bluuebunny/crossref_metadata_2025 huggingface dataset:
Modification of Cysteine Residues In Vitro and In Vivo Affects the Immunogenicity and Antigenicity of Major Histocompatibility Complex Class I–restricted Viral Determinants
Authors: Chen Weisan , Yewdell Jonathan W. , Levine Rodney L. , Bennink Jack R.
Published: July 2002

In studying the subdominant status of two cysteine-containing influenza virus nuclear protein (NP) determinants (NP39–47 and NP218–226) restricted by H-2Kd, we found that the antigenicity of synthetic peptides was enhanced 10–100-fold by treatment with reducing agents, despite the fact that the affinity for Kd was not enhanced. Reducing agents also markedly enhanced the immunogenicity of cysteine-containing peptides, as measured by propagation of long-term T cell lines in vitro. Similar enhancing effects were obtained by substituting cysteine with alanine or serine in the synthetic peptides, demonstrating that sulfhydryl modification of cysteine is responsible for the impaired antigenicity and immunogenicity of NP39–47 and NP218–226. We found similar effects for two widely studied, cysteine-containing peptides from lymphocytic choriomeningitis virus. The major modifications of cysteine-containing synthetic peptides are cysteinylation and dimerization occurring through cysteine residues. We demonstrate that both of these modifications occur in cells synthesizing a cytosolic NP218–226 minigene product and, further, that T cells specific for cysteinylated NP218–226 are induced by influenza virus infection in mice, demonstrating that this modification occurs in vivo. These findings demonstrate that posttranslational modifications affect the immunogenicity and antigenicity of cysteine-containing viral peptides and that this must be considered in studying the status of such peptides in immunodominance hierarchies.
Commitment to the B Lymphoid Lineage Occurs before DH-JH Recombination
Authors: Allman David , Li Jin , Hardy Richard R.
Published: July 2002

Lineage commitment in B lymphopoiesis remains poorly understood due to the inability to clearly define newly committed B lineage progenitors and their multipotential descendants. We examined the potential of three recently described progenitor populations in adult mouse bone marrow to differentiate into each hematopoietic lineage. The earliest of these, termed fraction (Fr.) A0, exhibited myeloid, erythroid, and B and T lymphoid progenitor activity and included individual cells with myeloid/B lymphoid potential. In sharp contrast, two later populations, termed Frs. A1 and A2 and characterized by surface B220 expression and transcription of the germline immunoglobulin heavy chain (IgH) locus, lacked progenitor activity for all hematopoietic lineages except B lymphocytes. These observations, together with single cell polymerase chain reaction analysis showing a lack of DHJH rearrangements in each population and experiments showing identical precursor potentials when these populations were derived from recombination activating gene (Rag)-1−/− and JH−/− mice, demonstrate that commitment to the B lymphoid lineage occurs before and independently of VHDHJH recombination.
Calcium-Induced Calcium Release in Smooth Muscle
Authors: Collier M.L. , Ji G. , Wang Y.-X. , Kotlikoff M.I.
Published: July 2002

Calcium-induced calcium release (CICR) has been observed in cardiac myocytes as elementary calcium release events (calcium sparks) associated with the opening of L-type Ca2+ channels. In heart cells, a tight coupling between the gating of single L-type Ca2+ channels and ryanodine receptors (RYRs) underlies calcium release. Here we demonstrate that L-type Ca2+ channels activate RYRs to produce CICR in smooth muscle cells in the form of Ca2+ sparks and propagated Ca2+ waves. However, unlike CICR in cardiac muscle, RYR channel opening is not tightly linked to the gating of L-type Ca2+ channels. L-type Ca2+ channels can open without triggering Ca2+ sparks and triggered Ca2+ sparks are often observed after channel closure. CICR is a function of the net flux of Ca2+ ions into the cytosol, rather than the single channel amplitude of L-type Ca2+ channels. Moreover, unlike CICR in striated muscle, calcium release is completely eliminated by cytosolic calcium buffering. Thus, L-type Ca2+ channels are loosely coupled to RYR through an increase in global [Ca2+] due to an increase in the effective distance between L-type Ca2+ channels and RYR, resulting in an uncoupling of the obligate relationship that exists in striated muscle between the action potential and calcium release.
Predecessors of preprint servers
Authors: Till James E.
Published: July 2002

Although there was an early experiment in the 1960s with the central distribution of paper preprints in the biomedical sciences, these sciences have not been early adopters of electronic preprint servers. Some barriers to the development of a ‘preprint culture’ in the biomedical sciences are described. Multiple factors that, from the 1960s, fostered the transition from a paper‐based preprint culture in high energy physics to an electronic one are also described. A new revolution in scientific publishing, in which journals come to be regarded as an overlay on electronic preprint databases, will probably overtake some areas of research much more quickly than others.
Removable sets for continuous solutions of quasilinear elliptic equations
Authors: Kilpeläinen Tero , Zhong Xiao
Published: July 2002

We show that sets of

n
−
p
+
α
(
p
−
1
)

n-p+\alpha (p-1)

Hausdorff measure zero are removable for

α
\alpha

-Hölder continuous solutions to quasilinear elliptic equations similar to the

p
p

-Laplacian. The result is optimal. We also treat larger sets in terms of a growth condition. In particular, our results apply to quasiregular mappings.
The multiplier operators on the weighted product spaces
Authors: Chen Lung-Kee , Fan Dashan
Published: July 2002

