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PubMed2003

Analysis of various beamlet sizes for IMRT with 6 MV photons.

Application of intensity modulated radiation therapy (IMRT) using multileaf collimation often requires the use of small beamlets to optimize the delivered radiation distribution. Small-beam dose distribution measurements were compared to dose distributions calculated using a commercial treatment planning system that models its data acquired using measurements from relatively large fields. We wanted to evaluate only the penumbra, percent depth-dose (PDD) and output model, so we avoided dose distribution features caused by rounded leaf ends and interleaf leakage by making measurements using the secondary collimators. We used a validated radiochromic film dosimetry system to measure high-resolution dose distributions of 6 MV photon beams. A commercial treatment planning system using the finite size pencil beam (FSPB) dose calculation algorithm was commissioned using measured central axis outputs from 4.0x4.0 to 40.0x40.0 cm2 beams and radiographic-film profile measurements of a 4.0x4.0 cm2 beam at twice the depth of maximum dose (dmax). Calculated dose distributions for square fields of 0.5x0.5 cm2, and 1.0x1.0 cm2, to 6.0x6.0 cm2, in 1.0x1.0 cm2, increments were compared against radiochromic film measurements taken with the film oriented parallel to the beam central axis in a water equivalent phantom. The PDD of the smaller field sizes exhibited behavior typical of small fields, namely a decrease in dmax with decreasing field size. The FSPB accurately modeled the depth-dose and central axis output for depths deeper than the nominal dmax of 1.5 cm plus 0.5 cm. The dose distribution in the build-up and penumbra regions was not accurately modeled for depths less than 2 cm, especially for the fields of 2.0x2.0 cm2 and smaller. Using the gamma function with 2 mm and 2% criteria, the dose model was shown to accurately predict the penumbra. While for single small beams the compared dose distributions passed the gamma function criteria, the clinical appropriateness of these criteria is not clear for a composite IMRT plan. Further investigation of the cumulative impact of the observed dose discrepancies is warranted. We speculate that the observed differences in the penumbra regions arise from some energy dependent artifact in the radiographic-film profiles used for commissioning. In the future, radiochromic film based commissioning might provide a more accurate data set for dose modeling.

Calibration↗
PubMed2003

Wavelength-scanning interferometry of a transparent parallel plate with refractive-index dispersion.

Testing for flatness of an optical parallel plate in a Fizeau interferometer suffers from problems caused by multiple-beam interference noise. Each internal-reflection component can be separated from the signal by its modulation frequency in a wavelength-scanned interferometer; however, the frequency depends on the thickness and the refractive-index dispersion of the test plate and on the nonlinearity of the scanning source. With a new 19-sample wavelength-scanning algorithm we demonstrate the elimination of the reflection noise, the effect of the dispersion up to the second order of the reflectance of the test plate, and as the nonlinearity of the source. The algorithm permits large tolerance in the air-gap distance, thus making it somewhat independent of the thickness of the test plate. The minimum residual reflection noise with this algorithm for testing a glass plate is approximately lambda/600. Experimental results show that the front surface of the test plate was measured within 1 nm rms of its true shape over a 230-mm-diameter aperture.

Journal Article↗
PubMed2001

Guest-to-host proton transfer in melatonin-beta-cyclodextrin inclusion complex by ionspray, fast atom bombardment and tandem mass spectrometry.

Ionspray (IS) and fast atom bombardment (FAB) positive ionization mass spectrometry (MS) of 1 : 1 beta-cyclodextrin (beta-CD)-melatonin (MLT) host-guest complex allowed the detection of gaseous protonated 1 : 1 beta-CD-MLT. Tandem MS collision-induced dissociation (CID) of such protonated 1 : 1 beta-CD-MLT species showed the proton (charge) to be retained to a significant extent by the host and by its cage fragmentation products, in spite of the higher proton affinity of MLT with respect to that of beta-CD. This requires an endothermic guest-to-host proton transfer to occur within the gaseous association. Collisional activation could be accounted for by the promotion of such an endothermic process; however, the proton affinity decrease of the guest determined by the loss of the elements of acetamide, which is a dominant MS dissociation reaction of pure protonated MLT, could also provide a rationale for such an endothermic guest-to-host proton transfer. This proposal parallels the reaction scheme we had previously formulated for the analogous MS and tandem MS behaviour of 1 : 1 beta-CD-5-methoxytryptamine inclusion complex with the protonated 5-methoxytryptamine guest undergoing deamination.

