bluuebunny/crossref_metadata_2025 huggingface dataset:
Accurate two‐dimensional IMRT verification using a back‐projection EPID dosimetry method
Authors: Wendling Markus , Louwe Robert J. W. , McDermott Leah N. , Sonke Jan‐Jakob , van Herk Marcel , Mijnheer Ben J.
Published: February 2006

The use of electronic portal imaging devices (EPIDs) is a promising method for the dosimetric verification of external beam, megavoltage radiation therapy—both pretreatment and in vivo. In this study, a previously developed EPID back‐projection algorithm was modified for IMRT techniques and applied to an amorphous silicon EPID. By using this back‐projection algorithm, two‐dimensional dose distributions inside a phantom or patient are reconstructed from portal images. The model requires the primary dose component at the position of the EPID. A parametrized description of the lateral scatter within the imager was obtained from measurements with an ionization chamber in a miniphantom. In addition to point dose measurements on the central axis of square fields of different size, we also used dose profiles of those fields as reference input data for our model. This yielded a better description of the lateral scatter within the EPID, which resulted in a higher accuracy in the back‐projected, two‐dimensional dose distributions. The accuracy of our approach was tested for pretreatment verification of a five‐field IMRT plan for the treatment of prostate cancer. Each field had between six and eight segments and was evaluated by comparing the back‐projected, two‐dimensional EPID dose distribution with a film measurement inside a homogeneous slab phantom. For this purpose, the ‐evaluation method was used with a dose‐difference criterion of 2% of dose maximum and a distance‐to‐agreement criterion of . Excellent agreement was found between EPID and film measurements for each field, both in the central part of the beam and in the penumbra and low‐dose regions. It can be concluded that our modified algorithm is able to accurately predict the dose in the midplane of a homogeneous slab phantom. For pretreatment IMRT plan verification, EPID dosimetry is a reliable and potentially fast tool to check the absolute dose in two dimensions inside a phantom for individual IMRT fields. Film measurements inside a phantom can therefore be replaced by EPID measurements.
Improving retrospective sorting of 4D computed tomography data
Authors: Rietzel Eike , Chen George T. Y.
Published: February 2006

Respiratory correlated CT is commercially available, and we have implemented its routine clinical use in planning lung tumor patients. Its value is determined by the fidelity of the spatiotemporal data set after processing the acquired reconstructed slices. Retrospective sorting of reconstructed slices is based on respiratory phase. However, the existing commercial software inadequately models respiratory phase for about 30% of the patients, mainly due to irregularities in the respiratory cycle. We have developed software that improves phase determination and consequently leads to an improvement of retrospective data sorting to make 4DCT data acquisition feasible for routine clinical use. Peak inhalation and exhalation respiratory states are selected manually; intermediate phases are interpolated. Residual motion artifacts in the resulting 4DCT volumes are reduced and allow use of the 4D imaging studies for treatment planning.
Performance comparison of two dual‐head coincidence cameras of the first and latest generation
Authors: Schelper Lutz Frank , Gosink Hans‐Juergen , Meller Birgit , Richter Eckart , Baehre Manfred
Published: February 2006

This study compares the performance and image quality of two gamma camera based PET systems of the first and latest generation. We investigated two dual head coincidence gamma cameras (PRISM 2000XP and AXIS, manufactured in 1997 and 2001 by Picker/Philips) predominantly in accordance with the NEMA NU2‐1994 and NU2‐2001 protocols. All performance parameters except for spatial resolution and image quality were determined after measuring a standard cylinder over several half‐life periods. Scatter and random fractions were evaluated with the sinogram technique. In order to determine spatial resolution and image quality we used phantoms as described in the NEMA NU2‐2001 protocol. The efficiency of the new system was found to be increased. True count rate at activity levels used in clinical conditions is improved and scatter fraction is decreased substantially. Accordingly, improved spatial resolution and image quality were observed with the new system. Altogether, the AXIS represents a further approach to the performance of dedicated positron emission tomographs
Monte Carlo calculations of thermal neutron capture in gadolinium: A comparison of GEANT4 and MCNP with measurements
Authors: Enger Shirin A. , Munck af Rosenschöld Per , Rezaei Arash , Lundqvist Hans
Published: February 2006

GEANT4 is a Monte Carlo code originally implemented for high‐energy physics applications and is well known for particle transport at high energies. The capacity of GEANT4 to simulate neutron transport in the thermal energy region is not equally well known. The aim of this article is to compare MCNP, a code commonly used in low energy neutron transport calculations and GEANT4 with experimental results and select the suitable code for gadolinium neutron capture applications. To account for the thermal neutron scattering from chemically bound atoms in biological materials a comparison of thermal neutron fluence in tissue‐like poly(methylmethacrylate) phantom is made with MCNP4B, GEANT4 6.0 patch1, and measurements from the neutron capture therapy (NCT) facility at the Studsvik, Sweden. The fluence measurements agreed with MCNP calculated results considering . The location of the thermal neutron peak calculated with MCNP without and GEANT4 is shifted by about towards a shallower depth and is 25%–30% lower in amplitude. Dose distribution from the gadolinium neutron capture reaction is then simulated by MCNP and compared with measured data. The simulations made by MCNP agree well with experimental results. As long as thermal neutron scattering from chemically bound atoms are not included in GEANT4 it is not suitable for NCT applications.
Reconstruction of electron spectra from depth doses with adaptive regularization
Authors: Wei Jikun , Sandison George A. , Chvetsov Alexei V.
Published: February 2006

