bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of objective functions for estimation of kinetic parameters
Authors: Muzic Raymond F. , Christian Bradley T.
Published: February 2006

There is growing interest in quantitatively analyzing in vivo image data, as this facilitates objective comparisons and measurement of effect. In this regard, people increasingly turn to pharmacokinetic models and estimation of parameters of such models. In this work several parameter estimation methodologies were compared within the context of the most common pharmacokinetic model used in positron emission tomography imaging to describe glucose metabolism and receptor‐ligand interactions at tracer concentrations. Simulated data were generated with 1000 realizations at each of 5 different noise levels. Estimates of the kinetic parameters were made for each realization using seven iterative, nonlinear estimation methodologies: ordinary least squares (OLS), weighted least squares (WLS), penalized weighted least squares (PWLS), iteratively reweighted least squares (IRLS), and variations of extended least squares (ELS0, ELS1, ELS3). Additionally, generalized linear least squares (GLLS) was also used. With relatively noise‐free data, the iterative nonlinear estimation methods generally produced low‐bias, high‐precision parameter estimates, whereas with GLLS the bias was more prominent. Greater distinction between the estimation methods was seen at the higher, more realistic noise levels, with ELS and IRLS methods generally achieving better precision than the other methods. At the high noise levels WLS, GLLS, and PWLS yielded parameter estimates with large bias for some kinetic parameters. In general, there are more favorable estimator methodologies than the frequently employed WLS. Methods that determine values of weights based on model output—IRLS, ELS0, ELS1 and ELS3—generally perform better than methods that determine values of weights based directly on the experimental data.
Calculation of effective dose from measurements of secondary neutron spectra and scattered photon dose from dynamic MLC IMRT for , , and beam energies
Authors: Howell Rebecca M. , Hertel Nolan E. , Wang Zhonglu , Hutchinson Jesson , Fullerton Gary D.
Published: February 2006

Effective doses were calculated from the delivery of , , and conventional and intensity‐modulated radiation therapy (IMRT) prostate treatment plans. ICRP‐60 tissue weighting factors were used for the calculations. Photon doses were measured in phantom for all beam energies. Neutron spectra were measured for and and ICRP‐74 quality conversion factors used to calculate ambient dose equivalents. The ambient dose equivalents were corrected for each tissue using neutron depth dose data from the literature. The depth corrected neutron doses were then used as a measure of the neutron component of the ICRP protection quantity, organ equivalent dose. IMRT resulted in an increased photon dose to many organs. However, the IMRT treatments resulted in an overall decrease in effective dose compared to conventional radiotherapy. This decrease correlates to the ability of an intensity‐modulated field to minimize dose to critical normal structures in close proximity to the treatment volume. In a comparison of the three beam energies used for the IMRT treatments, resulted in the lowest effective dose, while resulted in the highest effective dose. This is attributed to the large neutron contribution for compared to no neutron contribution for .
Performance evaluation of a computed radiography imaging device using a typical “front side” and novel “dual side” readout storage phosphors
Authors: Fetterly Kenneth A. , Schueler Beth A.
Published: February 2006

The Fourier‐space modulation transfer function (MTF), normalized noise power spectrum (nNPS), and detective quantum efficiency (DQE) of a computed radiography (CR) x‐ray imaging device were measured. Two different storage phosphor screens were used in conjunction with a single CR reader (Fuji, Clearview, CS). One of the storage phosphor plates (ST‐BD) had a clear backing material which allowed “dual side read” of the latent image from both the “front” and “back” sides of the phosphor. The other phosphor plate had a light occluding backing material, limiting the readout to front side only (ST‐VI). The standard RQA‐5 beam quality was used. The MTF was measured using a thick tungsten edge device. Compared to the ST‐55BD phosphor, the ST‐VI phosphor was found to have modestly higher MTF at all spatial frequencies. The and were measured for nominal incident exposure levels ranging from . The dual side read phosphor demonstrated superior DQE, especially at low spatial frequencies. At the frequency , the DQE values for the exposure were 0.36 and 0.21 for the ST‐55BD and ST‐VI phosphor plates, respectively. The differences between the spatial‐frequency dependent DQE of the two plates can be attributed to the increased signal collection efficiency of the dual side read plates and differences in storage phosphor structure noise.
Decomposition analysis of differential dose volume histograms
Authors: Van den Heuvel Frank
Published: February 2006

Dose volume histograms are a common tool to assess the value of a treatment plan for various forms of radiation therapy treatment. The purpose of this work is to introduce, validate, and apply a set of tools to analyze differential dose volume histograms by decomposing them into physically and clinically meaningful normal distributions. A weighted sum of the decomposed normal distributions (e.g., weighted dose) is proposed as a new measure of target dose, rather than the more unstable point dose. The method and its theory are presented and validated using simulated distributions. Additional validation is performed by analyzing simple four field box techniques encompassing a predefined target, using different treatment energies inside a water phantom. Furthermore, two clinical situations are analyzed using this methodology to illustrate practical usefulness. A comparison of a treatment plan for a breast patient using a tangential field setup with wedges is compared to a comparable geometry using dose compensators. Finally, a normal tissue complication probability (NTCP) calculation is refined using this decomposition. The NTCP calculation is performed on a liver as organ at risk in a treatment of a mesothelioma patient with involvement of the right lung. The comparison of the wedged breast treatment versus the compensator technique yields comparable classical dose parameters (e.g., conformity index and equal dose at the ICRU dose point). The methodology proposed here shows a 4% difference in weighted dose outlining the difference in treatment using a single parameter instead of at least two in a classical analysis (e.g., mean dose, and maximal dose, or total dose variance). NTCP‐calculations for the mesothelioma case are generated automatically and show a 3% decrease with respect to the classical calculation. The decrease is slightly dependant on the fractionation and on the ‐value utilized. In conclusion, this method is able to distinguish clinically important differences between treatment plans using a single parameter. This methodology shows promise as an objective tool for analyzing NTCP and doses in larger studies, as the only information needed is the dose volume histogram.
Resolution and noise measurements of five CRT and LCD medical displays
Authors: Saunders Robert S. , Samei Ehsan
Published: February 2006

