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At least 181 records · Page 10Linked to original sources
PubMed2004

Asynchronous adaptive time step in quantitative cellular automata modeling.

BACKGROUND: The behaviors of cells in metazoans are context dependent, thus large-scale multi-cellular modeling is often necessary, for which cellular automata are natural candidates. Two related issues are involved in cellular automata based multi-cellular modeling: how to introduce differential equation based quantitative computing to precisely describe cellular activity, and upon it, how to solve the heavy time consumption issue in simulation. RESULTS: Based on a modified, language based cellular automata system we extended that allows ordinary differential equations in models, we introduce a method implementing asynchronous adaptive time step in simulation that can considerably improve efficiency yet without a significant sacrifice of accuracy. An average speedup rate of 4-5 is achieved in the given example. CONCLUSIONS: Strategies for reducing time consumption in simulation are indispensable for large-scale, quantitative multi-cellular models, because even a small 100 x 100 x 100 tissue slab contains one million cells. Distributed and adaptive time step is a practical solution in cellular automata environment.

Animals↗
PubMed2004

An object model and database for functional genomics.

MOTIVATION: Large-scale functional genomics analysis is now feasible and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development of public data repositories and to improve data sharing. There is an established data format for microarrays (microarray gene expression markup language, MAGE-ML) and a draft standard for proteomics (PEDRo). We believe that all types of functional genomics experiments should be annotated in a consistent manner, and we hope to open up new ways of comparing multiple datasets used in functional genomics. RESULTS: We have created a functional genomics experiment object model (FGE-OM), developed from the microarray model, MAGE-OM and two models for proteomics, PEDRo and our own model (Gla-PSI-Glasgow Proposal for the Proteomics Standards Initiative). FGE-OM comprises three namespaces representing (i) the parts of the model common to all functional genomics experiments; (ii) microarray-specific components; and (iii) proteomics-specific components. We believe that FGE-OM should initiate discussion about the contents and structure of the next version of MAGE and the future of proteomics standards. A prototype database called RNA And Protein Abundance Database (RAPAD), based on FGE-OM, has been implemented and populated with data from microbial pathogenesis. AVAILABILITY: FGE-OM and the RAPAD schema are available from http://www.gusdb.org/fge.html, along with a set of more detailed diagrams. RAPAD can be accessed by registration at the site.

Abstracting and Indexing↗
PubMed2004

Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running.

BACKGROUND: Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. METHODS: We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. RESULTS: We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. CONCLUSIONS: Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods described.

Anisotropy↗
PubMed2006

GALGO: an R package for multivariate variable selection using genetic algorithms.

SUMMARY: The development of statistical models linking the molecular state of a cell to its physiology is one of the most important tasks in the analysis of Functional Genomics data. Because of the large number of variables measured a comprehensive evaluation of variable subsets cannot be performed with available computational resources. It follows that an efficient variable selection strategy is required. However, although software packages for performing univariate variable selection are available, a comprehensive software environment to develop and evaluate multivariate statistical models using a multivariate variable selection strategy is still needed. In order to address this issue, we developed GALGO, an R package based on a genetic algorithm variable selection strategy, primarily designed to develop statistical models from large-scale datasets.

Algorithms↗
PubMed2001

Reliable short-term memory in the trion model: toward a cortical language and grammar.

It has previously been shown that Hebb learning in a single column in the trion model of cortical organization occurs by selection. Motivated by von Neumann's solution for obtaining reliability and by models of circulating cortical activity, we introduce Hebb intercolumnar couplings to achieve dramatic enhancements in reliability in the firing of connected columns. In order for these enhancements to occur, specific temporal phase differences must exist between the same inherent spatial-temporal memory patterns in connected columns. We then generalize the criteria of large enhancements in the global firing of the entire connected columnar network to investigate the case when different inherent memory patterns are in the columns. The spatial rotations as well as the temporal phases now are crucial. Only certain combinations of inherent memory patterns meet these criteria with the symmetry properties playing a major role. The columnar order of these memory patterns not in the same symmetry family can be extremely important. This yields the first higher-level architecture of a cortical language and grammar within the trion model. The implications of this result with regard to an innate human language and grammar are discussed.

