in Amhara, Oromia and Southern Nations, Nationalities and Peoples' Regions of Ethiopia.

PubMed

Ngondi, Jeremiah M; Graves, Patricia M; Gebre, Teshome; Mosher, Aryc W; Shargie, Estifanos B; Emerson, Paul M; Richards, Frank O

2011-04-17

There has been recent large scale-up of malaria control interventions in Ethiopia where transmission is unstable. While household ownership of long-lasting insecticidal nets (LLIN) has increased greatly, there are concerns about inadequate net use. This study aimed to investigate factors associated with net use at two time points, before and after mass distribution of nets. Two cross sectional surveys were carried out in 2006 and 2007 in Amhara, Oromia and SNNP regions. The latter was a sub-sample of the national Malaria Indicator Survey (MIS 3R). Each survey wave used multi-stage cluster random sampling with 25 households per cluster (224 clusters with 5,730 households in Baseline 2006 and 245 clusters with 5,910 households in MIS 3R 2007). Net ownership was assessed by visual inspection while net utilization was reported as use of the net the previous night. This net level analysis was restricted to households owning at least one net of any type. Logistic regression models of association between net use and explanatory variables including net type, age, condition, cost and other household characteristics were undertaken using generalized linear latent and mixed models (GLLAMM). A total of 3,784 nets in 2,430 households were included in the baseline 2006 analysis while the MIS 3R 2007 analysis comprised 5,413 nets in 3,328 households. The proportion of nets used the previous night decreased from 85.1% to 56.0% between baseline 2006 and MIS 3R 2007, respectively. Factors independently associated with increased proportion of nets used were: LLIN net type (at baseline 2006); indoor residual spraying (at MIS 3R 2007); and increasing wealth index at both surveys. At both baseline 2006 and MIS 3R 2007, reduced proportion of nets used was independently associated with increasing net age, increasing damage of nets, increasing household net density, and increasing altitude (>2,000 m). This study identified modifiable factors affecting use of nets that were consistent across both surveys. While net replacement remains important, the findings suggest that: more education about use and care of nets; making nets more resistant to damage; and encouraging net mending are likely to maximize the huge investment in scale up of net ownership by ensuring they are used. Without this step, the widespread benefits of LLIN cannot be realized.

Understanding Randomness and Its Impact on Student Learning: Lessons Learned from Building the Biology Concept Inventory (BCI)

ERIC Educational Resources Information Center

Garvin-Doxas, Kathy; Klymkowsky, Michael W.

2008-01-01

While researching student assumptions for the development of the Biology Concept Inventory (BCI; http://bioliteracy.net), we found that a wide class of student difficulties in molecular and evolutionary biology appears to be based on deep-seated, and often unaddressed, misconceptions about random processes. Data were based on more than 500…

The development of the Project NetWork administrative records database for policy evaluation.

PubMed

Rupp, K; Driessen, D; Kornfeld, R; Wood, M

1999-01-01

This article describes the development of SSA's administrative records database for the Project NetWork return-to-work experiment targeting persons with disabilities. The article is part of a series of papers on the evaluation of the Project NetWork demonstration. In addition to 8,248 Project NetWork participants randomly assigned to receive case management services and a control group, the simulation identified 138,613 eligible nonparticipants in the demonstration areas. The output data files contain detailed monthly information on Supplemental Security Income (SSI) and Disability Insurance (DI) benefits, annual earnings, and a set of demographic and diagnostic variables. The data allow for the measurement of net outcomes and the analysis of factors affecting participation. The results suggest that it is feasible to simulate complex eligibility rules using administrative records, and create a clean and edited data file for a comprehensive and credible evaluation. The study shows that it is feasible to use administrative records data for selecting control or comparison groups in future demonstration evaluations.

Static cardiomyoplasty with synthetic elastic net suppresses ventricular dilatation and dysfunction after myocardial infarction in the rat: a chronic study.

PubMed

Kato, Nobusuke; Kawaguchi, Akira T; Kishida, Akio; Yamaoka, Tetsuji

2013-07-01

Although static cardiomyoplasty prevents the left ventricle (LV) from dilatation, it may interfere with diastolic relaxation, or cause restriction. We developed a synthetic net with dual elasticity and tested its effect late after myocardial infarction in the rat. LV pressure-volume relationships (PVR) were successively analyzed before, after intravenous volume load, and 10 minutes after occlusion of the left anterior descending artery. Rats were then randomized into groups receiving synthetic net wrapping around the heart (NET+, n = 8) and only partially behind LV (NET-, n = 9), and they underwent the same PVR studies 6 weeks later. End-diastolic and end-systolic PVR were defined, and LV size and function were compared under standardized loading conditions. Although there was no difference in Day 0, increase in LV end-diastolic and end-systolic volumes were significantly attenuated in NET+ rats 6 weeks later when there was a significant correlation between LV volumes by PVR estimation and actual measurements, with significant differences in both measures between the groups: NET+ < NET-. The presence or absence of net did not show restrictive hemodynamics under acute volume load. Static cardiomyoplasty using a synthetic elastic net significantly attenuated LV dilatation and dysfunction without restriction late after myocardial infarction in the rat. © 2013, Copyright the Authors. Artificial Organs © 2013, International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Metal oxide resistive random access memory based synaptic devices for brain-inspired computing

NASA Astrophysics Data System (ADS)

Gao, Bin; Kang, Jinfeng; Zhou, Zheng; Chen, Zhe; Huang, Peng; Liu, Lifeng; Liu, Xiaoyan

2016-04-01

The traditional Boolean computing paradigm based on the von Neumann architecture is facing great challenges for future information technology applications such as big data, the Internet of Things (IoT), and wearable devices, due to the limited processing capability issues such as binary data storage and computing, non-parallel data processing, and the buses requirement between memory units and logic units. The brain-inspired neuromorphic computing paradigm is believed to be one of the promising solutions for realizing more complex functions with a lower cost. To perform such brain-inspired computing with a low cost and low power consumption, novel devices for use as electronic synapses are needed. Metal oxide resistive random access memory (ReRAM) devices have emerged as the leading candidate for electronic synapses. This paper comprehensively addresses the recent work on the design and optimization of metal oxide ReRAM-based synaptic devices. A performance enhancement methodology and optimized operation scheme to achieve analog resistive switching and low-energy training behavior are provided. A three-dimensional vertical synapse network architecture is proposed for high-density integration and low-cost fabrication. The impacts of the ReRAM synaptic device features on the performances of neuromorphic systems are also discussed on the basis of a constructed neuromorphic visual system with a pattern recognition function. Possible solutions to achieve the high recognition accuracy and efficiency of neuromorphic systems are presented.

Adapting GNU random forest program for Unix and Windows

NASA Astrophysics Data System (ADS)

Jirina, Marcel; Krayem, M. Said; Jirina, Marcel, Jr.

2013-10-01

The Random Forest is a well-known method and also a program for data clustering and classification. Unfortunately, the original Random Forest program is rather difficult to use. Here we describe a new version of this program originally written in Fortran 77. The modified program in Fortran 95 needs to be compiled only once and information for different tasks is passed with help of arguments. The program was tested with 24 data sets from UCI MLR and results are available on the net.

Factors Associated With Time to Site Activation, Randomization, and Enrollment Performance in a Stroke Prevention Trial.

PubMed

Demaerschalk, Bart M; Brown, Robert D; Roubin, Gary S; Howard, Virginia J; Cesko, Eldina; Barrett, Kevin M; Longbottom, Mary E; Voeks, Jenifer H; Chaturvedi, Seemant; Brott, Thomas G; Lal, Brajesh K; Meschia, James F; Howard, George

2017-09-01

Multicenter clinical trials attempt to select sites that can move rapidly to randomization and enroll sufficient numbers of patients. However, there are few assessments of the success of site selection. In the CREST-2 (Carotid Revascularization and Medical Management for Asymptomatic Carotid Stenosis Trials), we assess factors associated with the time between site selection and authorization to randomize, the time between authorization to randomize and the first randomization, and the average number of randomizations per site per month. Potential factors included characteristics of the site, specialty of the principal investigator, and site type. For 147 sites, the median time between site selection to authorization to randomize was 9.9 months (interquartile range, 7.7, 12.4), and factors associated with early site activation were not identified. The median time between authorization to randomize and a randomization was 4.6 months (interquartile range, 2.6, 10.5). Sites with authorization to randomize in only the carotid endarterectomy study were slower to randomize, and other factors examined were not significantly associated with time-to-randomization. The recruitment rate was 0.26 (95% confidence interval, 0.23-0.28) patients per site per month. By univariate analysis, factors associated with faster recruitment were authorization to randomize in both trials, principal investigator specialties of interventional radiology and cardiology, pre-trial reported performance >50 carotid angioplasty and stenting procedures per year, status in the top half of recruitment in the CREST trial, and classification as a private health facility. Participation in StrokeNet was associated with slower recruitment as compared with the non-StrokeNet sites. Overall, selection of sites with high enrollment rates will likely require customization to align the sites selected to the factor under study in the trial. URL: http://www.clinicaltrials.gov. Unique identifier: NCT02089217. © 2017 American Heart Association, Inc.

Value of information analysis optimizing future trial design from a pilot study on catheter securement devices.

PubMed

Tuffaha, Haitham W; Reynolds, Heather; Gordon, Louisa G; Rickard, Claire M; Scuffham, Paul A

2014-12-01

Value of information analysis has been proposed as an alternative to the standard hypothesis testing approach, which is based on type I and type II errors, in determining sample sizes for randomized clinical trials. However, in addition to sample size calculation, value of information analysis can optimize other aspects of research design such as possible comparator arms and alternative follow-up times, by considering trial designs that maximize the expected net benefit of research, which is the difference between the expected cost of the trial and the expected value of additional information. To apply value of information methods to the results of a pilot study on catheter securement devices to determine the optimal design of a future larger clinical trial. An economic evaluation was performed using data from a multi-arm randomized controlled pilot study comparing the efficacy of four types of catheter securement devices: standard polyurethane, tissue adhesive, bordered polyurethane and sutureless securement device. Probabilistic Monte Carlo simulation was used to characterize uncertainty surrounding the study results and to calculate the expected value of additional information. To guide the optimal future trial design, the expected costs and benefits of the alternative trial designs were estimated and compared. Analysis of the value of further information indicated that a randomized controlled trial on catheter securement devices is potentially worthwhile. Among the possible designs for the future trial, a four-arm study with 220 patients/arm would provide the highest expected net benefit corresponding to 130% return-on-investment. The initially considered design of 388 patients/arm, based on hypothesis testing calculations, would provide lower net benefit with return-on-investment of 79%. Cost-effectiveness and value of information analyses were based on the data from a single pilot trial which might affect the accuracy of our uncertainty estimation. Another limitation was that different follow-up durations for the larger trial were not evaluated. The value of information approach allows efficient trial design by maximizing the expected net benefit of additional research. This approach should be considered early in the design of randomized clinical trials. © The Author(s) 2014.

Comparison of dietary phosphate absorption after single doses of lanthanum carbonate and sevelamer carbonate in healthy volunteers: a balance study.

PubMed

Martin, Patrick; Wang, Phillip; Robinson, Antoine; Poole, Lynne; Dragone, Jeffrey; Smyth, Michael; Pratt, Raymond

2011-05-01

Lanthanum carbonate and sevelamer carbonate are noncalcium phosphate binders used to treat hyperphosphatemia in patients with chronic kidney disease. This is the first study to compare phosphate absorption from a standardized meal ingested with a typical clinical dose of these binders. Randomized open-label crossover study. Healthy volunteers were confined to a clinical research center during 4 study periods. Of 31 volunteers randomly assigned, 19 completed all treatments and 18 were analyzed in the pharmacodynamic set (1 was excluded because of vomiting). Participants were assigned in random order to meal alone, meal plus lanthanum carbonate (1 tablet containing 1,000 mg of elemental lanthanum), and meal plus sevelamer carbonate (three 800-mg tablets). The gastrointestinal tract was cleared, the meal was ingested (± treatment), and rectal effluent was collected. In a fourth period, volunteers repeated the study procedures while fasting. The primary end point, net phosphate absorption, was analyzed using a mixed-effect linear model. Phosphorus content of effluent and duplicate meal samples were measured using inductively coupled plasma-optical emission spectroscopy. The standard meal contained ∼375 mg of phosphate, 75% of which was absorbed (net absorption, 281.7 ± 14.1 mg [adjusted mean ± standard error]). Lanthanum carbonate decreased net phosphate absorption by 45% (net absorption, 156.0 ± 14.2 mg) compared with 21% (net absorption, 221.8 ± 14.1 mg) for sevelamer carbonate (P < 0.001). Lanthanum carbonate bound 135.1 ± 12.3 mg of phosphate, whereas sevelamer carbonate bound 63.2 ± 12.3 mg, a 71.9-mg difference (95% CI, 40.0-103.8; P < 0.001). Per tablet, this equates to 135 mg of phosphate bound with lanthanum carbonate versus 21 mg with sevelamer carbonate. A single-dose study. In healthy volunteers, 1,000 mg of lanthanum carbonate decreased phosphate absorption by 45% compared with a 21% decrease with 2,400 mg of sevelamer carbonate. Copyright © 2011 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

Narrative exposure therapy for immigrant children traumatized by war: study protocol for a randomized controlled trial of effectiveness and mechanisms of change.

PubMed

Kangaslampi, Samuli; Garoff, Ferdinand; Peltonen, Kirsi

2015-06-17

Millions of children worldwide suffer from posttraumatic stress disorder (PTSD) symptoms and other mental health problems due to repeated exposure to war or organized violence. Forms of cognitive-behavioral therapy (CBT) are the most commonly used treatment for PTSD and appear to be effective for children as well, but little is known about the mechanisms of change through which they achieve their effectiveness. Here we present the study protocol of a randomized controlled trial (RCT) studying the effectiveness and mechanisms of change of Narrative Exposure Therapy (NET), a CBT-based, manualized, short-term intervention for PTSD symptoms resulting from repeated traumatization, in immigrant children traumatized by war. We are conducting a multicentre, pragmatic RCT in a usual care setting. Up to 80 9-17-year-old immigrant children who have experienced war and suffer from PTSD symptoms will be randomized into intervention (NET) and control (treatment as usual, TAU) groups of equal sizes. The effectiveness of NET treatment will be compared to both a waiting list and the parallel TAU positive control group, on the primary outcomes of PTSD and depressive symptoms, psychological distress, resilience, and level of cognitive performance. The effects of the intervention on traumatic memories and posttraumatic cognitions will be studied as potential mechanisms of change mediating overall treatment effectiveness. The possible moderating effects of peritraumatic dissociation, level of cognitive performance, and gender on treatment effectiveness will also be considered. We hypothesize that NET will be more effective than a waitlist condition or TAU in reducing PTSD and other symptoms and improving resilience, and that these effects will be mediated by changes in traumatic memories and posttraumatic cognitions. The results of this trial will provide evidence for the effectiveness of NET in treating trauma-related symptoms in immigrant children affected by war. The trial will also generate insights into the complex relationships between PTSD, memory functions, posttraumatic cognitions and cognitive performance in children, and help guide the future development and implementation of therapeutic interventions for PTSD in children. ClinicalTrials.gov NCT02425280 . Registered 15 April 2015.

Everolimus for the Treatment of Advanced Pancreatic Neuroendocrine Tumors: Overall Survival and Circulating Biomarkers From the Randomized, Phase III RADIANT-3 Study.

PubMed

Yao, James C; Pavel, Marianne; Lombard-Bohas, Catherine; Van Cutsem, Eric; Voi, Maurizio; Brandt, Ulrike; He, Wei; Chen, David; Capdevila, Jaume; de Vries, Elisabeth G E; Tomassetti, Paola; Hobday, Timothy; Pommier, Rodney; Öberg, Kjell

2016-11-10

Purpose Everolimus improved median progression-free survival by 6.4 months in patients with advanced pancreatic neuroendocrine tumors (NET) compared with placebo in the RADIANT-3 study. Here, we present the final overall survival (OS) data and data on the impact of biomarkers on OS from the RADIANT-3 study. Methods Patients with advanced, progressive, low- or intermediate-grade pancreatic NET were randomly assigned to everolimus 10 mg/day (n = 207) or placebo (n = 203). Crossover from placebo to open-label everolimus was allowed on disease progression. Ongoing patients were unblinded after final progression-free survival analysis and could transition to open-label everolimus at the investigator's discretion (extension phase). OS analysis was performed using a stratified log-rank test in the intent-to-treat population. The baseline levels of chromogranin A, neuron-specific enolase, and multiple soluble angiogenic biomarkers were determined and their impact on OS was explored. Results Of 410 patients who were enrolled between July 2007 and March 2014, 225 received open-label everolimus, including 172 patients (85%) randomly assigned initially to the placebo arm. Median OS was 44.0 months (95% CI, 35.6 to 51.8 months) for those randomly assigned to everolimus and 37.7 months (95% CI, 29.1 to 45.8 months) for those randomly assigned to placebo (hazard ratio, 0.94; 95% CI, 0.73 to 1.20; P = .30). Elevated baseline chromogranin A, neuron-specific enolase, placental growth factor, and soluble vascular endothelial growth factor receptor 1 levels were poor prognostic factors for OS. The most common adverse events included stomatitis, rash, and diarrhea. Conclusion Everolimus was associated with a median OS of 44 months in patients with advanced, progressive pancreatic NET, the longest OS reported in a phase III study for this population. Everolimus was associated with a survival benefit of 6.3 months, although this finding was not statistically significant. Crossover of patients likely confounded the OS results.

Defense of Cyber Infrastructures Against Cyber-Physical Attacks Using Game-Theoretic Models

DOE PAGES

Rao, Nageswara S. V.; Poole, Stephen W.; Ma, Chris Y. T.; ...

2015-04-06

The operation of cyber infrastructures relies on both cyber and physical components, which are subject to incidental and intentional degradations of different kinds. Within the context of network and computing infrastructures, we study the strategic interactions between an attacker and a defender using game-theoretic models that take into account both cyber and physical components. The attacker and defender optimize their individual utilities expressed as sums of cost and system terms. First, we consider a Boolean attack-defense model, wherein the cyber and physical sub-infrastructures may be attacked and reinforced as individual units. Second, we consider a component attack-defense model wherein theirmore » components may be attacked and defended, and the infrastructure requires minimum numbers of both to function. We show that the Nash equilibrium under uniform costs in both cases is computable in polynomial time, and it provides high-level deterministic conditions for the infrastructure survival. When probabilities of successful attack and defense, and of incidental failures are incorporated into the models, the results favor the attacker but otherwise remain qualitatively similar. This approach has been motivated and validated by our experiences with UltraScience Net infrastructure, which was built to support high-performance network experiments. In conclusion, the analytical results, however, are more general, and we apply them to simplified models of cloud and high-performance computing infrastructures.« less

Defense of Cyber Infrastructures Against Cyber-Physical Attacks Using Game-Theoretic Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Nageswara S. V.; Poole, Stephen W.; Ma, Chris Y. T.

The operation of cyber infrastructures relies on both cyber and physical components, which are subject to incidental and intentional degradations of different kinds. Within the context of network and computing infrastructures, we study the strategic interactions between an attacker and a defender using game-theoretic models that take into account both cyber and physical components. The attacker and defender optimize their individual utilities expressed as sums of cost and system terms. First, we consider a Boolean attack-defense model, wherein the cyber and physical sub-infrastructures may be attacked and reinforced as individual units. Second, we consider a component attack-defense model wherein theirmore » components may be attacked and defended, and the infrastructure requires minimum numbers of both to function. We show that the Nash equilibrium under uniform costs in both cases is computable in polynomial time, and it provides high-level deterministic conditions for the infrastructure survival. When probabilities of successful attack and defense, and of incidental failures are incorporated into the models, the results favor the attacker but otherwise remain qualitatively similar. This approach has been motivated and validated by our experiences with UltraScience Net infrastructure, which was built to support high-performance network experiments. In conclusion, the analytical results, however, are more general, and we apply them to simplified models of cloud and high-performance computing infrastructures.« less

Defense of Cyber Infrastructures Against Cyber-Physical Attacks Using Game-Theoretic Models.

PubMed

Rao, Nageswara S V; Poole, Stephen W; Ma, Chris Y T; He, Fei; Zhuang, Jun; Yau, David K Y

2016-04-01

The operation of cyber infrastructures relies on both cyber and physical components, which are subject to incidental and intentional degradations of different kinds. Within the context of network and computing infrastructures, we study the strategic interactions between an attacker and a defender using game-theoretic models that take into account both cyber and physical components. The attacker and defender optimize their individual utilities, expressed as sums of cost and system terms. First, we consider a Boolean attack-defense model, wherein the cyber and physical subinfrastructures may be attacked and reinforced as individual units. Second, we consider a component attack-defense model wherein their components may be attacked and defended, and the infrastructure requires minimum numbers of both to function. We show that the Nash equilibrium under uniform costs in both cases is computable in polynomial time, and it provides high-level deterministic conditions for the infrastructure survival. When probabilities of successful attack and defense, and of incidental failures, are incorporated into the models, the results favor the attacker but otherwise remain qualitatively similar. This approach has been motivated and validated by our experiences with UltraScience Net infrastructure, which was built to support high-performance network experiments. The analytical results, however, are more general, and we apply them to simplified models of cloud and high-performance computing infrastructures. © 2015 Society for Risk Analysis.

Efficacy of permethrin treated long-lasting insecticidal nets on malaria transmission and observations on the perceived side effects, collateral benefits and human safety in a hyperendemic tribal area of Orissa, India.

PubMed

Sharma, Surya K; Tyagi, Prajesh K; Upadhyay, Ashok K; Haque, Mohammed A; Mohanty, Suman S; Raghavendra, Kamaraju; Dash, Aditya P

2009-11-01

Studies were conducted on the efficacy of Olyset nets-a long-lasting insecticidal net (LLIN) factory treated with 2% (w/w) permethrin on malaria transmission in an area under the influence of pyrethroid susceptible vector species Anopheles culicifacies and A. fluviatilis in Sundargarh District, Orissa, India. The study area comprised 22 villages that were randomized into three clusters and designated as Olyset net, untreated net, and no net area. Malaria incidence in the study population was measured through longitudinal active surveillance at fortnightly intervals. There was a reduction of 65-70% in malaria incidence in Olyset net area as compared to the control areas. The attack rate of Plasmodium falciparum or number of episodes per person per year in different age groups also showed significant reduction in Olyset net area as compared to untreated net and no net areas. Cross-sectional point prevalence surveys showed 45.7% reduction of malaria prevalence in Olyset net users, whereas there was an increase of 33.3% and 51% in untreated net and no net villages respectively. The compliance rate of Olyset net usage in the study population was 80-98% during different months, whereas it was between 70% and 90% for untreated nets. There were minimal complains of skin irritation (4%), itching (8%) and eye irritation (1.2%). However, these effects were only transitory in nature lasting for few hours of the first usage. Olyset nets also provided collateral benefits in terms of relief not only from mosquitoes and malaria but also from other household pests such as head lice, bed bugs, cockroaches, ants and houseflies. The Olyset nets were found to be safe to humans as no adverse event was recorded in the net users that can be attributed to the use of net. The study showed that Olyset nets are effective personal protection tool that can be used in a community based intervention programme.

