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 469 records · Page 26Linked to original sources
PubMed1996

Teaching resources for dermatology on the WWW--quiz system and dynamic lecture scripts using a HTTP-database demon.

The World Wide Web (WWW) is becoming the major way of acquiring information in all scientific disciplines as well as in business. It is very well suitable for fast distribution and exchange of up to date teaching resources. However, to date most teaching applications on the Web do not use its full power by integrating interactive components. We have set up a computer based training (CBT) framework for Dermatology, which consists of dynamic lecture scripts, case reports, an atlas and a quiz system. All these components heavily rely on an underlying image database that permits the creation of dynamic documents. We used a demon process that keeps the database open and can be accessed using HTTP to achieve better performance and avoid the overhead involved by starting CGI-processes. The result of our evaluation was very encouraging.

Computer Communication Networks↗
PubMed2004

Knowledge acquisition in the fuzzy knowledge representation framework of a medical consultation system.

This paper describes the fuzzy knowledge representation framework of the medical computer consultation system MedFrame/CADIAG-IV as well as the specific knowledge acquisition techniques that have been developed to support the definition of knowledge concepts and inference rules. As in its predecessor system CADIAG-II, fuzzy medical knowledge bases are used to model the uncertainty and the vagueness of medical concepts and fuzzy logic reasoning mechanisms provide the basic inference processes. The elicitation and acquisition of medical knowledge from domain experts has often been described as the most difficult and time-consuming task in knowledge-based system development in medicine. It comes as no surprise that this is even more so when unfamiliar representations like fuzzy membership functions are to be acquired. From previous projects we have learned that a user-centered approach is mandatory in complex and ill-defined knowledge domains such as internal medicine. This paper describes the knowledge acquisition framework that has been developed in order to make easier and more accessible the three main tasks of: (a) defining medical concepts; (b) providing appropriate interpretations for patient data; and (c) constructing inferential knowledge in a fuzzy knowledge representation framework. Special emphasis is laid on the motivations for some system design and data modeling decisions. The theoretical framework has been implemented in a software package, the Knowledge Base Builder Toolkit. The conception and the design of this system reflect the need for a user-centered, intuitive, and easy-to-handle tool. First results gained from pilot studies have shown that our approach can be successfully implemented in the context of a complex fuzzy theoretical framework. As a result, this critical aspect of knowledge-based system development can be accomplished more easily.

Decision Making↗
PubMed2005

Coarse-grained computations for a micellar system.

We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms), and atomistic simulations of the Larson model of micelle formation. The procedure hinges on the (expected) evolution of a few slow, coarse-grained mesoscopic observables of the Monte Carlo simulation, and on (computational) time scale separation between these and the remaining "slaved," fast variables. Short bursts of appropriately initialized atomistic simulation are used to estimate the (coarse grained, deterministic) local dynamics of the evolution of the observables. These estimates are then in turn used to accelerate the evolution to computational stationarity through traditional continuum algorithms (forward Euler integration, Newton-Raphson fixed point computation). This "equation-free" framework, bypassing the derivation of explicit, closed equations for the observables (e.g., equations of state), may provide a computational bridge between direct atomistic/stochastic simulation and the analysis of its macroscopic, system-level consequences.

Journal Article↗
PubMed2006

Toward the comparison of rare earth element and actinide behavior in materials: a computational study of Ce- and U-bearing britholites.

We present a computational investigation into the nature of bonds formed by f-elements in materials. The paper presents an example of the incorporation of rare earth elements (REE) and actinides in minerals derived from fluorapatite: Ca(10)(PO(4))(6)F(2). These minerals, called britholites, allow many substitutions on all three Ca, P, and F sites and are considered as potential host phases for radioactive elements separated from nuclear waste. REE and actinides have very similar physical and chemical properties, but REE are not radioactive and much more easily handled. REE are, therefore, very often used as a surrogate for actinides in experimental studies. The representative elements of rare earths and actinides chosen for this first investigation are cerium and uranium, respectively. We have studied all the various configurations of Ca(9)X(PO(4))(6)(-)(y)()(SiO(4))(y)()F(2), where X stands for Ce(3+), Ce(4+), U(3+), and U(4+), and y is equal to 1 and 2 for three-time and four-time charged cations, respectively. Calculations have been performed within the density functional theory (DFT) framework according to the computation scheme determined in a previous study. The analysis of the energies of the various configurations shows that the incorporation of all the cations considered stabilizes the apatitic structure. This stabilization, however, is greater for four-time charged cations than for three-time charged ones, which shows that Ce and U are both preferentially substituted in the +IV oxidation state. In addition, the substitution in one of the two cationic sites of the apatitic structure is always more favorable. Then, the geometry analysis shows a larger decrease in size of this cationic site for U than for Ce, as well as different volume variations for Ce and U substitutions in the two cationic sites. This cannot be explained by steric effects alone. Finally, the electronic density analysis yields three essential results: U and Ce form significantly covalent bonds, U forms bonds more covalent than Ce, and finally four-time charged cations form more covalent bonds than three-time charged ones. The comparison of these results with the formation enthalpies of the various phases shows a positive correlation between the covalence degree of the bonds formed by the f-element and the stability of the structure. In addition, our results prove that Ce- and U-bearing britholites exhibit very similar energetic, structural, and electronic properties. Ce, therefore, appears to be a good simulant for U.

