bluuebunny/crossref_metadata_2025 huggingface dataset:
Loading Velocity Effect in the Load/Unload Systems With Multiple Flying Height States
Authors: Khan Polina V. , Hwang Pyung
Published: December 2008

The effect of the loading velocity on the loading process in the computer hard disk drive air slider system with multiple flying height states was studied numerically. The results of the static analysis were compared with the dynamic loading trajectories. The air lubrication problem was solved using the finite-element method. The static flying height states for variable suspension forces were considered as solution branches and were found by using a numerical continuation method. The dynamic loading trajectory was obtained iteratively by applying the Newmark method for the slider position and an implicit scheme for the air film pressure. Close agreement was found between the solution branches and the trajectories of dynamic loading with a velocity of 5 mm/s. At the higher velocities, the unstable negative pitching motion and the slider-disk contact at the slider’s leading edge were detected. Increasing the x-offset of the suspension point made it possible to complete loading with 10 mm/s. At the same time, increasing the x-offset led to the slider-disk contact at the slider’s trailing edge in the beginning of loading with a velocity exceeding 25 mm/s.
Feasibility study for linac‐based intensity modulated total marrow irradiation
Authors: Wilkie Joel R. , Tiryaki Hanifi , Smith Brett D. , Roeske John C. , Radosevich James A. , Aydogan Bulent
Published: December 2008

Total body irradiation (TBI) is used as a preconditioning regimen prior to bone marrow transplant for treatment of hematologic malignancies. During TBI, large volumes of normal tissue are irradiated, and this can lead to toxicities, most significantly in the lungs. Intensity modulated total marrow irradiation (IMTMI) may be able to reduce these toxicities by directly targeting the bone marrow while minimizing the dose to critical structures. The goal of this study was to assess the feasibility of IMTMI by following the planning and delivery process for a Rando phantom. A three isocenter technique was used to provide a full body plan for treatment on a linear accelerator. Thermoluminescent detectors (TLDs) were placed at 22 positions throughout the phantom to compare the delivered doses to the planned doses. Individual intensity modulated radiation therapy verification plans were delivered to a solid water phantom for the three isocenters, and doses measured from an ion chamber and film were compared to the planned doses. The treatment plan indicated that target coverage was achieved with this IMTMI technique, and that the doses to critical structures were reduced by 29%–65% compared to conventional TBI. TLD readings demonstrated accurate dose delivery, with an average difference of 3.5% from the calculated dose. Ion chamber readings for the verification plans were all within 3% of the expected dose, and film measurements showed accurate dose distributions. Results from this study suggest that IMTMI using the three isocenter technique can be accurately delivered and may result in substantial dose reductions to critical structures.
Development of a quantitative method for analysis of breast density based on three‐dimensional breast MRI
Authors: Nie Ke , Chen Jeon‐Hor , Chan Siwa , Chau Man‐Kwun I. , Yu Hon J. , Bahri Shadfar , Tseng Tiffany , Nalcioglu Orhan , Su Min‐Ying
Published: December 2008

Breast density has been established as an independent risk factor associated with the development of breast cancer. It is known that an increase of mammographic density is associated with an increased cancer risk. Since a mammogram is a projection image, different body position, level of compression, and the x‐ray intensity may lead to a large variability in the density measurement. Breast MRI provides strong soft tissue contrast between fibroglandular and fatty tissues, and three‐dimensional coverage of the entire breast, thus making it suitable for density analysis. To develop the MRI‐based method, the first task is to achieve consistency in segmentation of the breast region from the body. The method included an initial segmentation based on body landmarks of each individual woman, followed by fuzzy C‐mean (FCM) classification to exclude air and lung tissue, B‐spline curve fitting to exclude chest wall muscle, and dynamic searching to exclude skin. Then, within the segmented breast, the adaptive FCM was used for simultaneous bias field correction and fibroglandular tissue segmentation. The intraoperator and interoperator reproducibility was evaluated using 11 selected cases covering a broad spectrum of breast densities with different parenchymal patterns. The average standard deviation for breast volume and percent density measurements was in the range of 3%–4% among three trials of one operator or among three different operators. The body position dependence was also investigated by performing scans of two healthy volunteers, each at five different positions, and found the variation in the range of 3%–4%. These initial results suggest that the technique based on three‐dimensional MRI can achieve reasonable consistency to be applied in longitudinal follow‐up studies to detect small changes. It may also provide a reliable method for evaluating the change of breast density for risk management of women, or for evaluating the benefits/risks when considering hormonal replacement therapy or chemoprevention.
On the use of HDR source with the MammoSite® Radiation Therapy System
Authors: Baltas D. , Lymperopoulou G. , Zamboglou N.
Published: December 2008