SpectralNET – an application for spectral graph analysis and visualization

PubMed Central

Forman, Joshua J; Clemons, Paul A; Schreiber, Stuart L; Haggarty, Stephen J

2005-01-01

Background Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that can carry different weights. SpectralNET is a flexible application for analyzing and visualizing these biological and chemical networks. Results Available both as a standalone .NET executable and as an ASP.NET web application, SpectralNET was designed specifically with the analysis of graph-theoretic metrics in mind, a computational task not easily accessible using currently available applications. Users can choose either to upload a network for analysis using a variety of input formats, or to have SpectralNET generate an idealized random network for comparison to a real-world dataset. Whichever graph-generation method is used, SpectralNET displays detailed information about each connected component of the graph, including graphs of degree distribution, clustering coefficient by degree, and average distance by degree. In addition, extensive information about the selected vertex is shown, including degree, clustering coefficient, various distance metrics, and the corresponding components of the adjacency, Laplacian, and normalized Laplacian eigenvectors. SpectralNET also displays several graph visualizations, including a linear dimensionality reduction for uploaded datasets (Principal Components Analysis) and a non-linear dimensionality reduction that provides an elegant view of global graph structure (Laplacian eigenvectors). Conclusion SpectralNET provides an easily accessible means of analyzing graph-theoretic metrics for data modeling and dimensionality reduction. SpectralNET is publicly available as both a .NET application and an ASP.NET web application from . Source code is available upon request. PMID:16236170

SpectralNET--an application for spectral graph analysis and visualization.

PubMed

Forman, Joshua J; Clemons, Paul A; Schreiber, Stuart L; Haggarty, Stephen J

2005-10-19

Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that can carry different weights. SpectralNET is a flexible application for analyzing and visualizing these biological and chemical networks. Available both as a standalone .NET executable and as an ASP.NET web application, SpectralNET was designed specifically with the analysis of graph-theoretic metrics in mind, a computational task not easily accessible using currently available applications. Users can choose either to upload a network for analysis using a variety of input formats, or to have SpectralNET generate an idealized random network for comparison to a real-world dataset. Whichever graph-generation method is used, SpectralNET displays detailed information about each connected component of the graph, including graphs of degree distribution, clustering coefficient by degree, and average distance by degree. In addition, extensive information about the selected vertex is shown, including degree, clustering coefficient, various distance metrics, and the corresponding components of the adjacency, Laplacian, and normalized Laplacian eigenvectors. SpectralNET also displays several graph visualizations, including a linear dimensionality reduction for uploaded datasets (Principal Components Analysis) and a non-linear dimensionality reduction that provides an elegant view of global graph structure (Laplacian eigenvectors). SpectralNET provides an easily accessible means of analyzing graph-theoretic metrics for data modeling and dimensionality reduction. SpectralNET is publicly available as both a .NET application and an ASP.NET web application from http://chembank.broad.harvard.edu/resources/. Source code is available upon request.

Net use, care and repair practices following a universal distribution campaign in Mali.

PubMed

Leonard, Lori; Diop, Samba; Doumbia, Seydou; Sadou, Aboubacar; Mihigo, Jules; Koenker, Hannah; Berthe, Sara; Monroe, April; Bertram, Kathryn; Weber, Rachel

2014-11-18

The Government of Mali and the President's Malaria Initiative conducted a long-lasting, insecticidal net (LLIN) distribution campaign in April 2011 in the Sikasso region of Mali, with the aim of universal coverage, defined as one insecticide-treated net for every two persons. This study examines how households in post- and pre-campaign regions value and care for nets. The study was conducted in October 2012 in Sikasso and Kayes in the southeast and western regions of Mali, respectively. The regions were purposively selected to allow for comparison between areas that had already had a mass distribution campaign (Sikasso) and areas that had not yet had a mass distribution campaign (Kayes). Study sites and households were randomly selected. Sleeping space questionnaires and structured interviews with household heads were conducted to obtain information on net use, perceived value of free nets in relation to other malaria prevention activities, and net care and repair practices. The study included 40 households, split evenly across the two regions. Forty interviews were conducted with household heads and 151 sleeping spaces were inventoried using the sleeping space questionnaire. Nets obtained through the free distribution were reported to be highly valued in comparison to other malaria prevention strategies. Overall, net ownership and use were higher among households in areas that had already experienced a mass distribution. While participants reported using and valuing these nets, care and repair practices varied. National net use is high in Mali, and comparatively higher in the region covered by the universal distribution campaign than in the region not yet covered. While the Government of Mali and implementing partners have made strides to ensure high net coverage, some gaps remain related to communication messaging of correct and consistent net use throughout the year, and on improving net care and repair behaviour. By focusing on these areas as well as improved access to nets, coverage and use rates should continue to increase, contributing to improvements in malaria control.

Mobile Phone Intervention and Weight Loss Among Overweight and Obese Adults: A Meta-Analysis of Randomized Controlled Trials

PubMed Central

Liu, Fangchao; Kong, Xiaomu; Cao, Jie; Chen, Shufeng; Li, Changwei; Huang, Jianfeng; Gu, Dongfeng; Kelly, Tanika N.

2015-01-01

We conducted a meta-analysis of randomized controlled trials to examine the association of mobile phone intervention with net change in weight-related measures among overweight and obese adults. We searched electronic databases and conducted a bibliography review to identify articles published between the inception date of each database and March 27, 2014. Fourteen trials (including 1,337 participants in total) that met the eligibility criteria were included. Two investigators independently abstracted information on study characteristics and study outcomes. Net change estimates comparing the intervention group with the control group were pooled across trials using random-effects models. Compared with the control group, mobile phone intervention was associated with significant changes in body weight and body mass index (weight (kg)/height (m)2) of −1.44 kg (95% confidence interval (CI): −2.12, −0.76) and −0.24 units (95% CI: −0.40, −0.08), respectively. Subgroup analyses revealed that the associations were consistent across study-duration and intervention-type subgroups. For example, net body weight changes were −0.92 kg (95% CI: −1.58, −0.25) and −1.85 kg (95% CI: −2.99, −0.71) in trials of shorter (<6 months) and longer (≥6 months) duration, respectively. These findings provide evidence that mobile phone intervention may be a useful tool for promoting weight loss among overweight and obese adults. PMID:25673817

Bivalirudin or Unfractionated Heparin in Acute Coronary Syndromes.

PubMed

Valgimigli, Marco; Frigoli, Enrico; Leonardi, Sergio; Rothenbühler, Martina; Gagnor, Andrea; Calabrò, Paolo; Garducci, Stefano; Rubartelli, Paolo; Briguori, Carlo; Andò, Giuseppe; Repetto, Alessandra; Limbruno, Ugo; Garbo, Roberto; Sganzerla, Paolo; Russo, Filippo; Lupi, Alessandro; Cortese, Bernardo; Ausiello, Arturo; Ierna, Salvatore; Esposito, Giovanni; Presbitero, Patrizia; Santarelli, Andrea; Sardella, Gennaro; Varbella, Ferdinando; Tresoldi, Simone; de Cesare, Nicoletta; Rigattieri, Stefano; Zingarelli, Antonio; Tosi, Paolo; van 't Hof, Arnoud; Boccuzzi, Giacomo; Omerovic, Elmir; Sabaté, Manel; Heg, Dik; Jüni, Peter; Vranckx, Pascal

2015-09-10

Conflicting evidence exists on the efficacy and safety of bivalirudin administered as part of percutaneous coronary intervention (PCI) in patients with an acute coronary syndrome. We randomly assigned 7213 patients with an acute coronary syndrome for whom PCI was anticipated to receive either bivalirudin or unfractionated heparin. Patients in the bivalirudin group were subsequently randomly assigned to receive or not to receive a post-PCI bivalirudin infusion. Primary outcomes for the comparison between bivalirudin and heparin were the occurrence of major adverse cardiovascular events (a composite of death, myocardial infarction, or stroke) and net adverse clinical events (a composite of major bleeding or a major adverse cardiovascular event). The primary outcome for the comparison of a post-PCI bivalirudin infusion with no post-PCI infusion was a composite of urgent target-vessel revascularization, definite stent thrombosis, or net adverse clinical events. The rate of major adverse cardiovascular events was not significantly lower with bivalirudin than with heparin (10.3% and 10.9%, respectively; relative risk, 0.94; 95% confidence interval [CI], 0.81 to 1.09; P=0.44), nor was the rate of net adverse clinical events (11.2% and 12.4%, respectively; relative risk, 0.89; 95% CI, 0.78 to 1.03; P=0.12). Post-PCI bivalirudin infusion, as compared with no infusion, did not significantly decrease the rate of urgent target-vessel revascularization, definite stent thrombosis, or net adverse clinical events (11.0% and 11.9%, respectively; relative risk, 0.91; 95% CI, 0.74 to 1.11; P=0.34). In patients with an acute coronary syndrome, the rates of major adverse cardiovascular events and net adverse clinical events were not significantly lower with bivalirudin than with unfractionated heparin. The rate of the composite of urgent target-vessel revascularization, definite stent thrombosis, or net adverse clinical events was not significantly lower with a post-PCI bivalirudin infusion than with no post-PCI infusion. (Funded by the Medicines Company and Terumo Medical; MATRIX ClinicalTrials.gov number, NCT01433627.).

Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

EPA Science Inventory

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 t...

A Boolean Network Model of Nuclear Receptor Mediated Cell Cycle Progression

EPA Science Inventory

Nuclear receptors (NRs) are ligand-activated transcription factors that regulate a broad range of cellular processes. Hormones, lipids and xenobiotics have been shown to activate NRs with a range of consequences on development, metabolism, oxidative stress, apoptosis, and prolif...

A Boolean Network Model of Nuclear Receptor Mediated Cell Cycle Progression (S)

EPA Science Inventory

Nuclear receptors (NRs) are ligand-activated transcription factors that regulate a broad range of cellular processes. Hormones, lipids and xenobiotics have been shown to activate NRs with a range of consequences on development, metabolism, oxidative stress, apoptosis, and prolif...

Automatic Query Formulations in Information Retrieval.

ERIC Educational Resources Information Center

Salton, G.; And Others

1983-01-01

Introduces methods designed to reduce role of search intermediaries by generating Boolean search formulations automatically using term frequency considerations from natural language statements provided by system patrons. Experimental results are supplied and methods are described for applying automatic query formulation process in practice.…

Digital Equipment Corporation's CRDOM Software and Database Publications.

ERIC Educational Resources Information Center

Adams, Michael Q.

1986-01-01

Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

Topics for Mathematics Clubs.

ERIC Educational Resources Information Center

Dalton, LeRoy C., Ed.; Snyder, Henry D., Ed.

The ten chapters in this booklet cover topics not ordinarily discussed in the classroom: Fibonacci sequences, projective geometry, groups, infinity and transfinite numbers, Pascal's Triangle, topology, experiments with natural numbers, non-Euclidean geometries, Boolean algebras, and the imaginary and the infinite in geometry. Each chapter is…

Community-randomized trial of lambdacyhalothrin-treated hammock nets for malaria control in Yanomami communities in the Amazon region of Venezuela.

PubMed

Magris, M; Rubio-Palis, Y; Alexander, N; Ruiz, B; Galván, N; Frias, D; Blanco, M; Lines, J

2007-03-01

We conducted a community-randomized controlled trial in an area of moderate malaria transmission in the Amazon region, southern Venezuela, home of the Yanomami indigenous ethnic group. The aim was to compare the malaria incidence rate in villages with lambdacyhalothrin-treated hammock nets (ITHN) or with placebo-treated hammock nets (PTHN). In both arms of the study, intensive surveillance for early case detection was maintained and prompt malaria treatment was administered. Baseline data were collected before the intervention and a population of around 924 Yanomami was followed for 2 years. Despite the recent introduction of nets in the Yanomami villages and the adverse natural conditions in the area, the nets were accepted enthusiastically by the study population, used conscientiously and looked after carefully. The malaria incidence rate per thousand person-years at risk was 114.6 in the IHTN group and 186.8 in the PTHN group. The adjusted rate ratios indicated that ITHN prevent 56% [IRR: 0.44, 95% confidence interval (CI): 52-59%] of new malaria cases. ITHN reduced the prevalence of parasitaemia by 83% [relative risks (RR): 0.17, 95% CI: 47-100%], according to a cross-sectional survey carried out during the high transmission season. The prevalence of splenomegaly and anaemia was too low to detect any possible reduction as a result of ITHN. The main conclusion of the present study is that ITHN can reduce malaria incidence in the area and it is the most feasible method for malaria control in a forested area where indigenous villages are scattered over a large territory. This is the first community-level epidemiological trial to show that ITHN are highly effective against malaria transmitted by Anopheles darlingi.

Correcting bias due to missing stage data in the non-parametric estimation of stage-specific net survival for colorectal cancer using multiple imputation.

PubMed

Falcaro, Milena; Carpenter, James R

2017-06-01

Population-based net survival by tumour stage at diagnosis is a key measure in cancer surveillance. Unfortunately, data on tumour stage are often missing for a non-negligible proportion of patients and the mechanism giving rise to the missingness is usually anything but completely at random. In this setting, restricting analysis to the subset of complete records gives typically biased results. Multiple imputation is a promising practical approach to the issues raised by the missing data, but its use in conjunction with the Pohar-Perme method for estimating net survival has not been formally evaluated. We performed a resampling study using colorectal cancer population-based registry data to evaluate the ability of multiple imputation, used along with the Pohar-Perme method, to deliver unbiased estimates of stage-specific net survival and recover missing stage information. We created 1000 independent data sets, each containing 5000 patients. Stage data were then made missing at random under two scenarios (30% and 50% missingness). Complete records analysis showed substantial bias and poor confidence interval coverage. Across both scenarios our multiple imputation strategy virtually eliminated the bias and greatly improved confidence interval coverage. In the presence of missing stage data complete records analysis often gives severely biased results. We showed that combining multiple imputation with the Pohar-Perme estimator provides a valid practical approach for the estimation of stage-specific colorectal cancer net survival. As usual, when the percentage of missing data is high the results should be interpreted cautiously and sensitivity analyses are recommended. Copyright © 2017 Elsevier Ltd. All rights reserved.

The effect of trauma-focused therapy on the altered T cell distribution in individuals with PTSD: evidence from a randomized controlled trial.

PubMed

Morath, Julia; Gola, Hannah; Sommershof, Annette; Hamuni, Gilava; Kolassa, Stephan; Catani, Claudia; Adenauer, Hannah; Ruf-Leuschner, Martina; Schauer, Maggie; Elbert, Thomas; Groettrup, Marcus; Kolassa, Iris-Tatjana

2014-07-01

Posttraumatic stress disorder (PTSD) is associated with a reduced ratio of naïve cytotoxic T lymphocytes, an increased ratio of memory cytotoxic T lymphocytes, and a reduced proportion of FoxP3(+) regulatory T lymphocytes. This study investigated whether these immunological alterations are reversible through an evidence-based psychotherapeutic treatment. Therefore, 34 individuals with PTSD were randomly assigned to either a treatment condition of 12 sessions narrative exposure therapy (NET) or a waitlist control (WLC) group. PTSD symptoms were significantly reduced in the NET group, but not in the WLC group, four months post-therapy (effect size: Hedges' g = -1.61). One year after therapy, PTSD symptoms were improved even further in the NET group compared to baseline (Hedges' g = -1.96). This symptom improvement was mirrored in an increase in the originally reduced proportion of regulatory T cells (Tregs) in the NET group at the one-year follow-up, when comparing subgroups matched for baseline Treg numbers. However, no changes were found for the initially reduced proportion of CD45RA(+)CCR7(+) naïve T lymphocytes. In conclusion, NET was effective in reducing trauma-related PTSD symptoms and had a positive effect on the proportion of Tregs cells, thus demonstrating an effect of psychotherapy on an immunological level. Yet, the shift in the proportion of naïve and memory T lymphocytes in individuals with PTSD, discussed in the literature as a correlate of premature immunosenescence, was not reversible and thus might render these patients permanently more susceptible to infectious diseases. Copyright © 2014 Elsevier Ltd. All rights reserved.

Improving general flexibility with a mind-body approach: a randomized, controlled trial using neuro emotional Technique®.

PubMed

Jensen, Anne M; Ramasamy, Adaikalavan; Hall, Michael W

2012-08-01

General flexibility is a key component of health, well-being, and general physical conditioning. Reduced flexibility has both physical and mental/emotional etiologies and can lead to musculoskeletal injuries and athletic underperformance. Few studies have tested the effectiveness of a mind-body therapy on general flexibility. The aim of this study was to investigate if Neuro Emotional Technique® (NET), a mind-body technique shown to be effective in reducing stress, can also improve general flexibility. The sit-and-reach test (SR) score was used as a measure of general flexibility. Forty-five healthy participants were recruited from the general population and assessed for their initial SR score before being randomly allocated to receive (a) two 20-minute sessions of NET (experimental group); (b) two 20-minute sessions of stretching instruction (active control group); or (c) no intervention or instruction (passive control group). After intervention, the participants were reassessed in a similar manner by the same blind assessor. The participants also answered questions about demographics, usual water and caffeine consumption, and activity level, and they completed an anxiety/mood psychometric preintervention and postintervention. The mean (SD) change in the SR score was +3.1 cm (2.5) in the NET group, +1.2 cm (2.3) in the active control group and +1.0 cm (2.6) in the passive control group. Although all the 3 groups showed some improvement, the improvement in the NET group was statistically significant when compared with that of either the passive controls (p = 0.015) or the active controls (p = 0.021). This study suggests that NET could provide an effective treatment in improving general flexibility. A larger study is required to confirm these findings and also to assess longer term effectiveness of this therapy on general flexibility.

A comparison of lead lengths for mini-fyke nets to sample age-0 gar species

USGS Publications Warehouse

Long, James M.; Snow, Richard A.; Patterson, Chas P.

2016-01-01

Mini-fyke nets are often used to sample small-bodied fishes in shallow (<1 m depth) water, especially in vegetated shoreline habitats where seines are ineffective. Recent interest in gar (Lepisosteidae) ecology and conservation led us to explore the use of mini-fyke nets to capture age-0 gar and specifically how capture is affected by lead length of the fyke net. In the summers of 2012, 2013, and 2015, mini-fyke nets with two different lead lengths (4.57 m and 9.14 m) were set at random sites in backwaters and coves of the Red River arm of Lake Texoma, Oklahoma. Mean CPUE (catch-per-unit-effort; number per net night) was significantly lower for mini-fyke nets with short leads (0.52) compared to those with long leads (1.51). Additionally, Spotted Gar (Lepisosteus oculatus) were captured at a higher rate than the other three gar species present in Lake Texoma, although this could have been an artifact of sampling location. We found that differences in length-frequency of captured gar between gear types were nearly significant, with total length ranging from 47mm to 590mm. Mini-fyke nets with longer leads increased the efficiency of sampling for age-0 gar by increasing catch rate without affecting estimates of other population parameters and appear to be useful for this purpose. 

Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming.

PubMed

Chebouba, Lokmane; Miannay, Bertrand; Boughaci, Dalila; Guziolowski, Carito

2018-03-08

During the last years, several approaches were applied on biomedical data to detect disease specific proteins and genes in order to better target drugs. It was shown that statistical and machine learning based methods use mainly clinical data and improve later their results by adding omics data. This work proposes a new method to discriminate the response of Acute Myeloid Leukemia (AML) patients to treatment. The proposed approach uses proteomics data and prior regulatory knowledge in the form of networks to predict cancer treatment outcomes by finding out the different Boolean networks specific to each type of response to drugs. To show its effectiveness we evaluate our method on a dataset from the DREAM 9 challenge. The results are encouraging and demonstrate the benefit of our approach to distinguish patient groups with different response to treatment. In particular each treatment response group is characterized by a predictive model in the form of a signaling Boolean network. This model describes regulatory mechanisms which are specific to each response group. The proteins in this model were selected from the complete dataset by imposing optimization constraints that maximize the difference in the logical response of the Boolean network associated to each group of patients given the omic dataset. This mechanistic and predictive model also allow us to classify new patients data into the two different patient response groups. We propose a new method to detect the most relevant proteins for understanding different patient responses upon treatments in order to better target drugs using a Prior Knowledge Network and proteomics data. The results are interesting and show the effectiveness of our method.

ASP-G: an ASP-based method for finding attractors in genetic regulatory networks

PubMed Central

Mushthofa, Mushthofa; Torres, Gustavo; Van de Peer, Yves; Marchal, Kathleen; De Cock, Martine

2014-01-01

Motivation: Boolean network models are suitable to simulate GRNs in the absence of detailed kinetic information. However, reducing the biological reality implies making assumptions on how genes interact (interaction rules) and how their state is updated during the simulation (update scheme). The exact choice of the assumptions largely determines the outcome of the simulations. In most cases, however, the biologically correct assumptions are unknown. An ideal simulation thus implies testing different rules and schemes to determine those that best capture an observed biological phenomenon. This is not trivial because most current methods to simulate Boolean network models of GRNs and to compute their attractors impose specific assumptions that cannot be easily altered, as they are built into the system. Results: To allow for a more flexible simulation framework, we developed ASP-G. We show the correctness of ASP-G in simulating Boolean network models and obtaining attractors under different assumptions by successfully recapitulating the detection of attractors of previously published studies. We also provide an example of how performing simulation of network models under different settings help determine the assumptions under which a certain conclusion holds. The main added value of ASP-G is in its modularity and declarativity, making it more flexible and less error-prone than traditional approaches. The declarative nature of ASP-G comes at the expense of being slower than the more dedicated systems but still achieves a good efficiency with respect to computational time. Availability and implementation: The source code of ASP-G is available at http://bioinformatics.intec.ugent.be/kmarchal/Supplementary_Information_Musthofa_2014/asp-g.zip. Contact: Kathleen.Marchal@UGent.be or Martine.DeCock@UGent.be Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25028722

Intelligent Machines in the 21st Century: Automating the Processes of Inference and Inquiry

NASA Technical Reports Server (NTRS)

Knuth, Kevin H.