Journal Article↗
PubMed2004

A technique for fabricating patterns for removable partial denture frameworks using digitized casts and electronic surveying.

Although computer-aided design and manufacture techniques have shown some promising applications in the fabrication of crowns, inlays, and maxillofacial and oral surgery, the field of removable prosthodontics has not embraced these technologies so far. This article describes the development and investigation of computer-aided techniques that may eventually enable prosthodontic procedures such as surveying and the production of sacrificial patterns to be performed digitally. A 3-dimensional computer model of a conventional cast from a patient was obtained using an optical surface capture device (a scanner). The shape of a number of components of a removable partial denture framework was modeled on the 3-dimensional scan electronically, using computer-aided design software. A physical plastic shape of the components was produced using a Rapid Prototyping machine and used as a sacrificial pattern. Techniques to allow digital cast surveying before the production of sacrificial patterns were also developed. The results show that digital dental surveying and machine-produced sacrificial patterns can be accomplished. This article forms a basis for further developments leading to a fully integrated approach to the computer-aided design and fabrication of removable partial denture frameworks.

Computer Simulation↗
PubMed2006

Hydrogen atom and hydride anion addition to adenine: structures and energetics.

The radicals and anions derived from the 9H tautomer of adenine by adding a hydrogen atom to one of the four double bonds of the adenine framework have been studied. Computations were carried out using a carefully calibrated density functional (B3LYP) method and basis set (DZP++). Optimized geometries, energies, and vibrational frequencies are predicted for eight radicals and anions. The radicals are found to lie in a range of 22 kcal mol(-1), with the radical derived by addition to the C(8) carbon atom being the lowest lying energetically. The anions are predicted to be bound species in the gas phase with an energetic range of 43 kcal mol(-1). Anions produced by addition of a hydride ion to adenine carbon atoms are found to be the most favorable. Six of the anions are predicted to be stable species with respect to electron detachment. The adiabatic electron affinities, vertical electron affinities, and vertical detachment energies are computed for the first time. Electron affinities for these radicals range from 0.0 to 2.0 eV. Radicals produced by addition to a nitrogen atom have near-zero adiabatic electron affinities, while radicals produced by addition at carbon atoms have considerably higher electron affinities.

Adenine↗
PubMed2003

Implementation of a general multireference configuration interaction procedure with analytic gradients in a semiempirical context using the graphical unitary group approach.

The graphical unitary group approach has been applied in an efficient implementation of a general multireference configuration interaction (MRCI) method for use with small active molecular orbital spaces in a semiempirical framework. Gradients can be computed analytically for molecular orbitals from a closed-shell or a half-electron open-shell Hartree-Fock calculation. CPU times for single point energy and gradient calculations are reported. The code allows MRCI geometry optimizations of large molecules, as illustrated for the singlet ground state and the four lowest triplet states of fullerene C(76).

Journal Article↗
PubMed2001

MassKinetics: a theoretical model of mass spectra incorporating physical processes, reaction kinetics and mathematical descriptions.

