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PubMed2006

Optimisation and parallelisation strategies for Monte Carlo simulation of HIV infection.

In recent years, the study of immune response behaviour through mathematical and computational models has attracted considerable efforts. The dynamics of key cell types, and their interactions, has been a primary focus in terms of building a picture of how the immune system responds to a threat. Discrete methods, based on lattice Monte-Carlo (MC) models, with their flexibility and relative simplicity have previously been used to model the immune system behaviour. However, due to speed and memory constraints, large-scale simulations cannot be done on a single computer. Key issues in the reduction of simulation time are code optimisation and code parallelisation. In this paper, optimisation and parallelisation solutions are discussed, with reference to existing MC simulation code for dynamics of HIV infection.

Antibodies, Viral↗

PubMed1996

Syntactic recognition of regulatory regions in Escherichia coli.

MOTIVATION: One of the most common methodologies to identify cis-regulatory sites in regulatory regions in the DNA is that of weight matrices, as testified by several articles in this issue. An alternative to strengthen the computational predictions in regulatory regions is to develop methods that incorporate more biological properties present in such DNA regions. The grammatical implementation presented in this paper provides a concrete example in this direction. RESULTS: On the basis of the analysis of an exhaustive collection of regulatory regions in Escherichia coli, a grammatical model for the regulatory regions of sigma 70 promoters has been developed. The terminal symbols of the grammar represent individual sites for the binding of activator and repressor proteins, and include the precise position of sites in relation to transcription initiation. Combining these symbols, the grammar generates a large number of different sentences, each of which can be searched for matching against a collection of regulatory regions by means of weight matrices specific for each set of sites for individual proteins. On the basis of this grammatical model, a Prolog syntactic recognizer is presented here. Specific subgrammars for ArgR, LexA and TyrR were implemented. When parsing a collection of 128 sigma 70 promoter regions, the syntactic recognizer produces a much lower number of false-positive sites than the standard search using weight matrices.

Algorithms↗

PubMedDate not supplied

The influence of semantic and syntactic context constraints on lexical selection and integration in spoken-word comprehension as revealed by ERPs.

An event-related brain potential experiment was carried out to investigate the influence of semantic and syntactic context constraints on lexical selection and integration in spoken-word comprehension. Subjects were presented with constraining spoken sentences that contained a critical word that was either (a) congruent, (b) semantically and syntactically incongruent, but beginning with the same initial phonemes as the congruent critical word, or (c) semantically and syntactically incongruent, beginning with phonemes that differed from the congruent critical word. Relative to the congruent condition, an N200 effect reflecting difficulty in the lexical selection process was obtained in the semantically and syntactically incongruent condition where word onset differed from that of the congruent critical word. Both incongruent conditions elicited a large N400 followed by a left anterior negativity (LAN) time-locked to the moment of word category violation and a P600 effect. These results would best fit within a cascaded model of spoken-word processing, proclaiming an optimal use of contextual information during spoken-word identification by allowing for semantic and syntactic processing to take place in parallel after bottom-up activation of a set of candidates, and lexical integration to proceed with a limited number of candidates that still match the acoustic input.

Acoustic Stimulation↗

PubMed1995

Optimization of hemodynamic energy expenditure in the arterial system.

Experimental evaluations and comparisons of the passive and active biomechanical properties of isolated blood vessels from different species (dog, pig, calf, human), as well as the nature of different arterial pressure oscillations, reveal that: 1) Characteristic impedance of middle-size and large arteries changes with intraluminal mean pressure usually resulting in a U-shaped function with a minimum value around the normal physiological 100 mmHg pressure; 2) Similarly, pressure dependent adrenergic diameter responses (active strain) of different large arteries also exhibit parabolic shape with an extreme (maximum) value at 50-100 mmHg intraluminal pressure, suggesting that biomechanical characteristics of the vessel wall may define an optimum for hemodynamic operations; 3) Changes in the arterial smooth muscle tone shift the characteristic impedance curve along the pressure axis and alter the slopes of the parabola; 4) There are significant interactions between the fast 1st-order (pulsatile) and the slow 3rd-order arterial pressure wave components. These and some other characteristics of the circulatory system suggest the existence of an "extremal" forced oscillation blood pressure control mechanism in the body, optimizing the afterload of heart and the blood perfusion of systemic microvessels by minimizing the pulsatile energy expenditure at the physiological mean pressure operation level. A versatile mathematical model of this hypothetical mechanism was developed by us on an IBM PC using Pascal and 8086 Assembly languages. Simulation experiments show that such a physiological adaptive system could control arterial pressure effectively. The computer model is available on a PC disc.