In this paper, we proved the boundedness of multiplier operators on the weighted

L

p

L^{p}

product spaces.
The volume preserving mean curvature flow near spheres
Authors: Escher Joachim , Simonett Gieri
Published: July 2002

By means of a center manifold analysis we investigate the averaged mean curvature flow near spheres. In particular, we show that there exist global solutions to this flow starting from non-convex initial hypersurfaces.
Polynomials with integral coefficients, equivalent to a given polynomial
Authors: Kollár János
Published: July 2002

Let

f
(

x

0

,
…
,

x

n

)

f(x_{0},\dots ,x_{n})

be a homogeneous polynomial with rational coefficients. The aim of this paper is to find a polynomial with integral coefficients

F
(

x

0

,
…
,

x

n

)

F(x_{0},\dots ,x_{n})

which is “equivalent" to

f
f

and as “simple" as possible. The principal ingredient of the proof is to connect this question with the geometric invariant theory of polynomials. Applications to binary forms, class numbers, quadratic forms and to families of cubic surfaces are given at the end.
Nonvanishing of a certain sesquilinear form in the theta correspondence
Authors: He Hongyu
Published: July 2002

Suppose

2
n
+
1
≥
p
+
q

2n+1 \geq p+q

. In an earlier paper in 2000 we study a certain sesquilinear form

(
,

)

π

(,)_{\pi }

introduced by Jian-Shu Li in 1989. For

π
\pi

in the semistable range of

θ
(
M
O
(
p
,
q
)
→
M
S

p

2
n

(

R

)
)

\theta (MO(p,q) \rightarrow MSp_{2n}(\mathbb {R}))

, if

(
,

)

π

(,)_{\pi }

does not vanish, then it induces a sesquilinear form on

θ
(
π
)

\theta (\pi )

. In another work in 2000 we proved that

(
,

)

π

(,)_{\pi }

is positive semidefinite under a mild growth condition on the matrix coefficients of

π
\pi

. In this paper, we show that either

(
,

)

π

(,)_{\pi }

or

(
,

)

π
⊗
det

(,)_{\pi \otimes \det }

is nonvanishing. These results combined with one result of Przebinda suggest the existence of certain unipotent representations of

M

p

2
n

(

R

)

Mp_{2n}(\mathbb {R})

beyond unitary representations of low rank.
A computer-driven approach to PCR-based differential screening, alternative to differential display.
Authors: Consalez G G , Cabibbo A , Corradi A , Alli C , Sardella M , Sitia R , Fesce R
Published: July 2002

MOTIVATION: Polymerase chain reaction (PCR)-based RNA fingerprinting is a powerful tool for the isolation of differentially expressed genes in studies of neoplasia, differentiation or development. Arbitrarily primed RNA fingerprinting is capable of targeting coding regions of genes, as opposed to differential display techniques, which target 3' non-coding cDNA. In order to be of general use and to permit a systematic survey of differential gene expression, RNA fingerprinting has to be standardized and a number of highly efficient and selective arbitrary primers must be identified. RESULTS: We have applied a rational approach to generate a representative panel of high-efficiency oligonucleotides for RNA fingerprinting studies, which display marked affinity for coding portions of known genes and, as shown by preliminary results, of novel ones. The choice of oligonucleotides was driven by computer simulations of RNA fingerprinting reverse transcriptase (RT)-PCR experiments, performed on two custom-generated, non-redundant nucleotide databases, each containing the complete collection of deposited human or murine cDNAs. The simulation approach and experimental protocol proposed here permit the efficient isolation of coding cDNA fragments from differentially expressed genes. AVAILABILITY: Freely available on request from the authors. CONTACT: fesce.riccardo@hsr.it
TRITON: in silico construction of protein mutants and
prediction of their activities
Authors: Prokop Martin , Damborský Jir̆ı́ , Koc̆a Jaroslav
Published: July 2002

Motivation: One of the objectives of protein engineering is to propose and construct modified proteins with improved activity for the substrate of interest. Systematic computational investigation of many protein variants requires the preparation and handling of a large number of data files. The type of the data generated during the modelling of protein variants and the estimation of their activities offers the possibility of process automatization.

Results: The graphical program TRITON has been developed for modelling protein mutants and assessment of their activities. Protein mutants are modelled from the wild type structure by homology modelling using the external program MODELLER. Chemical reactions taking place in the mutants active site are modelled using the semi-empirical quantum mechanic program MOPAC. Semi-quantitative predictions of mutants activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of active site residues during the reaction. The program TRITON offers graphical tools for the preparation of the input data files, for calculation and for the analysis of the generated output data.

Availability: The program TRITON can run under operating systems IRIX, Linux and NetBSD. The software is available at http://www.chemi.muni.cz/lbsd/triton.html.

Contact: triton@chemi.muni.cz

* Dedicated to Professor Milan Kratochvı́l on the occasion of his 75th birthday.

