bluuebunny/crossref_metadata_2025 huggingface dataset:
Counter-Matching in Studies of Gene-Environment Interaction: Efficiency and Feasibility
Authors: Andrieu N. , Goldstein A. M. , Thomas D. C. , Langholz B.
Published: July 2002

The interest in studying gene-environment interaction is increasing for complex diseases. However, most methods of detecting gene-environment interactions may not be appropriate for the study of interactions involving rare genes (G) or uncommon environmental exposures (E), because of poor statistical power. To increase this power, the authors propose the counter-matching design. This design increases the number of subjects with the rare factor without increasing the number of measurements that must be performed. In this paper, the efficiency and feasibility (required sample sizes) of counter-matching designs are evaluated and discussed. Counter-matching on both G and E appears to be the most efficient design for detecting gene-environment interaction. The sensitivity and specificity of the surrogate measures, the frequencies of G and E, and, to a lesser extent, the value of the interaction effect are the most important parameters for determining efficiency. Feasibility is also more dependent on the exposure frequencies and the interaction effect than on the main effects of G and E. Although the efficiency of counter-matching is greatest when the risk factors are very rare, the study of such rare factors is not realistic unless one is interested in very strong interaction effects. Nevertheless, counter-matching appears to be more appropriate than most traditional epidemiologic methods for the study of interactions involving rare factors.
Neighborhood Socioeconomic Status and All-Cause Mortality
Authors: Bosma Hans , Dike van de Mheen H. , Borsboom Gerard J. J. M. , Mackenbach Johan P.
Published: July 2002

This study sought to determine the contribution of neighborhood socioeconomic status to all-cause mortality and to explore its correlates. As part of the longitudinal “Gezondheid en LevensOmstandigheden Bevolking en omstreken” (GLOBE) study in the Netherlands, 8,506 randomly selected men and women aged 15–74 years from 86 neighborhoods in the city of Eindhoven reported on their socioeconomic status in the 1991 baseline survey. During the 6-year follow-up, 487 persons died. Neighborhood socioeconomic status was derived from individual reports on socioeconomic status. Its effect on mortality was stringently controlled for four individual-level socioeconomic indicators. Persons living in a neighborhood with a high percentage of unemployed/disabled or poor persons had a higher mortality risk than did those living in a neighborhood with a low percentage of unemployed/disabled or poor persons. This was independent of individual socioeconomic characteristics, including individual unemployment/disability or reports of severe financial problems. Educational and occupational neighborhood indicators were similarly, but less strongly, related to mortality. The prevalence of poor housing conditions, social disintegration, and unhealthy psychologic profiles and behaviors was higher in neighborhoods with a low socioeconomic status. Contextual effects of socioeconomic status may thus be due to one or more of these specific circumstances. The findings indicate potential public health benefits of modifying socioeconomic characteristics of areas.
Incidence of Transitional Cell Carcinoma and Arsenic in Drinking Water: A Follow-up Study of 8,102 Residents in an Arseniasis-endemic Area in Northeastern Taiwan
Authors: Chiou Hung-Yi , Chiou Shu-Ti , Hsu Yi-Hsiang , Chou Yi-Li , Tseng Chin-Hsiao , Wei Min-Li , Chen Chien-Jen
Published: July 2002

A significant association between ingested arsenic and bladder cancer has been reported in an arseniasis-endemic area in southwestern Taiwan, where many households share only a few wells in their villages. In another arseniasis-endemic area in northeastern Taiwan, each household has its own well for obtaining drinking water. In 1991–1994, the authors examined risk of transitional cell carcinoma (TCC) in relation to ingested arsenic in a cohort of 8,102 residents in northeastern Taiwan. Estimation of each study subject's individual exposure to inorganic arsenic was based on the arsenic concentration in his or her own well water, which was determined by hydride generation combined with atomic absorption spectrometry. Information on duration of consumption of the well water was obtained through standardized questionnaire interviews. The occurrence of urinary tract cancers was ascertained by follow-up interview and by data linkage with community hospital records, the national death certification profile, and the cancer registry profile. Cox proportional hazards regression analysis was used to estimate multivariate-adjusted relative risks and 95% confidence intervals. There was a significantly increased incidence of urinary cancers for the study cohort compared with the general population in Taiwan (standardized incidence ratio = 2.05; 95% confidence interval (CI): 1.22, 3.24). A significant dose-response relation between risk of cancers of the urinary organs, especially TCC, and indices of arsenic exposure was observed after adjustment for age, sex, and cigarette smoking. The multivariate-adjusted relative risks of developing TCC were 1.9, 8.2, and 15.3 for arsenic concentrations of 10.1–50.0, 50.1–100, and >100 µg/liter, respectively, compared with the referent level of ≤10.0 µg/liter.
Plasma Concentrations of Carotenoids, Retinol, and Tocopherols in Preeclamptic and Normotensive Pregnant Women
Authors: Zhang Cuilin , Williams Michelle A. , Sanchez Sixto E. , King Irena B. , Ware-Jauregui Suzie , Larrabure Gloria , Bazul Victor , Leisenring Wendy M.
Published: July 2002