This work summarizes Monte Carlo results in order to evaluate the potential of using HDR sources in accelerated partial breast irradiation (APBI) with the MammoSite® applicator. Simulations have been performed using the MCNP5 Monte Carlo Code, in simple geometries comprised of two concentric spheres; the internal consisting of selected concentrations, C, of a radiographic contrast solution in water (Omnipaque 300™) to simulate the MammoSite balloon and the external consisting of water to simulate surrounding tissue. The magnitude of the perturbation of delivered dose due to the radiographic contrast medium used in the MammoSite® applicator is calculated. At the very close vicinity of the balloon surface, a dose build‐up region is observed, which leads to a dose overestimation by the treatment planning system (TPS) which depends on Omnipaque™ 300 solution concentration (and is in order of 2.3%, 3.0%, and 4.5%, respectively, at 1 mm away from the balloon ‐ water interface, for C=10%, 15%, and 20%). However, dose overestimation by the TPS is minimal for points lying at the prescription distance ( cm) or beyond, for all simulated concentrations and radii of MammoSite® balloon. An analytical estimation of the integral dose outside the CTV in the simple geometries simulated shows that dose to the breast for MammoSite® applications is expected to be comparable using HDR and sources, and higher than that for . The higher enegies of sources result to approximately twice radiation protection requirements as compared to sources. However, they allow for more accurate dosimetry calculation with currently used treatment planning algorithms for sources, compared to .
In vivo accuracy assessment of a needle‐based navigation system for CT‐guided radiofrequency ablation of the liver
Authors: Maier‐Hein Lena , Tekbas Aysun , Seitel Alexander , Pianka Frank , Müller Sascha A. , Satzl Stefanie , Schawo Simone , Radeleff Boris , Tetzlaff Ralf , Franz Alfred M. , Müller‐Stich Beat P. , Wolf I. , Kauczor H.‐U. , Schmied B. M. , Meinzer H.‐P.
Published: December 2008

Computed tomography (CT)‐guided percutaneous radiofrequency ablation (RFA) has become a commonly used procedure in the treatment of liver tumors. One of the main challenges related to the method is the exact placement of the instrument within the lesion. To address this issue, a system was developed for computer‐assisted needle placement which uses a set of fiducial needles to compensate for organ motion in real time. The purpose of this study was to assess the accuracy of the system in vivo. Two medical experts with experience in CT‐guided interventions and two nonexperts used the navigation system to perform 32 needle insertions into contrasted agar nodules injected into the livers of two ventilated swine. Skin‐to‐target path planning and real‐time needle guidance were based on preinterventional CT data slices. The lesions were hit in 97% of all trials with a mean user error of , a mean target registration error (TRE) of , and a mean overall targeting error of . The nonexperts achieved significantly better results than the experts with an overall error of compared to . The mean time for performing four needle insertions based on one preinterventional planning CT was with a mean setup time of , which includes the steps fiducial insertion , planning CT acquisition , and registration . The mean time for path planning and targeting was and , respectively. Apart from the fiducial insertion step, experts and nonexperts performed comparably fast. It is concluded that the system allows for accurate needle placement into hepatic tumors based on one planning CT and could thus enable considerable improvement to the clinical treatment standard for RFA procedures and other CT‐guided interventions in the liver. To support clinical application of the method, optimization of individual system modules to reduce intervention time is proposed.
Mechanically assisted 3D ultrasound guided prostate biopsy system
Authors: Bax Jeffrey , Cool Derek , Gardi Lori , Knight Kerry , Smith David , Montreuil Jacques , Sherebrin Shi , Romagnoli Cesare , Fenster Aaron
Published: December 2008

There are currently limitations associated with the prostate biopsy procedure, which is the most commonly used method for a definitive diagnosis of prostate cancer. With the use of two‐dimensional (2D) transrectal ultrasound (TRUS) for needle‐guidance in this procedure, the physician has restricted anatomical reference points for guiding the needle to target sites. Further, any motion of the physician's hand during the procedure may cause the prostate to move or deform to a prohibitive extent. These variations make it difficult to establish a consistent reference frame for guiding a needle. We have developed a 3D navigation system for prostate biopsy, which addresses these shortcomings. This system is composed of a 3D US imaging subsystem and a passive mechanical arm to minimize prostate motion. To validate our prototype, a series of experiments were performed on prostate phantoms. The 3D scan of the string phantom produced minimal geometric distortions, and the geometric error of the 3D imaging subsystem was . The accuracy of 3D prostate segmentation was determined by comparing the known volume in a certified phantom to a reconstructed volume generated by our system and was shown to estimate the volume with less then 5% error. Biopsy needle guidance accuracy tests in agar prostate phantoms showed that the mean error was and the 3D location of the biopsy core was recorded with a mean error of . In this paper, we describe the mechanical design and validation of the prototype system using an in vitro prostate phantom. Preliminary results from an ongoing clinical trial show that prostate motion is small with an in‐plane displacement of less than during the biopsy procedure.
A genetic algorithm for variable selection in logistic regression analysis of radiotherapy treatment outcomes
Authors: Gayou Olivier , Das Shiva K. , Zhou Su‐Min , Marks Lawrence B. , Parda David S. , Miften Moyed
Published: December 2008

