bluuebunny/crossref_metadata_2025 huggingface dataset:
Large Eddy Simulation Using a High-Order Nodal Discontinuous Galerkin Method on Unstructured Grids
Authors: Sengupta K. , Mashayek F. , Jacobs G. B.
Published: April 2008

In this paper we discuss the development of a robust, high-order Discontinuous Galerkin (DG) spectral element method for LES of compressible flows. The method secures geometrical flexibility through a fully unstructured grid (triangles in 2D and tetrahedral elements in 3D), allows for arbitrary order of accuracy and has excellent stability properties. An element based filtering technique is used in conjunction with the dynamic procedure to model the effect of sub-grid scales.
Nonlinear Stress and Temperature Creep Relations in Polymer Nanocomposites
Authors: Shaito Ali A. , D'Souza Nandika A. , Fairbrother Debora , Sterling Jerry
Published: April 2008

Stress and temperature response of Polyethylene (PE) nanocomposites is mapped and predicted using creep-recovery measurements. The results indicate that the PE nanocomposite exhibit nonlinear response. When montmorillonite layered silicates (MLS) are introduced into the polymer, the stress response deviates substantially. Recovery curves of the nanocomposites were lower than those of the creep response. Viscoplastic strain was lower in the case of the nanocomposites. The material responses are analyzed using mechanical analogs.
Damage Detection in Composite Beam Using the Temperature Distribution
Authors: Medici Ezequiel , Cecchini Andres , Serrano David , Just Frederick
Published: April 2008

Marine, aerospace, ground and civil structures can receive unexpected loading that may compromise integrity during their life span. Therefore, improvement in detecting damage can save revenue and lives depending upon the application. The prognostic capability is usually a function of the examiner's experience, background and data collection during the evaluation. Nondestructive evaluation (NDE) methods are varied and specific to a given type of system (material, damage type, loading and environmental scenarios). As a result, one method of damage detection alone cannot examine all possible conditions and may even give false readings. This work examined the transient thermal response technique to assess damage in a sandwich composite structure. The mathematical formulation of the problem is presented. Then, a numerical approximation technique is used to solve the governing equations. The thermal distribution on the surface of a beam model is analyzed when damage is introduced. Then, an experimental setup with an Infrared (IR) thermography camera was assembled in order to provide the necessary information about the surface temperature distribution over the beam. Several damages scenarios will be tested by the technique with the purpose of determining the limitations of the method. The obtained experimental data was used to validate the numerical model. Finally, the feasibility of this feature to use in damage detection is discussed.
In-Situ Frequency Tuning of Electrostatically Actuated Vibrating Nano Structures Using Focused Ion Beam
Authors: Chang Jiyoung , Kim Jongbaeg , Min Byung-Kwon , Lee Sang Jo , Lin Liwei
Published: April 2008

Schemes for in-situ resonant frequency tuning of nano scale vibrating structures using Focused Ion Beam (FIB) sputtering and FIB-Chemical Vapor Deposition (CVD) are presented. This approach introduces precisely controlled permanent increase or decrease of resonant frequencies on processed nano structures, enabling the frequency adjustment when the desired resonant frequency is higher or lower than the actual frequency of the fabricated resonators. The vibration is induced by electrostatic force between resonator and stator using 0~10V AC input and all the processes including fabrication of nanostructure, electrostatic actuation, vibration observation and frequency tuning in either higher or lower direction were successfully conducted in single FIB chamber. The range of the frequency tuned from 600kHz initial resonant frequency is +6kHz with -1.9μm and -65kHz with +1.1μm length change of the nano-resonator respectively. Structural FEM analysis result is compared with the experimental result.
Transient Experiments and Modeling of Soil Response to Extreme Heat
Authors: Hu Xianxu , Yong Mengwah , Marshall Andre´ W. , Goodings Deborah J.
Published: April 2008

This study investigates the transient response of saturated soil to extreme heat under severe tunnel fires by both experiments and CFD simulation. A basic soil-column configuration heated from below is chosen to examine the transport dynamics experimentally. The temperature rise, thermal transport, and pore pressure increases in saturated soils are measured in this fundamental configuration. A 2-D CFD simulation with a similar geometry sizes and boundary conditions is performed. The CFD simulations have shown correctly qualitative behavior observed in experiments, including the saturation front moving upward and the distinct regions developed in the soil medium.
A Thermoeconomic Based Tool for the Real-Time Management of a Cogenerative Combined Cycle
Authors: Verda Vittorio , Chirio Matteo , Ponta Andrea
Published: April 2008