Electron spectral reconstruction of medical accelerators from measured depth doses is a practical method for providing the input initial phase space distribution at the patient surface that is required by Monte Carlo treatment planning systems. The posed inverse problem of spectral reconstruction is ill conditioned and this may lead to nonphysical oscillations in the reconstructed spectra. Use of a variational method of solution with a regularization technique removes the oscillations but tends to smooth the sharp (deltalike) energy peak that is a common feature in electron spectra generated by medical accelerators. Because the sharp peak contains a large percentage of the electrons in the spectrum, an accurate estimate of the peak width, height and position is critical to the success of the technique for spectrum reconstruction with regularization. We propose use of an adaptive regularization term as a special form of the general Tichonov regularization function. The variational method with the adaptive regularization term is applied to reconstruct electron spectra for the 6, 9, and electron beams of a Varian Clinac 2100C accelerator and proves to be a very simple, effective and accurate approach. Results using this variational method with adaptive regularization almost perfectly reconstruct electron spectra from depth dose distributions.
Image blurring due to light‐sharing in PET block detectors
Authors: James Sara St. , Thompson Christopher J.
Published: February 2006

The spatial resolution in PET is poorer than that of CT or MRI. All modern PET scanners use block detectors, i.e., clusters of scintillation crystals coupled to four photomultiplier tubes. Some of the loss of spatial resolution in PET is attributed to the use of block detectors, because a photon that interacts with one crystal in the cluster may be incorrectly positioned, resulting in blurring of the reconstructed image. This is called the “block effect.” The block effect was measured for detectors from the CTI HR+ scanner, and the GE Advance scanner; two popular clinical PET scanners. The effect of changing the depth of first interaction of a gamma ray in the scintillation crystals was also studied to determine if it may be a contributor to the block effect. The block effect was found to be for the central crystals and negligible for the edge crystals in the CTI HR+ block. It was in the central crystals of the GE Advance detector, and in the edge crystals of the GE Advance detector. In the CTI HR+ detector, a depth dependence on the positioning of the event was observed, as was a dependence on the crystal location (edge versus center). In the GE Advance detector events that occurred at different interaction depths were positioned consistently. The percentage of events that may be positioned inaccurately was also calculated for both detectors. In the CTI HR+ detector as many as 16% of all events in the block detector may be positioned incorrectly. In the GE Advance detector as many as 13% of all events in the block detector may be positioned inaccurately. These results suggest that the depth of interaction of an annihilation photon may contribute to the block effect in detectors that use crystals cut from a single scintillation crystal (pseudodiscrete crystals), and is less dominant a factor for detectors that use discrete crystals with light sharing between the crystals. Investigating the effect of changing photon interaction depth in PET detectors can lead to better detector design, and an intuitive explanation of what sources of blurring may exist in the detector examined.
Direct cone‐beam cardiac reconstruction algorithm with cardiac banding artifact correction
Authors: Taguchi Katsuyuki , Chiang Beshan S. , Hein Ilmar A.
Published: February 2006

Multislice helical computed tomography (CT) is a promising noninvasive technique for coronary artery imaging. Various factors can cause inconsistencies in cardiac CT data, which can result in degraded image quality. These inconsistencies may be the result of the patient physiology (e.g., heart rate variations), the nature of the data (e.g., cone‐angle), or the reconstruction algorithm itself. An algorithm which provides the best temporal resolution for each slice, for example, often provides suboptimal image quality for the entire volume since the cardiac temporal resolution (TRc) changes from slice to slice. Such variations in TRc can generate strong banding artifacts in multi‐planar reconstruction images or three‐dimensional images. Discontinuous heart walls and coronary arteries may compromise the accuracy of the diagnosis. A ‐blocker is often used to reduce and stabilize patients' heart rate but cannot eliminate the variation. In order to obtain robust and optimal image quality, a software solution that increases the temporal resolution and decreases the effect of heart rate is highly desirable. This paper proposes an ECG‐correlated direct cone‐beam reconstruction algorithm (TCOT‐EGR) with cardiac banding artifact correction (CBC) and disconnected projections redundancy compensation technique (DIRECT). First the theory and analytical model of the cardiac temporal resolution is outlined. Next, the performance of the proposed algorithms is evaluated by using computer simulations as well as patient data. It will be shown that the proposed algorithms enhance the robustness of the image quality against inconsistencies by guaranteeing smooth transition of heart cycles used in reconstruction.
A proposed alternative to phase‐space recycling using the adaptive kernel density estimator method
Authors: Tyagi Neelam , Martin William R. , Du J. , Bielajew A. F. , Chetty Indrin J.
Published: February 2006