This case-control study was conducted in Lima, Peru, from June 1997 through January 1998 to assess whether plasma concentrations of carotenoids (α-carotene, β-carotene, lycopene, lutein, zeaxanthin, β-cryptoxanthin), retinol, and tocopherols (α-tocopherol and γ-tocopherol) are decreased in women with preeclampsia. A total of 125 pregnant women with preeclampsia and 179 normotensive pregnant women were included. Plasma concentrations of antioxidants were determined using high performance liquid chromatography. After adjusting for maternal demographic, behavioral, and reproductive characteristics and total plasma lipid concentrations, the authors found a linear increase in risk of preeclampsia with increasing concentrations of α-tocopherol (odds ratio of the highest quartile = 3.13; 95% confidence interval: 1.06, 9.23, with the lowest quartile as the reference group; p value of the test of linear trend = 0.040). The risk of preeclampsia decreased across increasing quartiles of concentrations for retinol (odds ratio of the highest quartile = 0.32; 95% confidence interval: 0.15, 0.69, with the lowest quartile as the reference group; p value of the test of linear trend = 0.001). Some of these results are inconsistent with the prevailing hypothesis that preeclampsia is an antioxidant-deficient state. Preliminary findings confirm an earlier observation of increased plasma concentrations of α-tocopherol among women with preeclampsia as compared with normotensive pregnant women.
Estimating the Relative Incidence of Heroin Use: Application of a Method for Adjusting Observed Reports of First Visits to Specialized Drug Treatment Agencies
Authors: Hickman Matthew , Seaman Shaun , de Angelis Daniela
Published: July 2002

In this paper, the authors propose a method for estimating the incidence of heroin use by adjusting reported numbers of heroin users visiting drug treatment agencies for the time lag between onset of heroin use and first treatment request (lag distribution). The adjusted incidence is relative, since it represents the number of individuals beginning heroin use in each year whose cases will be reported within 8 years of starting use. Users with longer lag times or whose cases are never reported are excluded. Utilizing data from southeastern England (1991–1998), the authors analyzed the effects of covariates (sex, age group, ethnic group, route of consumption, and year of onset of drug use) on the lag distribution. Trends in the adjusted incidence of heroin use were very different for injectors and noninjectors: Incidence among injectors seemed to be stable, while in noninjectors it increased twofold between 1991 and 1996–1997. These results must be interpreted cautiously, especially in relation to the wider context of underlying trends in the population. Potential biases derive from underreporting and from changes in the proportion of heroin users in treatment. The lag correction method adds substantially to the value of routine treatment data, at least for heroin use, and is potentially the best method for obtaining estimates of incidence.
Family Size, Day-Care Attendance, and Breastfeeding in Relation to the Incidence of Childhood Asthma
Authors: Infante-Rivard Claire , Amre Devendra , Gautrin Denyse , Malo Jean-Luc
Published: July 2002

A hypothesis has been suggested stating that children exposed early to infections are less likely to develop atopy or asthma. The authors investigated the relation between risk of childhood asthma and number of siblings as well as day-care attendance, as factors possibly increasing the likelihood of early infections, and breastfeeding as a factor reducing them. A case-control study was carried out in Montréal, Canada, between 1988 and 1995 that included 457 children diagnosed with asthma at 3–4 years of age and 457 healthy controls. Cases followed for 6 years were later classified as persistent or transient by the symptoms and use of medication after diagnosis. Among cases diagnosed at 3–4 years of age, the adjusted odds ratio for asthma was 0.54 (95% confidence interval (CI): 0.36, 0.80) for one sibling and 0.49 (95% CI: 0.30, 0.81) for two or more. The adjusted odds ratio for day-care attendance before 1 year of age was 0.59 (95% CI: 0.40, 0.87). Results were similar with persistent cases. Among transient cases (who possibly had an infection with wheezing at 3–4 years of age), day-care attendance and a short duration of breastfeeding resulted in increased risk. The results support the hypothesis that opportunity for early infections reduces the risk of asthma.
Polymer chromosome models and Monte Carlo simulations of
radiation breaking DNA
Authors: L.Ponomarev A. , K.Sachs R.
Published: July 2002

Motivation: Chromatin breakage by ionizing radiation is relevant to studies of carcinogenesis, tumor radiotherapy, biodosimetry and molecular biology. This article focuses on computer analysis of chromosome irradiation in mammalian cells.

Methods: Polymer physics and Monte Carlo numerical methods are used to develop a coarse-grained computational approach. Chromatin is modeled as a random walk on a cubic lattice, and the radiation tracks hitting the chromatin are modeled as straight lines hitting lattice sites. Each track can make a cluster of DSBs on a chromosome.

Results: The results obtained replace conjectured DNA fragment-size distribution functions in the recently developed RLC formalism by more mechanistically motivated distributions. The discrete lattice algorithm reproduces features of current radiation experiments relevant to chromatin on large scales. It approximates the continuous formalism and experimental data with adequate precision. It was also found that assuming either fixed chromatin with correlations among different clusters of DSBs or moving chromatin with no such correlations gives virtually identical numerical predictions.