In this paper a tool for the management of large cogeneration plants based on thermoeconomic analysis is presented and applied to a combined cycle. The tool is constituted of two thermodynamic models of the plant and a thermoeconomic model. The first model is a plant simulator whose characteristic parameters are obtained from measured data or information available in literature. Inputs are the electric and the thermal loads and the ambient conditions. This model determines the corresponding fuel consumption, mass and energy fluxes exchanged between the components and the thermodynamic state of all the mass flows. It can be used to determine how variations in the loads, in the ambient conditions, in the setpoints affect the plant operating condition as well as to generate a proper reference condition for the analysis. The second model performs data reconciliation. This is directly based on measured data corresponding with the current operating condition. The unavailable quantities are obtained by applying the balance equations together with some proper hypotheses. The value assumed by the characteristic performance parameters in the current condition constitutes an output of this model. The thermoeconomic model provides the costs associated with the plant products (heat supplied to the district heating network and electricity) as well as some evaluation parameters for diagnosis purposes. Future operating conditions can also be forecasted. In this case, the information provided by diagnosing the status of the components is introduced as an additional input in the simulator. The results can be used for planning the plant production, in particular for the day after, and for taking decisions about maintenance.
Heat Transfer Characteristics of Liquid Suspensions Containing Fluid-Filled Carbon Nanotubes
Authors: Sun K. , Bazilevsky A. A. , Megaridis C. M.
Published: April 2008

Fast and efficient dissipation of heat is necessary in high-demand applications of miniaturized microelectronics and optoelectronics. Solid nanoparticle suspensions in liquids (a.k.a. nanofluids) have been found to display thermal conductivities dramatically higher than those of the host fluids, which are typically heat transfer liquids, such as water, oil, ethylene glycol, etc. The present work focuses on fluid-filled carbon nanotubes, which serve in suspension to improve thermal properties of the host fluid. Hydrothermal treatment is applied to produce carbon nanotubes encapsulating an aqueous multiphase fluid. Transmission electron microscopy (TEM) is employed to confirm the entrapment of water inside the tubes. Controlled experiments are carried out to study the effect of filled-nanotube properties and concentration on the values of heat capacity of the host fluid.
A Large-Scale Simulation on Two-Phase Flow Characteristics Around Duel Rods in a Tight-Lattice Core
Authors: Takase K. , Yoshida H. , Ose Y. , Akimoto H.
Published: April 2008

Water-vapor two-phase flow structure in a fuel bundle of an advanced light water reactor was analyzed numerically by large-scale direct simulations. A newly developed two-phase flow analysis code was used. It can precisely predict the interface behavior between the liquid and gas phase by using the interface tracking method. The present analytical geometry simulates a tight-lattice fuel bundle with 37 fuel rods and four spacers. The fuel rod outer diameter is 13 mm and gap spacing between each rod is 1.3 mm. Each spacer is installed in an arbitrary axial position in order to keeping the gap width. Water flows upward from the bottom of the fuel bundle. The inlet conditions of water are as follows: temperature 283°C, pressure 7.2 MPa, flow rate 400 kg/m2s, and the Reynolds number 40,000. In the present study three-dimensional computations were carried out under the non-heated isothermal flow condition in order to remove the effect of heat transfer by the fuel rods. The average mesh size in the present numerical study was 0.15 mm. From results of a series of the numerical simulations, the following consideration was derived: 1)The fuel rod surface is encircled with thin water film; 2)The bridge phenomenon by the water film appears in the region where the spacing between fuel rods is narrow; 3)Vapor flows downward the triangular region where the spacing between fuel rods is large; and, 4)A flow configuration of vapor shows the streak structure in the vertical direction.
A Computational Study on Particle/Turbulence Interaction
Authors: Zhang N. , Zheng Z. Charlie
Published: April 2008

In a typical complex particle flow with turbulence, particles can directly interact with small turbulent eddies. The presence of particles changes the turbulence field, and at the same time, the turbulent eddies also influence the particle motion and coagulation. The problem for this computational study is modeled as a turbulent flow passing over a solid spherical particle. The background turbulence field is first generated using an LES turbulence simulation in a large domain. An improved direct-forcing immersed-boundary method is then used to place a particle in a truncated smaller domain to start the simulation for particle/turbulence interaction. The results show that turbulence causes different patterns of vortex shedding in the wake that appears as turbulent fluctuations. The effect of the particle on the background turbulence is detected in the spectral analysis where the particle removes some turbulent energy at the low frequency range and returns the energy to the frequency range corresponding to vortex shedding.
Model Uncertainty in Fluid-Structure Impact Risk Analysis
Authors: Mitchell Kenneth N. , Mahadevan Sankaran
Published: April 2008

This paper investigates the issue of model uncertainty in risk assessments of fluid-structure impact problems. Model-based risk assessments of complex phenomena such as the space shuttle solid rocket booster (SRB) splashdown event is affected by significant model uncertainty and approximations in finite element discretization, damage modeling, and the probabilistic analysis. Model verification and validation (V&V) helps in systematic assessment of modeling error, and suitable V&V techniques are explored in this paper. Since experimental testing of the SRB is infeasible, a simplified experimental framework is devised using an aluminum cylinder hinged at one end, with the objective of providing insights into the required model form (validation) as well as the required model resolution (verification). Preliminary results from error quantification as well as experimental validation are presented and discussed. Such information could be used to develop confidence and credibility in real-world reliability predictions of fluid-structure impact problems such as SRB splashdown.
Numerical Simulation on Short Pulsed Laser Heating of Semiconductor Thin Films: The Case of GaAs
Authors: Cheng Gary J. , Pirzada Daniel , Ai Xin , Li Ben
Published: April 2008

