Scanning laser reflection tool for alignment and period measurement of critical-angle transmission gratings

NASA Astrophysics Data System (ADS)

Song, Jungki; Heilmann, Ralf K.; Bruccoleri, Alexander R.; Hertz, Edward; Schatternburg, Mark L.

2017-08-01

We report progress toward developing a scanning laser reflection (LR) tool for alignment and period measurement of critical-angle transmission (CAT) gratings. It operates on a similar measurement principle as a tool built in 1994 which characterized period variations of grating facets for the Chandra X-ray Observatory. A specularly reflected beam and a first-order diffracted beam were used to record local period variations, surface slope variations, and grating line orientation. In this work, a normal-incidence beam was added to measure slope variations (instead of the angled-incidence beam). Since normal incidence reflection is not coupled with surface height change, it enables measurement of slope variations more accurately and, along with the angled-incidence beam, helps to reconstruct the surface figure (or tilt) map. The measurement capability of in-grating period variations was demonstrated by measuring test reflection grating (RG) samples that show only intrinsic period variations of the interference lithography process. Experimental demonstration for angular alignment of CAT gratings is also presented along with a custom-designed grating alignment assembly (GAA) testbed. All three angles were aligned to satisfy requirements for the proposed Arcus mission. The final measurement of roll misalignment agrees with the roll measurements performed at the PANTER x-ray test facility.

Alignment error envelopes for single particle analysis.

PubMed

Jensen, G J

2001-01-01

To determine the structure of a biological particle to high resolution by electron microscopy, image averaging is required to combine information from different views and to increase the signal-to-noise ratio. Starting from the number of noiseless views necessary to resolve features of a given size, four general factors are considered that increase the number of images actually needed: (1) the physics of electron scattering introduces shot noise, (2) thermal motion and particle inhomogeneity cause the scattered electrons to describe a mixture of structures, (3) the microscope system fails to usefully record all the information carried by the scattered electrons, and (4) image misalignment leads to information loss through incoherent averaging. The compound effect of factors 2-4 is approximated by the product of envelope functions. The problem of incoherent image averaging is developed in detail through derivation of five envelope functions that account for small errors in 11 "alignment" parameters describing particle location, orientation, defocus, magnification, and beam tilt. The analysis provides target error tolerances for single particle analysis to near-atomic (3.5 A) resolution, and this prospect is shown to depend critically on image quality, defocus determination, and microscope alignment. Copyright 2001 Academic Press.

Effects of alignment layer thickness on the pretilt angle of liquid crystals

NASA Astrophysics Data System (ADS)

Son, Jong-Ho; Zin, Wang-Cheol

2010-12-01

Mixture solutions of vertical- and planar-aligning polyimide precursors were coated on bare glass. The concentrations of the solutions were varied to control the thicknesses of the films. The resulting blend films were baked to induce imidization and then rubbed. The thicknesses (t) of the blend film and of the pure vertical-alignment film affected their surface energies; the pretilt angle can be fully controlled in the range 5.5°≤Θ0≤87° by adjusting t. The surface energy of pure planar-alignment layers was independent of t.

Swimming in an anisotropic fluid: How speed depends on alignment angle

NASA Astrophysics Data System (ADS)

Shi, Juan; Powers, Thomas R.

2017-12-01

Orientational order in a fluid affects the swimming behavior of flagellated microorganisms. For example, bacteria tend to swim along the director in lyotropic nematic liquid crystals. To better understand how anisotropy affects propulsion, we study the problem of a sheet supporting small-amplitude traveling waves, also known as the Taylor swimmer, in a nematic liquid crystal. For the case of weak anchoring of the nematic director at the swimmer surface and in the limit of a minimally anisotropic model, we calculate the swimming speed as a function of the angle between the swimmer and the nematic director. The effect of the anisotropy can be to increase or decrease the swimming speed, depending on the angle of alignment. We also show that elastic torque dominates the viscous torque for small-amplitude waves and that the torque tends to align the swimmer along the local director.

Dependence of field-aligned electron precipitation on season, altitude and pitch angle

NASA Technical Reports Server (NTRS)

Berko, F. W.; Hoffman, R. A.

