bluuebunny/crossref_metadata_2025 huggingface dataset:
Homology modeling, model and software evaluation: three related resources.
Authors: Rodriguez R , Chinea G , Lopez N , Pons T , Vriend G
Published: July 2002

MOTIVATION: Homology modeling is rapidly becoming the method of choice for obtaining three-dimensional coordinates for proteins because genome projects produce sequences at a much higher rate than NMR and X-ray laboratories can solve the three-dimensional structures. The quality of protein models will not be immediately clear to novices and support with the evaluation seems to be needed. Expert users are sometimes interested in evaluating the quality of modeling programs rather than the quality of the models themselves. RESULTS: Three servers have been made available to the scientific community: a homology modeling server, a model quality evaluation server and a server that evaluates models built of proteins for which the structure is already known, thereby implicitly evaluating the quality of the modeling program. AVAILABILITY: The modeling-related servers and several structure analysis servers are freely available at http://swift.embl-heidelberg.de/servers/ CONTACT: gert.vriend@embl-heidelberg.de
Decoding apparatus for eukaryotic selenocysteine insertion
Authors: Tujebajeva Rosa M , Copeland Paul R , Xu Xue‐Ming , Carlson Bradley A , Harney John W , Driscoll Donna M , Hatfield Dolph L , Berry Marla J
Published: July 2002

Decoding UGA as selenocysteine requires a unique tRNA, a specialized elongation factor, and specific secondary structures in the mRNA, termed SECIS elements. Eukaryotic SECIS elements are found in the 3′ untranslated region of selenoprotein mRNAs while those in prokaryotes occur immediately downstream of UGA. Consequently, a single eukaryotic SECIS element can serve multiple UGA codons, whereas prokaryotic SECIS elements only function for the adjacent UGA, suggesting distinct mechanisms for recoding in the two kingdoms. We have identified and characterized the first eukaryotic selenocysteyl‐tRNA‐specific elongation factor. This factor forms a complex with mammalian SECIS binding protein 2, and these two components function together in selenocysteine incorporation in mammalian cells. Expression of the two functional domains of the bacterial elongation factor–SECIS binding protein as two separate proteins in eukaryotes suggests a mechanism for rapid exchange of charged for uncharged selenocysteyl‐tRNA–elongation factor complex, allowing a single SECIS element to serve multiple UGA codons.
Non‐specific activation of the epithelial sodium channel by the CFTR chloride channel
Authors: Nagel Georg , Szellas Tanjef , Riordan John R , Friedrich Thomas , Hartung Klaus
Published: July 2002

The genetic disease cystic fibrosis is caused by mutation of the gene coding for the cystic fibrosis transmembrane conductance regulator (CFTR). Controversial studies reported regulation of the epithelial sodium channel (ENaC) by CFTR. We found that uptake of 22Na+ through ENaC is modulated by activation of CFTR in oocytes, coexpressing CFTR and ENaC, depending on extracellular chloride concentration. Furthermore we found that the effect of CFTR activation could be mimicked by other chloride channels. Voltage– and patch–clamp measurements, however, showed neither stimulation nor inhibition of ENaC‐mediated conductance by activated CFTR. We conclude that the observed modulation of 22Na+ uptake by activated CFTR is due to the effect of CFTR‐mediated chloride conductance on the membrane potential. These findings argue against the notion of a specific influence of CFTR on ENaC and emphasize the chloride channel function of CFTR.
SEK‐1 MAPKK mediates Ca2+ signaling to determine neuronal asymmetric development in Caenorhabditis elegans
Authors: Tanaka‐Hino Miho , Sagasti Alvaro , Hisamoto Naoki , Kawasaki Masato , Nakano Shunji , Ninomiya‐Tsuji Jun , Bargmann Cornelia I , Matsumoto Kunihiro
Published: July 2002

The mitogen‐activated protein kinase (MAPK) pathway is a highly conserved signaling cascade that converts extracellular signals into various outputs. In Caenorhabditis elegans, asymmetric expression of the candidate odorant receptor STR‐2 in either the left or the right of two bilaterally symmetrical olfactory AWC neurons is regulated by axon contact and Ca2+ signaling. We show that the MAPK kinase (MAPKK) SEK‐1 is required for asymmetric expression in AWC neurons. Genetic and biochemical analyses reveal that SEK‐1 functions in a pathway downstream of UNC‐43 and NSY‐1, Ca2+/calmodulin‐dependent protein kinase II (CaMKII) and MAPK kinase kinase (MAPKKK), respectively. Thus, the NSY‐1–SEK‐1–MAPK cascade is activated by Ca2+ signaling through CaMKII and establishes asymmetric cell fate decision during neuronal development.
The Money Pitt: Lord Londonderry and the South Sea Bubble; or, How to Manage Risk in an Emerging Market
Authors: Neal Larry
Published: July 2002

