bluuebunny/crossref_metadata_2025 huggingface dataset:
Heavy-ion induced desorption of a TiZrV coated vacuum chamber bombarded with 5MeV∕u Ar8+ beam at grazing incidence
Authors: Hedlund E. , Malyshev O. B. , Westerberg L. , Krasnov A. , Semenov A. S. , Leandersson M. , Zajec B. , Kollmus H. , Bellachioma M. C. , Bender M. , Krämer A. , Reich-Sprenger H.
Published: January 2009

TiZrV nonevaporable getter (NEG) coated vacuum chambers is a new vacuum technology which is already used in many particle accelerators worldwide. This coating is also of interest for heavy-ion accelerator vacuum chambers. Heavy-ion desorption yields from an activated as well as a CO saturated NEG coated tube have been measured with 5MeV∕u Ar8+ beam. The sticking probability of the NEG film was obtained by using the partial pressure ratios on two sides of the NEG coated tube. These ratios were compared to results of modeling of the experimental setup with test particle Monte Carlo and angular coefficient methods. The partial pressures inside the saturated NEG coated tube bombarded with heavy ions were up to 20 times larger than those inside the activated one. However, the partial pressure of methane remained the same. The value of the total desorption yield from the activated NEG coated tube is 2600molecules/ion. The desorption yields after saturation for CH4, H2, and CO2 were found to be very close to the yields measured after the activation, while CO increased by up to a factor of 5. The total desorption yield for the saturated tube is up to 7000molecules/ion. The large value of the desorption yield of the activated NEG coated tube, an order of magnitude higher than the desorption yield from a stainless steel tube at normal incident angle, could be explained by the grazing incident angle.
Analysis of surface roughness and its relationship with photoluminescence properties of silicon-rich oxide films
Authors: Luna-López J. A. , Morales-Sánchez A. , Aceves-Mijares M. , Yu Z. , Domínguez C.
Published: January 2009

It is well known that silicon-rich oxide (SRO) shows intense photoluminescence (PL). In this work, the authors studied the relationship of the surface morphology and the PL emission. PL spectra of SRO as a function of the excess silicon, temperature, and time of thermal annealing were obtained. The same samples were studied using transmission electronic microscopy and atomic force microscopy to determine their microstructure and surface morphology. A relationship between silicon agglomerates in the SRO and the surface morphology was obtained. Then, the red PL emission was related to the surface morphology. The authors found that the surface roughness is an important parameter for the high red emission of SRO.
The influence of bowtie filtration on cone‐beam CT image quality
Authors: Mail N. , Moseley D. J. , Siewerdsen J. H. , Jaffray D. A.
Published: January 2009

The large variation of x‐ray fluence at the detector in cone‐beam CT (CBCT) poses a significant challenge to detectors’ limited dynamic range, resulting in the loss of skinline as well as reduction of CT number accuracy, contrast‐to‐noise ratio, and image uniformity. The authors investigate the performance of a bowtie filter implemented in a system for image‐guided radiation therapy (Elekta oncology system, XVI) as a compensator for improved image quality through fluence modulation, reduction in x‐ray scatter, and reduction in patient dose. Dose measurements with and without the bowtie filter were performed on a CTDI Dose phantom and an empirical fit was made to calculate dose for any radial distance from the central axis of the phantom. Regardless of patient size, shape, anatomical site, and field of view, the bowtie filter results in an overall improvement in CT number accuracy, image uniformity, low‐contrast detectability, and imaging dose. The implemented bowtie filter offers a significant improvement in imaging performance and is compatible with the current clinical system for image‐guided radiation therapy.
Optimization of an adaptive neural network to predict breathing
Authors: Murphy Martin J. , Pokhrel Damodar
Published: January 2009

Purpose: To determine the optimal configuration and performance of an adaptive feed forward neural network filter to predict breathing in respiratory motion compensation systems for external beam radiation therapy. Method and Materials: A two‐layer feed forward neural network was trained to predict future breathing amplitudes for 27 recorded breathing histories. The prediction intervals ranged from . The optimal sampling frequency, number of input samples, training rate, and number of training epochs were determined for each breathing history and prediction interval. The overall optimal filter configuration was determined from this parameter survey, and its accuracy for each breathing example was compared to the individually optimal filter setups. Prediction accuracy was also compared to breathing stability as measured by the autocorrelation of the breathing signal. Results: The survey of filter configurations converged on a standard setup for all examples of breathing. For 24 of the 27 breathing histories the accuracy of the standard filter for a prediction interval was within a few percent of the individually optimized filter setups; for the remaining three histories the standard filter was 5%–15% less accurate. Conclusions: A standard adaptive neural network filter setup can provide approximately optimal breathing prediction for a wide range of breathing patterns. The filter accuracy has a clear correlation with the stability of breathing.
Prediction of DVH parameter changes due to setup errors for breast cancer treatment based on 2D portal dosimetry
Authors: Nijsten S. M. J. J. G. , van Elmpt W. J. C. , Mijnheer B. J. , Minken A. W. H. , Persoon L. C. G. G. , Lambin P. , Dekker A. L. A. J.
Published: January 2009