2003-01-01

The last century saw the application of Boolean algebra toward the construction of computing machines, which work by applying logical transformations to information contained in their memory. The development of information theory and the generalization of Boolean algebra to Bayesian inference have enabled these computing machines. in the last quarter of the twentieth century, to be endowed with the ability to learn by making inferences from data. This revolution is just beginning as new computational techniques continue to make difficult problems more accessible. However, modern intelligent machines work by inferring knowledge using only their pre-programmed prior knowledge and the data provided. They lack the ability to ask questions, or request data that would aid their inferences. Recent advances in understanding the foundations of probability theory have revealed implications for areas other than logic. Of relevance to intelligent machines, we identified the algebra of questions as the free distributive algebra, which now allows us to work with questions in a way analogous to that which Boolean algebra enables us to work with logical statements. In this paper we describe this logic of inference and inquiry using the mathematics of partially ordered sets and the scaffolding of lattice theory, discuss the far-reaching implications of the methodology, and demonstrate its application with current examples in machine learning. Automation of both inference and inquiry promises to allow robots to perform science in the far reaches of our solar system and in other star systems by enabling them to not only make inferences from data, but also decide which question to ask, experiment to perform, or measurement to take given what they have learned and what they are designed to understand.

Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model

PubMed Central

Lu, Wei; Song, Jiangning; Akutsu, Tatsuya

2015-01-01

Abstract This article considers the problem whereby, given two metabolic networks N1 and N2, a set of source compounds, and a set of target compounds, we must find the minimum set of reactions whose removal (knockout) ensures that the target compounds are not producible in N1 but are producible in N2. Similar studies exist for the problem of finding the minimum knockout with the smallest side effect for a single network. However, if technologies of external perturbations are advanced in the near future, it may be important to develop methods of computing the minimum knockout for multiple networks (MKMN). Flux balance analysis (FBA) is efficient if a well-polished model is available. However, that is not always the case. Therefore, in this article, we study MKMN in Boolean models and an elementary mode (EM)-based model. Integer linear programming (ILP)-based methods are developed for these models, since MKMN is NP-complete for both the Boolean model and the EM-based model. Computer experiments are conducted with metabolic networks of clostridium perfringens SM101 and bifidobacterium longum DJO10A, respectively known as bad bacteria and good bacteria for the human intestine. The results show that larger networks are more likely to have MKMN solutions. However, solving for these larger networks takes a very long time, and often the computation cannot be completed. This is reasonable, because small networks do not have many alternative pathways, making it difficult to satisfy the MKMN condition, whereas in large networks the number of candidate solutions explodes. Our developed software minFvskO is available online. PMID:25684199

The accuracy and efficiency of electronic screening for recruitment into a clinical trial on COPD.

PubMed

Schmickl, Christopher N; Li, Man; Li, Guangxi; Wetzstein, Marnie M; Herasevich, Vitaly; Gajic, Ognjen; Benzo, Roberto P

2011-10-01

Participant recruitment is an important process in successful conduct of randomized controlled trials. To facilitate enrollment into a National Institutes of Health-sponsored clinical trial involving patients with chronic obstructive pulmonary disease (COPD), we developed and prospectively validated an automated electronic screening tool based on boolean free-text search of admission notes in electronic medical records. During a 2-week validation period, all patients admitted to prespecified general medical services were screened for eligibility by both the electronic screening tool and a COPD nurse. Group discussion was the gold standard for confirmation of true-positive results. Compared with the gold standard, electronic screening yielded 100% sensitivity, 92% specificity, 100% negative predictive value, and 72% positive predictive value. Compared with traditional manual screening, electronic screening demonstrated time-saving potential of 76%. Thus, the electronic screening tool accurately identifies potential study subjects and improves efficiency of patient accrual for a clinical trial on COPD. This method may be expanded into other institutional and clinical settings. Copyright © 2011 Elsevier Ltd. All rights reserved.

Long-lasting insecticidal net source, ownership and use in the context of universal coverage: a household survey in eastern Rwanda.

PubMed

Kateera, Fredrick; Ingabire, Chantal M; Hakizimana, Emmanuel; Rulisa, Alexis; Karinda, Parfait; Grobusch, Martin P; Mutesa, Leon; van Vugt, Michèle; Mens, Petra F

2015-10-06

Universal long-lasting insecticidal net (LLIN) coverage (ULC) has reduced malaria morbidity and mortality across Africa. Although information is available on bed net use in specific groups, such as pregnant women and children under 5 years, there is paucity of data on their use among the general population. Bed net source, ownership and determinants of use among individuals from households in an eastern Rwanda community 8 months after a ULC were characterized. Using household-based, interviewer-administered questionnaires and interviewer-direct observations, data on bed net source, ownership and key determinants of net use, including demographics, socio-economic status indicators, house structure characteristics, as well as of bed net quantity, type and integrity, were collected from 1400 randomly selected households. Univariate and mixed effects logistic regression modelling was done to assess for determinants of bed net use. A total of 1410 households and 6598 individuals were included in the study. Overall, the proportion of households with at least one net was 92 % while bed net usage was reported among 72 % of household members. Of the households surveyed, a total ownership of 2768 nets was reported, of which about 96 % were reportedly LLINs received from the ULC. By interviewer-physical observation, 88 % of the nets owned were of the LLIN type with the remaining 12 % did not carry any mark to enable type recognition. The odds of bed net use were significantly lower among males and individuals: from households of low socio-economic status, from households with

Wealth, mother's education and physical access as determinants of retail sector net use in rural Kenya

PubMed Central

2006-01-01

Background Insecticide-treated bed nets (ITN) provide real hope for the reduction of the malaria burden across Africa. Understanding factors that determine access to ITN is crucial to debates surrounding the optimal delivery systems. The influence of homestead wealth on use of nets purchased from the retail sector is well documented, however, the competing influence of mother's education and physical access to net providers is less well understood. Methods Between December 2004 and January 2005, a random sample of 72 rural communities was selected across four Kenyan districts. Demographic, assets, education and net use data were collected at homestead, mother and child (aged < 5 years) levels. An assets-based wealth index was developed using principal components analysis, travel time to net sources was modelled using geographic information systems, and factors influencing the use of retail sector nets explored using a multivariable logistic regression model. Results Homestead heads and guardians of 3,755 children < 5 years of age were interviewed. Approximately 15% (562) of children slept under a net the night before the interview; 58% (327) of the nets used were purchased from the retail sector. Homestead wealth (adjusted OR = 10.17, 95% CI = 5.45–18.98), travel time to nearest market centres (adjusted OR = 0.51, 95% CI = 0.37–0.72) and mother's education (adjusted OR = 2.92, 95% CI = 1.93–4.41) were significantly associated with use of retail sector nets by children aged less than 5 years. Conclusion Approaches to promoting access to nets through the retail sector disadvantage poor and remote communities where mothers are less well educated. PMID:16436216

Long-term field performance of a polyester-based long-lasting insecticidal mosquito net in rural Uganda

PubMed Central

Kilian, Albert; Byamukama, Wilson; Pigeon, Olivier; Atieli, Francis; Duchon, Stephan; Phan, Chi

2008-01-01

Background In order to evaluate whether criteria for LLIN field performance (phase III) set by the WHO Pesticide Evaluation Scheme are met, first and second generations of one of these products, PermaNet®, a polyester net using the coating technology were tested. Methods A randomized, double blinded study design was used comparing LLIN to conventionally treated nets and following LLIN for three years under regular household use in rural conditions. Primary outcome measures were deltamethrin residue and bioassay performance (60 minute knock-down and 24 hour mortality after a three minute exposure) using a strain of Anopheles gambiae s.s. sensitive to pyrethroid insecticides. Results Baseline concentration of deltamethrin was within targets for all net types but was rapidly lost in conventionally treated nets and first generation PermaNet® with median of 0.7 and 2.5 mg/m2 after six months respectively. In contrast, second generation PermaNet® retained insecticide well and had 41.5% of baseline dose after 36 months (28.7 mg/m2). Similarly, vector mortality and knockdown dropped to 18% and 70% respectively for first generation LLIN after six months but remained high (88.5% and 97.8% respectively) for second generation PermaNet® after 36 months of follow up at which time 90.0% of nets had either a knockdown rate ≥ 95% or mortality rate ≥ 80%. Conclusion Second generation PermaNet® showed excellent results after three years of field use and fulfilled the WHOPES criteria for LLIN. Loss of insecticide on LLIN using coating technology under field conditions was far more influenced by factors associated with handling rather than washing. PMID:18355408

Comparison of serum and cervical mucus hormone levels during hormone-free interval of 24/4 vs. 21/7 combined oral contraceptives.

PubMed

Fels, Heather; Steward, Rachel; Melamed, Alexander; Granat, Anna; Stanczyk, Frank Z; Mishell, Daniel R

2013-06-01

This study analyzes levels of progesterone, estradiol, norethindrone (NET) and ethinyl estradiol (EE) in serum and levels of NET in cervical mucus on the last day of the hormone-free interval (HFI) in users of 24/4 [norethindrone acetate (NETA)/EE-24] vs. 21/7 (NETA/EE-21) regimens. This was a randomized controlled, crossover, equivalency trial. Subjects were randomized to receive NETA/EE-24 or NETA/EE-21 for 2 months and then switched between study drugs. Blood and cervical mucus samples were obtained on Days 12-16 and on the last day of the HFI. From April 2010 to November 2011, 32 subjects were enrolled with 18 subjects completing all study visits. There were no statistically significant differences in either day 12-16 (p=.54) or last hormone-free day (p=.33) cervical mucus NET concentrations between the regimens. On the last day of the HFI, median serum progesterone levels did not differ significantly; however, users of NETA/EE-24 had higher levels of serum NET (p<.001) and users of NETA/EE-21 had higher levels of serum estradiol (p=.01). This data supports the fact that inhibition of the pituitary-ovarian axis occurs during oral contraceptive use and during the HFI. We demonstrated that a reduced HFI of 4 days resulted in better suppression of the ovarian hormone production, thereby reducing the risk of ovulation and potential contraceptive failure. Copyright © 2013 Elsevier Inc. All rights reserved.

Make Mine a Metasearcher, Please!

ERIC Educational Resources Information Center

Repman, Judi; Carlson, Randal D.

2000-01-01

Describes metasearch tools and explains their value in helping library media centers improve students' Web searches. Discusses Boolean queries and the emphasis on speed at the expense of comprehensiveness; and compares four metasearch tools, including the number of search engines consulted, user control, and databases included. (LRW)

Boolean Approaches in Digital Diagnosis

DTIC Science & Technology

1989-12-04

Automation Conference, pages 64-70, 1983. 16. Barry W. Johnson. Design and A nalysis of Fault-Tolerant Digital Systems. Addison- Wesley Publishing...Mitchell. On a new algebra of logic. In C.S. Peirce, edhitor, Studies in Logic. Little, Brown. Boston. 1883. 2:3. Roger S. Pressman . Softwrare Engineering

Presentation of Repeated Phrases in a Computer-Assisted Abstracting Tool Kit.

ERIC Educational Resources Information Center

Craven, Timothy C.

2001-01-01

Discusses automatic indexing methods and describes the development of a prototype computerized abstractor's assistant. Highlights include the text network management system, TEXNET; phrase selection that follows indexing; phrase display, including Boolean capabilities; results of preliminary testing; and availability of TEXNET software. (LRW)

Stochastic Pseudo-Boolean Optimization

DTIC Science & Technology

2011-07-31

Right-Hand Side,” 2009 IN- FORMS Annual Meeting, San Diego, CA, October 11-14, 2009. 113 References [1] A.-Ghouila-Houri. Caracterisation des matrices...Optimization, 10:7–21, 2005. [30] P. Camion. Caracterisation des matrices unimodulaires. Cahiers Centre Etudes Rech., 5(4), 1963. [31] P. Camion

Order or chaos in Boolean gene networks depends on the mean fraction of canalizing functions

NASA Astrophysics Data System (ADS)

Karlsson, Fredrik; Hörnquist, Michael

2007-10-01

We explore the connection between order/chaos in Boolean networks and the naturally occurring fraction of canalizing functions in such systems. This fraction turns out to give a very clear indication of whether the system possesses ordered or chaotic dynamics, as measured by Derrida plots, and also the degree of order when we compare different networks with the same number of vertices and edges. By studying also a wide distribution of indegrees in a network, we show that the mean probability of canalizing functions is a more reliable indicator of the type of dynamics for a finite network than the classical result on stability relating the bias to the mean indegree. Finally, we compare by direct simulations two biologically derived networks with networks of similar sizes but with power-law and Poisson distributions of indegrees, respectively. The biologically motivated networks are not more ordered than the latter, and in one case the biological network is even chaotic while the others are not.

Two classes of ODE models with switch-like behavior.

PubMed

Just, Winfried; Korb, Mason; Elbert, Ben; Young, Todd

2013-12-01

In cases where the same real-world system can be modeled both by an ODE system ⅅ and a Boolean system , it is of interest to identify conditions under which the two systems will be consistent, that is, will make qualitatively equivalent predictions. In this note we introduce two broad classes of relatively simple models that provide a convenient framework for studying such questions. In contrast to the widely known class of Glass networks, the right-hand sides of our ODEs are Lipschitz-continuous. We prove that if has certain structures, consistency between ⅅ and is implied by sufficient separation of time scales in one class of our models. Namely, if the trajectories of are "one-stepping" then we prove a strong form of consistency and if has a certain monotonicity property then there is a weaker consistency between ⅅ and . These results appear to point to more general structure properties that favor consistency between ODE and Boolean models.

Evolution of Boolean networks under selection for a robust response to external inputs yields an extensive neutral space

NASA Astrophysics Data System (ADS)

Szejka, Agnes; Drossel, Barbara

2010-02-01

We study the evolution of Boolean networks as model systems for gene regulation. Inspired by biological networks, we select simultaneously for robust attractors and for the ability to respond to external inputs by changing the attractor. Mutations change the connections between the nodes and the update functions. In order to investigate the influence of the type of update functions, we perform our simulations with canalizing as well as with threshold functions. We compare the properties of the fitness landscapes that result for different versions of the selection criterion and the update functions. We find that for all studied cases the fitness landscape has a plateau with maximum fitness resulting in the fact that structurally very different networks are able to fulfill the same task and are connected by neutral paths in network (“genotype”) space. We find furthermore a connection between the attractor length and the mutational robustness, and an extremely long memory of the initial evolutionary stage.

Comparison of Seven Methods for Boolean Factor Analysis and Their Evaluation by Information Gain.

PubMed

Frolov, Alexander A; Húsek, Dušan; Polyakov, Pavel Yu

2016-03-01

An usual task in large data set analysis is searching for an appropriate data representation in a space of fewer dimensions. One of the most efficient methods to solve this task is factor analysis. In this paper, we compare seven methods for Boolean factor analysis (BFA) in solving the so-called bars problem (BP), which is a BFA benchmark. The performance of the methods is evaluated by means of information gain. Study of the results obtained in solving BP of different levels of complexity has allowed us to reveal strengths and weaknesses of these methods. It is shown that the Likelihood maximization Attractor Neural Network with Increasing Activity (LANNIA) is the most efficient BFA method in solving BP in many cases. Efficacy of the LANNIA method is also shown, when applied to the real data from the Kyoto Encyclopedia of Genes and Genomes database, which contains full genome sequencing for 1368 organisms, and to text data set R52 (from Reuters 21578) typically used for label categorization.

Pseudo-random properties of a linear congruential generator investigated by b-adic diaphony

NASA Astrophysics Data System (ADS)

Stoev, Peter; Stoilova, Stanislava

2017-12-01

In the proposed paper we continue the study of the diaphony, defined in b-adic number system, and we extend it in different directions. We investigate this diaphony as a tool for estimation of the pseudorandom properties of some of the most used random number generators. This is done by evaluating the distribution of specially constructed two-dimensional nets on the base of the obtained random numbers. The aim is to see how the generated numbers are suitable for calculations in some numerical methods (Monte Carlo etc.).

Sparse Forward-Backward for Fast Training of Conditional Random Fields

DTIC Science & Technology

2006-01-01

knowledge- based systems. Proceedings of the 6th Conference on Uncertainty in Artifcial Intelligence , 1990. Appears to be unavailable. [4] Michael I...response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and...task, the NetTalk text-to-speech data set [5], we can now train a conditional random field (CRF) in about 6 hours for which training previously

The net effects of the Project NetWork return-to-work case management experiment on participant earnings, benefit receipt, and other outcomes.

PubMed

Kornfeld, R; Rupp, K

2000-01-01

The Social Security Administration (SSA) initiated Project NetWork in 1991 to test case management as a means of promoting employment among persons with disabilities. The demonstration, which targeted Social Security Disability Insurance (DI) beneficiaries and Supplemental Security Income (SSI) applicants and recipients, offered intensive outreach, work-incentive waivers, and case management/referral services. Participation in Project NetWork was voluntary. Volunteers were randomly assigned to the "treatment" group or the "control" group. Those assigned to the treatment group met individually with a case or referral manager who arranged for rehabilitation and employment services, helped clients develop an individual employment plan, and provided direct employment counseling services. Volunteers assigned to the control group could not receive services from Project NetWork but remained eligible for any employment assistance already available in their communities. For both treatment and control groups, the demonstration waived specific DI and SSI program rules considered to be work disincentives. The experimental impact study thus measures the incremental effects of case and referral management services. The eight demonstration sites were successful in implementing the experimental design roughly as planned. Project NetWork staff were able to recruit large numbers of participants and to provide rehabilitation and employment services on a substantial scale. Most of the sites easily reached their enrollment targets and were able to attract volunteers with demographic characteristics similar to those of the entire SSI and DI caseload and a broad range of moderate and severe disabilities. However, by many measures, volunteers were generally more "work-ready" than project eligible in the demonstration areas who did not volunteer to receive NetWork services. Project NetWork case management increased average annual earnings by $220 per year over the first 2 years following random assignment. This statistically significant impact, an approximate 11-percent increase in earnings, is based on administrative data on earnings. For about 70 percent of sample members, a third year of followup data was available. For this limited sample, the estimated effect of Project NetWork on annual earnings declined to roughly zero in the third followup year. The findings suggest that the increase in earnings may have been short-lived and may have disappeared by the time Project NetWork services ended. Project NetWork did not reduce reliance on SSI or DI benefits by statistically significant amounts over the 30-42 month followup period. The services provided by Project NetWork thus did not reduce overall SSI and DI caseloads or benefits by substantial amounts, especially given that only about 5 percent of the eligible caseload volunteered to participate in Project NetWork. Project NetWork produced modest net benefits to persons with disabilities and net costs to taxpayers. Persons with disabilities gained mainly because the increases in their earnings easily outweighed the small (if any) reduction in average SSI and DI benefits. For SSA and the federal government as a whole, the costs of Project NetWork were not sufficiently offset by increases in tax receipts resulting from increased earnings or reductions in average SSI and DI benefits. The modest net benefits of Project NetWork to persons with disabilities are encouraging. How such benefits of an experimental intervention should be weighed against costs of taxpayers depends on value judgments of policymakers. Because different case management projects involve different kinds of services, these results cannot be directly generalized to other case management interventions. They are nevertheless instructive for planning new initiatives. Combining case and referral management services with various other interventions, such as longer term financial support for work or altered provider incentives, could produc

Willingness to pay for insecticide-treated nets in Berehet District, Amhara Region, Northern Ethiopia: implication of social marketing.

PubMed

Aleme, Adisu; Girma, Eshetu; Fentahun, Netsanet

2014-01-01

Understanding the feasibility of achieving widespread coverage with Insecticide-Treated Nets has to be preceded by learning how people value the Insecticide-Treated Nets and estimating the potential demand and willingness to pay so that sustainability of the intervention can be assured. The objective of this study was to determine willingness to pay for Insecticide-Treated Nets among households in Berehet District, Northern Ethiopia. A community-based cross-sectional study was conducted using both quantitative and qualitative methods in five randomly selected Kebeles from January-February 2012. Open ended contingent valuation technique with follow-up method was used. Qualitative data were collected through focus group discussions and observation methods. Binary logistic regression was used to determine the association between dependent and independent variables. The average number of individuals per Insecticide-Treated Nets was 3.83. Nearly 68.5% persons had willingness to buy Insecticide-Treated Nets if they have access to these Nets. The median maximum price a person is willingness to pay for blue rectangular Insecticide-Treated Net was 20 ETB. People had willingness to pay 30 ETB for blue and white conical insecticide-treated nets. Working on knowledge of malaria (OR=0.68, CI (0.47, 0.98; p<0.05), perceived benefit of Insecticide-Treated Nets (OR=0.28, CI (0.2-0.4; p<0.05), perceived susceptibility (OR=0.64(0.44-0.93; p<0.05) and perceived severity of malaria (OR=0.65(0.47-0.91, p<0.05) had significant association with a willingness to pay Insecticide-Treated Nets. Respondents who prefer Kebele/place/ to buy Insecticide-Treated Net for rectangular shape had a significant association with a willingness to pay for Insecticide-Treated Nets (OR=1.92, CI= 1.07-3.92). Promotions, products, price and place had significant association with willingness to pay for Insecticide-Treated Nets. Designing a social marketing strategy helps ensure sustainable supply of Insecticide-Treated Nets and proper use of Insecticide-Treated Nets.

Modeling Nuclear Receptor-Mediated Activity and Hepatotoxicity with Boolean Networks

EPA Science Inventory

Predicting the human health risk of chronic exposure to environmental contaminants remains an open problem. Chronic exposure to a wide array of chemicals – e.g., conazoles, perfluourinated chemicals and phthalates – has been associated with a range of hepatic lesions in rodents t...

Guide to Human Factors Information Sources.

DTIC Science & Technology

1984-11-01

intermediary, a computer search is sometimes unnecessary. A lucid way of presenting a search objective is either by Boolean (and/or) expressions or by Venn...1965). Human factors evaluation in system development. New York: John Wiley & Sons. 56. Murray, E. J. (1965). Sleep, dreams , and arousal. New York

Probabilistic Relational Structures and Their Applications

ERIC Educational Resources Information Center

Domotor, Zoltan

The principal objects of the investigation reported were, first, to study qualitative probability relations on Boolean algebras, and secondly, to describe applications in the theories of probability logic, information, automata, and probabilistic measurement. The main contribution of this work is stated in 10 definitions and 20 theorems. The basic…

Massive Query Resolution for Rapid Selective Dissemination of Information.

ERIC Educational Resources Information Center

Cohen, Jonathan D.

1999-01-01

Outlines an efficient approach to performing query resolution which, when matched with a keyword scanner, offers rapid selecting and routing for massive Boolean queries, and which is suitable for implementation on a desktop computer. Demonstrates the system's operation with large examples in a practical setting. (AEF)

Inference of gene regulatory networks from time series by Tsallis entropy

PubMed Central

2011-01-01

Background The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 ≤ q ≤ 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/. PMID:21545720

Norepinephrine transporter inhibition alters the hemodynamic response to hypergravitation.