We have implemented a nonparametric density estimation technique, the adaptive kernel density estimator (AKDE), to generate additional phase space (PS) variables in the vicinity of simulated PS points in Monte Carlo linear accelerator simulation. The method involves the placement of kernels at simulated PS points that have a “window width” that depends on the density of simulated PS points. This method has been tested on known one‐dimensional (1‐D) and two‐dimensional (2‐D) probability density functions (PDFs) and has been used to sample (photons only) from PS files generated from accelerator simulations. The original simulated PS vector was reduced to a rotationally invariant PS vector that takes advantage of the azimuthal symmetry above the collimating jaws. The new PS vector is sampled in the vicinity of the sampled PS vector . The first step in assessing the accuracy of the method was a correlation analysis among the AKDE generated PS variables compared with correlations among the original PS variables. “In‐air” particle fluence distributions between AKDE samples and the original PS distribution showed agreement within 2% ( to 6.8%) across the entire phase space plane. Central axis energy distributions and angular distributions agreed on average to within 1.5% ( to 6.6%) and 0.1% ( to 3.0%), respectively. Dose profiles were calculated for field sizes , , and for AKDE and compared against calculations performed with PS recycling. AKDE calculated depth doses and profiles were within 2% and , respectively, of those computed using PS recycling.
A direct voxel tracking method for four‐dimensional Monte Carlo dose calculations in deforming anatomy
Authors: Heath Emily , Seuntjens Jan
Published: February 2006

In this work we present a method of calculating dose in deforming anatomy where the position and shape of each dose voxel is tracked as the anatomy changes. The EGSnrc/DOSXYZnrc Monte Carlo code was modified to calculate dose in voxels that are deformed according to deformation vectors obtained from a nonlinear image registration algorithm. The defDOSXYZ code was validated by consistency checks and by comparing calculations against DOSXYZnrc calculations. Calculations in deforming phantoms were compared with a dose remapping method employing trilinear interpolation. Dose calculations with the deforming voxels agree with DOSXYZnrc calculations within 1%. In simple deforming rectangular phantoms the trilinear dose remapping method was found to underestimate the dose by up to 29% for a voxel size within the field, with larger discrepancies in regions of steep dose gradients. The agreement between the two calculation methods improved with smaller voxel size and deformation magnitude. A comparison of dose remapping from Inhale to Exhale in an anatomical breathing phantom demonstrated that dose deformations are underestimated by up to 16% in the penumbra and 8% near the surface with trilinear interpolation.
An improved method for flat‐field correction of flat panel x‐ray detector
Authors: Kwan Alexander L. C. , Seibert J. Anthony , Boone John M.
Published: February 2006

In this Technical Note, the effects of different flat‐field techniques are examined for a cesium iodide flat panel detector, which exhibited a slightly nonlinear exposure response. The results indicate that the variable flat‐field correction method with the appropriate polynomial fit provides excellent correction throughout the entire exposure range. The averaged normalized variation factor, used to assess the nonuniformity of the flat‐field correction, decreased from 30.76 for the fixed correction method to 4.13 for the variable flat‐field correction method with a fourth‐order polynomial fit for the spectrum, and from 16.42 to 3.97 for the spectrum.
Computerized mass detection for digital breast tomosynthesis directly from the projection images
Authors: Reiser I. , Nishikawa R. M. , Giger M. L. , Wu T. , Rafferty E. A. , Moore R. , Kopans D. B.
Published: February 2006

Digital breast tomosynthesis (DBT) has recently emerged as a new and promising three‐dimensional modality in breast imaging. In DBT, the breast volume is reconstructed from 11 projection images, taken at source angles equally spaced over an arc of . Reconstruction algorithms for this modality are not fully optimized yet. Because computerized lesion detection in the reconstructed breast volume will be affected by the reconstruction technique, we are developing a novel mass detection algorithm that operates instead on the set of raw projection images. Mass detection is done in three stages. First, lesion candidates are obtained for each projection image separately, using a mass detection algorithm that was initially developed for screen‐film mammography. Second, the locations of a lesion candidate are backprojected into the breast volume. In this feature volume, voxel intensities are a combined measure of detection frequency (e.g., the number of projections in which a given lesion candidate was detected), and a measure of the angular range over which a given lesion was detected. Third, features are extracted after reprojecting the three‐dimensional (3‐D) locations of lesion candidates into projection images. Features are combined using linear discriminant analysis. The database used to test the algorithm consisted of 21 mass cases (13 malignant, 8 benign) and 15 cases without mass lesions. Based on this database, the algorithm yielded a sensitivity of 90% at 1.5 false positives per breast volume. Algorithm performance is positively biased because this dataset was used for development, training, and testing, and because the number of algorithm parameters was approximately the same as the number of patient cases. Our results indicate that computerized mass detection in the sequence of projection images for DBT may be effective despite the higher noise level in those images.
A material sensitivity study on the accuracy of deformable organ registration using linear biomechanical modelsa)
Authors: Chi Y. , Liang J. , Yan D.
Published: February 2006

