Alignment Uncertainty Research Articles

Alignment of the central DØ detector

The alignment procedure of the Silicon Microstrip Tracker (SMT) and the Central Fiber Tracker (CFT) is described. Alignment uncertainties and resulting systematic errors in physics analyses are addressed.

Practical Field Alignment of Parabolic Trough Solar Concentrators

In this paper a new technique for parabolic trough mirror alignment based on the use of an innovative theoretical overlay photographic (TOP) approach is described. The technique is a variation on methods used to align mirrors on parabolic dish systems. It involves overlaying theoretical images of the heat collection element (HCE) in the mirrors onto carefully surveyed photographic images and adjustment of mirror alignment until they match. From basic geometric principles, for any given viewer location the theoretical shape and location of the reflected HCE image in the aligned mirrors can be predicted. The TOP approach promises to be practical and straightforward, and inherently aligns the mirrors to the HCE. Alignment of an LS-2 mirror module on the rotating platform at the National Solar Thermal Test Facility (NSTTF) with the TOP technique along with how it might be implemented in a large solar field is described. Comparison of the TOP alignment to the distant observer approach on the NSTTF LS-2 is presented and the governing equations used to draw the theoretical overlays are developed. Alignment uncertainty associated with this technique is predicted to be less than the mirror slope error.

Impact of CMS silicon tracker misalignment on track and vertex reconstruction

The alignment uncertainties of the CMS tracker detector, made of a huge amount of independent silicon sensors with an excellent position resolution, affect the performances of the track reconstruction, the track parameters measurement and the vertex reconstruction. In order to study the impact of the misalignment of the CMS tracking devices on the previous procedures, realistic estimates for the expected displacements of the tracking systems are supplied in two different scenarios, the first supposed to reproduce the misalignment conditions during the first data taking while the second one related to long-term data taking condition. Results on the track reconstruction are expressed in terms of the resolution on track parameters, the global efficiency of the track reconstruction and the fake rate in the two scenarios of misalignment, by comparing them with the scenario of a perfect alignment of the tracking devices. Primary vertex finding efficiency and position resolution are affected by the tracker misalignment, too.

TH‐C‐ValB‐02: Clinical Implementation of Cone‐Beam CT for Image‐Guided Radiation Therapy

Purpose: A linear accelerator equipped with cone‐beam CT (CBCT) was commissioned for image‐guided radiation therapy in an IMPAC's Multi‐Access environment. The purpose of this work is to report our experience of clinical implementation of CBCT in a multi‐vendor environment. Method and Materials: The mechanical accuracy of the system was tested using a stereotactic method to verify the imaging isocenter congruent with the therapy isocenter of the accelerator (Trilogy, Varian). Image qualities, including the high contrast resolution (HCR) and low contrast resolution (LCR), were evaluated and compared with the conventional CT (Catphan 600). Imaging doses were measured using TLDs in several anthropomorphic phantoms for the intended treatment sites (head, chest, and pelvis). There are connectivity issues with current vendor provided software, the clinical implementation of CBCT relies on in‐house CT‐assisted targeting (CAT) software, which is used for aligning CBCT images to the planning CT to determine daily setup shifts. The alignment uncertainties and its dependence on imaging dose were verified in phantom with various known couch shifts. Results: The imaging isocenter was found to within 1 mm of the therapy isocenter. The CBCT HCR is similar to the conventional CT, approximately 6∼7 lp/cm, while the LCR is inferior. The CBCT LCR with bow‐tie appears better than without. With bow‐tie, the average imaging doses using built‐in protocols were 7.1, 6.7 and 4.3 cGy in head, chest, and pelvis phantoms, respectively; without bow‐tie, doses were 5.4 and 2.4 cGy for head and pelvic phantoms. Workflow was implemented to use the in‐house CAT software with vendor supplied CBCT acquisition software. The CAT software can predict overall sub‐millimeter accuracy in a phantom experiment with many known couch shifts. Conclusion: We have successfully implemented CBCT for clinical use. Major challenges included various component testing, connectivity, and in‐house software implementations.