Electronic portal imaging devices (EPIDs) are increasingly used for portal dosimetry applications. In our department, EPIDs are clinically used for two‐dimensional (2D) transit dosimetry. Predicted and measured portal dose images are compared to detect dose delivery errors caused for instance by setup errors or organ motion. The aim of this work is to develop a model to predict dose‐volume histogram (DVH) changes due to setup errors during breast cancer treatment using 2D transit dosimetry. First, correlations between DVH parameter changes and 2D gamma parameters are investigated for different simulated setup errors, which are described by a binomial logistic regression model. The model calculates the probability that a DVH parameter changes more than a specific tolerance level and uses several gamma evaluation parameters for the planning target volume (PTV) projection in the EPID plane as input. Second, the predictive model is applied to clinically measured portal images. Predicted DVH parameter changes are compared to calculated DVH parameter changes using the measured setup error resulting from a dosimetric registration procedure. Statistical accuracy is investigated by using receiver operating characteristic (ROC) curves and values for the area under the curve (AUC), sensitivity, specificity, positive and negative predictive values. Changes in the mean PTV dose larger than 5%, and changes inandlarger than 10% are accurately predicted based on a set of 2D gamma parameters. Most pronounced changes in the three DVH parameters are found for setup errors in the lateral‐medial direction. AUC, sensitivity, specificity, and negative predictive values were between 85% and 100% while the positive predictive values were lower but still higher than 54%. Clinical predictive value is decreased due to the occurrence of patient rotations or breast deformations during treatment, but the overall reliability of the predictive model remains high. Based on our predictive model, 2D transit dosimetry measurements can now directly be translated in clinically more relevant DVH parameter changes for the PTV during conventional breast treatment. In this way, the possibility to design decision protocols based on extracted DVH changes is created instead of undertaking elaborate actions such as repeated treatment planning or 3D dose reconstruction for a large group of patients.
Report on a randomized trial comparing two forms of immobilization of the head for fractionated stereotactic radiotherapy
Authors: Bednarz Greg , Machtay Mitchell , Werner‐Wasik Maria , Downes Beverly , Bogner Joachim , Hyslop Terry , Galvin James , Evans James , Curran Walter , Andrews David
Published: January 2009

Fractionated stereotactic radiotherapy (SRT) requires accurate and reproducible immobilization of the patient's head. This randomized study compared the efficacy of two commonly used forms of immobilization used for SRT. Two routinely used methods of immobilization, which differ in their approach to reproduce the head position from day to day, are the Gill–Thomas–Cosman (GTC) frame and the BrainLab thermoplastic mask. The GTC frame fixates on the patient's upper dentition and thus is in direct mechanical contact with the cranium. The BrainLab mask is a two‐part masking system custom fitted to the front and back of the patient's head. After patients signed an IRB‐approved informed consent form, eligible patients were randomized to either GTC frame or mask for their course of SRT. Patients were treated as per standard procedure; however, prior to each treatment a set of digital kilovolt images (ExacTrac, BrainLabAB, Germany) was taken. These images were fused with reference digitally reconstructed radiographs obtained from treatment planning CT to yield lateral, longitudinal, and vertical deviations of isocenter and head rotations about respective axes. The primary end point of the study was to compare the two systems with respect to mean and standard deviations using the distance to isocenter measure. A total of 84 patients were enrolled (69 patients evaluable with detailed positioning data). A mixed‐effect linear regression and two‐tiled t test were used to compare the distance measure for both the systems. There was a statistically significant difference between mean distances for these systems, suggesting that the GTC frame was more accurate. The mean 3D displacement and standard deviations were for mask and for frame. Both immobilization techniques were highly effective, but the GTC frame was more accurate. To optimize the accuracy of SRT, daily kilovolt image guidance is recommended with either immobilization system.
Effect of nonlinear three‐dimensional optimized reconstruction algorithm filter on image quality and radiation dose: Validation on phantoms
Authors: Bai Mei , Chen Jiuhong , Raupach Rainer , Suess Christoph , Tao Ying , Peng Mingchen
Published: January 2009

A new technique called the nonlinear three‐dimensional optimized reconstruction algorithm filter (3D ORA filter) is currently used to improve CT image quality and reduce radiation dose. This technical note describes the comparison of image noise, slice sensitivity profile (SSP), contrast‐to‐noise ratio, and modulation transfer function (MTF) on phantom images processed with and without the 3D ORA filter, and the effect of the 3D ORA filter on CT images at a reduced dose. For CT head scans the noise reduction was up to 54% with typical bone reconstruction algorithms (H70) and a slice thickness; for liver CT scans the noise reduction was up to 30% with typical high‐resolution reconstruction algorithms (B70) and a slice thickness. MTF and SSP did not change significantly with the application of 3D ORA filtering , whereas noise was reduced . The low contrast detectability and MTF of images obtained at a reduced dose and filtered by the 3D ORA were equivalent to those of standard dose CT images; there was no significant difference in image noise of scans taken at a reduced dose, filtered using 3D ORA and standard dose CT . The 3D ORA filter shows good potential for reducing image noise without affecting image quality attributes such as sharpness. By applying this approach, the same image quality can be achieved whilst gaining a marked dose reduction.
Diminishing the impact of the partial volume effect in cardiac SPECT perfusion imaging
Authors: Pretorius P. Hendrik , King Michael A.
Published: January 2009

