Translational Coordinates Research Articles

Clinical Evaluation of an Immbolization System for Stereotactic Body Radiotherapy Using Helical Tomotherapy

In this study, a clinical evaluation of the Body Pro-Lok™ System combined with the TomoTherapy megavoltage computed tomography (MVCT) was performed for lung and liver stereotactic body radiotherapy (SBRT) to reduce interfractional setup uncertainty. Twenty patients treated with 3–5 fractions of SBRT were analyzed retrospectively. The Body Pro-Lok™ system was used in both CT simulation and during patient treatment setup. Patients were immobilized with a vacuum cushion placed posteriorly over the thoracic region, an abdominal compression plate, and a knee and foot sponge. Pretreatment MVCT scans of the TomoTherapy HI-ART II unit were fused with the planning kVCT before delivery of each fraction to determine the interfractional setup error. A total of 84 shifts were analyzed to assess the interfractional setup accuracy. Results showed that the mean interfractional setup errors and standard deviations were –0.9 ± 3.1 mm, 1.2 ± 5.5 mm, and 6.5 ± 2.6 mm for lateral (IEC-X), longitudinal (IEC-Y), and vertical (IEC-Z) variations, respectively. The maximum motion was 17.1 mm in the longitudinal direction. When all 3 translational coordinates were analyzed, a mean composite displacement vector of 8.2 ± 2.0 mm (range 4.1–11.7 mm) was obtained for all patients. Based on the findings, image-guided SBRT using the Body Pro-Lok™ system in conjunction with the MVCT of TomoTherapy is capable of minimizing interfractional setup error and improving treatment accuracy.

DOSIMETRIC IMPACT OF DAILY SETUP VARIATIONS DURING TREATMENT OF CANINE NASAL TUMORS USING INTENSITY‐MODULATED RADIATION THERAPY

Intensity-modulated radiation therapy (IMRT) can be employed to yield precise dose distributions that tightly conform to targets and reduce high doses to normal structures by generating steep dose gradients. Because of these sharp gradients, daily setup variations may have an adverse effect on clinical outcome such that an adjacent normal structure may be overdosed and/or the target may be underdosed. This study provides a detailed analysis of the impact of daily setup variations on optimized IMRT canine nasal tumor treatment plans when variations are not accounted for due to the lack of image guidance. Setup histories of ten patients with nasal tumors previously treated using helical tomotherapy were replanned retrospectively to study the impact of daily setup variations on IMRT dose distributions. Daily setup shifts were applied to IMRT plans on a fraction-by-fraction basis. Using mattress immobilization and laser alignment, mean setup error magnitude in any single dimension was at least 2.5 mm (0-10.0 mm). With inclusions of all three translational coordinates, mean composite offset vector was 5.9 +/- 3.3 mm. Due to variations, a loss of equivalent uniform dose for target volumes of up to 5.6% was noted which corresponded to a potential loss in tumor control probability of 39.5%. Overdosing of eyes and brain was noted by increases in mean normalized total dose and highest normalized dose given to 2% of the volume. Findings suggest that successful implementation of canine nasal IMRT requires daily image guidance to ensure accurate delivery of precise IMRT distributions when non-rigid immobilization techniques are utilized. Unrecognized geographical misses may result in tumor recurrence and/or radiation toxicities to the eyes and brain.

Processed splitting algorithms for rigid-body molecular dynamics simulations

An approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudovariables in a modified phase space, while the real translational and orientational coordinates are decoded by processing transformations. This allows one to overcome the barrier on the order of precision of the integration at a given number of force-torque evaluations per time step. Testing in dynamics of water versus previous methods shows that the algorithms obtained significantly improve the accuracy of the simulations without extra computational costs.

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring.