1973-01-01

The occurrence of field-aligned 2.3 keV electron precipitation was examined by using data from more than 7500 orbits of the polar-orbiting satellite, OGO-4. The frequency of occurrence of field aligned precipitation was highest at actual pitch angles between 7 and 10 deg, being highest in the winter months, at highest satellite altitudes. Acceleration by a localized parallel electric field established by electrostatic charge layers is proposed to explain particle observations.

Comparison of Alignment Correction Angles Between Fixed-Bearing and Mobile-Bearing UKA.

PubMed

Inoue, Atsuo; Arai, Yuji; Nakagawa, Shuji; Inoue, Hiroaki; Yamazoe, Shoichi; Kubo, Toshikazu

2016-01-01

Good outcomes have been reported with both fixed-bearing and mobile-bearing unicompartmental knee arthroplasty (UKA). However, overcorrected alignment could induce the progression of arthritis on the non-arthroplasty side. Changes of limb alignment after UKA with both types of bearings (fixed bearing: 24 knees, mobile bearing: 28 knees) were investigated. The mean difference between the preoperative standing femoral-tibial angle (FTA) and postoperative standing FTA was significantly larger in mobile bearing UKA group. In fixed-bearing UKA, there must be some laxity in MCL tension so that a 2-mm tension gauge can be inserted. In mobile-bearing UKA, appropriate MCL tension is needed to prevent bearing dislocation. This difference in MCL tension may have caused the difference in the correction angle between the groups. Copyright © 2016 Elsevier Inc. All rights reserved.

An error analysis perspective for patient alignment systems.

PubMed

Figl, Michael; Kaar, Marcus; Hoffman, Rainer; Kratochwil, Alfred; Hummel, Johann

2013-09-01

This paper analyses the effects of error sources which can be found in patient alignment systems. As an example, an ultrasound (US) repositioning system and its transformation chain are assessed. The findings of this concept can also be applied to any navigation system. In a first step, all error sources were identified and where applicable, corresponding target registration errors were computed. By applying error propagation calculations on these commonly used registration/calibration and tracking errors, we were able to analyse the components of the overall error. Furthermore, we defined a special situation where the whole registration chain reduces to the error caused by the tracking system. Additionally, we used a phantom to evaluate the errors arising from the image-to-image registration procedure, depending on the image metric used. We have also discussed how this analysis can be applied to other positioning systems such as Cone Beam CT-based systems or Brainlab's ExacTrac. The estimates found by our error propagation analysis are in good agreement with the numbers found in the phantom study but significantly smaller than results from patient evaluations. We probably underestimated human influences such as the US scan head positioning by the operator and tissue deformation. Rotational errors of the tracking system can multiply these errors, depending on the relative position of tracker and probe. We were able to analyse the components of the overall error of a typical patient positioning system. We consider this to be a contribution to the optimization of the positioning accuracy for computer guidance systems.

Error tracking control for underactuated overhead cranes against arbitrary initial payload swing angles

NASA Astrophysics Data System (ADS)

Zhang, Menghua; Ma, Xin; Rong, Xuewen; Tian, Xincheng; Li, Yibin

2017-02-01

This paper exploits an error tracking control method for overhead crane systems for which the error trajectories for the trolley and the payload swing can be pre-specified. The proposed method does not require that the initial payload swing angle remains zero, whereas this requirement is usually assumed in conventional methods. The significant feature of the proposed method is its superior control performance as well as its strong robustness over different or uncertain rope lengths, payload masses, desired positions, initial payload swing angles, and external disturbances. Owing to the same attenuation behavior, the desired error trajectory for the trolley for each traveling distance is not needed to be reset, which is easy to implement in practical applications. By converting the error tracking overhead crane dynamics to the objective system, we obtain the error tracking control law for arbitrary initial payload swing angles. Lyapunov techniques and LaSalle's invariance theorem are utilized to prove the convergence and stability of the closed-loop system. Simulation and experimental results are illustrated to validate the superior performance of the proposed error tracking control method.

The Lumbar Pelvic Angle, the Lumbar Component of the T1 Pelvic Angle, Correlates With HRQOL, PI-LL Mismatch, and it Predicts Global Alignment.