Animals↗

PubMed2005

Behavioral assessment of prelingually deaf children before cochlear implantation.

OBJECTIVES/HYPOTHESIS: To determine whether scores from a behavioral assessment of prelingually deafened children who present for cochlear implant surgery are predictive of audiological outcomes. STUDY DESIGN: Retrospective review of longitudinal data collected from 42 children with prelingual hearing loss who presented for a cochlear implant before age 5 years. METHODS: The Vineland Adaptive Behavioral Scales (VABS) was administered during the preimplant workup. Standardized scores reflect daily living skills, socialization, and motor development compared with a normative sample. Regression analyses were conducted to determine whether any subject variables were related to VABS scores. Mixed-model analyses were computed to determine whether preimplant VABS scores were predictive of longitudinal spoken-language data obtained after cochlear implant surgery. RESULTS: Motor scores tended to be higher than nonmotor scores. Nonmotor scores were significantly lower than the normative mean and decreased with testing age. Children with acquired deafness demonstrated lower motor scores than children with congenital causes. Children with higher motor scores demonstrated significantly higher performance on language, vocabulary, and word recognition tests than children with lower motor scores. Nonmotor domains were not as robustly related to spoken-language measures, although similar trends were observed. CONCLUSION: Profound deafness and language delay may confound the assessment of daily living skills and socialization in the population studied. Motor development appears to proceed normally in prelingually deafened children and is a preimplant predictor of spoken-language outcome in young infants and children with cochlear implants, a finding consistent with the large body of work establishing links between perceptual-motor and language development.

Activities of Daily Living↗

PubMed2005

Visualization methods for statistical analysis of microarray clusters.

BACKGROUND: The most common method of identifying groups of functionally related genes in microarray data is to apply a clustering algorithm. However, it is impossible to determine which clustering algorithm is most appropriate to apply, and it is difficult to verify the results of any algorithm due to the lack of a gold-standard. Appropriate data visualization tools can aid this analysis process, but existing visualization methods do not specifically address this issue. RESULTS: We present several visualization techniques that incorporate meaningful statistics that are noise-robust for the purpose of analyzing the results of clustering algorithms on microarray data. This includes a rank-based visualization method that is more robust to noise, a difference display method to aid assessments of cluster quality and detection of outliers, and a projection of high dimensional data into a three dimensional space in order to examine relationships between clusters. Our methods are interactive and are dynamically linked together for comprehensive analysis. Further, our approach applies to both protein and gene expression microarrays, and our architecture is scalable for use on both desktop/laptop screens and large-scale display devices. This methodology is implemented in GeneVAnD (Genomic Visual ANalysis of Datasets) and is available at http://function.princeton.edu/GeneVAnD. CONCLUSION: Incorporating relevant statistical information into data visualizations is key for analysis of large biological datasets, particularly because of high levels of noise and the lack of a gold-standard for comparisons. We developed several new visualization techniques and demonstrated their effectiveness for evaluating cluster quality and relationships between clusters.

Algorithms↗

PubMed2006

Physical activity and Native Americans: a review.

The physical activity behaviors of Native-American populations in the United States and Canada have received little attention in the health literature. The purpose of this review was to unite the literature regarding the physical activity behaviors of Native Americans. A majority of the literature was obtained using online databases. Reference lists were also reviewed to gain further access to the literature. Key-word searches included various combinations of Aboriginal, Native Indian, American Indian, Native American, First Nation, Métis, or Alaska Native with physical activity, exercise, and health behavior. Articles included were those published in English-language, peer-reviewed journals from 1990 until November 2005 that focused on participants aged 18 years and older. This review is organized according to ecologic models of health behavior, which take into account several correlates to explain human behavior, including demographic, personal health, environmental, and psychosocial. Correlates were included if they appeared at least three times in the literature. As a result of these inclusion criteria, the number of reviewed articles includes 28 quantitative, 4 qualitative, and 3 intervention studies. Results indicate that age, gender, and social support are important factors associated with physical activity. The remaining correlates show inconsistent or indeterminate results due in part to the paucity of research. It is suggested that an increase in the number of studies, especially those using longitudinal designs, is needed. Further, the application of psychosocial models to understand physical activity motivations as well as culturally appropriate and validated measurement tools are largely absent in the Native-American physical activity literature.