Algorithms↗
PubMed1997

The b matrix in diffusion tensor echo-planar imaging.

In diffusion tensor imaging (DTI) an effective diffusion tensor in each voxel is measured by using a set of diffusion-weighted images (DWIs) in which diffusion gradients are applied in a multiplicity of oblique directions. However, to estimate the diffusion tensor accurately, one must account for the effects of all imaging and diffusion gradient pulses on each signal echo, which are embodied in the b matrix. For DTI to be practical clinically, one must also acquire DWIs rapidly and free of motion artifacts, which is now possible with diffusion-weighted echo-planar imaging (DW-EPI). An analytical expression for the b matrix of a general DW-EPI pulse sequence is presented and then validated experimentally by measuring the diffusion tensor in an isotropic phantom whose diffusivity is already known. The b matrix is written in a convenient tabular form as a sum of individual pair-wise contributions arising from gradient pulses applied along parallel and perpendicular directions. While the contributions from readout and phase-encode gradient pulse trains are predicted to have a negligible effect on the echo, the contributions from other imaging and diffusion gradient pulses applied in both parallel and orthogonal directions are shown to be significant in our sequence. In general, one must understand and account for the multiplicity of interactions between gradient pulses and the echo signal to ensure that diffusion tensor imaging is quantitative.

Algorithms↗
PubMed1996

Segmentation of brain tissue from magnetic resonance images.

Segmentation of medical imagery is a challenging problem due to the complexity of the images, as well as to the absence of models of the anatomy that fully capture the possible deformations in each structure. The brain is a particularly complex structure, and its segmentation is an important step for many problems, including studies in temporal change detection of morphology, and 3-D visualizations for surgical planning. We present a method for segmentation of brain tissue from magnetic resonance images that is a combination of three existing techniques from the computer vision literature: expectation/maximization segmentation, binary mathematical morphology, and active contour models. Each of these techniques has been customized for the problem of brain tissue segmentation such that the resultant method is more robust than its components. Finally, we present the results of a parallel implementation of this method on IBM's supercomputer Power Visualization System for a database of 20 brain scans each with 256 x 256 x 124 voxels and validate those results against segmentations generated by neuroanatomy experts.

Algorithms↗
PubMedDate not supplied

High-density hydration layer of lysozymes: molecular dynamics decomposition of solution scattering data.

A characterization of the physical properties of protein hydration water is critical for understanding protein structure and function. Recent small-angle X-ray and neutron scattering data indicate that the density of water on the surface of lysozyme is significantly higher than in bulk water. Here, we provide an interpretation of the scattering results using a molecular dynamics simulation, which allows us to make quantitative predictions about density variations in the first hydration shell. The perturbation relative to bulk water involves statistically significant changes in the average water structure in the first hydration layer. The water density in the first hydration shell is increased by 5% with respect to the bulk. In regions of higher water density, the water dipoles align more parallel to each other and the number of hydrogen bonds per water molecule is higher. Increased water density is found for water molecules interacting with hydrogen and carbon atoms in the backbone or with nonpolar or negatively charged side-chain groups.

Algorithms↗
PubMed2006

Planar membranes interaction.

The system of two parallel planar, arbitrarily charged surfaces immersed in a solution containing only one ionic species, the counterions, is completely analyzed under a mean field Poisson-Boltzmann approach. Results for the pressure, reduced potential, and counterionic concentration are graphically displayed for two dissociating membranes and for a dissociating and an adsorbing membrane. The results indicate that the system of two planar parallel dissociating membranes acts as a buffer for pressure values and for counterionic concentration values in regions interior to and far from the membranes. The results are related to properties of planar or quasiplanar structures in biological cells.

Adsorption↗
PubMed2002

Computational techniques for solving the bidomain equations in three dimensions.

The bidomain equations are the most complete description of cardiac electrical activity. Their numerical solution is, however, computationally demanding, especially in three dimensions, because of the fine temporal and spatial sampling required. This paper methodically examines computational performance when solving the bidomain equations. Several techniques to speed up this computation are examined in this paper. The first step was to recast the equations into a parabolic part and an elliptic part. The parabolic part was solved by either the finite-element method (FEM) or the interconnected cable model model (ICCM). The elliptic equation was solved by FEM on a coarser grid than the parabolic problem and at a reduced frequency. The performance of iterative and direct linear equation system solvers was analyzed as well as the scalability and parallelizability of each method. Results indicate that the ICCM was twice as fast as the FEM for solving the parabolic problem, but when the total problem was considered, this resulted in only a 20% decrease in computation time. The elliptic problem could be solved on a coarser grid at one-quarter of the frequency at which the parabolic problem was solved and still maintain reasonable accuracy. Direct methods were faster than iterative methods by at least 50% when a good estimate of the extracellular potential was required. Parallelization over four processors was efficient only when the model comprised at least 500,000 nodes. Thus, it was possible to speed up solution of the bidomain equations by an order of magnitude with a slight decrease in accuracy.