A given outcome of radiotherapy treatment can be modeled by analyzing its correlation with a combination of dosimetric, physiological, biological, and clinical factors, through a logistic regression fit of a large patient population. The quality of the fit is measured by the combination of the predictive power of this particular set of factors and the statistical significance of the individual factors in the model. We developed a genetic algorithm (GA), in which a small sample of all the possible combinations of variables are fitted to the patient data. New models are derived from the best models, through crossover and mutation operations, and are in turn fitted. The process is repeated until the sample converges to the combination of factors that best predicts the outcome. The GA was tested on a data set that investigated the incidence of lung injury in NSCLC patients treated with 3DCRT. The GA identified a model with two variables as the best predictor of radiation pneumonitis: the V30and the ongoing use of tobacco at the time of referral. This two‐variable model was confirmed as the best model by analyzing all possible combinations of factors. In conclusion, genetic algorithms provide a reliable and fast way to select significant factors in logistic regression analysis of large clinical studies.
Technical Note: Rapid prototyping of 3D grid arrays for image guided therapy quality assurance
Authors: Kittle David , Holshouser Barbara , Slater James M. , Guenther Bob D. , Pitsianis Nikos P. , Pearlstein Robert D.
Published: December 2008

Three dimensional grid phantoms offer a number of advantages for measuring imaging related spatial inaccuracies for image guided surgery and radiotherapy. The authors examined the use of rapid prototyping technology for directly fabricating 3D grid phantoms from CAD drawings. We tested three different fabrication process materials, photopolymer jet with acrylic resin (PJ/AR), selective laser sintering with polyamide (SLS/P), and fused deposition modeling with acrylonitrile butadiene styrene (FDM/ABS). The test objects consisted of rectangular arrays of control points formed by the intersections of posts and struts ( rectangular cross section) and spaced apart in the , , and directions. The PJ/AR phantom expanded after immersion in water which resulted in permanent warping of the structure. The surface of the FDM/ABS grid exhibited a regular pattern of depressions and ridges from the extrusion process. SLS/P showed the best combination of build accuracy, surface finish, and stability. Based on these findings, a grid phantom for assessing machine‐dependent and frame‐induced MR spatial distortions was fabricated to be used for quality assurance in stereotactic neurosurgical and radiotherapy procedures. The spatial uniformity of the SLS/P grid control point array was determined by CT imaging ( resolution) and found suitable for the application, with over 97.5% of the control points located within of the position specified in CAD drawing and none of the points off by more than . Rapid prototyping is a flexible and cost effective alternative for development of customized grid phantoms for medical physics quality assurance.
Technical note: Heterogeneity dose calculation accuracy in IMRT: Study of five commercial treatment planning systems using an anthropomorphic thorax phantom
Authors: Davidson Scott E. , Popple Richard A. , Ibbott Geoffrey S. , Followill David S.
Published: December 2008

The purpose of this study was to determine the accuracy of five commonly used intensity‐modulated radiation therapy (IMRT) treatment planning systems (TPSs), 3 using convolution superposition algorithms or the analytical anisotropic algorithm (CSA/AAAs) and 2 using pencil beam algorithms (PBAs), in calculating the absorbed dose within a low‐density, heterogeneous region when compared with measurements made in an anthropomorphic thorax phantom. The dose predicted in the target center met the test criteria (5% of the dose normalization point or 3 mm distance to agreement) for all TPSs tested; however, at the tumor‐lung interface and at the peripheral lung in the vicinity of the tumor, the CSA/AAAs performed better than the PBAs (85% and 50%, respectively, of pixels meeting the 5%/3‐mm test criteria), and thus should be used to determine dose in heterogeneous regions.
Scale‐based scatter correction for computer‐aided polyp detection in CT colonography
Authors: Liu Jiamin , Yao Jianhua , Summers Ronald M.
Published: December 2008

CT colonography (CTC) is a feasible and minimally invasive method for the detection of colorectal polyps and cancer screening. Computer‐aided detection (CAD) of polyps can improve consistency and sensitivity of virtual colonoscopy interpretation and reduce interpretation burden. However, high‐density orally administered contrast agents have scatter effects on neighboring tissues. The scattering manifests itself as an artificial elevation in the observed CT attenuation values of the neighboring tissues. This pseudoenhancement phenomenon presents a problem for the application of computer‐aided polyp detection, especially when polyps are submerged in the contrast agents. The authors have developed a scale‐based correction method that minimizes scatter effects in CTC data by subtraction of the estimated scatter components from observed CT attenuations. By bringing a locally adaptive structure, object scale, into the correction framework, the region of neighboring tissues affected by contrast agents is automatically specified and adaptively changed in different parts of the image. The method was developed as one preprocessing step in the authors’ CAD system and was tested by using leave‐one‐patient‐out evaluation on 56 clinical CTC scans (supine or prone) from 28 patients. There were 50 colonoscopy‐confirmed polyps measuring . Visual evaluation indicated that the method reduced CT attenuation of pseudoenhanced polyps to the usual polyp Hounsfield unit range without affecting luminal air regions. For polyps submerged in contrast agents, the sensitivity of CAD with correction is increased 24% at a rate of ten false‐positive detections per scan. For all polyps within , the sensitivity of the authors’ CAD with scatter correction is increased 8% at a rate of ten false‐positive detections per scan. The authors’ results indicated that CAD with this correction method as a preprocessing step can yield a high sensitivity and a relatively low FP rate in CTC.
Image reconstruction and image quality evaluation for a dual source CT scanner
Authors: Flohr T. G. , Bruder H. , Stierstorfer K. , Petersilka M. , Schmidt B. , McCollough C. H.
Published: December 2008

