Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “computational frameworks”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,477 records · Page 82Linked to original sources
PubMed1998

Dynamic model of the vergence eye movement system: simulations using MATLAB/SIMULINK.

A dynamic model of the vergence eye movement system was developed and simulated using MATLAB/SIMULINK. The model was based on a dual-mode dynamic model previously written in FORTRAN. It consisted of a fast open-loop component and a slow closed-loop component. The new model contained several important modifications. For example, in the fast component, a zero-order hold element replaced the sampler and the target trajectory estimator in the earlier model to provide more stable and accurate responses. Also, a periodicity detector was added to automatically detect periodicity in the stimulus waveform. The stored periodic stimulus, with a reduction in latency, was used to drive the fast component output. Moreover, a connection representing the efference copy signal was added from the fast component output to the disparity input to provide an accurate estimate of the stimulus waveform. Further, Robinson's model of the extraocular muscles replaced the earlier 2nd-order plant to provide more realistic muscle dynamics. The entire model, containing the fast and slow components, was simulated using a variety of stimuli such as pulses, positive and negative ramps, square-wave, and sine-wave. The responses showed dynamic characteristics similar to experimental results. Thus, this new MATLAB/SIMULINK program provides a relatively easy-to-use, versatile, and powerful simulation environment for investigating the basic as well as clinical aspects of vergence dynamics. Moreover, the simulation program has general characteristics that can be modified to represent other oculomotor systems such as the versional and accommodation systems. This provides a framework for future investigation of dynamic interactions between oculomotor systems.

Computer Simulation↗
PubMed1998

Modelling and simulation of motility in actomyosin systems.

We present a model mechanism for simulating the diffusive motion and fluctuations inherent in myofibrillar sarcomere and its subunits at the molecular level. The model couples Langevin dynamics with Huxley kinetics to reproduce the transient patterns of momentum transfer, force generation and resulting motility due to the interactive activities of actin and myosin crossbridges. When myosin is detached from actin, our model predicts Brownian displacements centered at 0 +/- 8 nm (mean +/- SD, n = 265,308) and it is broadly distributed due to the Brownian noise. Attachment events produced displacements with step sizes of approximately 8 +/- 6 nm (mean +/- SD, n = 34,693), which is in agreement with some recent optical-tweezers transducer experimental results. The proposed model could form the basis for a complete qualitative and quantitative description of the evolving complex interactions of the molecular proteins--actin and myosin--in the overall framework of muscular contraction studies.

Actins↗
PubMed2004

Bayesian models for the analysis of genetic structure when populations are correlated.

MOTIVATION: Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of population genetic structure. In this study, we propose a mixture beta model to characterize the allele frequency distribution among populations. This formulation incorporates the correlation among populations as well as extending the model to data with different clusters of populations. RESULTS: Using simulated data, we show that in general, the mixture model provides a good approximation of the among-population allele frequency distribution and a good estimate of correlation among populations. Results from fitting the mixture model to a dataset of genotypes at 377 autosomal microsatellite loci from human populations indicate high correlation among populations, which may not be appropriate to neglect. Traditional measures of population structure tend to overestimate the amount of genetic differentiation when correlation is neglected. Inference is performed in a Bayesian framework. CONTACT: fur@ohsu.edu.

Bayes Theorem↗
PubMed2005

Light source position and reflectance estimation from a single view without the distant illumination assumption.

Several techniques have been developed for recovering reflectance properties of real surfaces under unknown illumination. However, in most cases, those techniques assume that the light sources are located at inifinity, which cannot be applied safely to, for example, reflectance modeling of indoor environments. In this paper, we propose two types of methods to estimate the surface reflectance property of an object, as well as the position of a light source from a single view without the distant illumination assumption, thus relaxing the conditions in the previous methods. Given a real image and a 3D geometric model of an object with specular reflection as inputs, the first method estimates the light source position by fitting to the Lambertian diffuse component, while separating the specular and diffuse components by using an iterative relaxation scheme. Our second method extends that first method by using as input a specular component image, which is acquired by analyzing multiple polarization images taken from a single view, thus removing its constraints on the diffuse reflectance property. This method simultaneously recovers the reflectance properties and the light source positions by optimizing the linearity of a log-transformed Torrance-Sparrow model. By estimating the object's reflectance property and the light source position, we can freely generate synthetic images of the target object under arbitrary lighting conditions with not only source direction modification but also source-surface distance modification. Experimental results show the accuracy of our estimation framework.

Algorithms↗
PubMed2005

Chain orientation in natural rubber, Part I: the inverse yielding effect.

