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At least 613 records · Page 34Linked to original sources
PubMed2005

Isomolar semigrand ensemble molecular dynamics: development and application to liquid-liquid equilibria.

An extended system molecular dynamics method for the isomolar semigrand ensemble (fixed number of particles, pressure, temperature, and fugacity fraction) is developed and applied to the calculation of liquid-liquid equilibria (LLE) for two Lennard-Jones mixtures. The method utilizes an extended system variable to dynamically control the fugacity fraction xi of the mixture by gradually transforming the identity of particles in the system. Two approaches are used to compute coexistence points. The first approach uses multiple-histogram reweighting techniques to determine the coexistence xi and compositions of each phase at temperatures near the upper critical solution temperature. The second approach, useful for cases in which there is no critical solution temperature, is based on principles of small system thermodynamics. In this case a coexistence point is found by running N-P-T-xi simulations at a common temperature and pressure and varying the fugacity fraction to map out the difference in chemical potential between the two species A and B (mu(A)-mu(B)) as a function of composition. Once this curve is known the equal-distance/equal-area criterion is used to determine the coexistence point. Both approaches give results that are comparable to those of previous Monte Carlo (MC) simulations. By formulating this approach in a molecular dynamics framework, it should be easier to compute the LLE of complex molecules whose intramolecular degrees of freedom are often difficult to properly sample with MC techniques.

Journal Article↗
PubMed1985

Computer-based information systems models. Perspectives for nursing.

A synthesis of theories from the management information systems (MIS) field provided the conceptual framework to describe how to design and develop effective computer-based information systems. An analysis of activities and interviews with nurse managers in a tertiary care medical center provided the basis for describing five major nursing department functions and the information requirements arising from those functions. The MIS framework was applied to the nursing department information requirements in order to derive MNIS, a normative model of a nursing information system, which was then used to "bench mark" the current status of commercially available nursing information systems. The researchers compared the MNIS with 28 nursing information systems that vendors are currently developing or marketing. The comparison revealed large gaps between nursing department needs and vendor-provided solutions.

Commerce↗
PubMed2004

From FNS to HEIV: a link between two vision parameter estimation methods.

Problems requiring accurate determination of parameters from image-based quantities arise often in computer vision. Two recent, independently developed frameworks for estimating such parameters are the FNS and HEIV schemes. Here, it is shown that FNS and a core version of HEIV are essentially equivalent, solving a common underlying equation via different means. The analysis is driven by the search for a nondegenerate form of a certain generalized eigenvalue problem and effectively leads to a new derivation of the relevant case of the HEIV algorithm. This work may be seen as an extension of previous efforts to rationalize and interrelate a spectrum of estimators, including the renormalization method of Kanatani and the normalized eight-point method of Hartley.

Algorithms↗
PubMedDate not supplied

A computer-based AIDS education program for nursing students.

A multidisciplinary team has developed a computer-based software program for educating nursing students and other college students about six sexually transmitted diseases (STDs). The program for educating about Acquired Immune Deficiency Syndrome (AIDS) is the first of the six "Smartbooks" to be completed, using the Hypercard Expert System shell on the Macintosh computer. Information is organized within a framework known as a concept map, and the student user progresses through the program in a self-directed way by "clicking" on the portion of the concept map that is of interest. Thus, the knowledge base can be accessed in many different ways, and is not restricted to a linear format. Comparative quantitative analysis using a control program shows consistently better student retention of information presented within the program that features concept maps. Qualitative results indicate that students find the conceptually-arranged knowledge base implicitly easy to understand, "fun" to use, and interesting to explore. Educational theory suggests that the success of such a format may be related to the schematic nature of memory.

Acquired Immunodeficiency Syndrome↗
PubMed2001

Good dynamics versus bad kinematics: is entanglement needed for quantum computation?