The authors present and evaluate concepts for image reconstruction in dual source CT (DSCT). They describe both standard spiral (helical) DSCT image reconstruction and electrocardiogram (ECG)‐synchronized image reconstruction. For a compact mechanical design of the DSCT, one detector (A) can cover the full scan field of view, while the other detector (B) has to be restricted to a smaller, central field of view. The authors develop an algorithm for scan data completion, extrapolating truncated data of detector (B) by using data of detector (A). They propose a unified framework for convolution and simultaneous 3D backprojection of both (A) and (B) data, with similar treatment of standard spiral, ECG‐gated spiral, and sequential (axial) scan data. In ECG‐synchronized image reconstruction, a flexible scan data range per measurement system can be used to trade off temporal resolution for reduced image noise. Both data extrapolation and image reconstruction are evaluated by means of computer simulated data of anthropomorphic phantoms, by phantom measurements and patient studies. The authors show that a consistent filter direction along the spiral tangent on both detectors is essential to reduce cone‐beam artifacts, requiring truncation of the extrapolated (B) data after convolution in standard spiral scans. Reconstructions of an anthropomorphic thorax phantom demonstrate good image quality and dose accumulation as theoretically expected for simultaneous 3D backprojection of the filtered (A) data and the truncated filtered (B) data into the same 3D image volume. In ECG‐gated spiral modes, spiral slice sensitivity profiles (SSPs) show only minor dependence on the patient's heart rate if the spiral pitch is properly adapted. Measurements with a thin gold plate phantom result in effective slice widths (full width at half maximum of the SSP) of for the nominal slice and for the nominal slice. The visually determined through‐plane ( axis) spatial resolution in a bar pattern phantom is for the nominal slice and for the nominal slice, again almost independent of the patient's heart rate. The authors verify the theoretically expected temporal resolution of at gantry rotation time by blur free images of a moving coronary artery phantom with rest phase and demonstrate image noise reduction as predicted for increased reconstruction data ranges per measurement system. Finally, they show that the smoothness of the transition between image stacks acquired in different cardiac cycles can be efficiently controlled with the proposed approach for ECG‐synchronized image reconstruction.
Investigation of psychophysical similarity measures for selection of similar images in the diagnosis of clustered microcalcifications on mammograms
Authors: Muramatsu Chisako , Li Qiang , Schmidt Robert , Shiraishi Junji , Doi Kunio
Published: December 2008

The presentation of images with lesions of known pathology that are similar to an unknown lesion may be helpful to radiologists in the diagnosis of challenging cases for improving the diagnostic accuracy and also for reducing variation among different radiologists. The authors have been developing a computerized scheme for automatically selecting similar images with clustered microcalcifications on mammograms from a large database. For similar images to be useful, they must be similar from the point of view of the diagnosing radiologists. In order to select such images, subjective similarity ratings were obtained for a number of pairs of clustered microcalcifications by breast radiologists for establishment of a “gold standard” of image similarity, and the gold standard was employed for determination and evaluation of the selection of similar images. The images used in this study were obtained from the Digital Database for Screening Mammography developed by the University of South Florida. The subjective similarity ratings for 300 pairs of images with clustered microcalcifications were determined by ten breast radiologists. The authors determined a number of image features which represent the characteristics of clustered microcalcifications that radiologists would use in their diagnosis. For determination of objective similarity measures, an artificial neural network (ANN) was employed. The ANN was trained with the average subjective similarity ratings as teacher and selected image features as input data. The ANN was trained to learn the relationship between the image features and the radiologists’ similarity ratings; therefore, once the training was completed, the ANN was able to determine the similarity, called a psychophysical similarity measure, which was expected to be close to radiologists’ impressions, for an unknown pair of clustered microcalcifications. By use of a leave‐one‐out test method, the best combination of features was selected. The correlation coefficient between the gold standard and the psychophysical similarity measure through the use of seven features was relatively high and was comparable to the correlation coefficients between the ratings by one radiologist and the average ratings by nine radiologists . The correlation coefficient was improved compared to that of a distance‐based method . The result indicated that similar images selected by the psychophysical similarity measure may be useful to radiologists in the diagnosis of clustered microcalcifications on mammograms.
Optical Absorption and Radiative Thermal Conductivity of Silicate Perovskite to 125 Gigapascals
Authors: Keppler Hans , Dubrovinsky Leonid S. , Narygina Olga , Kantor Innokenty
Published: December 2008

Mantle convection and plate tectonics are driven by the heat flow from Earth's core to the surface. The radiative contribution to heat transport is usually assumed to be negligible. Here, we report the near-infrared and optical absorption spectra of silicate perovskite, the main constituent of the lower mantle, to 125 gigapascals. Silicate perovskite remains quite transparent up to the pressures at the core-mantle boundary. Estimates of radiative thermal conductivity derived from these spectra approach 10 watts meter
–1
kelvin
–1
at lowermost mantle conditions, implying that heat conduction is dominated by radiation. However, the increase in radiative conductivity with temperature (
T
) is less pronounced than expected from a
T
3
dependency.
Design and Validation of a Microarray for Detection, Hemagglutinin Subtyping, and Pathotyping of Avian Influenza Viruses
Authors: Gall Astrid , Hoffmann Bernd , Harder Timm , Grund Christian , Höper Dirk , Beer Martin
Published: December 2008