Algorithms↗
PubMed2002

Contact order and ab initio protein structure prediction.

Although much of the motivation for experimental studies of protein folding is to obtain insights for improving protein structure prediction, there has been relatively little connection between experimental protein folding studies and computational structural prediction work in recent years. In the present study, we show that the relationship between protein folding rates and the contact order (CO) of the native structure has implications for ab initio protein structure prediction. Rosetta ab initio folding simulations produce a dearth of high CO structures and an excess of low CO structures, as expected if the computer simulations mimic to some extent the actual folding process. Consistent with this, the majority of failures in ab initio prediction in the CASP4 (critical assessment of structure prediction) experiment involved high CO structures likely to fold much more slowly than the lower CO structures for which reasonable predictions were made. This bias against high CO structures can be partially alleviated by performing large numbers of additional simulations, selecting out the higher CO structures, and eliminating the very low CO structures; this leads to a modest improvement in prediction quality. More significant improvements in predictions for proteins with complex topologies may be possible following significant increases in high-performance computing power, which will be required for thoroughly sampling high CO conformations (high CO proteins can take six orders of magnitude longer to fold than low CO proteins). Importantly for such a strategy, simulations performed for high CO structures converge much less strongly than those for low CO structures, and hence, lack of simulation convergence can indicate the need for improved sampling of high CO conformations. The parallels between Rosetta simulations and folding in vivo may extend to misfolding: The very low CO structures that accumulate in Rosetta simulations consist primarily of local up-down beta-sheets that may resemble precursors to amyloid formation.

Algorithms↗
PubMed1991

Computer design and fabrication of custom-contoured seating.

This article describes the development of a computer-controlled system for measuring anatomical contours and forces at the interface with seat surfaces. The system was designed to eliminate the cause of pressure sores, which are a major problem for wheelchair-bound individuals. A parallel and compatible system also has been developed for the rapid, precise, and cost-effective fabrication of custom-contoured seat cushions and other body supports from a range of open- and closed-cell foam materials.

Algorithms↗
PubMed2000

[A computer-aided analysis system for counting the synaptic numerical density based on disector technique].

The change in the numbers of synapse is of importance in various kinds of physiological and pathological processes. The numerical density is the structural parameter measuring up the numbers of the particles in the space. A new stereological technique, the disector technique, has been described to count the number of particles in a given volume of tissue. It is a technique for counting the number of arbitrary particles in 3-dimensional space using adjacent parallel sections at known distance apart. In this article also discussed is the software for computer assisted count of the synaptic numerical density based on the physical director technique with Visual Basic 4.0.

Algorithms↗
PubMed1994

Instruction in the techniques and concept of supportive care in oncology.

Cancer education merits a coordinated, vertical curriculum and an integrated planning strategy. It has become clear that it is as important to teach the techniques of supportive care in oncology as it is to teach the concepts of cancer biology, pathology, epidemiology, prevention, detection and aggressive treatments. Our aim is to determine whether the medical school and nursing school curricula give the students an introduction to the concepts of supportive care of the cancer patient. The spectrum of such supportive care encompasses a wide range of issues working towards a common goal of providing overall comfort with an emphasis on quality of life, and runs parallel with specific therapeutic strategies and associated problems. Do the graduate medical student and nursing student understand that cancer management is multidisciplinary and team-based? That the approach to pain management not only includes the administration of pain medications, but should also evaluate pain assessment and anesthetic, neurosurgical and behavioral approaches? That nausea and vomiting associated with chemotherapy can be ameliorated to a certain extent? That infections are common but algorithms exist for prevention and therapy? That certain metabolic complications are unique to cancer patients? That transfusions are vital procedures in patients with neoplasms undergoing aggressive treatments but are associated with certain risks and complications? That there are serious psychosocial, ethical and legal needs to be considered? To address these issues, the American Cancer Society Professors of Clinical Oncology, the American Cancer Society Professors of Oncology Nursing and the United States Cancer Center Directors were surveyed.(ABSTRACT TRUNCATED AT 250 WORDS)

Curriculum↗
PubMed2006

Localizing complex neural circuits with MEG data.