Inhomogeneous deformations are observed in stretched natural rubber of different crosslink density; the conditions of observation, nucleation and propagation are given in the first part of the paper. In samples of low crosslink density these inhomogeneities recall necking observed in others materials and in glassy polymers when the materials are drawn above a critical draw ratio. The difference is that in natural rubbers, NR, they nucleate and propagate at constant stress during unloading. This phenomenon, called inverse yielding appears during recovery only if the samples have been drawn previously in the hardening domain. During necking propagation the stress is constant. The mechanical and crystallinity properties of samples with and without inverse yielding are studied as a function of draw ratio, crosslink density and temperature. In the second part of the paper this transition zone (neck) of thickness 2 mm is studied by WAXS at the synchrotron source. From the orientation of NR crystallites and from the orientation of the stearic acid (2%, present in this type of rubber) we conclude that the deformation in the neck follows the flow lines. From the local crystallinity of the NR crystallites one deduces the local draw ratio across this transition zone. We suggest that in all these rubbers, which present a plateau of the recovery stress strain curve, micronecking exists. This effect is discussed in the framework of the Flory theory.

Computer Simulation↗
PubMed1995

Learning in recurrent finite difference networks.

A recurrent learning algorithm based on a finite difference discretization of continuous equations for neural networks is derived. This algorithm has the simplicity of discrete algorithms while retaining some essential characteristics of the continuous equations. In discrete networks learning smooth oscillations is difficult if the period of oscillation is too large. The network either grossly distorts the waveforms or is unable to learn at all. We show how the finite difference formulation can explain and overcome this problem. Formulas for learning time constants and time delays in this framework are also presented.

Algorithms↗
PubMed2005

Molecular dynamics simulation of a high-affinity antibody-protein complex: the binding site is a mosaic of locally flexible and preorganized rigid regions.

One nanosecond molecular dynamic (MD) simulation of anti-hen egg white lysozyme (HEL) antibody HyHEL63 (HH63) complexed with HEL reveals rigid and flexible regions of the HH63 binding site. Fifty conformations, extracted from the MD trajectory at regular time intervals were superimposed on HH63-HEL X-ray crystal structure, and the root mean squared deviations (RMSDs) and deviations in Calpha atom positions between the X-ray structure and the MD conformer were measured. Residue positions showing the large deviations in both light chain and heavy chain of the antibody were same in all the MD conformers. The residue positions showing smallest deviations were same for all the conformers in the case of light chain, whereas relatively variable in the heavy chain. Positions of large and small deviations fell in the complementarity determining regions (CDRs), for both heavy and light chains. The larger deviations were in CDR-2 of light and CDR-1 of heavy chain. Smaller deviations were in CDR-3 of light and CDR-2 and CDR-3 of heavy chains. The large and small deviating regions highlight flexible and rigid regions of HH63 binding site and suggest a mosaic binding mechanism, including both "induced fit" and preconfigured "lock-and-key" type of binding. Combined "induced fit" and "lock-and-key" binding would be a better definition for the formation of large complexes, which bury larger surface area on binding, as in the case of antibody-HEL complex. We further show that flexible regions, comprising mostly charged and polar residues, form intermolecular interactions with HEL, whereas rigid regions do not. Electrostatic complementarity between HH63 and HEL also imply optimized binding affinity. Flexible and rigid regions of a high-affinity antibody are selected during the affinity maturation of the antibody and have specific functional significance. The functional importance of local inherently flexible regions is to establish intermolecular contacts or they play a key role in molecular recognition, whereas local rigid regions provide the structural framework.

Antibodies↗
PubMed1994

Information management and quality improvement: the Joint Commission's perspective.

Health care is an information-intensive endeavor. Its improvement is even more information intensive. The core processes of health care and their improvement are dependent on effective and efficient management of information in health care organizations and integrated health care networks. The authors describe a framework for effective information management in health care organizations and discuss the implications of a framework for improving performance on information management.

Computer Communication Networks↗
PubMed2005

High stakes assessment using simulation -- an Australian experience.

The use of simulation for high stakes assessment has been embedded in the New South Wales Medical Practice Act and has been used for high stakes assessment on a number of occasions. Simulation has rarely been used in this manner elsewhere in the world. We outline the use of simulation in particular focussing on its relationship to a performance assessment programme featuring performance focus, peer assessment of standards, an educative, remedial and protective framework, strong legislative support and system awareness.

Clinical Competence↗
PubMed2005

A design of multiagent-based framework for volume image construction and analysis.