PubMed

Protopsaltis, Themistocles S; Lafage, Renaud; Smith, Justin S; Passias, Peter G; Shaffrey, Christopher I; Kim, Han Jo; Mundis, Gregory M; Ames, Christopher P; Burton, Douglas C; Bess, Shay; Klineberg, Eric; Hart, Robert A; Schwab, Frank J; Lafage, Virginie

2018-05-15

Prospective multicenter analysis of adult spinal deformity (ASD) patients. The aim of this study was to introduce the lumbar pelvic angle (LPA), a novel parameter of spinopelvic alignment. The T1 pelvic angle (TPA), a measure of global spinopelvic alignment, correlates with health-related quality of life (HRQOL), but it may not be measureable on all intraoperative x-rays. In patients with previous interbody fusion at L5-S1, the plane of the S1 endplate can be blurred, creating error in pelvic incidence and lumbar lordosis (PI-LL) measure. The LPA is more readily measured on intraoperative imaging than the TPA. ASD patients were included with either coronal Cobb angle >20°, sagittal vertical axis (SVA) >5 cm, thoracic kyphosis >60°, or pelvic tilt (PT) >25°. Measures of disability included Oswestry Disability Index (ODI), Scoliosis Research Society (SRS), and Short Form (SF)-36. Baseline and 2-year follow-up radiographic and HRQOL outcomes were evaluated. Linear regressions compared LPA with radiographic parameters and HRQOL. A total of 852 ASD patients (407 operative) were enrolled (mean age 53.7). Baseline LPA correlated with PI-LL (r = 0.79), PT (r = 0.78), TPA (r = 0.82), and SVA (r = 0.61) (all P < 0.001). PI-LL, LPA, and TPA correlated with ODI (r = 0.42/0.29/0.45), SF-36 physical component score (-0.43/-0.28/-0.45) SRS (-0.354/-0.23/-0.37) with all P < 0.001. At 2 years' follow-up, LPA correlated with PI-LL (r = 0.77), PT (r = 0.78), TPA (r = 0.83), and SVA (r = 0.57) (all P < 0.001). Categorizing patients by increasing LPA (<7°; 7°-15°; >15°) revealed progressive increases in all HRQOL, PI-LL (-3.2°/12.7°/32.4°), and TPA (9.7°/20.1°/34.6°) with all P < 0.001. Moderate disability (ODI = 40) corresponded to LPA 10.1°, PI-LL 12.6°, and TPA 20.6°. Mild disability (ODI = 20) corresponded to LPA 7.2°, PI-LL 4.2°, and TPA 14.7°. LPA correlates with TPA, PI-LL, and HRQOL in ASD patients

Initial Alignment for SINS Based on Pseudo-Earth Frame in Polar Regions.

PubMed

Gao, Yanbin; Liu, Meng; Li, Guangchun; Guang, Xingxing

2017-06-16

An accurate initial alignment must be required for inertial navigation system (INS). The performance of initial alignment directly affects the following navigation accuracy. However, the rapid convergence of meridians and the small horizontalcomponent of rotation of Earth make the traditional alignment methods ineffective in polar regions. In this paper, from the perspective of global inertial navigation, a novel alignment algorithm based on pseudo-Earth frame and backward process is proposed to implement the initial alignment in polar regions. Considering that an accurate coarse alignment of azimuth is difficult to obtain in polar regions, the dynamic error modeling with large azimuth misalignment angle is designed. At the end of alignment phase, the strapdown attitude matrix relative to local geographic frame is obtained without influence of position errors and cumbersome computation. As a result, it would be more convenient to access the following polar navigation system. Then, it is also expected to unify the polar alignment algorithm as much as possible, thereby further unifying the form of external reference information. Finally, semi-physical static simulation and in-motion tests with large azimuth misalignment angle assisted by unscented Kalman filter (UKF) validate the effectiveness of the proposed method.

Evaluation of alignment error due to a speed artifact in stereotactic ultrasound image guidance.

PubMed

Salter, Bill J; Wang, Brian; Szegedi, Martin W; Rassiah-Szegedi, Prema; Shrieve, Dennis C; Cheng, Roger; Fuss, Martin

