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Results for “computational frameworks”

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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↗

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↗

PubMed2004

A quantum chemical approach to the free energy calculations in condensed systems: the QM/MM method combined with the theory of energy representation.

A methodology has been proposed to compute the solvation free energy of a molecule described quantum chemically by means of quantum mechanical/molecular mechanical method combined with the theory of energy representation (QM/MM-ER). The present approximate approach is quite simple to implement and requires much less computational cost as compared with the free energy perturbation or thermodynamic integration. Furthermore, the electron distribution can be treated faithfully as a quantum chemical object, and it is no longer needed to employ the artificial interaction site model, a reduced form of the realistic electron distribution, which is commonly used in the conventional solution theory. The point of the present approach is to employ the QM solute with electron density fixed at its average distribution in order to make the solute-solvent interaction pairwise. Then, the solvation free energy can be computed within the standard framework of the energy representation. The remaining minor contribution originating from the many-body effect inherent in the quantum mechanical description can be evaluated separately within a similar framework if necessary. As a test calculation, the method has been applied to a QM water solute solvated by MM water solvent in ambient and supercritical states. The results of the QM/MM-ER simulations have been in excellent agreement with the experimental values.

Journal Article↗

PubMed2004

Electronic structure, vibrational stability, and predicted infrared-Raman spectra of the As20, As @ Ni12, and As @ Ni12 @ As20 clusters.

Recently an inorganic fullerine-like [As@Ni(12)@As(20)](3-) onion with near-perfect icosahedral symmetry in the crystalline phase was reported [M. J. Moses, J. C. Fettinger, and B. W. Eichhorn, Science 300, 778 (2003)]. This paper presents a detailed computational study in the framework of density functional theory on various aspects of this molecule. The electronic structure of the As@Ni(12)@As(20) is investigated in its neutral as well as -3 charged state together with its subunits As(20) and As@Ni(12) by the all electron linear combination of Gaussian-type orbitals method. The bonding is studied by examining the integrated charge within atomic sphere, the electron localization function, changes in the electron density distribution, and from vibrational modes. We find that strong covalent As-As bonds seen in isolated As(20) become weaker in the As@Ni(12)@As(20) and strong covalent As-Ni bonds are formed. The structural stability of all four clusters is examined by analyzing the energetics and by calculating the vibrational frequencies. Further, the infrared and Raman spectra is predicted for both the neutral and charged As@Ni(12)@As(20) clusters. Finally, the energy barrier for removal of a single arsenic atom is calculated for the neutral As@Ni(12)@As(20) cluster.

Journal Article↗

PubMed2002

Progress in and prospects for fluvial flood modelling.

Recent floods in the UK have raised public and political awareness of flood risk. There is an increasing recognition that flood management and land-use planning are linked, and that decision-support modelling tools are required to address issues of climate and land-use change for integrated catchment management. In this paper, the scientific context for fluvial flood modelling is discussed, current modelling capability is considered and research challenges are identified. Priorities include (i) appropriate representation of spatial precipitation, including scenarios of climate change; (ii) development of a national capability for continuous hydrological simulation of ungauged catchments; (iii) improved scientific understanding of impacts of agricultural land-use and land-management change, and the development of new modelling approaches to represent those impacts; (iv) improved representation of urban flooding, at both local and catchment scale; (v) appropriate parametrizations for hydraulic simulation of in-channel and flood-plain flows, assimilating available ground observations and remotely sensed data; and (vi) a flexible decision-support modelling framework, incorporating developments in computing, data availability, data assimilation and uncertainty analysis.

Climate↗

PubMed2004

Simplified methods of implant treatment in the edentulous lower jaw. Part II: Early loading.

