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 1,603 records · Page 89Linked to original sources
PubMed2004

Automated computer result reporting for haemoglobinopathy screening.

The anticipated introduction of universal antenatal screening can be expected to increase the workload of haemoglobinopathy laboratories throughout the country. We have devised a rule-based system to process those results that does not require skilled interpretation, thereby freeing staff time for more specialized work. The system relies on a calculated test to create a total haemoglobin peak value, which incorporates the values for HbA, HbA2 and HbF, the MCV and MCH from the full blood count. Each parameter has a series of defined ranges which, when subjected to an interpretation process within the laboratory computer system, generates an automated result text for the sample. During a 6-month verification period, the automated result interpretation system in conjunction with laboratory information systems (LIS) validation reduced the number of samples requiring manual review by 60%. The system was found to be 100% sensitive and 61.8% specific. We feel that the current specificity is acceptable in order to maintain a safe system. The ability to concentrate on potentially abnormal results will allow laboratories and health care workers more time to develop appropriate and timely frameworks to deal with abnormal results.

Clinical Laboratory Information Systems↗
PubMed1998

Anatomy of the orbit.

The normal orbit arguably contains the most complex anatomy of the human body. The orbit's small size, complex anatomy, and elaborate function make it a diagnostic challenge to evaluate. Magnetic resonance imaging (MRI) and computed tomography (CT) are essential studies for visualization of most normal and abnormal orbital structures. These studies also can help to understand some of the functional anatomical relationships within the orbit. This article attempts to review and illustrate the normal anatomical structures that can be identified on CT and MR images. These structures include the bony orbit, globe and optic nerve, extraocular muscles, lid retractor system, fibrous tissue framework, vascular system, neural structures, and lacrimal system.

Eye↗
PubMed2006

Parameter estimation using Simulated Annealing for S-system models of biochemical networks.

MOTIVATION: High-throughput technologies now allow the acquisition of biological data, such as comprehensive biochemical time-courses at unprecedented rates. These temporal profiles carry topological and kinetic information regarding the biochemical network from which they were drawn. Retrieving this information will require systematic application of both experimental and computational methods. RESULTS: S-systems are non-linear mathematical approximative models based on the power-law formalism. They provide a general framework for the simulation of integrated biological systems exhibiting complex dynamics, such as genetic circuits, signal transduction and metabolic networks. We describe how the heuristic optimization technique simulated annealing (SA) can be effectively used for estimating the parameters of S-systems from time-course biochemical data. We demonstrate our methods using three artificial networks designed to simulate different network topologies and behavior. We then end with an application to a real biochemical network by creating a working model for the cadBA system in Escherichia coli. AVAILABILITY: The source code written in C++ is available at http://www.engg.upd.edu.ph/~naval/bioinformcode.html. All the necessary programs including the required compiler are described in a document archived with the source code. SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

Biochemistry↗
PubMed1984

The clinical importance of bacterial urinary tract infections during pregnancy. I. Premature delivery, dismaturity.

Using computer analysis the authors studied the relationship between the various clinical forms of urinary tract infections and premature deliveries, i.e. dysmaturity in a population including several thousands of individuals. In the frameworks of uniform and monitored perinatal obstetric and neonatologic care system--the uniform diagnostics of bacteriuria was established. The standard birth-weights for the regions involved by our care were calculated, too. The basic observations of Kass were still found to be valid. In case of urinary tract infections, an increased rate of premature deliveries with respect to both birth-weights and gestational age of pregnancy should be reckoned with. Computer analysis proved not only a tendency for premature deliveries but also retarded intrauterine growth of the foetus.

Bacterial Infections↗
PubMed2003

The virtual microscope.

We present the design and implementation of the Virtual Microscope, a software system employing a client/server architecture to provide a realistic emulation of a high power light microscope. The system provides a form of completely digital telepathology, allowing simultaneous access to archived digital slide images by multiple clients. The main problem the system targets is storing and processing the extremely large quantities of data required to represent a collection of slides. The Virtual Microscope client software runs on the end user's PC or workstation, while database software for storing, retrieving and processing the microscope image data runs on a parallel computer or on a set of workstations at one or more potentially remote sites. We have designed and implemented two versions of the data server software. One implementation is a customization of a database system framework that is optimized for a tightly coupled parallel machine with attached local disks. The second implementation is component-based, and has been designed to accommodate access to and processing of data in a distributed, heterogeneous environment. We also have developed caching client software, implemented in Java, to achieve good response time and portability across different computer platforms. The performance results presented show that the Virtual Microscope systems scales well, so that many clients can be adequately serviced by an appropriately configured data server.

Computer Graphics↗
PubMed2005

Indexing hierarchical structures using graph spectra.