Business history forces historians and economists to take a wider view of individuals' actions as economic agents. The risk-managing strategies of Lord Londonderry (also known as “the Money Pitt”) during the financial boom and bust of the South Sea Bubble illustrate this theme well. He dealt in staggering sums for the time but hedged his bets along at least three dimensions: the pecuniary, the personal, and the political. His skills, however, remain unappreciated because he could not manage the ultimate uncertainty always present in human affairs—when will fate bring down the final curtain on one's partners, family and friends, patrons, or one's own person?
The neural correlates of consciousness: an analysis of cognitive skill learning
Authors:   The American Association for Research into Nervous and Mental Diseases, Raichle M. E.
Published: July 2002

This paper presents a functional brain–imaging strategy designed to isolate neural correlates of consciousness in humans. This strategy is based on skill learning. In the example presented (rapidly generating verbs for visually presented nouns), a cognitive skill is examined before and after practice. As shown, there are marked qualitative differences in the neural circuitry supporting performance of this task in the naive and practised state that include, importantly, both increases and decreases from the baseline activity of the brain.
The terminology problem for T cells: a discussion paper
Authors: Doherty Peter C.
Published: July 2002

The school of thought that owes allegiance to Ludwig Wittgenstein teaches that language conditions perceptions. When we use the term ‘cytotoxic T lymphocyte’ or ‘helper Tcell’ we tend to orientate our own thinking processes, and those of listeners or readers, down particular paths. Part of the problem is that we are often describing cell populations by functions that may either be a property of only a proportion of those that are being assayed, or are simply inferred from the expression of various cell–surface markers. The consequence can be a measure of confusion that might be avoided if we could communicate with greater clarity. Is it possible to achieve a better terminology that will be accepted generally? The following are some examples of why there may be some value in thinking about this.
Cooperation between C/EBPα TBP/TFIIB and SWI/SNF recruiting domains is required for adipocyte differentiation
Authors: Pedersen Thomas Åskov , Kowenz-Leutz Elisabeth , Leutz Achim , Nerlov Claus
Published: July 2002

Chromatin remodeling is an important step in promoter activation during cellular lineage commitment and differentiation. We show that the ability of the C/EBPα transcription factor to direct adipocyte differentiation of uncommitted fibroblast precursors and to activate SWI/SNF-dependent myeloid-specific genes depends on a domain, C/EBPα transactivation element III (TE-III), that binds the SWI/SNF chromatin remodeling complex. TE-III collaborates with C/EBPα TBP/TFIIB interaction motifs during induction of adipogenesis and adipocyte-specific gene expression. These results indicate that C/EBPα acts as a lineage-instructive transcription factor through SWI/SNF-dependent modification of the chromatin structure of lineage-specific genes, followed by direct promoter activation via recruitment of the basal transcription–initiation complex, and provide a mechanism by which C/EBPα can mediate differentiation along multiple cellular lineages.
Analysis of serine proteinase–inhibitor interaction by alanine shaving
Authors: Buczek Olga , Koscielska‐Kasprzak Katarzyna , Krowarsch Daniel , Dadlez Michał , Otlewski Jacek
Published: July 2002

We analyzed the energetic importance of residues surrounding the hot spot (the P1 position) of bovine pancreatic trypsin inhibitor (BPTI) in interaction with two proteinases, trypsin and chymotrypsin, by a procedure called molecular shaving. One to eight residues of the structural epitope, composed of two extended and exposed loops, were mutated to alanine(s). Although truncation of the side chains of residues surrounding the P1 position to methyl groups caused a decrease in ΔGden values up to 6.4 kcal mole−1, it did not influence the overall conformation of the inhibitor. We found that the replacement of up to six residues with alanines was fully additive at the level of protein stability. To analyze the influence of the structural epitope on the association energy, we determined association constants for BPTI variants and both enzymes and applied the additivity analysis. Shaving of two binding loops led to a progressive drop in the association energy, more pronounced for trypsin (decrease up to 9.6 kcal mole−1) than chymotrypsin (decrease up to 3.5 kcal mole−1). In the case of extensively mutated variants interacting with chymotrypsin, the association energies agreed very well with the values calculated from single mutational effects. However, when P1‐neighboring residues were shaved to alanine(s), their contribution to the association energy was not fully removed because of the presence of methyl groups and main chain–main chain intermolecular hydrogen bonds. Moreover, the hot spot had a different contribution to the complex stability in the fully shaved BPTI variant compared with the wild type, which was caused by perturbations of the P1–S1 electrostatic interaction.
The sequence determinants of cadherin molecules
Authors: Kister Alexander E. , Roytberg Michael A , Chothia Cyrus , Vasiliev Jurii M. , Gelfand Israel M.
Published: July 2002

The sequence and structural analysis of cadherins allow us to find sequence determinants—a few positions in sequences whose residues are characteristic and specific for the structures of a given family. Comparison of the five extracellular domains of classic cadherins showed that they share the same sequence determinants despite only a nonsignificant sequence similarity between the N‐terminal domain and other extracellular domains. This allowed us to predict secondary structures and propose three‐dimensional structures for these domains that have not been structurally analyzed previously. A new method of assigning a sequence to its proper protein family is suggested: analysis of sequence determinants. The main advantage of this method is that it is not necessary to know all or almost all residues in a sequence as required for other traditional classification tools such as BLAST, FASTA, and HMM. Using the key positions only, that is, residues that serve as the sequence determinants, we found that all members of the classic cadherin family were unequivocally selected from among 80,000 examined proteins. In addition, we proposed a model for the secondary structure of the cytoplasmic domain of cadherins based on the principal relations between sequences and secondary structure multialignments. The patterns of the secondary structure of this domain can serve as the distinguishing characteristics of cadherins.
Variability and accuracy of measurements of prostate brachytherapy seed position in vitro using three‐dimensional ultrasound: An intra‐ and inter‐observer study
Authors: Blake C. C. , Elliot T. L. , Slomka P. J. , Downey D. B. , Fenster A.
Published: July 2002