The results of numerical simulation of heat transfer phenomena in GaAs thin films irradiated by a pulsed laser are presented. A numerical algorithm involving a discontinuous Galerkin finite element method for the solution of hyperbolic heat conduction is used to solve the dual-phase-lag heat conduction equation The effects of different process parameters on heat propagation are analyzed. The heat conduction mode after pulsed laser irradiation is strongly dependent upon the incident laser energy density, film thickness and pulse duration. The heat transfer behavior for nano-, pico- and femto- second pulses has been studied and compared. A wave-type heat transfer phenomena was observed when pulse duration is of the order of relaxation time of the material being heated. It was found that for sub-picosecond pulses, the heat transfer occurs only by a thermal shock wave.
Full Band-Gap Silicon Phononic Crystals for Surface Acoustic Waves
Authors: Mohammadi Saeed , Khelif Abdelkrim , Westafer Ryan , Massey Eric , Hunt William D. , Adibi Ali
Published: April 2008

Periodic elastic structures, called phononic crystals, show interesting frequency domain characteristics that can greatly influence the performance of acoustic and ultrasonic devices for several applications. Phononic crystals are acoustic counterparts of the extensively-investigated photonic crystals that are made by varying material properties periodically. Here we demonstrate the existence of phononic band-gaps for surface acoustic waves (SAWs) in a half-space of two dimensional phononic crystals consisting of hexagonal (honeycomb) arrangement of air cylinders in a crystalline Silicon background with low filling fraction. A theoretical calculation of band structure for bulk wave using finite element method is also achieved and shows that there is no complete phononic band gap in the case of the low filling fraction. Fabrication of the holes in Silicon is done by optical lithography and deep Silicon dry etching. In the experimental characterization, we have used slanted finger interdigitated transducers deposited on a thin layer of Zinc oxide (sputtered on top of the phononic crystal structure to excite elastic surface waves in Silicon) to cover a wide range of frequencies. We believe this to be the first reported demonstration of phononic band-gap for SAWs in a hexagonal lattice phononic crystal at such a high frequency.
Rimming Flow of a Power-Law Fluid: Qualitative Analysis of the Mathematical Model
Authors: Fomin Sergei , Hubbard Richard
Published: April 2008

Rimming flow of the non-Newtonian fluid on the inner surface of a horizontal rotating cylinder is investigated. Simple lubrication theory is applied since the Reynolds number is small and liquid film is thin. For the steady-state flow of a power-law fluid the mathematical model reduces to a simple algebraic equation regarding the thickness of the liquid film. The qualitative analysis of this equation is carried out and the existence of two possible solutions is rigorously proved. Based on this analysis qualitative analysis, different regimes of the rimming flow are defined and analyzed analytically.
Experimental Analysis of the Temperature and Voltage Distribution of a SOFC Generator Varying the Air Stoichiometry and Pre-Heating Temperature
Authors: Santarelli M. , Leone P. , Garglio M. , Cali` M. , Orsello G.
Published: April 2008

GTT, a subsidiary of Siemens Power Corporation, started in 2004 the EOS Project (Energy from Solid Oxides) with Politecnico of Torino, an applied research activity in Stationary Fuel Cells based on SOFC technology. The project (2004-2009) has the purpose to test a pilot plant for Combined Heat and Power. The operation of a SOFC generator is strictly affected by some regulation variables, among which there are the air stoichiometry and pre-heating temperature: sensitivity tests have been performed and are analyzed in the paper to characterize the single sector operation in a 100 kWe SOFC stack. In the experimental domain of air stoichiometry (4.6-4.8) and air pre-heating temperature (609-612°C), it is shown that air stoichiometry has a deeper contribution to the behavior of the stack. Its effect is linked essentially to the modification of the temperature distribution inside the generator. In the experimental domain, the generator voltage can be expressed as a linear function of the air stoichiometry, so that the voltage sensitivity to the air stoichiometry has been outlined for single generator sectors of the whole generator. In particular, the results of the experimental session suggest that different sensitivities can be associated with the position of the sectors in the stack arrangement. Moreover, it is observed that air stoichiometry sensitivity tests can provide useful information about the assessment and problems of thermal management and temperature distribution inside the SOFC generator: this can be an interesting tool to address the optimal design of a air supply system and distribution inside the generator. Finally, the correlation between the voltage and temperature sensitivity to the air stoichiometry have been discussed.
Investigation of the Microstructures and Mechanical Properties of Nano- and Sub-Micron Composite Low Carbon Alloy Steel
Authors: Jia Chunde , Duan Zhanqiang , Yang Shutong , Zhang Guohui , Xu Zhuangzhi
Published: April 2008

