bluuebunny/crossref_metadata_2025 huggingface dataset:
Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.
Authors: Ponomarenko M P , Ponomarenko J V , Frolov A S , Podkolodnaya O A , Vorobyev D G , Kolchanov N A , Overton G C
Published: July 2002

MOTIVATION: Recognition of functional sites remains a key event in the course of genomic DNA annotation. It is well known that a number of sites have their own specific oligonucleotide content. This pinpoints the fact that the preference of the site-specific nucleotide combinations at adjacent positions within an analyzed functional site could be informative for this site recognition. Hence, Web-available resources describing the site-specific oligonucleotide content of the functional DNA sites and applying the above approach for site recognition are needed. However, they have been poorly developed up to now. RESULTS: To describe the specific oligonucleotide content of the functional DNA sites, we introduce the oligonucleotide alphabets, out of which the frequency matrix for a given site could be constructed in addition to a traditional nucleotide frequency matrix. Thus, site recognition accuracy increases. This approach was implemented in the activated MATRIX database accumulating oligonucleotide frequency matrices of the functional DNA sites. We have demonstrated that the false-positive error of the functional site recognition decreases if the oligonucleotide frequency matrixes are added to the nucleotide frequency matrixes commonly used. AVAILABILITY: The MATRIX database is available on the Web, http://wwwmgs.bionet.nsc.ru/Dbases/MATRIX/ and the mirror site, http://www.cbil.upenn.edu/mgs/systems/c onsfreq/.
SISEQ: manipulation of multiple sequence and large database
files for common platforms
Authors: Sato Naoki
Published: July 2002

Summary: A multiple sequence file converter for common platforms, SISEQ, is described, which performs extraction of DNA sequences that correspond to CDS or RNA field of a large database file as well as subsequent multi-sequence conversions for phylogenetic or molecular biological analysis. Command-line interface as well as a GUI and a script-driven operation mode are provided.

Availability: The program is freely available to academic users in the form of Macintosh FAT binary, DOS executable, or UNIX source code at http://www.molbiol.saitama-u.ac.jp/~naoki/Software.html.

Contact: naokisat@molbiol.saitama-u.ac.jp
Systemic properties of ensembles of metabolic networks:
application of graphical and statistical methods to simple
unbranched pathways
Authors: Alves Rui , Savageau Michael A.
Published: July 2002

Motivation: Mathematical models are the only realistic method for representing the integrated dynamic behavior of complex biochemical networks. However, it is difficult to obtain a consistent set of values for the parameters that characterize such a model. Even when a set of parameter values exists, the accuracy of the individual values is questionable. Therefore, we were motivated to explore statistical techniques for analyzing the properties of a given model when knowledge of the actual parameter values is lacking.

Results: The graphical and statistical methods presented in the previous paper are applied here to simple unbranched biosynthetic pathways subject to control by feedback inhibition. We represent these pathways within a canonical nonlinear formalism that provides a regular structure that is convenient for randomly sampling the parameter space. After constructing a large ensemble of randomly generated sets of parameter values, the structural and behavioral properties of the model with these parameter sets are examined statistically and classified. The results of our analysis demonstrate that certain properties of these systems are strongly correlated, thereby revealing aspects of organization that are highly probable independent of selection. Finally, we show how specification of a given behavior affects the distribution of acceptable parameter values.

Contact: Savageau@umich.edu

* To whom correspondence should be addressed.
Identifying target sites for cooperatively binding factors
Authors: GuhaThakurta Debraj , Stormo Gary D.
Published: July 2002

Motivation: Transcriptional activation in eukaryotic organisms normally requires combinatorial interactions of multiple transcription factors. Though several methods exist for identification of individual protein binding site patterns in DNA sequences, there are few methods for discovery of binding site patterns for cooperatively acting factors. Here we present an algorithm, Co-Bind (for COperative BINDing), for discovering DNA target sites for cooperatively acting transcription factors. The method utilizes a Gibbs sampling strategy to model the cooperativity between two transcription factors and defines position weight matrices for the binding sites. Sequences from both the training set and the entire genome are taken into account, in order to discriminate against commonly occurring patterns in the genome, and produce patterns which are significant only in the training set.

Results: We have tested Co-Bind on semi-synthetic and real data sets to show it can efficiently identify DNA target site patterns for cooperatively binding transcription factors. In cases where binding site patterns are weak and cannot be identified by other available methods, Co-Bind, by virtue of modeling the cooperativity between factors, can identify those sites efficiently. Though developed to model protein–DNA interactions, the scope of Co-Bind may be extended to combinatorial, sequence specific, interactions in other macromolecules.

Availability: The program is available upon request from the authors or may be downloaded from http://ural.wustl.edu.

Contact: dg@genetics.wustl.edu; stormo@genetics.wustl.edu
Exploring the pathway structure of metabolism: decomposition
into subnetworks and application to Mycoplasma pneumoniae
Authors: Schuster S. , Pfeiffer T. , Moldenhauer F. , Koch I. , Dandekar T.
Published: July 2002

Motivation: Reconstructing and analyzing the metabolic map of microorganisms is an important challenge in bioinformatics. Pathway analysis of large metabolic networks meets with the problem of combinatorial explosion of pathways. Therefore, appropriate algorithms for an automated decomposition of these networks into smaller subsystems are needed.