Hierarchical image structures are abundant in computer vision and have been used to encode part structure, scale spaces, and a variety of multiresolution features. In this paper, we describe a framework for indexing such representations that embeds the topological structure of a directed acyclic graph (DAG) into a low-dimensional vector space. Based on a novel spectral characterization of a DAG, this topological signature allows us to efficiently retrieve a promising set of candidates from a database of models using a simple nearest-neighbor search. We establish the insensitivity of the signature to minor perturbation of graph structure due to noise, occlusion, or node split/merge. To accommodate large-scale occlusion, the DAG rooted at each nonleaf node of the query "votes" for model objects that share that "part," effectively accumulating local evidence in a model DAG's topological subspaces. We demonstrate the approach with a series of indexing experiments in the domain of view-based 3D object recognition using shock graphs.

Algorithms↗
PubMed2006

Development and quality assurance of computer-based assessment batteries.

The purpose of this article is to outline critical elements in the development and quality assurance (QA) assessment of a computer-based assessment battery (CAB). The first section of the article provides an overview of the life cycle of a representative CAB, typical evolutionary stages, and many of the essential considerations for designing and developing a CAB. The second section of the article presents a model for conducting a quality assurance assessment of a CAB. A general narrative of several steps in the QA process is supported by a table of recommended QA assessment elements. Although this QA process model may not be definitive for all cases, it provides a general framework within which a systematic assessment of any CAB can be conducted.

Diagnosis, Computer-Assisted↗
PubMed2003

Conformon-driven biopolymer shape changes in cell modeling.

Conceptual models of the atom preceded the mathematical model of the hydrogen atom in physics in the second decade of the 20th century. The computer modeling of the living cell in the 21st century may follow a similar course of development. A conceptual model of the cell called the Bhopalator was formulated in the mid-1980s, along with its twin theories known as the conformon theory of molecular machines and the cell language theory of biopolymer interactions [Ann. N.Y. Acad. Sci. 227 (1974) 211; BioSystems 44 (1997) 17; Ann. N.Y. Acad. Sci. 870 (1999a) 411; BioSystems 54 (2000) 107; Semiotica 138 (1-4) (2002a) 15; Fundamenta Informaticae 49 (2002b) 147]. The conformon theory accounts for the reversible actions of individual biopolymers coupled to irreversible chemical reactions, while the cell language theory provides a theoretical framework for understanding the complex networks of dynamic interactions among biopolymers in the cell. These two theories are reviewed and further elaborated for the benefit of both computational biologists and computer scientists who are interested in modeling the living cell and its functions. One of the critical components of the mechanisms of cell communication and cell computing has been postulated to be space- and time-organized teleonomic (i.e. goal-directed) shape changes of biopolymers that are driven by exergonic (free energy-releasing) chemical reactions. The generalized Franck-Condon principle is suggested to be essential in resolving the apparent paradox arising when one attempts to couple endergonic (free energy-requiring) biopolymer shape changes to the exergonic chemical reactions that are catalyzed by biopolymer shape changes themselves. Conformons, defined as sequence-specific mechanical strains of biopolymers first invoked three decades ago to account for energy coupling in mitochondria, have been identified as shape changers, the agents that cause shape changes in biopolymers. Given a set of space- and time-organized teleonomic shape changes of biopolymers driven by conformons, all of the functions of the cell can be accounted for in molecular terms-at least in principle. To convert a conceptual model of the cell into a computer model, it is necessary to represent the conceptual model in an algebraic language. To this end, we have begun to apply the process algebra of Milner [Communicating and Mobile Systems: The pi-calculus, Cambridge University Press, Cambridge, 1999] to develop what is here called the "shape algebra," capable of describing complex and mobile patterns of interactions among biomolecules leading to cell functions.

Algorithms↗
PubMed1999

Virtual cutting of anatomical structures.

In the context of medicine cutting is one of the most important operations. Many surgical tasks start with an incision, allowing the surgeon to access the region of interest, using either conventional or minimal invasive surgery techniques. The work presented herein should be seen in the context of surgical training and preoperative planning using computer assisted medical simulation systems. The main result of this work is the proposed cutting algorithm based on predefined templates. To integrate this approach in the existing surgical training simulator and to handle additional tasks like soft tissue deformation, needed by the medical environment, a generic simulation framework was developed. This framework is able to utilize given multiprocessor- and network-environments to achieve the desired realtime interactivity.

Algorithms↗
PubMed2007

Evidence-based sample size calculations based upon updated meta-analysis.

