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At least 559 records · Page 31Linked to original sources
PubMed2006

Comparison of PENELOPE Monte Carlo dose calculations with Fricke dosimeter and ionization chamber measurements in heterogeneous phantoms (18 MeV electron and 12 MV photon beams).

Different measurements of depth-dose curves and dose profiles were performed in heterogeneous phantoms and compared to dose distributions calculated by a Monte Carlo code. These heterogeneous phantoms consisted of lung and/or bone heterogeneities. Irradiations and simulations were carried out for an 18 MeV electron beam and a 12 MV photon beam. Depth-dose curves were measured with Fricke dosimeters and with plane and cylindrical ionization chambers. Dose profiles were measured with a small cylindrical ionization chamber at different depths. The LINAC was modelled using the PENELOPE code and phase space files were used as input data for the calculations of the dose distributions in every simulation. The detectors (Fricke dosimeters and ionization chambers) were not modelled in the geometry. There is generally a good agreement between the measurements and PENELOPE. Some discrepancies exist, near interfaces, between the ionization chamber and PENELOPE due to the attenuation of the lower energy electrons by the wall of the ionization chamber.

Body Burden↗
PubMed2006

Performance comparison of independent component analysis algorithms for fetal cardiac signal reconstruction: a study on synthetic fMCG data.

Independent component analysis (ICA) algorithms have been successfully used for signal extraction tasks in the field of biomedical signal processing. We studied the performances of six algorithms (FastICA, CubICA, JADE, Infomax, TDSEP and MRMI-SIG) for fetal magnetocardiography (fMCG). Synthetic datasets were used to check the quality of the separated components against the original traces. Real fMCG recordings were simulated with linear combinations of typical fMCG source signals: maternal and fetal cardiac activity, ambient noise, maternal respiration, sensor spikes and thermal noise. Clusters of different dimensions (19, 36 and 55 sensors) were prepared to represent different MCG systems. Two types of signal-to-interference ratios (SIR) were measured. The first involves averaging over all estimated components and the second is based solely on the fetal trace. The computation time to reach a minimum of 20 dB SIR was measured for all six algorithms. No significant dependency on gestational age or cluster dimension was observed. Infomax performed poorly when a sub-Gaussian source was included; TDSEP and MRMI-SIG were sensitive to additive noise, whereas FastICA, CubICA and JADE showed the best performances. Of all six methods considered, FastICA had the best overall performance in terms of both separation quality and computation times.

Algorithms↗
PubMed2006

Comparison of a finite-element multigroup discrete-ordinates code with Monte Carlo for radiotherapy calculations.

Radiotherapy calculations often involve complex geometries such as interfaces between materials of vastly differing atomic number, such as lung, bone and/or air interfaces. Monte Carlo methods have been used to calculate accurately the perturbation effects of the interfaces. However, these methods can be computationally expensive for routine clinical calculations. An alternative approach is to solve the Boltzmann equation deterministically. We present one such deterministic code, Attila. Further, we computed a brachytherapy example and an external beam benchmark to compare the results with data previously calculated by MCNPX and EGS4. Our data suggest that the presented deterministic code is as accurate as EGS4 and MCNPX for the transport geometries examined in this study.

Body Burden↗
PubMed2003

An overview of attenuation and scatter correction of planar and SPECT data for dosimetry studies.

A number of factors impact the accuracy of activity quantitation in planar and single photon emission computed tomographic (SPECT) imaging. Two important such factors are attenuation and scattering in the medium containing the activity. The first removes photons which otherwise would have been included in the images, and the second adds events to the images from photons which would not have otherwise been imaged. A number of methods have been developed to compensate for these biases to activity quantitation. This review will briefly introduce planar quantitation which is commonly used for dosimetric purposes, and then present a slightly more detailed overview of SPECT quantitation which is arguably more accurate. It will conclude by cautioning users of commercial reconstruction software to validate it for quantitation before using it for dosimetric purposes.

Algorithms↗
PubMed2002

Effectiveness of virtual reality for teaching pedestrian safety.