Adult↗

PubMed2002

Lateralized spatial processes and their lexical implications.

Numerous lateralized tasks have been identified as involving spatial processing, but the extent to which they use the same spatial process is largely unknown. The present research investigated relationships among significant asymmetries from seven visuo-spatial and two verbal tasks, combining samples from previous factor analytic experiments with those from three new studies (combined N=789). All of the spatial intercorrelations were negligible (r<0.20), unlike previous outcomes finding robust correlations within certain clusters of verbal asymmetries. However, lateral differences involving spatial quantitative processing on the one hand and figure-ground separation on the other, showed significant but independent correlations with one from visual lexical processing (word recognition). The results support three major conclusions. First, there are at least several and possibly many lateralized spatial processes. Second, hemispheric processes follow a modular architecture in preference to a diffuse or parallel distributed architecture. Finally, the dissociated correlations are consistent with a visual lexical processing model having both occipital and parietal components, potentially reconciling a current controversy over the cerebral localization of language.

Adult↗

PubMed1994

Use of phonological information in a word-finding treatment for children.

Two children with word-finding deficits characterized largely by semantic substitutions participated in a treatment involving phonological information about target words. The treatment was motivated by models of naming where semantic information and phonological information are stored in independent ordered components. Given such models, it is possible to characterize some semantic word-finding substitutions as well as phonological word-finding substitutions as the result of breakdown at the level of the phonological output representation. The treatment was organized according to a single-subject multiple baseline design across behaviors and subjects. As hypothesized, the phonologically based treatment resulted in reduction not only of occasional phonological word-finding substitutions but also of the large number of semantic word-finding substitutions displayed during baseline and control measures of confrontation naming. In light of these data, the possible source of word-finding breakdowns in these children is explored.

Child, Preschool↗

PubMed1998

Implications of global change and climate variability for vector-borne diseases: generic approaches to impact assessments.

Global change is pervasive and occurring at a dramatic rate. It involves changes in land use, vegetation cover, species translocations and even the climate of the planet. The consequences for the biosphere are uncertain. Past research emphasis has been on the science of climate change as the major driver of policy. The present priority in the global-change community is to define the likely nature and extent of those impacts on biodiversity and the functioning of ecosystems. In addition, increasing consideration is now being given to adaptation measures. The way in which that is being initiated is to develop adaptation measures to respond to medium-term climate variability in the form of altered El Nino and similar cycles, and changes in the frequency of extreme events. Given the large number of stakeholders in agriculture, human health and environment, there is a need for great efficiencies if the scientific community is going to be able to respond in a meaningful way with foreseeable resources. The plethora of problems means that generic approaches are needed. The present situation, with parasitologists each doing their own thing in terms of developing and using software tools, is like the tower of Babel. Parasitologists need common tools and languages to facilitate communication and collaboration. Advances in computing, with object-oriented programming languages and seamless exchange of information between different packages and platforms, are providing some exciting opportunities to overcome these problems.

Adaptation, Biological↗

PubMedDate not supplied

KBSIM: a system for interactive knowledge-based simulation.

The KBSIM system integrates quantitative simulation with symbolic reasoning techniques, under the control of a user interface management system, using a relational database management system for data storage and interprocess communication. The system stores and processes knowledge from three distinct knowledge domains, viz. (i) knowledge about the processes of the system under investigation, expressed in terms of a Continuous System Simulation Language (CSSL); (ii) heuristic knowledge on how to reach the goals of the simulation experiment, expressed in terms of a Rule Description Language (RDL); and (iii) knowledge about the requirements of the intended users, expressed in terms of a User Interface Description Language (UIDL). The user works in an interactive environment controlling the simulation course with use of a mouse and a large screen containing a set of 'live' charts and forms. The user is assisted by an embedded 'expert system' module continuously watching both the system's behavior and the user's action, and producing alerts, alarms, comments and advice. The system was developed on a Hewlett-Packard 9000/350 workstation under the HP-Unix and HP-Windows operating systems, using the MIMER database management system, and Fortran, Prolog/Lisp and C as implementation languages. The KBSIM system has great potentials for supporting problem solving, design of working procedures and teaching related to management of highly dynamic systems.

Artificial Intelligence↗

PubMed2006

Association between polymorphism of tumour necrosis factor alpha-308 gene promoter and asthma: a meta-analysis.