Baffled‐Probe Cluster for Simultaneous, Single‐Point Monitoring of Magnetized Plasma Fluctuations

AbstractAn array of baffled probes for the real‐time monitoring of oscillating values of space potential, electric field and electron/ion temperature in magnetized plasma is assembled and tested. The multi‐probe array samples a region with dimensions on the order or less than an ion gyroradius, essentially a single point, and does not require voltage sweeps. We refer to an array of probes contained within such a single point as a probe cluster. Here, we describe two versions of the baffled‐probe cluster. In the first cluster, four independent coils of collection wire are mounted at 90‐degree intervals around the circumference of a short, thin, cylindrical, four‐bore ceramic tube. This tube slides into a larger‐diameter, single bore, ceramic tube having four azimuthally separated masks (baffles), each lining up with a coil‐coil gap on the 4‐bore tube, and four baffle‐to‐baffle gaps, each lining up with a coil on the 4‐bore tube. The second cluster uses a single four‐bore ceramic tube, with four longitudinal slots to allow side access to each bore, and probes made from a single strand of collection wire. With the tubes oriented perpendicular to the magnetic field, the baffled‐probe cluster is rotated around its axis in order to regulate the ratio between electron and ion currents to the baffled probes and, thereby, change the probes' relative sensitivity to space potential and temperature oscillations. This probe‐cluster design has the advantages of realtime monitoring of magnetized‐plasma fluctuations, post‐acquisition determination of electron‐temperature or ion‐temperature time series, post‐acquisition determination of cross‐phase and coherence between fluctuations of individual plasma parameters, compact size, minimal plasma perturbation (probes are non‐emissive), and relative insensitivity to alignment uncertainty. The clusters have been used for distinguishing temperature fluctuations from potential fluctuations in plasma of the WVU Q‐machine. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Joint Bayesian Estimation of Alignment and Phylogeny

We describe a novel model and algorithm for simultaneously estimating multiple molecular sequence alignments and the phylogenetic trees that relate the sequences. Unlike current techniques that base phylogeny estimates on a single estimate of the alignment, we take alignment uncertainty into account by considering all possible alignments. Furthermore, because the alignment and phylogeny are constructed simultaneously, a guide tree is not needed. This sidesteps the problem in which alignments created by progressive alignment are biased toward the guide tree used to generate them. Joint estimation also allows us to model rate variation between sites when estimating the alignment and to use the evidence in shared insertion/deletions (indels) to group sister taxa in the phylogeny. Our indel model makes use of affine gap penalties and considers indels of multiple letters. We make the simplifying assumption that the indel process is identical on all branches. As a result, the probability of a gap is independent of branch length. We use a Markov chain Monte Carlo (MCMC) method to sample from the posterior of the joint model, estimating the most probable alignment and tree and their support simultaneously. We describe a new MCMC transition kernel that improves our algorithm's mixing efficiency, allowing the MCMC chains to converge even when started from arbitrary alignments. Our software implementation can estimate alignment uncertainty and we describe a method for summarizing this uncertainty in a single plot.

Polarimetric RCS Calibration using Reference Reflectors

A new polarimetric radar cross section (RCS) calibration technique using two reference reflectors is developed and verified experimentally in the anechoic chamber of Multimedia University. The antenna system and the two orthogonal channels are modeled as a two-port network. The technique utilizes two electrically large reflectors, namely a rectangular flat plate and a 45° rotated dihedral corner reflector as the calibration targets to provide large reflections for co-polarization and cross-polarization returns, respectively. The orientation of the reflectors is not critical, and their theoretical RCS are not required in the calibration process. Therefore the alignment problem and uncertainties in the computation of the theoretical responses are eliminated. A metallic sphere with known theoretical RCS is used to verify the calibration accuracy and determine the correction factor for absolute RCS measurement. Scattering measurements are performed using a Vector Network Analyzer (VNA). Raw data are acquired and stored in the PC for further processing. Time domain gating technique is applied to remove the target-chamber coupling effect in the measurements.

Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model

BackgroundCertain protein families are highly conserved across distantly related organisms and belong to large and functionally diverse superfamilies. The patterns of conservation present in these protein sequences presumably are due to selective constraints maintaining important but unknown structural mechanisms with some constraints specific to each family and others shared by a larger subset or by the entire superfamily. To exploit these patterns as a source of functional information, we recently devised a statistically based approach called contrast hierarchical alignment and interaction network (CHAIN) analysis, which infers the strengths of various categories of selective constraints from co-conserved patterns in a multiple alignment. The power of this approach strongly depends on the quality of the multiple alignments, which thus motivated development of theoretical concepts and strategies to improve alignment of conserved motifs within large sets of distantly related sequences.ResultsHere we describe a hidden Markov model (HMM), an algebraic system, and Markov chain Monte Carlo (MCMC) sampling strategies for alignment of multiple sequence motifs. The MCMC sampling strategies are useful both for alignment optimization and for adjusting position specific background amino acid frequencies for alignment uncertainties. Associated statistical formulations provide an objective measure of alignment quality as well as automatic gap penalty optimization. Improved alignments obtained in this way are compared with PSI-BLAST based alignments within the context of CHAIN analysis of three protein families: Giα subunits, prolyl oligopeptidases, and transitional endoplasmic reticulum (p97) AAA+ ATPases.ConclusionWhile not entirely replacing PSI-BLAST based alignments, which likewise may be optimized for CHAIN analysis using this approach, these motif-based methods often more accurately align very distantly related sequences and thus can provide a better measure of selective constraints. In some instances, these new approaches also provide a better understanding of family-specific constraints, as we illustrate for p97 ATPases. Programs implementing these procedures and supplementary information are available from the authors.

Two Active Nuclei in 3C 294

The z = 1.786 radio galaxy 3C 294 lies < 10'' from a 12 mag star and has been the target of at least three previous investigations using adaptive optics (AO) imaging. A major problem in interpreting these results is the uncertainty in the precise alignment of the radio structure with the H- or K-band AO imaging. Here we report observations of the position of the AO guide star with the Hubble Space Telescope Fine Guidance Sensor, which, together with positions from the second United States Naval Observatory's CCD Astrograph Catalog (UCAC2), allow us to register the infrared and radio frames to an accuracy of better than 01. The result is that the nuclear compact radio source is not coincident with the brightest discrete object in the AO image, an essentially unresolved source on the eastern side of the light distribution, as Quirrenbach and coworkers had suggested. Instead, the radio source is centered about 09 to the west of this object, on one of the two apparently real peaks in a region of diffuse emission. Nevertheless, the conclusion of Quirrenbach and coworkers that 3C 294 involves an ongoing merger appears to be correct: analysis of a recent deep Chandra image of 3C 294 obtained from the archive shows that the nucleus comprises two X-ray sources, which are coincident with the radio nucleus and the eastern stellar object. The X-ray/optical flux ratio of the latter makes it extremely unlikely that it is a foreground Galactic star.

A kilohertz frame rate cinemagraphic PIV system for laboratory-scale turbulent and unsteady flows

A kilohertz frame rate cinemagraphic particle image velocimetry (PIV) system has been developed for acquiring time-resolved image sequences of laboratory-scale gas and liquid-phase turbulent flows. Up to 8000 instantaneous PIV images per second are obtained, with sequence lengths exceeding 4000 images. The two-frame cross-correlation method employed precludes directional ambiguity and has a higher signal-to-noise ratio than single-frame autocorrelation or cross-correlation methods, facilitating acquisition of long uninterrupted sequences of valid PIV images. Low and high velocities can be measured simultaneously with similar accuracy by adaptively cross-correlating images with the appropriate time delay. Seed particle illumination is provided by two frequency-doubled Nd:YAG lasers producing Q-switched pulses at the camera frame rate. PIV images are acquired using a 16 mm high-speed rotating prism camera. Frame-to-frame registration is accomplished by imaging two pairs of crossed lines onto each frame and aligning the digitized image sequence to these markers using image processing algorithms. No flow disturbance is created by the markers because only their image is projected to the PIV imaging plane, with the physical projection device residing outside the flow field. The frame-to-frame alignment uncertainty contributes 2% to the overall velocity measurement uncertainty, which is otherwise comparable to similar film-based PIV methods.