PubMed

Strempel, Sebastian; Schroeder, Christoph; Hemmersbach, Ruth; Boese, Andrea; Tank, Jens; Diedrich, André; Heer, Martina; Luft, Friedrich C; Jordan, Jens

2008-03-01

Sympathetically mediated tachycardia and vasoconstriction maintain blood pressure during hypergravitational stress, thereby preventing gravitation-induced loss of consciousness. Norepinephrine transporter (NET) inhibition prevents neurally mediated (pre)syncope during gravitational stress imposed by head-up tilt testing. Thus it seems reasonable that NET inhibition could increase tolerance to hypergravitational stress. We performed a double-blind, randomized, placebo-controlled crossover study in 11 healthy men (26 +/- 1 yr, body mass index 24 +/- 1 kg/m2), who ingested the selective NET inhibitor reboxetine (4 mg) or matching placebo 25, 13, and 1 h before testing on separate days. We monitored heart rate, blood pressure, and thoracic impedance in three different body positions (supine, seated, standing) and during a graded centrifuge run (incremental steps of 0.5 g for 3 min each, up to a maximal vertical acceleration load of 3 g). NET inhibition increased supine blood pressure and heart rate. With placebo, blood pressure increased in the seated position and was well maintained during standing. However, with NET inhibition, blood pressure decreased in the seated and standing position. During hypergravitation, blood pressure increased in a graded fashion with placebo. With NET inhibition, the increase in blood pressure during hypergravitation was profoundly diminished. Conversely, the tachycardic responses to sitting, standing, and hypergravitation all were greatly increased with NET inhibition. In contrast to our expectation, short-term NET inhibition did not improve tolerance to hypergravitation. Redistribution of sympathetic activity to the heart or changes in baroreflex responses could explain the excessive tachycardia that we observed.

Quantification of nonenhancing tumor burden in gliomas using effective T2 maps derived from dual echo turbo spin echo MRI

PubMed Central

Ellingson, Benjamin M.; Lai, Albert; Nguyen, Huytram N.; Nghiemphu, Phioanh L.; Pope, Whitney B.; Cloughesy, Timothy F.

2015-01-01

Purpose Evaluation of nonenhancing tumor (NET) burden is an important, yet challenging part of brain tumor response assessment. The current study focuses on using dual echo turbo spin echo MRI as a means of quickly estimating tissue T2, which can be used to objectively define NET burden. Experimental Design A series of experiments were performed to establish the use of T2 maps for defining NET burden. First, variation in T2 was determined using ACR water phantoms in 16 scanners evaluated over 3 years. Next, sensitivity and specificity of T2 maps for delineating NET from other tissues was examined. Then, T2-defined NET was used to predict survival in separate subsets of glioblastoma patients treated with radiation therapy, concurrent radiation and chemotherapy, or bevacizumab at recurrence. Results Variability in T2 in the ACR phantom was 3-5%. In training data, ROC analysis suggested that 125ms < T2 < 250ms could delineate NET with a sensitivity >90% and specificity >65%. Using this criterion, NET burden after completion of radiation therapy alone, or concurrent radiation therapy and chemotherapy, was shown to be predictive of survival (Cox, P<0.05), and the change in NET volume before and after bevacizumab therapy in recurrent glioblastoma was also a predictive of survival (P<0.05). Conclusions T2 maps using dual echo data are feasible, stable, and can be used to objectively define NET burden for use in brain tumor characterization, prognosis, and response assessment. The use of effective T2 maps for defining NET burden should be validated in a randomized clinical trial. PMID:25901082

Permethrin-impregnated bed nets for the prevention of malaria in schoolchildren on the Thai-Burmese border.

PubMed

Luxemburger, C; Perea, W A; Delmas, G; Pruja, C; Pecoul, B; Moren, A

1994-01-01

A double-blind controlled trial was undertaken from August 1990 to February 1991 among Karen children on the Thai-Burmese border to evaluate the effects on malaria incidence and prevalence of permethrin-treated bed nets. Three hundred and fifty schoolchildren, aged 4 to 15 years, were allocated at random to receive either a permethrin-impregnated net or a non-treated net. The incidence of malaria infections, confirmed by a blood film, was assessed during 6 months. Three surveys were conducted, on admission and 3 and 6 months later, to measure the prevalence of infections and spleen rates. Compliance was assessed by monthly home visiting. The use of permethrin-treated bed nets reduced the number of parasitaemic Plasmodium falciparum infections by 38% and the number of symptomatic episodes by 42%. The number of P. vivax malaria attacks was similar in each group. The prevalence of positive blood films in the 2 groups did not change significantly during the study. A reduction in spleen rate by 50% in both groups at the end of the study period could not be related to the overall use of nets. Compliance was high and no side-effect was reported. The long-term effects on morbidity and mortality need to be assessed after distribution of permethrin treated bed nets at the village level.

Markets, voucher subsidies and free nets combine to achieve high bed net coverage in rural Tanzania.

PubMed

Khatib, Rashid A; Killeen, Gerry F; Abdulla, Salim M K; Kahigwa, Elizeus; McElroy, Peter D; Gerrets, Rene P M; Mshinda, Hassan; Mwita, Alex; Kachur, S Patrick

2008-06-02

Tanzania has a well-developed network of commercial ITN retailers. In 2004, the government introduced a voucher subsidy for pregnant women and, in mid 2005, helped distribute free nets to under-fives in small number of districts, including Rufiji on the southern coast, during a child health campaign. Contributions of these multiple insecticide-treated net delivery strategies existing at the same time and place to coverage in a poor rural community were assessed. Cross-sectional household survey in 6,331 members of randomly selected 1,752 households of 31 rural villages of Demographic Surveillance System in Rufiji district, Southern Tanzania was conducted in 2006. A questionnaire was administered to every consenting respondent about net use, treatment status and delivery mechanism. Net use was 62.7% overall, 87.2% amongst infants (0 to 1 year), 81.8% amongst young children (>1 to 5 years), 54.5% amongst older children (6 to 15 years) and 59.6% amongst adults (>15 years). 30.2% of all nets had been treated six months prior to interview. The biggest source of nets used by infants was purchase from the private sector with a voucher subsidy (41.8%). Half of nets used by young children (50.0%) and over a third of those used by older children (37.2%) were obtained free of charge through the vaccination campaign. The largest source of nets amongst the population overall was commercial purchase (45.1% use) and was the primary means for protecting adults (60.2% use). All delivery mechanisms, especially sale of nets at full market price, under-served the poorest but no difference in equity was observed between voucher-subsidized and freely distributed nets. All three delivery strategies enabled a poor rural community to achieve net coverage high enough to yield both personal and community level protection for the entire population. Each of them reached their relevant target group and free nets only temporarily suppressed the net market, illustrating that in this setting that these are complementary rather than mutually exclusive approaches.

Statistical-learning strategies generate only modestly performing predictive models for urinary symptoms following external beam radiotherapy of the prostate: A comparison of conventional and machine-learning methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yahya, Noorazrul, E-mail: noorazrul.yahya@research.uwa.edu.au; Ebert, Martin A.; Bulsara, Max

Purpose: Given the paucity of available data concerning radiotherapy-induced urinary toxicity, it is important to ensure derivation of the most robust models with superior predictive performance. This work explores multiple statistical-learning strategies for prediction of urinary symptoms following external beam radiotherapy of the prostate. Methods: The performance of logistic regression, elastic-net, support-vector machine, random forest, neural network, and multivariate adaptive regression splines (MARS) to predict urinary symptoms was analyzed using data from 754 participants accrued by TROG03.04-RADAR. Predictive features included dose-surface data, comorbidities, and medication-intake. Four symptoms were analyzed: dysuria, haematuria, incontinence, and frequency, each with three definitions (grade ≥more » 1, grade ≥ 2 and longitudinal) with event rate between 2.3% and 76.1%. Repeated cross-validations producing matched models were implemented. A synthetic minority oversampling technique was utilized in endpoints with rare events. Parameter optimization was performed on the training data. Area under the receiver operating characteristic curve (AUROC) was used to compare performance using sample size to detect differences of ≥0.05 at the 95% confidence level. Results: Logistic regression, elastic-net, random forest, MARS, and support-vector machine were the highest-performing statistical-learning strategies in 3, 3, 3, 2, and 1 endpoints, respectively. Logistic regression, MARS, elastic-net, random forest, neural network, and support-vector machine were the best, or were not significantly worse than the best, in 7, 7, 5, 5, 3, and 1 endpoints. The best-performing statistical model was for dysuria grade ≥ 1 with AUROC ± standard deviation of 0.649 ± 0.074 using MARS. For longitudinal frequency and dysuria grade ≥ 1, all strategies produced AUROC>0.6 while all haematuria endpoints and longitudinal incontinence models produced AUROC<0.6. Conclusions: Logistic regression and MARS were most likely to be the best-performing strategy for the prediction of urinary symptoms with elastic-net and random forest producing competitive results. The predictive power of the models was modest and endpoint-dependent. New features, including spatial dose maps, may be necessary to achieve better models.« less

Dataflow Computation for the J-Machine

DTIC Science & Technology

1990-06-01

MOVE 8. 1 CALL ClrTVCTO1 ;((:LkBEL (:LITERAL (:SYIBOL : BBD -IF-4)))) ZIDIF.4: ROVE [1,133, 3.3 ROV 13. A2 ((:TERIXATM)) SUSPEND ;((:LAEL (:LITBUAL...deftostant syn 0) (detconstant int-tag ’int) (detconatant Int 1) (detconstant id-tag ’ td ) (defconstant td 9) (Aotconstaut boolean-tag lbool

Exploiting the Maximum Entropy Principle to Increase Retrieval Effectiveness.

ERIC Educational Resources Information Center

Cooper, William S.

1983-01-01

Presents information retrieval design approach in which queries of computer-based system consist of sets of terms, either unweighted or weighted with subjective term precision estimates, and retrieval outputs ranked by probability of usefulness estimated by "maximum entropy principle." Boolean and weighted request systems are discussed.…

"Back-Stage" Dissent: Student Twitter Use Addressing Instructor Ideology

ERIC Educational Resources Information Center

Linvill, Darren L.; Boatwright, Brandon C.; Grant, Will J.

2018-01-01

In this content analysis, we explored how students address instructor ideology in the university classroom through the social media platform Twitter. We employed Boolean search operators through Salesforce Marketing Cloud Radian6 software to gather tweets and identified English language tweets by how students referenced their instructor's…

Optimization of digital designs

NASA Technical Reports Server (NTRS)

Miles, Lowell H. (Inventor); Whitaker, Sterling R. (Inventor)

2009-01-01

An application specific integrated circuit is optimized by translating a first representation of its digital design to a second representation. The second representation includes multiple syntactic expressions that admit a representation of a higher-order function of base Boolean values. The syntactic expressions are manipulated to form a third representation of the digital design.

Topology of Document Retrieval Systems.

ERIC Educational Resources Information Center

Everett, Daniel M.; Cater, Steven C.

1992-01-01

Explains the use of a topological structure to examine the closeness between documents in retrieval systems and analyzes the topological structure of a vector-space model, a fuzzy-set model, an extended Boolean model, a probabilistic model, and a TIRS (Topological Information Retrieval System) model. Proofs for the results are appended. (17…

Must "Hard Problems" Be Hard?

ERIC Educational Resources Information Center

Kolata, Gina

1985-01-01

To determine how hard it is for computers to solve problems, researchers have classified groups of problems (polynomial hierarchy) according to how much time they seem to require for their solutions. A difficult and complex proof is offered which shows that a combinatorial approach (using Boolean circuits) may resolve the problem. (JN)

The Impact of Text Browsing on Text Retrieval Performance.

ERIC Educational Resources Information Center

Bodner, Richard C.; Chignell, Mark H.; Charoenkitkarn, Nipon; Golovchinsky, Gene; Kopak, Richard W.

2001-01-01

Compares empirical results from three experiments using Text Retrieval Conference (TREC) data and search topics that involved three different user interfaces. Results show that marking Boolean queries on text, which encourages browsing, and hypertext interfaces to text retrieval systems can benefit recall and can also benefit novice users.…

LISA's Move from SilverPlatter to Bowker--Looking at the Interface.

ERIC Educational Resources Information Center

Stein, Jonathan

1994-01-01

Compares LISA (Library and Information Science Abstracts) on SilverPlatter's CD-ROM with its replacement version, Bowker-Saur's LISA Plus. Features reviewed include entry to the databases; use of Boolean search facilities; indexes and browsing; displaying and printing records; subsidiary functions; on-screen help; and interfaces. (Contains eight…

Library Dream Machines: Helping Students Master Super Online Catalogs.

ERIC Educational Resources Information Center

Webb, T. D.

1992-01-01

Describes how automation has transformed the library and how super-catalogs have affected the process of doing research. Explains how faculty and librarians can work together to help students to use the available databases effectively, by teaching them Boolean logic, standard record formats, filing rules, etc. (DMM)

Fundamentals of Digital Logic.

ERIC Educational Resources Information Center

Noell, Monica L.

This course is designed to prepare electronics personnel for further training in digital techniques, presenting need to know information that is basic to any maintenance course on digital equipment. It consists of seven study units: (1) binary arithmetic; (2) boolean algebra; (3) logic gates; (4) logic flip-flops; (5) nonlogic circuits; (6)…

Conducting a Web Search.

ERIC Educational Resources Information Center

Miller-Whitehead, Marie

Keyword and text string searches of online library catalogs often provide different results according to library and database used and depending upon how books and journals are indexed. For this reason, online databases such as ERIC often provide tutorials and recommendations for searching their site, such as how to use Boolean search strategies.…

Community Information Centers and the Computer.

ERIC Educational Resources Information Center

Carroll, John M.; Tague, Jean M.

Two computer data bases have been developed by the Computer Science Department at the University of Western Ontario for "Information London," the local community information center. One system, called LONDON, permits Boolean searches of a file of 5,000 records describing human service agencies in the London area. The second system,…

Cryptographic Properties of the Hidden Weighted Bit Function

DTIC Science & Technology

2013-12-23

valid OMB control number. 1. REPORT DATE 23 DEC 2013 2. REPORT TYPE 3. DATES COVERED 00-00-2013 to 00-00-2013 4. TITLE AND SUBTITLE...K. Feng, An Infinite Class of Balanced Vectorial Boolean Functions with Optimum Algebraic Immunity and Good Nonlinearity, in: IWCC 2009, In: LNCS

Assessing Institutional Ineffectiveness: A Strategy for Improvement.

ERIC Educational Resources Information Center

Cameron, Kim S.

1984-01-01

Based on the theory that institutional change and improvement are motivated more by knowledge of problems than by knowledge of successes, a fault tree analysis technique using Boolean logic for assessing institutional ineffectiveness by determining weaknesses in the system is presented. Advantages and disadvantages of focusing on weakness rather…

Subject Retrieval from Full-Text Databases in the Humanities

ERIC Educational Resources Information Center

East, John W.

2007-01-01

This paper examines the problems involved in subject retrieval from full-text databases of secondary materials in the humanities. Ten such databases were studied and their search functionality evaluated, focusing on factors such as Boolean operators, document surrogates, limiting by subject area, proximity operators, phrase searching, wildcards,…

Kolmogorov proof of the Clauser, Horne, Shimony and Holt inequalities

NASA Astrophysics Data System (ADS)

Revzen, M.

Boolean logic is used to prove the CHSH inequalities. The proof elucidates the connection between Einstein elements of reality and quantum non-locality. The violation of the CHSH inequality by quantum theory is discussed and the two-stage view of quantum measurement relevance to incompatible observables is outlined.

Petri net modelling of buffers in automated manufacturing systems.

PubMed

Zhou, M; Dicesare, F

1996-01-01

This paper presents Petri net models of buffers and a methodology by which buffers can be included in a system without introducing deadlocks or overflows. The context is automated manufacturing. The buffers and models are classified as random order or order preserved (first-in-first-out or last-in-first-out), single-input-single-output or multiple-input-multiple-output, part type and/or space distinguishable or indistinguishable, and bounded or safe. Theoretical results for the development of Petri net models which include buffer modules are developed. This theory provides the conditions under which the system properties of boundedness, liveness, and reversibility are preserved. The results are illustrated through two manufacturing system examples: a multiple machine and multiple buffer production line and an automatic storage and retrieval system in the context of flexible manufacturing.

An Economical Analytical Equation for the Integrated Vertical Overlap of Cumulus and Stratus

NASA Astrophysics Data System (ADS)

Park, Sungsu

2018-03-01

By extending the previously proposed heuristic parameterization, the author derived an analytical equation computing the overlap areas between the precipitation (or radiation) areas and the cloud areas in a cloud system consisting of cumulus and stratus. The new analytical equation is accurate and much more efficient than the previous heuristic equation, which suffers from the truncation error in association with the digitalization of the overlap areas. Global test simulations with the new analytical formula in an offline mode showed that the maximum cumulus overlap simulates more surface precipitation flux than the random cumulus overlap. On the other hand, the maximum stratus overlap simulates less surface precipitation flux than random stratus overlap, which is due to the increase in the evaporation rate of convective precipitation from the random to maximum stratus overlap. The independent precipitation approximation (IPA) marginally decreases the surface precipitation flux, implying that IPA works well with other parameterizations. In contrast to the net production rate of precipitation and surface precipitation flux that increase when the cumulus and stratus are maximally and randomly overlapped, respectively, the global mean net radiative cooling and longwave cloud radiative forcing (LWCF) increase when the cumulus and stratus are randomly overlapped. On the global average, the vertical cloud overlap exerts larger impacts on the precipitation flux than on the radiation flux. The radiation scheme taking the subgrid variability of water vapor between the cloud and clear portions into account substantially increases the global mean LWCF in tropical deep convection and midlatitude storm track regions.

Net macromineral requirements in male and female Saanen goats.

PubMed

Santos Neto, J M; Resende, K T; Teixeira, I A M A; Vargas, J A C; Lima, A R C; Leite, R F; Figueiredo, F O M; Tedeschi, L O; Fernandes, M H M R

2016-08-01

These experiments estimated Ca, P, Mg, K, and Na requirements of intact male, castrated male, and female Saanen goats. Two experiments were performed: one to determine the net macromineral requirements for maintenance (Exp. 1) and another to determine net macromineral requirements for growth (Exp. 2). In Exp. 1, 75 goats (26 intact males, 25 castrated males, and 24 females) with initial BW (iBW) of 15.76 ± 0.10 kg were used. These animals were divided in 2 groups: baseline animals and pair-fed animals. Twenty-one goats (8 intact males, 7 castrated males, and 6 females) were slaughtered (16.6 ± 0.96 kg BW) at the beginning of the experiment to be used as the baseline group. The 54 remaining goats (18 intact males, 18 castrated males, and 18 females) were pair fed in 6 blocks of 3 goats per sex. The goats within each block were then randomly allocated to 1 of 3 levels of intake: ad libitum, restricted fed to 75% of the ad libitum intake, and restricted fed to 50% of ad libitum intake. When the animal fed ad libitum reached 31.2 ± 0.58 kg BW, it and the other goats from the same block were slaughtered. The effects of sex and level of intake were evaluated in a split-plot design, where sex was the main plot observation and level of intake was the subplot. Daily net macromineral requirements for maintenance did not differ among the sexes ( > 0.05), and the average values obtained were 35.4 mg Ca, 24.7 mg P, 2.5 mg Mg, 5.0 mg K, and 3.30 mg Na per kg BW∙d. The net requirements for growth in Exp. 2 were obtained using 58 goats (20 intact males, 20 castrated males, and 18 females) with 15.8 ± 0.11 kg iBW, all fed ad libitum. These animals were assigned in a completely randomized design and allocated in 3 slaughter weight groups: 16.6 ± 0.96, 23.1 ± 1.33, and 31.2 ± 0.58 kg BW. The net Ca, P, and Mg requirements for growth were not different among the sexes ( > 0.05). There was a sex effect on net K and Na requirements for growth ( < 0.05). The net K requirements for growth (g/kg ADG) of intact males were greater ( = 0.03) and increased approximately 16%, whereas females and castrated males decreased approximately 11% as BW increased from 15 to 30 kg BW. The net Na requirements for growth (g/kg ADG) increased 9.5% for intact males and decreased 22% for females when the goats grew from 15 to 30 kg BW. Sex, therefore, affects net K and Na requirements for growth, but it does not affect net macromineral requirements for maintenance in Saanen goats.

A multispin algorithm for the Kob-Andersen stochastic dynamics on regular lattices

NASA Astrophysics Data System (ADS)

Boccagna, Roberto

2017-07-01

The aim of the paper is to propose an algorithm based on the Multispin Coding technique for the Kob-Andersen glassy dynamics. We first give motivations to speed up the numerical simulation in the context of spin glass models [M. Mezard, G. Parisi, M. Virasoro, Spin Glass Theory and Beyond (World Scientific, Singapore, 1987)]; after defining the Markovian dynamics as in [W. Kob, H.C. Andersen, Phys. Rev. E 48, 4364 (1993)] as well as the related interesting observables, we extend it to the more general framework of random regular graphs, listing at the same time some known analytical results [C. Toninelli, G. Biroli, D.S. Fisher, J. Stat. Phys. 120, 167 (2005)]. The purpose of this work is a dual one; firstly, we describe how bitwise operators can be used to build up the algorithm by carefully exploiting the way data are stored on a computer. Since it was first introduced [M. Creutz, L. Jacobs, C. Rebbi, Phys. Rev. D 20, 1915 (1979); C. Rebbi, R.H. Swendsen, Phys. Rev. D 21, 4094 (1980)], this technique has been widely used to perform Monte Carlo simulations for Ising and Potts spin systems; however, it can be successfully adapted to more complex systems in which microscopic parameters may assume boolean values. Secondly, we introduce a random graph in which a characteristic parameter allows to tune the possible transition point. A consistent part is devoted to listing the numerical results obtained by running numerical simulations.

Estimation of insecticide persistence, biological activity and mosquito resistance to PermaNet® 2 long-lasting insecticidal nets over three to 32 months of use in Ethiopia.