The low carbon alloy steel was single face treated by a special hot diffusion method, and thus the gradual composite steel was produced. The microstructures of composite steel were very different from the matrix steel, white layer speared near the treated surface, and nano- and sub-micron particles were existed in the white layer. The results of ramon spectrum test indicated that the nano- and sub-micron particles can transfer several millimeters, several centimeters or even more. The mechanical properties changed sharply compared with the matrix steel. The hardness and the tensile strength near the treated surface were much higher than the matrix steel, and decreased gradually with the increase of distance to the treated surface. The composite steel has high strength, high hardness, high wear-resistance, high corrosion-resistance and etc. From the engineering application point of view, this technique can be used to produce super high qualities alloy steels, which can be used to the field as: metallurgy, mine, automobile, manufacture, energy sources, and etc.
Maximum Drag Reduction Asymptote of Polymeric Fluid Flow in Coiled Tubing
Authors: Shah Subhash N. , Zhou Yunxu
Published: April 2008

This study experimentally investigates the drag reduction characteristics of the most commonly used polymer fluids in coiled tubing applications. The flow loop employed consists of 1/2-in. straight and coiled tubing sections. The curvature ratio (a/R where a and R are the radii of the tubing and the reel drum respectively) investigated is from 0.01 to 0.076 which covers the typical curvature ratio range encountered in the oil and gas industry applications. Fluids tested include xanthan gum, guar gum, and HPG (hydroxypropyl guar) at various polymer concentrations. It is found that the drag reduction in coiled tubing is significantly lower than that in straight tubing, probably due to the effect of secondary flow in curved geometry. The onset of drag reduction is also found to be delayed as the curvature ratio was increased. A correlation for the maximum drag reduction (MDR) asymptote in coiled tubing is developed. When the curvature ratio is set to zero, the new correlation reduces to the famous Virk's MDR asymptote for dilute polymer solutions in straight pipes. A new drag reduction envelope is also proposed for the analysis of drag reduction behavior of polymeric fluids in coiled tubing. Application of the new drag reduction envelope is also discussed.
Electrothermo Convective Instability With Inclined Temperature Gradient
Authors: Kaloni P. N. , Lou J. X.
Published: April 2008

The linear convective stability analysis of a poorly conducting liquid with inclined temperature gradient and under a vertical d. c. electric field is investigated. The liquid is placed between a parallel plate electrode system with the upper electrode heated. The eigenvalue problem is solved by the Chebyshev Tau-QZ method. Consideration is also given to the case when there is no horizontal flow and some interesting results are obtained. For inclined temperature gradient case, it is found that the onset of convection is governed by six parameters RV, RH, Re, Pr, Pe and Se. The effect of varying Re upon critical RV and RH is discussed and some considerations to the occurrence of transverse or longitudinal mode is pointed out.
Use of an Infrared Laser to Determine Separated Flow
Authors: Weyker Evelyn , Poor Andrew , van Treuren Kenneth W.
Published: April 2008

This experiment used an infrared laser technique to determine where flow separation and reattachment occurred on a backward facing step. The step size was 6.35 cm, and the overall length of the model was 60.96 cm, with 30.48 cm for the bottom step. Two types of tufts were used in this experiment to define the flow field: string tufts and thermochromic liquid crystal (TLC) tufts. In this experiment, the string tuft was attached to the end of a wand that was placed in the flow path. String tufts are intrusive to the flow and give a less accurate surface visualization because the weight of the string affects the results. Consequently, string tufts do not respond well to low flow velocities. In contrast, TLC tufts do not have these limitations. Thermochromic liquid crystals do not impede the flow and they give accurate surface visualizations. They respond to changing temperature by reflecting light at different wavelengths, resulting in a changing observable color as the temperature changes. An infrared laser heated the surface of the model in a circular spot resulting in crystal color change. Airflow over the heated surface convected energy in the direction of the flow. This resulted in a visible TLC "tail" pointing in the direction of the flow. With this technique, both forward and reverse flow can be detected. Images of these tufts were recorded with a digital video camera. Eccentricity of the tufts indicated the direction of flow. Two velocities of upstream flow were tested: 100% of the blower's voltage, a velocity of 1.13 m/s, and 80% of the blower's voltage, a velocity of 1.07 m/s. For both velocities, reattachment occurred using the TLC tuft method at approximately 17.145 cm from the step. Using the string tuft attached to a wand, these results were verified as the reattachment region was between 16.51 cm and 17.78 cm.
Dosimetric investigation of lung tumor motion compensation with a robotic respiratory tracking system: An experimental study
Authors: Nioutsikou Elena , Seppenwoolde Yvette , Symonds‐Tayler J. Richard N. , Heijmen Ben , Evans Phil , Webb Steve
Published: April 2008