Availability: This set of subroutines comprises the DNABreak package available at the UC Berkeley mathematical radiobiology site: http://math.berkeley.edu/~sachs/ponomarev/artem.index.html

Contact: alp17@math.berkeley.edu

Abbreviations: Mbp, megabasepair; DSB, DNA double strand break; RLC, randomly-located-clusters Sachs et al. (1999);PBC, periodic boundary conditions Binder (1995); RW, random walk Sokal (1995); size, genomic content in Mbp.
Alignment of 3D structures of macromolecular assemblies
Authors: Lanzavecchia Salvatore , Cantele Francesca , Bellon Pier Luigi
Published: July 2002

Motivation: A number of macromolecular assemblies are being reconstructed in 3D from electron micrographs. The analysis yields a 3D matrix representing the protein density map. In reconstruction processes and in comparing the results of different experiments, it is often necessary to obtain all models oriented the same way in three dimensions. The problem is not trivial since there exist no 3D counterpart of correlation analysis used for 2D images. It is usually solved by time consuming trial and error algorithms.

Results: 3D density distributions can be brought to a ‘canonical’ orientation. The tensor of inertia of the distribution is determined and its eigenvectors are oriented along the coordinate axes. The method is fast and essentially free of reference. It is suitable for structures whose inertial axes do not completely degenerate as they do in icosahedral viruses or if symmetry is cubic. Applications are presented for asymmetric objects and for molecules possessing symmetry axes higher than twofold.

Implementation: The implementation simply requires the accumulation of the inertial tensor and its diagonalisation. Volume data rotation has been already illustrated in this journal by the authors.

Availability: The software is available upon request to the authors.

Contact: salvator@csmtbo.mi.cnr.it

* To whom correspondence should be addressed.
Extensive feature detection of N-terminal protein sorting
signals
Authors: Bannai Hideo , Tamada Yoshinori , Maruyama Osamu , Nakai Kenta , Miyano Satoru
Published: July 2002

Motivation: The prediction of localization sites of various proteins is an important and challenging problem in the field of molecular biology. TargetP, by Emanuelsson et al. (J. Mol. Biol. , 300, 1005–1016, 2000) is a neural network based system which is currently the best predictor in the literature for N-terminalsorting signals. One drawback of neural networks, however, is that it is generally difficult to understand and interpret how and why they make such predictions. In this paper, we aim to generate simple and interpretable rules as predictors, and still achieve a practical prediction accuracy. We adopt an approach which consists of an extensive search for simple rules and various attributes which is partially guided by human intuition.

Results: We have succeeded in finding rules whose prediction accuracies come close to that of TargetP, while still retaining a very simple and interpretable form. We also discuss and interpret the discovered rules.

Availability: An (experimental) web service usingrules obtained by our method is provided at http://hypothesiscreator.net/iPSORT/.

Contact: bannai@ims.u-tokyo.ac.jp
Multiple sequence alignment using partial order graphs
Authors: Lee Christopher , Grasso Catherine , Sharlow Mark F.
Published: July 2002

Motivation: Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment step. However, this leads to loss of information needed for accurate alignment, and gap scoring artifacts.

Results: We present a graph representation of an MSA that can itself be aligned directly by pairwise dynamic programming, eliminating the need to reduce the MSA to a profile. This enables our algorithm (Partial Order Alignment (POA)) to guarantee that the optimal alignment of each new sequence versus each sequence in the MSA will be considered. Moreover, this algorithm introduces a new edit operator, homologous recombination, important for multidomain sequences. The algorithm has improved speed (linear time complexity) over existing MSA algorithms, enabling construction of massive and complex alignments (e.g. an alignment of 5000 sequences in 4 h on a Pentium II). We demonstrate the utility of this algorithm on a family of multidomain SH2 proteins, and on EST assemblies containing alternative splicing and polymorphism.

Availability: The partial order alignment program POA is available at http://www.bioinformatics.ucla.edu/poa.

Contact: leec@mbi.ucla.edu

* To whom correspondence should be addressed.

2 Current address: center for Applied Mathematics, 657 Rhodes Hall, Cornell University, Ithaca NY 14853, USA.
Environments of Crystallization and Compositional Diversity of Mauna Loa Xenoliths
Authors: GAFFNEY AMY M.
Published: July 2002

Two picrite flows from the SW rift zone of Mauna Loa contain xenoliths of dunite, harzburgite, lherzolite, plagioclase-bearing lherzolite and harzburgite, troctolite, gabbro, olivine gabbro, and gabbronorite. Textures and olivine compositions preclude a mantle source for the xenoliths, and rare earth element concentrations of xenoliths and clinopyroxene indicate that the xenolith source is not old oceanic crust, but rather a Hawaiian, tholeiitic-stage magma. Pyroxene compositions, phase assemblages and textural relationships in xenoliths indicate at least two different crystallization sequences. Calculations using the pMELTS algorithm show that the two sequences result from crystallization of primitive Mauna Loa magmas at 6 kbar and 2 kbar. Independent calculations of olivine Ni–Fo compositional variability in the plagioclase-bearing xenoliths over these crystallization sequences are consistent with observed olivine compositional variability. Two parents of similar bulk composition, but which vary in Ni content, are necessary to explain the olivine compositional variability in the dunite and plagioclase-free peridotitic xenoliths. Xenoliths probably crystallized in a small magma storage area beneath the rift zone, rather than the large sub-caldera magma reservoir. Primitive, picritic magmas are introduced to isolated rift zone storage areas during periods of high magma flux. Subsequent eruptions reoccupy these areas, and entrain and transport xenoliths to the surface.
Transcranial magnetic stimulation: studying the brain--behaviour relationship by induction of ‘virtual lesions’
Authors: Pascual-Leone Alvaro
Published: July 2002