To whom correspondence should be addressed.
PlantSat: a specialized database for plant satellite repeats
Authors: Macas Jir̆ı́ , Mészáros Tibor , Nouzová Marcela
Published: July 2002

Motivation: Tandemly organized repetitive sequences (satellite DNA) are widespread in complex eukaryotic genomes. In plants, satellite repeats often represent a substantial part of nuclear DNA but only a little is known about the molecular mechanisms of their amplification and their possible role(s) in genome evolution and function. Unfortunately, addressing these questions via characterization of general sequence properties of known satellite repeats has been hindered by a difficulty in obtaining a complete and unbiased set of sequence data for this analysis. This is mainly due to the presence of multiple entries of homologous sequences and of single entries that contain more than one repeated unit (monomer) in the public databases.

Results: We have established a computer database specialized for plant satellite repeats (PlantSat) that integrates sequence data available from various resources with supplementary information including repeat consensus sequences, abundances, and chromosomal localizations. The sequences are stored as individual repeat monomers grouped into families, which simplifies their computer analysis and makes it more accurate. Using this feature, we have performed a basic sequence analysis of the whole set of plant satellite repeats with respect to their monomer length and nucleotide composition. The analysis revealed several preferred length ranges of the monomers (∼165 bp and its multiples) and an over-representation of the AA/TT dinucleotide in the repeats. We have also detected an enrichment of satellite DNA sequences for the motif CAAAA that is supposed to be involved in breakage–reunion of repeated sequences.

Availability: The PlantSat database is accessible via a web interface (http://w3lamc.umbr.cas.cz/PlantSat) and can be searched for keywords, sequence motifs, and sequence homologies, or it can be used as a source of organized sequence data for further analyses.

Contact: macas@umbr.cas.cz

* To whom correspondence should be addressed.
INFLATION TARGETERS IN PRACTICE: A LUCKY LOT?
Authors: Simone Francisco De A. Nadal‐De
Published: July 2002

Some observers have attributed the success of inflation targeters in reducing inflation to the global disinflation of the 1990s. As a result, inflation targeting countries have been considered to be a lucky lot. One key policyimplication of that is that if the international environment becomes again hostile to low inflation in the future, inflation targeting will prove to have been a mere fad. This article views inflation targeting not just as a rule but as a framework for the conduct of monetary policy, and it argues that currently available analyses of the experience of inflation targeting countries have serious weaknesses. One weakness is that those studies have not taken into account that regime changes may alter the quantitative and qualitative interaction among small, open economies and the rest of the world. Another weakness is that those studies have not recognized that the extraction of common trends and cycles is contingent on the nature of the monetary policy regime. It is likely that inflation targeting frameworks may imply a new beneficial trend in monetary policy making. This suggests that if the international environment becomes again hostile to low inflation in the future, an inflation targeting framework may become a viable alternative to a central bank that remains committed to price stability.
CURRENCY CONVERTIBILITY AND LINKAGE BETWEEN CHINESE OFFICIAL AND SWAP MARKET EXCHANGE RATES
Authors: Yang Jian , Leatham David J.
Published: July 2002

This article investigates the impact of currency convertibility under the current account on the informational linkage between official and swap market exchange rates for Chinese currency (renminbi). Findings indicate that currency convertibility increased the informational connection between the government's official exchange rate and the swap market exchange rate, exclusively traded by foreign investors, and thus improved the information content of renminbi exchange rates. Moreover, the results also suggest that more complete currency convertibility was needed for more informed renminbi exchange rates.
WAGES AND EMPLOYMENT IN THE U.S. APPAREL INDUSTRY
Authors: Brown Bruce C.
Published: July 2002

This article uses individual‐level data from the U.S. Census, Public Use Microdata Sample (PUMS), to examine wages and employment in the U.S. apparel industry. Total employment in this sector has been falling since 1970, and its overall average wage is the lowest of 25 industry aggregates. But disaggregation by gender, education, and nativity reveals that groups of highly educated male native workers earn higher average wages in apparel than in other industries. Moreover, after adjusting for observed individual differences in human capital (in addition to the three characteristics used to form worker subsets), highly educated male natives earn positive wage premiums in this sector. In contrast, most categories of immigrants and female natives earn relatively low average wages and experience negative wage premiums in apparel. This variation in the adjusted industry wage premiums across worker groups may be related to apparel's relative exposure to imports and immigrant workers.
An inner membrane platform in the type II secretion machinery of Gram‐negative bacteria
Authors: Py Béatrice , Loiseau Laurent , Barras Frédéric
Published: July 2002

The type II secretion machinery allows most Gram‐negative bacteria to deliver virulence factors into their surroundings. We report that in Erwinia chrysanthemi, GspE (the putative NTPase), GspF, GspL and GspM constitute a complex in the inner membrane that is presumably used as a platform for assembling other parts of the secretion machinery. The GspE–GspF–GspL–GspM complex was demonstrated by two methods: (i) co‐immunoprecipitation of GspE–GspF–GspL with antibodies raised against either GspE or GspF; (ii) interactions in the yeast two‐hybrid system between GspF and GspE, GspF and GspL, GspL and GspM. GspL was found to have an essential role in complex formation. We propose a model in which the GspE–GspF–GspL–GspM proteins constitute a building block within the secretion machinery on top of which another building block, referred to as a pseudopilus, assembles. By analogy, we predict that a similar platform is required for the biogenesis of the type IV pilus.
Myc/Max/Mad regulate the frequency but not the duration of productive cell cycles
Authors: Hölzel Michael , Kohlhuber Franz , Schlosser Isabel , Hölzel Dieter , Lüscher Bernhard , Eick Dirk
Published: July 2002