The benefits of using Synchrony™ Respiratory Tracking System (RTS) in conjunction with the CyberKnife robotic treatment device to treat a “breathing tumor” in an anthropomorphic, tissue‐equivalent, thoracic phantom have been investigated. The following have been studied: (a) Synchrony's ability to allow the CyberKnife to deliver accurately a planned dose distribution to the free‐breathing phantom and (b) the dosimetric implications when irregularities in the breathing cycle and phase differences between internal (tumor) and external (chest) motion exist in the course of one treatment fraction. The breathing phantom PULMONE (phantom used in lung motion experiments) has been used, which can imitate regular or irregular breathing patterns. The breathing traces from two patients with lung cancer have been selected as input. Both traces were irregular in amplitude, frequency, and base line. Patient B demonstrated a phase difference between internal and external motion, whereas patient A did not. The experiment was divided into three stages: In stage I‐static, the treatment was delivered to the static phantom. In stage II‐motion, the phantom was set to breathe, following the breathing trace of each of the two patients. Synchrony™ was switched off, so no motion compensation was made. In stage III‐compensation, the phantom was set to breathe and Synchrony™ was switched on. A linear correspondence model was chosen to allow for phase differences between internal and external motion. Gafchromic EBT film was inserted in the phantom tumor to measure dose. To eradicate small errors in film alignment during readout, a gamma comparison with pass criteria of 3%/3 mm was selected. For a more quantitative approach, the percentage of pixels in each gamma map that exceeded the value of 1 was also used. For both breathing signals, the dose blurring caused by the respiratory motion of the tumor in stage II was degraded considerably compared with stage I ( for patient A and 8% for patient B). The motion compensation via the linear correspondence model was sufficient to provide a dose distribution that satisfied the set gamma criteria ( for patient A and 2% for patient B). Synchrony™ RTS has been found satisfactory in recovering the initial detail in dose distribution, for realistic breathing signals, even in the case where a phase delay between internal tumor motion and external chest displacement exists. For the signals applied here, a linear correspondence model provided an acceptable degree of motion compensation.
Automatic segmentation of the prostate in 3D MR images by atlas matching using localized mutual information
Authors: Klein Stefan , van der Heide Uulke A. , Lips Irene M. , van Vulpen Marco , Staring Marius , Pluim Josien P. W.
Published: April 2008

An automatic method for delineating the prostate (including the seminal vesicles) in three‐dimensional magnetic resonance scans is presented. The method is based on nonrigid registration of a set of prelabeled atlas images. Each atlas image is nonrigidly registered with the target patient image. Subsequently, the deformed atlas label images are fused to yield a single segmentation of the patient image. The proposed method is evaluated on 50 clinical scans, which were manually segmented by three experts. The Dice similarity coefficient (DSC) is used to quantify the overlap between the automatic and manual segmentations. We investigate the impact of several factors on the performance of the segmentation method. For the registration, two similarity measures are compared: Mutual information and a localized version of mutual information. The latter turns out to be superior (median , with a paired two‐sided Wilcoxon test) and comes at no added computational cost, thanks to the use of a novel stochastic optimization scheme. For the atlas fusion step we consider a majority voting rule and the “simultaneous truth and performance level estimation” algorithm, both with and without a preceding atlas selection stage. The differences between the various fusion methods appear to be small and mostly not statistically significant . To assess the influence of the atlas composition, two atlas sets are compared. The first set consists of 38 scans of healthy volunteers. The second set is constructed by a leave‐one‐out approach using the 50 clinical scans that are used for evaluation. The second atlas set gives substantially better performance , stressing the importance of a careful atlas definition. With the best settings, a median DSC of around 0.85 is achieved, which is close to the median interobserver DSC of 0.87. The segmentation quality is especially good at the prostate‐rectum interface, where the segmentation error remains below in 50% of the cases and below in 75% of the cases.
Classifier performance prediction for computer‐aided diagnosis using a limited dataset
Authors: Sahiner Berkman , Chan Heang‐Ping , Hadjiiski Lubomir
Published: April 2008

In a practical classifier design problem, the true population is generally unknown and the available sample is finite‐sized. A common approach is to use a resampling technique to estimate the performance of the classifier that will be trained with the available sample. We conducted a Monte Carlo simulation study to compare the ability of the different resampling techniques in training the classifier and predicting its performance under the constraint of a finite‐sized sample. The true population for the two classes was assumed to be multivariate normal distributions with known covariance matrices. Finite sets of sample vectors were drawn from the population. The true performance of the classifier is defined as the area under the receiver operating characteristic curve (AUC) when the classifier designed with the specific sample is applied to the true population. We investigated methods based on the Fukunaga–Hayes and the leave‐one‐out techniques, as well as three different types of bootstrap methods, namely, the ordinary, 0.632, and bootstrap. The Fisher's linear discriminant analysis was used as the classifier. The dimensionality of the feature space was varied from 3 to 15. The sample size from the positive class was varied between 25 and 60, while the number of cases from the negative class was either equal to or . Each experiment was performed with an independent dataset randomly drawn from the true population. Using a total of 1000 experiments for each simulation condition, we compared the bias, the variance, and the root‐mean‐squared error (RMSE) of the AUC estimated using the different resampling techniques relative to the true AUC (obtained from training on a finite dataset and testing on the population). Our results indicated that, under the study conditions, there can be a large difference in the RMSE obtained using different resampling methods, especially when the feature space dimensionality is relatively large and the sample size is small. Under this type of conditions, the 0.632 and bootstrap methods have the lowest RMSE, indicating that the difference between the estimated and the true performances obtained using the 0.632 and bootstrap will be statistically smaller than those obtained using the other three resampling methods. Of the three bootstrap methods, the bootstrap provides the lowest bias. Although this investigation is performed under some specific conditions, it reveals important trends for the problem of classifier performance prediction under the constraint of a limited dataset.
Improvement of the spatial resolution of the MicroPET R4 scanner by wobbling the bed
Authors: Suk Joon Young , Thompson Christopher J. , Labuda Aleks , Goertzen Andrew L.
Published: April 2008