This paper describes a design of a multiagent-based system that can be used to manage the acquisition and analysis of ultrasonograph images. The major concept is to design a management framework consisting of multiple intelligent agents to direct the ultrasonograph image acquisition and analysis operations carried out using a high-speed bit-parallel architecture efficiently as well as to allow for the construction of 3D images from 2D ones. Volume image operations need reactivity, autonomy, and intelligence of software. Therefore, agents can play an important role in enhancing the overall operation of medical image analysis. The system suggests a set of image analysis operations including smoothing, noise removal, and enhancing techniques. These operations will be implemented using parallel processing architectures while the management framework will consist of different agent types such as: simple reflex agents, agents that keep track of the world, goal-based agents, and utility-based agents. These agents interact with each other and exchange data among themselves in order to achieve a comprehensive speed in performing the volume image construction operations. Guided with the fact that the agent consists of program and architecture, the system deploys parallel processing architectures to implement the image analysis operations. The system is considered a step towards a complete multiagent-based framework for medical image acquisition and analysis.

Algorithms↗
PubMed2006

High-accuracy peak picking of proteomics data using wavelet techniques.

A new peak picking algorithm for the analysis of mass spectrometric (MS) data is presented. It is independent of the underlying machine or ionization method, and is able to resolve highly convoluted and asymmetric signals. The method uses the multiscale nature of spectrometric data by first detecting the mass peaks in the wavelet-transformed signal before a given asymmetric peak function is fitted to the raw data. In an optional third stage, the resulting fit can be further improved using techniques from nonlinear optimization. In contrast to currently established techniques (e.g. SNAP, Apex) our algorithm is able to separate overlapping peaks of multiply charged peptides in ESI-MS data of low resolution. Its improved accuracy with respect to peak positions makes it a valuable preprocessing method for MS-based identification and quantification experiments. The method has been validated on a number of different annotated test cases, where it compares favorably in both runtime and accuracy with currently established techniques. An implementation of the algorithm is freely available in our open source framework OpenMS.

Algorithms↗
PubMed1988

Computer graphics in medicine: a survey.

Increased interest is presently given to three-dimensional (3-D) medical applications due to simultaneous emergence of high-resolution imaging systems and computer graphics techniques. This paper intends to present a survey of this field together with discussion and prospective views. The general framework is composed of six parts: data acquisition and preprocessing, polygonal object representation, voxel description, system architecture, medical applications, and prospects. Data base acquisition includes characterization of imaging modalities and medical specificity. Preprocessing schemes are directed to improvements (filtering), windowing, and spatial anisotropy (linear or spline interpolation). The two following sections are devoted to descriptions of the main object representations. Particular emphasis is given to optimal contour approximation, surface triangulation, mathematical surfaces on one hand, and cuberille and voxel representations on the other. Display capabilities--hidden surface removal, surface normal shading, structure enhancement--and data base structuration--hierarchical and nonhierarchical (graph and tree encoding)--are, respectively, described. An overview of 3-D systems is further given (Section V), and features of medical applications are reviewed and gathered in basic functionalities, surgery, and radiotherapy specifications (Section VI). The last section provides some prospective views on reconstruction from a few projections, model-guided labeling, multimodality image overlay, and local image network. Some of these issues are illustrated by examples of 3-D images.

Computer Graphics↗
PubMed2006

A classification-based framework for predicting and analyzing gene regulatory response.

BACKGROUND: We have recently introduced a predictive framework for studying gene transcriptional regulation in simpler organisms using a novel supervised learning algorithm called GeneClass. GeneClass is motivated by the hypothesis that in model organisms such as Saccharomyces cerevisiae, we can learn a decision rule for predicting whether a gene is up- or down-regulated in a particular microarray experiment based on the presence of binding site subsequences ("motifs") in the gene's regulatory region and the expression levels of regulators such as transcription factors in the experiment ("parents"). GeneClass formulates the learning task as a classification problem--predicting +1 and -1 labels corresponding to up- and down-regulation beyond the levels of biological and measurement noise in microarray measurements. Using the Adaboost algorithm, GeneClass learns a prediction function in the form of an alternating decision tree, a margin-based generalization of a decision tree. METHODS: In the current work, we introduce a new, robust version of the GeneClass algorithm that increases stability and computational efficiency, yielding a more scalable and reliable predictive model. The improved stability of the prediction tree enables us to introduce a detailed post-processing framework for biological interpretation, including individual and group target gene analysis to reveal condition-specific regulation programs and to suggest signaling pathways. Robust GeneClass uses a novel stabilized variant of boosting that allows a set of correlated features, rather than single features, to be included at nodes of the tree; in this way, biologically important features that are correlated with the single best feature are retained rather than decorrelated and lost in the next round of boosting. Other computational developments include fast matrix computation of the loss function for all features, allowing scalability to large datasets, and the use of abstaining weak rules, which results in a more shallow and interpretable tree. We also show how to incorporate genome-wide protein-DNA binding data from ChIP chip experiments into the GeneClass algorithm, and we use an improved noise model for gene expression data. RESULTS: Using the improved scalability of Robust GeneClass, we present larger scale experiments on a yeast environmental stress dataset, training and testing on all genes and using a comprehensive set of potential regulators. We demonstrate the improved stability of the features in the learned prediction tree, and we show the utility of the post-processing framework by analyzing two groups of genes in yeast--the protein chaperones and a set of putative targets of the Nrg1 and Nrg2 transcription factors--and suggesting novel hypotheses about their transcriptional and post-transcriptional regulation. Detailed results and Robust GeneClass source code is available for download from http://www.cs.columbia.edu/compbio/robust-geneclass.