A modified kinematic model for particle flow in moving beds

Granular materials are utilized in a wide variety of industrial applications. The complex hydrodynamics of granular flow is still not fully understood. The flow characteristics of solid particles in a two-dimensional moving bed were studied experimentally and theoretically. The effects of mass velocity, properties of particles and the shape of moving bed on flow pattern were examined. The experiments show that the mass velocity of solid particles and the placement of baffles in stagnant zones have no effect on flow pattern. The shape, size and repose angle of particles affect the flow pattern greatly. The particles have more liquidity and the mixture between particles is easier with the increasing of sphericity degree of particles and the decreasing of particle size. The shape of flowing zone becomes more sharp-angled with the increasing of the repose angle, and the stagnant zone becomes larger. The kinematic model was used to simulate the particle flow. For center discharge the simulation results are in agreement with experiment data very well, while for eccentric discharge the simulation couldn't show the effects of side walls on particle flow. An analytic solution of kinematic model was obtained by Lie transformation group. It shows that the velocity of particle flow is the maximum when x equals 0. The method of translational coordinate was used to modify the traditional kinematic model in order to make sure the x value of each point on the maximum particles velocity distribution lines is zero. The modified kinematic model could simulate the eccentric discharge well, and the field of kinematic model applications was expanded.

A Computational Method for Planar Kinematic Analysis of Beam Pumping Units

A generalized computational method for planar kinematic analysis of pumping units is presented in this study. In this method, a local coordinate system is assigned to each body with respect to a fixed global coordinate system. The position of each point in a body is determined by specifying the global translational coordinates of the local coordinate system origin and its rotational angle relative to the global coordinate system. Constraint equations of motion are developed using the vector of coordinates of the connected bodies. These equations are solved to yield the position, velocity, and acceleration of the individual linkages at each instance of time. Both rotational and translational types of joints are considered in the analysis. The translational joint analysis is not discussed in this paper as they are not applicable for beam pumping units. This method can be used as an effective tool for pumping unit design and optimization. An example is provided to show the application of this method.

Measurement of vehicle parameters of motion without gyro-stabilized platforms

Spatial position of vehicle C.G. as well as angular parameters of body rotation are of major importance for analysis of vehicle dynamics, handling vibrational comfort, safe service in traffic etc. The mentioned parameters are determined by use of methods of dynamic simulation in phase of development, and by means of test measurement for vehicles in real service conditions. The problem that is to be taken into consideration here is related to practical measurement of vehicle motion parameters. Translational coordinates of vehicle C.G. are usually measured on the basis of registered linear accelerations of vehicle C.G. (once or twice integrated later, for calculation of displacement or velocity) and body angles are usually measured on gyroscope-stabilized platforms. The problem which occurs in these cases is the platform price (up to 100.000 EUR), not easily affordable for researchers. This paper attempts to determine vehicle motion parameters on the ground of six registered linear accelerations of specific body spots.

Quantum adiabatic polarons by translationally invariant perturbation theory

The translationally invariant diagrammatic quantum perturbation theory (TPT) is applied to the polaron problem on the 1D lattice, modeled through the Holstein Hamiltonian with the phonon frequency omega0, the electron hopping t and the electron-phonon coupling constant g. The self-energy diagrams of the fourth-order in g are calculated exactly for an intermittently added electron, in addition to the previously known second-order term. The corresponding quadratic and quartic corrections to the polaron ground state energy become comparable at t/omega0>1 for g/omega0~(t/omega0)^{1/4} when the electron self-trapping and translation become adiabatic. The corresponding non adiabatic/adiabatic crossover occurs while the polaron width is large, i.e. the lattice coarsening negligible. This result is extended to the range (t/omega0)^{1/2}>g/omega0>(t/omega0)^{1/4}>1 by considering the scaling properties of the high-order self-energy diagrams. It is shown that the polaron ground state energy, its width and the effective mass agree with the results found traditionally from the broken symmetry side, kinematic corrections included. The Landau self trapping of the electron in the classic self-consistent, localized displacement potential, the restoration of the translational symmetry by the classic translational Goldstone mode and the quantization of the polaronic translational coordinate are thus all encompassed by a quantum theory which is translationally invariant from the outset.