The performance of soft‐copy displays plays a significant role in the overall image quality of a digital radiographic system. In this work, we discuss methods to characterize the resolution and noise of both cathode ray tube (CRT) and liquid crystal display (LCD) devices. We measured the image quality of five different commercial display devices, representing both CRT and LCD technologies, using a high‐quality charge‐coupled device (CCD) camera. The modulation transfer function (MTF) was calculated using the line technique, correcting for the MTF of the CCD camera and the display pixel size. The normalized noise power spectrum (NPS) was computed from two‐dimensional Fourier analysis of uniform images. To separate the effects of pixel structure from interpixel luminance variations, we created structure‐free images by eliminating the pixel structures of the display device. The NPS was then computed from these structure‐free images to isolate interpixel luminance variations. We found that the MTF of LCDs remained close to the theoretical limit dictated by their inherent pixel size ( at Nyquist frequency), in contrast to the MTF for the two CRT displays, which dropped to at the Nyquist frequency. However, the NPS of LCDs showed significant peaks due to the subpixel structure, while the NPS of CRT displays exhibited a nearly flat power spectrum. After removing the pixel structure, the structured noise peaks for LCDs were eliminated and the overall noise magnitude was significantly reduced. The average total noise‐to‐signal ratio for CRT displays was , of which was due to interpixel luminance variations, while LCD displays had total noise to signal ratios of of which were due to interpixel luminance variations. Depending on the extent of the blurring and prewhitening processes of the human visual system, the magnitude of the display noise (including pixel structure) potentially perceived by the observer was reduced to (accounting for blurring only) and (accounting for blurring and prewhitening) for CRTs, and (accounting for blurring only) and (accounting for blurring and prewhitening) for LCDs.
Real‐time 3D‐surface‐guided head refixation useful for fractionated stereotactic radiotherapy
Authors: Li Shidong , Liu Dezhi , Yin Gongjie , Zhuang Ping , Geng Jason
Published: February 2006

Accurate and precise head refixation in fractionated stereotactic radiotherapy has been achieved through alignment of real‐time 3D‐surface images with a reference surface image. The reference surface image is either a 3D optical surface image taken at simulation with the desired treatment position, or a CT/MRI‐surface rendering in the treatment plan with corrections for patient motion during CT/MRI scans and partial volume effects. The real‐time 3D surface images are rapidly captured by using a 3D video camera mounted on the ceiling of the treatment vault. Any facial expression such as mouth opening that affects surface shape and location can be avoided using a new facial monitoring technique. The image artifacts on the real‐time surface can generally be removed by setting a threshold of jumps at the neighboring points while preserving detailed features of the surface of interest. Such a real‐time surface image, registered in the treatment machine coordinate system, provides a reliable representation of the patient head position during the treatment. A fast automatic alignment between the real‐time surface and the reference surface using a modified iterative‐closest‐point method leads to an efficient and robust surface‐guided target refixation. Experimental and clinical results demonstrate the excellent efficacy of set‐up time, the desired accuracy and precision of in isocenter shifts, and in rotation.
A computed tomography implementation of multiple‐image radiography
Authors: Brankov Jovan G. , Wernick Miles N. , Yang Yongyi , Li Jun , Muehleman Carol , Zhong Zhong , Anastasio Mark A.
Published: February 2006

Conventional x‐ray computed tomography (CT) produces a single volumetric image that represents the spatially variant linear x‐ray attenuation coefficient of an object. However, in many situations, differences in the x‐ray attenuation properties of soft tissues are very small and difficult to measure in conventional x‐ray imaging. In this work, we investigate an analyzer‐based imaging method, called computed tomography multiple‐image radiography (CT‐MIR), which is a tomographic implementation of the recently proposed multiple‐image radiography method. The CT‐MIR method reconstructs concurrently three physical properties of the object. In addition to x‐ray attenuation, CT‐MIR produces volumetric images that represent the refraction and ultrasmall‐angle scattering properties of the object. These three images can provide a rich description of the object's physical properties that are revealed by the probing x‐ray beam. An imaging model for CT‐MIR that is based on the x‐ray transform of the object properties is established. The CT‐MIR method is demonstrated by use of experimental data acquired at a synchroton radiation imaging beamline, and is compared to the pre‐existing diffraction‐enhanced imaging CT method. We also investigate the merit of an iterative reconstruction method for use with future clinical implementations of CT‐MIR, which we anticipate would be photon limited.
Evaluation of an automated deformable image matching method for quantifying lung motion in respiration‐correlated CT images
Authors: Pevsner A. , Davis B. , Joshi S. , Hertanto A. , Mechalakos J. , Yorke E. , Rosenzweig K. , Nehmeh S. , Erdi Y. E. , Humm J. L. , Larson S. , Ling C. C. , Mageras G. S.
Published: February 2006