Upregulation of the proto‐oncoprotein Myc, a basic, helix–loop–helix, leucin zipper domain transcription factor has profound consequences on cell proliferation, cell growth and apoptosis. Cell cultures of somatic c‐myc−/− rat fibroblasts show extremely prolonged doubling times of 52 h. Using time‐lapse microscopy, we show here that individual c‐myc−/− cells proceeded within ∼24 h through the cell cycle as fast as c‐myc+/+ cells. However, c‐myc−/− cells were highly sensitive to contact inhibition and readily arrested in the cell cycle already at low density. Activation of conditional MycER overcame cell cycle arrest in c‐myc−/− cells and led to continuous proliferation at the expense of increased apoptosis at high cell density. Conditional expression of Mad1, a Myc antagonist, represses proliferation of different cell types including U2OS cells. In analogy to the effect of Myc, this occurs mainly by reducing the probability of cells remaining in the cycle. Our data demonstrate that the Myc/Max/Mad network does not regulate the duration of the cell cycle, but the decision of cells to enter or exit the cell cycle.
Human Asf1 and CAF‐1 interact and synergize in a repair‐coupled nucleosome assembly pathway
Authors: Mello Jill A , Silljé Herman H W , Roche Danièle M J , Kirschner Doris B , Nigg Erich A , Almouzni Geneviève
Published: July 2002

The efficient assembly of newly replicated and repaired DNA into chromatin is essential for proper genome function. Based on genetic studies in Saccharomyces cerevisiae, the histone chaperone anti‐silencing function 1 (Asf1) has been implicated in the DNA repair response. Here, the human homologs are shown to function synergistically with human CAF‐1 to assemble nucleosomes during nucleotide excision repair in vitro. Furthermore, we demonstrate that hAsf1 proteins can interact directly with the p60 subunit of hCAF‐1. In contrast to hCAF‐1 p60, the nuclear hAsf1 proteins are not significantly associated with chromatin in cells before or after the induction of DNA damage, nor specifically recruited to damaged DNA during repair in a bead‐linked DNA assay. A model is proposed in which the synergism between hAsf1 and CAF‐1 for nucleosome formation during DNA repair is achieved through a transient physical interaction allowing histone delivery from Asf1 to CAF‐1.
Cluster size distributions: signatures of self–organization in spatial ecologies
Authors: Pascual Mercedes , Roy Manojit , Guichard Frédéric , Flierl Glenn
Published: July 2002

Three different lattice–based models for antagonistic ecological interactions, both nonlinear and stochastic, exhibit similar power–law scalings in the geometry of clusters. Specifically, cluster size distributions and perimeter–area curves follow power–law scalings. In the coexistence regime, these patterns are robust: their exponents, and therefore the associated Korcak exponent characterizing patchiness, depend only weakly on the parameters of the systems. These distributions, in particular the values of their exponents, are close to those reported in the literature for systems associated with self–organized criticality (SOC) such as forest–fire models; however, the typical assumptions of SOC need not apply. Our results demonstrate that power–law scalings in cluster size distributions are not restricted to systems for antagonistic interactions in which a clear separation of time–scales holds. The patterns are characteristic of processes of growth and inhibition in space, such as those in predator–prey and disturbance–recovery dynamics. Inversions of these patterns, that is, scalings with a positive slope as described for plankton distributions, would therefore require spatial forcing by environmental variability.
The Swi5 activator recruits the Mediator complex to theHOpromoter without RNA polymerase II
Authors: Bhoite Leena T. , Yu Yaxin , Stillman David J.
Published: July 2002

Regulation ofHOgene expression in the yeastSaccharomyces cerevisiaeis intricately orchestrated by an assortment of gene-specific DNA-binding and non-DNA binding regulators. Binding of the early G1transcription factor Swi5 to the distal URS1 element of theHOpromoter initiates a cascade of events through recruitment of the Swi/Snf and SAGA complexes. In late G1, binding of transcription factor SBF to promoter proximal sequences results in the timely expression ofHO. In this work we describe an important additional layer of complexity to the current model by identifying a connection between Swi5 and the Mediator/RNA polymerase II holoenzyme complex. We show that Swi5 recruits Mediator toHOby specific interaction with the Gal11 module of the Mediator complex. Importantly, binding of both the Gal11 and Srb4 mediator components to the upstream region ofHOis independent of the SBF factor. Swi/Snf is required for Mediator binding, and genetic suppression experiments suggest that Swi/Snf and Mediator act in the same genetic pathway ofHOactivation. Experiments examining the kinetics of binding show that Mediator binds toHOpromoter elements 1.5 kb upstream of the transcription start site in early G1, but this binding occurs without RNA Pol II. RNA Pol II does not bind toHOuntil late G1, whenHOis actively transcribed, and binding occurs exclusively to the TATA region.
A variable resolution x‐ray detector for computed tomography: II. Imaging theory and performance
Authors: DiBianca F. A. , Zou P. , Jordan L. M. , Laughter J. S. , Zeman H. D. , Sebes J.
Published: July 2002