BACKGROUND: Most implant treatment is performed with a two-stage surgical procedure. A disadvantage of these implant treatments is that they are time-consuming. PURPOSE: The aim of the present study was to evaluate the results of early loading in the edentulous mandible and to compare those results with treatment results of one-stage surgery followed by a healing period and with two-stage surgery. MATERIAL AND METHODS: The material comprises four treatment groups with a total of 108 patients with edentulous lower jaws and 432 implants. All patients were treated with Brånemark implants (Nobel Biocare AB, Gothenburg, Sweden) with a turned surface and fixed prostheses in the lower jaw, supported by four implants. The patients in group A were treated with a one-stage procedure, a two-piece implant, and a 3-month healing period before loading. Group B (control group) had a two-stage procedure, a two-piece implant, and a 3-month healing period. Group C had a one-stage procedure, a one-piece implant, and a 3-month healing period. Group D was treated with a one-stage surgical procedure, a two-piece implant, and early loading (within 3 weeks). All patients were provided with a Procera Implant Bridge (Nobel Biocare) with a framework made by computer-assisted milling of one piece of pure titanium. All patients have been followed up for 1 year. RESULTS: The survival rates were 93.2 to 93.3% in the experimental groups and 97.5% in the control group. The difference was not statistically significant. The measurements of the marginal bone level demonstrated a mean bone loss of 0.8 mm between fixture insertion and the 1-year examination in patients with early loading (group D) whereas the bone loss in patients who underwent a healing period before loading was 1.3 to 1.6 mm. The difference between the control group and the group with early loading was significant. CONCLUSIONS: Survival rates for patients treated with a one-stage procedure were lower than survival rates for patients treated according to a "classical concept," but the differences were not statistically significant. There was no difference between treatment results with one-piece and two-piece implants. The implant loss in patients with early loading was probably caused by overloading, and careful supervision of occlusal loading is recommended. Early loading gave significantly less marginal bone loss when compared with two-stage surgery.

Adult↗

PubMed2002

[CRANIO--development of a system for computer- and robot-assisted craniotomy].

In the framework of the DFG project CRANIO, we are dealing with the problems of computer-assisted planning and robot-assisted realization of craniotomy, with optional skull reconstruction. A CT dataset was obtained from a phantom skull model and basic operation planning as well as different registration methods were performed. As one option it is possible to mill a contour on the skull or even to remove the entire area with a robot-guided microsurgical milling tool. In this context, work space tests were performed with a hexapod parallel robot. The milling of any contour geometry could be realized with different tool angles using the existing CRIGOS robot system without additional axes.

Computer Simulation↗

PubMed2000

Federation of the Person Identification Service between enterprises.

The Person Identification Service (PIDS) is a standard that has been adopted by the Object Management Group for managing identities of persons within a particular domain. That standard includes an interface that supports the ability to connect multiple PIDS servers together in a federated manner. The specification leaves great flexibility as to how to accomplish the federation. In this paper, we examine some of the federated approaches being considered by the Government Computer-based Patient Record Framework (G-CPR) project and discuss their advantages and disadvantages and the details of a specific, scalable approach to federation.

Government Agencies↗

PubMed1991

Population density and development potential in rural Zimbabwe: an assessment based on the 1969 and 1982 censuses.

"Based on 1969 and 1982 census data, this paper examines the spatial association between high rural population density and development potential in Zimbabwe and its significance for national development policy. A 1982 grid cell density map was compiled on the same geographical frame as an existing 1969 density map, yielding an intercensal density change map. A land classification map and a composite map of development constraints were rasterized on the same spatial framework and subjected to computer analysis. Areas of critically high (and generally increasing) densities showed strong spatial associations with areas of severe development constraints...."

Africa↗

PubMed2002

[Registration statistical program for the Rehabilitation Center for Patients with Cleft Lip and Palate in Uzbekistan].

The authors suggest an information computer support within the framework of a complex system for the diagnosis and treatment of patients with cleft lip and palate. This program will ensure operative information exchange for specialists of various spheres. Such information, united in the data base, will become the base for creation of a universal system of complex rehabilitation of patients with cleft lip and palate.

Cleft Lip↗

PubMed2005

Mathematical modeling and optimization of drug delivery from intratumorally injected microspheres.

PURPOSE: Paclitaxel is a highly promising phase-sensitive antitumor drug that could conceivably be improved by extended lower dosing as opposed to intermittent higher dosing. Although intratumoral delivery of paclitaxel to the whole tumor at different loads and rates has already been achieved, determining an optimal release mode of paclitaxel for tumor eradication remains difficult. This study set out to rationally design such an optimal microsphere release mode based on mathematical modeling. EXPERIMENTAL DESIGN: A computational reaction-diffusion framework was used to model drug release from intratumorally injected microspheres, drug transport and binding in tumor interstitum, and drug clearance by microvasculature and intracellular uptake and binding. RESULTS: Numerical simulations suggest that interstitial drug concentration is characterized by a fast spatially inhomogeneous rise phase, during which interstitial and intracellular binding sites are saturated, followed by a slow spatially homogeneous phase that is governed by the rate of drug release from microspheres. For zero-order drug release, the slow phase corresponds to a plateau drug concentration that is proportional to the ratio of the rate of blood clearance of drug to the rate of drug release from microspheres. Consequently, increasing the duration of intratumoral drug release extends the duration of cell exposure to the drug but lowers the plateau drug concentration. This tradeoff implies that intratumoral drug release can be designed to optimize tumor cell kill. Synthesizing our modeling predictions with published dose-response data, we propose an optimal protocol for the delivery of paclitaxel-loaded microspheres to small solid tumors.