We study the role of entanglement in quantum computation. We consider the case of a pure state contaminated by "white noise." This framework arises, for example, in pseudopure state implementations of quantum computing using NMR. We analyze quantum computational protocols which aim to solve exponential classical problems with polynomial resources and ask whether or not entanglement of the pseudopure states is needed to achieve this aim. We show that, for a large class of such protocols, including Shor's factorization, entanglement is necessary. We also show that achieving entanglement is not sufficient: If the state is sufficiently noisy, exponential resources are needed even if entanglement is present.

Journal Article↗
PubMed1989

Computer applications for staff development and patient education.

The changing and evolving profession of nursing necessitates extensive staff development activities on the part of nursing management. This ongoing responsibility is essential to maintaining the currency and competence of practicing nurses and facilitating their professional growth. Simultaneously there are economic constraints coinciding with increased consumer demands for patient education. The purpose of this paper is to explore an innovative teaching method, the use of instructional computing for staff development and patient education programs. The theoretical frameworks for this instructional modality are identified and general advantages and disadvantages of instructional computing applications are described. Specific examples of programs from the literature are briefly discussed.

Attitude to Computers↗
PubMed2002

Computational study on monkey VOR adaptation and smooth pursuit based on the parallel control-pathway theory.

Much controversy remains about the site of learning and memory for vestibuloocular reflex (VOR) adaptation in spite of numerous previous studies. One possible explanation for VOR adaptation is the flocculus hypothesis, which assumes that this adaptation is caused by synaptic plasticity in the cerebellar cortex. Another hypothesis is the model proposed by Lisberger that assumes that the learning that occurs in both the cerebellar cortex and the vestibular nucleus is necessary for VOR adaptation. Lisberger's model is characterized by a strong positive feedback loop carrying eye velocity information from the vestibular nucleus to the cerebellar cortex. This structure contributes to the maintenance of a smooth pursuit driving command with zero retinal slip during the steady-state phase of smooth pursuit with gain 1 or during the target blink condition. Here, we propose an alternative hypothesis that suggests that the pursuit driving command is maintained in the medial superior temporal (MST) area based on MST firing data during target blink and during ocular following blank, and as a consequence, we assume a much smaller gain for the positive feedback from the vestibular nucleus to the cerebellar cortex. This hypothesis is equivalent to assuming that there are two parallel neural pathways for controlling VOR and smooth pursuit: a main pathway of the semicircular canals to the vestibular nucleus for VOR, and a main pathway of the MST-dorsolateral pontine nuclei (DLPN)-flocculus/ventral paraflocculus to the vestibular nucleus for smooth pursuit. First, we theoretically demonstrate that this parallel control-pathway theory can reproduce the various firing patterns of horizontal gaze velocity Purkinje cells in the flocculus/ventral paraflocculus dependent on VOR in the dark, smooth pursuit, and VOR cancellation as reported in Miles et al. at least equally as well as the gaze velocity theory, which is the basic framework of Lisberger's model. Second, computer simulations based on our hypothesis can stably reproduce neural firing data as well as behavioral data obtained in smooth pursuit, VOR cancellation, and VOR adaptation, even if only plasticity in the cerebellar cortex is assumed. Furthermore, our computer simulation model can reproduce VOR adaptation automatically based on a heterosynaptic interaction model between parallel fiber inputs and climbing fiber inputs. Our results indicate that different assumptions about the site of pursuit driving command maintenance computationally lead to different conclusions about where the learning for VOR adaptation occurs. Finally, we propose behavioral and physiological experiments capable of discriminating between these two possibilities for the site of pursuit driving command maintenance and hence for the sites of learning and memory for VOR adaptation.

Adaptation, Physiological↗
PubMed2004

ProteomeGRID: towards a high-throughput proteomics pipeline through opportunistic cluster image computing for two-dimensional gel electrophoresis.