The partial volume effect (PVE) significantly restricts the absolute quantification of regional myocardial uptake and thereby limits the accuracy of absolute measurement of blood flow and coronary flow reserve by SPECT. The template‐projection‐reconstruction method has been previously developed for PVE compensation. This method assumes the availability of coregistered high‐spatial resolution anatomical information as is now becoming available with commercial dual‐modality imaging systems such as SPECT/CTs. The objective of this investigation was to determine the extent to which the impact of the PVE on cardiac perfusion SPECT imaging can be diminished if coregistered high‐spatial resolution anatomical information is available. For this investigation the authors introduced an additional parameter into the template‐projection‐reconstruction compensation equation called the voxel filling fraction . This parameter specifies the extent to which structure edge voxels in the emission reconstruction are filled by the structure in question as determined by the higher spatial‐resolution imaging modality and the fractional presence of the structure at different states of physiological motion as in combining phases of cardiac motion. During correction the removal of spillover to the cardiac region from the surrounding structures is performed first by using reconstructed templates of neighboring structures (liver, blood pool, lungs) to calculate spillover fractions. This is followed by determining recovery coefficients for all voxels within the heart wall from the reconstruction of the template projections of the left and right ventricles (LV and RV). The emission data are subsequently divided by these recovery coefficients taking into account the filling fraction . The mathematical cardiac torso phantom was used for investigation correction of PVE for a normal LV distribution, a defect in the inferior wall, and a defect in the anterior wall. PVE correction resulted in a dramatic visual reduction in the impact of extracardiac activity, improved the uniformity of the normally perfused heart wall, and enhanced defect visibility without undue noise amplification. No significant artifacts were seen with PVE correction in the presence of mild (one voxel) misregistration. A statistically significant improvement in the accuracy of the count levels within the normal heart wall was also noted. However, residual spillover of counts from within the myocardium creates a bias in regions of decreased wall counts (perfusion defects/abnormal wall motion) when the anatomical imaging modality does not allow definition of templates for defects present in the heart during emission imaging.
Determination of x‐ray spectra from Al attenuation data by imposing a priori physical features of the spectrum: Theory and experimental validation
Authors: Delgado Víctor
Published: January 2009

The determination of the spectral distribution of an x‐ray beam from attenuation measurements in a narrow beam is an ill‐conditioned problem that has aroused great interest since it was first proposed by Silberstein in 1932. In this work, the explicit reconstruction of the spectral distribution directly from the attenuation curve, without differentiating it, is carried out by a maximum likelihood method that allows one to impose a priori physical features of an x‐ray spectral distribution, such as the positiveness of the solution, the boundness of its support, and the position and shape of the spikes and edges associated with the characteristic radiation. The numerical simulations made and the experimental validation of the proposed method have shown that it is possible to reconstruct x‐ray spectra that, having a realistic shape, accurately fit the attenuation curve and predict the energy fluence. Nevertheless, the reconstruction of spectra including the K x rays of W is less accurate than the reconstruction of spectra including L x rays of W or K x rays of Mo, even when a priori information about the position and shape of the spikes and edges associated with the characteristic radiation is used.
Spectroscopic output of and low dose rate brachytherapy sources
Authors: Usher‐Moga Jacqueline , Beach Stephen M. , DeWerd Larry A.
Published: January 2009

The spectroscopic output of low dose rate (LDR) brachytherapy sources is dependent on the physical design and construction of the source. Characterization of the emitted photons from 12 and 3 LDR brachytherapy source models is presented. Photon spectra, both along the transverse bisector and at several polar angles, were measured in air with a high‐purity reverse electrode germanium (REGe) detector. Measured spectra were corrected to in vacuo conditions via Monte Carlo and analytical methods. The tabulated and plotted spectroscopic data provide a more complete understanding of each source model's output characteristics than can be obtained with other measurement techniques. The variation in fluorescence yield of the sources containing silver caused greater differences in the emitted spectra and average energies among these seed models than was observed for the sources or the sources that do not contain silver. Angular spectroscopic data further highlighted the effects of source construction unique to each model, as well as the asymmetric output of many seeds. These data demonstrate the need for the incorporation of such physically measured output characteristics in the Monte Carlo modeling process.
Localization of transient signal high‐values in laser Doppler flowmetry signals with an empirical mode decomposition
Authors: Humeau Anne , Trzepizur Wojciech , Rousseau David , Chapeau‐Blondeau François , Abraham Pierre
Published: January 2009