This paper is a step in investigating whether three‐dimensional (3D) ultrasound can be used intra‐operatively to replace Computed Tomography (CT) for localization of brachytherapy seeds. In order to quantify the accuracy and variability of seed localization without introducing effects due to tissues, we first report our results with test phantoms. An inter‐ and intra‐observer study was performed to assess the variability of 2 3D ultrasound scan acquisition methods: Tilt 3D scanning and pull‐back 3D scanning. Seven observers measured the positions of gold seed markers in an agar phantom twice in each of the three orthogonal image planes. An analysis of variance (ANOVA) was performed to determine the intra‐ and inter‐observer standard errors of measurement (SEM) and the minimum detectable changes in marker position Average intra‐ and inter‐observer SEMs for the tilt scan 3D image were 0.36 and 0.40 mm, respectively. Measurements of the pull‐back scan 3D image yielded average intra‐ and inter‐observer SEM of 0.46 and 0.49 mm, respectively. A paired difference analysis showed that the lower SEM for the tilt 3D scan image were statistically significant at a significance level of The accuracy of the US measurements was tested by determining marker coordinates from CT images of the phantom in a stereotactic head frame. CT coordinates were matched to the ultrasound (US) coordinates by means of an affine transform. Average matching errors in x, y, and z were 0.02, 0.10, and −0.02 mm, respectively.
Dosimetric effects of contrast media for catheter‐based intravascular brachytherapy
Authors: Li X. Allen
Published: July 2002

The purpose of this work is to calculate the dose perturbations due to the presence of iodine contrast media in catheter‐based intravascular brachytherapy (IVBT). The EGSnrc Monte Carlo system was used to perform the calculation for the two most commonly used β and γ sources and as well as for a variety of monoenergetic photon and electron sources. Various contrast media with cylindrical‐shell shapes were considered. The dose perturbations due to the presence of iodine contrast media were found to be significant for IVBT. In the region outside of the contrast media (usually the treatment target region for IVBT), the dose is generally increased for the γ source, while it is decreased for the β source. In the presence of a 1.0‐mm‐thick common clinical contrast medium, the dose enhancement can be as high as 30% for the source, while the dose can be reduced by up to 25% for the source. The dose enhancement region for the γ source extends approximately 1.0 mm away from the contrast medium, while the dose reduction for the β source affects the entire target region. The dose perturbation depends on (1) the volume (thickness) of the contrast medium, (2) the iodine concentration in contrast media, and (3) the type and energy of radioactive source. The dose effects due to the contrast medium as well as the differences between β and γ sources, revealed in this study, should be recognized and may be considered in the dose prescription for intravascular brachytherapy. These effects should also be taken into account in analyzing the treatment outcome for those IVBT clinical trials involving a contrast medium.
An iterative EPID calibration procedure for dosimetric verification that considers the EPID scattering factor
Authors: Chang Jenghwa , Mageras Gikas S. , Ling Clifton C. , Lutz Wendell
Published: July 2002

There has been an increasing interest in the application of electronic portal imaging devices (EPIDs) to dosimetric verification, particularly for intensity modulated radiotherapy. Although not water equivalent, the phantom scatter factor of an EPID, is generally assumed to be that of a full phantom, a slab phantom, or a mini phantom. This assumption may introduce errors in absolute dosimetry using EPIDs. A calibration procedure that iteratively updates and the calibration curve (pixel value to dose rate) is presented. The EPID (Varian Portal Vision) is irradiated using a field with different beam intensities. The initial guess of dose rates in the EPID is calculated from ionization chamber measurements in air, multiplied by or The calibration curve is obtained by fitting EPID readings from pixels near the beam central axis and dose rates in EPID to a quadratic equation. The is obtained from EPID measurements in and field and from the calibration curve, and is in turn used to adjust the dose rate measurements and hence the calibration curve. The above procedure is repeated until it converges. The final calibration curve is used to convert portal dose to dose in the slab phantom, using the calibrated or assuming or The converted doses are then compared with the dose measured using an ionization chamber. We also apply this procedure to off‐axis points and study its dependence on the energy spectrum. The hypothesis testing results (on the 95% significance level) indicate that systematic errors are introduced when assuming or and the dose calculated using is more consistent with ionization chamber measurements. Differences between and are as large as 2% for large field sizes. The measured relative dose profile at using the EPID agrees well with the measured profile at of the isocentric plane using film in a polystyrene phantom with full buildup and full backup, for open and wedged fields, and for a broad range of field sizes of interest. The dependence of the EPID response on the energy spectrum is removed once the calibration is performed under the same conditions as the actual measurements.
Accelerator‐based neutron brachytherapy
Authors: Song Haijun , Yanch Jacquelyn C. , Klinkowstein Robert E.
Published: July 2002

