| 1. |
- Dewaraja, YK, et al.
(författare)
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A parallel Monte Carlo code for planar and SPECT imaging: implementation, verification and applications in I-131 SPECT
- 2002
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Ingår i: Computer Methods and Programs in Biomedicine. - 0169-2607. ; 67:2, s. 115-124
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Tidskriftsartikel (refereegranskat)abstract
- This paper reports the implementation of the SIMIND Monte Carlo code on an IBM SP2 distributed memory parallel computer. Basic aspects of running Monte Carlo particle transport calculations on parallel architectures are described. Our parallelization is based on equally partitioning photons among the processors and uses the Message Passing Interface (MPI) library for interprocessor communication and the Scalable Parallel Random Number Generator (SPRNG) to generate uncorrelated random number streams. These parallelization techniques are also applicable to other distributed memory architectures. A linear increase in computing speed with the number of processors is demonstrated for Lip to 32 processors. This speed-up is especially significant in Single Photon Emission Computed Tomography (SPECT) simulations involving higher energy photon emitters, where explicit modeling of the phantom and collimator is required. For I-131, the accuracy of the parallel code is demonstrated by comparing simulated and experimental SPECT images from a heart/thorax phantom. Clinically realistic SPECT simulations using the voxel-man phantom are carried out to assess scatter and attenuation correction.
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| 2. |
- Edvardsson, Hannes, et al.
(författare)
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Compact and efficient 3D shape description through radial function approximation
- 2003
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Ingår i: Computer Methods and Programs in Biomedicine. - 0169-2607 .- 1872-7565. ; 72:2, s. 89-97
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Tidskriftsartikel (refereegranskat)abstract
- A fast and simple method for three-dimensional shape description is described. The method views a 3D object as a radial distance function on the unit sphere, and thus reduces the dimensionality of the description problem by one. The radial distance function is approximated by Fourier methods in the basis of the spherical harmonic polynomials. The necessary integration is carried out on the object boundary, rather than on the unit sphere. Consequently, there is no need of a parameterisation of the object surface. The description makes it possible to compare shapes in a computationally very simple way. Solutions on how to cope with translated and rotated objects are discussed. The method is developed for star-shaped objects, but is stable even if the input image is non-star-shaped. The method is tested in a data set from magnetic resonance imaging (MRI) of the brain. Potential medical applications are discussed. ⌐ 2002 Elsevier Science Ireland Ltd. All rights reserved.
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| 3. |
- Foracchia, Marco, et al.
(författare)
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POPED, a software for optimal experiment design in population kinetics.
- 2004
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Ingår i: Computer Methods and Programs in Biomedicine. - 0169-2607 .- 1872-7565. ; 74:1, s. 29-46
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Tidskriftsartikel (refereegranskat)abstract
- Population kinetic analysis is the methodology used to quantify inter-subject variability in kinetic studies. It entails the collection of (possibly sparse) data from dynamic experiments in a group of subjects and their quantitative interpretation by means of a mathematical model. This methodology is widely used in the pharmaceutical industry (where it is termed "pharmacokinetic population analysis") and recently it is becoming increasingly used in other areas of biomedical research. Unlike traditional kinetic studies, where the number of subjects can be quite small, population kinetic studies require large numbers of subjects. It is, therefore, of great interest to design these studies in the most efficient manner possible, to maximize the information content provided by the data. In this paper we propose an algorithm and a computer program, POPED, for the optimal design of a population kinetic experiment. In particular, the number of samples for each subject and the design of the individual sampling strategies, i.e. the number and location of the time points at which the output variable is sampled, will be considered. Among the various criteria proposed in the literature, D and ED optimality are the ones implemented in our software program, since they are the most widely used. A brief description of the techniques employed to perform design optimization is given, together with some details on their actual implementation. Some examples are then presented to show the program usage and the results provided.
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| 4. |
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| 5. |
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| 6. |
- Persson, Mats, 1954-, et al.
(författare)
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Development and maintenance of guideline-based decision support for pharmacological treatment of hypertension
- 2000
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier. - 0169-2607 .- 1872-7565. ; 61:3, s. 209-219
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Tidskriftsartikel (refereegranskat)abstract
- The objective was to build a computer-based decision support system (DSS), which could apply the formal rules embedded in guidelines regarding pharmacological treatment of hypertension. The aim was also to test VISUAL BASIC as a development tool for DSS's in health care. From the Swedish guidelines for treatment of hypertension, the most widely accepted and scientifically best proved treatment strategies were chosen and implemented as rules. A DSS that is capable of applying the evidence-based rules extracted from guidelines regarding drug treatment of hypertension, to any patient's medical profile, was constructed. The output consists of a recommendation regarding preferred generic drug class and also a written report, reflecting decision steps provided by the rule-base and inference engine. We also provide methods for formalising an implementable language of guidelines. A mainstream programming language like VISUAL BASIC can be an alternative when building complicated decision support systems. A logic formal notation can facilitate communication between the expert and the programmer. The program is a stand-alone product independent of computerized medical records and thereby easy to install and maintain.