We have evaluated an automated registration procedure for predicting tumor and lung deformation based on CT images of the thorax obtained at different respiration phases. The method uses a viscous fluid model of tissue deformation to map voxels from one CT dataset to another. To validate the deformable matching algorithm we used a respiration‐correlated CT protocol to acquire images at different phases of the respiratory cycle for six patients with nonsmall cell lung carcinoma. The position and shape of the deformable gross tumor volumes (GTV) at the end‐inhale (EI) phase predicted by the algorithm was compared to those drawn by four observers. To minimize interobserver differences, all observers used the contours drawn by a single observer at end‐exhale (EE) phase as a guideline to outline GTV contours at EI. The differences between model‐predicted and observer‐drawn GTV surfaces at EI, as well as differences between structures delineated by observers at EI (interobserver variations) were evaluated using a contour comparison algorithm written for this purpose, which determined the distance between the two surfaces along different directions. The mean and 90% confidence interval for model‐predicted versus observer‐drawn GTV surface differences over all patients and all directions were 2.6 and , respectively, whereas the mean and 90% confidence interval for interobserver differences were 2.1 and . We have also evaluated the algorithm's ability to predict normal tissue deformations by examining the three‐dimensional (3‐D) vector displacement of 41 landmarks placed by each observer at bronchial and vascular branch points in the lung between the EE and EI image sets (mean and 90% confidence interval displacements of 11.7 and , respectively). The mean and 90% confidence interval discrepancy between model‐predicted and observer‐determined landmark displacements over all patients were 2.9 and , whereas interobserver discrepancies were 2.8 and . Paired tests indicate no significant statistical differences between model predicted and observer drawn structures. We conclude that the accuracy of the algorithm to map lung anatomy in CT images at different respiratory phases is comparable to the variability in manual delineation. This method has therefore the potential for predicting and quantifying respiration‐induced tumor motion in the lung.
Computerized detection of intracranial aneurysms for three‐dimensional MR angiography: Feature extraction of small protrusions based on a shape‐based difference image technique
Authors: Arimura Hidetaka , Li Qiang , Korogi Yukunori , Hirai Toshinori , Katsuragawa Shigehiko , Yamashita Yasuyuki , Tsuchiya Kazuhiro , Doi Kunio
Published: February 2006

We have improved a computerized scheme for the detection of intracranial aneurysms for three‐dimensional (3‐D) magnetic resonance angiography (MRA) by the use of image features of small protrusions extracted based on a shape‐based difference image (SBDI) technique. Initial candidates were identified by use of a multiple gray‐level thresholding technique in dot enhanced images, and by finding short branches in skeleton images. Image features related to aneurysms were determined based on candidate regions segmented by use of a region growing technique. For extracting additional features on small protrusions or small aneurysms, we have developed an SBDI technique, which was based on the shape‐based difference between an original segmented vessel and a vessel with suppressed local change in thickness. The SBDI technique was useful for obtaining local changes in vessel thickness, i.e., SBD regions, which could be small aneurysms in the case of true positives, but thin or very small regions in the case of false positives. Many false positives were removed by means of rule‐based schemes and linear discriminant analysis on various 3‐D localized image features, including SBDI features. We tested the computerized scheme on 53 cases with 61 aneurysms and 62 nonaneurysm cases based on a leave‐one‐out‐by‐patient test method. As a result, false positives per patient decreased from 5.8 to 3.8, while a high sensitivity of 97% was maintained by use of the SBDI technique, in which SBDI features were effective for removing some false positives. The computer‐aided diagnostic (CAD) scheme may be robust and useful in assisting radiologists in the detection of intracranial aneurysms for MRA.
Registration of MR prostate images with biomechanical modeling and nonlinear parameter estimation
Authors: Alterovitz Ron , Goldberg Ken , Pouliot Jean , Hsu I‐Chow Joe , Kim Yongbok , Noworolski Susan Moyher , Kurhanewicz John
Published: February 2006

Magnetic resonance imaging (MRI) and magnetic resonance spectroscopic imaging (MRSI) have been shown to be very useful for identifying prostate cancers. For high sensitivity, the MRI/MRSI examination is often acquired with an endorectal probe that may cause a substantial deformation of the prostate and surrounding soft tissues. Such a probe is removed prior to radiation therapy treatment. To register diagnostic probe‐in magnetic resonance (MR) images to therapeutic probe‐out MR images for treatment planning, a new deformable image registration method is developed based on biomechanical modeling of soft tissues and estimation of uncertain tissue parameters using nonlinear optimization. Given two‐dimensional (2‐D) segmented probe‐in and probe‐out images, a finite element method (FEM) is used to estimate the deformation of the prostate and surrounding tissues due to displacements and forces resulting from the endorectal probe. Since FEM requires tissue stiffness properties and external force values as input, the method estimates uncertain parameters using nonlinear local optimization. The registration method is evaluated using images from five balloon and five rigid endorectal probe patient cases. It requires on average of computation time on a Pentium‐M PC. Comparing the prostate outline in deformed probe‐out images to corresponding probe‐in images, the method obtains a mean Dice Similarity Coefficient (DSC) of 97.5% for the balloon probe cases and 98.1% for the rigid probe cases. The method improves significantly over previous methods with greater improvement for balloon probe cases with larger tissue deformations.
MCNPX simulation of a multileaf collimator
Authors: Pönisch Falk , Titt Uwe , Kry Stephen F. , Vassiliev Oleg N. , Mohan Radhe
Published: February 2006