The MicroPET R4 scanner was designed for imaging small rodents such as mice and rats. In many cases the spatial resolution of this system is not sufficient for resolving structures of interest. In order to improve the spatial resolution of the MicroPET R4 through improved spatial sampling, the authors have implemented a variable radius eccentric motion, commonly referred to as wobbling, which is applied to the animal bed during scanning. The wobble motion is incorporated into the sinograms using modified histogramming software, capable of reading the bed wobble position from the list‐mode data. The histogramming software corrects the data for the dwell time, apparent crystal location, and crystal‐pair efficiency and applies a resolution matching filter. The data acquisition, reconstruction, and image display programs provided from the manufacturer required no modifications. For all studies a wobble period of 8 s was used. The optimal wobble radius was found to be 1.50 mm. The wobbled bed acquisition technique was tested by scanning a resolution phantom and a rat. Images from both studies acquired when using the wobble motion showed an improved spatial resolution when compared with comparable images acquired without the wobble motion. The bed wobbling mechanism can be added to any MicroPET system without major changes and without compromising any imaging modes. Implementing the wobble mechanism may represent a cost‐effective method to upgrade the spatial resolution of a MicroPET when compared to the purchase of a newer generation system.
The root percent depth dose method for calculating monitor units for irregularly shaped electron fields
Authors: Kehwar Than S. , Huq M. Saiful
Published: April 2008

This study outlines an improved method for calculating dose per monitor unit values for irregularly shaped electron fields using the root percent depth dose method. This method calculates the percent depth dose and output factors for an irregularly shaped electron field directly from the measured electron beam percent depth dose curves and output factors for circular fields. The percent depth dose curves and output factors for circular fields are normalized and measured at a fixed depth of maximum dose for a reference field, respectively. When compared with the sector integral lateral buildup ratio method, the percent depth dose data calculated using the root method accounts more accurately for the change in lateral scatter with decreasing field size. Therefore, it provides more accurate values of dose per monitor unit at different depths for all type of field shapes and beam energies. For beam energies in the range of 6–21 MeV, the differences between measured and calculated dose per monitor unit values, at different depths, were found to be within when the root percent depth dose method was used for calculation and when the sector integral lateral buildup ratio method was used. The root percent depth dose method was tested and compared with the sector integral lateral buildup ratio method for ten clinically used irregularly shaped inserts (cutouts). For small irregularly shaped fields, a maximum difference of was found between calculated dose per monitor unit values and measurements when the root percent depth dose method was used; this difference changed to when comparisons were made between measurements and calculations based on the sector integral lateral buildup ration method. For large irregular fields this difference was found to be within and , respectively.
Technical note: The calibration of ‐labeled SIR‐Spheres® using a nondestructive spectroscopic assay
Authors: Selwyn R. , Micka J. , DeWerd L. , Nickles R. , Thomadsen B.
Published: April 2008

‐labeled SIR‐Spheres® are currently used to treat patients with hepatic metastases secondary to colorectal adenocarcinoma. In general, the prescribed activity is based on empirical data collected during clinical trials. The activity of the source vial is labeled by the manufacturer as and is not independently verified by the end user. This technical note shows that the results of a nondestructive spectroscopic assay of a SIR‐Spheres® sample was 26% higher than the activity stated by the manufacturer. This difference should not impact the current empirical prescription method but may be problematic for patient‐specific dosimetry applications, such as image‐based dosimetry.
Automatic nonrigid registration of whole body CT mice images
Authors: Li Xia , Yankeelov Thomas E. , Peterson Todd E. , Gore John C. , Dawant Benoit M.
Published: April 2008

Three‐dimensional intra‐ and intersubject registration of image volumes is important for tasks that include quantification of temporal/longitudinal changes, atlas‐based segmentation, computing population averages, or voxel and tensor‐based morphometry. While a number of methods have been proposed to address this problem, few have focused on the problem of registering whole body image volumes acquired either from humans or small animals. These image volumes typically contain a large number of articulated structures, which makes registration more difficult than the registration of head images, to which the majority of registration algorithms have been applied. This article presents a new method for the automatic registration of whole body computed tomography (CT) volumes, which consists of two main steps. Skeletons are first brought into approximate correspondence with a robust point‐based method. Transformations so obtained are refined with an intensity‐based nonrigid registration algorithm that includes spatial adaptation of the transformation's stiffness. The approach has been applied to whole body CT images of mice, to CT images of the human upper torso, and to human head and neck CT images. To validate the authors method on soft tissue structures, which are difficult to see in CT images, the authors use coregistered magnetic resonance images. They demonstrate that the approach they propose can successfully register image volumes even when these volumes are very different in size and shape or if they have been acquired with the subjects in different positions.
Revealing Magnetic Interactions from Single-Atom Magnetization Curves
Authors: Meier Focko , Zhou Lihui , Wiebe Jens , Wiesendanger Roland
Published: April 2008