The laser Doppler flowmetry (LDF) technique provides the monitoring of microvascular blood flow perfusion. However, LDF monitors based on fiber‐optic transducers have the serious drawback of generating TRAnsient Signal High‐values (TRASH) in signals. These TRASH correspond to artifacts for clinicians as they prevent interpretations of the signal when they are numerous. Moreover, TRASH exclude the possibility of direct signal processing and analyses. Therefore, in clinical routines, a human visual inspection of LDF signals is necessary to detect TRASH and to process the signals accordingly. This may be very time consuming. An algorithm able to localize TRASH automatically for their removal is therefore of interest. However, the development of such an algorithm is not an easy task as TRASH amplitude can be lower, higher, or in the same amplitude range as responses to stimuli such as post‐occlusive hyperemia. The recently introduced empirical mode decomposition (EMD) has the advantage of splitting any kind of signal into fast and slow oscillations. Relying on these properties, the authors evaluate the possibility for EMD to localize TRASH automatically. For this purpose, LDF signals from 28 men of different ages are recorded at rest, during a vascular occlusion of , followed by a post‐occlusive hyperemia. For each signal containing TRASH, the first intrinsic mode function obtained with the EMD is processed with a running window‐based analysis in which a thresholding of the local maxima is carried out for the localization of TRASH. From the data, the use of a window width of is suggested. The results show effective and potential usefulness of this algorithm for an automatic localization of TRASH. Moreover, the method proposed has the advantage of being insensitive to the rapid increases of blood flow induced by post‐occlusive hyperemia, which is of interest for clinicians. Because it is both local and fully data adaptive, EMD appears as an appealing processing technique for overcoming some of the limitations of the LDF.
RNA interference screening demystified
Authors: Lord C J , Martin S A , Ashworth A
Published: January 2009

Genetic screens, where the effects of modifying gene function on cell behaviour are assessed in a systematic fashion, have for some time provided useful information to those interested in disease pathogenesis and treatment. Genetic screens exploiting the phenomenon of RNA interference (RNAi) are now becoming commonplace. This article explains the different RNAi screen formats and describes some of the applications of RNAi screening that may be pertinent to the research pathologist.
CD30-positive diffuse large B-cell lymphoma with microvillous features: so-called microvillous lymphoma
Authors: Liu A , Sugisaki Y , Hosone M , Namimatsu S , Maeda S , Naito Z , Ghazizadeh M
Published: January 2009

A case of CD30-positive microvillous lymphoma (MVL) in an 87-year-old man who was encountered generalised lymphadenopathy is presented. Histopathologically, the tumour showed a morphological mimic of anaplastic large cell lymphoma (ALCL) with sinusoidal growth pattern. Immunohistochemically (IHC), the tumour cells were CD30+, CD20+, CD45+, BCL-2+, BCL-6+, MUM1+, Ki-67+, CD45RO−, CD3−, CD10−, CD15−, CD56−, EMA−, TIA-1−and ALK−. Flow cytometry confirmed the IHC. In situ hybridisation for Epstein–Barr virus RNA was negative. Electron microscopically, the tumour cells were similar to large transformed lymphocytes and had circumferentially profuse microvillous projections resembling those of epithelial mesothelioma cells. In conclusion, CD30-positive MVLs are indistinguishable from ALCLs that have ultrastructural microvillous projections by morphology alone. However, the lack of EMA, TIA-1 and ALK expression in this MVL case facilitated a definite distinction from ALCLs. The results of a panel of three markers (CD10−, Bcl-6+and MUM1+) suggested that the present case of CD30-positive MVLs has an activated non-germinal centre B-cell origin.
Histological scoring of fibrosis and activity in HIV–chronic hepatitis B related liver disease: performance of the METAVIR score assessed on virtual slides
Authors: Wendum D , Lacombe K , Chevallier M , Callard P , Valet F , Miailhes P , Bonnard P , Molina J-M , Lascoux-Combe C , Fléjou J-F , Girard P-M
Published: January 2009

Background:

The METAVIR score, which is the most widely used score in France, was specifically elaborated and evaluated in chronic hepatitis C and has never been validated in HIV–hepatitis virus B (HBV) co-infected patients.

Aims:

To validate the use of the METAVIR scoring system for activity and fibrosis on liver biopsies in co-infected HIV–HBV patients.

Methods:

METAVIR scoring for activity and fibrosis was first conducted on both original and virtual slides by one pathologist for comparison. Then 55 biopsies turned into virtual slides were scored by three pathologists independently.

Results:

The scoring comparison between virtual slides and glass slides showed an almost perfect agreement for fibrosis (weighted κ (κw) 0.8) and a substantial agreement for activity (κw0.68). The inter-observer agreement on virtual slides was moderate to almost perfect (κw0.52 to 0.84) for fibrosis and was dependent on the pair of pathologists considered. The best agreement was obtained in scoring advanced fibrosis and cirrhosis versus significant fibrosis versus no or mild fibrosis (κw0.70 to 0.84). The agreement for cirrhosis was rated moderate to substantial (κw0.54 to 0.79). Agreement for activity was substantial (κw0.66 to 0.8).