Continuing threats of devastating outbreaks in poultry and of human infections caused by highly pathogenic avian influenza virus (HPAIV) H5N1 emphasize the need for the further development of rapid and reliable methods of virus detection and characterization. Here we report on the design and comprehensive validation of a low-density microarray as a diagnostic tool for the detection and typing of avian influenza virus (AIV). The array consists of one probe for the conserved matrix gene and 97 probes targeting the HA
0
cleavage-site region. Following fragment amplification by a generic PCR approach, the array enables AIV detection, hemagglutinin (HA) subtyping, and pathotyping within a single assay. For validation, a panel of 92 influenza A viruses which included 43 reference strains representing all 16 HA subtypes was used. All reference strains were correctly typed with respect to their HA subtypes and pathotypes, including HPAIV H5N1/Asia, which caused outbreaks in Germany in 2006 and 2007. In addition, differentiation of strains of the Eurasian and North American lineages of the H5 and H7 subtypes was possible. The sensitivity of the microarray for the matrix gene is comparable to that of real-time reverse transcription-PCR (RT-PCR). It is, however, 10- to 100-fold lower than that of real-time RT-PCR with respect to HA subtyping and pathotyping. The specificity of the array was excellent, as no pathogens relevant for differential diagnosis yielded a positive reaction. Validation with field samples included 19 cloacal swab specimens from wild and domestic birds. Influenza A virus was verified in all samples, whereas the HA subtypes could be determined for 14 samples. The results demonstrate that the microarray assay described complements current methods and can accelerate the diagnosis and characterization of AIV.
Longer Intestinal Persistence of
Enterococcus faecalis
Compared to
Enterococcus faecium
Clones in Intensive-Care-Unit Patients
Authors: Ruiz-Garbajosa Patricia , del Campo Rosa , Coque Teresa M. , Asensio Angel , Bonten Marc , Willems Rob , Baquero Fernando , Cantón Rafael
Published: December 2008

The dynamics of intestinal colonization with enterococcal clones in intensive-care-unit (ICU) patients was evaluated. Eight patients admitted directly to the neurosurgical ICU at the Ramón y Cajal University Hospital (Madrid, Spain) from the community and with no overlapping stay during a 10-month period in 2006 were studied. Rectal swab specimens were collected on admission and daily until the patients were discharged. Clonality was determined by pulsed-field gel electrophoresis and multilocus sequence typing. Clonal colonization dynamics were estimated by using two new parameters: the clonal diversity per patient per day (CDPD) and the clonal persistence ratio (CPR).
Enterococcus faecalis
isolates (
n
= 123) and
Enterococcus faecium
isolates (
n
= 66) were resolved into 13 and 15 clones, respectively. The CDPD of
E. faecalis
steadily increased during admission, and
E. faecalis
showed a higher (
P
= 0.001) CPR value than
E. faecium
(0.86 and 0.42, respectively).
E. faecium
, with the exception of an ampicillin-resistant clone belonging to clonal complex 17, frequently appeared as a short-term colonizer, even though the
E. faecalis
clones had significantly (
P
= 0.03) more days under antibiotic exposure than
E. faecium
(77.5 and 65 days/100 colonization days, respectively).
E. faecalis
had a longer persistence than
E. faecium
, except for the CC17 ampicillin-resistant clone, and
E. faecalis
showed a cumulative increase in CDPD, whereas
E. faecium
did not. CDPD and CPR were useful for measuring the dynamics of intestinal colonization with enterococcal clones.
Detection and Isolation of
Campylobacter
Species Other than
C. jejuni
from Children with Crohn's Disease
Authors: Zhang Li , Man Si Ming , Day Andrew S. , Leach Steven T. , Lemberg Daniel A. , Dutt Shoma , Stormon Michael , Otley Anthony , O'Loughlin Edward V. , Magoffin Annabel , Ng Patrick H. Y. , Mitchell Hazel
Published: December 2008

The presence of
Campylobacter
species other than
Campylobacter jejuni
and antibodies to
Campylobacter concisus
in children were investigated. A significantly greater presence of
C. concisus
and higher levels of antibodies to
C. concisus
were detected in children with Crohn's disease (CD) than in controls.
Campylobacter
species other than
C. jejuni
were isolated from intestinal biopsy specimens of children with CD.
Clinic-Based Evaluation of a Rapid Point-of-Care Test for Detection of
Chlamydia trachomatis
in Specimens from Sex Workers in Escuintla, Guatemala
Authors: Sabidó M. , Hernández G. , González V. , Vallès X. , Montoliu A. , Figuerola J. , Isern V. , Viñado B. , Figueroa L. , Casabona J.
Published: December 2008