2008-12-07

Ultrasound (US) image guidance systems used in radiotherapy are typically calibrated for soft tissue applications, thus introducing errors in depth-from-transducer representation when used in media with a different speed of sound propagation (e.g. fat). This error is commonly referred to as the speed artifact. In this study we utilized a standard US phantom to demonstrate the existence of the speed artifact when using a commercial US image guidance system to image through layers of simulated body fat, and we compared the results with calculated/predicted values. A general purpose US phantom (speed of sound (SOS) = 1540 m s(-1)) was imaged on a multi-slice CT scanner at a 0.625 mm slice thickness and 0.5 mm x 0.5 mm axial pixel size. Target-simulating wires inside the phantom were contoured and later transferred to the US guidance system. Layers of various thickness (1-8 cm) of commercially manufactured fat-simulating material (SOS = 1435 m s(-1)) were placed on top of the phantom to study the depth-related alignment error. In order to demonstrate that the speed artifact is not caused by adding additional layers on top of the phantom, we repeated these measurements in an identical setup using commercially manufactured tissue-simulating material (SOS = 1540 m s(-1)) for the top layers. For the fat-simulating material used in this study, we observed the magnitude of the depth-related alignment errors resulting from the speed artifact to be 0.7 mm cm(-1) of fat imaged through. The measured alignment errors caused by the speed artifact agreed with the calculated values within one standard deviation for all of the different thicknesses of fat-simulating material studied here. We demonstrated the depth-related alignment error due to the speed artifact when using US image guidance for radiation treatment alignment and note that the presence of fat causes the target to be aliased to a depth greater than it actually is. For typical US guidance systems in use today, this will

Do CAS measurements correlate with EOS 3D alignment measurements in primary TKA?

PubMed

Meijer, Marrigje F; Boerboom, Alexander L; Bulstra, Sjoerd K; Reininga, Inge H F; Stevens, Martin

2017-09-01

Objective of this study was to compare intraoperative computer-assisted surgery (CAS) alignment measurements during total knee arthroplasty (TKA) with pre- and postoperative coronal alignment measurements using EOS 3D reconstructions. In a prospective study, 56 TKAs using imageless CAS were performed and coronal alignment measurements were recorded twice: before bone cuts were made and after implantation of the prosthesis. Pre- and postoperative coronal alignment measurements were performed using EOS 3D reconstructions. Thanks to the EOS radiostereography system, measurement errors due to malpositioning and deformity during acquisition are eliminated. CAS measurements were compared with EOS 3D reconstructions. Varus/valgus angle (VV), mechanical lateral distal femoral angle (mLDFA) and mechanical medial proximal tibial angle (mMPTA) were measured. Significantly different VV angles were measured pre- and postoperatively with CAS compared to EOS. For preoperative measurements, mLDFA did not differ significantly, but a significantly larger mMPTA in valgus was measured with CAS. Results of this study indicate that differences in alignment measurements between CAS measurements and pre- and postoperative EOS 3D are due mainly to the difference between weight-bearing and non-weight-bearing position and potential errors in validity and reliability of the CAS system. EOS 3D measurements overestimate VV angle in lower limbs with substantial mechanical axis deviation. For lower limbs with minor mechanical axis deviation as well as for mMPTA measurements, CAS measures more valgus than EOS. Eventually the results of this study are of clinical relevance, since it raises concerns regarding the validity and reliability of CAS systems in TKA. IIb.

A line-source method for aligning on-board and other pinhole SPECT systems

PubMed Central

Yan, Susu; Bowsher, James; Yin, Fang-Fang

2013-01-01

Purpose: In order to achieve functional and molecular imaging as patients are in position for radiation therapy, a robotic multipinhole SPECT system is being developed. Alignment of the SPECT system—to the linear accelerator (LINAC) coordinate frame and to the coordinate frames of other on-board imaging systems such as cone-beam CT (CBCT)—is essential for target localization and image reconstruction. An alignment method that utilizes line sources and one pinhole projection is proposed and investigated to achieve this goal. Potentially, this method could also be applied to the calibration of the other pinhole SPECT systems. Methods: An alignment model consisting of multiple alignment parameters was developed which maps line sources in three-dimensional (3D) space to their two-dimensional (2D) projections on the SPECT detector. In a computer-simulation study, 3D coordinates of line-sources were defined in a reference room coordinate frame, such as the LINAC coordinate frame. Corresponding 2D line-source projections were generated by computer simulation that included SPECT blurring and noise effects. The Radon transform was utilized to detect angles (α) and offsets (ρ) of the line-source projections. Alignment parameters were then estimated by a nonlinear least squares method, based on the α and ρ values and the alignment model. Alignment performance was evaluated as a function of number of line sources, Radon transform accuracy, finite line-source width, intrinsic camera resolution, Poisson noise, and acquisition geometry. Experimental evaluations were performed using a physical line-source phantom and a pinhole-collimated gamma camera attached to a robot. Results: In computer-simulation studies, when there was no error in determining angles (α) and offsets (ρ) of the measured projections, six alignment parameters (three translational and three rotational) were estimated perfectly using three line sources. When angles (α) and offsets (ρ) were provided by

A line-source method for aligning on-board and other pinhole SPECT systems.