Transcranial magnetic stimulation (TMS) provides a non-invasive method of induction of a focal current in the brain and transient modulation of the function of the targeted cortex. Despite limited understanding about focality and mechanisms of action, TMS provides a unique opportunity of studying brain-behaviour relations in normal humans. TMS can enhance the results of other neuroimaging techniques by establishing the causal link between brain activity and task performance, and by exploring functional brain connectivity.
Thoughts on the development, structure and evolution of the mammalian and avian telencephalic pallium
Authors: Puelles Luis
Published: July 2002

Various lines of evidence suggest that the development and evolution of the mammalian isocortex cannot be easily explained without an understanding of correlative changes in surrounding areas of the telencephalic pallium and subpallium. These are close neighbours in a common morphogenetic field and are postulated as sources of some cortical neuron types (and even of whole cortical areas). There is equal need to explain relevant developmental evolutionary changes in the dorsal thalamus, the major source of afferent inputs to the telencephalon (to both the pallium and subpallium). The mammalian isocortex evolved within an initially small dorsal part of the pallium of vertebrates, surrounded by other pallial parts, including some with a non–cortical, nuclear structure. Nuclear pallial elements are markedly voluminous in reptiles and birds, where they build the dorsal ventricular ridge, or hypopallium, which has been recently divided molecularly and structurally into a lateral pallium and a ventral pallium. Afferent pallial connections are often simplified as consisting of thalamic fibres that project either to focal cell aggregates in the ventral pallium (predominant in reptiles and birds) or to corticoid areas in the dorsal pallium (predominant in mammals). Karten's hypothesis, put forward in 1969, on the formation of some isocortical areas postulates an embryonic translocation into the nascent isocortex of the ventropallial thalamorecipient foci and respective downstream ventropallial target populations, as specific layer IV, layers II– III, or layers V–VI neuron populations. This view is considered critically in the light of various recent data, contrasting with the alternative possibility of a parallel, separate evolution of the different pallial parts. The new scenario reveals as well a separately evolving tiered structure of the dorsal thalamus, some of whose parts receive input from midbrain sensory centres (collothalamic nuclei), whereas other parts receive oligosynaptic ‘lemniscal’ connections bypassing the midbrain (lemnothalamic nuclei). An ampler look into known hodological patterns from this viewpoint suggests that ancient collothalamic pathways, which target ventropallial foci, are largely conserved in mammals, while some emergent cortical connections can be established by means of new collaterals in some of these pathways. The lemnothalamic pathways, which typically target ancestrally the dorsopallial isocortex, show parallel increments of relative size and structural diversification of both the thalamic cell populations and the cortical recipient areas. The evolving lemnothalamic pathways may interact developmentally with collothalamic corticopetal collaterals in the modality–specific invasion of the emergent new areas of isocortex.
Alkaline phosphatase from the hyperthermophilic bacterium T. maritima requires cobalt for activity
Authors: Wojciechowski Cheryl L. , Cardia James P. , Kantrowitz Evan R.
Published: July 2002

The hyperthermophilic bacterium Thermotoga maritima encodes a gene sharing sequence similarities with several known genes for alkaline phosphatase (AP). The putative gene was isolated and the corresponding protein expressed in Escherichia coli, with and without a predicted signal sequence. The recombinant protein showed phosphatase activity toward the substrate p‐nitrophenyl‐phosphate with a kcat of 16 s−1 and a Km of 175 μM at a pH optimum of 8.0 when assayed at 25°C. T. maritima phosphatase activity increased at high temperatures, reaching a maximum kcat of 100 s−1, with a Km of 93 μM at 65°C. Activity was stable at 65°C for >24 h and at 90°C for 5 h. Phosphatase activity was dependent on divalent metal ions, specifically Co(II) and Mg(II). Circular dichroism spectra showed that the enzyme gains secondary structure on addition of these metals. Zinc, the most common divalent metal ion required for activity in known APs, was shown to inhibit the T. maritima phosphatase enzyme at concentrations above 0.3 moles Zn: 1 mole monomer. All activity was abolished in the presence of 0.1 mM EDTA. The T. maritima AP primary sequence is 28% identical when compared with E. coli AP. Based on a structural model, the active sites are superimposable except for two residues near the E. coli AP Mg binding site, D153 and K328 (E. coli numbering) corresponding to histidine and tryptophan in T. maritima AP, respectively. Sucrose‐density gradient sedimentation experiments showed that the protein exists in several quaternary forms predominated by an octamer.
Magnetic fields with photon beams: Monte Carlo calculations for a model magnetic field
Authors: Jette David
Published: July 2002