Our purpose in this work was to validate a very detailed Monte Carlo model, developed in MCNPX, of a Millennium 120 multileaf collimator integrated into a Varian Clinac 21EX treatment head. The Monte Carlo results were compared with measurements for both the and photon modes. The following comparisons were performed: depth‐dose curves, lateral profiles, multileaf collimator leakage, the tongue‐and‐grove test, and the round leaf‐end test. The good agreement between the Monte Carlo simulations and measurements showed that our model is accurate. Consequently, the benchmarks provided by our study can be used in future Monte Carlo studies.
SemiSPECT: A small‐animal single‐photon emission computed tomography (SPECT) imager based on eight cadmium zinc telluride (CZT) detector arrays
Authors: Kim Hyunki , Furenlid Lars R. , Crawford Michael J. , Wilson Donald W. , Barber H. Bradford , Peterson Todd E. , Hunter William C. J. , Liu Zhonglin , Woolfenden James M. , Barrett Harrison H.
Published: February 2006

The first full single‐photon emission computed tomography (SPECT) imager to exploit eight compact high‐intrinsic‐resolution cadmium zinc telluride (CZT) detectors, called SemiSPECT, has been completed. Each detector consists of a CZT crystal and a customized application‐specific integrated circuit (ASIC). The CZT crystal is a slab with a continuous top electrode and a bottom electrode patterned into a array by photolithography. The ASIC is attached to the bottom of the CZT crystal by indium‐bump bonding. A bias voltage of is applied to the continuous electrode. The eight detectors are arranged in an octagonal lead‐shielded ring. Each pinhole in the eight‐pinhole aperture placed at the center of the ring is matched to each individual detector array. An object is imaged onto each detector through a pinhole, and each detector is operated independently with list‐mode acquisition. The imaging subject can be rotated about a vertical axis to obtain additional angular projections. The performance of SemiSPECT was characterized using . When a diameter pinhole is used, the spatial resolution on each axis is about as estimated by the Fourier crosstalk matrix, which provides an algorithm‐independent average resolution over the field of view. The energy resolution achieved by summing neighboring pixel signals in a window is about 10% full‐width‐at‐half‐maximum of the photopeak. The overall system sensitivity is about with the energy window of from the photopeak. Line‐phantom images are presented to visualize the spatial resolution provided by SemiSPECT, and images of bone, myocardium, and human tumor xenografts in mice demonstrate the feasibility of preclinical small‐animal studies with SemiSPECT.
Molecular characterization and chromosomal mapping of the 5S rRNA gene in Solea senegalensis: a new linkage to the U1, U2, and U5 small nuclear RNA genes
Authors: Manchado Manuel , Zuasti Eugenia , Cross Ismael , Merlo Alejandro , Infante Carlos , Rebordinos Laureana
Published: February 2006

Some units of the 5S rDNA of Solea senegalensis were amplified by PCR and sequenced. Three main PCR products (227, 441, and 2166 bp) were identified. The 227- and 441-bp fragments were characterized by highly divergent nontranscribed spacer sequences (referred to as NTS-I and NTS-II) that were 109 and 324 bp long, respectively, yet their coding sequences were nearly identical. The 2166-bp 5S rDNA unit was composed of two 5S rRNA genes separated by NTS-I and followed by a 1721-bp spacer containing the U2, U5, and U1 small nuclear RNA genes (snRNAs). They were inverted and arranged in the transcriptional direction opposite that of the 5S rRNA gene. This simultaneous linkage of 3 different snRNAs had never been observed before. The PCR products were used as probes in fluorescence in situ hybridization experiments to locate the corresponding loci on the chromosomes of S. senegalensis. A major 5S rDNA chromosomal site was located along most of the short arm of a submetacentric pair, while a minor site was detected near the centromeric region of an acrocentric pair.Key words: soleidae, pleuronectiformes, 5S rDNA, Solea, snRNAs linkage.
Varying signals of the effects of natural selection during teleost growth hormone gene evolution
Authors: Ryynänen Heikki J , Primmer Craig R
Published: February 2006

The growth hormone (GH) gene of teleost fish exhibits a higher degree of variability compared with other vertebrate groups. However, the different selective constraints at the sequence level are not well understood. In this study, maximum-likelihood (ML) models of codon substitutions were used to investigate Darwinian adaptive evolution of the GH gene in teleost fishes. Complete GH gene sequences of 54 fish species were classified into 4 orders, and the variable nature of GH was examined by determining the dNand dSrate variation and the rates of molecular evolution for each teleost order. The results indicate that although the overall evolution rate for teleost GH is high ((1.15 ± 0.01) × 10–9substitutions/(aa site·y)) compared with the "slow phases" in mammals ((0.21 to 0.28 ± 0.05) × 10–9), the vital structure of this gene has been retained. While the majority of the amino acid changes appear to be due to relaxation of purifying selection, some positively selected sites were detected in regions with no specifically identified role in protein function. The positively selected regions observed in salmoniformes lineage suggests a possible role for positive selection driving functional divergence in paralogous forms of the GH gene after whole-genome duplication in this lineage.Key words: teleost fish, growth hormone, positive selection, synonymous substitution, non-synonymous substitution, molecular evolution.
Genetic diversity of the Andean tuber-bearing species, oca (Oxalis tuberosa Mol.), investigated by inter-simple sequence repeats
Authors: Pissard A , Ghislain M , Bertin P
Published: February 2006