The development and evaluation of a new approach to neutron brachytherapy is described. This approach, accelerator‐based fast neutron brachytherapy, involves the interstitial or intracavity insertion of a narrow, evacuated accelerator beam tube such that its tip, containing the neutron‐producing target, is placed in or near the tumor. Tumor irradiation via brachytherapy should result in a reduction in the healthy tissue complication rate observed when poorly collimated and/or low energy external neutron beam are used for treatment. Use of a variable energy accelerator provides an advantage over isotope sources for neutron brachytherapy in that the neutron beam can be turned on and off and the neutron energy spectrum varied for different treatment applications. A prototype accelerator‐based fast neutron brachytherapy device, 10 cm long and 6 mm outer diameter, has been constructed and evaluated in terms of its dosimetric output, treatment time, and practical feasibility. The prototype device is a tube‐in‐tube design with cooling water running between the inner and outer tubes to cool a beryllium target located at the tip of the inner tube. Cooling experiments were performed and coupled with Monte Carlo simulations to determine treatment times as a function of heat load for various neutron‐producing reactions. Using the reaction at MeV, 66 RBE‐Gy (12 Gy physical dose) can be delivered to the boundary of a 4.5‐cm‐diam treatment volume in 8 min at a heat load of 130 W. Other reactions offer similar treatment times at somewhat higher bombarding energies and also show higher potential for dose enhancement with the boron‐10 neutron capture reaction due to their softer neutron spectra. Dose distributions in a water phantom were measured with the prototype brachytherapy tube using the dual‐ion chamber technique for the reaction at MeV. The measurements and simulations agree within uncertainties and demonstrate that fast neutrons contribute more than 90% of the dose to the target volume.
Effect of multileaf collimator leaf width on physical dose distributions in the treatment of CNS and head and neck neoplasms with intensity modulated radiation therapy
Authors: Fiveash J. B. , Murshed H. , Duan J. , Hyatt M. , Caranto J. , Bonner J. A. , Popple R. A.
Published: July 2002

The purpose of this work is to examine physical radiation dose differences between two multileaf collimator (MLC) leaf widths (5 and 10 mm) in the treatment of CNS and head and neck neoplasms with intensity modulated radiation therapy (IMRT). Three clinical patients with CNS tumors were planned with two different MLC leaf sizes, 5 and 10 mm, representing Varian‐120 and Varian‐80 Millennium multileaf collimators, respectively. Two sets of IMRT treatment plans were developed. The goal of the first set was radiation dose conformality in three dimensions. The goal for the second set was organ avoidance of a nearby critical structure while maintaining adequate coverage of the target volume. Treatment planning utilized the CadPlan/Helios system (Varian Medical Systems, Milpitas CA) for dynamic MLC treatment delivery. All beam parameters and optimization (cost function) parameters were identical for the 5 and 10 mm plans. For all cases the number of beams, gantry positions, and table positions were taken from clinically treated three‐dimensional conformal radiotherapy plans. Conformality was measured by the ratio of the planning isodose volume to the target volume. Organ avoidance was measured by the volume of the critical structure receiving greater than 90% of the prescription dose For three patients with squamous cell carcinoma of the head and neck (T2‐T4 N0‐N2c M0) 5 and 10 mm leaf widths were compared for parotid preservation utilizing nine coplanar equally spaced beams delivering a simultaneous integrated boost. Because modest differences in physical dose to the parotid were detected, a NTCP model based upon the clinical parameters of Eisbruch et al. was then used for comparisons. The conformality improved in all three CNS cases for the 5 mm plans compared to the 10 mm plans. For the organ avoidance plans, also improved in two of the three cases when the 5 mm leaf width was utilized for IMRT treatment delivery. In the third case, both the 5 and 10 mm plans were able to spare the critical structure with none of the structure receiving more than 90% of the prescription dose, but in the moderate dose range, less dose was delivered to the critical structure with the 5 mm plan. For the head and neck cases both the 5 and beamlets dMLC sliding window techniques spared the contralateral parotid gland while maintaining target volume coverage. The mean parotid dose was modestly lower with the smaller beamlet size (21.04 Gy vs 22.36 Gy). The resulting average NTCP values were 13.72% for 10 mm dMLC and 8.24% for 5 mm dMLC. In conclusion, five mm leaf width results in an improvement in physical dose distribution over 10 mm leaf width that may be clinically relevant in some cases. These differences may be most pronounced for single fraction radiosurgery or in cases where the tolerance of the sensitive organ is less than or close to the target volume prescription.
Digital radiology using active matrix readout of amorphous selenium: Theoretical analysis of detective quantum efficiency
Authors: Zhao Wei , Rowlands J. A.
Published: July 2002