Strong transverse magnetic fields can produce very large dose enhancements and reductions in localized regions of a patient under irradiation by a photon beam. We have suggested a model magnetic field which can be expected to produce such large dose enhancements and reductions, and we have carried out EGS4 Monte Carlo calculations to examine this effect for a 6×6 cm2photon beam of energy 15, 30, or 45 MV penetrating a water phantom. Our model magnetic field has a nominal (center) strengthranging between 1 and 5 T, and a maximum strength within the geometric beam which isFor all three beam energies, there is significant dose enhancement forwhich increases greatly forbut stronger magnetic fields increase the enhancement further only for the 45‐MV beam. Correspondingly, there is major reduction in the dose just distal to this region of large dose enhancement, resulting from secondary electrons and positrons originating upstream which are depositing energy in the dose‐enhancement region rather than continuing further into the patient. The dose peak region is fairly narrow (in depth), but the magnetic field can be shifted along the longitudinal axis to produce a flat peak region of medium width (∼2 cm) or of large width (∼4 cm), with rapid dose dropoffs on either side. For the 30‐MV beam withwe found a dose enhancement of 55% for the narrow‐width configuration, 32% for the medium‐width configuration, and 23% for the large‐width configuration; for the 45‐MV beam withthe enhancements were quite similar, but for the 15‐MV beam they were considerably less. For all of these 30‐MV configurations, the dose reductions were ∼30%, and they were ∼40% for the 45‐MV configurations.
Comparison of the Batho, ETAR and Monte Carlo dose calculation methods in CT based patient models
Authors: du Plessis F. C. P. , Willemse C. A. , Lötter M. G. , Goedhals L.
Published: July 2002

This paper shows the contribution that Monte Carlo methods make in regard to dose distribution calculations in CT based patient models and the role it plays as a gold standard to evaluate other dose calculation algorithms. The EGS4 based BEAM code was used to construct a generic 8 MV accelerator to obtain a series of x‐ray field sources. These were used in the EGS4 based DOSXYZ code to generate beam data in a mathematical water phantom to set up a beam model in a commercial treatment planning system (TPS), CADPLAN V.2.7.9. Dose distributions were calculated with the Batho and ETAR inhomogeneity correction algorithms in head/sinus, lung, and prostate patient models forandopen x‐ray beams. Corresponding dose distributions were calculated with DOSXYZ that were used as a benchmark. The dose comparisons are expressed in terms of 2D isodose distributions, percentage depth dose data, and dose difference volume histograms (DDVH's). Results indicated that the Batho and ETAR methods contained inaccuracies of 20%–70% in the maxillary sinus region in the head model. Large lung inhomogeneities irradiated with small fields gave rise to absorbed dose deviations of 10%–20%. It is shown for afield that DOSXYZ models lateral scatter in lung that is not present in the Batho and ETAR methods. The ETAR and Batho methods are accurate within 3% in a prostate model. We showed how the performance of these inhomogeneity correction methods can be understood in realistic patient models using validated Monte Carlo codes such as BEAM and DOSXYZ.
Reducing loss in lateral charged‐particle equilibrium due to air cavities present in x‐ray irradiated media by using longitudinal magnetic fields
Authors: Naqvi Shahid A. , Li X. Allen , Ramahi Shada W. , Chu James C. , Ye Sung‐Joon
Published: July 2002

The underdosing of lesions distal to air cavities, such as those found in upper respiratory passages, occurs due to the loss in lateral charged‐particle equilibrium (CPE). The degree of underdosing worsens for smaller field sizes, resulting in more frequent recurrence of the cancer treated. Higher photon energies further aggravate the outcome by producing longer second build‐up regions beyond the cavity. Besides underdosing, the larger lateral spread of secondary electron fluence in the air cavity produces diffuse dose distributions at the tissue‐air interface for shaped or intensity modulated fields. These disequilibrium effects create undesirable deviations from the intended treatment. The clinical concern is further intensified by the failure of traditional treatment planning systems to even account for such defects. In this work, the use of longitudinal magnetic fields on the order of 0.5 T is proposed for alleviating lateral electronic disequilibrium due to the presence of air cavities in the irradiated volume. The magnetic field enforces lateral CPE by restricting the lateral range of electrons in the air cavity. The problem is studied in a simple water‐air‐water slab geometry usingEGS4Monte Carlo simulations for 6 MV photons. Electronic disequilibrium is evaluated for beams of various sizes, shapes and intensity distributions constructed by linear superposition of the dose distributions forbeamlets. Comparison is also made withirradiation. The results indicate that the lateral confinement of secondary electrons in the air cavity by sub‐MRI strength longitudinal fields is effective in reducing deterioration of dose distributions near tissue‐air interfaces. This can potentially reduce recurrence rates of cancers such as the larynx carcinoma.
A simple method for bremsstrahlung spectra reconstruction from transmission measurements
Authors: Krmar M. , Nikolić D. , Krstonošić P. , Cora S. , Francescon P. , Chiovati P. , Rudić A.
Published: July 2002

A new method for evaluation of bremsstrahlung spectra from transmission measurements has been developed. In this method some very well known facts relating to thick target bremsstrahlung spectra area prioriincluded in the calculation procedure. Some characteristics of the method are preliminarily illustrated on a 6 MV therapy linear accelerator.
Tissue–air ratios for narrow gamma‐ray beams
Authors: Nizin Paul S. , Mooij Rob B.
Published: July 2002