Results: A decomposition algorithm for metabolic networks based on the local connectivity of metabolites is presented. Interrelations of this algorithm with alternative methods proposed in the literature and the theory of small world networks are discussed. The applicability of our method is illustrated by an analysis of the metabolism of Mycoplasma pneumoniae , which is an organism of considerable medical interest. The decomposition gives rise to 19 subnetworks. Three of these are here discussed in biochemical terms: arginine degradation, the tetrahydrofolate system, and nucleotide metabolism. The interrelations of pathway analysis of biochemical networks with Petri net theory are outlined.

Availability: Metatoolis available from ftp://mudshark.brookes.ac.uk/pub/software/ibmpc or http://www.bioinf.mdc-berlin.de/metabolic/. The program Separatorfor decomposing metabolic networks is available from http://www.bioinf.mdc-berlin.de/metabolic/.

Supplementary information: http://www.bioinf.mdc-berlin.de/metabolic/metatool/http://www.bork.embl-heidelberg.de/Annot/MP/ (re-annotation of M. pneumoniae genome)

Contact: dandekar@embl-heidelberg.de; koch_i@molgen.mpg.de; pfeiffer@eco.umnw.ethz.ch; stschust@mdc-berlin.de
A heterochromatin protein 1 homologue in Caenorhabditis elegans acts in germline and vulval development
Authors: Couteau Florence , Guerry Fréderic , Müller Fritz , Palladino Francesca
Published: July 2002

Proteins of the highly conserved heterochromatin protein 1 (HP1) family have been found to function in the dynamic organization of nuclear architecture and in gene regulation throughout the eukaryotic kingdom. In addition to being key players in heterochromatin‐mediated gene silencing, HP1 proteins may also contribute to the transcriptional repression of euchromatic genes via the recruitment to specific promoters. To investigate the role played by these different activities in specific developmental pathways, we identified HP1 homologues in the genome of Caenorhabditis elegans and used RNA‐mediated interference to study their function. We show that one of the homologues, HPL‐2, is required for the formation of a functional germline and for the development of the vulva by acting in an Rb‐related pathway. We suggest that, by acting as repressors of gene expression, HP1 proteins may fulfil specific functions in both somatic and germline differentiation processes throughout development.
Informal Financial Service Institutions for Survival: African Women and Stokvels in Urban South Africa, 1930–1998
Authors: Verhoef Grietjie
Published: July 2002

Traditional kinship relations denied African women access to property and cash income. As they moved out of the traditional sector to urban centers, women created opportunities for independent earnings, and they displayed remarkable entrepreneurial spirit in undertaking informal economic activities. One of their tactics was the utilization of a type of rotating credit and savings organization (ROSCA), the stokvel, to mobilize savings outside the formal financial structure. This article brings together scattered research on stokvels, traces their past and present uses by African women, and concludes with an exploration of the reasons for the persistence of these forms despite the development of sophisticated financial structures in modern South Africa.
The role of gene splicing, gene amplification and regulation in mosquito insecticide resistance
Authors: Hemingway J. , Hawkes N. , Prapanthadara L. , Jayawardenal K. G. I. , Ranson H.
Published: July 2002

The primary routes of insecticide resistance in all insects are alterations in the insecticide target sites or changes in the rate at which the insecticide is detoxified. Three enzyme systems, glutathione S–transferases, esterases and monooxygenases, are involved in the detoxification of the four major insecticide classes. These enzymes act by rapidly metabolizing the insecticide to non–toxic products, or by rapidly binding and very slowly turning over the insecticide (sequestration). InCulexmosquitoes, the most common organophosphate insecticide resistance mechanism is caused by co–amplification of two esterases. The amplified esterases are differentially regulated, with three times more Estβ21being produced than Estα21.Cis–acting regulatory sequences associated with these esterases are under investigation. All the amplified esterases in differentCulexspecies act through sequestration. The rates at which they bind with insecticides are more rapid than those for their non–amplified counterparts in the insecticide–susceptible insects. In contrast, esterase–based organophosphate resistance inAnophelesis invariably based on changes in substrate specificities and increased turnover rates of a small subset of insecticides. The up–regulation of both glutathione S–transferases and monooxygenases in resistant mosquitoes is due to the effect of a single major gene in each case. The products of these major genes up–regulate a broad range of enzymes. The diversity of glutathione S–transferases produced byAnophelesmosquitoes is increased by the splicing of different 5' ends of genes, with a single 3' end, within one class of this enzyme family. Thetrans–acting regulatory factors responsible for the up–regulation of both the monooxygenase and glutathione S–transferases still need to be identified, but the recent development of molecular tools for positional cloning inAnopheles gambiaenow makes this possible.
Mixed chimerism
Authors: Sykes Megan , Sachs David H.
Published: July 2002