PubMed

Anshebo, Gedeon Yohannes; Graves, Patricia M; Smith, Stephen C; Wills, Aprielle B; Damte, Mesele; Endeshaw, Tekola; Shargie, Estifanos Biru; Gebre, Teshome; Mosher, Aryc W; Patterson, Amy E; Emerson, Paul M

2014-03-06

Information is needed on the expected durability of insecticidal nets under operational conditions. The persistence of insecticidal efficacy is important to estimate the median serviceable life of nets under field conditions and to plan for net replacement. Deltamethrin residue levels were evaluated by the proxy method of X-ray fluorescence spectrometry on 189 nets used for three to six months from nine sites, 220 nets used for 14-20 months from 11 sites, and 200 nets used for 26-32 months from ten sites in Ethiopia. A random sample of 16.5-20% of nets from each time period (total 112 of 609 nets) were tested by bioassay with susceptible mosquitoes, and nets used for 14-20 months and 26-32 months were also tested with wild caught mosquitoes. Mean insecticide levels estimated by X-ray fluorescence declined by 25.9% from baseline of 66.2 (SD 14.6) mg/m2 at three to six months to 44.1 (SD 21.2) mg/m2 at 14-20 months and by 30.8% to 41.1 (SD 18.9) mg/m2 at 26-32 months. More than 95% of nets retained greater than 10 mg/m2 of deltamethrin and over 79% had at least 25 mg/m2 at all time periods. By bioassay with susceptible Anopheles, mortality averaged 89.0% on 28 nets tested at three to six months, 93.3% on 44 nets at 14-20 months and 94.1% on 40 nets at 26-32 months. With wild caught mosquitoes, mortality averaged 85.4% (range 79.1 to 91.7%) at 14-20 months but had dropped significantly to 47.2% (39.8 to 54.7%) at 26-32 months. Insecticide residue level, as estimated by X-ray fluorescence, declined by about one third between three and six months and 14-20 months, but remained relatively stable and above minimum requirements thereafter up to 26-32 months. The insecticidal activity of PermaNet® 2.0 long-lasting insecticidal nets in the specified study area may be considered effective to susceptible mosquitoes at least for the duration indicated in this study (32 months). However, results indicated that resistance in the wild population is already rendering nets with optimum insecticide concentrations less effective in practice.

The Relationship of Financial Pressures and Community Characteristics to Closure of Private Safety Net Clinics.

PubMed

Li, Suhui; Dor, Avi; Pines, Jesse M; Zocchi, Mark S; Hsia, Renee Y

2016-10-01

In order to better understand what threatens vulnerable populations' access to primary care, it is important to understand the factors associated with closing safety net clinics. This article examines how a clinic's financial position, productivity, and community characteristics are associated with its risk of closure. We examine patterns of closures among private-run primary care clinics (PCCs) in California between 2006 and 2012. We use a discrete-time proportional hazard model to assess relative hazard ratios of covariates, and a random-effect hazard model to adjust for unobserved heterogeneity among PCCs. We find that lower net income from patient care, smaller amount of government grants, and lower productivity were associated with significantly higher risk of PCC closure. We also find that federally qualified health centers and nonfederally qualified health centers generally faced the same risk factors of closure. These results underscore the critical role of financial incentives in the long-term viability of safety net clinics. © The Author(s) 2015.

Outcome in early-onset fetal growth restriction is best combining computerized fetal heart rate analysis with ductus venosus Doppler: insights from the Trial of Umbilical and Fetal Flow in Europe.

PubMed

Frusca, Tiziana; Todros, Tullia; Lees, Christoph; Bilardo, Caterina M

2018-02-01

Early-onset fetal growth restriction represents a particular dilemma in clinical management balancing the risk of iatrogenic prematurity with waiting for the fetus to gain more maturity, while being exposed to the risk of intrauterine death or the sequelae of acidosis. The Trial of Umbilical and Fetal Flow in Europe was a European, multicenter, randomized trial aimed to determine according to which criteria delivery should be triggered in early fetal growth restriction. We present the key findings of the primary and secondary analyses. Women with fetal abdominal circumference <10th percentile and umbilical pulsatility index >95th percentile between 26-32 weeks were randomized to 1 of 3 monitoring and delivery protocols. These were: fetal heart rate variability based on computerized cardiotocography; and early or late ductus venosus Doppler changes. A safety net based on fetal heart rate abnormalities or umbilical Doppler changes mandated delivery irrespective of randomized group. The primary outcome was normal neurodevelopmental outcome at 2 years. Among 511 women randomized, 362/503 (72%) had associated hypertensive conditions. In all, 463/503 (92%) of fetuses survived and cerebral palsy occurred in 6/443 (1%) with known outcome. Among all women there was no difference in outcome based on randomized group; however, of survivors, significantly more fetuses randomized to the late ductus venosus group had a normal outcome (133/144; 95%) than those randomized to computerized cardiotocography alone (111/131; 85%). In 118/310 (38%) of babies delivered <32 weeks, the indication was safety-net criteria: 55/106 (52%) in late ductus venosus, 37/99 (37%) in early ductus venosus, and 26/105 (25%) in computerized cardiotocography groups. Higher middle cerebral artery impedance adjusted for gestation was associated with neonatal survival without severe morbidity (odds ratio, 1.24; 95% confidence interval, 1.02-1.52) and infant survival without neurodevelopmental impairment at 2 years (odds ratio, 1.33; 95% confidence interval, 1.03-1.72) although birthweight and gestational age were more important determinants. Perinatal and 2-year outcome was better than expected in all randomized groups. Among survivors, 2-year neurodevelopmental outcome was best in those randomized to delivery based on late ductus venosus changes. Given a high rate of delivery based on the safety-net criteria, deciding delivery based on late ductus venosus changes and abnormal computerized fetal heart rate variability seems prudent. There is no rationale for delivery based on cerebral Doppler changes alone. Of note, most women with early-onset fetal growth restriction develop hypertension. Copyright © 2018 Elsevier Inc. All rights reserved.

Measured Effects of Turbulence on the Loudness and Waveforms of Conventional and Shaped Minimized Sonic Booms

NASA Technical Reports Server (NTRS)

Plotkin, Kenneth J.; Maglieri, Domenic J.; Sullivan, Brenda M.

2005-01-01

Turbulence has two distinctive effects on sonic booms: there is distortion in the form of random perturbations that appear behind the shock waves, and shock rise times are increased randomly. A first scattering theory by S.C. Crow in the late 1960s quantified the random distortions, and Crow's theory was shown to agree with available flight test data. A variety of theories for the shock thickness have been presented, all supporting the role of turbulence in increasing rise time above that of a basic molecular-relaxation structure. The net effect of these phenomena on the loudness of shaped minimized booms is of significant interest. Initial analysis suggests that there would be no change to average loudness, but this had not been experimentally investigated. The January 2004 flight test of the Shaped Sonic Boom Demonstrator (SSBD), together with a reference unmodified F-5E, included a 12500- foot linear ground sensor array with 28 digitally recorded sensor sites. This data set provides an opportunity to re-test Crow's theory for the post-shock perturbations, and to examine the net effect of turbulence on the loudness of shaped sonic booms.

Safety and immunogenicity of a combined Tetanus, Diphtheria, recombinant acellular Pertussis vaccine (TdaP) in healthy Thai adults.

PubMed

Sirivichayakul, Chukiat; Chanthavanich, Pornthep; Limkittikul, Kriengsak; Siegrist, Claire-Anne; Wijagkanalan, Wassana; Chinwangso, Pailinrut; Petre, Jean; Hong Thai, Pham; Chauhan, Mukesh; Viviani, Simonetta

2017-01-02

An acellular Pertussis (aP) vaccine containing recombinant genetically detoxified Pertussis Toxin (PTgen), Filamentous Hemagglutinin (FHA) and Pertactin (PRN) has been developed by BioNet-Asia (BioNet). We present here the results of the first clinical study of this recombinant aP vaccine formulated alone or in combination with tetanus and diphtheria toxoids (TdaP). A phase I/II, observer-blind, randomized controlled trial was conducted at Mahidol University in Bangkok, Thailand in healthy adult volunteers aged 18-35 y. The eligible volunteers were randomized to receive one dose of either BioNet's aP or Tetanus toxoid-reduced Diphtheria toxoid-acellular Pertussis (TdaP) vaccine, or the Tdap Adacel® vaccine in a 1:1:1 ratio. Safety follow-up was performed for one month. Immunogenicity was assessed at baseline, at 7 and 28 d after vaccination. Anti-PT, anti-FHA, anti-PRN, anti-tetanus and anti-diphtheria IgG antibodies were assessed by ELISA. Anti-PT neutralizing antibodies were assessed also by CHO cell assay. A total of 60 subjects (20 per each vaccine group) were enrolled and included in the safety analysis. Safety laboratory parameters, incidence of local and systemic post-immunization reactions during 7 d after vaccination and incidence of adverse events during one month after vaccination were similar in the 3 vaccine groups. One month after vaccination, seroresponse rates of anti-PT, anti-FHA and anti-PRN IgG antibodies exceeded 78% in all vaccine groups. The anti-PT IgG, anti-FHA IgG, and anti-PT neutralizing antibody geometric mean titers (GMTs) were significantly higher following immunization with BioNet's aP and BioNet's TdaP than Adacel® (P< 0.05). The anti-PRN IgG, anti-tetanus and anti-diphtheria GMTs at one month after immunization were comparable in all vaccine groups. All subjects had seroprotective titers of anti-tetanus and anti-diphtheria antibodies at baseline. In this first clinical study, PTgen-based BioNet's aP and TdaP vaccines showed a similar tolerability and safety profile to Adacel® and elicited significantly higher immune responses to PT and FHA.

Effectiveness of post-campaign, door-to-door, hang-up, and communication interventions to increase long-lasting, insecticidal bed net utilization in Togo (2011–2012): a cluster randomized, control trial

PubMed Central

2014-01-01

Background It is well established that insecticide-treated bed nets (ITNs), in particular long-lasting, insecticidal nets (LLINs), can be used as one of the primary interventions for effective malaria control. A consistent gap between net ownership and use has been observed, indicating that factors exist that prevent an owned mosquito net from being used. One approach used in the context of LLIN campaigns is a post-distribution, door-to-door visit of households with educational messages and to physically assist with hang-up of nets. Methods A cluster randomized trial was conducted in the Plateaux Region of Togo to evaluate the effectiveness of different approaches to post-LLIN campaign home visits (number of visits and timing) by volunteers to enhance LLIN hang-up and utilization. Results It was found that, in general, households that received intervention visits, particularly the most recent intervention visit, had levels of use that were typically 5 to 10% higher than the control households, while access did not differ among control and intervention households. Eight months post-campaign, ITN use by all individuals, children under five years and women of reproductive age was 11.3 to 14.4 percentage points greater in the study arm that received all three intervention visits than in the control communities. In households that received one or two additional door-to-door visits, the majority of respondents indicated that the volunteer provided new information during the visit regarding the use and importance of ITNs despite having received previous multiple visits. Conclusions The impact of the interventions appears to have been primarily through the delivery and reinforcement of key behaviour-change communication (BCC) messages regarding the importance of using an ITN and its care. Regardless of whether the respondents in fact received new information or had forgotten earlier information, this suggests that regular visits from community agents are useful in reinforcing key BCC messages. PMID:25005572

AGARD Flight Test Instrumentation Series. Volume 14. The Analysis of Random Data

DTIC Science & Technology

1981-11-01

obtained at arbitrary times during a number of flights. No constraints have been placed upon the controlling parameters, so that the process is non ...34noisy" environment controlling a non -linear system (the aircraft) using a redundant net of control parameters. when aircraft were flown manually with...structure. Cuse 2. Non -Stationary Measurements. When the 114S value of a random signal varies with parameters which cannot be controlled , then the method

Impact of permethrin-treated bed nets on entomologic indices in an area of intense year-round malaria transmission.

PubMed

Gimnig, John E; Vulule, John M; Lo, Terrence Q; Kamau, Luna; Kolczak, Margarette S; Phillips-Howard, Penelope A; Mathenge, Evan M; ter Kuile, Feiko O; Nahlen, Bernard L; Hightower, Allen W; Hawley, William A

2003-04-01

The effect of permethrin-treated bed nets (ITNs) on malaria vectors was studied as part of a large-scale, randomized, controlled trial in western Kenya. Indoor resting densities of fed Anopheles gambiae s.l. and An. funestus in intervention houses were 58.5% (P = 0.010) and 94.5% (P = 0.001) lower, respectively, compared with control houses. The sporozoite infection rate in An. gambiae s.l. was 0.8% in intervention areas compared with 3.4% (P = 0.026) in control areas, while the sporozoite infection rates in An. funestus were not significantly different between the two areas. We estimated the overall transmission of Plasmodium falciparum in intervention areas to be 90% lower than in control areas. Permethrin resistance was not detected during the study period. As measured by densities of An. gambiae s.l., the efficacy of bed nets decreased if one or more residents did not sleep under a net or if bed nets had not been re-treated within six months. These results indicate that ITNs are optimally effective if used every night and if permethrin is reapplied at least biannually.

EBMPracticeNet: A Bilingual National Electronic Point-Of-Care Project for Retrieval of Evidence-Based Clinical Guideline Information and Decision Support

PubMed Central

2013-01-01

Background In Belgium, the construction of a national electronic point-of-care information service, EBMPracticeNet, was initiated in 2011 to optimize quality of care by promoting evidence-based decision-making. The collaboration of the government, health care providers, evidence-based medicine (EBM) partners, and vendors of electronic health records (EHR) is unique to this project. All Belgian health care professionals get free access to an up-to-date database of validated Belgian and nearly 1000 international guidelines, incorporated in a portal that also provides EBM information from other sources than guidelines, including computerized clinical decision support that is integrated in the EHRs. Objective The objective of this paper was to describe the development strategy, the overall content, and the management of EBMPracticeNet which may be of relevance to other health organizations creating national or regional electronic point-of-care information services. Methods Several candidate providers of comprehensive guideline solutions were evaluated and one database was selected. Translation of the guidelines to Dutch and French was done with translation software, post-editing by translators and medical proofreading. A strategy is determined to adapt the guideline content to the Belgian context. Acceptance of the computerized clinical decision support tool has been tested and a randomized controlled trial is planned to evaluate the effect on process and patient outcomes. Results Currently, EBMPracticeNet is in "work in progress" state. Reference is made to the results of a pilot study and to further planned research including a randomized controlled trial. Conclusions The collaboration of government, health care providers, EBM partners, and vendors of EHRs is unique. The potential value of the project is great. The link between all the EHRs from different vendors and a national database held on a single platform that is controlled by all EBM organizations in Belgium are the strengths of EBMPracticeNet. PMID:23842038

Using Expected Value to Introduce the Laplace Transform

ERIC Educational Resources Information Center

Lutzer, Carl V.

2015-01-01

We propose an introduction to the Laplace transform in which Riemann sums are used to approximate the expected net change in a function, assuming that it quantifies a process that can terminate at random. We assume only a basic understanding of probability.

Introducing Online Bibliographic Service to its Users: The Online Presentation

ERIC Educational Resources Information Center

Crane, Nancy B.; Pilachowski, David M.

1978-01-01

A description of techniques for introducing online services to new user groups includes discussion of terms and their definitions, evolution of online searching, advantages and disadvantages of online searching, production of the data bases, search strategies, Boolean logic, costs and charges, "do's and don'ts," and a user search questionnaire. (J…

A Study of Search Intermediary Working Notes: Implications for IR System Design.

ERIC Educational Resources Information Center

Spink, Amanda; Goodrum, Abby

1996-01-01

Reports findings from an exploratory study investigating working notes created during encoding and external storage (EES) processes by human search intermediaries (librarians at the University of North Texas) using a Boolean information retrieval (IR) system. Implications for the design of IR interfaces and further research is discussed.…

Recognition vs Reverse Engineering in Boolean Concepts Learning

ERIC Educational Resources Information Center

Shafat, Gabriel; Levin, Ilya

2012-01-01

This paper deals with two types of logical problems--recognition problems and reverse engineering problems, and with the interrelations between these types of problems. The recognition problems are modeled in the form of a visual representation of various objects in a common pattern, with a composition of represented objects in the pattern.…

Target-Based Maintenance of Privacy Preserving Association Rules

ERIC Educational Resources Information Center

Ahluwalia, Madhu V.

2011-01-01

In the context of association rule mining, the state-of-the-art in privacy preserving data mining provides solutions for categorical and Boolean association rules but not for quantitative association rules. This research fills this gap by describing a method based on discrete wavelet transform (DWT) to protect input data privacy while preserving…

Information Resources Usage in Project Management Digital Learning System

ERIC Educational Resources Information Center

Davidovitch, Nitza; Belichenko, Margarita; Kravchenko, Yurii

2017-01-01

The article combines a theoretical approach to structuring knowledge that is based on the integrated use of fuzzy semantic network theory predicates, Boolean functions, theory of complexity of network structures and some practical aspects to be considered in the distance learning at the university. The paper proposes a methodological approach that…

Algebraic grid adaptation method using non-uniform rational B-spline surface modeling

NASA Technical Reports Server (NTRS)

Yang, Jiann-Cherng; Soni, B. K.

1992-01-01

An algebraic adaptive grid system based on equidistribution law and utilized by the Non-Uniform Rational B-Spline (NURBS) surface for redistribution is presented. A weight function, utilizing a properly weighted boolean sum of various flow field characteristics is developed. Computational examples are presented to demonstrate the success of this technique.

A Characterization of Banach Spaces Containing l1

PubMed Central

Rosenthal, Haskell P.

1974-01-01

It is proved that a Banach space contains a subspace isomorphic to l1 if (and only if) it has a bounded sequence with no weak-Cauchy subsequence. The proof yields that a sequence of subsets of a given set has a subsequence that is either convergent or Boolean independent. PMID:16592162

Deriving Laws from Ordering Relations

NASA Technical Reports Server (NTRS)

Knuth, Kevin H.

2004-01-01

The effect of Richard T. Cox's contribution to probability theory was to generalize Boolean implication among logical statements to degrees of implication, which are manipulated using rules derived from consistency with Boolean algebra. These rules are known as the sum rule, the product rule and Bayes Theorem, and the measure resulting from this generalization is probability. In this paper, I will describe how Cox s technique can be further generalized to include other algebras and hence other problems in science and mathematics. The result is a methodology that can be used to generalize an algebra to a calculus by relying on consistency with order theory to derive the laws of the calculus. My goals are to clear up the mysteries as to why the same basic structure found in probability theory appears in other contexts, to better understand the foundations of probability theory, and to extend these ideas to other areas by developing new mathematics and new physics. The relevance of this methodology will be demonstrated using examples from probability theory, number theory, geometry, information theory, and quantum mechanics.

Networks and games for precision medicine.

PubMed

Biane, Célia; Delaplace, Franck; Klaudel, Hanna

2016-12-01

Recent advances in omics technologies provide the leverage for the emergence of precision medicine that aims at personalizing therapy to patient. In this undertaking, computational methods play a central role for assisting physicians in their clinical decision-making by combining data analysis and systems biology modelling. Complex diseases such as cancer or diabetes arise from the intricate interplay of various biological molecules. Therefore, assessing drug efficiency requires to study the effects of elementary perturbations caused by diseases on relevant biological networks. In this paper, we propose a computational framework called Network-Action Game applied to best drug selection problem combining Game Theory and discrete models of dynamics (Boolean networks). Decision-making is modelled using Game Theory that defines the process of drug selection among alternative possibilities, while Boolean networks are used to model the effects of the interplay between disease and drugs actions on the patient's molecular system. The actions/strategies of disease and drugs are focused on arc alterations of the interactome. The efficiency of this framework has been evaluated for drug prediction on a model of breast cancer signalling. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The logical primitives of thought: Empirical foundations for compositional cognitive models.

PubMed

Piantadosi, Steven T; Tenenbaum, Joshua B; Goodman, Noah D

2016-07-01

The notion of a compositional language of thought (LOT) has been central in computational accounts of cognition from earliest attempts (Boole, 1854; Fodor, 1975) to the present day (Feldman, 2000; Penn, Holyoak, & Povinelli, 2008; Fodor, 2008; Kemp, 2012; Goodman, Tenenbaum, & Gerstenberg, 2015). Recent modeling work shows how statistical inferences over compositionally structured hypothesis spaces might explain learning and development across a variety of domains. However, the primitive components of such representations are typically assumed a priori by modelers and theoreticians rather than determined empirically. We show how different sets of LOT primitives, embedded in a psychologically realistic approximate Bayesian inference framework, systematically predict distinct learning curves in rule-based concept learning experiments. We use this feature of LOT models to design a set of large-scale concept learning experiments that can determine the most likely primitives for psychological concepts involving Boolean connectives and quantification. Subjects' inferences are most consistent with a rich (nonminimal) set of Boolean operations, including first-order, but not second-order, quantification. Our results more generally show how specific LOT theories can be distinguished empirically. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Stability Depends on Positive Autoregulation in Boolean Gene Regulatory Networks

PubMed Central

Pinho, Ricardo; Garcia, Victor; Irimia, Manuel; Feldman, Marcus W.

2014-01-01

Network motifs have been identified as building blocks of regulatory networks, including gene regulatory networks (GRNs). The most basic motif, autoregulation, has been associated with bistability (when positive) and with homeostasis and robustness to noise (when negative), but its general importance in network behavior is poorly understood. Moreover, how specific autoregulatory motifs are selected during evolution and how this relates to robustness is largely unknown. Here, we used a class of GRN models, Boolean networks, to investigate the relationship between autoregulation and network stability and robustness under various conditions. We ran evolutionary simulation experiments for different models of selection, including mutation and recombination. Each generation simulated the development of a population of organisms modeled by GRNs. We found that stability and robustness positively correlate with autoregulation; in all investigated scenarios, stable networks had mostly positive autoregulation. Assuming biological networks correspond to stable networks, these results suggest that biological networks should often be dominated by positive autoregulatory loops. This seems to be the case for most studied eukaryotic transcription factor networks, including those in yeast, flies and mammals. PMID:25375153

Utilization of Large Scale Surface Models for Detailed Visibility Analyses

NASA Astrophysics Data System (ADS)

Caha, J.; Kačmařík, M.

2017-11-01

This article demonstrates utilization of large scale surface models with small spatial resolution and high accuracy, acquired from Unmanned Aerial Vehicle scanning, for visibility analyses. The importance of large scale data for visibility analyses on the local scale, where the detail of the surface model is the most defining factor, is described. The focus is not only the classic Boolean visibility, that is usually determined within GIS, but also on so called extended viewsheds that aims to provide more information about visibility. The case study with examples of visibility analyses was performed on river Opava, near the Ostrava city (Czech Republic). The multiple Boolean viewshed analysis and global horizon viewshed were calculated to determine most prominent features and visibility barriers of the surface. Besides that, the extended viewshed showing angle difference above the local horizon, which describes angular height of the target area above the barrier, is shown. The case study proved that large scale models are appropriate data source for visibility analyses on local level. The discussion summarizes possible future applications and further development directions of visibility analyses.

A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks.