A computed tomography (CT) imaging technique called variable resolution x‐ray (VRX) detection provides variable image resolution ranging from that of clinical body scanning (1 cy/mm) to that of microscopy (100 cy/mm). In this paper, an experimental VRX CT scanner based on a rotating subject table and an angulated storage phosphor screen detector is described and tested. The measured projection resolution of the scanner is ⩾ 20 lp/mm. Using this scanner, 4.8‐s CT scans are made of specimens of human extremities and of in vivo hamsters. In addition, the system's projected spatial resolution is calculated to exceed 100 cy/mm for a future on‐line CT scanner incorporating smaller focal spots (0.1 mm) than those currently used and a 1008‐channel VRX detector with 0.6‐mm cell spacing.
A study to assess and improve dose computations in photon beam therapy
Authors: Aspradakis Maria M.
Published: July 2002

The thesis provides a comprehensive and critical review of existing photon dose calculation models.\sTwo applications of the Monte Carlo method to radiotherapy have been studied using the EGS4 Monte Carlo system.\sThe first is the generation of total and total‐scatter energy deposition kernels (EDK) (scored and stored on a Cartesian coordinate system), and the second the use of the Monte Carlo method as a benchmarking tool.\sAn EGS4 usercode (XYZSIM) is presented that calculates total and total‐scatter dose deposited in a Cartesian geometry from divergent, polyenergetic photon beams. A superposition model is further developed from the dose deposition point of view.\sDose at a point is obtained from knowledge of the total energy released per unit mass in the medium (TERMA) and the total EDK.\sEffective energy spectrum information is used to calculate dose for clinical beams.\sThe performance of this model is examined in homogeneous and heterogeneous media.\sCalculation time is decreased by reducing the number of dose points calculated with superposition and by appropriately using results from a fast, conventional inhomogeneity correction model.\sThis technique speeds up the computation of a 3D dose distribution by at least a factor of 100 with no significant losses in accuracy.
Maximum likelihood image reconstruction in positron emission tomography (PET):\sConvergence characteristics and stopping rules
Authors: Kontaxakis Georgios
Published: July 2002

Maximum likelihood estimation image reconstruction algorithms for emission tomography received much attention during the last decade because of their potential to produce high quality images.\sA detailed study of the convergence properties of the expectation–maximization (EM) algorithm for PET image reconstruction is presented.\sThe main problems associated with this technique are addressed, namely, its high computational cost and the lack of a robust stopping criterion for this iterative algorithm.\sA practical implementation of the EM algorithm on a modern workstation is presented.\sA PET scanner is simulated using Monte Carlo techniques.\sDifferent kinds of data sets are produced and used in order to study the properties of the algorithm and develop a stopping rule, which are then validated with the use of real sinogram data from a commercial PET scanner.\sOther algorithms of the same iterative class are studied and modified versions of the EM algorithm are proposed with stopping rules, all based on the properties of the image vector updating coefficients in each iteration.\sA practical implementation of the EM algorithm is the final result, with optimal performance on the conventional computing systems available today, producing tomographic reconstructions in clinically meaningful times.
Large discrepancies between calculated and diode readings for small field sizes and small SSDs of 15 MV photon beams
Authors: Wierzbicki Jacek G. , Waid David S.
Published: July 2002

Clinical observations have revealed that diode readings from 15 MV photon beams with small field sizes and small SSD values were consistently 5%–10% higher than doses calculated at the maximum depth. Dose at depth depends on the collimator scattering factor and the phantom scattering factor—both field size dependent. Diodes are placed on the skin surface, and therefore the phantom scatter factor is different than at depth. In addition, inverse square corrections should be calculated with respect to the location of the diode itself rather than the location of within the tissue. This may account for about 8% difference between calculated and diode readings for very small radiation fields and small SSDs, e.g., a prostate boost.
Use of CEA TVS film for measuring high energy photon beam dose distributions
Authors: Cadman Patrick
Published: July 2002

CEA TVS film is a therapy verification film that has been recently introduced in the North American market. This film features linear characteristic curves for photon energies from to 18 MV as reported by Cheng and Das [Med. Phys. 23, 1225 (1996)]. In Saskatoon, TVS film was investigated for its application in the measurement of dose distributions with 4 and 18 MV linacs and a unit. The TVS film jacket has a layer of conductive material that has a minimal effect on the film's response. Film sensitivity generally increases for exposures normal to the incident beam as compared with parallel exposures, but was highly dependent on beam energy and depth of measurement. Fractional depth doses obtained in the parallel orientation agreed well with ion chamber measurements for the linac beams at depths beyond ion chamber measurements differed by a maximum of 1.6% and 2.6% for the 4 and 18 MV beams, respectively. In the buildup region, an increase in film response was found when compared to the ion chamber measurements for both linac beams. With the beam, the TVS film showed an increase in sensitivity with depth as the proportion of scattered soft x rays increases; the maximum difference between ion chamber and film fractional depth doses was 7.8%. The TVS film demonstrates a substantial improvement over Kodak X‐Omat V film for measuring depth doses in the parallel orientation, for all beams considered. Generally, the results confirm TVS film as an accurate and practical dosimeter for the measurement of dose distributions in high energy photon beams.
Analysis of methods for reducing false positives in the automated detection of clustered microcalcifications in mammograms
Authors: Nagel Rufus H. , Nishikawa Robert M. , Papaioannou John , Doi Kunio
Published: July 2002