Model‐based deformable organ registration techniques using the finite element method (FEM) have recently been investigated intensively and applied to image‐guided adaptive radiotherapy (IGART). These techniques assume that human organs are linearly elastic material, and their mechanical properties are predetermined. Unfortunately, the accurate measurement of the tissue material properties is challenging and the properties usually vary between patients. A common issue is therefore the achievable accuracy of the calculation due to the limited access to tissue elastic material constants. In this study, we performed a systematic investigation on this subject based on tissue biomechanics and computer simulations to establish the relationships between achievable registration accuracy and tissue mechanical and organ geometrical properties. Primarily we focused on image registration for three organs: rectal wall, bladder wall, and prostate. The tissue anisotropy due to orientation preference in tissue fiber alignment is captured by using an orthotropic or a transversely isotropic elastic model. First we developed biomechanical models for the rectal wall, bladder wall, and prostate using simplified geometries and investigated the effect of varying material parameters on the resulting organ deformation. Then computer models based on patient image data were constructed, and image registrations were performed. The sensitivity of registration errors was studied by perturbating the tissue material properties from their mean values while fixing the boundary conditions. The simulation results demonstrated that registration error for a subvolume increases as its distance from the boundary increases. Also, a variable associated with material stability was found to be a dominant factor in registration accuracy in the context of material uncertainty. For hollow thin organs such as rectal walls and bladder walls, the registration errors are limited. Given 30% in material uncertainty, the registration error is limited to within . For a solid organ such as the prostate, the registration errors are much larger. Given 30% in material uncertainty, the registration error can reach . However, the registration error distribution for prostates shows that most of the subvolumes have a much smaller registration error. A deformable organ registration technique that uses FEM is a good candidate in IGART if the mean material parameters are available.
Development and evaluation of an exact fan‐beam reconstruction algorithm using an equal weighting scheme via locally compensated filtered backprojection (LCFBP)
Authors: Chen Guang‐Hong , Tokalkanahalli Ranjini , Zhuang Tingliang , Nett Brian E. , Hsieh Jiang
Published: February 2006

A novel exact fan‐beam image reconstruction formula is presented and validated using both phantom data and clinical data. This algorithm takes the form of the standard ramp filtered backprojection (FBP) algorithm plus local compensation terms. This algorithm will be referred to as a locally compensated filtered backprojection (LCFBP). An equal weighting scheme is utilized in this algorithm in order to properly account for redundantly measured projection data. The algorithm has the desirable property of maintaining a mathematically exact result for: the full scan mode , the short scan mode ( full fan angle), and the supershort scan mode [less than ( full fan angle)]. Another desirable feature of this algorithm is that it is derivative‐free. This feature is beneficial in preserving the spatial resolution of the reconstructed images. The third feature is that an equal weighting scheme has been utilized in the algorithm, thus the new algorithm has better noise properties than the standard filtered backprojection image reconstruction with a smooth weighting function. Both phantom data and clinical data were utilized to validate the algorithm and demonstrate the superior noise properties of the new algorithm.
Distribution of Ty3-gypsy- and Ty1-copia-like DNA sequences in the genus Helianthus and other Asteraceae
Authors: Natali L , Santini S , Giordani T , Minelli S , Maestrini P , Cionini P G , Cavallini A
Published: February 2006

Two repeated DNA sequences, pHaS13 and pHaS211, which revealed similarity to the int gene of Ty3-gypsy retrotransposons and the RNAse-H gene of Ty1-copia retroelements, respectively, were surveyed in Asteraceae species and within the genus Helianthus. Southern analysis of the genome of selected Asteraceae that belong to different tribes showed that pHaS13- and pHaS211-related subfamilies of gypsy- and copia-like retroelements are highly redundant only in Helianthus and, to a lesser extent, in Tithonia, a Helianthus strict relative. However, under low stringency posthybridization washes, bands were observed in almost all the other Asteraceae tested when pHaS13 was used as a probe, and in several species when pHaS211 was hybridized. FISH analysis of pHaS13 or pHaS211 probes was performed in species in which labelling was observed in Southern hybridizations carried out under high stringency conditions (Helianthus annuus, Tithonia rotundifolia, Ageratum spp., Leontopodium spp., Senecio vulgaris for pHaS13, and H. annuus, Tithonia rotundifolia, and S. vulgaris for pHaS211). Scattered labelling was observed over all metaphase chromosomes, indicating a large dispersal of both Ty3-gypsy- and Ty1-copia-like retroelements. However, preferential localization of Ty3-gypsy-like sequences at centromeric chromosome regions was observed in all of the species studies but one, even in species in which pHaS13-related elements are poorly represented. Ty1-copia -like sequences showed preferential localization at the chromosome ends only in H. annuus. To study the evolution of gypsy- and copia-like retrotransposons in Helianthus, cladograms were built based on the Southern blot hybridization patterns of pHaS13 or pHaS211 sequences to DNA digests of several species of this genus. Both cladograms agree in splitting the genomes studied into annuals and perennials. Differences that occurred within the clades of perennial and annual species between gypsy- and copia-like retroelements indicated that these retrotransposons were differentially active during Helianthus speciation, suggesting that the evolution of the 2 retroelement families was, within limits, independent.Key words: Asteraceae, FISH, genome evolution, Helianthus, retrotransposons, Ty1-copia, Ty3-gypsy.
5S rDNA gene diversity in tea (Camellia sinensis (L.) O. Kuntze) and its use for variety identification
Authors: Singh Dharam , Ahuja Paramvir Singh
Published: February 2006