Induction of mixed chimerism has the potential to overcome the current limitations of transplantation, namely chronic rejection, complications of immunosuppressive therapy and the need for xenografts to overcome the current shortage of allogeneic organs. Successful achievement of mixed chimerism had been shown to tolerize T cells, B cells and possibly natural killer cells, the lymphocyte subsets that pose major barriers to allogeneic and xenogeneic transplants. Current understanding of the mechanisms involved in tolerization of each cell type is reviewed. Considerable advances have been made in reducing the potential toxicity of conditioning regimens required for the induction of mixed chimerism in rodent models, and translation of these strategies to large animal models and in a patient are important advances toward more widespread clinical application of the mixed chimerism approach for tolerance induction.
Establishment of a Chemical Synthetic Lethality Screen in Cultured Human Cells
Authors: Simons Arnold , Dafni Naomi , Dotan Iris , Oron Yoram , Canaani Dan
Published: July 2002

The synthetic lethality screen is a powerful genetic method for unraveling functional interactions between proteins in yeast. Here we demonstrate the feasibility of a chemical synthetic lethality screen in cultured human cells, based in part on the concept of the yeast method. The technology employs both an immortalized human cell line, deficient in a gene of interest, which is complemented by an episomal survival plasmid expressing the gene of interest, and the use of a novel double-label fluorescence system. Selective pressure imposed by any one of several synthetic lethal metabolic inhibitors prevented the spontaneous loss of the episomal survival plasmid. Retention or loss over time of this plasmid could be sensitively detected in a blind test, while cells were grown in microtiter plates. Application of this method should thus permit high throughput screening of drugs, which are synthetically lethal with any mutant human gene of interest, whose normal counterpart can be expressed. This usage is particularly attractive for the search of drugs, which kill malignant cells in a gene-specific manner, based on their predetermined cellular genotype. Moreover, by replacing the chemicals used in this example with a library of either DNA oligonucleotides or expressible dominant negative genetic elements, one should be able to identify synthetic lethal human genes.
QTL Analysis in a Complex Autopolyploid: Genetic Control of Sugar Content in Sugarcane
Authors: Ming Ray , Liu Sin-Chieh , Moore Paul H. , Irvine James E. , Paterson Andrew H.
Published: July 2002

QTL mapping in autopolyploids is complicated by the possibility of segregation for three or more alleles at a locus and by a lack of preferential pairing, however the subset of polymorphic alleles that show simplex segregation ratios can be used to locate QTLs. In autopolyploid Saccharum, 36 significant associations between variation in sugar content and unlinked loci detected by 31 different probes were found in two interspecific F1populations. Most QTL alleles showed phenotypic effects consistent with the parental phenotypes, but occasional transgressive QTLs revealed opportunities to purge unfavorable alleles from cultivars or introgress valuable alleles from exotics. Several QTLs on homologous chromosomes appeared to correspond to one another–multiple doses of favorable ‘alleles’ at such chromosomal region(s) yielded diminishing returns–such negative epistasis may contribute to phenotypic buffering. Fewer sugar content QTLs were discovered from the highest-sugar genotype than from lower-sugar genotypes, perhaps suggesting that many favorable alleles have been fixed by prior selection, i.e. that the genes for which allelic variants (QTLs) persist in improved sugarcanes may be a biased subset of the population of genes controlling sugar content. Comparison of these data to mutations and QTLs previously mapped in maize hinted that seed and biomass crops may share a partly-overlapping basis for genetic variation in carbohydrate deposition. However, many QTLs do not correspond to known candidate genes, suggesting that other approaches will be necessary to isolate the genetic determinants of high sugar content of vegetative tissues.
Selecting beam weight and wedge filter on the basis of dose gradient analysis
Authors: Dai Jianrong , Zhu Yunping
Published: July 2002

This study proposes an algorithm for selecting beam weight, wedge angle, and wedge orientation for three‐dimensional radiation therapy treatment planning. According to dose gradient analysis, the necessary and sufficient condition for achieving a homogeneous dose over the target volume is that the total vector sum of the dose gradients of all beams be zero everywhere in the target volume. This study presents equations for calculating the beam weight, wedge angle, and collimator angle (because the collimator angle determines wedge orientation when beam direction is known) for treatment plans using two angled beams or three coplanar or noncoplanar beams. It also provides suggestions for calculations of treatment plans using more than three beams, for which many feasible solutions will be available. When tested using two clinical cases, this algorithm achieved homogeneous dose distributions over target volumes. With this algorithm, repeated manual adjustments are reduced, and the quality and efficiency of treatment planning are improved.
Signal to noise ratio based filter optimization in triple energy window scatter correction
Authors: Blokland Koos (J.) A. K. , Winn R. D. R. , Pauwels E. K. J.
Published: July 2002