During cognitive processing, the various cortical areas, with specialized functions, supply for different tasks. In most cases then, the information flows are processed in a parallel way by brain networks which work together integrating the single performances for a common goal. Such a step is generally performed at higher processing levels in the associative areas. The frequency range at which neuronal pools oscillate is generally wider than the one which is detectable by bold changes in fMRI studies. A high time resolution technique like magnetoencephalography or electroencephalography is therefore required as well as new data processing algorithms for detecting different coherent brain areas cooperating for one cognitive task. Our experiments show that no algorithm for the inverse problem solution is immune from bias. We propose therefore, as a possible solution, our software LOCANTO (LOcalization and Coherence ANalysis TOol). This new package features a set of tools for the detection of coherent areas. For such a task, as a default, it employs the algorithm with best performances for the neural landscape to be detected. If the neural landscape under attention involves more than two interacting areas the SLoreta algorithm is used. Our study shows in fact that SLoreta performance is not biased when the correlation among multiple sources is high. On the other hand, the Beamforming algorithm is more precise than SLoreta at localizing single or double sources but it gets a relevant localization bias when the sources are more than three and are highly correlated.

Bias↗
PubMed2005

Multiplexing schemes for generic SNP genotyping assays.

Association studies in populations relate genomic variation among individuals with medical condition. Key to these studies is the development of efficient and affordable genotyping techniques. Generic genotyping assays are independent of the target SNPs and offer great flexibility in the genotyping process. Efficient use of such assays calls for identifying sets of SNPs that can be interrogated in parallel under constraints imposed by the genotyping technology. In this paper, we study problems arising in the design of genotyping experiments using generic assays. Our problem formulation deals with two main factors that affect the genotyping cost: the number of assays used and the number of PCR reactions required for sample preparation. We prove that the resulting computational problems are hard, but provide approximate and heuristic solutions to these problems. Our algorithmic approach is based on recasting the multiplexing problems as partitioning and packing problems on a bipartite graph. We tested our algorithmic approaches on an extensive collection of synthetic data and on data that was simulated using real SNP sequences. Our results show that the algorithms achieve near-optimal designs in many cases and demonstrate the applicability of generic assays to SNP genotyping.

Algorithms↗
PubMed2004

Cardiac cine parallel imaging on a 0.7T open system.

BACKGROUND: Parallel imaging can be applied to cardiac imaging with a cylindrical MRI (magnetic resonance imaging) apparatus. Studies of open MRI, however, are few. This study sought to achieve cardiac cine parallel imaging (or RAPID, for "rapid acquisition through parallel imaging design") with an open 0.7T MRI apparatus. MATERIALS AND METHODS: Imaging time was shortened in all slice directions with the use of a dedicated four-channel RF receiving coil comprising solenoid coils and butterfly coils. Coil shape was designed through an RF-coil simulation that considered biological load. The auto-calibration of a 0.7T open MRI apparatus incorporated a modified image-domain reconstruction algorithm. Cine images were obtained with a BASG, or balanced SARGE (steady-state acquisition with rewound gradient echo), sequence. Image quality was evaluated with cylindrical phantoms and five healthy volunteers. RESULTS: Multi-slice phantom images showed no visible artifacts. Cine images taken under breath-hold with an acceleration factor of two were evaluated carefully. With auto-calibration, the images revealed no visible unfolded artifacts or motion artifacts. RAPID thus improved the acquisition speed, time resolution, and spatial resolution of short-axis, long-axis, and four-chamber images. CONCLUSION: The use of a dedicated RF coil enabled cardiac cine RAPID to be performed with an open MRI apparatus.

Artifacts↗
PubMed2006

Molecular subtyping of breast cancer from traditional tumor marker profiles using parallel clustering methods.