A flat‐panel x‐ray imaging detector using a layer of amorphous selenium (‐Se) for direct conversion of x rays (to charge) and an active matrix for self‐scanned readout is being investigated for digital radiology. A theoretical analysis of the spatial frequency dependent detective quantum efficiency of the self‐scanned ‐Se detector is performed based on a model of signal and noise propagation in a cascaded imaging system. Because of the high intrinsic resolution of ‐Se and the pixelated active matrix readout method, such detectors are inherently undersampled and aliasing is present. The presampling modulation transfer function (MTF) and aliased noise power spectrum (NPS) of the detector were used in the analysis of It is proven that the aliased NPS for the self‐scanned ‐Se detectors is white. Since the shape of is determined by the ratio of MTF squared and the NPS, the shape of follows the square of the presampling MTF of the detector as a result of the white NPS. The analysis also shows that DQE(0) is proportional to the pixel fill factor, i.e., the fraction of each pixel area used for image charge collection. The DQE analysis is applied to detector parameters for three x‐ray imaging applications: mammography, chest radiography, and fluoroscopy. The effects of pixel fill factor, imaging geometry (i.e., incident angle of x rays), and various sources of electronic noise on the detector are discussed. Strategies for maximizing detector DQE for each x‐ray imaging application are proposed.
TG‐21 versus TG‐25: A comparison for electrons
Authors: Followill David S. , Davis Denise S. , Hanson William F.
Published: July 2002

Since 1984, the Radiological Physics Center (RPC) has used the American Association of Physicists in Medicine Task Group 21 (TG‐21) protocol (absorbed dose determination) as the basis of its On‐site Dosimetry Review visits to institutions participating in the National Cancer Institute's cooperative clinical trials. Subsequent to the TG‐21 protocol, the Task Group 25 (TG‐25) report on electron‐beam dosimetry was published. The TG‐25 report was not intended to supercede the TG‐21 protocol, but to supplement it for depths other than However, both reports included measurement techniques and data regarding the calibration of electron beams. TG‐25 was not intended for absolute calibrations made clear by the fact that it does not present all of the data required for plastic phantom calibrations, i.e., unrestricted stopping power ratios. As a result, some confusion has arisen at various institutions as to which protocol should be used for machine calibration. In this study, possible discrepancies that arise when using TG‐21, a version of TG‐21 modified by the RPC, and TG‐25 are compared. The differences in the results are calculated as a function of energy (6 and 20 MeV), chamber type (cylindrical or parallel plate), and the type of phantom material (water, polystyrene, or acrylic). The largest discrepancies noted were between TG‐25 and the two TG‐21 methods for low‐energy electrons in either water or polystyrene. The mean difference for all conditions was 0.8% with a maximum value of 3.3% in polystyrene. The definition of the effective point of measurement; determination of the mean nominal incident energy mean energy at depth and most probable energy at the surface for each protocol, and subsequent stopping power ratio, chamber replacement factor, and electron fluence correction factor are the major contributors to the calculated differences.
Physical imaging performance of a compact computed radiography acquisition device
Authors: Kengyelics S. M. , Launders J. H. , Cowen A. R.
Published: July 2002

A comprehensive investigation of the physical imaging performance of a Philips AC3 computed radiography system using fifth‐generation image plate technology has been undertaken. Measurements include characteristic response, modulation transfer function (MTF) and Wiener spectra (WS) for standard and high resolution image plates sampled at 10 pixels/mm. These results were used to calculate noise equivalent quanta (NEQ) and detective quantum efficiency (DQE) spectral descriptions of system performance. Luminescence noise and x‐ray quantum noise components were separated. From an estimate of the luminescence noise power, the average system gain was calculated and results show a substantial improvement over earlier generations of computed radiography systems for standard image plates.
Portal dose image (PDI) prediction for dosimetric treatment verification in radiotherapy. I. An algorithm for open beams
Authors: Pasma K. L. , Heijmen B. J. M. , Kroonwijk M. , Visser A. G.
Published: July 2002

A method is presented for calculation of transmission functions for high energy photon beams through patients. These functions are being used in our clinic for prediction of portal dose images (PDIs) which are compared with PDIs measured with an electronic portal imaging device (EPID). The calculations are based on the planning CT‐scan of the patient and on the irradiation geometry as determined in the treatment planning process. For each beam quality, the required input data for the algorithm for transmission prediction are derived from a limited number of measured beam data. The method has been tested for a PDI‐plane at 160 cm from the focus, in agreement with the fixed focus‐to‐detector distance of our fluoroscopic EPIDs. For 6, 23 and 25 MV photon beams good agreement (∼1%) has been found between calculated and measured transmissions through anthropomorphic phantoms.
Attenuation correction for a combined 3D PET/CT scanner
Authors: Kinahan P. E. , Townsend D. W. , Beyer T. , Sashin D.
Published: July 2002