PubMed

Laomettachit, Teeraphan; Chen, Katherine C; Baumann, William T; Tyson, John J

2016-01-01

To understand the molecular mechanisms that regulate cell cycle progression in eukaryotes, a variety of mathematical modeling approaches have been employed, ranging from Boolean networks and differential equations to stochastic simulations. Each approach has its own characteristic strengths and weaknesses. In this paper, we propose a "standard component" modeling strategy that combines advantageous features of Boolean networks, differential equations and stochastic simulations in a framework that acknowledges the typical sorts of reactions found in protein regulatory networks. Applying this strategy to a comprehensive mechanism of the budding yeast cell cycle, we illustrate the potential value of standard component modeling. The deterministic version of our model reproduces the phenotypic properties of wild-type cells and of 125 mutant strains. The stochastic version of our model reproduces the cell-to-cell variability of wild-type cells and the partial viability of the CLB2-dbΔ clb5Δ mutant strain. Our simulations show that mathematical modeling with "standard components" can capture in quantitative detail many essential properties of cell cycle control in budding yeast.

A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks

PubMed Central

Laomettachit, Teeraphan; Chen, Katherine C.; Baumann, William T.

2016-01-01

To understand the molecular mechanisms that regulate cell cycle progression in eukaryotes, a variety of mathematical modeling approaches have been employed, ranging from Boolean networks and differential equations to stochastic simulations. Each approach has its own characteristic strengths and weaknesses. In this paper, we propose a “standard component” modeling strategy that combines advantageous features of Boolean networks, differential equations and stochastic simulations in a framework that acknowledges the typical sorts of reactions found in protein regulatory networks. Applying this strategy to a comprehensive mechanism of the budding yeast cell cycle, we illustrate the potential value of standard component modeling. The deterministic version of our model reproduces the phenotypic properties of wild-type cells and of 125 mutant strains. The stochastic version of our model reproduces the cell-to-cell variability of wild-type cells and the partial viability of the CLB2-dbΔ clb5Δ mutant strain. Our simulations show that mathematical modeling with “standard components” can capture in quantitative detail many essential properties of cell cycle control in budding yeast. PMID:27187804

Programmable bioelectronics in a stimuli-encoded 3D graphene interface

NASA Astrophysics Data System (ADS)

Parlak, Onur; Beyazit, Selim; Tse-Sum-Bui, Bernadette; Haupt, Karsten; Turner, Anthony P. F.; Tiwari, Ashutosh

2016-05-01

The ability to program and mimic the dynamic microenvironment of living organisms is a crucial step towards the engineering of advanced bioelectronics. Here, we report for the first time a design for programmable bioelectronics, with `built-in' switchable and tunable bio-catalytic performance that responds simultaneously to appropriate stimuli. The designed bio-electrodes comprise light and temperature responsive compartments, which allow the building of Boolean logic gates (i.e. ``OR'' and ``AND'') based on enzymatic communications to deliver logic operations.The ability to program and mimic the dynamic microenvironment of living organisms is a crucial step towards the engineering of advanced bioelectronics. Here, we report for the first time a design for programmable bioelectronics, with `built-in' switchable and tunable bio-catalytic performance that responds simultaneously to appropriate stimuli. The designed bio-electrodes comprise light and temperature responsive compartments, which allow the building of Boolean logic gates (i.e. ``OR'' and ``AND'') based on enzymatic communications to deliver logic operations. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr02355j

Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation

PubMed Central

Honigberg, Saul M.

2016-01-01

Diploid budding yeast (Saccharomyces cerevisiae) can adopt one of several alternative differentiation fates in response to nutrient limitation, and each of these fates provides distinct biological functions. When different strain backgrounds are taken into account, these various fates occur in response to similar environmental cues, are regulated by the same signal transduction pathways, and share many of the same master regulators. I propose that the relationships between fate choice, environmental cues and signaling pathways are not Boolean, but involve graded levels of signals, pathway activation and master-regulator activity. In the absence of large differences between environmental cues, small differences in the concentration of cues may be reinforced by cell-to-cell signals. These signals are particularly essential for fate determination within communities, such as colonies and biofilms, where fate choice varies dramatically from one region of the community to another. The lack of Boolean relationships between cues, signaling pathways, master regulators and cell fates may allow yeast communities to respond appropriately to the wide range of environments they encounter in nature. PMID:27917388

Two classes of ODE models with switch-like behavior

PubMed Central

Just, Winfried; Korb, Mason; Elbert, Ben; Young, Todd

2013-01-01

In cases where the same real-world system can be modeled both by an ODE system ⅅ and a Boolean system 𝔹, it is of interest to identify conditions under which the two systems will be consistent, that is, will make qualitatively equivalent predictions. In this note we introduce two broad classes of relatively simple models that provide a convenient framework for studying such questions. In contrast to the widely known class of Glass networks, the right-hand sides of our ODEs are Lipschitz-continuous. We prove that if 𝔹 has certain structures, consistency between ⅅ and 𝔹 is implied by sufficient separation of time scales in one class of our models. Namely, if the trajectories of 𝔹 are “one-stepping” then we prove a strong form of consistency and if 𝔹 has a certain monotonicity property then there is a weaker consistency between ⅅ and 𝔹. These results appear to point to more general structure properties that favor consistency between ODE and Boolean models. PMID:24244061

Mood and anxiety disorders as early manifestations of medical illness: a systematic review.

PubMed

Cosci, Fiammetta; Fava, Giovanni A; Sonino, Nicoletta

2015-01-01

Affective disturbances involving alterations of mood, anxiety and irritability may be early symptoms of medical illnesses. The aim of this paper was to provide a systematic review of the literature with qualitative data synthesis. MEDLINE, PsycINFO, EMBASE, Cochrane, and ISI Web of Science were systematically searched from inception to February 2014. Search terms were 'prodrome/early symptom', combined using the Boolean 'AND' operator with 'anxiety/depression/mania/hypomania/irritability/irritable mood/hostility', combined with the Boolean 'AND' operator with 'medical illness/medical disorder'. PRISMA guidelines were followed. A total of 21 studies met the inclusion criteria and were analyzed. Depression was found to be the most common affective prodrome of medical disorders and was consistently reported in Cushing's syndrome, hypothyroidism, hyperparathyroidism, pancreatic and lung cancer, myocardial infarction, Wilson's disease, and AIDS. Mania, anxiety and irritability were less frequent. Physicians may not pursue medical workup of cases that appear to be psychiatric in nature. They should be alerted that disturbances in mood, anxiety and irritability may antedate the appearance of a medical disorder.

Two Methods for Efficient Solution of the Hitting-Set Problem

NASA Technical Reports Server (NTRS)

Vatan, Farrokh; Fijany, Amir

2005-01-01

A paper addresses much of the same subject matter as that of Fast Algorithms for Model-Based Diagnosis (NPO-30582), which appears elsewhere in this issue of NASA Tech Briefs. However, in the paper, the emphasis is more on the hitting-set problem (also known as the transversal problem), which is well known among experts in combinatorics. The authors primary interest in the hitting-set problem lies in its connection to the diagnosis problem: it is a theorem of model-based diagnosis that in the set-theory representation of the components of a system, the minimal diagnoses of a system are the minimal hitting sets of the system. In the paper, the hitting-set problem (and, hence, the diagnosis problem) is translated from a combinatorial to a computational problem by mapping it onto the Boolean satisfiability and integer- programming problems. The paper goes on to describe developments nearly identical to those summarized in the cited companion NASA Tech Briefs article, including the utilization of Boolean-satisfiability and integer- programming techniques to reduce the computation time and/or memory needed to solve the hitting-set problem.

General method to find the attractors of discrete dynamic models of biological systems.

PubMed

Gan, Xiao; Albert, Réka

2018-04-01

Analyzing the long-term behaviors (attractors) of dynamic models of biological networks can provide valuable insight. We propose a general method that can find the attractors of multilevel discrete dynamical systems by extending a method that finds the attractors of a Boolean network model. The previous method is based on finding stable motifs, subgraphs whose nodes' states can stabilize on their own. We extend the framework from binary states to any finite discrete levels by creating a virtual node for each level of a multilevel node, and describing each virtual node with a quasi-Boolean function. We then create an expanded representation of the multilevel network, find multilevel stable motifs and oscillating motifs, and identify attractors by successive network reduction. In this way, we find both fixed point attractors and complex attractors. We implemented an algorithm, which we test and validate on representative synthetic networks and on published multilevel models of biological networks. Despite its primary motivation to analyze biological networks, our motif-based method is general and can be applied to any finite discrete dynamical system.

General method to find the attractors of discrete dynamic models of biological systems

NASA Astrophysics Data System (ADS)

Gan, Xiao; Albert, Réka

2018-04-01

Analyzing the long-term behaviors (attractors) of dynamic models of biological networks can provide valuable insight. We propose a general method that can find the attractors of multilevel discrete dynamical systems by extending a method that finds the attractors of a Boolean network model. The previous method is based on finding stable motifs, subgraphs whose nodes' states can stabilize on their own. We extend the framework from binary states to any finite discrete levels by creating a virtual node for each level of a multilevel node, and describing each virtual node with a quasi-Boolean function. We then create an expanded representation of the multilevel network, find multilevel stable motifs and oscillating motifs, and identify attractors by successive network reduction. In this way, we find both fixed point attractors and complex attractors. We implemented an algorithm, which we test and validate on representative synthetic networks and on published multilevel models of biological networks. Despite its primary motivation to analyze biological networks, our motif-based method is general and can be applied to any finite discrete dynamical system.

Color is processed less efficiently than orientation in change detection but more efficiently in visual search.

PubMed

Huang, Liqiang

2015-05-01

Basic visual features (e.g., color, orientation) are assumed to be processed in the same general way across different visual tasks. Here, a significant deviation from this assumption was predicted on the basis of the analysis of stimulus spatial structure, as characterized by the Boolean-map notion. If a task requires memorizing the orientations of a set of bars, then the map consisting of those bars can be readily used to hold the overall structure in memory and will thus be especially useful. If the task requires visual search for a target, then the map, which contains only an overall structure, will be of little use. Supporting these predictions, the present study demonstrated that in comparison to stimulus colors, bar orientations were processed more efficiently in change-detection tasks but less efficiently in visual search tasks (Cohen's d = 4.24). In addition to offering support for the role of the Boolean map in conscious access, the present work also throws doubts on the generality of processing visual features. © The Author(s) 2015.

Net endogenous acid production is associated with a faster decline in GFR in African Americans

PubMed Central

Scialla, Julia J.; Appel, Lawrence J.; Astor, Brad C.; Miller, Edgar R.; Beddhu, Srinivasan; Woodward, Mark; Parekh, Rulan S.; Anderson, Cheryl A. M.

2012-01-01

Increased acid excretion may promote renal injury. To evaluate this in African Americans with hypertensive nephrosclerosis, we studied the association between the net endogenous acid production and progression of kidney disease in 632 patients in the AASK trial. Protein and potassium intakes were estimated from 24-hour urea nitrogen and potassium excretion, and used to estimate net endogenous acid production, averaged over 2 years, approximating routine intake. The link between net endogenous acid production and the I125iothalamate glomerular filtration rate (iGFR) and time to end stage renal disease or doubling of serum creatinine was analyzed using mixed models and Cox proportional hazards regressions. The trend in higher net endogenous acid production was significantly associated with a faster decline in iGFR over a median of 3.2 years. After adjustment for age, body mass index, baseline iGFR, urine protein to creatinine ratio and randomized treatment group, the trend in higher net endogenous acid production remained significantly associated with a faster decline in iGFR at a rate 1.01 mL/min/1.73 m2 per year faster in the highest to the lowest quartile. However, in time to event analyses over a median of 7.7 years, the adjusted hazard ratio (1.10) for composite renal events per 25 mEq/day higher net endogenous acid production was not significant. Hence, our findings implicate endogenous acid production as a potential modifiable risk factor for progressive kidney disease. PMID:22475819

Clustering of host-seeking activity of Anopheles gambiae mosquitoes at the top surface of a human-baited bed net

PubMed Central

2013-01-01

Background Knowledge of the interactions between mosquitoes and humans, and how vector control interventions affect them, is sparse. A study exploring host-seeking behaviour at a human-occupied bed net, a key event in such interactions, is reported here. Methods Host-seeking female Anopheles gambiae activity was studied using a human-baited ‘sticky-net’ (a bed net without insecticide, coated with non-setting adhesive) to trap mosquitoes. The numbers and distribution of mosquitoes captured on each surface of the bed net were recorded and analysed using non-parametric statistical methods and random effects regression analysis. To confirm sticky-net reliability, the experiment was repeated using a pitched sticky-net (tilted sides converging at apex, i.e., neither horizontal nor vertical). The capture efficiency of horizontal and vertical sticky surfaces were compared, and the potential repellency of the adhesive was investigated. Results In a semi-field experiment, more mosquitoes were caught on the top (74-87%) than on the sides of the net (p < 0.001). In laboratory experiments, more mosquitoes were caught on the top than on the sides in human-baited tests (p < 0.001), significantly different to unbaited controls (p < 0.001) where most mosquitoes were on the sides (p = 0.047). In both experiments, approximately 70% of mosquitoes captured on the top surface were clustered within a 90 × 90 cm (or lesser) area directly above the head and chest (p < 0.001). In pitched net tests, similar clustering occurred over the sleeper’s head and chest in baited tests only (p < 0.001). Capture rates at horizontal and vertical surfaces were not significantly different and the sticky-net was not repellent. Conclusion This study demonstrated that An. gambiae activity occurs predominantly within a limited area of the top surface of bed nets. The results provide support for the two-in-one bed net design for managing pyrethroid-resistant vector populations. Further exploration of vector behaviour at the bed net interface could contribute to additional improvements in insecticide-treated bed net design or the development of novel vector control tools. PMID:23902661

Beneficial effects of Korean red ginseng on lymphocyte DNA damage, antioxidant enzyme activity, and LDL oxidation in healthy participants: a randomized, double-blind, placebo-controlled trial.

PubMed

Kim, Ji Young; Park, Ju Yeon; Kang, Hee Jung; Kim, Oh Yoen; Lee, Jong Ho

2012-07-17

The reported health benefits of Korean red ginseng (KRG) include antioxidant, antitumor, antimutagenic, and immunomodulatory activities; however, the effects on oxidative stress have not yet been evaluated. Therefore, we assessed the effect of KRG on antioxidant enzymes and oxidative stress markers in humans. We conducted a randomized, double-blind, placebo-controlled study with three groups, including placebo, low-dose (3 g/day), and high-dose (6 g/day), which were randomly assigned to healthy subjects aged 20-65 years. Lymphocyte DNA damage, antioxidative enzyme activity, and lipid peroxidation were assessed before and after the 8-week supplementation. Fifty-seven subjects completed the protocol. Plasma superoxide dismutase (SOD) activity after the 8-week KRG supplementation was significantly higher in the low-and high-dose groups compared to baseline. Plasma glutathione peroxidase (GPx) and catalase activities were also increased after the high-dose supplementation. Furthermore, the DNA tail length and tail moment were significantly reduced after the supplementation (low-dose and high-dose), and plasma oxidized low-density lipoprotein (LDL) levels were reduced in low-dose and high-dose groups, but increased in the placebo group. The net changes in oxidized LDL after the supplementation differed significantly between both KRG supplementation groups and the placebo group. Net changes in GPx, SOD and catalase activities, and DNA tail length and tail moment were significantly different between the high-dose group and the placebo group. Additionally, the net changes in urinary 8-epi-PGF(2α) were significantly different between the KRG supplementation groups and the placebo group. KRG supplementation may attenuate lymphocyte DNA damage and LDL oxidation by upregulating antioxidant enzyme activity.

Beneficial effects of Korean red ginseng on lymphocyte DNA damage, antioxidant enzyme activity, and LDL oxidation in healthy participants: a randomized, double-blind, placebo-controlled trial

PubMed Central

2012-01-01

Background The reported health benefits of Korean red ginseng (KRG) include antioxidant, antitumor, antimutagenic, and immunomodulatory activities; however, the effects on oxidative stress have not yet been evaluated. Therefore, we assessed the effect of KRG on antioxidant enzymes and oxidative stress markers in humans. Methods We conducted a randomized, double-blind, placebo-controlled study with three groups, including placebo, low-dose (3 g/day), and high-dose (6 g/day), which were randomly assigned to healthy subjects aged 20–65 years. Lymphocyte DNA damage, antioxidative enzyme activity, and lipid peroxidation were assessed before and after the 8-week supplementation. Results Fifty-seven subjects completed the protocol. Plasma superoxide dismutase (SOD) activity after the 8-week KRG supplementation was significantly higher in the low-and high-dose groups compared to baseline. Plasma glutathione peroxidase (GPx) and catalase activities were also increased after the high-dose supplementation. Furthermore, the DNA tail length and tail moment were significantly reduced after the supplementation (low-dose and high-dose), and plasma oxidized low-density lipoprotein (LDL) levels were reduced in low-dose and high-dose groups, but increased in the placebo group. The net changes in oxidized LDL after the supplementation differed significantly between both KRG supplementation groups and the placebo group. Net changes in GPx, SOD and catalase activities, and DNA tail length and tail moment were significantly different between the high-dose group and the placebo group. Additionally, the net changes in urinary 8-epi-PGF2α were significantly different between the KRG supplementation groups and the placebo group. Conclusions KRG supplementation may attenuate lymphocyte DNA damage and LDL oxidation by upregulating antioxidant enzyme activity. PMID:22805313

Design of the Lifestyle Improvement through Food and Exercise (LIFE) study: a randomized controlled trial of self-management of type 2 diabetes among African American patients from safety net health centers.

PubMed

Lynch, Elizabeth B; Liebman, Rebecca; Ventrelle, Jennifer; Keim, Kathryn; Appelhans, Bradley M; Avery, Elizabeth F; Tahsin, Bettina; Li, Hong; Shapera, Merle; Fogelfeld, Leon

2014-11-01

The Lifestyle Improvement through Food and Exercise (LIFE) study is a community-based randomized-controlled trial to measure the effectiveness of a lifestyle intervention to improve glycemic control among African Americans with type 2 diabetes attending safety net clinics. The study enrolled African American adults with a diagnosis of type 2 diabetes and HbA1c ≥ 7.0 who had attended specific safety net community clinics in the prior year. 210 patients will be enrolled and randomized to either the LIFE intervention or a standard of care control group, which consists of two dietitian-led diabetes self-management classes. The LIFE intervention was delivered in 28 group sessions over 12 months and focused on improving diet through dietitian-led culturally-tailored nutrition education, increasing physical activity through self-monitoring using an accelerometer, increasing ability to manage blood sugar through modifications to lifestyle, and providing social support for behavior change. In addition to the group sessions, peer supporters made regular telephone calls to participants to monitor progress toward behavioral goals and provide social support. The 12-month intervention phase was followed by a six-month maintenance phase consisting of two group sessions. The primary outcome of the study is change in A1C from baseline to 12 months, and an additional follow-up will occur at 18 months. The hypothesis of the study is that the participants in the LIFE intervention will show a greater improvement in glycemic control over 12 months than participants in the control group. Copyright © 2014 Elsevier Inc. All rights reserved.

Intelligent machines in the twenty-first century: foundations of inference and inquiry.

PubMed

Knuth, Kevin H

2003-12-15

The last century saw the application of Boolean algebra to the construction of computing machines, which work by applying logical transformations to information contained in their memory. The development of information theory and the generalization of Boolean algebra to Bayesian inference have enabled these computing machines, in the last quarter of the twentieth century, to be endowed with the ability to learn by making inferences from data. This revolution is just beginning as new computational techniques continue to make difficult problems more accessible. Recent advances in our understanding of the foundations of probability theory have revealed implications for areas other than logic. Of relevance to intelligent machines, we recently identified the algebra of questions as the free distributive algebra, which will now allow us to work with questions in a way analogous to that which Boolean algebra enables us to work with logical statements. In this paper, we examine the foundations of inference and inquiry. We begin with a history of inferential reasoning, highlighting key concepts that have led to the automation of inference in modern machine-learning systems. We then discuss the foundations of inference in more detail using a modern viewpoint that relies on the mathematics of partially ordered sets and the scaffolding of lattice theory. This new viewpoint allows us to develop the logic of inquiry and introduce a measure describing the relevance of a proposed question to an unresolved issue. Last, we will demonstrate the automation of inference, and discuss how this new logic of inquiry will enable intelligent machines to ask questions. Automation of both inference and inquiry promises to allow robots to perform science in the far reaches of our solar system and in other star systems by enabling them not only to make inferences from data, but also to decide which question to ask, which experiment to perform, or which measurement to take given what they have learned and what they are designed to understand.

Can electronic search engines optimize screening of search results in systematic reviews: an empirical study.

PubMed

Sampson, Margaret; Barrowman, Nicholas J; Moher, David; Clifford, Tammy J; Platt, Robert W; Morrison, Andra; Klassen, Terry P; Zhang, Li

2006-02-24

Most electronic search efforts directed at identifying primary studies for inclusion in systematic reviews rely on the optimal Boolean search features of search interfaces such as DIALOG and Ovid. Our objective is to test the ability of an Ultraseek search engine to rank MEDLINE records of the included studies of Cochrane reviews within the top half of all the records retrieved by the Boolean MEDLINE search used by the reviewers. Collections were created using the MEDLINE bibliographic records of included and excluded studies listed in the review and all records retrieved by the MEDLINE search. Records were converted to individual HTML files. Collections of records were indexed and searched through a statistical search engine, Ultraseek, using review-specific search terms. Our data sources, systematic reviews published in the Cochrane library, were included if they reported using at least one phase of the Cochrane Highly Sensitive Search Strategy (HSSS), provided citations for both included and excluded studies and conducted a meta-analysis using a binary outcome measure. Reviews were selected if they yielded between 1000-6000 records when the MEDLINE search strategy was replicated. Nine Cochrane reviews were included. Included studies within the Cochrane reviews were found within the first 500 retrieved studies more often than would be expected by chance. Across all reviews, recall of included studies into the top 500 was 0.70. There was no statistically significant difference in ranking when comparing included studies with just the subset of excluded studies listed as excluded in the published review. The relevance ranking provided by the search engine was better than expected by chance and shows promise for the preliminary evaluation of large results from Boolean searches. A statistical search engine does not appear to be able to make fine discriminations concerning the relevance of bibliographic records that have been pre-screened by systematic reviewers.

Recurrent-neural-network-based Boolean factor analysis and its application to word clustering.