Variability in the organization of repeats of 5S rDNA is useful for phylogenetic studies in various crops. We found variable repeats of 5S rDNA gene in the genome of tea (Camellia sinensis (L.) O. Kuntze) during Southern hybridization. Variability in the repeats of 5S rDNA with specific restriction endonuleases (Sau3AI, BamHI, and ApoI) was analyzed in 28 different tea clones representing 3 types of tea. Our results clearly show that the 5S rDNA gene in tea could be used as a molecular marker to distinguish C. sinensis Chinary tea from the other important types of tea, namely Assamica and Cambod. Upon analysis with restriction endonucleases, the 5S rDNA gene in the tea genome was found to be heavily methylated.Key words: Camellia sinensis, 5S rDNA, DNA methylation, restriction endonucleases, molecular marker.
Identification of all chromosome arms and their involvement in meiotic homoeologous associations at metaphase I in 2Hordeum vulgareL. ×Hordeum bulbosumL. hybrids
Authors: Pickering R , Klatte S , Butler R C
Published: February 2006

We have identified all Hordeum bulbosum chromosomes in 2 diploid Hordeum vulgare × Hordeum bulbosum hybrids using suitable probes and fluorescence in situ hybridization. Using the parental idiograms allowed us to carry out a full analysis of chromosome associations among all chromosome arms in the hybrids. Association frequencies were generally lower for the short arms than for the long arms. There were also significant differences among the chromosome arms in association frequencies, partly correlated with the absolute length of the chromosome arm, as well as with the frequency of recombinant lines, which were recovered from partially fertile interspecific hybrids. The H. bulbosum idiogram will be useful for further chromosome association studies and will enable the identification of H. bulbosum chromosomes involved in chromosome addition or substitution lines.Key words: Hordeum vulgare, Hordeum bulbosum, interspecific hybrids, chromosome associations, meiosis, fluorescence in situ hybridization.
Linkage and mapping of resistance genes toXanthomonas axonopodispv.passifloraein yellow passion fruit
Authors: Lopes Ricardo , Lopes Maria Teresa Gomes , Carneiro Monalisa Sampaio , de Pina Matta Frederico , Camargo Luis Eduardo Aranha , Vieira Maria Lucia Carneiro
Published: February 2006

The cultivated passion fruit (Passiflora edulis f. flavicarpa) is a cross-pollinated species native to South America. In the current study, a segregating F1population derived from a single cross between the clones IAPAR-06 and IAPAR-123 was used to construct AFLP-based linkage maps and to map resistance genes to bacterial spot caused by Xanthomonas axonopodis pv. passiflorae. Linkage analysis was performed by the 2-way pseudo-testcross mapping method using markers that segregated in a 1:1 ratio. The IAPAR-06 linkage map was constructed using 115 markers, 112 of which were allocated to 9 linkage groups (LG) covering 790.2 cM. The map of IAPAR-123 was constructed using 140 markers, 138 of which were allocated to 9 LG covering 488.9 cM. In both maps, clusters of markers were detected, indicating that the AFLP markers were not distributed at random. Bacterial resistance was assessed by measuring the diseased leaf area after wound-inoculating the leaves of F1plants. Quantitative resistance loci (QRLs) mapping was carried out by composite interval mapping and 1 QRL was detected, which explained 15.8% of the total phenotypic variation. The possibility of considering these data for marker-assisted selection in passion fruit breeding programs is discussed.Key words: Passiflora, linkage map, bacterial leaf spot, quantitative resistance loci.
Integrative strategies to identify candidate genes in rodent models of human alcoholism
Authors: Treadwell Julie A
Published: February 2006

The search for genes underlying alcohol-related behaviours in rodent models of human alcoholism has been ongoing for many years with only limited success. Recently, new strategies that integrate several of the traditional approaches have provided new insights into the molecular mechanisms underlying ethanol's actions in the brain. We have used alcohol-preferring C57BL/6J (B6) and alcohol-avoiding DBA/2J (D2) genetic strains of mice in an integrative strategy combining high-throughput gene expression screening, genetic segregation analysis, and mapping to previously published quantitative trait loci to uncover candidate genes for the ethanol-preference phenotype. In our study, 2 genes, retinaldehyde binding protein 1 (Rlbp1) and syntaxin 12 (Stx12), were found to be strong candidates for ethanol preference. Such experimental approaches have the power and the potential to greatly speed up the laborious process of identifying candidate genes for the animal models of human alcoholism.Key words: alcoholism, ethanol preference, gene expression, mouse model, retinoic acid signalling, syntaxin.
DNA methylation, histone H3 methylation, and histone H4 acetylation in the genome of a crustacean
Authors: Barzotti Rita , Pelliccia Franca , Rocchi Angela
Published: February 2006