Cerebral Cortex↗
PubMed1984

Computer programs as theories in biology.

Complex theories in biology may be developed, refined, and tested by the use of computer programmed simulations. The computer is recognized as a powerful tool for theory development; it is, in fact, the only means of thoroughly testing and examining a large and intricate theory. A program as a text is a statement of a theory and when run on the computer it is model of that theory. As the program's behavior is then the major argument for the credibility of a large and complex theory, the program itself is the only irrefutable statement of the theory. Bur programs written in the currently available programming languages tend to be incomprehensible. We argue that the program should be the definitive statement of the theory. In addition, the program plus a series of abstractions is a vehicle for effective communication of complex theories in biology. Several techniques of computer science are borrowed, for the purpose of developing a methodology for abstraction and a language for representing abstractions. The arguments are fully illustrated with a recently published biological theory.

Communication↗
PubMed2005

Cellular automata with object-oriented features for parallel molecular network modeling.

Cellular automata are an important modeling paradigm for studying the dynamics of large, parallel systems composed of multiple, interacting components. However, to model biological systems, cellular automata need to be extended beyond the large-scale parallelism and intensive communication in order to capture two fundamental properties characteristic of complex biological systems: hierarchy and heterogeneity. This paper proposes extensions to a cellular automata language, Cellang, to meet this purpose. The extended language, with object-oriented features, can be used to describe the structure and activity of parallel molecular networks within cells. Capabilities of this new programming language include object structure to define molecular programs within a cell, floating-point data type and mathematical functions to perform quantitative computation, message passing capability to describe molecular interactions, as well as new operators, statements, and built-in functions. We discuss relevant programming issues of these features, including the object-oriented description of molecular interactions with molecule encapsulation, message passing, and the description of heterogeneity and anisotropy at the cell and molecule levels. By enabling the integration of modeling at the molecular level with system behavior at cell, tissue, organ, or even organism levels, the program will help improve our understanding of how complex and dynamic biological activities are generated and controlled by parallel functioning of molecular networks. Index Terms-Cellular automata, modeling, molecular network, object-oriented.

Algorithms↗
PubMed2000

A centralised telephone service for tobacco cessation: the California experience.

OBJECTIVE: To provide an overview of the California Smokers' Helpline, an increasingly popular telephone program for tobacco cessation in California since 1992. As many states, regions, and nations are contemplating various telephone programs as part of large scale anti-tobacco campaigns, this paper presents a practical model. DESIGN: The Helpline provides Californians with free cessation services that include counselling, self help quit kits, and cessation related information. Services are provided in six spoken languages plus a line for the hearing impaired. The program is promoted statewide by media campaigns, health care providers, local tobacco control programs, and the public school system. SETTING: The Helpline is centrally operated through the University of California, San Diego and provides services statewide via telephone. RESULTS: The Helpline has served over 100 000 tobacco users and has become the chief cessation resource for the Comprehensive Tobacco Control Program in California. Media was the most important referral source for Helpline callers (50%), followed by health care providers (20%). About one third of the callers were ethnic minorities and 17% were 24 years old or younger. Compared to California smokers in general, the callers were more dependent on nicotine and more likely to live with other smokers, but they were also more likely to have tried to quit recently and were more ready to try again. Two randomised trials have demonstrated the efficacy of the Helpline's counselling protocol. CONCLUSION: A centralised helpline operation can be an accessible and effective service for tobacco users and should be included in any large scale, comprehensive tobacco control program.

Adolescent↗
PubMed2005

Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import and export of SBML models. In this way the toolbox connects nicely to other SBML-enabled modelling packages. Models are represented in an internal model format and can be described either by entering ordinary differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis.

Database Management Systems↗
PubMed2003

Competitive exclusion and coexistence of universal grammars.