PubMed

Frolov, Alexander A; Husek, Dusan; Polyakov, Pavel Yu

2009-07-01

The objective of this paper is to introduce a neural-network-based algorithm for word clustering as an extension of the neural-network-based Boolean factor analysis algorithm (Frolov , 2007). It is shown that this extended algorithm supports even the more complex model of signals that are supposed to be related to textual documents. It is hypothesized that every topic in textual data is characterized by a set of words which coherently appear in documents dedicated to a given topic. The appearance of each word in a document is coded by the activity of a particular neuron. In accordance with the Hebbian learning rule implemented in the network, sets of coherently appearing words (treated as factors) create tightly connected groups of neurons, hence, revealing them as attractors of the network dynamics. The found factors are eliminated from the network memory by the Hebbian unlearning rule facilitating the search of other factors. Topics related to the found sets of words can be identified based on the words' semantics. To make the method complete, a special technique based on a Bayesian procedure has been developed for the following purposes: first, to provide a complete description of factors in terms of component probability, and second, to enhance the accuracy of classification of signals to determine whether it contains the factor. Since it is assumed that every word may possibly contribute to several topics, the proposed method might be related to the method of fuzzy clustering. In this paper, we show that the results of Boolean factor analysis and fuzzy clustering are not contradictory, but complementary. To demonstrate the capabilities of this attempt, the method is applied to two types of textual data on neural networks in two different languages. The obtained topics and corresponding words are at a good level of agreement despite the fact that identical topics in Russian and English conferences contain different sets of keywords.

Floral Morphogenesis: Stochastic Explorations of a Gene Network Epigenetic Landscape

PubMed Central

Aldana, Maximino; Benítez, Mariana; Cortes-Poza, Yuriria; Espinosa-Soto, Carlos; Hartasánchez, Diego A.; Lotto, R. Beau; Malkin, David; Escalera Santos, Gerardo J.; Padilla-Longoria, Pablo

2008-01-01

In contrast to the classical view of development as a preprogrammed and deterministic process, recent studies have demonstrated that stochastic perturbations of highly non-linear systems may underlie the emergence and stability of biological patterns. Herein, we address the question of whether noise contributes to the generation of the stereotypical temporal pattern in gene expression during flower development. We modeled the regulatory network of organ identity genes in the Arabidopsis thaliana flower as a stochastic system. This network has previously been shown to converge to ten fixed-point attractors, each with gene expression arrays that characterize inflorescence cells and primordial cells of sepals, petals, stamens, and carpels. The network used is binary, and the logical rules that govern its dynamics are grounded in experimental evidence. We introduced different levels of uncertainty in the updating rules of the network. Interestingly, for a level of noise of around 0.5–10%, the system exhibited a sequence of transitions among attractors that mimics the sequence of gene activation configurations observed in real flowers. We also implemented the gene regulatory network as a continuous system using the Glass model of differential equations, that can be considered as a first approximation of kinetic-reaction equations, but which are not necessarily equivalent to the Boolean model. Interestingly, the Glass dynamics recover a temporal sequence of attractors, that is qualitatively similar, although not identical, to that obtained using the Boolean model. Thus, time ordering in the emergence of cell-fate patterns is not an artifact of synchronous updating in the Boolean model. Therefore, our model provides a novel explanation for the emergence and robustness of the ubiquitous temporal pattern of floral organ specification. It also constitutes a new approach to understanding morphogenesis, providing predictions on the population dynamics of cells with different genetic configurations during development. PMID:18978941

Intelligent machines in the twenty-first century: foundations of inference and inquiry

NASA Technical Reports Server (NTRS)

Knuth, Kevin H.

2003-01-01

The last century saw the application of Boolean algebra to the construction of computing machines, which work by applying logical transformations to information contained in their memory. The development of information theory and the generalization of Boolean algebra to Bayesian inference have enabled these computing machines, in the last quarter of the twentieth century, to be endowed with the ability to learn by making inferences from data. This revolution is just beginning as new computational techniques continue to make difficult problems more accessible. Recent advances in our understanding of the foundations of probability theory have revealed implications for areas other than logic. Of relevance to intelligent machines, we recently identified the algebra of questions as the free distributive algebra, which will now allow us to work with questions in a way analogous to that which Boolean algebra enables us to work with logical statements. In this paper, we examine the foundations of inference and inquiry. We begin with a history of inferential reasoning, highlighting key concepts that have led to the automation of inference in modern machine-learning systems. We then discuss the foundations of inference in more detail using a modern viewpoint that relies on the mathematics of partially ordered sets and the scaffolding of lattice theory. This new viewpoint allows us to develop the logic of inquiry and introduce a measure describing the relevance of a proposed question to an unresolved issue. Last, we will demonstrate the automation of inference, and discuss how this new logic of inquiry will enable intelligent machines to ask questions. Automation of both inference and inquiry promises to allow robots to perform science in the far reaches of our solar system and in other star systems by enabling them not only to make inferences from data, but also to decide which question to ask, which experiment to perform, or which measurement to take given what they have learned and what they are designed to understand.

IL-33 and soluble ST2 levels as novel predictors for remission and progression of carotid plaque in early rheumatoid arthritis: A prospective study.

PubMed

Shen, Jiayun; Shang, Qing; Wong, Chun-Kwok; Li, Edmund K; Wang, Shang; Li, Rui-Jie; Lee, Ka-Lai; Leung, Ying-Ying; Ying, King-Yee; Yim, Cheuk-Wan; Kun, Emily W; Leung, Moon-Ho; Li, Martin; Li, Tena K; Zhu, Tracy Y; Yu, Shui-Lian; Kuan, Woon-Pang; Yu, Cheuk-Man; Tam, Lai-Shan

2015-08-01

To study the association between the baseline IL-33 and soluble ST2 (sST2) levels with disease remission and progression of carotid atherosclerosis in early rheumatoid arthritis (ERA) patients. A total of 98 ERA patients were enrolled. Disease activity and the presence of carotid plaque were evaluated at baseline and 12 months later. Plasma IL-33 and sST2 levels were determined using enzyme-linked immunosorbent assay kits. Baseline IL-33 and sST2 levels were associated with inflammatory markers and cardiovascular (CV) risk factors. Overall, 44(45%), 18(18%), and 21(21%) patients achieved remission based on 28-joint disease activity score (DAS28), Boolean, and simplified disease activity score (SDAI) criteria at 12 months, respectively. Patients with detectable IL-33 at baseline were less likely to achieve DAS28 (P = 0.010) and SDAI remission (P = 0.021), while a lower baseline sST2 level was able to predict DAS28, Boolean, and SDAI remission (P = 0.005, 0.001, and <0.001, respectively). Using multivariate analysis, a lower baseline sST2 level independently predict Boolean (OR = 0.789; P = 0.005) and SDAI remission (0.812; P = 0.008). Regarding carotid atherosclerosis, 9/98(9.2%) patients had plaque progression at 12 months. Baseline IL-33 was detectable in 8/9(89%) and 42/83(51%) of patients with and without plaque progression respectively (P = 0.029). Baseline detectable IL-33 was an independent predictor for plaque progression after adjusting for traditional CV risk factors (P = 0.017). Lower baseline sST2 levels independently predict disease remission and baseline detectable IL-33 independently predicts carotid plaque progression in ERA patients. This study suggests that inflammation induced by the IL-33/ST2 axis may play a significant role in the development of cardiovascular disease in RA. Copyright © 2015 Elsevier Inc. All rights reserved.

Physical exercise and blood pressure with reference to the angiotensinogen M235T polymorphism.

PubMed

Rauramaa, Rainer; Kuhanen, Raimo; Lakka, Timo A; Väisänen, Sari B; Halonen, Pirjo; Alén, Markku; Rankinen, Tuomo; Bouchard, Claude

2002-08-14

We investigated the role of the angiotensinogen (AGT) gene M235T polymorphism in determining blood pressure (BP) response to moderate intensity exercise in a 6-yr randomized controlled trial in 140 middle-aged men. Sitting, supine, and standing blood pressures were measured annually. Of the randomized men, 86% participated in the trial for 6 yr. Submaximal cardiorespiratory fitness increased by 16% in the exercise group. In the M homozygotes, sitting systolic BP decreased by 1.0 mmHg in the exercise but increased by 14.6 mmHg in the reference group (P = 0.007 for net effect). Sitting and supine diastolic BP decreased by 6.2 and 3.3 mmHg in the exercise but increased by 2.8 and 3.2 mmHg in the reference group (P = 0.026 and 0.024 for net effects), respectively. Regular moderate intensity exercise attenuates aging-related increase in systolic BP and decreases diastolic BP among the M homozygotes of the AGT gene M235T polymorphism.

Application of stochastic processes in random growth and evolutionary dynamics

NASA Astrophysics Data System (ADS)

Oikonomou, Panagiotis

We study the effect of power-law distributed randomness on the dynamical behavior of processes such as stochastic growth patterns and evolution. First, we examine the geometrical properties of random shapes produced by a generalized stochastic Loewner Evolution driven by a superposition of a Brownian motion and a stable Levy process. The situation is defined by the usual stochastic Loewner Evolution parameter, kappa, as well as alpha which defines the power-law tail of the stable Levy distribution. We show that the properties of these patterns change qualitatively and singularly at critical values of kappa and alpha. It is reasonable to call such changes "phase transitions". These transitions occur as kappa passes through four and as alpha passes through one. Numerical simulations are used to explore the global scaling behavior of these patterns in each "phase". We show both analytically and numerically that the growth continues indefinitely in the vertical direction for alpha greater than 1, goes as logarithmically with time for alpha equals to 1, and saturates for alpha smaller than 1. The probability density has two different scales corresponding to directions along and perpendicular to the boundary. Scaling functions for the probability density are given for various limiting cases. Second, we study the effect of the architecture of biological networks on their evolutionary dynamics. In recent years, studies of the architecture of large networks have unveiled a common topology, called scale-free, in which a majority of the elements are poorly connected except for a small fraction of highly connected components. We ask how networks with distinct topologies can evolve towards a pre-established target phenotype through a process of random mutations and selection. We use networks of Boolean components as a framework to model a large class of phenotypes. Within this approach, we find that homogeneous random networks and scale-free networks exhibit drastically different evolutionary paths. While homogeneous random networks accumulate neutral mutations and evolve by sparse punctuated steps, scale-free networks evolve rapidly and continuously towards the target phenotype. Moreover, we show that scale-free networks always evolve faster than homogeneous random networks; remarkably, this property does not depend on the precise value of the topological parameter. By contrast, homogeneous random networks require a specific tuning of their topological parameter in order to optimize their fitness. This model suggests that the evolutionary paths of biological networks, punctuated or continuous, may solely be determined by the network topology.

Two- and three-input TALE-based AND logic computation in embryonic stem cells.

PubMed

Lienert, Florian; Torella, Joseph P; Chen, Jan-Hung; Norsworthy, Michael; Richardson, Ryan R; Silver, Pamela A

2013-11-01

Biological computing circuits can enhance our ability to control cellular functions and have potential applications in tissue engineering and medical treatments. Transcriptional activator-like effectors (TALEs) represent attractive components of synthetic gene regulatory circuits, as they can be designed de novo to target a given DNA sequence. We here demonstrate that TALEs can perform Boolean logic computation in mammalian cells. Using a split-intein protein-splicing strategy, we show that a functional TALE can be reconstituted from two inactive parts, thus generating two-input AND logic computation. We further demonstrate three-piece intein splicing in mammalian cells and use it to perform three-input AND computation. Using methods for random as well as targeted insertion of these relatively large genetic circuits, we show that TALE-based logic circuits are functional when integrated into the genome of mouse embryonic stem cells. Comparing construct variants in the same genomic context, we modulated the strength of the TALE-responsive promoter to improve the output of these circuits. Our work establishes split TALEs as a tool for building logic computation with the potential of controlling expression of endogenous genes or transgenes in response to a combination of cellular signals.

Detection of colorectal masses in CT colonography: application of deep residual networks for differentiating masses from normal colon anatomy

NASA Astrophysics Data System (ADS)

Näppi, Janne J.; Hironaka, Toru; Yoshida, Hiroyuki

2018-02-01

Even though the clinical consequences of a missed colorectal cancer far outweigh those of a missed polyp, there has been little work on computer-aided detection (CADe) for colorectal masses in CT colonography (CTC). One of the problems is that it is not clear how to manually design mathematical image-based features that could be used to differentiate effectively between masses and certain types of normal colon anatomy such as ileocecal valves (ICVs). Deep learning has demonstrated ability to automatically determine effective discriminating features in many image-based problems. Recently, residual networks (ResNets) were developed to address the practical problems of constructing deep network architectures for optimizing the performance of deep learning. In this pilot study, we compared the classification performance of a conventional 2D-convolutional ResNet (2D-ResNet) with that of a volumetric 3D-convolutional ResNet (3D-ResNet) in differentiating masses from normal colon anatomy in CTC. For the development and evaluation of the ResNets, 695 volumetric images of biopsy-proven colorectal masses, ICVs, haustral folds, and rectal tubes were sampled from 196 clinical CTC cases and divided randomly into independent training, validation, and test datasets. The training set was expanded by use of volumetric data augmentation. Our preliminary results on the 140 test samples indicate that it is feasible to train a deep volumetric 3D-ResNet for performing effective image-based discriminations in CTC. The 3D-ResNet slightly outperformed the 2D-ResNet in the discrimination of masses and normal colon anatomy, but the statistical difference between their very high classification accuracies was not significant. The highest classification accuracy was obtained by combining the mass-likelihood estimates of the 2D- and 3D-ResNets, which enabled correct classification of all of the masses.

Cost analysis of a patient navigation system to increase screening colonoscopy adherence among urban minorities.

PubMed

Jandorf, Lina; Stossel, Lauren M; Cooperman, Julia L; Graff Zivin, Joshua; Ladabaum, Uri; Hall, Diana; Thélémaque, Linda D; Redd, William; Itzkowitz, Steven H

2013-02-01

Patient navigation (PN) is being used increasingly to help patients complete screening colonoscopy (SC) to prevent colorectal cancer. At their large, urban academic medical center with an open-access endoscopy system, the authors previously demonstrated that PN programs produced a colonoscopy completion rate of 78.5% in a cohort of 503 patients (predominantly African Americans and Latinos with public health insurance). Very little is known about the direct costs of implementing PN programs. The objective of the current study was to perform a detailed cost analysis of PN programs at the authors' institution from an institutional perspective. In 2 randomized controlled trials, average-risk patients who were referred for SC by primary care providers were recruited for PN between May 2008 and May 2010. Patients were randomized to 1 of 4 PN groups. The cost of PN and net income to the institution were determined in a cost analysis. Among 395 patients who completed colonoscopy, 53.4% underwent SC alone, 30.1% underwent colonoscopy with biopsy, and 16.5% underwent snare polypectomy. Accounting for the average contribution margins of each procedure type, the total revenue was $95,266.00. The total cost of PN was $14,027.30. Net income was $81,238.70. In a model sample of 1000 patients, net incomes for the institutional completion rate (approximately 80%), the historic PN program (approximately 65%), and the national average (approximately 50%) were compared. The current PN program generated additional net incomes of $35,035.50 and $44,956.00, respectively. PN among minority patients with mostly public health insurance generated additional income to the institution, mainly because of increased colonoscopy completion rates. Copyright © 2012 American Cancer Society.

Health impact and cost-effectiveness of a private sector bed net distribution: experimental evidence from Zambia.

PubMed

Sedlmayr, Richard; Fink, Günther; Miller, John M; Earle, Duncan; Steketee, Richard W

2013-03-18

Relatively few programmes have attempted to actively engage the private sector in national malaria control efforts. This paper evaluates the health impact of a large-scale distribution of insecticide-treated nets (ITNs) conducted in partnership with a Zambian agribusiness, and its cost-effectiveness from the perspective of the National Malaria Control Programme (NMCP). The study was designed as a cluster-randomized controlled trial. A list of 81,597 cotton farmers was obtained from Dunavant, a contract farming company in Zambia's cotton sector, in December 2010. 39,963 (49%) were randomly selected to obtain one ITN each. Follow-up interviews were conducted with 438 farmers in the treatment and 458 farmers in the control group in June and July 2011. Treatment and control households were compared with respect to bed net ownership, bed net usage, self-reported fever, and self-reported confirmed malaria. Cost data was collected throughout the programme. The distribution effectively reached target beneficiaries, with approximately 95% of households in the treatment group reporting that they had received an ITN through the programme. The average increase in the fraction of household members sleeping under an ITN the night prior to the interview was 14.6 percentage points (p-value <0.001). Treatment was associated with a 42 percent reduction in the odds of self-reported fever (p-value <0.001) and with a 49 percent reduction in the odds of self-reported malaria (p-value 0.002). This was accomplished at a cost of approximately five US$ per ITN to Zambia's NMCP. The results illustrate that existing private sector networks can efficiently control malaria in remote rural regions. The intra-household allocation of ITNs distributed through this channel was comparable to that of ITNs received from other sources, and the health impact remained substantial.

Changes of attachment characteristics during psychotherapy of patients with social anxiety disorder: Results from the SOPHO-Net trial

PubMed Central

Strauß, Bernhard; Altmann, Uwe; Manes, Susanne; Tholl, Anne; Koranyi, Susan; Nolte, Tobias; Beutel, Manfred E.; Wiltink, Jörg; Herpertz, Stephan; Hiller, Wolfgang; Hoyer, Jürgen; Joraschky, Peter; Nolting, Björn; Ritter, Viktoria; Stangier, Ulrich; Willutzki, Ulrike; Salzer, Simone; Leibing, Eric; Leichsenring, Falk; Kirchmann, Helmut

2018-01-01

Objectives Within a randomized controlled trial contrasting the outcome of manualized cognitive-behavioral (CBT) and short term psychodynamic therapy (PDT) compared to a waiting list condition (the SOPHO-Net trial), we set out to test whether self-reported attachment characteristics change during the treatments and if these changes differ between treatments. Research design and methods 495 patients from the SOPHO-Net trial (54.5% female, mean age 35.2 years) who were randomized to either CBT, PDT or waiting list (WL) completed the partner-related revised Experiences in Close Relationships Questionnaire (ECR-R) before and after treatment and at 6 and 12 months follow-up. The Liebowitz Social Anxiety Scale (LSAS) was administered at pre-treatment, post-treatment, and at 6-month and 1-year follow-up. ECR-R scores were first compared to a representative healthy sample (n = 2508) in order to demonstrate that the clinical sample differed significantly from the non-clinical sample with respect to attachment anxiety and avoidance. Results LSAS scores correlated significantly with both ECR-R subscales. Post-therapy, patients treated with CBT revealed significant changes in attachment anxiety and avoidance whereas patients treated with PDT showed no significant changes. Changes between post-treatment and the two follow-ups were significant in both conditions, with minimal (insignificant) differences between treatments at the 12- month follow-up. Conclusions The current study supports recent reviews of mostly naturalistic studies indicating changes in attachment as a result of psychotherapy. Although there were differences between conditions at the end of treatment, these largely disappeared during the follow-up period which is line with the other results of the SOPHO-NET trial. Trial registration Controlled-trials.com ISRCTN53517394 PMID:29518077

Establishing a national knowledge translation and generation network in kidney disease: the CAnadian KidNey KNowledge TraNslation and GEneration NeTwork.

PubMed

Manns, Braden; Barrett, Brendan; Evans, Michael; Garg, Amit; Hemmelgarn, Brenda; Kappel, Joanne; Klarenbach, Scott; Madore, Francois; Parfrey, Patrick; Samuel, Susan; Soroka, Steven; Suri, Rita; Tonelli, Marcello; Wald, Ron; Walsh, Michael; Zappitelli, Michael

2014-01-01

Patients with chronic kidney disease (CKD) do not always receive care consistent with guidelines, in part due to complexities in CKD management, lack of randomized trial data to inform care, and a failure to disseminate best practice. At a 2007 conference of key Canadian stakeholders in kidney disease, attendees noted that the impact of Canadian Society of Nephrology (CSN) guidelines was attenuated given limited formal linkages between the CSN Clinical Practice Guidelines Group, kidney researchers, decision makers and knowledge users, and that further knowledge was required to guide care in patients with kidney disease. The idea for the Canadian Kidney Knowledge Translation and Generation Network (CANN-NET) developed from this meeting. CANN-NET is a pan-Canadian network established in partnership with CSN, the Kidney Foundation of Canada and other professional societies to improve the care and outcomes of patients with and at risk for kidney disease. The initial priority areas for knowledge translation include improving optimal timing of dialysis initiation, and increasing the appropriate use of home dialysis. Given the urgent need for new knowledge, CANN-NET has also brought together a national group of experienced Canadian researchers to address knowledge gaps by encouraging and supporting multicentre randomized trials in priority areas, including management of cardiovascular disease in patients with kidney failure.

Proto-experiences and subjective experiences: classical and quantum concepts.

PubMed

Vimal, Ram Lakhan Pandey

2008-03-01

Deterministic reductive monism and non-reductive substance dualism are two opposite views for consciousness, and both have serious problems. An alternative view is needed. For this, we hypothesize that strings or elementary particles (fermions and bosons) have two aspects: (i) elemental proto-experiences (PEs) as phenomenal aspect, and (ii) mass, charge, and spin as material aspect. Elemental PEs are hypothesized to be the properties of elementary particles and their interactions, which are composed of irreducible fundamental subjective experiences (SEs)/PEs that are in superimposed form in elementary particles and in their interactions. Since SEs/PEs are superimposed, elementary particles are not specific to any SE/PE; they (and all inert matter) are carriers of SEs/PEs, and hence, appear as non-experiential material entities. Furthermore, our hypothesis is that matter and associated elemental PEs co-evolved and co-developed into neural-nets and associated neural-net PEs (neural Darminism), respectively. The signals related to neural PEs interact in a neural-net and neural-net PEs emerges from random process of self-organization. The neural-net PEs are a set of SEs embedded in the neural-net by a non-computational or non-algorithmic process. The non-specificity of elementary particles is transformed into the specificity of neural-nets by neural Darwinism. The specificity of SEs emerges when feedforward and feedback signal interacts in the neuropil and are dependent on wakefulness (i.e., activation) attention, re-entry between neural populations, working memory, stimulus at above threshold, and neural net PE signals. This PE-SE framework integrates reductive and non-reductive views, complements the existing models, bridges the explanatory gaps, and minimizes the problem of causation.

Cost-effective sampling of ¹³⁷Cs-derived net soil redistribution: part 1--estimating the spatial mean across scales of variation.

PubMed

Li, Y; Chappell, A; Nyamdavaa, B; Yu, H; Davaasuren, D; Zoljargal, K

2015-03-01

The (137)Cs technique for estimating net time-integrated soil redistribution is valuable for understanding the factors controlling soil redistribution by all processes. The literature on this technique is dominated by studies of individual fields and describes its typically time-consuming nature. We contend that the community making these studies has inappropriately assumed that many (137)Cs measurements are required and hence estimates of net soil redistribution can only be made at the field scale. Here, we support future studies of (137)Cs-derived net soil redistribution to apply their often limited resources across scales of variation (field, catchment, region etc.) without compromising the quality of the estimates at any scale. We describe a hybrid, design-based and model-based, stratified random sampling design with composites to estimate the sampling variance and a cost model for fieldwork and laboratory measurements. Geostatistical mapping of net (1954-2012) soil redistribution as a case study on the Chinese Loess Plateau is compared with estimates for several other sampling designs popular in the literature. We demonstrate the cost-effectiveness of the hybrid design for spatial estimation of net soil redistribution. To demonstrate the limitations of current sampling approaches to cut across scales of variation, we extrapolate our estimate of net soil redistribution across the region, show that for the same resources, estimates from many fields could have been provided and would elucidate the cause of differences within and between regional estimates. We recommend that future studies evaluate carefully the sampling design to consider the opportunity to investigate (137)Cs-derived net soil redistribution across scales of variation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Relative net vertical impulse determines jumping performance.