In this work, we used antibodies against histone H3 trimethylated at lysine 9 (H3K9m3); against histone H4 acetylated at lysines 5, 8, 12, and 16 (H4ac); and against DNA methylated at 5C cytosine (m5C) to study the presence and distribution of these markers in the genome of the isopod crustacean Asellus aquaticus. The use of these 3 antibodies to immunolabel spermatogonial metaphases yields reproducible patterns on the chromosomes of this crustacean. The X and Y chromosomes present an identical banding pattern with each of the antibodies. The heterochromatic telo meric regions and the centromeric regions are rich in H3K9m3, but depleted in m5C and H4ac. Thus, m5C does not seem to be required to stabilize the silence of these regions in this organism.Key words: DNA methylation, H3 methylation, H4 acetylation, crustacean, Asellus aquaticus.
Cloning and characterization of resistance gene analogs from Avena species
Authors: Irigoyen M L , Ferrer E , Loarce Y
Published: February 2006

Sequences analogous to plant resistance genes of the NBS–LRR class were cloned from the genomic DNA of 11 Avena species with different genomes and levels of ploidy. Three pairs of degenerate primers were used, based on conserved DNA sequence motifs belonging to the NBS domain, and 33 sequences were identified. These were subdivided into 7 classes depending on nucleotide sequence identity. Despite the high level of degeneracy, the primers behaved in a highly selective way; the majority of sequences from the different species obtained with every primer combin ation showed strong identity and were considered homologous. For most species, only one sequence of each class was identified in each genome, suggesting that duplicated sequences are fairly divergent. The strong identity among specific NBS sequences precludes any conclusions being made on the evolution of these species. The genomic organization of the RGA sequences was explored using those of A. strigosa as probes in Southern blots involving digested DNA from 15 Avena species. The hybridization patterns showed wide diversity both among sequences within a species and among species for each sequence. However, the dendrogram generated using the RFLPs showed relationships among species to be in good agreement with those previously established using other molecular markers.Key words: resistance gene analog (RGA), disease resistance genes, diversity, Avena, oats.
An evaluation of warranty contracting in the United States of America
Authors: Bayraktar Mehmet Emre , Cui Qingbin , Hastak Makarand , Minkarah Issam
Published: February 2006

It is believed that warranty contracting would benefit state highway agencies by improving quality, saving money and time, and encouraging contractors' innovations. However, the challenges associated with warranties could be substantial, including higher costs, early failures, a reduction or even elimination of small contractors from the bidding process, and an increase in contract disputes and litigation. The actual impact of warranty provisions on state Department of Transportation (DOT) projects in the United States of America is still unclear because of limited industry experience. This paper provides a detailed discussion of warranty provisions and the benefits and problems associated with the subject matter. The advantages and disadvantages of warranty provisions are evaluated from the conflicting perspectives of state Departments of Transportation (DOTs), contractors, and surety companies. The future prospects of warranty provisions are established based on the findings of a recent study of warranty provisions and existing literature. Also, several options are proposed that have a strong potential to improve the application of warranties on DOT projects.Key words: warranties, highway construction, innovation, highway maintenance, contract administration, construction costs, construction inspection.
Monotonic and cyclic load behaviour of helical pile connectors in the vertical direction
Authors: Youssef M A , El Naggar M H , Ahmed M
Published: February 2006

The helical pile is a foundation system that is used to support new residential and commercial buildings and to stabilize repairs of existing structures. It represents an attractive option to upgrade the seismic resistance of foundations. This necessitates a good understanding of the seismic performance of the specialized connectors linking the pile shaft to the concrete foundation. An experimental program is initiated at The University of Western Ontario to investigate the seismic performance of these connectors, to develop models that can be used in finite element analysis to describe their behaviour, and to propose modifications to enhance their seismic performance, if necessary. In this program, eight specimens were tested to assess the behaviour of two types of these connectors under different loading modes. It was concluded that connectors with an uplift bracket are required for seismic applications to control uplift displacement due to rocking of the foundation.Key words: helical pile, connector, experimental, model, monotonic load, cyclic load, foundation, stiffness, strength.
Design of erosion protection at diversion tunnel outlets with concrete prisms
Authors: Emami Soleyman , Schleiss Anton J
Published: February 2006

Concrete prisms obtained by dividing cubes diagonally have been used successfully in some dam projects in Iran as a flexible and economical erosion protection measure at diversion tunnel outlets ending in a mobile river bed. To establish appropriate design criteria for this new protection measure, systematic hydraulic model tests have been performed. The physical tests allowed us to highlight the performance of the concrete prisms placed at a diversion tunnel outlet compared with an unprotected erodable riverbed. The concrete prisms are placed in such a way that in case of undermining, the protection system is able to deform and limit erosion and scour by always covering most of the river bed at the outlet. Based on the tests results, general applicable design criteria and equations, for estimating the scour hole geometry, its location, and the required size of the prisms as well as the total area to be protected, have been developed.Key words: diversion tunnel, scour, erosion protection, hydraulic model tests, concrete prisms, river diversion.
Prediction of flow patterns in scoured beds caused by submerged horizontal jets
Authors: Gunal M , Guven A
Published: February 2006