Sixty percent to 70% of pedestrian injuries in children under the age of 10 years are the result of the child either improperly crossing intersections or dashing out in the street between intersections. The purpose of this injury prevention research study was to evaluate a desktop virtual reality (VR) program that was designed to educate and train children to safely cross intersections. Specifically, the objectives were to determine whether children can learn pedestrian safety skills while working in a virtual environment and whether pedestrian safety learning in VR transfers to real world behavior. Following focus groups with a number of key experts, a virtual city with eight interactive intersections was developed. Ninety-five children participated in a community trial from two schools (urban and suburban). Approximately half were assigned to a control group who received an unrelated VR program, and half received the pedestrian safety VR intervention. Children were identified by group and grade by colored tags on their backpacks, and actual street crossing behavior of all children was observed 1 week before and 1 week after the interventions. There was a significant change in performance after three trials with the VR intervention. Children learned safe street crossing within the virtual environment. Learning, identified as improved street-crossing behavior, transferred to real world behavior in the suburban school children but not in the urban school. The results are discussed in relation to possibilities for future VR interventions for injury prevention.

Accidents, Traffic↗
PubMed2001

Simulating glycosylated hemoglobin (HbA1c) levels in diabetes using an interactive educational virtual diabetes patient simulator.

In 1996, an interactive educational diabetes simulator called AIDA was released without charge on the Internet as a noncommercial contribution to continuing diabetes education. Over the past 5 years, over 100,000 people have visited the AIDA Web pages at http://www.2aida.org and over 25,000 copies of the program have been downloaded free-of-charge. Previous Diabetes Information Technology & WebWatch columns have described various user feedback comments about the AIDA software. This current column overviews the method applied for modelling glycosylated hemoglobin (HbA1c) levels within an updated version of the AIDA program (v4.3). The result seems to be a useful and novel addition to the diabetes simulations, providing a parameter with which most users will be familiar, and able to relate. It is expected that the HbA1c indicator may prove useful in enhancing the educational value of the diabetes simulations.

Computer Simulation↗
PubMed2003

Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.

A large-scale in silico evaluation of gene deletions in Saccharomyces cerevisiae was conducted using a genome-scale reconstructed metabolic model. The effect of 599 single gene deletions on cell viability was simulated in silico and compared to published experimental results. In 526 cases (87.8%), the in silico results were in agreement with experimental observations when growth on synthetic complete medium was simulated. Viable phenotypes were correctly predicted in 89.4% (496 out of 555) and lethal phenotypes were correctly predicted in 68.2% (30 out of 44) of the cases considered. The in silico evaluation was solely based on the topological properties of the metabolic network which is based on well-established reaction stoichiometry. No interaction or regulatory information was accounted for in the in silico model. False predictions were analyzed on a case-by-case basis for four possible inadequacies of the in silico model: (1) incomplete media composition, (2) substitutable biomass components, (3) incomplete biochemical information, and (4) missing regulation. This analysis eliminated a number of false predictions and suggested a number of experimentally testable hypotheses. A genome-scale in silico model can thus be used to systematically reconcile existing data and fill in our knowledge gaps about an organism.

Computational Biology↗
PubMed1997

Building human genome maps with radiation hybrids.

Genome maps are crucial tools in human genetic research, providing known landmarks for locating disease genes and frameworks for large-scale sequencing. Radiation hybrid mapping is one technique for building genome maps. In this paper, we describe the methods used to build radiation hybrid maps of the entire human genome. We present the hidden Markov model that we employ to estimate the likelihood of a map despite uncertainty about the data, and we discuss the problem of searching for maximum-likelihood maps. We describe the graph algorithms used to find sparse but reliable initial maps and our methods of extending them. Finally, we show results validating our software on simulated data, and we describe our genome-wide human radiation hybrid maps and the evidence supporting them.

Chromosome Mapping↗
PubMed2004

Vector NTI, a balanced all-in-one sequence analysis suite.

Vector NTI is a well-balanced desktop application integrated for molecular sequence analysis and biological data management. It has a centralised database and five application modules: Vector NTI, AlignX, BioAnnotator, ContigExpress and GenomBench. In this review, the features and functions available in this software are examined. These include database management, primer design, virtual cloning, alignments, sequence assembly, 3D molecular viewer and internet tools. Some problems encountered when using this software are also discussed. It is hoped that this review will introduce this software to more molecular biologists so they can make better-informed decisions when choosing computational tools to facilitate their everyday laboratory work. This tool can save time and enhance analysis but it requires some learning on the user's part and there are some issues that need to be addressed by the developer.