PubMed

Kirby, Tyler J; McBride, Jeffrey M; Haines, Tracie L; Dayne, Andrea M

2011-08-01

The purpose of this investigation was to determine the relationship between relative net vertical impulse and jump height in a countermovement jump and static jump performed to varying squat depths. Ten college-aged males with 2 years of jumping experience participated in this investigation (age: 23.3 ± 1.5 years; height: 176.7 ± 4.5 cm; body mass: 84.4 ± 10.1 kg). Subjects performed a series of static jumps and countermovement jumps in a randomized fashion to a depth of 0.15, 0.30, 0.45, 0.60, and 0.75 m and a self-selected depth (static jump depth = 0.38 ± 0.08 m, countermovement jump depth = 0.49 ± 0.06 m). During the concentric phase of each jump, peak force, peak velocity, peak power, jump height, and net vertical impulse were recorded and analyzed. Net vertical impulse was divided by body mass to produce relative net vertical impulse. Increasing squat depth corresponded to a decrease in peak force and an increase in jump height and relative net vertical impulse for both static jump and countermovement jump. Across all depths, relative net vertical impulse was statistically significantly correlated to jump height in the static jump (r = .9337, p < .0001, power = 1.000) and countermovement jump (r = .925, p < .0001, power = 1.000). Across all depths, peak force was negatively correlated to jump height in the static jump (r = -0.3947, p = .0018, power = 0.8831) and countermovement jump (r = -0.4080, p = .0012, power = 0.9050). These results indicate that relative net vertical impulse can be used to assess vertical jump performance, regardless of initial squat depth, and that peak force may not be the best measure to assess vertical jump performance.

Efficient convex-elastic net algorithm to solve the Euclidean traveling salesman problem.

PubMed

Al-Mulhem, M; Al-Maghrabi, T

1998-01-01

This paper describes a hybrid algorithm that combines an adaptive-type neural network algorithm and a nondeterministic iterative algorithm to solve the Euclidean traveling salesman problem (E-TSP). It begins with a brief introduction to the TSP and the E-TSP. Then, it presents the proposed algorithm with its two major components: the convex-elastic net (CEN) algorithm and the nondeterministic iterative improvement (NII) algorithm. These two algorithms are combined into the efficient convex-elastic net (ECEN) algorithm. The CEN algorithm integrates the convex-hull property and elastic net algorithm to generate an initial tour for the E-TSP. The NII algorithm uses two rearrangement operators to improve the initial tour given by the CEN algorithm. The paper presents simulation results for two instances of E-TSP: randomly generated tours and tours for well-known problems in the literature. Experimental results are given to show that the proposed algorithm ran find the nearly optimal solution for the E-TSP that outperform many similar algorithms reported in the literature. The paper concludes with the advantages of the new algorithm and possible extensions.

Compile-Time Schedulability Analysis of Communicating Concurrent Programs

DTIC Science & Technology

2006-06-28

synchronize via the read and write operations on the FIFO channels. These operations have been implemented with the help of semaphores , which...3 1.1.2 Synchronous Dataflow . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1.1.3 Boolean Dataflow...described by concurrent programs . . . . . . . . . 4 1.3 A synchronous dataflow model, its topology matrix, and repetition vector . 10 1.4 Select and

Learning Boolean Networks in HepG2 cells using ToxCast High-Content Imaging Data (SOT annual meeting)

EPA Science Inventory

Cells adapt to their environment via homeostatic processes that are regulated by complex molecular networks. Our objective was to learn key elements of these networks in HepG2 cells using ToxCast High-content imaging (HCI) measurements taken over three time points (1, 24, and 72h...

A Model of Knowledge Based Information Retrieval with Hierarchical Concept Graph.

ERIC Educational Resources Information Center

Kim, Young Whan; Kim, Jin H.

1990-01-01

Proposes a model of knowledge-based information retrieval (KBIR) that is based on a hierarchical concept graph (HCG) which shows relationships between index terms and constitutes a hierarchical thesaurus as a knowledge base. Conceptual distance between a query and an object is discussed and the use of Boolean operators is described. (25…

The Local Minima Problem in Hierarchical Classes Analysis: An Evaluation of a Simulated Annealing Algorithm and Various Multistart Procedures

ERIC Educational Resources Information Center

Ceulemans, Eva; Van Mechelen, Iven; Leenen, Iwin

2007-01-01

Hierarchical classes models are quasi-order retaining Boolean decomposition models for N-way N-mode binary data. To fit these models to data, rationally started alternating least squares (or, equivalently, alternating least absolute deviations) algorithms have been proposed. Extensive simulation studies showed that these algorithms succeed quite…

Bringing Federal Documents to the Forefront for Library Users: Selective Cataloging Using an OPAC.

ERIC Educational Resources Information Center

Oliva, Victor T.

2000-01-01

Reviews the value of federal depository document titles and discuses reasons why many are worth cataloging. Several approaches to cataloging these titles to make them more readily accessible are profiled. The Adelphi University Library (New York) has devised a system, using Boolean logic and an online public access catalog to choose which titles…

Qualitative Comparative Analysis, Necessary Conditions, and Limited Diversity: Some Problematic Consequences of Schneider and Wagemann's Enhanced Standard Analysis

ERIC Educational Resources Information Center

Cooper, Barry; Glaesser, Judith

2016-01-01

We discuss a recent development in the set theoretic analysis of data sets characterized by limited diversity. Ragin, in developing his Qualitative Comparative Analysis (QCA), developed a standard analysis that produces parsimonious, intermediate, and complex Boolean solutions of truth tables. Schneider and Wagemann argue this standard analysis…

Crisp Sets and Boolean Algebra: A Research Strategy for Student Affairs

ERIC Educational Resources Information Center

Banning, James; Eversole, Barbara; Most, David; Kuk, Linda

2008-01-01

A review of student affairs journals clearly points out that most, if not all, research strategies within the field fall within traditional approaches based on quantitative methods and, more recently, qualitative methods. The purpose of this article is not to discourage use of these time honored research strategies, but to suggest the inclusion of…

Impact of a Primary Care CKD Registry in a US Public Safety-Net Health Care Delivery System: A Pragmatic Randomized Trial.

PubMed

Tuot, Delphine S; McCulloch, Charles E; Velasquez, Alexandra; Schillinger, Dean; Hsu, Chi-Yuan; Handley, Margaret; Powe, Neil R

2018-04-23

Many individuals with chronic kidney disease (CKD) do not receive guideline-concordant care. We examined the impact of a team-based primary care CKD registry on clinical measures and processes of care among patients with CKD cared for in a public safety-net health care delivery system. Pragmatic trial of a CKD registry versus a usual-care registry for 1 year. Primary care providers (PCPs) and their patients with CKD in a safety-net primary care setting in San Francisco. The CKD registry identified at point of care all patients with CKD, those with blood pressure (BP)>140/90mmHg, those without angiotensin-converting enzyme (ACE) inhibitor/angiotensin receptor blocker (ARB) prescription, and those without albuminuria quantification in the past year. It also provided quarterly feedback pertinent to these metrics to promote "outreach" to patients with CKD. The usual-care registry provided point-of-care cancer screening and immunization data. Changes in systolic BP at 12 months (primary outcome), proportion of patients with BP control, prescription of ACE inhibitors/ARBs, quantification of albuminuria, severity of albuminuria, and estimated glomerular filtration rate. The patient population (n=746) had a mean age of 56.7±12.1 (standard deviation) years, was 53% women, and was diverse (8% non-Hispanic white, 35.7% black, 24.5% Hispanic, and 24.4% Asian). Randomization to the CKD registry (30 PCPs, 285 patients) versus the usual-care registry (49 PCPs, 461 patients) was associated with 2-fold greater odds of ACE inhibitor/ARB prescription (adjusted OR, 2.25; 95% CI, 1.45-3.49) and albuminuria quantification (adjusted OR, 2.44; 95% CI, 1.38-4.29) during the 1-year study period. Randomization to the CKD registry was not associated with changes in systolic BP, proportion of patients with uncontrolled BP, or degree of albuminuria or estimated glomerular filtration rate. Potential misclassification of CKD; missing baseline medication data; limited to study of a public safety-net health care system. A team-based safety-net primary care CKD registry did not improve BP parameters, but led to greater albuminuria quantification and more ACE inhibitor/ARB prescriptions after 1 year. Adoption of team-based CKD registries may represent an important step in translating evidence into practice for CKD management. Copyright © 2018 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

Impact of lambdacyhalothrin capsule suspension treated bed nets on malaria in tribal villages of Malkangiri district, Orissa, India.

PubMed

Sahu, S S; Vijayakumar, T; Kalyanasundaram, M; Subramanian, S; Jambulingam, P

2008-09-01

Insecticide treated mosquito nets are increasingly being used in malaria control programmes. One of the problems with the treatment of bed nets with conventional formulations of insecticides was that regular washing of treated nets diminish insecticidal effect. Lambdacyhalothrin 2.5 capsule suspension (CS) (2.5% a.i., w/v), a new water-based microencapsulated formulation is reported to have wash-resistant property and longer persistence on the netting material than other formulations. We evaluated the impact of the use of nylon bed nets treated with lambdacyhalothrin 2.5 CS at 10 mg (a.i.)/m(2) in comparison to untreated nets and no nets on malaria in tribal villages in Orissa. Nine foothill villages, highly endemic for falciparum malaria, from the Primary Health Centre (PHC) areas of Khairput and Kudumulugumma of Malkangiri district, Orissa, were divided into three groups, each with a population of about 500 and allocated randomly for treated (TN) and untreated nets (UN) and no nets (NN). Bed nets were distributed in September 2001 and retreatment was done in June 2002. The impact was assessed based on the changes in vector density, parous rate, malaria incidence and parasite rates. Indoor-resting collections of Anopheles fluviatilis and An. culicifacies were made at fortnightly intervals from fixed human dwellings. Mass blood surveys before and after distribution of nets and fortnightly active surveillance were carried out to assess the change in parasite rates and malaria incidence. Bioassays were conducted at fortnightly intervals on the bed nets supplied to the villagers. The reductions in indoor resting catches of An. fluviatilis and An. culicifacies were 96 and 38 per cent in villages with treated nets and 2.6 and 23 per cent in villages with untreated nets respectively compared to no net villages. For six months following treatment, 100 per cent mortality of An. fluviatilis was observed on the unwashed nets and on the nets washed once or twice. After re-treatment, 100 per cent mortality of An. fluviatilis or An. culicifacies was observed for nine months even after two washes. Usage rates of treated and untreated nets varied seasonally; 58.9 and 46.3 per cent in rainy season, 48.6 and 37.1 per cent in winter season and 38.1 and 31.6 per cent in summer season respectively. Reductions in malaria parasite rates were about 65 per cent in the treated net villages and 39 per cent in the untreated net villages compared to no net villages. About 75 per cent of treated nets and 60 per cent of untreated nets were in usable condition 19 months after distribution. The estimated protection factor based on malaria incidence was 86 per cent for the treated nets during both post-treatment and post-retreatment periods and 34 and 51 per cent for untreated nets for the corresponding periods compared to no nets. The results of the study showed that the use of bed nets treated nets with CS formulation of lambdacyhalothrin at 10 mg (a.i.)/m(2) was acceptable to the community and re-treatment of nets at nine-monthly intervals can significantly reduce density and survival of An. fluviatilis and incidence of falciparum malaria.

The effect of delivery mechanisms on the uptake of bed net re-impregnation in Kilifi District, Kenya.

PubMed

Snow, R W; McCabe, E; Mbogo, C N; Molyneux, C S; Some, E S; Mung'ala, V O; Nevill, C G

1999-03-01

The results of recently completed trials in Africa of insecticide-treated bed nets (ITBN) offer new possibilities for malaria control. These experimental trials aimed for high ITBN coverage combined with high re-treatment rates. Whilst necessary to understand protective efficacy, the approaches used to deliver the intervention provide few indications of what coverage of net re-treatment would be under operational conditions. Varied delivery and financing strategies have been proposed for the sustainable delivery of ITBNs and re-treatment programmes. Following the completion of a randomized, controlled trial on the Kenyan coast, a series of suitable delivery strategies were used to continue net re-treatment in the area. The trial adopted a bi-annual, house-to-house re-treatment schedule free of charge using research project staff and resulted in over 95% coverage of nets issued to children. During the year following the trial, sentinel dipping stations were situated throughout the community and household members informed of their position and opening times. This free re-treatment service achieved between 61-67% coverage of nets used by children for three years. In 1997 a social marketing approach, that introduced cost-retrieval, was used to deliver the net re-treatment services. The immediate result of this transition was that significantly fewer of the mothers who had used the previous re-treatment services adopted this revised approach and coverage declined to 7%. The future of new delivery services and their financing are discussed in the context of their likely impact upon previously defined protective efficacy and cost-effectiveness estimates.

Using deep learning for detecting gender in adult chest radiographs

NASA Astrophysics Data System (ADS)

Xue, Zhiyun; Antani, Sameer; Long, L. Rodney; Thoma, George R.

2018-03-01

In this paper, we present a method for automatically identifying the gender of an imaged person using their frontal chest x-ray images. Our work is motivated by the need to determine missing gender information in some datasets. The proposed method employs the technique of convolutional neural network (CNN) based deep learning and transfer learning to overcome the challenge of developing handcrafted features in limited data. Specifically, the method consists of four main steps: pre-processing, CNN feature extractor, feature selection, and classifier. The method is tested on a combined dataset obtained from several sources with varying acquisition quality resulting in different pre-processing steps that are applied for each. For feature extraction, we tested and compared four CNN architectures, viz., AlexNet, VggNet, GoogLeNet, and ResNet. We applied a feature selection technique, since the feature length is larger than the number of images. Two popular classifiers: SVM and Random Forest, are used and compared. We evaluated the classification performance by cross-validation and used seven performance measures. The best performer is the VggNet-16 feature extractor with the SVM classifier, with accuracy of 86.6% and ROC Area being 0.932 for 5-fold cross validation. We also discuss several misclassified cases and describe future work for performance improvement.

Analysis of Phase-Type Stochastic Petri Nets With Discrete and Continuous Timing

NASA Technical Reports Server (NTRS)

Jones, Robert L.; Goode, Plesent W. (Technical Monitor)

2000-01-01

The Petri net formalism is useful in studying many discrete-state, discrete-event systems exhibiting concurrency, synchronization, and other complex behavior. As a bipartite graph, the net can conveniently capture salient aspects of the system. As a mathematical tool, the net can specify an analyzable state space. Indeed, one can reason about certain qualitative properties (from state occupancies) and how they arise (the sequence of events leading there). By introducing deterministic or random delays, the model is forced to sojourn in states some amount of time, giving rise to an underlying stochastic process, one that can be specified in a compact way and capable of providing quantitative, probabilistic measures. We formalize a new non-Markovian extension to the Petri net that captures both discrete and continuous timing in the same model. The approach affords efficient, stationary analysis in most cases and efficient transient analysis under certain restrictions. Moreover, this new formalism has the added benefit in modeling fidelity stemming from the simultaneous capture of discrete- and continuous-time events (as opposed to capturing only one and approximating the other). We show how the underlying stochastic process, which is non-Markovian, can be resolved into simpler Markovian problems that enjoy efficient solutions. Solution algorithms are provided that can be easily programmed.

Multipartnered Fertility and Depression among Fragile Families

ERIC Educational Resources Information Center

Turney, Kristin; Carlson, Marcia J.

2011-01-01

We used data from the Fragile Families and Child Wellbeing Study to examine the association between multipartnered fertility (MPF)--when parents have children with more than one partner--and depression. Random-effects models suggested that MPF is associated with a greater likelihood of depression, net of family structure and other covariates.…

Simulation of diffuse-charge capacitance in electric double layer capacitors

NASA Astrophysics Data System (ADS)

Sun, Ning; Gersappe, Dilip

2017-01-01

We use a Lattice Boltzmann Model (LBM) in order to simulate diffuse-charge dynamics in Electric Double Layer Capacitors (EDLCs). Simulations are carried out for both the charge and the discharge processes on 2D systems of complex random electrode geometries (pure random, random spheres and random fibers). The steric effect of concentrated solutions is considered by using a Modified Poisson-Nernst-Planck (MPNP) equations and compared with regular Poisson-Nernst-Planck (PNP) systems. The effects of electrode microstructures (electrode density, electrode filler morphology, filler size, etc.) on the net charge distribution and charge/discharge time are studied in detail. The influence of applied potential during discharging process is also discussed. Our studies show how electrode morphology can be used to tailor the properties of supercapacitors.

Rapid dark-blood carotid vessel-wall imaging with random bipolar gradients in a radial SSFP acquisition.

PubMed

Lin, Hung-Yu; Flask, Chris A; Dale, Brian M; Duerk, Jeffrey L

2007-06-01

To investigate and evaluate a new rapid dark-blood vessel-wall imaging method using random bipolar gradients with a radial steady-state free precession (SSFP) acquisition in carotid applications. The carotid artery bifurcations of four asymptomatic volunteers (28-37 years old, mean age = 31 years) were included in this study. Dark-blood contrast was achieved through the use of random bipolar gradients applied prior to the signal acquisition of each radial projection in a balanced SSFP acquisition. The resulting phase variation for moving spins established significant destructive interference in the low-frequency region of k-space. This phase variation resulted in a net nulling of the signal from flowing spins, while the bipolar gradients had a minimal effect on the static spins. The net effect was that the regular SSFP signal amplitude (SA) in stationary tissues was preserved while dark-blood contrast was achieved for moving spins. In this implementation, application of the random bipolar gradient pulses along all three spatial directions nulled the signal from both in-plane and through-plane flow in phantom and in vivo studies. In vivo imaging trials confirmed that dark-blood contrast can be achieved with the radial random bipolar SSFP method, thereby substantially reversing the vessel-to-lumen contrast-to-noise ratio (CNR) of a conventional rectilinear SSFP "bright-blood" acquisition from bright blood to dark blood with only a modest increase in TR (approximately 4 msec) to accommodate the additional bipolar gradients. Overall, this sequence offers a simple and effective dark-blood contrast mechanism for high-SNR SSFP acquisitions in vessel wall imaging within a short acquisition time.

A cost-benefit analysis of three older adult fall prevention interventions.

PubMed

Carande-Kulis, Vilma; Stevens, Judy A; Florence, Curtis S; Beattie, Bonita L; Arias, Ileana

2015-02-01

One out of three persons aged 65 and older falls annually and 20% to 30% of falls result in injury. The purpose of this cost-benefit analysis was to identify community-based fall interventions that were feasible, effective, and provided a positive return on investment (ROI). A third-party payer perspective was used to determine the costs and benefits of three effective fall interventions. Intervention effectiveness was based on randomized controlled trial results. National data were used to estimate the average annual benefits from averting the direct medical costs of a fall. The net benefit and ROI were estimated for each of the interventions. For the Otago Exercise Program delivered to persons aged 65 and older, the net benefit was $121.85 per participant and the ROI was 36% for each dollar invested. For Otago delivered to persons aged 80 and older, the net benefit was $429.18 and the ROI was 127%. Tai chi: Moving for Better Balance had a net benefit of $529.86 and an ROI of 509% and Stepping On had a net benefit of $134.37 and an ROI of 64%. All three fall interventions provided positive net benefits. The ROIs showed that the benefits not only covered the implementation costs but also exceeded the expected direct program delivery costs. These results can help health care funders and other community organizations select appropriate and effective fall interventions that also can provide positive returns on investment. Published by Elsevier Ltd.

Verification of VLSI designs

NASA Technical Reports Server (NTRS)

Windley, P. J.

1991-01-01

In this paper we explore the specification and verification of VLSI designs. The paper focuses on abstract specification and verification of functionality using mathematical logic as opposed to low-level boolean equivalence verification such as that done using BDD's and Model Checking. Specification and verification, sometimes called formal methods, is one tool for increasing computer dependability in the face of an exponentially increasing testing effort.

An Analysis of Cryptographically Significant Boolean Functions With High Correlation Immunity by Reconfigurable Computer

DTIC Science & Technology

2010-12-01

with high correlation immunity and then evaluate these functions for other desirable cryptographic features. C. METHOD The only known primary methods...out if not used) # ---------------------------------- # PRIMARY = < primary file 1> < primary file 2> #SECONDARY = <secondary file 1...finding the fuction value for a //set u and for each value of v. end end

Sequential, progressive, equal-power, reflective beam-splitter arrays

NASA Astrophysics Data System (ADS)

Manhart, Paul K.

2017-11-01

The equations to calculate equal-power reflectivity of a sequential series of beam splitters is presented. Non-sequential optical design examples are offered for uniform illumination using diode lasers. Objects created using Boolean operators and Swept Surfaces can create objects capable of reflecting light into predefined elevation and azimuth angles. Analysis of the illumination patterns for the array are also presented.

Study of Strategies Used in Online Searching: 2. Positional Logic--an Example of the Importance of Selecting the Right Boolean Operator.

ERIC Educational Resources Information Center

Oldroyd, Betty K.; Schroder, J. J.

1982-01-01

Reviews the advantages and disadvantages of different types of term combination using the positional logic capability of online information retrieval systems and describes a study in which searches for material on "microwave integrated circuits" were conducted in order to find the most economical way of generating the most relevant…

Developing and Testing an Online Tool for Teaching GIS Concepts Applied to Spatial Decision-Making

ERIC Educational Resources Information Center

Carver, Steve; Evans, Andy; Kingston, Richard

2004-01-01

The development and testing of a Web-based GIS e-learning resource is described. This focuses on the application of GIS for siting a nuclear waste disposal facility and the associated principles of spatial decision-making using Boolean and weighted overlay methods. Initial student experiences in using the system are analysed as part of a research…

An Investigation of the Mathematical Models of Piaget's Psychological Theory of Cognitive Learning. Final Report.

ERIC Educational Resources Information Center

Kalechofsky, Robert

This research paper proposes several mathematical models which help clarify Piaget's theory of cognition on the concrete and formal operational stages. Some modified lattice models were used for the concrete stage and a combined Boolean Algebra and group theory model was used for the formal stage. The researcher used experiments cited in the…