Clustered microcalcifications are often the first sign of breast cancer in a mammogram. Nevertheless, all clustered microcalcifications are not found by an individual radiologist reading a mammogram. The use of a second reader may find those clusters of microcalcifications not found by the first reader, thereby improving the sensitivity of detecting clustered microcalcifications. Our laboratory has developed a computerized scheme for the detection of clustered microcalcifications, which can act like a second reader, that is undergoing clinical evaluation. This paper concerns the feature analysis stage of the computer scheme, which is designed to remove some of the false‐computer detections. We have examined three methods of feature analysis, namely, rule based (the method currently used), an artificial neural network (ANN), and a combined method. In an independent database of 50 images, at a sensitivity of 83%, the average number of false positive (FP) detections per image was: 1.9 for rule‐based, 1.6 for ANN, and 0.8 for the combined method. We demonstrate that the combined method performs best because each of the two stages eliminates different types of false positives.
Three‐dimensional reconstruction of cerebral vasculature from limited digital subtraction angiographic projections
Authors: Sen Anindya
Published: July 2002

An integrated approach is developed for three‐dimensional (3D) cone beam reconstruction of cerebral vasculature (both morphology and gray scale) from a limited number (4–6) of digital subtraction angiographic (DSA) projections, obtained using a standard biplane C‐arm x‐ray system, using the Algebraic Reconstruction Technique (ART) with non‐negativity constraint. The accuracy of ART is improved by determining weights based on the intersection volume between a pyramidal ray and cubic voxel. The input data are segmented and corrected for spatial image distortion. The reconstruction (volume ) is accelerated by retaining only the voxels containing vasculature (masking), multiscaling, and partitioning the algorithm to run in parallel. Problems in using ART are evaluated. Limited view reconstruction is demonstrated to be unstable. In addition, errors arising from geometric uncertainty, noise, and partial voluming are assessed with simulations. Corrective measures in reconstructions are described and demonstrated with experimental data. Reconstruction of a phantom containing fiducial markers at known locations demonstrated that the reconstructed geometry is accurate to less than a pixel width (0.23 mm). The reconstruction algorithm with corrective measures is tested using a thin wire phantom, and anatomic skull phantom, a human carotid artery, and human cerebral vasculature with an aneurysm. The use of weight norm cutoff and averaging ART for different terminal conditions is found to be effective. The reconstruction results are also validated with reprojections of the 3D reconstructions.
Monte Carlo dose calculations for a new ovoid shield system for carcinoma of the uterine cervix
Authors: Weeks K. J.
Published: July 2002

The dose distribution for an ovoid with a new tungsten shielding design was determined using Monte Carlo simulation. Standard Cesium‐137 tube sources, tungsten shielding, and aluminum ovoid applicator were each modeled as a collection of solid objects. Dose was calculated in planes above, below, in front of, and on the sides of the colpostat. The Monte Carlo results were compared with the results from a parametrized calculation algorithm and good agreement was obtained. The dose distribution matrix derived from the parametrized algorithm can be used for clinical treatment planning.
A test tool for the visual verification of light and radiation fields using film or an electronic portal imaging device
Authors: Dunscombe Peter , Humphreys Sonja , Leszczynski Konrad
Published: July 2002

We describe the design and evaluation of a simple test tool which can be used in conjunction with either film or an electronic portal imaging device (EPID) to verify light and radiation fields and their congruence. The precision of the technique is better than 0.5 mm under all conditions tested. When used with film the accuracy or offset of the technique (the difference between test tool observations and a scanned conventional film) is better than 0.5 mm but, with an EPID as the image receptor, the accuracy dropped to, in one trial, 0.86 mm. The offset may be due to a systematic observer bias in determining the 50% O.D. level on the image, compounded, in the case of EPID measurements, by image acquisition and display parameters. Thus, when used with an EPID, calibration of the system will be required if absolute field dimensions are required. When used with film, the test tool method described here is of sufficient accuracy and precision to confirm the compliance of light and radiation field parameters with currently accepted quality control protocols.
Optical density dependence on postirradiation temperature and time for MD‐55‐2 type radiochromic film
Authors: Reinstein L. E. , Gluckman G. R.
Published: July 2002

Various forms of GAFChromic film (GC) have been used for several years as radiographic media for measuring dose distributions of brachytherapy sources and small radiation fields. A new double layer film, referred to as MD‐55‐2 is now offered and is useful for clinical dose ranges. In this paper we study the effect of postirradiation storage and the reversible effects of temperature during optical density measurements for this new radiochromic film. The reversible change in optical density measured with a He–Ne laser densitometer (632.8 nm) was found to vary by less than 1% over the range 18–30 °C, but with densitometers whose light source falls on the left‐hand side (i.e., shorter wavelengths) of the GC film's major absorbance peak the dependence was found to be as high as 2%/°C. The rate at which the film darkens irreversibly (postirradiation) was found to depend on the storage temperature. In typical clinical conditions (20–25 °C), the initial rate at which the film darkens can vary by as much as a factor of 1.5. Furthermore, the storage temperature was found to affect the asymptotic value for the optical absorbance. For storage temperatures of 20–35 °C, the limiting values of the absorbance were approximately 4% higher than samples stored at lower temperatures, which had been irradiated to the same dose.
Dosimetric characteristics of a double‐focused miniature multileaf collimator
Authors: Meeks Sanford L. , Bova Francis J. , Kim Siyong , Tomé Wolfgang A. , Buatti John M. , Friedman William A.
Published: July 2002