Coupling between local vibrations and charge transport in discotic materials

Charge transport between molecular units is sensitive to coupling between thermal motion and the electronic structure of these units. The thermal motion of a short column of discotic molecules is simulated by a molecular dynamics simulation in order to provide the correct distribution of distorted molecular units, including the effects of the alkoxy tails. Ab initio calculations are then used to determine the electronic structure of the distorted triphenylene cores and the time dependence of the interaction between these. This goes beyond previous works that have calculated changes in charge transfer by finite displacement of rigid molecular units along translational and rotational coordinates. Two timescales and types of motion are distinguished: slow whole body motions of the disks, and internal vibrational modes of the aromatic cores. The effects of these motions are separated via their different timescales, and are found to be of equal importance in the interaction between the HOMOs of neighbouring molecules. Electron/phonon coupling from these small molecular distortions may be important not only for charge transport, but also for loss of carriers via relaxation of electronically excited states.

Multidimensional reactive scattering with quantum trajectories

Ensembles of quantum trajectories are evolved to study time-dependent reaction dynamics in multidimensional systems with up to 25 vibrational modes. The equations of motion are formulated in curvilinear reaction path coordinates and all coupling terms are retained, including those involving curvature of the reaction path. The model potential is a Gaussian barrier along the translational coordinate coupled to M vibrational modes. Spatial derivatives needed to propagate the trajectories are evaluated by least squares fitting in a contracted basis set. Stable propagation of the trajectory ensembles was carried out until complete bifurcation into reflected and reactive subensembles. The reaction probabilities were evaluated by Monte Carlo integration of the multidimensional smooth transmitted densities. Computational results, including trajectory plots and time-dependent reaction probabilities, are presented for M = 1, 5, and 25 vibrational modes.

Real Time Prostate Translation, Rotation, Deformation Evaluated with Calypso Beacon™ Transponders

Real Time Prostate Translation, Rotation, Deformation Evaluated with Calypso Beacon™ Transponders

Theoretical Study of the Benzene Excimer Using Time-Dependent Density Functional Theory

A theoretical characterization of the potential energy surfaces of the singlet benzene excimer states derived from the B2u monomer excited state has been performed using time-dependent density functional theory. The excited-state potential energy surfaces were initially characterized by computations along the parallel and perpendicular intermolecular translational coordinates. These calculations predict that the lowest excited state for parallel translation is bound with a minimum at 3.15 angstroms and with a binding energy of 0.46 eV, while the perpendicular translational coordinate was essentially found to be a repulsive state. At the calculated minimum distance, the effect of in-plane rotation, out-of-plane rotation, and slipped-parallel translation were examined. The rotational calculations predict that deviations from the D6h geometry lead to a destabilization of the excimer state; however, small angular variations in the range of 0 degrees -10 degrees are predicted to be energetically feasible. The slipped-parallel translational calculations also predict a destabilizing effect on the excimer state and were found to possess barriers to this type of dissociation in the range of 0.50-0.61 eV. When compared to experimentally determined values for the benzene excimer energetics, the calculated values were found to be in semiquantitative agreement. Overall, this study suggests that the time-dependent density functional theory method can be used to characterize the potential energy surfaces and the energetics of aromatic excimers with reasonable accuracy.

Kinematic Analysis of the Cervical Spine Following Implantation of an Artificial Cervical Disc