Conclusions:

This study validates the use of virtual slide technology to assess fibrosis and activity on liver biopsies. It also validates the use of the METAVIR score in co-infected HIV–HBV patients and illustrates the challenges in establishing the histological diagnosis of cirrhosis in the HIV–HBV context.
The role of immunohistochemistry in the differential diagnosis of papillary lesions of the breast
Authors: Tse G M , Tan P H , Moriya T
Published: January 2009

Papillary lesions of the breast represent a heterogeneous group with differing biological behaviour. Correct diagnosis is crucial but may be difficult, as many benign and malignant papillary lesions have similar appearances. Immunohistochemistry plays a useful role in their differentiation. Myoepithelial markers can help in differentiating papilloma from papillary carcinoma, as the former usually shows a continuous layer of myoepithelial cells. In intracystic papillary carcinoma, there is controversy as to the presence of a complete myoepithelial cell layer around these lesions. p63 is the marker of choice as the staining is nuclear, cross-reactivity is minimal, and sensitivity is high. Papilloma may frequently be complicated by superimposed different types of epithelial hyperplasia, which range from usual to atypical or even ductal carcinoma in situ, and they many be morphologically similar. Basal cytokeratins (CKs) are useful to differentiate these entities; as usual hyperplasia is positive for basal CKs with a mosaic staining pattern. CK5/6 is probably the best marker. Neuroendocrine markers (chromogranin A and synaptophysin) may be positive in papillary carcinoma, particularly in the solid type, and there may be some overlap with the ductal carcinoma in situ with spindle cells or endocrine ductal carcinoma in situ. A panel of CK5/6, p63 and neuroendocrine markers can be useful in the diagnostic investigation of problematic papillary lesions of the breast. As the experience with these markers remains rather limited, it is too early to recommend basing treatment choices on these marker studies alone. Complete removal of lesion is probably still the treatment of choice.
A molecular marker closely linked to the region of Rht-D1c and Ms2 genes in common wheat (Triticum aestivum)
Authors: Cao Wenguang , Somers Daryl J. , Fedak George
Published: January 2009

A male sterile wheat mutant, Triticum aestivum L. ‘Taigu’, was found in a wheat field in China in 1972. The male sterility was controlled by a single dominant gene that was referred to as Ms2. Recently, this gene was found to be linked to a dwarfing gene through crossing Taigu with the short wheat T. aestivum ‘Ai-Bian 1’ carrying the dwarfing gene Rht-D1c. The objective of this study was to develop molecular markers linked to the male sterility Ms2 gene in common wheat. One hundred and twenty-two near-isogenic lines were developed through backcrossing and sib intercrossing and used as the mapping population for the development of molecular markers. Bulked segregant analysis was used to screen 48 pairs of SSR primers, and a marker, MS2-WMC617, was identified closely linked to the male sterile Ms2 gene that mapped at the distal position of chromosome arm 4DS. The use of the molecular marker MS2-WMC617 can facilitate recurrent selection in a wheat breeding program based on marker-assisted selection.
Robustness of QTLs across germplasm pools using a model quantitative trait
Authors: Lee E. A. , Staebler J. M. , Grainger C. , Snook M. E.
Published: January 2009

Knowledge of the inheritance of C-glycosyl flavone synthesis in maize ( Zea mays L.) silk tissues has been acquired through detailed genetic studies involving primarily germplasm from the Corn Belt Dent race. To test the robustness of this genetic knowledge, we examined C-glycosyl flavone synthesis in a genetically distinct germplasm pool, popcorn. C-glycosyl flavone profiles and levels and the involvement of three specific genes/quantitative trait loci (p, pr1, and sm1) in C-glycosyl flavone synthesis were examined in popcorn germplasm representing at least two races and various diverse geographic regions. Twenty-four inbred lines and 23 hybrids involving these inbred lines and inbred line R17 were characterized for their flavone profiles and levels in silk tissues. Two F2mapping populations were constructed to examine the involvement of p, pr1, and sm1 on C-glycosyl flavone synthesis. C-glycosyl flavone levels threefold higher than previously reported in Corn Dent Belt materials and a novel class of compounds were discovered. The gene action of sm1 was different, the functional p allele was not always dominant, and pr1 did not affect maysin synthesis. Based on this rather simplistic “model” quantitative trait, it appears that caution should be exercised when attempting to apply quantitative trait locus knowledge accumulated in one germplasm base to a germplasm base that is known to be distinctly unique.
Identification and characterization of the WRKY transcription factor family in Pinus monticola
Authors: Liu Jun-Jun , Ekramoddoullah Abul K.M.
Published: January 2009