BACKGROUND: Asthma is a complex polygenic disease in which gene-environment interactions are important. The gene encoding tumour necrosis factor alpha (TNFalpha) is one of several candidate loci for asthma pathogenesis and is highly polymorphic. A number of studies have investigated the polymorphism of TNFalpha-308 gene promoter (substitution G-->A, designated as TNF1 and TNF2) in relation to asthma susceptibility in different populations. However, the results of individual studies have been inconsistent. METHODS: To address the inconsistent findings in studies of the association of the polymorphism of TNFalpha-308 gene promoter with susceptibility to asthma, a systematic review was undertaken of the published data and a meta-analysis was performed. The MEDLINE database was searched for case-control studies published in English language journals from 1966 to October 2005. Data were extracted using standardised forms and pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. RESULTS: Fifteen eligible studies, comprising 2409 patients with asthma and 3266 controls, were included in the meta-analysis. Using the random effects model, the pooled result showed that the TNF2 allele is associated with overall susceptibility to asthma (OR 1.37, 95% CI 1.02 to 1.84, p=0.04). The ORs for asthma susceptibility in TNF2 homozygote individuals were significantly increased at 2.01 (95% CI 1.26 to 3.20, p=0.009) and 1.51 (95% CI 1.02 to 2.22, p=0.041) compared with TNF1 homozygotes and TNF2/1 heterozygotes, respectively. In addition, the pooled OR for asthma risk in TNF2/1 heterozygotes was also significantly higher than that in TNF1/1 homozygotes (OR 1.47, 95% CI 1.01 to 2.13, p=0.045). CONCLUSIONS: The TNF2 allele confers a significant risk for developing asthma. A large scale case-control study is needed to clarify the functional effect of the polymorphism of the TNFalpha gene in the pathogenesis of asthma.

Adolescent↗

PubMed2003

Component-based mediation services for the integration of medical applications.

Allowing exchange of information and cooperation among network-wide distributed and heterogeneous applications is a major need of current health-care information systems. The European project SynEx aims at developing an integration platform for both new and legacy applications on each partner's site. We developed, in this project, mediation services based on the generic and reusable software components that facilitate the construction of an integration platform and ease the communication and the meaningful transformation among distributed and heterogeneous applications. The main component of the mediation services is named Pilot, which serves as an intelligent broker. It uses a multi-agents service model allowing the integration platform to be multi-servers. It transforms a client request into a valid high level service on the platform. Each service is broken up into several elementary steps by the Pilot. For each step, the Pilot uses an agent to realize the operation configured by the step. At runtime, the Pilot synchronizes the execution of different steps. To ease the communication and the interaction with the heterogeneous systems, an agent can integrate a Mediator. The Mediators are the communication and interpretation tools within the mediation services. We have developed a generic model that can be specialized for creating specific mediators for the different use cases. The mediator model uses two interfaces to connect the mediator with two systems that need to communicate. Each interface deals with the three aspects through three managers (the Communication Manager, the Syntax Manager and the Semantic Manager). Some ready-to-use specializations are developed for some well defined cases which can reduce the development effort. Once a manager is specialized, it can be used in different combinations with other managers to resolve different problems. The meaningful transformation is ensured on a semantic level in each mediator through the Semantic Model component. This last component allows the mapping among different vocabularies used by different systems through a shared ontology which allows the mapping process to focus on the meaning of the transformed information. We have used XML in different components of the mediation services as the interchange format and the description format. This has enhanced the flexibility of the components. The component based approach allows the generic components to be reused in different contexts and also allows the mediations services to be open to integrate other available technologies thus largely reduce the development efforts.

Artificial Intelligence↗

PubMed1998

Moderators of gender effects on parents' talk to their children: a meta-analysis.

Two sets of meta-analyses of studies examining gender effects on parents' observed language with their children were conducted. One looked at studies comparing mothers and fathers in amount of talking, supportive speech, negative speech, directive speech, informing speech, and questions and requests. The other looked at studies comparing mothers' interactions with daughters versus with sons in amount of talking, supportive speech, and directive speech. Across studies, mothers tended to talk more (d = .26), use more supportive (d = .23) and negative (d = .13) speech, and use less directive (d = .19) and informing (d = .15) speech than did fathers. Also, mothers tended to talk more (d = .29) and use more supportive speech (d = .22) with daughters than with sons. Medium or large effect sizes occurred in most analyses when particular moderator variables were taken into account. Effect sizes varied, depending on aspects of the interactive setting, the child's age, sampling and measurement, and publication characteristics. The results are interpreted in relation to a contextual-interactive model of gender typing.