The quest for high-throughput proteomics has revealed a number of critical issues. Whilst improved two-dimensional gel electrophoresis (2-DE) sample preparation, staining and imaging issues are being actively pursued by industry, reliable high-throughput spot matching and quantification remains a significant bottleneck in the bioinformatics pipeline, thus restricting the flow of data to mass spectrometry through robotic spot excision and protein digestion. To this end, it is important to establish a full multi-site Grid infrastructure for the processing, archival, standardisation and retrieval of proteomic data and metadata. Particular emphasis needs to be placed on large-scale image mining and statistical cross-validation for reliable, fully automated differential expression analysis, and the development of a statistical 2-DE object model and ontology that underpins the emerging HUPO PSI GPS (Human Proteome Organization Proteomics Standards Initiative General Proteomics Standards). The first step towards this goal is to overcome the computational and communications burden entailed by the image analysis of 2-DE gels with Grid enabled cluster computing. This paper presents the proTurbo framework as part of the ProteomeGRID, which utilises Condor cluster management combined with CORBA communications and JPEG-LS lossless image compression for task farming. A novel probabilistic eager scheduler has been developed to minimise make-span, where tasks are duplicated in response to the likelihood of the Condor machines' owners evicting them. A 60 gel experiment was pair-wise image registered (3540 tasks) on a 40 machine Linux cluster. Real-world performance and network overhead was gauged, and Poisson distributed worker evictions were simulated. Our results show a 4:1 lossless and 9:1 near lossless image compression ratio and so network overhead did not affect other users. With 40 workers a 32x speed-up was seen (80% resource efficiency), and the eager scheduler reduced the impact of evictions by 58%.

Algorithms↗
PubMed2004

Depth-map-based scene analysis for active navigation in virtual angioscopy.

This paper presents a new approach dealing with virtual exploratory navigation inside vascular structures. It is based on the notion of active vision in which only visual perception drives the motion of the virtual angioscope. The proposed fly-through approach does not require a premodeling of the volume dataset or an interactive control of the virtual sensor during the fly-through. Active navigation combines the on-line computation of the scene view and its analysis, to automatically define the three-dimensional sensor path. The navigation environment and the camera-like model are first sketched. The basic stages of the active navigation framework are then described: the virtual image computation (based on ray casting), the scene analysis process (using depth map), the navigation strategy, and the virtual path estimation. Experimental results obtained from phantom model and patient computed tomography data are finally reported.

Algorithms↗
PubMed2025

SIGEL: a context-aware genomic representation learning framework for spatial genomics analysis.

Spatial transcriptomics (ST) integrates spatial information into genomics, yet methods for generating spatially-informed gene representations are limited and computationally intensive. We present SIGEL, a cost-effective framework that derives gene manifolds from ST data by exploiting spatial genomic context. The resulting SIGEL-generated gene representations (SGRs) are context-aware, biologically meaningful, and robust across samples, making them highly effective for key downstream tasks, including imputing missing genes, detecting spatial expression patterns, identifying disease-related genes and interactions, and improving spatial clustering. Extensive experiments across diverse ST datasets validate SIGEL's effectiveness and highlight its potential in advancing spatial genomics research.

Genomics↗
PubMed2003

Level set-based integration of segmentation and computational fluid dynamics for flow correction in phase contrast angiography.

RATIONALE AND OBJECTIVES: A novel method to correct flow data from magnetic resonance phase contrast (MR-PC) angiography, based on combining computational fluid dynamics and segmentation in a level set framework, was developed and tested in this study. MATERIALS AND METHODS: The MR-PC velocity data was used in a partial differential equation-based level set method for vessel segmentation. The results were supplied as the quantitative description of the vessel wall to the flow field solver using computational fluid dynamics, based on the level set method, to obtain a physically meaningful flow. The most significant characteristic of our novel approach is that it requires light computational loads, especially insofar as it avoids generation of complex computational grid system. The integration of segmentation and computational fluid dynamics in a level set framework is shown to be both robust and economic, and yet yields a physically correct velocity field and optimal vessel geometry. RESULTS: The application to the flow field in a straight tube with circular cross section of constant radius demonstrated the validity of out new approach, especially the treatment of the velocity boundary conditions on the solid wall. Simulation of the velocity field in both common carotid artery and bifurcation of basilar and vertebral arteries, based on clinical MR-PC data, provided with smooth and stable results. CONCLUSION: Applying this procedure to both synthetic and clinical data, significant improvement of the blood velocity field, such as a smooth velocity distribution aligned along the vessels and removal of burst or error vectors, could be observed. This procedure also offers possibilities for improved vessel segmentation.