Algorithms↗
PubMed1998

Transcription regulatory region analysis using signal detection and fuzzy clustering.

MOTIVATION: Presently available programs for the recognition of potential transcription factor binding sites in genomic sequences generally yield a huge amount of output. These output lists have to be filtered to obtain biologically significant elements, which is highly laborious work to be done manually. RESULTS: We developed a strategy for systematic verification and improvement of the underlying profiles, and for their contextual analysis by a fuzzy clustering approach using non-redundant libraries of search profiles as a prerequisite. AVAILABILITY: The tools mentioned in the paper are available upon request. CONTACT: ewi@gbf.de

Algorithms↗
PubMed1998

A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily.

MOTIVATION: Massive oligonucleotide hybridization is one of the most promising technologies of functional genome analysis. The critical point is to design appropriate sets of oligonucleotides that can be used effectively in identification by hybridization. RESULTS: Using a genetic algorithm approach, we have attempted to design sets of oligo probes capable of identifying new genes belonging to a defined gene family within a cDNA or genomic library. It is not limited by oligonucleotide length and admits the letter 'N' in the structure of the oligonucleotides selected. One of the major advantages of this approach is the low homology required to identify functional families of sequences with little homology. We have designed the oligonucleotide sets that are most selective for the cDNA clones of transmembrane G protein-coupled receptors (GPCRs), a large family of proteins that form part of a modular system of extracellular signal transduction to the intracellular second messenger pathways. The accuracy of identification has been checked on the EST library containing 713 870 cDNA sequences. A set of 15 oligos between 7 and 14 bases in length has correctly identified 70% of the GPCR cDNA collection sequences with 0.02% false positives. AVAILABILITY: The developed software is available by ftp://ftp.bionet.nsc. ru/pub/biology/ and on the Web page http://www.bionet.nsc. ru/SRCG/Oligoselector/. CONTACT: kel@.bionet.nsc.ru; sebastian. meier-ewert@gpc-ag.com

Algorithms↗
PubMed1998

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.

MOTIVATION: The untranslated regions (UTRs) of mRNA upstream (5'UTR) and downstream (3'UTR) of the open reading frame, as well as the mRNA precursor, carry important regulatory sequences. To reveal unidentified regulatory signals, we combine information from experiments with computational approaches. Depending on available knowledge, three different strategies are employed. RESULTS: Searching with a consensus template, new RNAs with regulatory RNA elements can be identified in genomic screens. By this approach, we identify new candidate regulatory motifs resembling iron-responsive elements in the 5'UTRs of HemA, FepB and FrdB mRNA from Escherichia coli. If an RNA element is not yet defined, it may be analyzed by combining results from SELEX (selective enrichment of ligands by exponential amplification) and a search of databases from RNA or genomic sequences. A cleavage stimulating factor (CstF) binding element 3 of the polyadenylation site in the mRNA precursor serves as a test example. Alternatively, the regulatory RNA element may be found by studying different RNA foldings and their correlation with simple experimental tests. We delineate a novel instability element in the 3'UTR of the estrogen receptor mRNA in this way. AVAILABILITY: Strategy, methods and programs are available on request from T.Dandekar. CONTACT: dandekar@embl-heidelberg.de

3' Untranslated Regions↗
PubMed1998

Statistics of large-scale sequence searching.

MOTIVATION: Database search programs such as FASTA, BLAST or a rigorous Smith-Waterman algorithm produce lists of database entries, which are assumed to be related to the query. The computation of statistical significance of similarity scores is well established for single pairs of sequences and using purely random models. However, the multi-trial context of a database search poses new problems. The credibility of a certain score obtained in a database search decreases with the amount of data that is compared. To improve p-value computation for database search experiments, statistical properties of the databases, such as the distribution of sequence length and effects induced by frequently repeated sequence patterns, need to be taken into account. RESULTS: We investigated the SWISS-PROT protein database Release 31.0 running extensive simulations of database searches. A discrepancy is observed between the theoretical predictions and the empirical distribution. To correct for this, we evaluate the statistical significance of scores in the context of a database search by a contrasting semi-random model. This model enhances purely random models by one additional parameter reflecting individual statistical properties of real databases. We call this parameter the effective size of the database. CONTACT: r.spang@dkfz-heidelberg.de;m.vingron@dkfz-hei del berg.de

Computational Biology↗
PubMed1998

Towards detection of orthologues in sequence databases.