This study introduces a table of tissue–air ratios (TAR) for narrowgamma‐ray beams. The table is consistent with recently published TAR data for broadgamma‐ray beams [Table 4.1, Br. J. Radiol. Suppl.25(1996)]. Narrow‐beam TARs are derived analytically from broad‐beam data of Table 4.1 and are tabulated for circular fields ranging from 0.2 to 2.2 cm in radius— an approximate equivalent of atosquare‐field range. The extent of depths is from 0.5 to 30 cm in water.
Astigmatic single photon emission computed tomography imaging with a displaced center of rotation
Authors: Wang Huili , Smith Mark F. , Stone Craig D. , Jaszczak Ronald J.
Published: July 2002

A filtered backprojection algorithm is developed for single photon emission computed tomography (SPECT) imaging with an astigmatic collimator having a displaced center of rotation. The astigmatic collimator has two perpendicular focal lines, one that is parallel to the axis of rotation of the gamma camera and one that is perpendicular to this axis. Using SPECT simulations of projection data from a hot rod phantom and point source arrays, it is found that a lack of incorporation of the mechanical shift in the reconstruction algorithm causes errors and artifacts in reconstructed SPECT images. The collimator and acquisition parameters in the astigmatic reconstruction formula, which include focal lengths, radius of rotation, and mechanical shifts, are often partly unknown and can be determined using the projections of a point source at various projection angles. The accurate determination of these parameters by a least squares fitting technique using projection data from numerically simulated SPECT acquisitions is studied. These studies show that the accuracy of parameter determination is improved as the distance between the point source and the axis of rotation of the gamma camera is increased. The focal length to the focal line perpendicular to the axis of rotation is determined more accurately than the focal length to the focal line parallel to this axis.
Modeling photon output caused by backscattered radiation into the monitor chamber from collimator jaws using a Monte Carlo technique
Authors: Liu H. Helen , Mackie T. Rockwell , McCullough Edwin C.
Published: July 2002

Dose per monitor unit in photon fields generated by clinical linear accelerators can be affected by the backscattered radiation into the monitor chamber from collimator jaws. Thus, it is necessary to account for the backscattered radiation in computing monitor unit setting for a treatment field. In this work, we investigated effects of the backscatter from collimator jaws based on Monte Carlo simulations of a clinical linear accelerator. The backscattered radiation scored within the monitor chamber was identified as originating either from the upper jaws (Y jaws), or from the lower jaws (X jaws). From the results of Monte Carlo simulations, ratios of the monitor‐chamber‐scored dose caused by the backscatter to the dose caused by the forward radiation, were modeled as functions of the individual X and Y jaw positions. The amount of the backscattered radiation for any field setting was then computed as a compound contribution from both the X and Y jaws. The dose ratios of were then used to calculate the change in photon output caused by the backscatter, Results of these calculations were compared with available measured data based on counting the electron pulses or charge from the electron target of an accelerator. Data from this study showed that the backscattered radiation contributes approximately 3% to the monitor‐chamber‐scored dose. A majority of the backscattered radiation comes from the upper jaws, which are located closer to the monitor chamber. The amount of the backscatter decreases approximately in a linear fashion with the jaw opening. This results in about a 2% increase of photon output from a field to a field. The off‐axis location of the jaw opening does not have a significant effect on the magnitude of the backscatter. The backscatter effect is significant for monitor chambers using kapton windows, particularly for treatment fields using moving jaws. Applying the backscatter correction improves the accuracy of monitor‐unit calculation using a model‐based dose calculation algorithm such as the convolution method.
Field pattern of a magnetic dipole
Authors: Mc Tavish J. P.
Published: July 2002

A calculation is presented which gives the field pattern due to a dipole field. The approach should be within the reach of an undergraduate student.
Incorporation of loudness measures in active noise control
Authors: Sommerfeldt Scott D. , Samuels Timothy O.
Published: July 2002

An attempt has been made to use a modified version of a standard active noise control algorithm in order to take into account the unique response of the human auditory system. It has been shown in the past that decreasing the sound pressure level at a location does not guarantee a similar decrease in the perceived loudness at that location. Typically, active noise control is based on minimizing the “error signal” from a mechanical device such as a microphone, whose response is nominally flat across the frequency response range of the human ear. However, if the response of the ear can be approximated by digitally filtering the error signal before it reaches the adaptive controller, one can, in effect, minimize the more subjective loudness level, as opposed to the sound pressure level. The work reported here entails simulating active noise control based upon minimizing perceived loudness for a collection of input noise signals. A comparison of the loudness of the resulting error signal is made to the loudness of that resulting from standard sound pressure level minimization. It has been found that the effectiveness of this technique is largely dependent upon the nature of the input noise signal. Furthermore, this technique is judged to be worth considering for use with applications of active noise control where the uncontrolled noise more prominently constitutes low range audio frequencies (approximately 30 Hz–100 Hz) than medium range audio frequencies (approximately 300 Hz–600 Hz).
Scattering and active acoustic control from a submerged spherical shell
Authors: Scandrett Clyde
Published: July 2002