Basilar Artery↗
PubMed2005

Penalized-likelihood sinogram smoothing for low-dose CT.

We have developed a sinogram smoothing approach for low-dose computed tomography (CT) that seeks to estimate the line integrals needed for reconstruction from the noisy measurements by maximizing a penalized-likelihood objective function. The maximization is performed by an algorithm derived by use of the separable paraboloidal surrogates framework. The approach overcomes some of the computational limitations of a previously proposed spline-based penalized-likelihood sinogram smoothing approach, and it is found to yield better resolution-variance tradeoffs than this spline-based approach as well an existing adaptive filtering approach. Such sinogram smoothing approaches could be valuable when applied to the low-dose data acquired in CT screening exams, such as those being considered for lung-nodule detection.

Algorithms↗
PubMed2006

A survey of motif discovery methods in an integrated framework.

BACKGROUND: There has been a growing interest in computational discovery of regulatory elements, and a multitude of motif discovery methods have been proposed. Computational motif discovery has been used with some success in simple organisms like yeast. However, as we move to higher organisms with more complex genomes, more sensitive methods are needed. Several recent methods try to integrate additional sources of information, including microarray experiments (gene expression and ChlP-chip). There is also a growing awareness that regulatory elements work in combination, and that this combinatorial behavior must be modeled for successful motif discovery. However, the multitude of methods and approaches makes it difficult to get a good understanding of the current status of the field. RESULTS: This paper presents a survey of methods for motif discovery in DNA, based on a structured and well defined framework that integrates all relevant elements. Existing methods are discussed according to this framework. CONCLUSION: The survey shows that although no single method takes all relevant elements into consideration, a very large number of different models treating the various elements separately have been tried. Very often the choices that have been made are not explicitly stated, making it difficult to compare different implementations. Also, the tests that have been used are often not comparable. Therefore, a stringent framework and improved test methods are needed to evaluate the different approaches in order to conclude which ones are most promising. REVIEWERS: This article was reviewed by Eugene V. Koonin, Philipp Bucher (nominated by Mikhail Gelfand) and Frank Eisenhaber.

Journal Article↗
PubMed2000

GLIF3: the evolution of a guideline representation format.

The Guideline Interchange Format (GLIF) is a language for structured representation of guidelines. It was developed to facilitate sharing clinical guidelines. GLIF version 2 enabled modeling a guideline as a flowchart of structured steps, representing clinical actions and decisions. However, the attributes of structured constructs were defined as text strings that could not be parsed, and such guidelines could not be used for computer-based execution that requires automatic inference. GLIF3 is a new version of GLIF designed to support computer-based execution. GLIF3 builds upon the framework set by GLIF2 but augments it by introducing several new constructs and extending GLIF2 constructs to allow a more formal definition of decision criteria, action specifications and patient data. GLIF3 enables guideline encoding at three levels: a conceptual flowchart, a computable specification that can be verified for logical consistency and completeness, and an implementable specification that can be incorporated into particular institutional information systems.

Decision Support Techniques↗
PubMed2001

"Non-VSEPR" Structures and Bonding in d(0) Systems.