MOTIVATION: Numerous homologous sequences from diverse species can be retrieved from databases using programs such as BLAST. However, due to multigene families, evolutionary relationship often cannot be easily determined and proper functional assignment becomes difficult. Thus, discrimination between orthologues and paralogues within BLAST output lists of homologous sequences becomes more and more important. RESULT: We therefore developed a method that attempts to construct a reconciled tree from a gene tree of selected sequences and its corresponding phylogenetic tree of the species involved (species tree). An interface on the Web is developed to enable users to analyse the BLAST result. BLAST outputs are parsed and, for the selected sequences, multiple alignments are constructed either globally or for local regions. Bootstrapped trees are returned and compared with the expected species tree. In cases of discrepancies, gene duplications are assumed and a reconciled tree is computed. The reconciled tree shows probable orthologues and paralogues as predicted.

Computational Biology↗
PubMed1998

DIALIGN: finding local similarities by multiple sequence alignment.

MOTIVATION: DIALIGN is a new method for pairwise as well as multiple alignment of nucleic acid and protein sequences. While standard alignment programs rely on comparing single residues and imposing gap penalties, DIALIGN constructs alignments by comparing whole segments of the sequences. No gap penalty is employed. This point of view is especially adequate if sequences are not globally related, but share only local similarities, as is the case in genomic DNA sequences and in many protein families. RESULTS: Using four different data sets, we show that DIALIGN is able correctly to align conserved motifs in protein sequences. Alignments produced by DIALIGN are compared systematically to the results of five other alignment programs. AVAILABILITY: DIALIGN is available to the scientific community free of charge for non-commercial use. Executables for various UNIX platforms including LINUX can be downloaded at http://www.gsf.de/biodv/dialign.html CONTACT: werner, morgenstern@gsf.de

Algorithms↗
PubMed1998

New scoring schemes for protein fold recognition based on Voronoi contacts.

MOTIVATION: The genome projects produce a wealth of protein sequences. Theoretical methods to predict possible structures and functions are needed for screening purposes, large-scale comparisons and in-depth analysis to identify worthwhile targets for further experimental research. Sequence-structure alignment is a basic tool for the identification of model folds for protein sequences and the construction of crude structural models. Empirical contact potentials (potentials of mean force) are used to optimize and evaluate such alignments. RESULTS: We propose new scoring schemes based on a contact definition derived from Voronoi decompositions of the three-dimensional coordinates of protein structures. We demonstrate that Voronoi potentials are superior to pure distance-based contact potentials with respect to recognition rate and significance for native folds. Moreover, the scoring scheme has the potential to provide a reasonable balance of detail and ion such that it is also useful for the recognition of distantly related (both homologous and non-homologous) proteins. This is demonstrated here on a set of structural alignments showing much better correspondence of native and model scores for the Voronoi potentials as compared to conventional distance-based potentials. AVAILABILITY: The potentials are made available via the program system ToPLign (URL: http://cartan.gmd.de/ToPLign.html). CONTACT: Ralf.Zimmer,Ralf.Thiele@gmd.de

Algorithms↗
PubMed1999

FramePlus: aligning DNA to protein sequences.

MOTIVATION: Automated annotation of Expressed Sequence Tags (ESTs) is becoming increasingly important as EST databases continue to grow rapidly. A common approach to annotation is to align the gene fragments against well-documented databases of protein sequences. The sensitivity of the alignment algorithm is key to the success of such methods. RESULTS: This paper introduces a new algorithm, FramePlus, for DNA-protein sequence alignment. The SCOP database was used to develop a general framework for testing the sensitivity of such alignment algorithms when searching large databases. Using this framework, the performance of FramePlus was found to be somewhat better than other algorithms in the presence of moderate and high rates of frameshift errors, and comparable to Translated Search in the absence of sequencing errors. AVAILABILITY: The source code for FramePlus and the testing datasets are freely available at ftp.compugen.co.il/pub/research. CONTACT: raveh@compugen.co.il.

Algorithms↗