We evaluated a rapid point-of-care test for the detection of
Chlamydia trachomatis
in specimens from 278 sex workers attending sexually transmitted infection clinics in Guatemala. The sensitivity and the specificity of the test compared to the results of PCR were 62.96% and 99.60%, respectively. The test performed moderately well as a screening tool in a context in which clinical follow-up visits are infrequent.
Identification of Sendai Virus L Protein Amino Acid Residues Affecting Viral mRNA Cap Methylation
Authors: Murphy Andrea M. , Grdzelishvili Valery Z.
Published: December 2008

Viruses of the order
Mononegavirales
all encode a large (L) polymerase protein responsible for the replication and transcription of the viral genome as well as all posttranscriptional modifications of viral mRNAs. The L protein is conserved among all members of the
Mononegavirales
and has six conserved regions (“domains”). Using vesicular stomatitis virus (VSV) (family
Rhabdoviridae
) experimental system, we and others recently identified several conserved amino acid residues within L protein domain VI which are required for viral mRNA cap methylation. To verify that these critical amino acid residues have a similar function in other members of the
Mononegavirales
, we examined the Sendai virus (SeV) (family
Paramyxoviridae
) L protein by targeting homologous amino acid residues important for cap methylation in VSV which are highly conserved among all members of the
Mononegavirales
and are believed to constitute the L protein catalytic and
S
-adenosylmethionine-binding sites. In addition, an SeV L protein mutant with a deletion of the entire domain VI was generated. First, L mutants were tested for their abilities to synthesize viral mRNAs. While the domain VI deletion completely inactivated L, most of the amino acid substitutions had minor effects on mRNA synthesis. Using a reverse genetics approach, these mutations were introduced into the SeV genome, and recombinant infectious SeV mutants with single alanine substitutions at L positions 1782, 1804, 1805, and 1806 or a double substitution at positions 1804 and 1806 were generated. The mutant SeV virions were purified, detergent activated, and analyzed for their abilities to synthesize viral mRNAs methylated at their cap structures. In addition, further studies were done to examine these SeV mutants for a possible host range phenotype, which was previously shown for VSV cap methylation-defective mutants. In agreement with a predicted role of the SeV L protein invariant lysine 1782 as a catalytic residue, the recombinant virus with a single K1782A substitution was completely defective in cap methylation and showed a host range phenotype. In addition, the E1805A mutation within the putative
S
-adenosylmethionine-binding site of L resulted in a 60% reduction in cap methylation. In contrast to the homologous VSV mutants, other recombinant SeV mutants with amino acid substitutions at this site were neither defective in cap methylation nor host range restricted. The results of this initial study using an SeV experimental system demonstrate similarities as well as differences between the L protein cap methylation domains in different members of the
Mononegavirales
.
Nuclear Magnetic Resonance Structure Shows that the Severe Acute Respiratory Syndrome Coronavirus-Unique Domain Contains a Macrodomain Fold
Authors: Chatterjee Amarnath , Johnson Margaret A. , Serrano Pedro , Pedrini Bill , Joseph Jeremiah S. , Neuman Benjamin W. , Saikatendu Kumar , Buchmeier Michael J. , Kuhn Peter , Wüthrich Kurt
Published: December 2008

The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for “middle of the SARS-unique domain”) in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1"-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.
PB2 Protein of a Highly Pathogenic Avian Influenza Virus Strain A/chicken/Yamaguchi/7/2004 (H5N1) Determines Its Replication Potential in Pigs
Authors: Manzoor Rashid , Sakoda Yoshihiro , Nomura Naoki , Tsuda Yoshimi , Ozaki Hiroichi , Okamatsu Masatoshi , Kida Hiroshi
Published: December 2008

It has been shown that not all but most of the avian influenza viruses replicate in the upper respiratory tract of pigs (H. Kida et al., J. Gen. Virol. 75:2183-2188, 1994). It was shown that A/chicken/Yamaguchi/7/2004 (H5N1) [Ck/Yamaguchi/04 (H5N1)] did not replicate in pigs (N. Isoda et al., Arch. Virol. 151:1267-1279, 2006). In the present study, the genetic basis for this host range restriction was determined using reassortant viruses generated between Ck/Yamaguchi/04 (H5N1) and A/swine/Hokkaido/2/1981 (H1N1) [Sw/Hokkaido/81 (H1N1)]. Two in vivo-generated single-gene reassortant virus clones of the H5N1 subtype (virus clones 1 and 2), whose PB2 gene was of Sw/Hokkaido/81 (H1N1) origin and whose remaining seven genes were of Ck/Yamaguchi/04 (H5N1) origin, were recovered from the experimentally infected pigs. The replicative potential of virus clones 1 and 2 was further confirmed by using reassortant virus (rg-Ck-Sw/PB2) generated by reverse genetics. Interestingly, the PB2 gene of Ck/Yamaguchi/04 (H5N1) did not restrict the replication of Sw/Hokkaido/81 (H1N1), as determined by using reassortant virus rg-Sw-Ck/PB2. The rg-Sw-Ck/PB2 virus replicated to moderate levels and for a shorter duration than parental Sw/Hokkaido/81 (H1N1). Sequencing of two isolates recovered from the pigs inoculated with rg-Sw-Ck/PB2 revealed either the D256G or the E627K amino acid substitution in the PB2 proteins of the isolates. The D256G and E627K mutations enhanced viral polymerase activity in the mammalian cells, correlating with replication of virus in pigs. These results indicate that the PB2 protein restricts the growth of Ck/Yamaguchi/04 (H5N1) in pigs.
MULTISENSORY DETECTION SYSTEM FOR DAMAGE CONTROL AND SITUATIONAL AWARENESS
Authors: MINOR CHRISTIAN P. , STEINHURST DANIEL A. , JOHNSON KEVIN J. , ROSE-PEHRSSON SUSAN L. , OWRUTSKY JEFFREY C. , WALES STEPHEN C. , GOTTUK DANIEL T.
Published: December 2008