Algorithms↗
PubMed2004

TcruziDB: an integrated Trypanosoma cruzi genome resource.

TcruziDB (http://TcruziDB.org) is an integrated genome database for the parasitic organism Trypanosoma cruzi, the causative agent of Chagas' disease. The database currently incorporates all available sequence data (Genomic, BAC, EST) in a single user-friendly location. The database contains a variety of tools specifically designed for searching unannotated draft sequence via BLAST, keyword searches of pre-computed BLAST results, and protein motif searches. Release 1.0 of the database contains nearly 730 million bp of genome sequence from 1.1 million sequence reads generated by the TIGR-Karolinska-SBRI Trypanosoma cruzi Genome Consortium and 15 million bp of clustered EST and genomic sequence obtained from other sources. As annotation, microarray and proteomic data become available, the database will incorporate and integrate these data using the GUS (http://www.gusdb. org) relational framework.

Animals↗
PubMed2004

Spiral waves in disinhibited mammalian neocortex.

Spiral waves are a basic feature of excitable systems. Although such waves have been observed in a variety of biological systems, they have not been observed in the mammalian cortex during neuronal activity. Here, we report stable rotating spiral waves in rat neocortical slices visualized by voltage-sensitive dye imaging. Tissue from the occipital cortex (visual) was sectioned parallel to cortical lamina to preserve horizontal connections in layers III-V (500-mum-thick, approximately 4 x 6 mm(2)). In such tangential slices, excitation waves propagated in two dimensions during cholinergic oscillations. Spiral waves occurred spontaneously and alternated with plane, ring, and irregular waves. The rotation rate of the spirals was approximately 10 turns per second, and the rotation was linked to the oscillations in a one-cycle- one-rotation manner. A small (<128 mum) phase singularity occurred at the center of the spirals, about which were observed oscillations of widely distributed phases. The phase singularity drifted slowly across the tissue ( approximately 1 mm/10 turns). We introduced a computational model of a cortical layer that predicted and replicated many of the features of our experimental findings. We speculate that rotating spiral waves may provide a spatial framework to organize cortical oscillations.

Action Potentials↗
PubMed2003

Facilitating real-time volume interaction.

We report on efforts to provide high-level intuitive tools that exploit commodity-based computing to facilitate real-time and distributed interactions with volumetric data. These efforts include an open source volume-rendering library, a portable volume visualization application framework, and parallel volume-rendering exploiting commodity-based hardware. We present our design and implementations, as well as examples of some of the various groups currently utilizing these tools, and discuss the tradeoffs of our developments versus existing techniques.

Computer Simulation↗
PubMed1998

Functional endoscopic sinus surgery (FESS): what radiologists need to know.

The place of coronal computed tomography (CT) in the assessment of patients prior to functional endoscopic sinus surgery (FESS) is well established. The ability to accurately correlate radiological and surgical anatomy enhances precision and safety during FESS. This pictorial essay reviews the conceptual anatomical framework that forms the basis of FESS.

Endoscopy↗
PubMed2006

Ethics and lactation consultants: developing knowledge, skills, and tools.

This article studies the role of ethics in the context of the work of International Board Certified Lactation Consultants. It provides an overview of some of the main ethical approaches with the goal of contributing to the knowledge, skills, and tools required by lactation consultants. Five main sections structure the article: background, current literature, ethical theory and principles, implications for lactation consultants, and decision-making frameworks. Background about the International Board of Lactation Consultant Examiners and International Board Certified Lactation Consultants and the significance of applied ethics in their work are described. Current literature regarding ethics and lactation consultants is reviewed. Because a computer-based literature search yielded a lack of articles, ethics in nursing literature is also presented. Three main ethical theories and 5 key ethical principles are explored with a view to their implications for lactation consultants. Finally, decision-making frameworks are considered as systematic tools for making ethical decisions.

Breast Feeding↗