A theoretical framework and an accompanying computer program (MassKinetics, www.chemres.hu/ms/ masskinetics) is developed for describing reaction kinetics under statistical, but non-equilibrium, conditions, i.e. those applying to mass spectrometry. In this model all the important physical processes influencing product distributions are considered: reactions, including the effects of acceleration, collisions and photon exchange. These processes occur simultaneously and are taken into account by the master equation approach. The system is described by (independent) product, kinetic energy and internal energy distributions, and the time development of these distributions is studied using transition probability functions. The product distribution at the end of the experiment corresponds to the mass spectrum. Individual elements in this scheme are mostly well known: internal energy-dependent reaction rates are calculated by transition state theory (RRK or RRKM formalisms). In the course of collisions, energy transfer and other processes may occur (the latter usually resulting in the 'loss' of ion signal). Collisions are characterized by their probability and by energy transfer in a single collision. To describe single collisions, three collision models are used: long-lived collision complexes, partially inelastic collisions and partially inelastic collisions with cooling. The latter type has been developed here, and is capable of accounting for cooling effects occurring in collision cascades. Descriptions of photon absorption and emission are well known in principle, and these are also taken into account, in addition to changes in kinetic energy due to external (electric) fields. These changes in the system occur simultaneously, and are described by master equations (a set of differential equations). The usual form of the master equation (taking into account reactions and collisional excitation) was extended to consider also radiative energy transfer, kinetic energy changes, energy partitioning and ion loss collisions. Initial results show that close to experimental accuracy can be obtained with MassKinetics, using few or no adjustable parameters. The model/program can be used to model almost all types of mass spectrometric experiments (e.g. MIKE, CID, SORI and resonant excitation). Note that it was designed for mass spectrometric applications, but can also be used to study reaction kinetics in other non-equilibrium systems.

Energy Transfer↗
PubMed2006

A theoretical study of pentacyclo-undecane cage peptides of the type [Ac-X-Y-NHMe].

The conformational preferences of peptides of the type, Ac-X-Y-NHMe, where X and Y = Ala, cage and Pro, were studied by means of computational techniques within the framework of a molecular mechanics approach. For each of the eight peptide analogues, extensive conformational searches were carried out using molecular dynamics (MD) and simulated annealing (SA) protocols in an iterative fashion. Both results are in good agreement and complement each other. The conformational search indicates that the cage residue restricts the conformational freedom of the dipeptide considerably in comparison with the other model residues used. This study revealed that proline exhibits a greater tendency in promoting reverse-turn characteristics in comparison to the cage peptides, which show promising beta-turn characteristics. It was also found that 300-500 K is not sufficient to overcome rotational barriers for cage peptides. In all cases, the low-energy conformers have a tendency to form bent structures.

Models, Theoretical↗
PubMed2005

Spatial motion constraints for robot assisted suturing using virtual fixtures.

We address the problem of the stitching task in endoscopic surgery using a circular needle under robotic assistance. Our main focus is to present an algorithm for suturing using guidance virtual fixtures (VF) that assist the surgeon to move towards a desired goal. A weighted multi-objective, constraint optimization framework is used to compute the joint motions required for the tasks. We show that with the help of VF, suturing can be performed at awkward angles without multiple trials, thus avoiding damage to tissue. In this preliminary study we show the feasibility of our approach and demonstrate the promise of cooperative assistance in complex tasks such as suturing.

Feasibility Studies↗
PubMed1996

Flow cytometry for CD34 determination in hematopoietic grafts.

CD34 is a type I transmembrane protein that is expressed on lympho-hematopoietic progenitor and endothelial cells and has a potential adhesion function. Various monoclonal antibodies, whether characterized by glycosylated epitopes or not, are utilized to recognize different subsets of hematopoietic progenitors. Coexpression of membrane markers involving CD34 is an approach to the definition of those subpopulations of cells previously characterized by using in vitro cultures. Thus, in the autologous transplantation procedure, flow cytometry determination of CD34+ cells in the grafts themselves, especially as concerns cytapheresis products, was enhanced with CFU-GM enumeration. This methodology required a standardized protocol with regard to the choice of the monoclonal antibody, had to be to data acquisition and to computer analysis. Within the framework of a multicentric trial, various strategies had to be evaluated. Special attention was paid to obtaining a sensitivity level of 0.1%. New, standardized approaches are currently in the planning stage, in particular with a view to determining absolute count on the basis of readings generated by the flow-cytometer.

Antigens, CD34↗
PubMed2025

A dataset of estimated heterozygous individual and carrier couple frequencies for pan-ancestry carrier screening.

The data described in this publication supported the development and evaluation of pan-ancestry reproductive carrier screening panels for autosomal recessive (AR) and X-linked (XL) conditions. Raw data included combined sets of DNA variants in 1,350 AR/XL genes obtained from the ClinVar and gnomAD databases. The dataset enabled calculations of positive yield for individuals and couples across both ancestry-specific and pan-ancestry, optimised "Goldilocks"-ranked gene panels, addressing population-specific variations in the frequencies of heterozygous individuals and carrier couples. The positive yield analysis offered a performance metric for carrier screening panels, facilitating the modeling of screening performance for panels of varying sizes and composition and providing resources for optimizing panel content to ensure equity across underrepresented genetic ancestries The dataset can support ongoing research into the equitable application of carrier screening and offers significant reuse potential for refining population genetic screening practices, validating computational models, and developing frameworks to update carrier screening panels in alignment with evolving genomic data, including in underrepresented and minority populations.