The Andean tuber-bearing species, Oxalis tuberosa Mol., is a vegetatively propagated crop cultivated in the uplands of the Andes. Its genetic diversity was investigated in the present study using the inter-simple sequence repeat (ISSR) technique. Thirty-two accessions originating from South America (Argentina, Bolivia, Chile, and Peru) and maintained in vitro were chosen to represent the ecogeographic diversity of its cultivation area. Twenty-two primers were tested and 9 were selected according to fingerprinting quality and reproducibility. Genetic diversity analysis was performed with 90 markers. Jaccard's genetic distance between accessions ranged from 0 to 0.49 with an average of 0.28 ± 0.08 (mean ± SD). Dendrogram (UPGMA (unweighted pair-group method with arithmetic averaging)) and factorial correspondence analysis (FCA) showed that the genetic structure was influenced by the collection site. The two most distant clusters contained all of the Peruvian accessions, one from Bolivia, none from Argentina or Chile. Analysis by country revealed that Peru presented the greatest genetic distances from the other countries and possessed the highest intra-country genetic distance (0.30 ± 0.08). This suggests that the Peruvian oca accessions form a distinct genetic group. The relatively low level of genetic diversity in the oca species may be related to its predominating reproduction strategy, i.e., vegetative propagation. The extent and structure of the genetic diversity of the species detailed here should help the establishment of conservation strategies.Key words: oca, Oxalis tuberosa, Andean tuber, genetic diversity, ISSR, vegetative propagation.
Mapping genes for resistance to Leptosphaeria maculans in Brassica juncea
Authors: Christianson J A , Rimmer S R , Good A G , Lydiate D J
Published: February 2006

Blackleg disease of crucifers, caused by the fungus Leptosphaeria maculans, is a major concern to oilseed rape producers worldwide. Brassica species containing the B genome have high levels of resistance to blackleg. Brassica juncea F2 and first-backcross (B1) populations segregating for resistance to a PG2 isolate of L. maculans were created. Segregation for resistance to L. maculans in these populations suggested that resistance was controlled by two independent genes, one dominant and one recessive in nature. A map of the B. juncea genome was constructed using segregation in the F2 population of a combination of restriction fragment length polymorphism (RFLP) and microsatel lite markers. The B. juncea map consisted of 325 loci and was aligned with previous maps of the Brassica A and B genomes. The gene controlling dominant resistance to L. maculans was positioned on linkage group J13 based on segregation for resistance in the F2 population. This position was confirmed in the B1 population in which the resistance gene was definitively mapped in the interval flanked by pN199RV and sB31143F. The provisional location of the recessive gene controlling resistance to L. maculans on linkage group J18 was identified using a subset of informative F2 individuals.Key words: blackleg, B genome, phoma, recessive resistance.
Effectiveness of neuro-fuzzy recognition approach in evaluating steel bridge paint conditions
Authors: Chen Po-Han , Chang Luh-Maan
Published: February 2006

The development of digital image recognition techniques has contributed to increased precision in pattern recognition and led to numerous applications in industries. In September 1999, the Indiana Department of Transportation (INDOT) first tried out digital image recognition techniques to steel bridge coating assessment. The purpose of this tryout was to obtain a rust percentage, which was required in the INDOT bridge painting warranty contract, when conducting steel bridge coating investigation. Despite the advantages of digital image recognition, some problems that may cause inaccurate recognition results still exist. Nonuniform illumination (i.e., brightness or darkness or shadow) is one of them. The neuro-fuzzy recognition approach (NFRA) was developed to minimize the effect of nonuniform illumination. In this technical note, the framework of NFRA, its application to steel bridge coating assessment, and its performance comparison to three other image recognition methods will be presented.Key words: neuro-fuzzy recognition approach (NFRA), artificial neural network (ANN), double sampling plan, multiresolution pattern classification (MPC), iterated conditional modes (ICM).
Optimizing geometric design of roundabouts: multi-objective analysis
Authors: Mehmood Atif , Easa Said M
Published: February 2006

The main objectives of roundabout design are to maximize traffic safety and operational efficiency. Traditionally, because of the complexity of the system and the multiple objectives involved, the design process is iterative and time-consuming. A minor change in the geometry can result in significant changes in the system performance (operation and safety). This paper presents an optimization model that directly provides the roundabout geometry that optimizes two objectives: design consistency and operational efficiency. Design consistency is represented by the mean difference in operating speeds for various conflicting vehicle paths and operational efficiency is represented by the average roundabout delay. Vehicle paths (through, right, and left) and roundabout delay are modeled for all roundabout approaches. The input geometric data to the model can be easily obtained from an aerial photograph of the selected site using a geographic information systems (GIS) software. The system performance is optimized subject to geometric and traffic constraints. The proposed model is applicable to single-lane roundabouts (urban and rural) with four legs intersecting at right angles. Application of the model to an actual proposed roundabout site is presented. This proposed approach provides the optimum solution directly and is also more efficient than the traditional iterative approach. Key words: geometric design, roundabouts, horizontal curve, radius, optimization, consistency, capacity, traffic delay.
Applying the HEC-RAS model and GIS techniques in river network floodplain delineation
Authors: Yang Jie , Townsend Ronald D , Daneshfar Bahram
Published: February 2006