Meta-analyses of randomized controlled trials (RCTs) provide the highest level of evidence regarding the effectiveness of interventions and as such underpin much of evidence-based medicine. Despite this, meta-analyses are usually produced as observational by-products of the existing literature, with no formal consideration of future meta-analyses when individual trials are being designed. Basing the sample size of a new trial on the results of an updated meta-analysis which will include it, may sometimes make more sense than powering the trial in isolation. A framework for sample size calculation for a future RCT based on the results of a meta-analysis of the existing evidence is presented. Both fixed and random effect approaches are explored through an example. Bayesian Markov Chain Monte Carlo simulation modelling is used for the random effects model since it has computational advantages over the classical approach. Several criteria on which to base inference and hence power are considered. The prior expectation of the power is averaged over the prior distribution for the unknown true treatment effect. An extension to the framework allowing for consideration of the design for a series of new trials is also presented. Results suggest that power can be highly dependent on the statistical model used to meta-analyse the data and even very large studies may have little impact on a meta-analysis when there is considerable between study heterogeneity. This raises issues regarding the appropriateness of the use of random effect models when designing and drawing inferences across a series of studies.

Anti-Bacterial Agents↗
PubMed2001

A framework for modelling in S88 constructs for scheduling purposes.

ISA S88.01 [1] [ISA (ANSI/S88.01.1995), Standard batch control; part 1: models and terminology, Instrument Society of America, 1995] is a standard that provides a methodology for the dissemination of a batch into standard models and provides the terminology for defining the control requirements of batch plants. The nature of S88 is such that it is not only applicable to the development of computer control systems for a batch plant, but also could be utilised within batch management software, i.e. scheduling. This paper presents a method of interpreting multi-purpose/product batch plant into S88 constructs to provide an object oriented framework for the research and development of a batch scheduling Matlab tool-box. Such a framework provides a thorough and efficient method of articulating the model to effectively apply automatic scheduling/optimisation methods.

Journal Article↗
PubMed1992

[Three-dimensional reconstruction of cytoskeletons in rat salivary glands using confocal fluorescence microscopy and volume-rendering computer graphics].

A new reconstruction technique for the demonstration of three-dimensional architectural details from biological fluorescent specimens was used to determine the precise spacial organization of F-actin in rat sublingual glands. F-actin was stained with NBD-phallacidin in thick (20-30 microns) frozen sections and observed with a confocal laser scanning microscope to obtain thin (-1 micron) optically sectioned images. A series of optical sections taken successively at different focal levels in steps of 1 micron was then reconstructed with volume-rendering computer graphics. The rendered images viewed from several angles (e.g. top, bottom, sides) clearly revealed the presence of F-actin fluorescence along the hexagonal framework of the junctional complex within the acini and in the cytoplasm of star-shaped myoepithelial cells encircling the acini. The detailed structures and the topographical relations between the junctional complex and myoepithelial cells were more impressively observed when the rendered images were displayed by motion picture. These images are free from any artifacts caused by the mechanical sectioning and revealed well the delicate and complicated profiles of cellular structures that previously have been almost impossible to demonstrate by conventional reconstruction techniques. We expect that the combination of confocal microscopy and volume rendering will permit the dynamic observation of previously unseen phenomena in three dimensions, such as the behavior of biologically active molecules in living cells.

Animals↗
PubMedDate not supplied

Theoretical conformational investigation of thrombin-fibrinogen recognition complex.

Theoretical conformational investigation of the thrombin-fibrinogen recognition complex was fulfilled. At first preliminary study was carried out using space-filling molecular models. At the next stage computer simulation was conducted. For this purpose a package of programs for the theoretical conformational analysis of two interacting molecules has been developed in the framework of atom-atom potentials. The package contains an original algorithm for constructing initial approximation based on assumption that the structure of the complex is determined mainly by the ligand-ligand attraction and Van-der-Vaals repulsion. Complex structure with considerable binding energy was obtained. Molecules of that structure are bound mainly by four oppositely charged pairs of side chain groups. The beta -loop of thrombin in the complex is shown to undergo essential structural transformations. A hypothesis is suggested that this transformation may influence active sites allosterically. Some ways and mechanisms of this influence are discussed as well as an approach to its calculation.

Computer Simulation↗
PubMed1988

The Escherichia coli 30S ribosomal subunit; an optimized three-dimensional fit between the ribosomal proteins and the 16S RNA.

We have generated a computerized fit between the 3-dimensional map of the E.coli 30S ribosomal proteins, as determined by neutron scattering, and the recently published 3-dimensional model for the 16S RNA. To achieve this, the framework of coordinates for RNA-protein cross-link sites on the phosphate backbone in the RNA model was related to the corresponding framework of coordinates for the mass centres of the proteins by a least squares fitting procedure. The resulting structure, displayed on a computer graphics system, gives the first complete picture of the E.coli 30S ribosomal subunit showing both the proteins and the double-helical regions of the RNA. The root mean square distance between cross-link sites and protein centres is 32 A. The position of the mass centre of the combined double-helical regions was calculated from the model and compared with the position of the mass centre of the complete set of proteins. The two centres are displaced relative to one another by 20 A in the model structure, in good agreement with the experimental value of 25 A found by neutron scattering.