The dosimetric characteristics of a double‐focused miniature multileaf collimator (mMLC) attached to a Philips SL75/5 linear accelerator (linac) have been investigated. Output factors, percentage depth–dose, penumbra, leaf transmission, and leakage between the leaves were measured for the 6 MV x‐ray beam on this accelerator. Because leakage both through and between the leaves is minimal, the linac jaws can be kept fixed while the mMLC leaf configuration is modified for different aperture shapes. This allows for accurate output prediction using the equivalent square formalism. Percent depth–dose measured for fields defined by the mMLC show little deviation from the percent depth–dose measured for fields defined by the machine jaws or Lipowitz metal blocks. Because the mMLC matches beam divergence in both directions, allows minimal beam transmission, and has a large source‐to‐collimator distance, the penumbra is sharper for fields defined by the mMLC than for fields defined by the linac jaws or Lipowitz metal blocks. Based on these data, dose calculations for mMLC‐defined fields can be applied with no change in procedures from those used for fields defined using conventional methods.
Monte Carlo modeling of the transverse‐axis dose distribution of the Model 200 interstitial brachytherapy source
Authors: Williamson Jeffrey F.
Published: July 2002

This study presents the first theoretical analysis of the absolute dose‐rate distribution about the Model 200 interstitial brachytherapy source. Monte Carlo photon‐transport (MCPT) simulation techniques have been used to evaluate the transverse‐axis dose‐rate distribution of the Model 200 source as a function of thickness of the Pd metal coating (containing the plated onto the surfaces of right cylindrical graphite pellets contained within the seed. The dose‐rate constant, Λ, was realistically estimated by simulating the wide‐angle, free‐air chamber (WAFAC) calibration geometry. The WAFAC is the experimental realization of NIST's (National Institute of Standards and Technology) recently implemented primary standard of air‐kerma strength Our results show that polar angle‐ and distance‐dependent oblique filtration and shielding effects induce significant and unexpected photon fluence anisotropy near the transverse‐axis and inverse square law deviations at typical calibration distances. Any source consisting of radioactivity deposited on a highly attenuating surface with sharp edges may exhibit such effects. In the case of the Model 200 seed, the Pd metal thickness does not significantly influence the relative dose distribution in water at distances less than 5 cm, but does make Λ sensitive to the measurement geometry. Fortunately, the WAFAC averages fluence over a sufficiently large aperture that the resultant Λ, 0.68±0.02 cGy⋅h−1⋅U−1, is almost independent of Pd metal layer thickness and in close agreement with recent measurements and calculations. This value is 20% higher than that of the renormalized Task Group 43 Λ value.
Monte Carlo‐aided dosimetry of the symmetra model I25.S06 interstitial brachytherapy seed
Authors: Hedtjärn Håkan , Carlsson Gudrun Alm , Williamson Jeffrey F.
Published: July 2002

A dosimetric study of a new seed for permanent prostate implant, the Symmetra Seed model I25.S06, has been undertaken utilizing Monte Carlo photon transport calculations. All dosimetric quantities recommended by the AAPM Task Group 43 (TG‐43) report have been calculated. Quantities determined are dose rate constant, radial dose function, anisotropy function, anisotropy factor, and anisotropy constant. The recently (January 1999) revised NIST (National Institute of Standards and Technology) standard for air kerma strength calibration was taken into account as well as updated interaction cross‐section data. Calculations were done for the competing model 6702 source for the purpose of comparison. The calculated dose‐rate constants for the two seeds are 1.010 and 1.016 cGyh−1U−1 for the Symmetra and model 6702 seeds, respectively. The latter value deviates from the value, 1.039 cGyh−1U−1, recommended in the TG‐43 report. The calculated radial dose function for the Symmetra new seed is more penetrating than that of the model 6711 seed (by 20% at 5 cm distance) but agrees closely (within statistical errors) with that of the model 6702 seed up to distances of 10 cm. The anisotropy function for the seed is also close to that for the 6702 seed with a tendency of somewhat more pronounced anisotropy (lower values at small angles from the longitudinal axis). Compared to the model 6711 seed, the Symmetra new seed is more isotropic. The anisotropy constants (the anisotropy function averaged with respect to angle and distance) for the three seed models are within 2%.
Electric field outside a parallel plate capacitor
Authors: Parker G. W.
Published: July 2002

The problem of determining the electrostatic potential and field outside a parallel plate capacitor is reduced, using symmetry, to a standard boundary value problem in the half space z⩾0. In the limit that the gap d between plates approaches zero, the potential outside the plates is given as an integral over the surface of one plate. This integral is evaluated for several special cases. The magnitude of the field just outside and near the center of a two-dimensional strip capacitor of width W is shown to agree with finite difference calculations when W/d>4. The shapes of field lines outside a strip capacitor are determined, and circular lines are shown to occur near the edges. The determination of the electric field just outside and near the center of a parallel plate capacitor complements the recently published result for the magnetic field just outside and near the center of a long solenoid [J. A. Farley and R. H. Price, Am. J. Phys. 69, 751–754 (2001)].
Masking in three pinnipeds: Underwater, low-frequency critical ratios
Authors: Southall Brandon L. , Schusterman Ronald J. , Kastak David
Published: July 2002