The basic goal of this study is to present a numerical simulation model for turbulent water flow issued on frozen scoured beds. The model uses a finite volume method to solve the equations of motion and transport equations for two dimensions on a transformed rectangular domain using boundary-fitted coordinates. The internal characteristics of the mean flow of submerged horizontal jets including surface profiles on frozen scoured beds are computed by a two-dimensional k–ε turbulence model. Computations are carried out at different frozen-scoured bed profiles. A staggered grid system is adapted for variable arrangements to avoid the well-known checkerboard oscillations in pressure and velocity. The SIMPLE algorithm is adapted for the computation. No experimental studies were performed during this investigation. The diffusion characteristics of the submerged jet, growth of boundary layer thickness, velocity distribution within the boundary layer, and shear stress at the scour are investigated and compared with the results of others. Key words: boundary-fitted coordinates, local scour, k–ε model, finite volume method, horizontal jets, submerged jets.
Bed-load transport model based on fractional size distribution
Authors: Ashiq Muhammad , Doering John C , Hosoda Takashi
Published: February 2006

Two models based on the fractional size distribution approach, used in conjunction with the excess discharge theory, have been developed by using bed-load data collected from the Roaring River (Rocky Mountain National Park, Colorado) during the summer of 1995. The first model is based on the critical discharge value of individual fractional (IF) sizes, IF model (for log-normal and nonlog-normal size distribution modes), while the other is based on critical discharge value for total (combined) sizes, total fractional (TF) sizes model (for log-normal and nonlog-normal size distribution modes). The performance of the log-normal size distribution based models was tested with data from the Roaring River, Rich Creek, and Fourmile Creek (three Colorado streams), whereas the performance of the nonlog-normal size distribution based models was tested using Pitzbach River data. The performance of the models was also tested by comparing their results with the Inpasihardjo fractional size distribution based model. For all tests, the TF model performed better for both the log-normal and nonlog-normal grain size distributions.Key words: fractional size, critical discharge, IF model, TF model, discharge theory, Roaring River.
An analytic hierarchy process based model for risk and opportunity assessment of international construction projects
Authors: Dikmen Irem , Birgonul M Talat
Published: February 2006

Risk assessment of international projects is a complicated task because of the sensitivity of project success related to country specific risks as well as project risks. Decision makers face the difficulty of weighing project opportunities against risks and determining attractiveness of projects while giving bidding decisions. The aim of this paper is to propose a methodology for risk and opportunity assessment of international projects. The proposed model uses an analytic hierarchy process for calculation of risk and opportunity ratings. A risk breakdown structure, specific to international construction projects, is proposed as well as a list of factors that affect the ability of construction companies to manage risk. An application of the proposed methodology is demonstrated by using real data supplied by a construction company that is experienced in international markets. Ranking of project options is made according to the opportunity and risk ratings that are calculated by using the proposed methodology based on the judgments of company professionals.Key words: international construction, risk assessment, analytic hierarchy process.
Effect of silica fume and lateral confinement on fire endurance of high strength concrete columns
Authors: Kodur V K.R , McGrath R
Published: February 2006

Fire represents one of the most severe environmental conditions, and therefore should be properly accounted for in the design of structural members. The increased use of high strength concrete (HSC) in buildings has raised concerns regarding the behaviour of such concrete in fire. In particular, spalling at elevated temperatures, as identified in studies by a number of laboratories, is a main concern. In this paper, results from experimental studies on the fire resistance of HSC columns are presented. A comparison is made of the fire resistance performance of HSC columns with and without silica fume and with different confinement configurations. The effect of silica fume and the effect of confinement on the fire performance of HSC columns will be discussed. The results show that the fire endurance of HSC columns with higher silica fume content is lower and the reduced tie spacing and the provision of cross-ties are beneficial in minimizing the spalling in HSC.Key words: fire resistance, high strength concrete, reinforced concrete columns, spalling.
Identification of a family of DNA-binding proteins with homology to RNA splicing factors
Authors: Shipman Kristy L , Robinson Phillip J , King Bruce R , Smith Roger , Nicholson Richard C
Published: February 2006

We describe a unique family of human proteins that are capable of binding to the cAMP regulatory element (CRE) and that are homologous to RNA splicing proteins. A human cDNA was isolated that encodes a protein with a distinctive combination of modular domain structures: 2 leucine-zipper-like domains, a DNA-binding zinc-finger-like domain, an RNA-binding zinc-finger-like domain, and 2 coiled-coil protein–protein interaction domains. It also has a serine–arginine - rich domain, commonly found in proteins involved in RNA splicing. The protein was discovered using the CRE as bait in a yeast 1-hybrid assay. It was then shown to bind specifically to the CRE in vitro using gel shift assays. We have named the protein CRE-associated protein (CREAP). We show that it is widely expressed in human tissues but is highly expressed in several fetal tissues and in several regions of the adult brain. CREAP is closely related to 2 human proteins of unknown function. CREAP shows significant homology with a small nuclear ribonucleoprotein of yeast, Luc7p, involved in 5′ splice site recognition. The 3 human CREAP proteins form a unique family with the potential to act as transcription factors that link to RNA processing.Key words: multifunctional protein, zinc finger, bZIP, transcription factor, splicing factor, protein family, CRH, CRE.
The influence of cholesterol and lipid metabolism on host cell structure and hepatitis C virus replication
Authors: Sagan Selena M , Rouleau Yanouchka , Leggiadro Cynthia , Supekova Lubica , Schultz Peter G , Su Andrew I , Pezacki John Paul
Published: February 2006