A direct-processing approach to river system floodplain delineation is developed. Floodplain zones of part of the South Nation River system, located just east of Ottawa, Ontario, are mapped in two dimensions and three dimensions by integrating the hydraulic model of the choice with geographic information systems (GIS). The first objective was to construct and validate a Hydrologic Engineering Center's River Analysis System (HEC-RAS) river network model of the system using existing HEC-2 model-generated data. Next, HEC-RAS simulations were performed to generate water surface profiles throughout the system for six different design storm events. The in-channel spatial data of HEC-RAS were then geo-referenced and mapped in the GIS domain and integrated with digital elevation model (DEM) over-bank data to build a triangular irregular network (TIN) terrain model. In the final step, floodplain zones for the six design storms were reproduced in three dimensions by overlaying the integrated terrain model for the region with the corresponding water surface TIN.Key words: river, floodplain, delineation, GIS-approach, HEC-2 model, HEC-RAS model, data query.
Study on the interaction of bovine serum albumin with acid cyanine 5R and its application in analysis
Authors: Lu Fei , Pan Jing-Hao , Liu Yun , Zhang Hongfen , Guo Yujing , Wang Yingte
Published: February 2006

A supramolecular complex of bovine serum albumin (BSA) with acid cyanine 5R (AC 5R, C.I. acid blue 113, C.I.: 26360) has been shown to form in Tris–HCl buffer solution (pH 7.42) by linear sweep voltammetry (LSV), fluorimetry, and spectrophotometry. The binding ratio and binding constant of BSA with AC 5R have been detected by LSV and fluorimetry. The binding mechanism is also preliminarily discussed. In Tris–HCl buffer solution (pH 7.42), AC 5R can easily be reduced on the mercury electrode, and it has a well-defined LSV peak current (Ip) and peak potential (Ep) at –0.65 V (vs. SCE). In the presence of BSA, the Ipof AC 5R decreases, and the peak potential (Ep) shifts to a more positive potential. The decrease of the second-order derivative of reductive peak current (ΔIp") of AC 5R is proportional to the logarithm of BSA concentration in the range of 1.54 × 10–8mol·L–1– 1.54 × 10–5mol·L–1(r = 0.9931 – 0.9977). The limit of detection of BSA is 9.0 × 10–9mol·L–1. The relative standard deviation is 1.83% (n = 10), and the standard recovery is 97.5%–104.8%. This method can be used to determine BSA concentration on the basis of the interaction of BSA with AC 5R.Key words: bovine serum albumin (BSA), acid cyanine 5R (AC 5R), supramolecule, binding ratio, binding constant, fluorimetry, spectrophotometry, electroanalytical method.
Role of osmolytes as chemical chaperones during the refolding of aminoacylase
Authors: Kim Sung-Hye , Yan Yong-Bin , Zhou Hai-Meng
Published: February 2006

The refolding and reactivation of aminoacylase is particularly difficult because of serious off-pathway aggregation. The effects of 4 osmolytes — dimethylsulphoxide, glycerol, proline, and sucrose — on the refolding and reactivation of guanidine-denaturated aminoacylase were studied by measuring aggregation, enzyme activity, intrinsic fluorescence spectra, 1-anilino-8-naphthalenesulfonate (ANS) fluorescence spectra, and circular dishroism (CD) spectra. The results show that all the osmolytes not only inhibit aggregation but also recover the activity of aminoacylase during refolding in a concentration-dependent manner. In particularly, a 40% glycerol concentration and a 1.5 mol/L sucrose concentration almost completely suppressed the aminoacylase aggregation. The enzyme activity measurements revealed that the influence of glycerol is more significant than that of any other osmolyte. The intrinsic fluorescence results showed that glycerol, proline, and sucrose stabilized the aminoacylase conformation effectively, with glycerol being the most effective. All 4 kinds of osmolytes reduced the exposure of the hydrophobic surface, indicating that osmolytes facilitate the formation of protein hydrophobic collapse. The CD results indicate that glycerol and sucrose facilitate the return of aminoacylase to its native secondary structure. The results of this study suggest that the ability of the various osmolytes to facilitate the refolding and renaturation of aminoacylase is not the same. A survey of the results in the literature, as well as those presented here, suggests that although the protective effect of osmolytes on protein activity and structure is equal for different osmolytes, the ability of osmolytes to facilitate the refolding of various proteins differs from case to case. In all cases, glycerol was found to be the best stabilizer and a folding aid.Key words: protein aggregation, aminoacylase, chaperone, osmolytes, protein refolding.
Dose-dependent effect of hydrogen peroxide on calcium mobilization in mouse pancreatic acinar cells
Authors: Granados María P , Salido Ginés M , González Antonio , Pariente José A
Published: February 2006