Behavioral techniques were used to determine underwater masked hearing thresholds for a northern elephant seal (Mirounga angustirostris), a harbor seal (Phoca vitulina), and a California sea lion (Zalophus californianus). Octave-band white noise maskers were centered at five test frequencies ranging from 200 to 2500 Hz; a slightly wider noise band was used for testing at 100 Hz. Critical ratios were calculated at one masking noise level for each test frequency. Above 200 Hz, critical ratios increased with frequency. This pattern is similar to that observed in most animals tested, and indicates that these pinnipeds lack specializations for detecting low-frequency tonal sounds in noise. However, the individual pinnipeds in this study, particularly the northern elephant seal, detected signals at relatively low signal-to-noise ratios. These results provide a means of estimating zones of auditory masking for pinnipeds exposed to anthropogenic noise sources.
Acoustic measurements of boundary layer flow and sediment flux
Authors: Thorne Peter D. , Taylor Jon
Published: July 2002

Results are reported on an assessment of the application of coherent Doppler and cross-correlation techniques to measure nearbed boundary layer flow. The approaches use acoustic backscattering from sediments entrained into the water column from the bed, to obtain high-resolution profiles of the nearbed hydrodynamics. Measurements are presented from a wave tunnel experiment in which sediment was entrained by unidirectional, oscillatory, and combined flows. The data collected have been used to evaluate the capability of the two flow techniques to measure boundary layer mean, turbulent, and intrawave velocity profiles. Further, the backscattered signal has been used to measure suspended sediment concentration profiles, which have been combined with the velocity profiles to obtain high-resolution measurements of boundary layer sediment flux.
Tomographic inversion of geoacoustic properties in a range-dependent shallow-water environment
Authors: Pignot Patrick , Chapman N. Ross
Published: July 2002

This paper presents a matched-field tomographic method to estimate the geoacoustic properties of the ocean bottom for a range-dependent medium in shallow water. The inversion method has been developed in order to interpret experimental data from the Haro Strait PRIMER sea trial. This experiment was carried out in June ’96 and used low-frequency broadband signals that were received on three vertical line arrays. Inversion of the data is particularly difficult because of the complex bathymetry of the Haro Strait experimental site. For this inversion, a range-dependent ray code was developed to solve the forward problem, allowing an arbitrarily layered bottom environment. The inversion scheme is based on modeling the propagation time and the amplitude of the recorded data, and a simple new cost function is proposed. The signal ray paths are identified automatically using a simple process that compares calculated and measured travel times. Data from multiple source positions are used to invert the range dependence of the geoacoustic model. The environment is separated into segments, and within each segment the inversion is carried out layer by layer for a multilayer geoacoustic model. Starting with the topmost layer, the range-dependent thickness and sound speed are estimated via a Monte Carlo method. Inversion results are presented for synthetic and experimental data from the Haro Strait sea trial.
Comment on Apfel’s second comment
Authors: Frizzell Leon A. , Kramer Jeffery M. , Zachary James F. , O’Brien William D.
Published: July 2002

This is a comment to the preceding letter [R. E. Apfel, J. Acoust. Soc. Am. 110, 1740 (2001)].
Inversion of elastic waveform data in anisotropic solids using the delta-function representation of the Green’s function
Authors: Tewary V. K.
Published: July 2002

A method for inversion of measured data on elastic waveforms in anisotropic solids is proposed, using the delta-function representation of the Green’s function. The method requires integration over a closed 2-D (two-dimensional) space. In contrast, inversion using the traditional Fourier representation requires integration over an infinite 4-D space. The method can be used to determine the Green’s function for imaging applications and elastic constants for materials characterization. The method is illustrated by applying it to determine all six elastic constants of a model graphite fiber composite assuming a tetragonal structure and using simulated data.
A common origin for vocal accuracy and melodic expectancy: Vocal constraints
Authors: Russo Frank A. , Cuddy Lola L.
Published: July 2002

Participants were assigned to one of four groups (no music training, instrumental training, vocal training, and semiprofessional vocalists). Participants were asked to sing 16 three-note melodic sequences previously calibrated by listeners for the degree to which the third note fulfilled the perceptual expectancy established by the first two notes [L. L. Cuddy and C. A. Lunney, Percept. Psychophys. 57, 451–462 (1995)]. The current study assessed the sung accuracy of the entire three-note sequence with three measures (F0 tracking, expert judgment, and self-judgment). All measures revealed that, on average, semiprofessionals were most accurate and musically untrained participants the least accurate. The pattern of accuracy across the 16 sequences, however, was consistent across all groups; intersubject correlations were generally high and significant. Moreover, accuracy measures obtained from each group corresponded to the degree of fulfillment of perceptual expectancy. Two possible accounts of the findings are discussed. Vocal accuracy may reflect perceptual expectancy. Alternatively, vocal accuracy and perceptual expectancy may both reflect a common origin, that of vocal constraints. The latter account has been articulated as the motor theory of melodic perception [F. A. Russo and L. L. Cuddy, Conf. Musical Cognition & Behavior, Rome (1998)].