Universal grammar (UG) is a list of innate constraints that specify the set of grammars that can be learned by the child during primary language acquisition. UG of the human brain has been shaped by evolution. Evolution requires variation. Hence, we have to postulate and study variation of UG. We investigate evolutionary dynamics and language acquisition in the context of multiple UGs. We provide examples for competitive exclusion and stable coexistence of different UGs. More specific UGs admit fewer candidate grammars, and less specific UGs admit more candidate grammars. We will analyze conditions for more specific UGs to outcompete less specific UGs and vice versa. An interesting finding is that less specific UGs can resist invasion by more specific UGs if learning is more accurate. In other words, accurate learning stabilizes UGs that admit large numbers of candidate grammars.

Biological Evolution↗
PubMed1991

Finite dose percutaneous drug absorption: a BASIC program for the solution of the diffusion equation.

A BASIC program to obtain the solution for the diffusion equation describing the finite dose percutaneous absorption pharmacokinetics is shown. Drug amount in the solution matrix, Av, that in the skin which is regarded as a simple diffusion membrane. As, and the drug flux from the skin which is provided by the local circulation per unit area, J, and the blood drug concentration. C, expressed as functions of time are obtained using Fourier series. Usually, a small number (less than 10) of series is enough to obtain the accurate values for Av, As, J, and C. It is also shown that the solution of the diffusion equation reported previously for the specific case where both the diffusion coefficient of a drug through the vehicle and skin-capillary clearance are very large is expressed as a limit.

Administration, Cutaneous↗
PubMed1978

Speech development in hearing-impaired children.

Many hearing-impaired children are unable to speak intelligibly. Research indicates, however, that patterns of errors typically found in the speech of such children could be largely avoided by systematic teaching. The purpose of this paper is to present and discuss a model for the progressive development of speech skills to the levels of automaticity required for fluent spoken language.

Child↗
PubMed1994

Emergence of visual-graphic symbol combinations by youth with moderate or severe mental retardation.

Research and practice on augmentative communication for persons with moderate or severe mental retardation have primarily targeted the acquisition and use of single symbols. Symbol combinations, however, provide insight into how augmented communicators use individual symbols to build more complex communications. In Study 1, untaught symbol combinations produced during natural communication interactions by 7 subjects with mental retardation were examined for their semantic, ordering, and generalization patterns. The symbol combinations largely resembled those produced by young speaking language learners, suggesting that the augmented communicators were following typical patterns of communication in generating their symbol combinations. In Study 2, we examined the symbol combinations modeled for subjects by their partners. The structure of the modeled combinations did not resemble the children's productions, indicating that the children could not have relied on simple rote imitation for their combination production. These results suggest that augmented communicators with mental retardation may use their symbols as speaking children use oral words in the development of complex communications.

Adolescent↗
PubMedDate not supplied

Promoting father-friendly healthcare.

Fathers are taking a more active role in their children's lives and healthcare; consequently, healthcare providers need to be more aware of and attentive to fathers in clinical encounters. The literature on healthcare provider inclusion of fathers is sparse. The focus has been mainly on exhortations to include fathers, or has documented treatment of fathers as invisible in healthcare settings. While not overtly hostile to fathers, healthcare providers occasionally marginalize or ignore them. The purpose of this article is to help healthcare providers: (1) become aware of and assess their interactions with fathers and (2) be more intentional in their interactions with them. To that end, this article includes a self-assessment of one's practice, including the following components: introductions, body language, eye contact, obtaining/giving information, and beliefs about the role of fathers. Intentional interactions for developing more father-friendly healthcare are discussed including both small and large changes, guided by the PLISSIT model. Finally, best practices, challenges, issues, and resources related to father inclusion in healthcare are described. The major issue for providers is to no longer question whether to include fathers, but how.

Child↗
PubMed1998

Progress in modeling and simulation.