We have employed confocal laser scanning microscopy to investigate how intracellular free calcium concentration ([Ca2+]i) is influenced by hydrogen peroxide (H2O2) in collagenase-dispersed mouse pancreatic acinar cells. In the absence of extracellular calcium, treatment of cells with increasing concentrations of H2O2resulted in an increase in [Ca2+]i, indicating the release of calcium from intracellular stores. Micromolar concentrations of H2O2induced an oscillatory pattern, whereas 1 mmol H2O2/L caused a slow and sustained increase in [Ca2+]i. H2O2abolished the typical calcium release stimulated by thapsigargin or by the physiological agonist cholecystokinin octapeptide (CCK-8). Depletion of either agonist-sensitive or mitochondrial calcium pools was unable to prevent calcium release induced by 1 mmol H2O2/L, but depletion of both stores abolished it. Additionally, lower H2O2concentrations were able to release calcium only after depletion of mitochondrial calcium stores. Treatment with either the phospholipase C inhibitor U-73122 or the inhibitor of the inositol 1,4,5-trisphosphate (IP3) receptor xestospongin C did not modify calcium release from the agonist-sensitive pool induced by 100 µmol H2O2/L, suggesting the involvement of a mechanism independent of IP3 generation. In addition, H2O2reduced amylase release stimulated by CCK-8. Finally, either the H2O2-induced calcium mobilization or the inhibitory effect of H2O2on CCK-8-induced amylase secretion was abolished by dithiothreitol, a sulphydryl reducing agent. We conclude that H2O2at micromolar concentrations induces calcium release from agonist- sensitive stores, and at millimolar concentrations H2O2can also evoke calcium release from the mitochondria. The action of H2O2is mediated by oxidation of sulphydryl groups of calcium ATPases independently of IP3 generation.Key words: hydrogen peroxide, pancreatic acinar cells, intracellular calcium stores, amylase secretion.
TXM13 human melanoma cells: a novel source for the inhibition kinetics of human tyrosinase and for screening whitening agents
Authors: Park Yong-Doo , Kim So-yeon , Lyou You-Jeong , Lee Dong-Youn , Yang Jun-Mo
Published: February 2006

Research involving whitening agents requires several steps of experimentation, and the initial step is to test whitening agents with human melanocytes and those with human tyrosinase. Unfortunately, it takes a long time to gather human melanocytes, and these cells have some limitations when it comes to performing experiments, such as their passage difficulties and their cost. In this study, we suggest that the TXM13 human melanoma cells could be a useful cell candidate for studying human tyrosinase inhibition and depigmentation. We applied a tyrosinase inhibitor, such as dithioglycerine (DTGC), to validate the cell line's usefulness, and we tested the effect of DTGC on TXM13 melanogenesis. The results showed that human tyrosinase from TXM13 was appropriate, according to the inhibition kinetics, and that the conspicuous depigmentation of TXM13 occurred after DTGC treatment without downregulating the tyrosinase expression level. When taken together, our findings provide useful information regarding the use of the TXM13 melanoma cells for the development of whitening agents.Key words: TXM13, pigment cell, human tyrosinase, whitening agent.
Isolation and characterization of a new agglutinin from the red marine algaHypnea cervicornisJ. Agardh
Authors: Nascimento K S , Nagano C S , Nunes E V , Rodrigues R F , Goersch G V , Cavada B S , Calvete J J , Saker-Sampaio S , Farias W R.L , Sampaio A H
Published: February 2006

The biochemical characterization of a new lectin (Hypnea cervicornis agglutinin or HCA) isolated from the Brazilian red alga H. cervicornis is reported. The haemagglutinating activity of the lectin was only inhibited by the glycoprotein porcine stomach mucin at a minimum inhibitory concentration of 19 µg·mL–1. No haemagglutination inhibition was detected after the addition of simple sugars. The MALDI-TOF molecular masses of native and reduced and carbamidomethylated HCA were, respectively, 9196.6 Da and 9988.2 Da, indicating that the primary structure of the protein is crosslinked by 7 disulfide bonds. This unusual structural feature among lectins, along with its N-terminal sequence and amino-acid composition, clearly shows that HCA belongs to a protein family distinct from the isolectins Hypnin A1 and A2 isolated from the related Japanese alga Hypnea japonica. On the other hand, HCA displayed a high degree of similarity to the agglutinin from the Brazilian species Hypnea musciformis. Our data indicate the occurrence of structural diversity among lectins of closely related species living in distant ecosystems, i.e., the Pacific coast of Japan and the Atlantic coast of Brazil, and support the hypothesis that the lectin content (lectinome) might serve as a biomarker for taxonomical purposes.Key words: agglutinin, lectin, isolation, Hypnea cervicornis, red marine alga.
Expression and localization of PCSK9 in rat hepatic cells
Authors: Grozdanov Petar N , Petkov Petko M , Karagyozov L K , Dabeva Mariana D
Published: February 2006

Proprotein convertase subtilisin/kexin type 9 (PCSK9), recently cloned in several laboratories, including ours, causes a third form of autosomal dominant hypercholesterolemia. Its mechanism of action remains unclear. We studied the expression and subcellular localization of PCSK9 in fetal and adult rat tissues associated with cholesterol homeostasis using quantitative reverse transcriptase - PCR, Western blot analysis, subcellular fractionation, and confocal immuno fluorescent microscopy. PCSK9 mRNA is most abundant in yolk sac and fetal liver, but the highest expression of the protein was found in differentiated hepa toma FAO-1 cell line, which also shows the highest expression of LDLR. In FAO-1 cells PCSK9 expression is down regulated by cholesterol and 25-hydroxycholesterol and upregulated in the absence of sterols following the same pattern of expression as HMG-CoA reductase, synthase, and LDLR. Subcellular fractionation, combined with Western blotting, showed that PCSK9 is localized in the ER and intermediate vesicular compartment of the cell but not in Golgi cisternae. The mature enzyme is secreted from the liver and hepatoma cells. Double labeling with antibodies to PCSK9 and LDLR or clathrin revealed some colocalization of PCSK9 with clathrin-coated vesicles and LDLR. In conclusion, our results show that PCSK9 is processed in the ER, and the mature convertase is secreted in the plasma.Key words: PCSK9 expression, PCSK9 localization, hepatic cells.
Altered phosphorylation of topoisomerase I following overexpression in an ovarian cancer cell line
Authors: St-Amant Christiane , Lussier Stéphanie , Lehoux Jacques , Laberge Rémi-Martin , Boissonneault Guylain
Published: February 2006