Triple energy window (TEW) scatter correction estimates the contribution of scattered photons to the acquisition data by acquiring additional data through two narrow energy windows placed adjoined to the main (photopeak) energy window. The contribution is estimated by linear interpolation and then subtracted. Noise amplification is reduced by filtering both the photopeak scintigram and the scatter estimate. We have studied the filter settings of each filter using a physical phantom filled with a resulting in count densities comparable to clinical studies. The performance of order‐8 Butterworth filters at different cut‐off frequencies (CoFs) were compared based on signal to noise ratios (SNRs). The highest SNRs were obtained when the noisy scatter information was strongly filtered with the CoF less than or equal to 0.07 cycles/pixel (cpp). The best CoF for the filter of the photopeak image is object size dependent; smaller objects require a higher CoF. For objects with a size near the SPECT spatial resolution (∼15 mm) the optimal CoF is equal to 0.18 cpp. For larger objects (31.8 mm) the highest SNR was obtained with a CoF equal to 0.13 cpp. A CoF equal to 0.16 cpp is a good compromise for all objects with a diameter equal to the spatial resolution or larger. These results depend on the initial signal to noise ratio of the acquisition data and so on the count density.
Correcting organ motion artifacts in x‐ray CT systems based on tracking of motion phase by the spatial overlap correlator. II. Experimental study
Authors: Dhanantwari Amar C. , Stergiopoulos Stergios , Zamboglou Nikolaos , Baltas Dimos , Vogt Hans‐Georg , Karangelis Grigoris
Published: July 2002

This paper presents the experimental part of an investigation on tracking and eliminating organ motion artifacts in x‐ray CT cardiac applications with emphasis on imaging coronary calcification. The system methodology consists of a software implementation of the spatial overlap correlator (SSOC) concept in x‐ray CT scanners to track the net amplitude and phase of organ motion during the CT data acquisition process. A coherent sinogram synthesis (CSS) method is then used to identify the repeated phases of a periodic organ motion from the information provided by the SSOC process and hence synthesize a new sinogram with no motion effects. Since the SSOC scheme is capable of tracking cardiac motion, it identifies also the projection points associated with minimum amplitude cardiac motion effects. These points are used to identify a 180° plus the fan angle sinogram for image reconstruction. This leads to a retrospective gating (RG) scheme that is based on the output of the SSOC process. Performance comparison of the proposed methodology with the retrospective ECG gating using real data sets with phantoms and human patients provides a performance assessment of the merits of the proposed methods. Real results demonstrate that the new methodology eliminates the requirement for ECG gating. Moreover, the CSS and the new RG methods do not require breath holding and they can be implemented in x‐ray CT scanners to image coronary calcification and the heart's ventricles.
A study on computer‐aided diagnosis based on temporal subtraction of sequential chest radiographs (in Japanese)
Authors: Kano Akiko
Published: July 2002

An automated digital image subtraction technique for use with pairs of temporally sequential chest radiographs has been developed to aid radiologists in the detection of interval changes. Automated image registration based on nonlinear geometric warping is performed prior to subtraction in order to deal with complicated radiographic misregistration. Processing includes global matching, to achieve rough registration between the entire lung fields in the two images, and local matching, based on a cross‐correlation method, to determine local shift values for a number of small regions. A proper warping of is determined by fitting two‐dimensional polynomials to the distributions of the shift values. One image is warped and then subtracted from the other. The resultant subtraction images were able to enhance the conspicuity of various types of interval changes. Improved global matching based on a weighted template matching method achieved robust registration even with photofluorographs taken in chest mass screening programs, which had previously presented us with a relatively large number of poor‐registration images. The new method was applied to 129 pairs of chest mass screening images, and offered registration accuracy as good as manual global matching. An observer test using 114 cases including 57 lung cancer cases presented better sensitivity and specificity on average compared to conventional comparison readings. In addition, newly developed image processing that eliminates the rib edge artifacts in subtraction images was applied to 26 images having pathological interval changes; results showed the potential for application to automated schemes for the detection of interval change patterns. With its capacity to improve the diagnostic accuracy of chest radiographs, the chest temporal subtraction technique promises to become an important element of computer‐aided diagnosis (CAD) systems.
Producing parallel x rays with a bent‐crystal monochromator and an x‐ray tube
Authors: Zhong Z. , Dilmanian F. A. , Bacarian T. , Zhong N. , Chapman D. , Ren B. , Wu X. Y. , Weinmann H.‐J.
Published: July 2002

A bent Laue monochromator and a conventional x‐ray tube were used to produce a fan beam that was parallel in the plane perpendicular to the plane of the fan. The x‐ray fan beam was tunable in energy and had about 12% energy bandwidth at a slice height of 5 mm when tuned to 50 keV. The beam's energy was slightly coupled to the vertical position on the beam's height. The slice height could be varied from 1 to 10 mm. The flux at 50 keV was approximately photons/mm2/s with a rotating anode tungsten x‐ray tube operating at 120 kVp and 100 mA. The narrow energy bandwidth of the beam produced is advantageous over a conventional divergent polychromatic beam for all radiography applications, while the parallelism of the beam enhances its intensity by about threefold and offers some advantages for computed tomography.
Improvement of breast cancer irradiation techniques
Authors: Hurkmans Coen
Published: July 2002