A data fusion-based, multisensory detection system, called “Volume Sensor”, was developed under the Advanced Damage Countermeasures (ADC) portion of the US Navy's Future Naval Capabilities program (FNC) to meet reduced manning goals. A diverse group of sensing modalities was chosen to provide an automated damage control monitoring capability that could be constructed at a relatively low cost and also easily integrated into existing ship infrastructure. Volume Sensor employs an efficient, scalable, and adaptable design framework that can serve as a template for heterogeneous sensor network integration for situational awareness. In the development of Volume Sensor, a number of challenges were addressed and met with solutions that are applicable to heterogeneous sensor networks of any type. These solutions include: 1) a uniform, but general format for encapsulating sensor data, 2) a communications protocol for the transfer of sensor data and command and control of networked sensor systems, 3) the development of event specific data fusion algorithms, and 4) the design and implementation of modular and scalable system architecture. In full-scale testing on a shipboard environment, two prototype Volume Sensor systems demonstrated the capability to provide highly accurate and timely situational awareness regarding damage control events while simultaneously imparting a negligible footprint on the ship's 100 Mbps Ethernet network and maintaining smooth and reliable operation in a real-time fashion.
LINEAR AND NONLINEAR TAILS I: GENERAL RESULTS AND PERTURBATION THEORY
Authors: SZPAK NIKODEM
Published: December 2008

For nonlinear wave equations with a potential term, we prove pointwise space-time decay estimates and develop a perturbation theory for small initial data. We show that the perturbation series has a positive convergence radius by a method which reduces the wave equation to an algebraic one. We demonstrate that already first and second perturbation orders, satisfying linear equations, can provide precise information about the decay of the full solution to the nonlinear wave equation.
A PRIORI ESTIMATES FOR MANY-BODY HAMILTONIAN EVOLUTION OF INTERACTING BOSON SYSTEM
Authors: GRILLAKIS MANOUSSOS G. , MARGETIS DIONISIOS
Published: December 2008

We study the evolution of a many-particle system whose wave function obeys the N-body Schrödinger equation under Bose symmetry. The system Hamiltonian describes pairwise particle interactions in the absence of an external potential. We derive a priori dispersive estimates that express the overall repulsive nature of the particle interactions. These estimates hold for a wide class of two-body interaction potentials which are independent of the particle number, N. We discuss applications of these estimates to the BBGKY hierarchy for reduced density matrices analyzed by Elgart, Erdős, Schlein and Yau.
Emerging Insights into Antibiotic-Associated Diarrhea andClostridium difficileInfection through the Lens of Microbial Ecology
Authors: Walk Seth T. , Young Vincent B.
Published: December 2008

Antibiotics are the main, and often only, clinical intervention for prophylactic and active treatment of bacterial infections in humans. Perhaps it is not surprising that these drugs also shift the composition of commensal bacteria inside our bodies, especially those within the gut microbial community (microbiota). How these dynamics ultimately affect the function of the gut microbiota, however, is not fully appreciated. Likewise, how antibiotic induced changes facilitate the outgrowth and pathogenicity of certain bacterial strains remains largely enigmatic. Here, we discuss the merits of a microbial ecology approach toward understanding a common side effect of antibiotic use, antibiotic-associated diarrhea (AAD), and the opportunistic bacterial infections that sometimes underlie it. As an example, we discuss how this approach is being used to address complex disease dynamics duringClostridium difficileinfection.
A Novel and One-Pot Synthesis of 6-arylpyrimidin-4-ol
Authors: Gajera Jitendra M. , Tondlekar Shital N. , Gharat Laxmikant A.
Published: December 2008

We have developed a novel and one-pot synthesis of 6-arylpyrimidine-4-ol by reacting commercially available alkyl 3-oxo-3-arylpropanoate with formamide in the presence of stoichiometric amount of ammonium acetate.
IDE Gene Polymorphism Influences on BPSD in Mild Dementia of Alzheimer's Type
Authors: Sato Noriko , Ueki Akinori , Ueno Hideo , Shinjo Hidetaka , Morita Yoshio
Published: December 2008