The miniaturization of magnetic devices toward the limit of single atoms calls for appropriate tools to study their magnetic properties. We demonstrate the ability to measure magnetization curves of individual magnetic atoms adsorbed on a nonmagnetic metallic substrate with use of a scanning tunneling microscope with a spin-polarized tip. We can map out low-energy magnetic interactions on the atomic scale as evidenced by the oscillating indirect exchange between a Co adatom and a nanowire on Pt(111). These results are important for the understanding of variations that are found in the magnetic properties of apparently identical adatoms because of different local environments.
Reconstitution of Pilus Assembly Reveals a Bacterial Outer Membrane Catalyst
Authors: Nishiyama Mireille , Ishikawa Takashi , Rechsteiner Helene , Glockshuber Rudi
Published: March 2008

Type 1 pili from uropathogenic
Escherichia coli
are a prototype of adhesive surface organelles assembled and secreted by the conserved chaperone/usher pathway. We reconstituted type 1 pilus biogenesis from purified pilus proteins. The usher FimD acted as a catalyst to accelerate the ordered assembly of protein subunits independently of cellular energy. Its activity was highly dependent on the adhesin subunit FimH, which triggered the conversion of FimD into a high-efficiency assembly catalyst. Furthermore, a simple kinetic model adequately rationalized usher-catalyzed pilus assembly in vivo. Our results contribute to a mechanistic understanding of protein-catalyzed biogenesis of supramolecular protein complexes at the bacterial outer cell membrane.
Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia
Authors: Walsh Tom , McClellan Jon M. , McCarthy Shane E. , Addington Anjené M. , Pierce Sarah B. , Cooper Greg M. , Nord Alex S. , Kusenda Mary , Malhotra Dheeraj , Bhandari Abhishek , Stray Sunday M. , Rippey Caitlin F. , Roccanova Patricia , Makarov Vlad , Lakshmi B. , Findling Robert L. , Sikich Linmarie , Stromberg Thomas , Merriman Barry , Gogtay Nitin , Butler Philip , Eckstrand Kristen , Noory Laila , Gochman Peter , Long Robert , Chen Zugen , Davis Sean , Baker Carl , Eichler Evan E. , Meltzer Paul S. , Nelson Stanley F. , Singleton Andrew B. , Lee Ming K. , Rapoport Judith L. , King Mary-Claire , Sebat Jonathan
Published: March 2008

Schizophrenia is a devastating neurodevelopmental disorder whose genetic influences remain elusive. We hypothesize that individually rare structural variants contribute to the illness. Microdeletions and microduplications >100 kilobases were identified by microarray comparative genomic hybridization of genomic DNA from 150 individuals with schizophrenia and 268 ancestry-matched controls. All variants were validated by high-resolution platforms. Novel deletions and duplications of genes were present in 5% of controls versus 15% of cases and 20% of young-onset cases, both highly significant differences. The association was independently replicated in patients with childhood-onset schizophrenia as compared with their parents. Mutations in cases disrupted genes disproportionately from signaling networks controlling neurodevelopment, including neuregulin and glutamate pathways. These results suggest that multiple, individually rare mutations altering genes in neurodevelopmental pathways contribute to schizophrenia.
Expression of a Functional Single-Chain Variable-Fragment Antibody against Complement Receptor 1 inStreptococcus gordonii
Authors: Knight Jennifer B. , Halperin Scott A. , West Kenneth A. , Lee Song F.
Published: April 2008

Streptococcus gordonii, an oral commensal organism, is a candidate vector for oral-vaccine development. Previous studies have shown that recombinantS. gordoniiexpressing heterologous antigens was weakly immunogenic when delivered intranasally. In this study, antigen was specifically targeted to antigen-presenting cells (APC) in order to potentiate antigen-APC interactions and increase the humoral immune response to the antigen. To achieve this goal, a single-chain variable-fragment (scFv) antibody against complement receptor 1 (CR1) was constructed. Anti-CR1 scFv purified fromEscherichia coliwas able to bind to mouse mixed lymphocytes and bone marrow-derived dendritic cells. The in vivo function of the anti-CR1 scFv protein was assessed by immunizing mice intranasally with soluble scFv and determining the immune response against the hemagglutinin (HA) peptide located on the carboxy terminus of the scFv. The serum anti-HA immunoglobulin G (IgG) immune response was dose dependent; as little as 100 ng of anti-CR1 scFv induced a significant IgG immune response, while such a response was minimal when the animals were given an unrelated scFv. The anti-CR1 scFv was expressed inS. gordoniias a secreted protein, which was functional, as it bound to dendritic cells. Mice orally colonized by the anti-CR1-secretingS. gordoniiproduced an anti-HA IgG immune response, indicating that such an approach can be used to increase the immune response to antigens produced by this bacterium.
Evaluation of a Rapid New Stool Antigen Test for Diagnosis of
Helicobacter pylori
Infection in Adult Patients
Authors: Krausse Rea , Müller G. , Doniec M.
Published: April 2008