Determination of ventilatory liver movement via radiographic evaluation of diaphragm position

Purpose: To determine the accuracy of estimation of liver movement inferred by observing diaphragm excursion on radiographic images. Methods and Materials: Eight patients with focal liver cancer had platinum embolization microcoils implanted in their livers during catheterization of the hepatic artery for delivery of regional chemotherapy. These patients underwent fluoroscopy, during which normal breathing movement was recorded on videotape. Movies of breathing movement were digitized, and the relative projected positions of the diaphragm and coils were recorded. For 6 patients, daily radiographs were also acquired during treatment. Retrospective measurements of coil position were taken after the diaphragm was aligned with the superior portion of the liver on digitally reconstructed radiographs. Results: Coil movement of 4.9 to 30.4 mm was observed during normal breathing. Diaphragm position tracked inferior-superior coil displacement accurately (population σ 1.04 mm) throughout the breathing cycle. The range of coil movement was predicted by the range of diaphragm movement with an accuracy of 2.09 mm (σ). The maximum error observed measuring coil movement using diaphragm position was 3.8 mm for a coil 9.8 cm inferior to the diaphragm. However, the distance of the coil from the top of the diaphragm did not correlate significantly with the error in predicting liver excursion. Analysis of daily radiographs showed that the error in predicting coil position using the diaphragm as an alignment landmark was 1.8 mm (σ) in the inferior-superior direction and 2.2 mm in the left-right direction, similar in magnitude to the inherent uncertainty in alignment. Conclusions: This study demonstrated that the range of ventilatory movement of different locations within the liver is predicted by diaphragm position to an accuracy that matches or exceeds existing systems for ventilatory tracking. This suggests that the diaphragm is an acceptable anatomic landmark for radiographic estimation of liver movement in anterior-posterior projections for most patients.

Preliminary report: Monocular spatial localization in children with strabismic amblyopia

Defective spatial localization is an important feature of strabismic amblyopia. Based on our experience from testing adult strabismics under various test conditions, we developed a test for assessing vertical alignment in strabismic children. Patients had to align a vertical test line with the apices of two vertically arranged reference triangles, under the control of both the dominant eye and the amblyopic eye. Means and standard deviations of several judgements represent systematic errors and uncertainty of alignment. We tested 27 strabismic and 34 age-matched control children aged 4.5-10 years. Control children showed a scatter of mean systematic alignment around the correct position of up to 7 minarc. In the amblyopic eyes of strabismic children, uncertainty was consistently higher than in the eyes of the control children. Systematic errors outside the normal range frequently occurred. In children tested repeatedly during occlusion therapy, uncertainty decreased as visual acuity improved. In several cases we observed changes of systematic vertical alignment during therapy, sometimes unexpectedly in the sense of a change in the direction of mislocalization or an initial increase and later decrease of errors. Thus, children with strabismic amblyopia show spatial localization deficits which are similar to those of adult strabismic amblyopes. Both spatial uncertainty and systematic distortions are susceptible to change due to enforced use of the amblyopic eye during occlusion therapy.

Planning target volumes for radiotherapy: how much margin is needed?

Purpose: The radiotherapy planning target volume (PTV) encloses the clinical target volume (CTV) with anisotropic margins to account for possible uncertainties in beam alignment, patient positioning, organ motion, and organ deformation. Ideally, the CTV-PTV margin should be determined solely by the magnitudes of the uncertainties involved. In practice, the clinician usually also considers doses to abutting healthy tissues when deciding on the size of the CTV-PTV margin. This study calculates the ideal size of the CTV-PTV margin when only physical position uncertainties are considered. Methods and Materials: The position of the CTV for any treatment is assumed to be described by independent Gaussian distributions in each of the three Cartesian directions. Three strategies for choosing a CTV-PTV margin are analyzed. The CTV-PTV margin can be based on: 1. the probability that the CTV is completely enclosed by the PTV; 2. the probability that the projection of the CTV in the beam’s eye view (BEV) is completely enclosed by the projection of the PTV in the BEV; and 3. the probability that a point on the edge of the CTV is within the PTV. Cumulative probability distributions are derived for each of the above strategies. Results: Expansion of the CTV by 1 standard deviation (SD) in each direction results in the CTV being entirely enclosed within the PTV 24% of the time; the BEV projection of the CTV is enclosed within the BEV projection of the PTV 39% of the time; and a point on the edge of the CTV is within the PTV 84% of the time. To have the CTV enclosed entirely within the PTV 95% of the time requires a margin of 2.8 SD. For the BEV projection of the CTV to be within the BEV projection of the PTV 95% of the time requires a margin of 2.45 SD. To have any point on the surface of the CTV be within the PTV 95% of the time requires a margin of 1.65 SD. Conclusion: In the first two strategies for selecting a margin, the probability of finding the CTV within the PTV is unrelated to dose variations in the CTV. In the third strategy, the specified confidence limit is correlated with the minimum target dose. We recommend that the PTV be calculated from the CTV using a margin of 1.65 SD in each direction. This gives a minimum CTV dose that is greater than 95% of the minimum PTV dose. Additional sparing of adjoining healthy structures should be accomplished by modifying beam portals, rather than adjusting the PTV. Then, the dose distributions more accurately reflect the clinical compromise between treating the tumor and sparing the patient.