Prospective cohort study. To assess the biomechanical profile of the cervical spine following cervical arthroplasty. Spinal arthroplasty offers the promise of maintaining functional spinal motion, thereby potentially avoiding adjacent segment disease. Disc replacement may become the next gold standard for the treatment of degenerative cervical spine disease, and must be studied rigorously to ensure in vivo efficacy and safety. A total of 20 patients underwent single or 2-level implantation of the Bryan artificial cervical disc (Medtronic Sofamor Danek, Memphis TN) for treatment of cervical degenerative disc disease producing radiculopathy and/or myelopathy. Lateral neutral, flexion, and extension cervical radiographs were obtained before surgery and at intervals up to 24 months after surgery. Kinematic parameters, including sagittal rotation, horizontal translation, change in disc height, and center of rotation (COR), were assessed for each spinal level using quantitative motion analysis software. Motion was preserved in the operated spinal segments (mean range of motion 7.8 degrees) up to 24 months following surgery. The relative contribution of each spinal segment to overall spinal sagittal rotation differed depending on whether the disc was placed at C5-C6 or C6-C7. Overall cervical motion (C2-C7) was moderately but significantly increased during late follow-up. Sagittal rotation, anterior and posterior disc height, translation, and COR coordinates did not change significantly following surgery. The COR was most frequently located posterior and inferior to the center of the disc space. The Bryan artificial cervical disc provided in vivo functional spinal motion at the operated level, reproducing the preoperative kinematics of the spondylotic disc.

Pronounced non-Condon effects in the ultrafast infrared spectroscopy of water

In the context of vibrational spectroscopy in liquids, non-Condon effects refer to the dependence of the vibrational transition dipole moment of a particular molecule on the rotational and translational coordinates of all the molecules in the liquid. For strongly hydrogen-bonded systems, such as liquid water, non-Condon effects are large. That is, the bond dipole derivative of an OH stretch depends strongly on its hydrogen-bonding environment. Previous calculations of nonlinear vibrational spectroscopy in liquids have not included these non-Condon effects. We find that for water, inclusion of these effects is important for an accurate calculation of, for example, homodyned and heterodyned three-pulse echoes. Such echo experiments have been "inverted" to obtain the OH stretch frequency time-correlation function, but by necessity the Condon and other approximations are made in this inversion procedure. Our conclusion is that for water, primarily because of strong non-Condon effects, this inversion may not lead to the correct frequency time-correlation function. Nevertheless, one can still make comparison between theory and experiment by calculating the experimental echo observables themselves.

Effects of long-term ionic and osmotic stress conditions on photosynthesis in the cyanobacterium Synechocystis sp. PCC 6803.

Salinity is considered to be one of the most severe problems in worldwide agricultural production, but the published investigations give contradictory results of the effect of ionic and osmotic stresses on photosynthesis. In the present study, long-term effects of both ionic and osmotic stresses, especially on photosynthesis, were investigated using the moderately halotolerant cyanobacterium Synechocystis sp. PCC 6803. Our results show that the PSII activity and the photosynthetic capacity tolerated NaCl but a high concentration of sorbitol completely inhibited both activities. In line with these results, we show that the amount of the D1 protein of PSII was decreased under severe osmotic stress, whereas the levels of PsaA / B and NdhF3 proteins remained unchanged. However, high concentrations of sorbitol stress led to a drastic decrease of both psbA (encoding D1) and psaA (encoding PsaA) transcripts, suggesting that severe osmotic stress may abolish the tight coordination of transcription and translation normally present in bacteria, at least in the case of the psaA gene. Taken together, our results indicate that the osmotic stress component is more detrimental to photosynthesis than the ionic one and, furthermore, under osmotic stress, the D1 protein appears to be the target of this stress treatment.

Knowledge-based prediction of DNA atomic structure from nucleic sequence.

A simple knowledge-based method for DNA atomic structure prediction from nucleic sequence is presented. We used free B-DNA crystal structures to estimate the distribution of trinucleotide base pairs and tetranucleotide base-pair steps conformational coordinates. We used these distributions as a basis to predict the 3D position of the non-hydrogen atoms of the nucleic bases of any arbitrary DNA sequence of any length. The only constraint imposed was that the structure is a B-DNA one with Watson-Crick complementary base pairs. The method was tested on not seen DNA structures with sequence lengths varying from 6bp to 12bp. The obtained predictions have RMSE around 0.5 A for the translational conformational coordinates, and around 5 degrees for the rotational. For the estimation of the nucleic base non-hydrogen atom coordinates the RMSE is around 1.1 A. The knowledge-based method outperformed a technique based on genetic algorithms in the prediction of B-DNA structures.