Carrier screening↗
PubMed2005

Bayesian fMRI time series analysis with spatial priors.

We describe a Bayesian estimation and inference procedure for fMRI time series based on the use of General Linear Models (GLMs). Importantly, we use a spatial prior on regression coefficients which embodies our prior knowledge that evoked responses are spatially contiguous and locally homogeneous. Further, using a computationally efficient Variational Bayes framework, we are able to let the data determine the optimal amount of smoothing. We assume an arbitrary order Auto-Regressive (AR) model for the errors. Our model generalizes earlier work on voxel-wise estimation of GLM-AR models and inference in GLMs using Posterior Probability Maps (PPMs). Results are shown on simulated data and on data from an event-related fMRI experiment.

Bayes Theorem↗
PubMed1996

Inhibition of complement activity by humanized anti-C5 antibody and single-chain Fv.

Activation of the complement system contributes significantly to the pathogenesis of numerous acute and chronic diseases. Recently, a monoclonal antibody (5G1.1) that recognizes the human complement protein C5, has been shown to effectively block C5 cleavage, thereby preventing the generation of the pro-inflammatory complement components C5a and C5b-9. Humanized 5G1.1 antibody, Fab and scFv molecules have been produced by grafting the complementarity determining regions of 5G1.1 on to human framework regions. Competitive ELISA analysis indicated that no framework changes were required in the humanized variable regions for retention of high affinity binding to C5, even at framework positions predicted by computer modeling to influence CDR canonical structure. The humanized Fab and scFv molecules blocked complement-mediated lysis of chicken erythrocytes and porcine aortic endothelial cells in a dose-dependent fashion, with complete complement inhibition occurring at a three-fold molar excess, relative to the human C5 concentration. In contrast to a previously characterized anti-C5 scFv molecule, the humanized h5G1.1 scFv also effectively blocked C5a generation. Finally, an intact humanized h5G1.1 antibody blocked human complement lytic activity at concentrations identical to the original murine monoclonal antibody. These results demonstrate that humanized h5G1.1 and its recombinant derivatives retain both the affinity and blocking functions of the murine 5G1.1 antibody, and suggest that these molecules may serve as potent inhibitors of complement-mediated pathology in human inflammatory diseases.

Amino Acid Sequence↗
PubMed1999

A comparison of 3-D data correlation methods for fractionated stereotactic radiotherapy.

PURPOSE: Stereotactic radiosurgery is currently used to treat patients who are not good candidates for conventional neurosurgical procedures. For treatments of nonvascular tumor cells, it appears that fractionation offers a radiobiological advantage between tumor and normal tissues. Therefore, fractionated stereotactic radiotherapy (FSR) is preferred because it minimizes normal tissue complications and maximizes local tumor control probability. We have implemented a methodology clinically to perform the noninvasive patient repositioning technique. The 3-D data correlation method for high-precision and multiple fraction stereotactic treatments has been presented. METHODS AND MATERIALS: Three different optimization algorithms (Hooke and Jeeves optimization, simplex optimization, and simulated annealing optimization) are evaluated to calculate the transformation parameters necessary for FSR. A least-square object function is created to perform the 3-D data matching process. By minimizing the unconstrained object function value the best fit can be approached for the reference 3-D data sets. Simulation shows that these algorithms deliver results that are comparable to the previously published correlation algorithm (1,2) (singular value decomposition [SVD] method). The advantage for optimization algorithms is easily understood and can be readily implemented by using a personal computer (PC). The mathematical framework provides a tool to calculate the transformation matrix which can be used to adjust patient position for fractionated treatments. Therefore, using these algorithms for a high-precision fractionated treatment is possible without an invasive repeat fixation device and has been implemented clinically. A bite plate system was incorporated to acquire 3-D patient data. With a 3-D digital camera localization device, the patient motion can be followed in real time with the system calibrated to the isocenter. RESULTS: Two types of data sets are utilized to study the correlation results. One is using the digitized patient data which were retrieved clinically. The other is using the randomly generated data sets. Simulation errors for the optimization algorithms are all less than 1 mm in translation and less than 1 degree in rotation. Currently, FSR is performed using special designed repeat fixation devices which assure reproducible patient position for multiple fractions of radiation treatment. Clinical results indicated that this technique provided excellent treatment results. CONCLUSION: Three optimization algorithms have been applied and evaluated in calculating the transformation parameters between two 3-D contours or digitized data points. The mathematical functions behind these optimization algorithms are straightforward and can be easily implemented. When incorporated with the proper CT/MR image data with an electronic portal imaging (EPI) system, this process can possibly verify the patient's treatment position whenever there is doubt about the movement during the treatment procedure.