PURPOSE: Recent small-sized genomic studies on the identification of breast cancer bioprofiles have led to profoundly dishomogenous results. Thus, we sought to identify distinct tumor profiles with possible clinical relevance based on clusters of immunohistochemical molecular markers measured on a large, single institution, case series. EXPERIMENTAL DESIGN: Tumor biological profiles were explored on 633 archival tissue samples analyzed by immunohistochemistry. Five validated markers were considered, i.e., estrogen receptors (ER), progesterone receptors (PR), Ki-67/MIB1 as a proliferation marker, HER2/NEU, and p53 in their original scale of measurement. The results obtained were analyzed by three different clustering algorithms. Four different indices were then used to select the different profiles (number of clusters). RESULTS: The best classification was obtained creating four clusters. Notably, three clusters were identified according to low, intermediate, and high ER/PR levels. A further subdivision in two biologically distinct subtypes was determined by the presence/absence of HER2/NEU and of p53. As expected, the cluster with high ER/PR levels was characterized by a much better prognosis and response to hormone therapy compared to that with the lowest ER/PR values. Notably, the cluster characterized by high HER2/NEU levels showed intermediate prognosis, but a rather poor response to hormone therapy. CONCLUSIONS: Our results show the possibility of profiling breast cancers by means of traditional markers, and have novel clinical implications on the definition of the prognosis of cancer patients. These findings support the existence of a tumor subtype that responds poorly to hormone therapy, characterized by HER2/NEU overexpression.

Adult↗
PubMed2000

Exact radon rebinning algorithm for the long object problem in helical cone-beam CT.

This paper addresses the long object problem in helical cone-beam computed tomography. We present the PHI-method, a new algorithm for the exact reconstruction of a region-of-interest (ROI) of a long object from axially truncated data extending only slightly beyond the ROI. The PHI-method is an extension of the Radon-method, published by Kudo, Noo, and Defrise in issue 43 of journal Physics in Medicine and Biology. The key novelty of the PHI-method is the introduction of a virtual object fpsi(x) for each value of the azimuthal angle psi in the image space, with each virtual object having the property of being equal to the true object f(x) in some ROI omegam. We show that, for each psi, one can calculate exact Radon data corresponding to the two-dimensional (2-D) parallel-beam projection of fpsi(x) onto the meridian plane of angle psi. Given an angular range of length pi of such parallel-beam projections, the ROI omegam can be exactly reconstructed because f(x) is identical to fpsi(x) in Omegam. Simulation results are given for both the Radon-method and the PHI-method indicating that 1) for the case of short objects, the Radon- and PHI-methods produce comparable image quality, 2) for the case of long objects, the PHI-method delivers the same image quality as in the short object case, while the Radon-method fails, and 3) the image quality produced by the PHI-method is similar for a large range of pitch values.

Algorithms↗
PubMed2003

Thorium(IV) complexes of bidentate hydroxypyridinonates.

The coordination chemistry of actinide(IV) ions with hydroxypyridinone ligands has been initially explored by examining the complexation of Th(IV) ion with bidentate PR-1,2-HOPO (HL(1)()), PR-Me-3,2-HOPO (HL(2)()), and PR-3,4-HOPO-N (HL(3)()) ligands. The complexes Th(L(1)())(4), Th(L(2)())(4), and Th(L(3)())(4) were prepared in methanol solution from Th(acac)(4) and the corresponding ligand. Single-crystal X-ray diffraction analyses are reported for the free ligand PR-Me-3,2-HOPO (HL(2)()) [Ponemacr;, Z = 8, a = 8.1492(7) A, b = 11.1260(9) A, c = 23.402(2) A, alpha = 87.569(1) degrees, beta = 86.592(1) degrees, gamma = 87.480(1) degrees ], and the complex Th(L(2)())(4).H(2)O [Pna2(1) (No. 33), Z = 4, a = 17.1250(5) A, b = 12.3036(7) A, c = 23.880 (1) A]. A comparison of the structure of the metal complex Th-PR-Me-3,2-HOPO with that of free ligand PR-Me-3,2-HOPO reveals that the ligand geometry is the same in the free ligand and in the metal complex. Amide hydrogen bonds enhance the rigidity and stability of the complex and demonstrate that the Me-3,2-HOPO ligands are predisposed for metal chelation. Solution thermodynamic studies determined overall formation constants (log beta(140)) for Th(L(1)())(4), Th(L(2)())(4), and Th(L(3)())(4) of 36.0(3), 38.3(3), and 41.8(5), respectively. Species distribution calculations show that the 4:1 metal complex Th(L)(4) is the dominant species in the acidic range (pH < 6) for PR-1,2-HOPO, in weakly acidic to physiological pH range for PR-Me-3,2-HOPO and in the high-pH range (>8) for PR-3,4-HOPO-N. This finding parallels the relative acidity of these structurally related ligands. In the crystal of [Th(L(2)())(4)].H(2)O, the chiral complex forms an unusual linear coordination polymer composed of linked, alternating enantiomers.

Algorithms↗