Animals↗

PubMed2005

Multi-agent model for Indian rural health care.

PURPOSE: The objective of this paper is to present a model that uses multi-agent system (MAS) technology to assist doctors based at rural areas to receive timely expert opinions from specialist doctors working in medical institutions like the Postgraduate Institute of Medical Research, Chandigarh or the All India Institute of Medical Sciences, New Delhi. DESIGN/METHODOLOGY/APPROACH: A MAS is a software entity wherein agent metaphor is used to represent human-like intelligence and behavior. These agents are distributed over geographical areas and are part of software running at these sites. The foundation for this model lies in the fact that medical intelligence is distributed in nature and, if it is possible to bring this knowledge together, it could prove to be advantageous in providing improved health care to those people in rural areas. A few existing research works are included to demonstrate the usage of MAS in health care. FINDINGS: It has been observed that the health scenario in India is ranked poor world-wide by international organizations and, with the increasing population, this will worsen. RESEARCH LIMITATIONS/IMPLICATIONS: Initially, the aim is to concentrate on a few medical departments only. It can be extended into more detailed framework. PRACTICAL IMPLICATIONS: Physical computing and networking infrastructure are required for practical implementation along with training for the doctors. ORIGINALITY/VALUE: The primary beneficiaries of this system are likely to be those patients in the rural sector requiring expert medical opinion. The government health organizations will be able to provide quality medical facilities comparable with the medical facilities available in the developed nations. Currently this would seem to be a distant dream.

Delivery of Health Care↗

PubMed1996

A desktop image processing system for computer-assisted orthopedic surgery (DISOS).

Within the framework of our research activities in orthopedic surgery a PC-based imageprocessing system for the processing of x-ray computer-tomographic data has been developed. The system is used as a work platform for the investigations concerning interaction modalities, strategies and techniques for an efficient planning and execution of surgical interventions in orthopedic surgery by means of individual templates. The method of individual templates has been presented in /1,2/ and will not be subject of this paper.

Computer Peripherals↗

PubMed2004

GiPSi: an open source/open architecture software development framework for surgical simulation.

In this paper we propose an open source/open architecture framework for developing organ level surgical simulations. Our goal is to facilitate shared development of reusable models, to accommodate heterogeneous models of computation, and to provide a framework for interfacing multiple heterogeneous models. The framework provides an intuitive API for interfacing models with spatial relationships. It is specifically designed to be independent of the specifics of the modeling methods used and therefore facilitates seamless integration of heterogeneous models and processes. Furthermore, each model has separate geometries for visualization, simulation, and interfacing, allowing the modeler choose the most natural geometric representation for each case.

Computer Simulation↗

PubMed1998

Constrained optimization for neural map formation: a unifying framework for weight growth and normalization.

Computational models of neural map formation can be considered on at least three different levels of abstraction: detailed models including neural activity dynamics, weight dynamics that abstract from the neural activity dynamics by an adiabatic approximation, and constrained optimization from which equations governing weight dynamics can be derived. Constrained optimization uses an objective function, from which a weight growth rule can be derived as a gradient flow, and some constraints, from which normalization rules are derived. In this article, we present an example of how an optimization problem can be derived from detailed nonlinear neural dynamics. A systematic investigation reveals how different weight dynamics introduced previously can be derived from two types of objective function terms and two types of constraints. This includes dynamic link matching as a special case of neural map formation. We focus in particular on the role of coordinate transformations to derive different weight dynamics from the same optimization problem. Several examples illustrate how the constrained optimization framework can help in understanding, generating, and comparing different models of neural map formation. The techniques used in this analysis may also be useful in investigating other types of neural dynamics.

Animals↗

PubMed2005

Proposal for a framework for optimizing artificial environments based on physiological feedback.

We propose and then evaluate a new framework for finding the physical parameters of an artificial environment which give rise to given target physiological characteristics. We assume that a human is a system that takes as inputs the physical parameters of an artificial environment and outputs physiological parameters in response. We define our task as the inverse problem; we must find the best inputs from given target outputs. Our proposed framework solves the inverse problem using evolutionary computation techniques to optimize an artificial environment. We evaluate this framework using a simulation with a vibration environment and verify that it works.

Environment, Controlled↗