In this work we demonstrate the proof of principle of CT‐based attenuation correction of 3D positron emission tomography (PET) data by using scans of bone and soft tissue equivalent phantoms and scans of humans. This method of attenuation correction is intended for use in a single scanner that combines volume‐imaging (3D) PET with x‐ray computed tomography (CT) for the purpose of providing accurately registered anatomical localization of structures seen in the PET image. The goal of this work is to determine if we can perform attenuation correction of the PET emission data using accurately aligned CT attenuation information. We discuss possible methods of calculating the PET attenuation map at 511 keV based on CT transmission information acquired from 40 keV through 140 keV. Data were acquired on separate CT and PET scanners and were aligned using standard image registration procedures. Results are presented on three of the attenuation calculation methods: segmentation, scaling, and our proposed hybrid segmentation/scaling method. The results are compared with those using the standard 3D PET attenuation correction method as a gold standard. We demonstrate the efficacy of our proposed hybrid method for converting the CT attenuation map from an effective CT photon energy of 70 keV to the PET photon energy of 511 keV. We conclude that using CT information is a feasible way to obtain attenuation correction factors for 3D PET.
Monte Carlo method to study the proton fluence for treatment planning
Authors: Paganetti Harald
Published: July 2002

The proton beam at the Hahn Meitner Institute (HMI) in Berlin will be used for proton therapy of eye melanoma in the near future. As part of the pre‐therapeutic studies, Monte Carlo calculations have been performed to investigate the primary fluence distribution of the proton beam including the influence of scattering foils, range shifters, modulator wheels, and collimators. Any material in the beam path will modify the therapeutic beam because of energy loss, multiple scattering, range straggling, and nuclear reactions. The primary fluence information is a pre‐requisite for most pencil‐beam treatment planning algorithms. The measured beam penumbra has been used as one of the parameters to characterize a proton beam for further calculations in a treatment planning algorithm. However, this phenomenological quantity represents only indirect information about the properties of the proton beam. In this work, an alternative parameterization of the beam exiting the vacuum window of the accelerator, as well as the beam right in front of the patient collimator, is introduced. A beam is fully characterized if one knows (for instance from Monte Carlo simulations) the particle distribution in energy, position, and angle, i.e., the phase space distribution. Therefore, parameters derived from this distribution can provide an alternative input in treatment planning algorithms. In addition, the method of calculation is introduced as a tool to investigate the influence of modifications in the beam delivery system on the behavior of the therapeutic proton beam.
Optical density changes of Gafchromic MD‐55 film resulting from laser light exposure at wavelengths of 671 nm and 633 nm
Authors: Sullivan Paul R. , Hasson Brian F. , Grossman Carl H. , Simpson Larry D.
Published: July 2002

Laser‐based scanners provide a sensitive means for measuring optical density (OD) of Gafchromic films. Such instruments were reviewed in a recent AAPM report (task group 55) which provided recommendations and information on OD measurements (effect of wavelength, temperature, etc.). The present article reports that variable rate scanners and spot densitometers using laser diodes (671 nm) and HeNe lasers (633 nm) can cause polymerization of Gafchromic film. The light induced polymerization depends on light power, wavelength, beam spot size, dwell time, and prior radiation dose of the film. Measurements were made with a custom built scanner that provided accurate control of light power, light polarization, dwell time, and film position in relation to the beam focus. The results demonstrate that lasers operating with powers of 0.1, 0.5, 1.0, and 1.5 mW produce a nonlinear increase in OD of Gafchromic film. The measured change in OD after 1 min of exposure ranges from 0.150 to 0.244 for a laser diode operating at 0.5 and 1.5 mW, respectively. Tables are included that tabulate the increase in OD for laser power, dwell time, and prior dose. Laser light induced polymerization can have a significant impact on dosimetry measurements acquired using these laser‐based systems.
Surface acoustic impedance and causality
Authors: Berthelot Yves H.
Published: July 2002

Several models that are commonly used to calculate the surface acoustic impedance of porous materials are examined in light of the causality requirement in its nonlocal and its approximate local forms. Strict (nonlocal) causality requires that the imaginary part of the surface acoustic impedance be the Hilbert transform of the real part. It is found that the local approximation is not a good test of causality for these models and that, even in its general form, the equation describing the surface acoustic impedance of these porous materials is not strictly causal at high frequencies.
Numerical model for nonlinear standing waves and weak shocks in thermoviscous fluids
Authors: Vanhille Christian , Campos-Pozuelo Cleofé
Published: July 2002

Nonlinear standing waves in a one-dimensional tube are studied numerically by using a finite-difference algorithm. The numerical code models the acoustic field in resonators for homogeneous, thermoviscous fluids. Calculations are performed exclusively in the time domain, and all harmonic components are obtained by one resolution. The fully nonlinear differential equation is written in Lagrangian coordinates. It is solved without truncation. Effects of absorption are included. Displacement and pressure wave forms are calculated at different locations and results are shown for different excitation levels and tube lengths. Amplitude distributions along the resonator axis for every harmonic component are also evaluated. Simulations are performed for amplitudes ranging from linear to strongly nonlinear and weak shock. A very good concordance with classic experimental and analytical results is obtained.
Maturation of the human cochlear amplifier: Distortion product otoacoustic emission suppression tuning curves recorded at low and high primary tone levels
Authors: Abdala Carolina
Published: July 2002