For the modeling of systems, the computers are more and more used while the other "media" (including the human intellect) carrying the models are abandoned. For the modeling of knowledges, i.e. of more or less general concepts (possibly used to model systems composed of instances of such concepts), the object-oriented programming is nowadays widely used. For the modeling of processes existing and developing in the time, computer simulation is used, the results of which are often presented by means of animation (graphical pictures moving and changing in time). Unfortunately, the object-oriented programming tools are commonly not designed to be of a great use for simulation while the programming tools for simulation do not enable their users to apply the advantages of the object-oriented programming. Nevertheless, there are exclusions enabling to use general concepts represented at a computer, for constructing simulation models and for their easy modification. They are described in the present paper, together with true definitions of modeling, simulation and object-oriented programming (including cases that do not satisfy the definitions but are dangerous to introduce misunderstanding), an outline of their applications and of their further development. In relation to the fact that computing systems are being introduced to be control components into a large spectrum of (technological, social and biological) systems, the attention is oriented to models of systems containing modeling components.

Computer Simulation↗
PubMed2005

Ambiguity resolution analysis in incremental parsing of natural language.

Incremental parsing gains its importance in natural language processing and psycholinguistics because of its cognitive plausibility. Modeling the associated cognitive data structures, and their dynamics, can lead to a better understanding of the human parser. In earlier work, we have introduced a recursive neural network (RNN) capable of performing syntactic ambiguity resolution in incremental parsing. In this paper, we report a systematic analysis of the behavior of the network that allows us to gain important insights about the kind of information that is exploited to resolve different forms of ambiguity. In attachment ambiguities, in which a new phrase can be attached at more than one point in the syntactic left context, we found that learning from examples allows us to predict the location of the attachment point with high accuracy, while the discrimination amongst alternative syntactic structures with the same attachment point is slightly better than making a decision purely based on frequencies. We also introduce several new ideas to enhance the architectural design, obtaining significant improvements of prediction accuracy, up to 25% error reduction on the same dataset used in previous work. Finally, we report large scale experiments on the entire Wall Street Journal section of the Penn Treebank. The best prediction accuracy of the model on this large dataset is 87.6%, a relative error reduction larger than 50% compared to previous results.

Algorithms↗
PubMed1996

Variation in the application of natural processes: language-dependent constraints in the phonological acquisition of bilingual children.

This paper studies phonological processes and constraints on early phonological and lexical development, as well as the strategies employed by a young Spanish-, Portuguese-, and Hebrew-speaking child-Nurit (the author's niece)-in the construction of her early lexicon. Nurit's linguistic development is compared to that of another Spanish-, Portuguese-, and Hebrew-speaking child-Noam (the author's son). Noam and Nurit's linguistic development is contrasted to that of Berman's (1977) English- and Hebrew-speaking daughter (Shelli). The simultaneous acquisition of similar (closely related languages) such as Spanish and Portuguese versus that of nonrelated languages such as English and Hebrew yields different results: Children acquiring similar languages seem to prefer maintenance as a strategy for the construction of their early lexicon, while children exposed to nonrelated languages appear to prefer reduction to a large extent (Faingold, 1990). The Spanish- and Portuguese-speaking children's high accuracy stems from a wider choice of target words, where the diachronic development of two closely related languages provides a simplified model lexicon to the child.

Child Language↗
PubMed2006

Potential impact of advanced clinical information technology on cancer care in 2015.

New clinical information technologies now sporadically available will soon be in routine clinical use, bringing many changes to all phases of the cancer care continuum. For example, new technologies such as: (1) The next generation Internet; (2) Real-time clinical decision support systems; (3) Off-line, population-based systems; (4) Large, integrated, individual patient-level phenotypic and genotypic databases with intelligent data mining capabilities; (5) Wireless, invasive and non-invasive physiologic monitoring devices; (6) Natural Language Processing (NLP) systems; and (7) Mathematical models of complex biological systems all have the potential to impact significantly the provision of cancer care throughout its continuum. While new information management and communication techniques and technologies will reduce many of the inefficiencies and inaccuracies of our present systems, there will be an equal, and potentially far more dangerous, set of unintended consequences. Informatics investigators, cancer specialists, and health system administrators must focus on the study of what is working and what is not, as well as, on development and testing of the new clinical information management and communication technologies, if we are to be ready for the future.

Cancer Care Facilities↗