Temporal sampling requirements for the tracer kinetics modeling of breast disease

The physiological parameters measured in the tracer kinetics modeling of data from a dynamic contrast-enhanced magnetic resonance (MR) breast exam (blood flow-extraction fraction product [FE], volume of the extracellular extravascular space [V e], and blood volume [V b]) may enable non-invasive diagnosis of breast cancer. One of the factors that compromises the accuracy and precision of the parameter estimates, and therefore their diagnostic potential, is the temporal resolution of the MR scans used to measure contrast agent (gadolinium-diethylenetriamine pentaacetic acid [Gd-DTPA]) concentration in an artery (arterial input function [AIF]) and in the tissue (tissue residue function [TRF]). Using computer simulations, we have examined, for several AIF widths, the errors introduced into estimates of tracer kinetic parameters in breast tissue due to insufficient temporal sampling. Temporal sampling errors can be viewed as uncertainties and biases in the parameter estimates introduced by the uncertainty in the relative alignments of the AIF, TRF, and sampling grid. These effects arise from the model’s inherent sensitivity to error in either the AIF or TRF, which is dependent on the values of the tracer kinetic parameters and increases with AIF width. Based on the results of the simulations, to ensure that the error in FE and V e will be under 10% of their true values, we recommend a rapid bolus injection of contrast agent (∼10 s), that the AIF be sampled every second, and that the TRF be sampled every 16 s or less. An accurate measurement of V b requires that the TRF be sampled at least every 4 s. The results of these investigations can be used to set minimum dynamic imaging rates for tracer kinetics modeling of the breast.

Real-Time Optimal Attitude Estimation Using Horizon Sensor and Magnetometer Data

Full three-axis knowledge was desired for a momentum bias spacecraft employing only a horizon sensor for attitude determination. This sensor provided adequate knowledge for rotations about two axes but no information forrotationsaboutthenadiraxis.Though satisfactory formanyapplications,proximityand rendezvousoperations of a thrusting vehicle near the Shuttle are best supported with three-axis knowledge. The solution devised takes three-axis magnetometeroutputs, used on the spacecraft to scale magnetic torquer commands, and horizon sensor outputs to establish an overdetermined attitude matrix. The attitude matrix is solved by minimizing a chi-square loss function relating the measured vectors to internally modeled reference vectors. The reference vectors are provided by a Keplarian propagator modie ed for oblateness effects and the 1995 World Magnetic Model 12thorder geomagnetic e eld coefe cients. The approach is implemented on a laptop computer for real-time e ight operations. Ground simulations indicate three-sigma errors of about 1.3 deg in pitch and roll and 2.6 deg in yaw. Tests conducted on the Shuttle’ s robot arm prior to release of the spacecraft on STS-69 and STS-80 cone rmed theseexpectations. The system performed well during freee ight and provided valuable attitudeknowledgeduring perturbations due to tip-off and thruster alignment uncertainties.

The relationship model between the influence factors and the strategic applications of information systems

In previous studies, some researchers empirically suggested the influence factors on the strategic applications of information systems (IS). However, they did not empirically prove the effects of the relationships among the influence factors on the strategic applications of IS. The objectives of this study are to examine these relationships and to identify the moderating effects of support factors on the relationship between the facilitators of alignment and the strategic applications level of IS. For this study, the research model explaining the relationships among influence factors and strategic applications level was developed. The results suggested that there is significant positive correlation between perceived environmental uncertainty and facilitators of alignment. The intervening effect of alignment facilitators and the moderating effects of support factors were also proved. Based on the empirical results, the roles or functions of influence factors and the managerial implications are proposed.