The cochlear amplifier shows level-dependent function and works optimally at low levels. For this reason, manipulation of stimulus level is a route through which the human cochlear amplifier can be investigated in a noninvasive manner. Distortion product otoacoustic emissions (DPOAEs) evoked as a function of stimulus level provide a tool for exploration of human cochlear amplifier function and, when applied to neonates, for investigation of cochlear maturation. The current experiment generated 2f1−f2 DPOAE ipsilateral suppression tuning curves (STCs) at three primary tone levels and five f2 frequencies in a large group of premature and term neonates and adults. The differences between tuning generated with low- and high-level primary tones was measured to provide a gross estimate of the “tuning enhancement effect” attributed to the cochlear amplifier. Other features of the DPOAE suppression tuning curves were measured as well. Consistent with previous reports, at 1500 and 6000 Hz, STCs were narrower, with a steeper slope on the low-frequency flank of the tuning curve in premature neonates versus adults. Additionally, only DPOAE STCs from adults and term neonates became markedly broader and more shallow when recorded with high-level primary tones. It has been hypothesized that the excessive narrowness of suppression tuning and the absence of a level effect on DPOAE STCs recorded in premature neonates reflects a subtle immaturity in cochlear amplifier function just prior to term birth.
Pulse response of a nonlinear layer
Authors: Hedberg Claes M. , Rudenko Oleg V.
Published: July 2002

A simple analytical theory is developed for the description of the non-steady-state response of a thin nonlinear layer, which differs markedly in its linear properties from the surrounding medium. Such a layer can model the behavior of real inhomogeneities like a cloud of gas bubbles in a liquid, a crack or split plane in a solid, or the contact between two slightly tightened rough surfaces. Both weakly nonlinear pulse and harmonic responses are calculated and the general properties of the spectral and temporal structures of the scattered field are discussed. Exact strongly nonlinear solutions are derived for a special type of stress–strain relationship corresponding to the behavior of real condensed media under strong loads. Profiles and spectra shown conform with experimental results. The pulse response on the short δ-pulse shaped incident wave is calculated for arbitrary nonlinear properties of the layer. The possibilities to apply the sets of data on measured characteristics of pulse response in the solution of inverse problems are briefly discussed.
Review and status of sonic boom penetration into the ocean
Authors: Sparrow Victor W.
Published: July 2002

Since the 1970 Sonic Boom Symposium, held at the ASA’s 80th meeting in Houston, TX, substantial progress has been made in understanding the penetration of sonic booms into the ocean. The state of the art at that time was documented by J. C. Cook, T. Goforth, and R. K. Cook [J. Acoust. Soc. Am. 51, 729–741 (1972)]. Since then, additional experiments have been performed which corroborate Cook’s and Sawyers’ theory for sonic boom penetration into a flat ocean surface. In addition, computational simulations have validated that theory and extended the work to include arbitrarily shaped waveforms penetrating flat ocean surfaces. Further numerical studies have investigated realistic ocean surfaces including large-scale ocean swell. Research has also been performed on the effects of ocean inhomogeneities due to bubble plumes. This paper provides a brief overview of these developments.
Individual differences in the processing of speech and nonspeech sounds by normal-hearing listeners
Authors: Surprenant Aimée M. , Watson Charles S.
Published: July 2002

While a large portion of the variance among listeners in speech recognition is associated with the audibility of components of the speech waveform, it is not possible to predict individual differences in the accuracy of speech processing strictly from the audiogram. This has suggested that some of the variance may be associated with individual differences in spectral or temporal resolving power, or acuity. Psychoacoustic measures of spectral-temporal acuity with nonspeech stimuli have been shown, however, to correlate only weakly (or not at all) with speech processing. In a replication and extension of an earlier study [Watson et al., J. Acoust. Soc. Am. Suppl. 1 71, S73 (1982)] 93 normal-hearing college students were tested on speech perception tasks (nonsense syllables, words, and sentences in a noise background) and on six spectral-temporal discrimination tasks using simple and complex nonspeech sounds. Factor analysis showed that the abilities that explain performance on the nonspeech tasks are quite distinct from those that account for performance on the speech tasks. Performance was significantly correlated among speech tasks and among nonspeech tasks. Either, (a) auditory spectral-temporal acuity for nonspeech sounds is orthogonal to speech processing abilities, or (b) the appropriate tasks or types of nonspeech stimuli that challenge the abilities required for speech recognition have yet to be identified.
The perception of Cantonese lexical tones by early-deafened cochlear implantees
Authors: Ciocca Valter , Francis Alexander L. , Aisha Rani , Wong Lena
Published: July 2002

This study investigated whether cochlear implant users can identify Cantonese lexical tones, which differ primarily in their F0 pattern. Seventeen early-deafened deaf children (age=4 years, 6 months to 8 years, 11 months; postoperative period=11–41 months) took part in the study. Sixteen children were fitted with the Nucleus 24 cochlear implant system; one child was fitted with a Nucleus 22 implant. Participants completed a 2AFC picture identification task in which they identified one of the six contrastive Cantonese tones produced on the monosyllabic target word /ji/. Each target stimulus represented a concrete object and was presented within a carrier phrase in sentence-medial position. Group performance was significantly above chance for three contrasts. However, the cochlear implant listeners performed much worse than a 612-year-old, moderately hearing impaired control listener who was tested on the same task. These findings suggest that this group of cochlear implant users had great difficulty in extracting the pitch information needed to accurately identify Cantonese lexical tones.
The effects of decreased audibility produced by high-pass noise masking on cortical event-related potentials to speech sounds /ba/ and /da/
Authors: Martin Brett A. , Sigal Alain , Kurtzberg Diane , Stapells David R.
Published: July 2002