The WRKY gene family represents an ancient and highly complex group of transcription factors involved in signal transduction pathways of numerous plant developmental processes and host defense response. Up to now, most WRKY proteins have been identified in a few angiosperm species. Identification of WRKY genes in a conifer species would facilitate a comprehensive understanding of the evolutionary and function-adaptive process of this superfamily in plants. We performed PCR on genomic DNA to clone WRKY sequences from western white pine ( Pinus monticola ), one of the most valuable conifer species endangered by white pine blister rust ( Cronartium ribicola ). In total, 83 P. monticola WRKY (PmWRKY) sequences were identified using degenerate primers targeted to the WRKY domain. A phylogenetic analysis revealed that PmWRKY members fell into four major groups (1, 2a+2b, 2c, and 2d+2e) described in Arabidopsis and rice. Because of high genetic diversity of the PmWRKY family, a modified AFLP method was used to detect DNA polymorphism of this gene family. Polymorphic fragments accounted for 17%–35% of total PCR products in the AFLP profiles. Among them, one WRKY AFLP marker was linked to the major resistance gene (Cr2) against C. ribicola. The results of this study provide basic genomic information for a conifer WRKY gene family, which will pave the way for elucidating gene evolutionary mechanisms in plants and unveiling the precise roles of PmWRKY in conifer development and defense response.
Influence of overconsolidation on the freezing characteristics of a clayey silt
Authors: Konrad J.-M.
Published: January 2009

Laboratory freezing tests were performed on a saturated clayey silt at various overconsolidation ratios (OCR) to establish the relationship between initial void ratio and stress history, and the amount of moisture transfer during freezing. The frost heave tests were analysed in terms of the segregation potential as well as a function of the temperature of ice lens formation and the overall hydraulic conductivity of the frozen fringe. All other factors being the same, the segregation potential was found to increase with increasing values of OCR (decreasing initial void ratios). However, the combined effects of decreasing void ratio and increasing suction at the frost line, all other factors being identical in all freezing tests, resulted in decreasing segregation potentials. This trend was the result of a decrease in the temperature of ice lens formation and the concomitant decrease in overall hydraulic conductivity of the frozen fringe. A simple model showed that the capillary unfrozen water between clay particles increases when the particles pack closer together, as overconsolidation increases, allowing the migratory water to freeze within the frozen soil at a colder temperature. Key words: frost heave, clayey silt, overconsolidation, void ratio.
Fracture effects in the shallow groundwater zone in weathered Sarnia-area clay
Authors: D'Astous A. Y. , Ruland W. W. , Bruce J. R. G. , Cherry J. A. , Gillham R. W.
Published: January 2009

The Sarnia area of southwestern Ontario is underlain by thick deposits of clay-rich glacial till. From ground surface to between 4 and 6 m depth the clay till is fractured, oxidized, and penetrated by root holes. The water table fluctuates seasonally between the ground surface and the bottom of the weathered zone. Water-level response tests in conventional piezometers installed in augered holes in the weathered zone typically provide very low values of hydraulic conductivity (10−7–10−9 cm/s), which are similar to values obtained from the deeper unweathered and unfractured till. The augering process creates a smeared clay zone along the borehole walls that significantly reduces measured hydraulic conductivity values. In this study, the weathered-zone hydraulic conductivity was measured using unconventional piezometers, a large-diameter well, and a tracer experiment between two test pits. The smeared zone was removed or reduced around these installations, and the measured weathered-zone hydraulic conductivity was 10−5–10−7 cm/s, much higher than in the deep unweathered clay. These results, together with depth profiles of groundwater tritium and monitored water-level fluctuations, indicate that the weathered zone has hydraulic conductivity governed by fractures and has significant hydrologic activity in the fractures. Key words: clay, fractures, hydraulic conductivity, permeability, piezometer, tritium, tracer experiment, weathered zone.
Coquitlam Lake water tunnel upgrading—design and construction, a case history
Authors: Huber Frank
Published: January 2009

This paper describes geotechnical and construction aspects of a water supply tunnel upgrading project, in the Coquitlam River valley, northeast of Vancouver, British Columbia. This tunnel conveys potable water from Coquitlam Lake, a major source of water for the Vancouver area, to below Coquitlam dam, into large-diameter supply mains. This project involved the enlargement of the existing tunnel in rock, and sand and gravel, and the construction of a new tunnel through a wide variety of ground conditions, including stiff silt and clay, sand and gravel with up to 12 m of groundwater head at the tunnel horizon, and granodiorite rock. These difficult ground conditions required careful evaluation of numerous costly excavation methods.The entire project was on a very tight construction schedule, as Coquitlam Lake is an essential source of water during the warm summer months. In total, 786 m of tunnel or decline was driven. To facilitate timely project completion, a decline was driven to intersect the existing tunnel about halfway between the intake and south portal outlet, providing the contractor with two additional faces to work from. Numerous types of ground support were used, including rock bolts, steel sets, and fibre-reinforced shotcrete. Construction was started in July 1986 and completed in May 1987. Key words: tunnel, soft ground, shoring, ground load, rock bolts, shotcrete, blasting.
Geomembrane interface friction
Authors: Negussey D. , Wijewickreme W. K. D. , Vaid Y. P.
Published: January 2009

Interface friction between an HDPE geomembrane and an angular as well as a rounded sand, a gravel, and a geotextile was investigated in a ring shear apparatus. The results indicate development of peak resistance at small strain and constant residual interface friction angles at large strain. The magnitude and difference between peak and residual friction angles increase with angularity. Interface friction angles between a geotextile and geomembrane were very low with no distinction between peak and residual. At composite interfaces, sliding occurred much more readily at a finer grained than a coarsegrained geomembrane interface. Key words: geomembranes, geotextiles, interface friction, granular materials.
RECOVERING THE GLOBAL STRUCTURE FROM MULTIPLE LOCAL BAYESIAN NETWORKS
Authors: LI WEIHUA , LIU WEIYI , YUE KUN
Published: January 2009