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| 7. |
- Tammi, Martti, et al.
(författare)
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TRAP : Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences
- 2003
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Ingår i: Computer Methods and Programs in Biomedicine. - 0169-2607 .- 1872-7565. ; 70:1, s. 47-59
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Tidskriftsartikel (refereegranskat)abstract
- The software commonly used for assembly of shotgun sequence data has several limitations. One such limitation becomes obvious when repetitive sequences are encountered. Shotgun assembly is a difficult task, even for non-repetitive regions, but the use of quality assessments of the data and efficient matching algorithms have made it possible to assemble most sequences efficiently. In the case of highly repetitive sequences, however, these algorithms fail to distinguish between sequencing errors and single base differences in regions containing nearly identical repeats. None of the currently available fragment assembly programs are able to correctly assemble highly similar repetitive data, and we, therefore, present a novel shotgun assembly program, Tandem Repeat Assembly Program (TRAP). The main feature of this program is the ability to separate long repetitive regions from each other by distinguishing single base substitutions as well as insertions/deletions from sequencing errors. This is accomplished by using a novel multiple-alignment based analysis method. Since repeats are a common complication in most sequencing projects, this software should be of use for the whole sequencing community.
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| 8. |
- Lindbom, Lars, et al.
(författare)
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Perl-speaks-NONMEM (PsN) – a Perl module for NONMEM related programming
- 2004
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 75:2, s. 85-94
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Tidskriftsartikel (refereegranskat)abstract
- The NONMEM program is the most widely used nonlinear regression software in population pharmacokinetic/pharmacodynamic (PK/PD) analyses. In this article we describe a programming library, Perl-speaks-NONMEM (PsN), intended for programmers that aim at using the computational capability of NONMEM in external applications. The library is object oriented and written in the programming language Perl. The classes of the library are built around NONMEM's data, model and output files. The specification of the NONMEM model is easily set or changed through the model and data file classes while the output from a model fit is accessed through the output file class. The classes have methods that help the programmer perform common repetitive tasks, e.g. summarising the output from a NONMEM run, setting the initial estimates of a model based on a previous run or truncating values over a certain threshold in the data file. PsN creates a basis for the development of high-level software using NONMEM as the regression tool.
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| 9. |
- Sintorn, Ida-Maria, et al.
(författare)
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A refined circular template matching method for classification of human cytomegalovirus capsids in TEM images
- 2004
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607. ; 76, s. 95-102
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Tidskriftsartikel (refereegranskat)abstract
- An automatic image analysis method for describing, segmenting, and classifying Human Cyto\-megalo\-virus capsids in transmission electron micrograph (TEM) images of host cell nuclei has been developed. Three stages of the capsid assembly process in the host cell nucleus have been investigated. Each class is described by a radial density profile, which is the average grey-level at each radial distance from the centre. A template, constructed from the profile, is used to find possible capsid locations by correlation based matching. The matching results are further refined by size and distortion analysis of each possible capsid, resulting in a final segmentation and classification.
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| 10. |
- Wang, Peijun, et al.
(författare)
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A Web-based cost-effective training tool with possible application to brain injury rehabilitation
- 2004
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607. ; 74:3, s. 235-243
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Tidskriftsartikel (refereegranskat)abstract
- Virtual reality (VR) has provoked enormous interest in the medical community. In particular, VIR offers therapists new approaches for improving rehabilitation effects. However, most of these VR assistant toots are not very portable, extensible or economical. Due to the vast amount of 3D data, they are not suitable for Internet transfer. Furthermore, in order to run these VR systems smoothly, special hardware devices are needed. As a result, existing VIR assistant toots tend to be available in hospitals but not in patients' homes. To overcome these disadvantages, as a case study, this paper proposes a Web-based Virtual Ticket Machine, called WBVTM, using VRML [VRML Consortium, The Virtual Reality Modeling Language: International Standard ISO/IEC DIS 14772-1, 1997, available at http://www.vrml.org/Specifications/VRML97], Java and EAI (External Authoring Interface) [Silicon Graphics, Inc., The External Authoring Interface (EAI), available at http://cosmosoftware.com/developer/eai.htmt], to help people with acquired brain injury (ABI) to relearn basic living skills at home at a low cost. As these technologies are open standard and feature usability on the Internet, WBVTM achieves the goals of portability, easy accessibility and cost-effectiveness. (C) 2003 Elsevier Ireland Ltd. All rights reserved.
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