In this thesis a number of improvements of breast cancer radiotherapy techniques are described, resulting in a reduction of cardiac mortality. Target volume localization, patient positioning, and treatment planning studies were performed. The accuracy of localization of the internal mammary lymph nodes, using sonography, lymphoscintigraphy, and computer‐tomograpy, as well as the inter‐and intraobserver variations in the delineation of the breast CTV on CT‐scans, are quantified. The amount of heart and lung inside tangential treatment fields is quantified for patients lying supine with both arms in a forearm support and with the ipsilateral arm positioned using an “L‐bar.” Conventional rectangular tangential field irradiation is compared with newly developed conformal and IMRT tangential field irradiation techniques for irradiation of the left breast. For the combined treatment of the internal mammary lymph nodes and left‐sided breast the wide split tangent technique is compared with two new techniques: a tangential field IMRT technique and a technique using oblique electron‐photon fields to irradiate the lymph nodes combined with tangential fields to irradiate the breast. The CT‐based conformal and IMRT treatment techniques lead to better sparing of the heart. However, these techniques are at this moment more time consuming than conventional, simulator‐based treatments. Therefore, a patient selection criterion was developed using the maximum heart distance (MHD) as can be seen on a beam's eye view of a medio‐lateral tangential field. It was shown that the MHD is a good estimator for the probability of late cardiac mortality and can be used to select patients that should be treated with a conformal or IMRT treatment technique.
Monte Carlo‐aided dosimetry of the Theragenics TheraSeed® Model 200 interstitial brachytherapy seed
Authors: Monroe James I. , Williamson Jeffrey F.
Published: July 2002

A dosimetric study of a seed for permanent interstitial brachytherapy, the Theragenics Corporation Model 200 (TheraSeed®), has been undertaken utilizing Monte Carlo photon‐transport (MCPT) simulations. All dosimetric quantities recommended by the American Association of Physicists in Medicine (AAPM) Task Group 43 (TG‐43) [Med. Phys. 22, 209–234 (1995)] report have been calculated. This source contains graphite pellets coated with palladium metal, within which the radioactive is distributed. Due to the significant influence of this metal coating thickness on the dose distribution, two coating thicknesses, 2.2 μm (light seed, representing currently available seeds) and 10.5 μm (heavy seed, representing reactor‐produced seeds available before 1994), were analyzed. Quantities determined are the following: dose rate constant, radial dose function, anisotropy function, anisotropy factor, anisotropy constant, and “along and away” dose tables. The National Institute of Standards and Technology (NIST) Wide Angle Free Air Chamber (WAFAC) standard for air‐kerma strength was simulated, allowing a comparison to measured dosimetry data normalized to The calculated dose‐rate constants are 0.691 (light seed) and 0.694 cGy h−1 U−1 (heavy seed), where in contrast to the recommended TG‐43 value of 0.74 cGy h−1 U−1 and the value, 0.665 cGy h−1 U−1, recommended by AAPM report 69 [Med. Phys. 27, 634–642 (2000)]. Anisotropy constants weighted average, are 0.862 and 0.884 for the light seed and heavy seed, respectively. A generalization of the AAPM formalism [Med. Phys. 27, 634–642] for evaluating the time‐dependent ratio of an administered‐to‐prescribed dose is presented. The findings of this study, in combination with 5% corrections applied to WAFAC measurements performed in 1999, imply that changes in the AAPM's recommended ratios as large as 6%, are indicated.
Comparison of exposure standards in the mammography x‐ray region
Authors: Coletti J. G. , Pearson D. W. , DeWerd L. A. , O'Brien C. M. , Lamperti P. J.
Published: July 2002

Direct comparisons of the National Institute of Standards and Technology's (NIST) Ritz 20 kV to 100 kV standard free‐air ionization chamber and a portable variable‐length free‐air ionization chamber designed by the University of Wisconsin—Madison Accredited Dosimetry Calibration Laboratory (UW‐ADCL) were made on NISTs low‐energy tungsten x‐ray range. As a result of this direct comparison, NIST has established a UW‐ADCL designed chamber, the Attix chamber, as the national standard chamber for the mammography energy x‐ray range. The Ritz standard chamber and the Attix standard chamber have been extensively compared using the new molybdenum and rhodium beam qualities. The results indicate that exposure measurements in the mammography energy x‐ray region with the two free‐air chambers can be made with a discrepancy of less than 0.35%.
Effective dose and energy imparted in diagnostic radiology
Authors: Huda Walter , Gkanatsios Nikolaos A.
Published: July 2002

The patient effective dose, is an indicator of the stochastic radiation risk associated with radiographic or fluoroscopic x‐ray examinations. Determining effective doses for radiologic examinations by measurement or calculation is generally very difficult. By contrast, the energy imparted, ε, to the patient may be obtained from the x‐ray exposure‐area product incident on the patient. As energy imparted is approximately proportional to the effective dose for any given x‐ray radiographic view, the availability of ratios for common radiographic projections provides a convenient way for estimating effective doses. Ratios of were obtained for 68 projections using and ε values obtained from published dosimetry data computed using Monte Carlo techniques on an adult anthropomorphic phantom. The average ratio for the 68 projections in adults was 17.8±1.4 mSv/J, whereas uniform whole body irradiation corresponds to 14.1 mSv/J. The major determinant of ratios was the projection employed (the body region irradiated and x‐ray beam orientation), whereas the tube potential and beam filtration were of secondary importance. Adult ratios may also be used to obtain effective doses to pediatric patients undergoing x‐ray examinations by application of a correction factor based on the patient mass.
Calibration of a portal imaging device for high‐precision dosimetry: A Monte Carlo study
Authors: Keller Harald , Fix Michael , Rüegsegger Peter
Published: July 2002