The evaluation of a new rapid stool antigen test showed different levels of sensitivity for final readings of test results at 20 min (59.1%) and 30 min (76.9%). Significant differences in performance were observed between the two sexes and the various age categories, with higher efficiency in male patients and young adults. Generally, this test is efficient and can be used to detect
H. pylori
infection in adults. However, further studies are required to confirm its accuracy.
Roles of LEF-4 and PTP/BVP RNA Triphosphatases in Processing of Baculovirus Late mRNAs
Authors: Li Yi , Guarino Linda A.
Published: April 2008

The baculovirus
Autographa californica
nucleopolyhedrovirus encodes two proteins with RNA triphosphatase activity. Late expression factor LEF-4, which is an essential gene, is a component of the RNA polymerase and also encodes the RNA capping enzyme guanylyltransferase. PTP/BVP is also an RNA triphosphatase, but is not essential for viral replication, possibly because its activity is redundant to that of LEF-4. To elucidate the role of these proteins in mRNA cap formation, a mutant virus that lacked both RNA triphosphatase activities was constructed. Infection studies revealed that the double-mutant virus was viable and normal with respect to the production of budded virus. Pulse-labeling studies and immunoblot analyses showed that late gene expression in the double mutant was equivalent to that in the wild type, while polyhedrin expression was slightly reduced. Direct analysis of the mRNA cap structure indicated no alteration of cap processing in the double mutant. Together, these results reveal that baculoviruses replicate and express their late genes at normal levels in the absence of its two different types of RNA triphosphatases.
Translocation of photosynthetically assimilated carbon-14 in three arctic grasses in situ at Barrow, Alaska
Authors: Tieszen Larry L. , Johnson Douglas A. , Allessio Mary L.
Published: April 2008

A portable beta detector and counter were used under arctic field conditions to monitor 14C export in three tundra grasses. All species possessed a pattern of translocation at the low arctic temperatures similar to that of other temperate grasses under more moderate temperate zone conditions. Loss of label from loaded areas was rapid for the first 4 to 6 h and then decreased. Twenty to 35% of the original material remained after 24 h. There were no major differences in export among the three species, and patterns were similar throughout the season regardless of changing environmental conditions.
Morphology and ecology of Phialocephala fortinii in roots of Rhododendron brachycarpum
Authors: Currah R. S. , Tsuneda A. , Murakami S.
Published: April 2008

The morphology of the interaction of three strains of Phialocephala fortinii with the roots of Rhododendron brachycarpum was examined by light, scanning, and transmission electron microscopy using material grown in axenic Petri dish cultures and in nonsterile pot cultures. In Petri dish cultures, Phialocephala fortinii quickly overwhelmed root tips of young seedlings, causing distortion of cells of the root apex and inhibition of elongation. In older roots, mature, vacuolated, and moribund epidermal cells were penetrated. In pot-cultured plants the epidermis was heavily colonized by hyphae growing parallel to the long axis of the root. Microsclerotia formed within individual cells, between the epidermal and the subepidermal layers, and within cells surrounding the point of emergence of lateral roots. Hyphae did not invade the stele. The effects of two strains of Phialocephala fortinii on shoot dry weight accumulation of R. brachycarpum grown in pot culture were examined and compared with the effects of Hymenoscyphus ericae, Myxotrichum stipitatum, Oidiodendron echinulatum, and Pseudogymnoascus roseus. One strain of Phialocephala fortinii had a significant negative effect on dry weight accumulation, whereas a second had no effect. Hymenoscyphus ericae had a positive effect. The remaining fungi had no effect. One strain of Phialocephala fortinii gave rise to what appeared to be sterile discocarps on the surface of soil in 4-month-old pots of R. brachycarpum. Key words: Phialocephala fortinii, Hymenoscyphus ericae, microsclerotia, Rhododendron brachycarpum, ericoid mycorrhizas, Mycelium radicis atrovirens.
Quelques aspects d'une morphologie continuiste et dynamique
Authors: Jeune Bernard , Sattler Rolf
Published: April 2008

The authors discuss presuppositions of classical plant morphology and point out the difficulties of classical (classificatory) typology (based on typical forms that are mutually exclusive, categories such as shoot, root, leaf, or trichome), which have been known for a long time. It is shown how these difficulties can be overcome by a more open morphology concept that is continuous and dynamic. Furthermore, it is pointed out that such an approach works through an appropriate methodology based on principal components analysis and a decomposition of the plant into nested morphological articulations. Keywords: plant morphology, continuum morphology, dynamic morphology.
Vegetation zonation as related to the salt tolerance of species of brackish riverbanks
Authors: Wilson J. Bastow , King Warren McG. , Sykes Martin T. , Partridge Trevor R.
Published: April 2008

Nine riverbank species were grown in a range of salinities to estimate salt tolerances. These tolerances, and others calculated from previous studies, are compared with the species’ distributions upstream–downstream and upshore–downshore on brackish riverbanks. Downstream and downshore limits could predict the salt tolerance of the species, together accounting for 64% of the variation. Upstream and upshore limits accounted for 58%, but the relation with upstream limits was not statistically significant. There was a continuous range of tolerances. Keywords: adaptation, brackish marsh, ecological distribution, estuary, river marsh, RGR, salinity tolerance.