There is a growing interest regarding the use of camptothecins (CPTs) for the management of ovarian cancer. Since topoisomerase I has been established as a prime target of these drugs in other experimental models, it was important to determine whether sensitivity to CPTs in ovarian cancer cells is also correlated with the cellular level of this enzyme. Despite the 7-fold increase in topoisomerase expression achieved by adenovirus-mediated expression, the sensitivity to a CPT derivative (topotecan), was not improved compared with control cells harboring an endogenous level of the enzyme. This observation is in accordance with the similar level of topoisomerase I activity found in control and overexpressing cells and suggests that these cells may efficiently regulate the enzyme activity. Indeed, topoisomerase I overexpressing cells are characterized by a lack of alkaline phosphatase sensitivity and elimination of the hyperphosphorylated form of the protein. Taken together, these observations strongly suggest that an alteration in the phosphorylation state of topoisomerase I could limit its activity and prevent improvement of CPT response in ovarian cancer cells. In addition, a limited extent of topoisomerase I phosphorylating activity was found in nuclear extract of OVCAR-3 cells. Hence, providing enhancement in topoisomerase I expression may not result in improvement of CPT response in ovarian cancer cells because of an efficient control of the phosphorylation state of the enzyme.Key words: topoisomerase I, camptothecins, phosphorylation, chemotherapy, ovarian cancer.
Effect of geraniol on fatty-acid and mevalonate metabolism in the human hepatoma cell line Hep G2
Authors: Polo Monica P , de Bravo Margarita G
Published: February 2006

Monoterpenes have multiple pharmacological effects on the metabolism of mevalonate. Geraniol, a dietary monoterpene, has in vitro and in vivo anti-tumor activity against several cell lines. We have studied the effects of geraniol on growth, fatty-acid metabolism, and mevalonate metabolism in the human hepatocarcinoma cell line Hep G2. Up to 100 µmol geraniol/L inhibited the growth rate and 3-hydroxymethylglutaryl coenzyme A reductase (HMG-CoA) reductase activity of these cells. At the same concentrations, it increased the incorporation of cholesterol from the medium in a dose-dependent manner. Geraniol-treated cells incorporated less14C-acetate into nonsaponifiable lipids, inhibiting its incorporation into cholesterol but not into squalene and lanosterol. This is indicative of an inhibition in cholesterol synthesis at a step between lanosterol and cholesterol, a fact confirmed when cells were incubated with3H-mevalonate. The incorporation of3H-mevalonate into protein was also inhibited, whereas its incorporation into fatty acid increased. An inhibition of Δ5 desaturase activity was demonstrated by the inhibition of the conversion of14C-dihomo-γ-linolenic acid into arachidonic acid. Geraniol has multiple effects on mevalonate and lipid metabolism in Hep G2 cells, affecting cell proliferation. Although mevalonate depletion is not responsible for cellular growth, it affects cholesterogenesis, protein prenylation, and fatty-acid metabolism.Key words: geraniol, Hep G2, HMG-CoA reductase, mevalonate, fatty acids.
Intrinsic bioremediation of diesel-contaminated cold groundwater in bedrock
Authors: Cross Katharine M , Biggar Kevin W , Semple Kathy , Foght Julia , Guigard Selma E , Armstrong James E
Published: February 2006

In 1982 diesel fuel migrated from a well lease site into underlying fractured bedrock contaminating the groundwater-bearing zone approximately 30 m below ground surface. Historical contaminant concentrations, geochemical indicators, and microbiological data were analysed to evaluate natural attenuation, specifically intrinsic bioremediation. Evidence of microbial activity was provided by most probable number (MPN) and commercial biological activity reaction tests (BART). Laboratory microcosms using groundwater from the site were incubated under aerobic and anaerobic conditions with electron acceptor and nutrient amendment to assess microbial activity. Aerobic biodegradation rates were determined by measuring mineralization of 14C-dodecane. Nutrient amendment combined with a higher temperature (28 °C) increased the first-order aerobic biodegradation rate to 0.0066 d–1 from 0.0002 d–1 at 10 °C. Anaerobic biodegradation rates were calculated from depletion of total extractable hydrocarbons (TEH) over 717 d at 10 °C. Nutrient addition increased the anaerobic first-order biodegradation rate to 0.0016 from 0.0005 d–1. Data from these laboratory microcosms indicate that the current slow rates of intrinsic bioremediation may be enhanced with nutrient addition. Key words: intrinsic bioremediation, natural attenuation, groundwater, diesel fuel, hydrocarbon biodegradation, anaerobic hydrocarbon biodegradation, biological activity reaction test (BART).