This paper is concerned with the scattering from a submerged (heavy fluid) bilaminate spherical shell composed of an outer layer of steel, and an inner layer of radially polarized piezoelectric material. The methodology used includes separation formulas for the stresses and displacements, which in turn are used (coupled with spherical harmonics) to reduce the governing equations to linear systems of ordinary differential equations. This technique uses the full equations of elasticity rather than any of the various thin-shell approximations in determining the axisymmetric scattering from a shell, normal modes of vibration for the shell, as well as voltages necessary for annihilation of a scattered pressure due to insonification of the shell by an incident plane wave.
Power transmission from a vibrating body to a circular cylindrical shell through passive and active isolators
Authors: Howard Carl Q. , Hansen Colin H. , Pan Jiaqiang
Published: July 2002

The transmission of harmonic vibratory power from a vibrating rigid body into a thin supporting cylindrical shell through multiple passive and active isolators is investigated theoretically. The model allows for the transmission of vertical and horizontal harmonic forces and moments about all three coordinate axes. Results show that over a frequency range from 0 to 200 Hz, the real power transmission into the supporting shell can be reduced substantially by employing in parallel with existing passive isolators, active isolators adjusted to provide appropriate control force amplitudes and phases.
Resonant scattering of acoustic waves by ellipsoid air bubbles in liquids
Authors: Ye Zhen
Published: July 2002

This paper reports the first analytic study of resonant scattering of acoustic waves by ellipsoid air bubbles in liquids. Based on the Kirchhoff integral theorem, the function of sound scattering is derived in a simple closed form and is shown to bear analogy with the well-known expression for sound scattering from spherical air bubbles. The resonance frequency and the quality factor Q are also derived. For the special cases such as spherical and prolate spheroid bubbles, the results reduce to the previously known results.
The perceptual relevance of locus equations
Authors: Fruchter David , Sussman Harvey M.
Published: July 2002

Identification curves were estimated for the English consonants /b,d,g/ using five-formant CV synthetic stimuli comprehensively sampling the F2 onset–F2vowel acoustic space in the vicinity of /b,d,g/ locus equations [H. Sussman et al., J. Acoust. Soc. Am. 90, 1309–1325 (1991)]. The stimuli included 10 English monophthongal vowel contexts, 11 levels of F2 onset per vowel, and 3 levels of F3 onset orthogonally varied with the F2 variables (10 vowels×11 F2 onsets×3 F3 onsets=330 stimuli). After brief training, each of six subjects, three male and three female, was presented eight trials of each of the stimuli, one or two trials per day over a period of several days. Systems of identification curves were visualized as identification surfaces situated in locus equation acoustic space and were overlaid with acoustic data from five male speakers in order to judge the degree of correspondence between perception and acoustic data. A chi square analysis was also performed in order to quantify the correspondence between the observed perception data and expected frequencies derived from the acoustic data. The results, when interpreted in terms of a dominance hierarchy hypothesis, strongly indicate F2 onset and F2 vowel, in combination, serve as important cues for stop consonant place of articulation.
Sound scattering by several zooplankton groups. II. Scattering models
Authors: Stanton Timothy K. , Chu Dezhang , Wiebe Peter H.
Published: July 2002

Mathematical scattering models are derived and compared with data from zooplankton from several gross anatomical groups—fluidlike, elastic shelled, and gas bearing. The models are based upon the acoustically inferred boundary conditions determined from laboratory backscattering data presented in part I of this series [Stanton et al., J. Acoust. Soc. Am. 103, 225–235 (1998)]. The models use a combination of ray theory, modal-series solution, and distorted wave Born approximation (DWBA). The formulations, which are inherently approximate, are designed to include only the dominant scattering mechanisms as determined from the experiments. The models for the fluidlike animals (euphausiids in this case) ranged from the simplest case involving two rays, which could qualitatively describe the structure of target strength versus frequency for single pings, to the most complex case involving a rough inhomogeneous asymmetrically tapered bent cylinder using the DWBA-based formulation which could predict echo levels over all angles of incidence (including the difficult region of end-on incidence). The model for the elastic shelled body (gastropods in this case) involved development of an analytical model which takes into account irregularities and discontinuities of the shell. The model for gas-bearing animals (siphonophores) is a hybrid model which is composed of the summation of the exact solution to the gas sphere and the approximate DWBA-based formulation for arbitrarily shaped fluidlike bodies. There is also a simplified ray-based model for the siphonophore. The models are applied to data involving single pings, ping-to-ping variability, and echoes averaged over many pings. There is reasonable qualitative agreement between the predictions and single ping data, and reasonable quantitative agreement between the predictions and variability and averages of echo data.
Simplified models of transient elastic waves in finite axisymmetric layered media
Authors: El-Raheb Michael
Published: July 2002