Today electronic portal imaging devices (EPID's) are used primarily to verify patient positioning. They have, however, also the potential as 2D‐dosimeters and could be used as such for transit dosimetry or dose reconstruction. It has been proven that such devices, especially liquid filled ionization chambers, have a stable dose response relationship which can be described in terms of the physical properties of the EPID and the pulsed linac radiation. For absolute dosimetry however, an accurate method of calibration to an absolute dose is needed. In this work, we concentrate on calibration against dose in a homogeneous water phantom. Using a Monte Carlo model of the detector we calculated dose spread kernels in units of absolute dose per incident energy fluence and compared them to calculated dose spread kernels in water at different depths. The energy of the incident pencil beams varied between 0.5 and 18 MeV. At the depth of dose maximum in water for a 6 MV beam (1.5 cm) and for a 18 MV beam (3.0 cm) we observed large absolute differences between water and detector dose above an incident energy of 4 MeV but only small relative differences in the most frequent energy range of the beam energy spectra. It is shown that for a 6 MV beam the absolute reference dose measured at 1.5 cm water depth differs from the absolute detector dose by 3.8%. At depth 1.2 cm in water, however, the relative dose differences are almost constant between 2 and 6 MeV. The effects of changes in the energy spectrum of the beam on the dose responses in water and in the detector are also investigated. We show that differences larger than 2% can occur for different beam qualities of the incident photon beam behind water slabs of different thicknesses. It is therefore concluded that for high‐precision dosimetry such effects have to be taken into account. Nevertheless, the precise information about the dose response of the detector provided in this Monte Carlo study forms the basis of extracting directly the basic radiometric quantities photon fluence and photon energy fluence from the detector's signal using a deconvolution algorithm. The results are therefore promising for future application in absolute transit dosimetry and absolute dose reconstruction.
Mapping dose distributions
Authors: Beckett Craig , Dickof Peter
Published: July 2002

Clinical dose calculations are often performed by scaling distances from a dose distribution measured in one medium to calculate the dose in another. These perturbation calculations have the mathematical form of a mapping. In this paper we identify five conditions required for particle transport to reduce to this form and develop a new mapping for electrons which approximately satisfies these conditions. This continuous scattering mapping is based on two parameters, the scattering power of the medium which determines the shape of the scaling paths, and the stopping power of the medium which determines where the energy is deposited along these paths. Pencil beam dose distributions are calculated with EGS4 in one medium and mapped to other media. The resultant distributions are compared with EGS4 calculations done directly in the second medium. The accuracy of the mapping algorithm is shown to be superior to both linear density scaling and the MDAH electron pencil beam algorithm [Kenneth R. Hogstrom, Michael D. Mills, and Peter R. Almond, “Electron beam dose calculations,” Phys. Med. Biol. 26, 445–459 (1981)] for pencil beams in homogeneous media and inhomogeneous phantoms (both slab and nonslab geometries) for a variety of materials of clinical interest.
In‐phantom neutron fluence measurements in the orthogonal Birmingham boron neutron capture therapy beam
Authors: Tattam D. A. , Allen D. A. , Beynon T. D. , Constantine G. , Green S. , Scott M. C. , Weaver D. R.
Published: July 2002

This paper presents the results of an experimental investigation into the performance of the Birmingham accelerator‐based epithermal BNCT beam. In‐phantom gold foil activation and boron trifluoride tube measurements have been used. The results have been compared with calculated response rates using Monte Carlo modeling of the entire neutron system from source to phantom and detector. The excellent agreement obtained gives us confidence in the validity of the simulations and our ability to predict accurately the neutronic performance of our BNCT facility.
An evaluation of the signal and noise characteristics of four CCD‐based film digitizers
Authors: Hangiandreou N. J. , O'Connor T. J. , Felmlee J. P.
Published: July 2002

Film digitizers are common devices in radiology departments involved with picture archive and communication systems (PACS) and teleradiology. In this paper, we studied the performance of film digitizers based on charge‐coupled device detectors (CCD digitizers), and compared this with the performance of a laser digitizer (the de facto standard). Our focus was on the assessment of signal, noise and useful optical density range performance. A function derived from the Rose model was used to evaluate these parameters in absolute terms, based their predicted ability to detect objects of specific size and optical density difference with respect to background. We studied CCD digitizers from four different vendors and found that none was able to reliably operate up to the maximum density of 3.0 required to digitize plain radiographs, while the laser digitizer was capable of this task. Our analysis also indicated that two of the four CCD digitizers were adequate for digitizing laser‐printed cross‐sectional images in certain cases. Finally, our analysis indicated that digitization of SMPTE pattern films along with visual assessment of the 5% and 95% contrast patches was not sufficient for determining the utility of film digitizers for clinical tasks. Computation of the function provides a useful means of assessing the performance of film digitizers (e.g., for acceptance testing and quality control), and this technique may be adaptable for evaluation of other digital imaging modalities.
Chemical dosimetry in the near‐zone of brachytherapy sources
Authors: Hasson Brian F.
Published: July 2002