Complex signals in the genomic 3' nontranslated region of bovine viral diarrhea virus coordinate translation and replication of the viral RNA.

The genomes of positive-strand RNA viruses strongly resemble cellular mRNAs. However, besides operating as a messenger to generate the virus-encoded proteins, the viral RNA serves also as a template during replication. A central issue of the viral life cycle, the coordination of protein and RNA synthesis, is yet poorly understood. Examining bovine viral diarrhea virus (BVDV), we report here on the role of the variable 3'V portion of the viral 3' nontranslated region (3'NTR). Genetic studies and structure probing revealed that 3'V represents a complex RNA motif that is composed of synergistically acting sequence and structure elements. Correct formation of the 3'V motif was shown to be an important determinant of the viral RNA replication process. Most interestingly, we found that a proper conformation of 3'V is required for accurate termination of translation at the stop-codon of the viral open reading frame and that efficient termination of translation is essential for efficient replication of the viral RNA. Within the viral 3'NTR, the complex 3'V motif constitutes also the binding site of recently characterized cellular host factors, the so-called NFAR proteins. Considering that the NFAR proteins associate also with the 5'NTR of the BVDV genome, we propose a model where the viral 3'NTR has a bipartite functional organization: The conserved 3' portion (3'C) is part of the nascent replication complex; the variable 5' portion (3'V) is involved in the coordination of the viral translation and replication. Our data suggest the accuracy of translation termination as a sophisticated device determining viral adaptation to the host.

Members of the NF90/NFAR protein group are involved in the life cycle of a positive-strand RNA virus.

A major issue of current virology concerns the characterization of cellular proteins that operate as functional components of the viral multiplication process. Here we describe a group of host factors designated as 'NFAR proteins' that are recruited by the replication machinery of bovine viral diarrhea virus, a close relative of the human pathogen hepatitis C virus. The NFAR proteins associate specifically with both the termini of the viral RNA genome involving regulatory elements in the 5' and 3' non-translated regions. Modification of the protein interaction sites in the 3' non-translated region yielded viral RNAs that were replication deficient. Viral replication was also inhibited by RNAi approaches that reduced the concentration of RNA helicase A, a member of the NFAR group, in the host cell's cytoplasm. Further experimental data suggest that NFAR proteins mediate a circular conformation of the viral genome that may be important for the coordination of translation and replication. Because NFAR proteins are presumed components of the antiviral response, we suspect that viral recruitment may also serve to weaken cellular defense mechanisms.

Curbing the nonsense: the activation and regulation of mRNA surveillance.

Gene expression requires the coordination and integration of multiple processes, including transcription, splicing, polyadenylation, nucleocytoplasmic export, and translation of mRNAs. Such complexity inevitably results in errors, many of which ultimately lead to premature termination of translation. Additionally, nonsense mutations can be introduced during DNA replication and are the cause of 20% to 40% of human genetic diseases (Frischmeyer and Dietz 1999). The truncated proteins encoded by these mutant mRNAs are potentially toxic to the cell, and therefore, a mechanism, known as mRNA surveillance or nonsense-mediated mRNA decay (NMD), has evolved to recognize mRNAs containing premature termination codons (PTCs) and cause their degradation to be accelerated.

Molecular Dynamics Simulation of Collinear Polymer Nanoparticle Collisions: Reaction and Scattering

Collinear collisions of polyethylene nanoparticles are studied, with a particular emphasis on the transition between sticking and reactive scattering trajectories. The former are characterized by collisions where the two polymer particles form a particle dimer, the latter by collisions resulting in the gross change of particle structure, such as particle fragmentation or transfer of polymer chains from one particle to another. It is observed that in the collinear case there are no scattering trajectories where the particles undergo nearly elastic collisions and rebound with small energy change. This property is attributed to the fact that during the collision process the particles undergo reorganization, and the energy involved is difficult to recover. The result is that at all but extremely high velocities, particles undergo rapid and irreversible energy transfer from the relative translational coordinate into other internal coordinates, resulting in dimerization of the polymer particles.