This study investigated the effects of decreased audibility produced by high-pass noise masking on cortical event-related potentials (ERPs) N1, N2, and P3 to the speech sounds /ba/ and /da/ presented at 65 and 80 dB SPL. Normal-hearing subjects pressed a button in response to the deviant sound in an oddball paradigm. Broadband masking noise was presented at an intensity sufficient to completely mask the response to the 65-dB SPL speech sounds, and subsequently high-pass filtered at 4000, 2000, 1000, 500, and 250 Hz. With high-pass masking noise, pure-tone behavioral thresholds increased by an average of 38 dB at the high-pass cutoff and by 50 dB one octave above the cutoff frequency. Results show that as the cutoff frequency of the high-pass masker was lowered, ERP latencies to speech sounds increased and amplitudes decreased. The cutoff frequency where these changes first occurred and the rate of the change differed for N1 compared to N2, P3, and the behavioral measures. N1 showed gradual changes as the masker cutoff frequency was lowered. N2, P3, and behavioral measures showed marked changes below a masker cutoff of 2000 Hz. These results indicate that the decreased audibility resulting from the noise masking affects the various ERP components in a differential manner. N1 is related to the presence of audible stimulus energy, being present whether audible stimuli are discriminable or not. In contrast, N2 and P3 were absent when the stimuli were audible but not discriminable (i.e., when the second formant transitions were masked), reflecting stimulus discrimination. These data have implications regarding the effects of decreased audibility on cortical processing of speech sounds and for the study of cortical ERPs in populations with hearing impairment.
Dependence of frequency modulation detection on frequency modulation coherence across carriers: Effects of modulation rate, harmonicity, and roving of the carrier frequencies
Authors: Furukawa Shigeto , Moore Brian C. J.
Published: July 2002

Furukawa and Moore [S. Furukawa and B. C. J. Moore, J. Acoust. Soc. Am. 100, 2299–2312 (1996)] found that the detection of frequency modulation (FM) imposed on two inharmonically related carriers was better when the FM was coherent across carriers than when it was incoherent. Here, “coherence” refers to whether the pattern of frequency change over time was identical or different across carriers. The present paper was designed to explore three possible mechanisms underlying this effect. Thresholds were measured for the detection of a single cycle of sinusoidal FM imposed on two sinusoidal carriers. The FM of each carrier was equally detectable, as determined in preliminary experiments. A continuous pink-noise background was used to mask the outputs of auditory filters tuned between the two carrier frequencies. The modulation rate was either 2.5, 5, or 10 Hz. Three combinations of carrier frequencies were used, varying in the extent to which the carriers were harmonically related (1050 and 2069 Hz; 1100 and 2000 Hz; and 1100 and 1925 Hz). The carrier frequencies were either fixed at these values, or were randomly varied (roved) from one trial to another (±10%) keeping the frequency ratio constant. Performance for coherent FM was generally better than for incoherent FM. The effect of FM coherence was greater at the lowest modulation rate and was slightly greater when the carrier frequencies were fixed throughout a block of trials than when they were roved. For the two lowest modulation rates, the effect of FM coherence was greater for carriers that were (nearly) harmonically related. It is proposed that sensitivity to FM coherence depends partly on comparing patterns of phase locking to the carriers; this is done most effectively at low modulation rates. However, two other factors may play a small role. These are: sensitivity to the coherence of amplitude modulation induced in the auditory system by the FM (which is somewhat disrupted by roving the carrier frequencies); and sensitivity to fluctuations in the residue pitch evoked by the two carriers (the residue pitch being less salient for inharmonically related carriers).
Central auditory system plasticity: Generalization to novel stimuli following listening training
Authors: Tremblay Kelly , Kraus Nina , Carrell Thomas D. , McGee Therese
Published: July 2002

Behavioral perceptual abilities and neurophysiologic changes observed after listening training can generalize to other stimuli not used in the training paradigm, thereby demonstrating behavioral “transfer of learning” and plasticity in underlying physiologic processes. Nine normal-hearing monolingual English-speaking adults were trained to identify a prevoiced labial stop sound (one that is not used phonemically in the English language). After training, the subjects were asked to discriminate and identify a prevoiced alveolar stop. Mismatch negativity cortical evoked responses (MMN) were recorded to both labial and alveolar stimuli before and after training. Behavioral performance and MMNs also were evaluated in an age-matched control group that did not receive training. Listening training improved the experimental group’s ability to discriminate and identify an unfamiliar VOT contrast. That enhanced ability transferred from one place of articulation (labial) to another (alveolar). The behavioral training effects were reflected in the MMN, which showed an increase in duration and area when elicited by the training stimuli as well as a decrease in onset latency when elicited by the transfer stimuli. Interestingly, changes in the MMN were largest over the left hemisphere. The results demonstrate that training can generalize to listening situations beyond those used in training sessions, and that the preattentive central neurophysiology underlying perceptual learning are altered through auditory training.