Child↗

PubMed2000

On the "specifics" of specific reading disability and specific language impairment.

The reading and oral language scores of 110 children with a specific reading disability (SRD) and 102 children with a specific language impairment (SLI) indicated that approximately 53% of children with an SRD and children with an SLI could be equally classified as having an SRD or an SLI, 55% of children with an SRD have impaired oral language, and 51% of children with an SLI have a reading disability. Finding that a large percentage of children can be equally classified as SRD or SLI has repercussions for the criteria used to define an SRD, for conceptualising subgroups of learning disability, and for estimates of the incidence of SRD. Further, it highlights the need for future studies to assess both the reading and oral language abilities of SRD and SLI participants to determine how specifically impaired and homogeneous samples really are.

Adolescent↗

PubMed2002

[Describing language of spectra and rough set].

It is the traditional way to analyze spectra by experiences in astronomical field. And until now there has never been a suitable theoretical frame to describe spectra, which is may be owing to small spectra datasets that astronomers can get by low-level instruments. With the high-speed development of telescopes, especially on behalf of LAMOST, a large telescope which can collect more than 20,000 spectra in an observing night, spectra datasets are becoming larger and larger very fast. Facing these voluminous datasets, the traditional spectra-processing way simply depending on experiences becomes unfit. In this paper, we develop a brand-new language--describing language of spectra (DLS) to describe spectra of celestial bodies by defining BE (Basic element). And based on DLS, we introduce the method of RSDA (Rough set and data analysis), which is a technique of data mining. By RSDA we extract some rules of stellar spectra, and this experiment can be regarded as an application of DLS.

Algorithms↗

PubMed2005

A temporal constraint structure for extracting temporal information from clinical narrative.

INTRODUCTION: Time is an essential element in medical data and knowledge which is intrinsically connected with medical reasoning tasks. Many temporal reasoning mechanisms use constraint-based approaches. Our previous research demonstrates that electronic discharge summaries can be modeled as a simple temporal problem (STP). OBJECTIVE: To categorize temporal expressions in clinical narrative text and to propose and evaluate a temporal constraint structure designed to model this temporal information and to support the implementation of higher-level temporal reasoning. METHODS: A corpus of 200 random discharge summaries across 18 years was applied in a grounded approach to construct a representation structure. Then, a subset of 100 discharge summaries was used to tally the frequency of each identified time category and the percentage of temporal expressions modeled by the structure. Fifty random expressions were used to assess inter-coder agreement. RESULTS: Six main categories of temporal expressions were identified. The constructed temporal constraint structure models time over which an event occurs by constraining its starting time and ending time. It includes a set of fields for the endpoint(s) of an event, anchor information, qualitative and metric temporal relations, and vagueness. In 100 discharge summaries, 1961 of 2022 (97%) identified temporal expressions were effectively modeled using the temporal constraint structure. Inter-coder evaluation of 50 expressions yielded exact match in 90%, partial match with trivial differences in 8%, partial match with large differences in 2%, and total mismatch in 0%. CONCLUSION: The proposed temporal constraint structure embodies a sufficient and successful implementation method to encode the diversity of temporal information in discharge summaries. Placing data within the structure provides a foundational representation upon which further reasoning, including the addition of domain knowledge and other post-processing to implement an STP, can be accomplished.

Database Management Systems↗

PubMed2005

Using process diagrams for the graphical representation of biological networks.

With the increased interest in understanding biological networks, such as protein-protein interaction networks and gene regulatory networks, methods for representing and communicating such networks in both human- and machine-readable form have become increasingly important. Although there has been significant progress in machine-readable representation of networks, as exemplified by the Systems Biology Mark-up Language (SBML) (http://www.sbml.org) issues in human-readable representation have been largely ignored. This article discusses human-readable diagrammatic representations and proposes a set of notations that enhances the formality and richness of the information represented. The process diagram is a fully state transition-based diagram that can be translated into machine-readable forms such as SBML in a straightforward way. It is supported by CellDesigner, a diagrammatic network editing software (http://www.celldesigner.org/), and has been used to represent a variety of networks of various sizes (from only a few components to several hundred components).

Animals↗