The relationship model between the influence factors and the strategic applications of information systems

In previous studies, some researchers empirically suggested the influence factors on the strategic applications of information systems (IS). However, they did not empirically prove the effects of the relationships among the influence factors on the strategic applications of IS. The objectives of this study are to examine these relationships and to identify the moderating effects of support factors on the relationship between the facilitators of alignment and the strategic applications level of IS. For this study, the research model explaining the relationships among influence factors and strategic applications level was developed. The results suggested that there is significant positive correlation between perceived environmental uncertainty and facilitators of alignment. The intervening effect of alignment facilitators and the moderating effects of support factors were also proved. Based on the empirical results, the roles or functions of influence factors and the managerial implications are proposed.

Alignment uncertainties of the NIST watt experiment

The effects of alignment uncertainties of the NIST watt balance with respect to local gravity and the magnetic flux density of the balance have been analyzed. Techniques for measuring all quantities relevant to misalignment have been developed. The components of the relative combined standard uncertainty of the measured value of the watt due to alignment uncertainties have been reduced to 20 nW/W, and potential improvements in the balance design have been identified which could ultimately lead to a reduction of that uncertainty to below 10 nW/W.

Optimal radiation beam profiles considering the stochastic process of patient positioning in fractionated radiation therapy

We present a solution to the problem of finding optimal beam profiles in fractionated radiation therapy when taking the uncertainty in beam patient alignment into account. The problem was previously solved for the special cases of one single dose fraction and infinitely many fractions. For few fractions (<or=5), symmetry considerations reduce the problem so that it can be handled with ordinary numerical integration techniques. For the general case, including the frequently used 20-30 fractions, a Monte Carlo integration method has been developed. As may be expected, a linear response model for radiation sensitivity, based only on the total dose delivered, is insufficient for a large number of dose fractions with sharp beam edges. Under such circumstances the full linear quadratic model for cell survival has to be incorporated. The standard technique of opening up the fields to compensate for the positioning uncertainty is only feasible when the surrounding normal tissues tolerate radiation well. The present studies indicate that the probability of achieving tumour control without inducing severe injury to normal tissue can be increased if optimal non-uniform beams are used.

The spatial accuracy of cellular dose estimates obtained from 3D reconstructed serial tissue autoradiographs

In order to better predict and understand the effects of radiopharmaceuticals used for therapy, it is necessary to determine more accurately the radiation absorbed dose to cells in tissue. Using thin-section autoradiography, the spatial distribution of sources relative to the cells can be obtained from a single section with micrometre resolution. By collecting and analysing serial sections, the 3D microscopic distribution of radionuclide relative to the cellular histology, and therefore the dose rate distribution, can be established. Here, a method of 3D reconstruction of serial sections is proposed, and measurements are reported of (i) the accuracy and reproducibility of quantitative autoradiography and (ii) the spatial precision with which tissue features from one section can be related to adjacent sections. Uncertainties in the activity determination for the specimen result from activity losses during tissue processing (4-11%), and the variation of grain count per unit activity between batches of serial sections (6-25%). Correlation of the section activity to grain count densities showed deviations ranging from 6-34%. The spatial alignment uncertainties were assessed using nylon fibre fiduciary markers incorporated into the tissue block, and compared to those for alignment based on internal tissue landmarks. The standard deviation for the variation in nylon fibre fiduciary alignment was measured to be 41 mu m cm-1, compared to 69 mu m cm-1 when internal tissue histology landmarks were used. In addition, tissue shrinkage during histological processing of up to 10% was observed. The implications of these measured activity and spatial distribution uncertainties upon the estimate of cellular dose rate distribution depends upon the range of the radiation emissions. For long-range beta particles, uncertainties in both the activity and spatial distribution translate linearly to the uncertainty in dose rate of <15%. For short-range emitters (<100 mu m), such as alpha particle sources, the magnitude of the uncertainty in serial section alignment is comparable with the particle track length. Under these circumstances, dosimetric errors are introduced in proportion to the serial section alignment inaccuracy.