Bayesian networks are powerful tools for common knowledge representation and reasoning of partial beliefs under uncertainty. In the last decade, Bayesian networks have been successfully applied to a variety of problem domains and many Bayesian networks have been established. Confronted with many real-world applications, each Bayesian network established may be a local model of the whole knowledge domain. It is desirable to combine all local models of the whole domain into a global and more general representation. It is not realistic to expect the domain experts to construct the global model manually due to the too broad domain. As well, it is not feasible to relearn the model since the dataset may have been discarded or the whole domain may be distributed. Thus, constructing the global model by combining local models is doomed to be an alternative solution. This paper concentrates on finding a method of combination without loss of any information and free of datasets by capturing the graphical characterizations of global models. From the graphical perspective, this paper first captures two graphical characterizations to determine the skeleton and V-structure of global models. Moreover, a simple algorithm is elicited from these graphical characterizations to recover the global underlying model from multiple local models. A preliminary experiment demonstrates empirically that our algorithm is feasible.
ROBOCUP HUMANOID CHALLENGE
Authors: MAYER N. MICHAEL , ASADA MINORU
Published: January 2009

We describe here the humanoid challenge that is part of the RoboCup robot soccer competitions. We focus on how relevant research issues of humanoid robotics — for example, biped walking and human-like sensors and actuators — can be addressed, and we investigate how teams proceed to solve the given tasks. Thus, new technologies like artificial muscles and artificial skin might find their way into the competition very soon. We detail examples of these technologies and discuss in which way they may contribute to RoboCup, and in return how RoboCup may serve as a benchmark for achievements within these technologies. Further we describe how RoboCup works as an open, worldwide cooperative project in robotics and AI.
DEVELOPMENT OF A HIGH-PERFORMANCE HUMANOID SOCCER ROBOT
Authors: MATSUMURA REO , ISHIGURO HIROSHI
Published: January 2009

The RoboCup, which is a worldwide robot soccer competition, has set an ambitious goal for itself: to have a humanoid robot team win against human teams in World Cup Soccer by 2050. In order to achieve this goal, the robots require highly sophisticated sensory-data processing and decision-making functions. The development of robots for the RoboCup Humanoid League also has significant meaning for the development of robotics. However, this development is not easy and there are few papers covering it and its design policy. This paper reports the design policy for humanoids developed by Team Osaka, whose robots have been selected as the best humanoid robots four times in the last four years. In addition to the design policy, this paper also reports on the developmental process and comparisons among humanoid versions developed by Team Osaka. We believe that this paper will offer much information to other researchers who are developing humanoids for the RoboCup.
3D MODELS OF HUMANOID SOCCER ROBOT IN USARSim AND ROBOTICS STUDIO SIMULATORS
Authors: MENEGATTI EMANUELE , SILVESTRI GIOVANNI , PAGELLO ENRICO , GREGGIO NICOLA , CISTERNINO ANTONIO , MAZZANTI FEDERICO , SORBELLO ROSARIO , CHELLA ANTONIO
Published: January 2009

This paper describes our experience in the simulation of humanoid soccer robots using two general purposes 3D simulators, namely USARSim and Microsoft Robotics Studio. We address the problem of the simulation of a soccer match among two teams of small humanoid robots in the RoboCup Soccer Kid-Size Humanoid competitions. The paper reports the implementation of the virtual models of the Robovie-M humanoid robot platform in the two simulators. Robovie-M was the robot used by our team "Artisti" in the RoboCup 2006 competitions. This paper focuses on the procedures needed to implement the virtual models of the robot and in the details of the models. We describe experiments assessing the feasibility and the fidelity of the two simulators.
HIERARCHICAL REACTIVE CONTROL FOR HUMANOID SOCCER ROBOTS
Authors: BEHNKE SVEN , STÜCKLER JÖRG
Published: January 2009

Humanoid soccer serves as a benchmark problem for artificial intelligence research and robotics. Every year, more teams are competing, for example, in the RoboCup Humanoid League. As the robots improve in the basic skills of walking, kicking, and getting up, teams can focus on soccer skills and team coordination. The complexity of soccer behaviors and team play calls for structured behavior engineering.

In this paper, we describe the design of the behavior control software for the Humanoid League team NimbRo. The software is based on a framework that supports a hierarchy of reactive behaviors. It is structured both as an agent hierarchy (joint–body part–player–team) and as a time hierarchy. The speed of sensors, behaviors, and actuators decreases when moving up in the hierarchy. The lowest levels of this framework contain position control of individual joints and kinematic interfaces for body parts. At the next level, basic skills are implemented. Soccer behaviors like searching for the ball, approaching the ball, avoiding obstacles, and defending the goal reside on the player level. Finally, on the tactical level, the robots communicate via a wireless network to negotiate roles and use allocentric information to configure the soccer behaviors.