The treatment of neointimal‐hyperplasia, prostate cancer with seed implants, and transition zone effects in three‐dimensional conformal therapy has spurred the development of new dosimeters for evaluating steep dose‐gradient regions. This thesis describes two dosimetry systems to accurately measure the radial dose in the near‐zone (<5 mm) of clinically used and sources. A custom‐made polymer gel dosimeter was designed and implemented for this project. This dosimeter evaluated with a high field strength small‐bore MR (Magnetic Resonance) scanner provided precise measurement of the dose in the near‐zone. A second system consisted of gaf‐chromic film and a custom‐built precision scanner. The scanner, using a 670 nm diode laser and precision built micrometers, provided precise scanning of the gaf‐chromic film. The gaf‐chromic film dosimetry system gave results that were in good agreement (2%) with the polymer gel dosimeter for the radial dose in the near‐zone of clinically used and sources. The radial dose data from both dosimetry systems agreed to within 3% with Monte Carlo data at radial distances of less than 5 mm from the center of single and sources. This project has extended the reliable data in the near‐zone to 1 mm for Both dosimeters were shown to be satisfactory for near‐zone dosimetry, and provide an empirical benchmark for the Monte Carlo theorist.
Characteristics of metal‐plate/film detectors at therapy energies. I. Modulation transfer function
Authors: Falco T. , Fallone B. G.
Published: July 2002

Measurements of modulation transfer function (MTF) for front and back metal‐plate/film portal detectors are reported for the Cobalt‐60 and 10 MV spectra. The detectors consist of a double‐emulsion portal film secured between plates of Al, Cu, brass, or Pb with thicknesses varying from 0 to 4.81 mm. Secondary electrons produced within the front plate generate the main signal, but the MTF decreases with an increase in front plate thickness greater than the maximum range of electrons because of photon scatter in the front plate. Because the decrease of MTF with backplate thickness ceases for backplate thickness greater than the MTF is influenced more by the backscatter electrons than the backscatter photons.
Analysis of spectral blur effects in x‐ray scatter imaging
Authors: Leclair Robert J. , Johns Paul C.
Published: July 2002

Previous analysis in our research program investigating the potential use of scattered photons for medical x‐ray imaging has been for monoenergetic beams. In practice, polyenergetic beams are almost always used due to their higher photon fluence rate. The effects of beam polychromaticity on x‐ray scatter imaging are determined with the aid of our semianalytic model that images a target object against a background material of the same dimensions when both are situated within a water phantom. Our analysis involves four different photon beams with constant incident energy fluence: (1) a monoenergetic beam with photon energy (2) a dual peak beam with two separate monoenergetic peaks of energies and (3) a clinical x‐ray beam, and (4) a rectangular beam with uniform energy fluence between energies and A comparison between the polyenergetic spectra is accomplished by matching the centroids and standard deviations of the dual peak and rectangular spectra to those of the clinical x‐ray spectrum. For the task of imaging liver versus fat structures 1 cm thick in a 25‐cm‐diam spherical water phantom with the scattered photons between 2° and 12°, the predicted signal‐to‐noise ratio (SNR) obtained with a 100 kV beam is of the SNR acquired with the optimum monoenergetic beam The SNR for the corresponding dual peak beam is of and for the rectangular beam is Our analysis shows that monoenergetic x‐ray beams are not necessary for x‐ray scatter imaging.
Thermal dosimetry of a focused ultrasound beam in vivo by magnetic resonance imaging
Authors: Chung Andrew H. , Jolesz Ferenc A. , Hynynen Kullervo
Published: July 2002

Magnetic resonance imaging (MRI) thermometry has been utilized for in vivo evaluation of thermal exposure induced by a focused ultrasound beam. A simulation study of the focused ultrasound beam was conducted to select imaging parameters for reducing the error due to the spatial and temporal averaging of MRI. Temperature imaging based on the proton resonance frequency shift was utilized to obtain the temperature distribution during sonication in the skeletal muscle of eight rabbits. MRI‐derived temperature information was then used to calculate the thermal dose distribution induced by the sonication and to estimate the coagulated tissue volume. The tissue changes were also evaluated directly by taking the ‐weighted and the contrast agent enhanced ‐weighted MR images. Errors in the temperature and thermal dose measurements were found to be minimal using the following parameters: slice thickness=3 mm, voxel dimension=0.6 mm, and scan time per image=3.4 s. The estimated dimensions of the coagulated tissue volume were in good agreement with the tissue damages seen on the contrast agent enhanced ‐weighted images. The tissue damage seen on the histology was closely matched to the ones seen on the ‐weighted images. This study showed that MRI thermometry has significant potential for both monitoring the thermal exposure and evaluating the tissue damage. This would allow real‐time control of the sonication parameters to optimize clinical treatments.
Use of low‐pressure tissue equivalent proportional counters for the dosimetry of neutron beams used in BNCT and BNCEFNT
Authors: Kota Chandrasekhar , Maughan Richard L. , Tattam David , Beynon T. Derek
Published: July 2002