Insulin degrading enzyme (IDE) degrades amyloid (A), which may inhibit the accumulation of A in a brain affected with dementia of Alzheimer's type (DAT). A decrease in the activity of IDE results in changes in glucose utilization in the brain, which could affect the cognitive and psychiatric symptoms of DAT. We investigated a possible association of IDE gene polymorphism and the behavioral and psychological symptoms of dementia (BPSD) in mild DAT. The genotyping for IDE and apolipoprotein E (ApoE) was determined in 207 patients with mild DAT and 215 controls. The occurrence of BPSD was demonstrated using the Behavioral Pathology in Alzheimer's Disease Rating Scale (BEHAVE-AD). IDE gene polymorphism is unlikely to play a substantial role in conferring susceptibility to DAT, but it may be involved in the development of affective disturbance through the course of mild DAT, regardless of the presence of an ApoE 4 allele. The present data could be the result of a small sample size. Further investigations using larger samples are thus required to clarify the correlation between IDE gene polymorphism, susceptibility to DAT, and emergence of BPSD.
Culture and Implicit Self-Esteem
Authors: Boucher Helen C. , Kaiping Peng  , Junqi Shi  , Lei Wang
Published: December 2008

One explanation for the lower self-esteem of East Asians is that they have dialectical, or inconsistent, self-esteem in that they endorse both the positively and the negatively keyed items of the Rosenberg Self-Esteem Scale, relative to Euro-Americans. The following research extended this effect to implicit self-esteem. In two studies, Chinese, Euro-Americans (Studies 1 and 2), and Chinese Americans (Study 2) completed explicit and implicit measures of self-esteem. On both types of measures, Chinese scored most highly on various indices of dialectical self-esteem. In Study 2, the explicit self-esteem of Chinese Americans was similar to that of Chinese, but their implicit self-esteem was identical to that of Euro-Americans. In the discussion, we focus on how East Asians come to possess inconsistent self-esteem and pose questions for future research.
How to Order a Beer
Authors: Pika Simone , Nicoladis Elena , Marentette Paula
Published: December 2008

It is said that conventional gestures for numbers differ by culture. Conventional gestures are thought to imply consistency of form both across and within individuals. The present study tests the consistency of finger gestures of 60 participants of three different cultures and in three different mother tongues in nine different hypothetical scenarios. The first subject of analysis is whether participants differentiate between counting and signaling. The second subject is the consistency of gestures within and between groups. The third is how participants depict the number 1. Result show that most people use the same gestures for counting and signaling. In addition, Germans and English Canadians show relatively low degrees of individual differences whereas French Canadians show relatively high degrees of individual variability. Furthermore, only the Germans use the thumb to indicate the number 1, whereas the two North American cultures use the index finger. The present data suggest that finger gestures of some cultures clearly qualify as conventional gestures whereas others do not. It is suggested that the development of conventional gestures is influenced by cultural exposure, which can even result into the loosening of conventions.
Professional Identity and the Future of Rehabilitation Counseling
Authors: Patterson Jeanne B.
Published: December 2008

This article describes a vision of rehabilitation counseling, wherein both the profession of rehabilitation counseling and the diverse roles of rehabilitation counselors are recognized and valued by rehabilitation counselors, the general public, and other professionals in promoting social justice and equal opportunity for individuals with disabilities. Using parallels with psychology, this article describes opportunities and challenges related to the visibility and centrality of rehabilitation counseling in society. Marketing is a key element in moving rehabilitation counseling from a fringe activity to a central, well-known profession. Recommendations to make rehabilitation counseling central to society include rehabilitation professional associations and other constituencies (a) working together to market the profession, which can capitalize on the ever-expanding number of career opportunities for rehabilitation counselors and (b) leveraging resources for the common good while respecting our differences.
Judgment Deferred
Authors: Tarvydas Vilia , Leahy Michael J. , Zanskas Stephen A.
Published: December 2008

Fifteen years have passed since an analysis of the position of rehabilitation counselors in the national counselor licensure movement by Tarvydas and Leahy. This article addresses the question of how well their efforts to achieve licensure parity with other counselors have fared. This question will be addressed by discussing (a) rehabilitation counseling developments that have influenced licensure progress, (b) shifts in the nature of professionalization and efforts toward rehabilitation counseling parity, and (c) counselor licensure trends and rehabilitation counseling status within them. Specific recommendations are provided that would assist the field of rehabilitation counseling in meeting the urgent challenges that confront them in consolidating its position in the maturing counselor licensure movement before it is further disadvantaged.
Developmental Considerations and Acculturation of Children
Authors: López Francesca A.
Published: December 2008

This article presents the secondary validation of the Brief Acculturation Rating Scale for Mexican Americans-II (Brief ARSMA-II) for use with children— carried out using two samples of Mexican-descent children (ages = 9-11) from two states ( N = 295). The Brief ARSMA-II was originally normed on adolescents and adults but has been validated and used with children. Ethnic identity development perspectives suggest that the interpretation of scores derived from acculturation measures normed on adolescents and adults may not extend accurately to children. Convergent validity and differential discrimination between groups were examined using scores on the Brief ARSMA-II; scores on an acculturation measure designed for the present study, the Things About Me (TAM); and traditional proxy measures of acculturation. Results from this study do not support the use of the Brief ARSMA-II with children. The importance of considering contextual effects in the interpretation of scores of children's acculturation experience is discussed.