Algorithms↗
PubMed2005

[Demographic and socioeconomic factors associated with needs for home assistance among community-dwelling elderly: a study from the French Home Survey Handicaps-Disabilities-Dependence].

BACKGROUND: Gains in life expectancy in western countries have mainly come hand in hand with growing chronic diseases and disabilities related to the activities of daily living (ADL) and instrumental activities of daily living (IADL). Although these disabilities have been identified as predictors of institutionalization, the elderly in France continue to live at home, in the community, alone or with others. This work aims at identifying and assessing their needs for assistance and looks especially at the demographic and socioeconomic associated features. METHODS: Reported needs for assistance with ADL and IADL are studied through a representative sample of 8,745 people aged 60 years and older and living at home in 1999, taken from the French cross-sectional "Handicaps-Disabilities-Dependence" survey. Statistical associations (non-adjusted and adjusted Odds-Ratio-OR) have been computed in a conceptual framework derived from Andersen and Newman's behavioural model. RESULTS: More than 1 million people aged 60 years and older need assistance from another person to perform at least one ADL (bathing, dressing, going to toilet, eating, transferring, getting outside) and about 2.5 millions persons for at least one IADL (shopping, food preparation, housekeeping). Need for assistance for at least one ADL is associated with age (OR=1.4 for 70-79, 3.6 for 80+); male aged 80 and older (OR=0.5); low educational status (OR=1.5); being married (OR=1.7) or living with an other person (OR=2); a disposable income less than 540 euro per capita and per month or between 540 and 1,080 euro (OR=1.3); impairments: motor (OR=3), language (OR=2.1), visual (OR=1.7), mental (OR=1.5) and other (OR=1.2); availability of home equipment devices (OR=3.5), technical devices for moving inside (OR=3) and others (OR=2.1). Need for assistance is especially high among those who required assistance (OR=4) or proxies (OR=5.5) to answer. Declared need for assistance for at least one IADL is roughly associated with the same factors. CONCLUSION: These results suggest that the declared needs for human assistance are based not exclusively on functional limitations but are also related to the social and environmental setting.

Activities of Daily Living↗
PubMed2002

Biomechanical models to simulate consequences of maxillofacial surgery.

This paper presents the biomechanical finite element models that have been developed in the framework of the computer-assisted maxillofacial surgery. After a brief overview of the continuous elastic modelling method, two models are introduced and their use for computer-assisted applications discussed. The first model deals with orthognathic surgery and aims at predicting the facial consequences of maxillary and mandibular osteotomies. For this, a generic three-dimensional model of the face is automatically adapted to the morphology of the patient by the mean of elastic registration. Qualitative simulations of the consequences of an osteotomy of the mandible can thus be provided. The second model addresses the Sleep Apnoea Syndrome. Its aim is to develop a complete modelling of the interaction between airflow and upper airways walls during breathing. Dynamical simulations of the interaction during a respiratory cycle are computed and compared with observed phenomena.

Biomechanical Phenomena↗
PubMed2006

Effect of electronic polarization on charge-transport parameters in molecular organic semiconductors.

Theoretical investigations of charge transport in organic materials are generally based on the "energy splitting in dimer" method and routinely assume that the transport parameters (site energies and transfer integrals) determined from monomer and dimer calculations can be reliably used to describe extended systems. Here, we demonstrate that this transferability can fail even in molecular crystals with weak van der Waals intermolecular interactions, due to the substantial (but often ignored) impact of polarization effects, particularly on the site energies. We show that the neglect of electronic polarization leads to qualitatively incorrect values and trends for the transfer integrals computed with the energy splitting method, even in simple prototypes such as ethylene or pentacene dimers. The polarization effect in these systems is largely electrostatic in nature and can change dramatically upon transition from a dimer to an extended system. For example, the difference in site energy for a prototypical "face-to-edge" one-dimensional stack of pentacene molecules is calculated to be 30% greater than that in the "face-to-edge" dimer, whereas the site energy difference in the pentacene crystal is vanishingly small. Importantly, when computed directly in the framework of localized monomer orbitals, the transfer integral values for dimer and extended systems are very similar.

Journal Article↗