The absorbed dose in a phantom or patient in boron neutron capture therapy (BNCT) and boron neutron capture enhanced fast neutron therapy (BNCEFNT) is deposited by gamma rays, neutrons of a range of energies and the reaction products. These dose components are commonly measured with paired (TE/Mg) ion chambers and foil activation technique. In the present work, we have investigated the use of paired tissue equivalent (TE) and proportional counters as an alternate and complementary dosimetry technique for use in these neutron beams. We first describe various aspects of counter operation, uncertainties in dose measurement, and interpretation of the data. We then present measurements made in the following radiation fields: An epithermal beam at the University of Birmingham in the United Kingdom, a fast neutron therapy beam at Harper Hospital in Detroit, and a radiation field. In the epithermal beam, our measured gamma and neutron dose rates compare very well with the values calculated using Monte Carlo methods. The measured dose rates show a systematic difference of ∼35% when compared to the calculations. The measured dose rates in the fast neutron beam are in good agreement with those measured using a calibrated A‐150 TEP (tissue equivalent plastic) ion chamber. The measured dose rates compare very well with those measured using other methods. In the radiation field, the measured dose rates for all three components agree well with other Monte Carlo calculations and measurements. Based on these results, we conclude that the paired low‐pressure proportional counters can be used to establish an independent technique of dose measurement in these radiation fields.
On the use of the statistical definition of entropy to justify Planck’s form of the third law of thermodynamics
Authors: Mafé Salvador , Manzanares José A. , de la Rubia Juan
Published: July 2002

The statistical definition of entropy is often used to justify Planck’s form of the third law of thermodynamics in a very graphic form. Statements like for a nondegenerate ground state system at 0 K, the system should be in its lowest energy (ground) state and then S=0 according to the statistical definition of entropy are commonplace in many textbooks. These statements are useful, but might as well be supplemented with more empirical views concerning the physical limits of low temperatures in thermodynamics and the high number of states still accessible for a macroscopic system when the entropy takes small values. The purpose of this note is to emphasize the above points making use of four model systems: the Fermi ideal gas, the confined Bose ideal gas, the photon gas, and the noninteracting particles in a two-level system. Each of these physical systems has a characteristic temperature related to the nature and organization of its microscopic constituents and the third law should perhaps be expressed in terms of the behavior of the system when it approaches this temperature rather than the presumed behavior at exactly T=0 K.
A simple derivation of the recursion relation for 〈rN〉 in energy eigenstates
Authors: Balasubramanian S.
Published: July 2002

A simple derivation based on the generalized Hellmann–Feynman theorem is given for the three-term recursion relation for 〈rN〉 in the energy eigenstates of a hydrogenic atom and the harmonic oscillator in one, two, and three dimensions.
How to teach statistical thermal physics in an introductory physics course
Authors: Lee Koo-Chul
Published: July 2002

We report on several simulation programs (available through http://phys.snu.ac.kr/howto/ or http://phya.snu.ac.kr/∼kclee/howto/) which can be used to teach the statistical foundations of thermal physics in introductory college physics courses. These programs are simple applications of a technique for generating random configurations of many dice with a fixed total value. By merely simulating dice throwing we can demonstrate all the important principles of classical thermodynamics.
A closer look at tumbling toast
Authors: Bacon M. E. , Heald George , James Matt
Published: July 2002

The study of the mechanics of tumbling toast provides an informative and entertaining project for undergraduates. The relatively recent introduction of software packages to facilitate the analysis of video recordings, and the numerical solution of complex differential equations, makes such a study an attractive candidate for inclusion in an experimental physics course at the undergraduate level. In the study reported here it is found that the experimentally determined free fall angular velocity of a board, tumbling off the edge of a table, can only be predicted at all accurately if slipping is taken into account. The size and shape of the board used in the calculations and in the experiments were roughly the same as that of a piece of toast. In addition, it is found that the board, tumbling from a standard table of height 76 cm, will land butter-side down (neglecting any bounce) for two ranges of overhang (δ0). δ0 is defined as the initial distance from the table edge to a vertical line drawn through the center of mass when the board is horizontal. For our board (length 10.2 cm) the approximate ranges of overhang are 0–0.8 and 2.7–5.1 cm. The importance of the 0–0.8 cm (only 2% of all possible overhangs for which tumbling is possible) favoring a butter-side down landing should not be underestimated when pondering the widely held belief that toast, tumbling from a table, usually falls butter-side down.
Nice things about mean fields: Mean field potentials for the classroom
Authors: Cheng Leo , Goldstein Elisheva , Siegel P. B.
Published: July 2002

We present two examples which use a mean field potential to determine valence electron and nucleon energy levels in atoms and nuclei, respectively. In atoms, we compute the energy levels of the alkali elements, and in nuclei the binding energy of valence nucleons in mirror nuclei are calculated. In both cases, the student can compare the results with experiment and vary the parameters of the calculation to best fit the data.
Paradoxical behavior of an infinite ladder network of inductors and capacitors
Authors: van Enk S. J.
Published: July 2002

The behavior of the impedance of a standard ladder network of capacitors and inductors is analyzed as a function of the size of the network. This behavior may be unstable in the absence of dissipation so that the limit of an infinite network is not well defined. Standard textbooks do not always treat this case correctly.