Under certain circumstances, metal complexes with a formal d(0) electronic configuration may exhibit structures that violate the traditional structure models, such as the VSEPR concept or simple ionic pictures. Some examples of such behavior, such as the bent gas-phase structures of some alkaline earth dihalides, or the trigonal prismatic coordination of some early transition metal chalcogenides or pnictides, have been known for a long time. However, the number of molecular examples for "non-VSEPR" structures has increased dramatically during the past decade, in particular in the realm of organometallic chemistry. At the same time, various theoretical models have been discussed, sometimes controversially, to explain the observed, unusual structures. Many d(0) systems are important in homogeneous and heterogeneous catalysis, biocatalysis (e.g. molybdenum or tungsten enzymes), or materials science (e.g. ferroelectric perovskites or zirconia). Moreover, their electronic structure without formally nonbonding d orbitals makes them unique starting points for a general understanding of structure, bonding, and reactivity of transition metal compounds. Here we attempt to provide a comprehensive view, both of the types of deviations of d(0) and related complexes from regular coordination arrangements, and of the theoretical framework that allows their rationalization. Many computational and experimental examples are provided, with an emphasis on homoleptic mononuclear complexes. Then the factors that control the structures are discussed in detail. They are a) metal d orbital participation in sigma bonding, b) polarization of the outermost core shells, c) ligand repulsion, and d) pi bonding. Suggestions are made as to which of the factors are the dominant ones in certain situations. In heteroleptic complexes, the competition of sigma and pi bonding of the various ligands controls the structures in a complicated fashion. Some guidelines are provided that should help to better understand the interrelations. Bent's rule is of only very limited use in these types of systems, because of the paramount influence of pi bonding. Finally, computed and measured structures of multinuclear complexes are discussed, including possible consequences for the properties of bulk solids.

Journal Article↗
PubMed2003

Parallelization of four-component calculations. II. Symmetry-driven parallelization of the 4-Spinor CCSD algorithm.

Given the importance of the Coupled-cluster (CC) method as an efficient and accurate way to take electron correlation into account, we extend the parallelization technique in the second part of this series also to the 4-Spinor CCSD algorithm implemented in the Dirac-Fock packages DIRAC and MOLFDIR. The present implementation is based on the availability of the transformed molecular two-electron integrals on an external storage medium. The linearity of the CC equations in these two-electron integrals is used in a parallelization strategy that is based on distribution of the two largest integral classes that carry three or four virtual spinor indices. The corresponding partial contributions to the T(1) and T(2) amplitudes are calculated on each node and added using Message Passing Interface (MPI) library calls. Although we did not employ a master/slave principle, one specific node was assigned to also perform the remaining serial parts of the algorithm. In the critical sections considerable savings in storage requirements and computer time could be achieved, and this allows for computations on larger systems in the framework of four-component theory.

Journal Article↗
PubMed1998

Evaluation of Surface Ionization Parameters from AFM Data.

A new application of atomic force microscopy (AFM) for evaluation of surface ionization parameters on the basis of a charge-regulation model is demonstrated. Interactions between symmetrical silicon nitride and silica surfaces have been measured in aqueous electrolytic solutions at different pHs and separations from a few Debye lengths down to zero. The obtained experimental data are reported and interpreted on a quantitative level in the framework of Derjaguin's approximation; the computational procedure used for this purpose is outlined. Surface charge density, surface potential, and species concentrations are calculated as functions of pH and separation, unveiling the limits of applicability of classical constant-charge and constant-potential approximations. The integrity of the results on the charge properties of interacting surfaces is discussed in reference to electrokinetic and titration data, potential problems caused by the existence of non-DLVO forces and surface irregularities being highlighted. Copyright 1998 Academic Press.

Journal Article↗
PubMed1994

The hierarchical Bayesian approach to population pharmacokinetic modelling.

Compartmental models are widely used to model the profile of drug concentrations versus time from administration in an individual subject. Observed concentrations are then modelled as noisy departures from the underlying profile, the latter characterised for each individual by a small number of 'individual parameters'. When a population of individuals is studied, inter-individual variation is modelled by assuming that the individual profile parameters are drawn from a population distribution, the latter characterised by 'population parameters' describing, in effect, a mean population profile and individual variation around it. From a Bayesian statistical perspective, such models fit exactly into the so-called hierarchical modelling framework, which provides a coherent basis for individual and population inferences and prediction, as well as for decision-making (for example, the design of dosage regimens). This paper outlines the hierarchical model framework and describes how the required computations can be carried out in a straightforward manner by a Markov chain Monte Carlo technique known as Gibbs sampling, even when models involve mean-variance relationships and outliers.

Bayes Theorem↗