Computer Graphics↗
PubMed1996

Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly].

The design of enzyme mimics with therapeutic and industrial applications has interested both experimental and computational chemists for several decades. Recent advances in the computational methodology of restrained molecular dynamics, used in conjunction with data obtained from two-dimensional 1H NMR spectroscopy, make it a promising method to study peptide and protein structure and function. Several issues, however, need to be addressed in order to assess the validity of this method for its explanatory and predictive value. Among the issues addressed in this study are: the accuracy and generizability of the GROMOS peptide molecular mechanics force field; the effect of inclusion of solvent on the simulations; and the effect of different types of restraining algorithms on the computational results. The decapeptide Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly, which corresponds to the sequence of ACTH1-10, has been synthesized, cyclized, and studied by two-dimensional 1H NMR spectroscopy. Restrained molecular dynamics (RMD) and time-averaged restrained molecular dynamics (TARMD) simulations were carried out on four different distance-geometry starting structures in order to determine and contrast the behavior of cyclic ACTH1-10 in vacuum and in solution. For the RMD simulations, the structures did not fit the NOE data well, even at high values of the restraining potential. The TARMD simulation method, however, was able to give structures that fit the NOE data at high values of the restraining potential. In both cases, inclusion of explicit solvent molecules in the simulation had little effect on the quality of the fit, although it was found to dampen the motion of the cyclic peptide. For both simulation techniques, the number and size of the NOE violations increased as the restraining potential approached zero. This is due, presumably, to inadequacies in the force field. Additional TARMD vacuum-phase simulations, run with a larger memory length or with a larger sampling size (16 additional distance-geometry structures), yielded no significantly different results. The computed data were then analyzed to help explain the sparse NOE data and poor chymotryptic activity of the cyclic peptide. Cyclic ACTH1-10, which contains the functional moieties of the catalytic triad of chymotrypsin, was evaluated as a potential mimic of chymotrypsin by measurement of the rate of hydrolysis of esters of L- and D-phenylalanine. The poor rate of hydrolysis is attributed to the flexibility of the decapeptide, the motion of the side chains, which result in the absence of long-range NOEs, the small size of the macrocycle relative to that of the substrate, and the inappropriate orientation of the Gly, His, and Ser residues. The results demonstrate the utility of this method in computer-aided molecular design of cyclic peptides and suggest structural modifications for future work based on a larger and more rigid peptide framework.

Adrenocorticotropic Hormone↗
PubMed1993

Generalized pharmacokinetic modeling for drugs with nonlinear binding: I. Theoretical framework.

The following integrodifferential equation is proposed as the basis for a generalized treatment of pharmacokinetic systems in which nonlinear binding occurs phi'(cu)c'u = -q(cu)+g * cu+f where cu identical to unbound plasma drug concentration, f identical to drug input rate, ' indicates the derivative of a function, and * indicates the convolution operation: (g * cu) (t) = integral of t0 g(t-u)cu(u) du. Possible physical interpretations of the functions q, g and f are: q(cu) identical to rate at which drug leaves the sampling compartment, g * cu identical to rate at which drug returns to the sampling compartment from the peripheral system (tissues that are kinetically distinct from the sampling compartment), and phi(cu) identical to amount of drug in the sampling compartment. The approach assumes that drug binding is sufficiently rapid that it may be treated as an equilibrium process. It may be applied to systems in which nonlinear binding occurs within the sampling compartment, i.e., in the systemic circulation or in tissues to which drug is rapidly distributed. The proposed relationship is a generalization of most existing models for drugs with nonlinear binding. It can serve as a general theoretical framework for such models or as the basis for "model-independent" methods for analyzing the pharmacokinetics of drugs with nonlinear binding. Computer programs for the numerical solution of the integrodifferential equation are presented. Methods for pharmacokinetic system characterization, prediction and bioavailability are presented and demonstrated.

Biological Availability↗
PubMed2004

Reinforcement learning with via-point representation.

In this paper, we propose a new learning framework for motor control. This framework consists of two components: reinforcement learning and via-point representation. In the field of motor control, conventional reinforcement learning has been used to acquire control sequences such as cart-pole or stand-up robot control. Recently, researchers have become interested in hierarchical architecture, such as multiple levels, and multiple temporal and spatial scales. Our new framework contains two levels of hierarchical architecture. The higher level is implemented using via-point representation, which corresponds to macro-actions or multiple time scales. The lower level is implemented using a trajectory generator that produces primitive actions. Our framework can modify the ongoing movement by means of temporally localized via-points and trajectory generation. Successful results are obtained in computer simulation of the cart-pole swing up task.

Computer Simulation↗