A simplified model, termed the flexure model, is used to analyze elastic waves in a weakly coupled periodic stack of disks bonded by thin layers of a weak polymer. Comparison with results of a more complete two-dimensional (2-D) axisymmetric model reveals the importance of axial stress and nonlinear distribution of radial displacement across the thickness. Also, in the 2-D model, it is possible to eliminate extensional modes through the thickness and inertia of the bond without compromising accuracy. In the 2-D model and for low radial wave numbers for a defined mode, its phase and group velocities can be approximated by the 1-D mass–spring model. They undergo discontinuities at the boundaries of extensional propagation zones. The flexure model reproduces the 2-D characteristic speeds but with slightly wider propagation zones and faster wavefronts.
Monosyllabic word recognition at higher-than-normal speech and noise levels
Authors: Studebaker Gerald A. , Sherbecoe Robert L. , McDaniel D. Michael , Gwaltney Catherine A.
Published: July 2002

The effects of intensity on monosyllabic word recognition were studied in adults with normal hearing and mild-to-moderate sensorineural hearing loss. The stimuli were bandlimited NU#6 word lists presented in quiet and talker-spectrum-matched noise. Speech levels ranged from 64 to 99 dB SPL and S/N ratios from 28 to −4 dB. In quiet, the performance of normal-hearing subjects remained essentially constant; in noise, at a fixed S/N ratio, it decreased as a linear function of speech level. Hearing-impaired subjects performed like normal-hearing subjects tested in noise when the data were corrected for the effects of audibility loss. From these and other results, it was concluded that: (1) speech intelligibility in noise decreases when speech levels exceed 69 dB SPL and the S/N ratio remains constant; (2) the effects of speech and noise level are synergistic; (3) the deterioration in intelligibility can be modeled as a relative increase in the effective masking level; (4) normal-hearing and hearing-impaired subjects are affected similarly by increased signal level when differences in speech audibility are considered; (5) the negative effects of increasing speech and noise levels on speech recognition are similar for all adult subjects, at least up to 80 years; and (6) the effective dynamic range of speech may be larger than the commonly assumed value of 30 dB.
Time delay spectrometry for hydrophone calibrations below 1 MHz
Authors: Gammell Paul M. , Harris Gerald R.
Published: July 2002

Knowing the response of miniature ultrasonic hydrophones at frequencies below 1 MHz is important for assessing the accuracy of acoustic pressure pulse measurements in medical ultrasound applications. Therefore, a time delay spectrometry (TDS) system was developed as an efficient means to measure hydrophone sensitivity in this frequency range. In TDS a swept-frequency signal is transmitted. A tracking receiver distinguishes arrivals with different propagation delays by their frequency offset relative to the signal being transmitted, thus eliminating spurious signals such as those reflected from the water surface or tank walls. Two piezoelectric ceramic source transducers were used: a standard planar disk and a disk with varying thickness to broaden the thickness-resonance. This latter design was preferred for its more uniform response without significant sensitivity loss. TDS is not an absolute method, but it was demonstrated to provide efficient, accurate calibrations via comparison with a reference hydrophone using a substitution technique.
A possible neurophysiological basis of the octave enlargement effect
Authors: McKinney Martin F. , Delgutte Bertrand
Published: July 2002

Although the physical octave is defined as a simple ratio of 2:1, listeners prefer slightly greater octave ratios. [J. Acoust. Soc. Am. 73, 1694–1700 (1983)] suggested that a temporal model for octave matching would predict this octave enlargement effect because, in response to pure tones, auditory-nerve interspike intervals are slightly larger than the stimulus period. In an effort to test Ohgushi’s hypothesis, auditory-nerve single-unit responses to pure-tone stimuli were collected from Dial-anesthetized cats. It was found that although interspike interval distributions show clear phase-locking to the stimulus, intervals systematically deviate from integer multiples of the stimulus period. Due to refractory effects, intervals smaller than 5 msec are slightly larger than the stimulus period and deviate most for small intervals. On the other hand, first-order intervals are smaller than the stimulus period for stimulus frequencies less than 500 Hz. It is shown that this deviation is the combined effect of phase-locking and multiple spikes within one stimulus period. A model for octave matching was implemented which compares frequency estimates of two tones based on their interspike interval distributions. The model quantitatively predicts the octave enlargement effect. These results are consistent with the idea that musical pitch is derived from auditory-nerve interspike interval distributions.
Dynamic Rheological Studies of Coagulation and Fibrinolysis
Authors: Kirkpatrick J. P. , McIntire L. V. , Moake J. L. , Peterson D. L.
Published: July 2002

A Weissenberg rheogoniometer in the oscillatory mode was employed to determine the effect of fibrinolysis and fibrinogen degradation products (FDP) on the development of the dynamic shear moduli in coagulating platelet-free plasma (PFP) and platelet-rich plasma (PRP). While the FDP produced by incubation of PFP for 3 min with streptokinase (SK) increased the maximum  shear storage modulus (Gmax′) of PFP, these early FDP decreased the Gmax′ of PRP clots significantly. The FDP produced at longer incubation periods reduced the Gmax′ of PRP clots also. The decreased Gmax′ in PRP containing FDP appears due to FDP inhibiting the binding of polymerizing fibrin to the platelet membrane. While 10 μ/ml of SK did not produce FDP or induce significant fibrinolysis, clot lysis was complete and rapid in the presence of 20 μ/ml SK. Experiments with crosslinking inhibitors indicate that poorly crosslinked clots are more susceptible to fibrinolysis. In addition, a model for coagulation is presented which accurately fits the entire storage modulus-versus-time curve for PFP.