Our robots performed very well at RoboCup 2007, which took place in Atlanta, Georgia, USA. They won both the KidSize and the TeenSize humanoid soccer competitions.
On constructing optimistic simulation algorithms for the discrete event system specification
Authors: Nutaro James
Published: January 2009

This article describes a Time Warp simulation algorithm for discrete event models that are described in terms of the Discrete Event System Specification (DEVS). The article shows how the total state transition and total output function of a DEVS atomic model can be transformed into an event processing procedure for a logical process. A specific Time Warp algorithm is constructed around this logical process, and it is shown that the algorithm correctly simulates a DEVS coupled model that consists entirely of interacting atomic models. The simulation algorithm is presented abstractly; it is intended to provide a basis for implementing efficient and scalable parallel algorithms that correctly simulate DEVS models.
Direct address translation for virtual memory in energy-efficient embedded systems
Authors: Zhou Xiangrong , Petrov Peter
Published: January 2009

This article presents a methodology for virtual memory support in energy-efficient embedded systems. A holistic approach is proposed, where the combined efforts of compiler, operating system, and hardware architecture achieve a significant system power reductions. The application information extracted and analyzed by the compiler is utilized dynamically by the microarchitecture and the operating system to perform energy-efficient and, for many memory references, time-deterministic address translations. We demonstrate that by using application information regarding virtual memory layout, an efficient and conflict-free translation process can be implemented through the utilization of a small hardware direct translation table (DTT) accessed in an application-specific manner. The set of virtual pages is partitioned into groups, such that for each group only a few of the least significant bits are used as an index to obtain the physical page number. We outline an efficient compile-time algorithm for identifying these groups and allocate their translation entries optimally into the DTT. The introduced hardware is minimal in terms of area, performance, and power overhead, while offering the flexibility of software programmability. This is achieved through a small set of registers and tables, which are made software accessible. We have quantitatively evaluated the proposed methodology on a number of embedded applications, including voice, image, and video processing.
Analyzing the worst-case execution time for instruction caches with prefetching
Authors: Yan Jun , Zhang Wei
Published: January 2009

Time predictability is one of the most important design considerations for real-time systems. In this article, we study the impact of instruction prefetching on the worst-case performance of instruction caches. We extend the static cache simulation technique to model and compute the worst-case instruction cache performance with prefetching. The evaluation results show that instruction prefetching can benefit both the average-case and worst-case performance; however, the degree of the worst-case performance improvement due to instruction prefetching is less than that of the average-case performance. As a result, the time variation of computing is increased by instruction prefetching. Also, our experimental results indicate that the prefetching distance can significantly impact the worst-case performance of instruction caches with instruction prefetching. Specifically, when the prefetching distance is equal to the L1 miss penalty, the worst-case execution time with instruction prefetching is minimized.
Transition of instruments in The SINE WAVE ORCHESTRA
Authors: Jo Kazuhiro , Furudate Ken , Ishida Daisuke , Noguchi Mizuki
Published: January 2009

This article discusses the transition of instruments in The SINE WAVE ORCHESTRA (SWO), which is a participatory sound performance project. Its basic concept is that each participant plays a sine wave, to collectively create a sound representation. Although all SWO works use the same sound source (i.e., sine waves), each SWO work employs different instruments. The employment of various instruments results in different styles of collective sound representation. This article examines five of the instruments utilized in SWO works. In The SINE WAVE ORCHESTRA The Stairway, the participants played sine waves with light-sensitive instruments as well as other instruments. In The SINE WAVE ORCHESTRA stay, participants accumulated sine waves in an echoless chamber. In The SINE WAVE ORCHESTRA nomadic, each participants played and exhibitied a sine wave with a Linux-installed Pod. At The SINE WAVE ORCHESTRA at ZeroOne San Jose/ISEA 2006, each participant played a sine wave with a hand-held plastic egg instrument; in The SINE WAVE ORCHESTRA mediate, participants extended the recursion of sine waves with eight sets of boards. In this article we discuss which elements of the instrument affect how people create collective sound representations and describe the participants' experience with the instruments.
The Vestibulo-Auricular Reflex
Authors: Tollin Daniel J. , Ruhland Janet L. , Yin Tom C. T.
Published: January 2009

The mammalian orienting response to sounds consists of a gaze shift that can be a combination of head and eye movements. In animals with mobile pinnae, the ears also move. During head movements, vision is stabilized by compensatory rotations of the eyeball within the head because of the vestibulo-ocular reflex (VOR). While studying the gaze shifts made by cats to sounds, a previously uncharacterized compensatory movement was discovered. The pinnae exhibited short-latency, goal-directed movements that reached their target while the head was still moving. The pinnae maintained a fixed position in space by counter-rotating on the head with an equal but opposite velocity to the head movement. We call these compensatory ear movements the vestibulo-auricular reflex (VAR) because they shared many kinematic characteristics with the VOR. Control experiments ruled out efference copy of head position signals and acoustic tracking (audiokinetic) of the source as the cause of the response. The VAR may serve to stabilize the auditory world during head movements.