The hepatitis C virus (HCV) replicates on a membrane protein complex composed of viral proteins, replicating RNA, and altered cellular membranes. Small-molecule inhibitors of cellular lipid–cholesterol metabolism such as 25-hydroxycholesterol, cerulenin, lovastatin, and GGTI-286 all show a negative effect on HCV replication. Perturbation of host cell lipid and cholesterol metabolism can disrupt replication complexes by altering membranous structures where replication occurs. Changes in cholesterol and (or) lipid composition can have a general effect on membrane structure. Alternatively, metabolic changes can exert a more subtle influence over replication complexes by altering localization of host proteins through alterations in lipid anchoring. Here, we use Huh-7 cells harboring subgenomic HCV replicons to demonstrate that 25-hydroxycholesterol, cerulenin, lovastatin, and GGTI-286 do not disrupt the membranous web where replication occurs, whereas cholesterol-depleting agents such as β-cyclodextrin do. Cellular imaging suggests that the HCV RNA can remain associated with subcellular compartments connected with replication complexes in the presence of metabolic inhibitors. Therefore, at least 2 different molecular mechanisms are possible for the inhibition of HCV replication through the modulation of cellular lipid and cholesterol metabolism.Key words: hepatitis C virus, lipid metabolism, fluorescence microscopy, electron microscopy, membranous web, statins.
Cytokine-stimulated phosphorylation of GSK-3 is primarily dependent upon PKCs, not PKB
Authors: Vilimek Dino , Duronio Vincent
Published: February 2006

The regulation of glycogen synthase kinase-3 (GSK-3) by phosphorylation at inhibitory sites has been well documented. In many, but not all, cases, the phosphatidylinositol 3-kinase pathway, and particularly the downstream kinase protein kinase B (PKB) / akt, have been shown to be responsible for GSK-3 phosphorylation. Given that no studies have ever reported cytokine-mediated phosphorylation of GSK-3, we investigated the phosphorylation of this kinase in several hemopoietic cell types in response to either interleukin (IL)-3, IL-4 or granulocyte-macrophage colony stimulating factor (GM-CSF). Each of the cytokines was able to stimulate phosphorylation of the isoforms GSK-3α and GSK-3β. However, only in the case of IL-4 stimulation was there any dependence on PKB for this phosphorylation. We were clearly able to show that PKB was capable of phosphorylating GSK-3 in these cells, but studies using inhibitors of the protein kinase C (PKC) family of kinases have shown that these enzymes are more likely to play a key role in GSK-3 phosphorylation. Cytokine-mediated generation of diacylglycerol was demonstrated, supporting the possible activation of PKC family members. Thus, cytokine-dependent GSK-3 phosphorylation in hemopoietic cells proceeds primarily through PKB independent pathways.Key words: kinase, regulation, signal transduction, cytokine, apoptosis.
Effects of glucose and its modulation by insulin and estradiol on BMSC differentiation into osteoblastic lineages
Authors: Gopalakrishnan V , Vignesh R C , Arunakaran J , Aruldhas M M , Srinivasan N
Published: February 2006

It is well known that diabetes affects bone in human and animal models, and leads to osteopenia and osteoporosis. Bone-mineral density and other biochemical markers of bone turnover are very much affected in people with diabetes. Reduced bone mass, occurring with increased frequency in diabetes mellitus, has been attributed to poor glycemic control, but the pathogenic mechanisms remain unknown. High concentrations of glucose (hyperglycemia) in diabetics leads to this complication. Very few in vitro studies using bone-cell lines have been carried out to address this problem. In this study, we examined the effects of different doses of glucose concentration (5.5, 16.5, and 49.4 mmol/L), alone, with insulin (0.6 µg/mL), or with 17β-estradiol (E2) (10 nmol/L), on rat bone-marrow stromal cells (BMSCs) in the presence of an osteogenic medium. BMSC proliferation and alkaline phosphatase (ALP) were studied after 3 and 7 d of culture, respectively; the area stained for collagen and mineralized nodules was studied after 28 d of culture. With high concentrations of glucose, BMSC proliferation, ALP activity, the number of nodules formed, and the area stained for collagen were greatly reduced. Insulin treatment alone was able to increase [3H]-thymidine uptake or ALP activity, whereas both insulin and estradiol were able to increase the number of mineralized nodules and the area stained for collagen and mineralization. In conclusion, this study suggests that insulin and estradiol are able to contain the deleterious effect of high concentrations of glucose on BMSC-derived osteoblast proliferation and function.Key words: bone marrow cells, estradiol, glucose, insulin, mineralization.