PubMed

Yan, Susu; Bowsher, James; Yin, Fang-Fang

2013-12-01

In order to achieve functional and molecular imaging as patients are in position for radiation therapy, a robotic multipinhole SPECT system is being developed. Alignment of the SPECT system-to the linear accelerator (LINAC) coordinate frame and to the coordinate frames of other on-board imaging systems such as cone-beam CT (CBCT)-is essential for target localization and image reconstruction. An alignment method that utilizes line sources and one pinhole projection is proposed and investigated to achieve this goal. Potentially, this method could also be applied to the calibration of the other pinhole SPECT systems. An alignment model consisting of multiple alignment parameters was developed which maps line sources in three-dimensional (3D) space to their two-dimensional (2D) projections on the SPECT detector. In a computer-simulation study, 3D coordinates of line-sources were defined in a reference room coordinate frame, such as the LINAC coordinate frame. Corresponding 2D line-source projections were generated by computer simulation that included SPECT blurring and noise effects. The Radon transform was utilized to detect angles (α) and offsets (ρ) of the line-source projections. Alignment parameters were then estimated by a nonlinear least squares method, based on the α and ρ values and the alignment model. Alignment performance was evaluated as a function of number of line sources, Radon transform accuracy, finite line-source width, intrinsic camera resolution, Poisson noise, and acquisition geometry. Experimental evaluations were performed using a physical line-source phantom and a pinhole-collimated gamma camera attached to a robot. In computer-simulation studies, when there was no error in determining angles (α) and offsets (ρ) of the measured projections, six alignment parameters (three translational and three rotational) were estimated perfectly using three line sources. When angles (α) and offsets (ρ) were provided by the Radon transform, estimation

Helicity-dependent single-walled carbon nanotube alignment on graphite for helical angle and handedness recognition

PubMed Central

Chen, Yabin; Shen, Ziyong; Xu, Ziwei; Hu, Yue; Xu, Haitao; Wang, Sheng; Guo, Xiaolei; Zhang, Yanfeng; Peng, Lianmao; Ding, Feng; Liu, Zhongfan; Zhang, Jin

2013-01-01

Aligned single-walled carbon nanotube arrays provide a great potential for the carbon-based nanodevices and circuit integration. Aligning single-walled carbon nanotubes with selected helicities and identifying their helical structures remain a daunting issue. The widely used gas-directed and surface-directed growth modes generally suffer the drawbacks of mixed and unknown helicities of the aligned single-walled carbon nanotubes. Here we develop a rational approach to anchor the single-walled carbon nanotubes on graphite surfaces, on which the orientation of each single-walled carbon nanotube sensitively depends on its helical angle and handedness. This approach can be exploited to conveniently measure both the helical angle and handedness of the single-walled carbon nanotube simultaneously at a low cost. In addition, by combining with the resonant Raman spectroscopy, the (n,m) index of anchored single-walled carbon nanotube can be further determined from the (d,θ) plot, and the assigned (n,m) values by this approach are validated by both the electronic transition energy Eii measurement and nanodevice application. PMID:23892334

Image defects from surface and alignment errors in grazing incidence telescopes

NASA Technical Reports Server (NTRS)

Saha, Timo T.

1989-01-01

The rigid body motions and low frequency surface errors of grazing incidence Wolter telescopes are studied. The analysis is based on surface error descriptors proposed by Paul Glenn. In his analysis, the alignment and surface errors are expressed in terms of Legendre-Fourier polynomials. Individual terms in the expression correspond to rigid body motions (decenter and tilt) and low spatial frequency surface errors of mirrors. With the help of the Legendre-Fourier polynomials and the geometry of grazing incidence telescopes, exact and approximated first order equations are derived in this paper for the components of the ray intercepts at the image plane. These equations are then used to calculate the sensitivities of Wolter type I and II telescopes for the rigid body motions and surface deformations. The rms spot diameters calculated from this theory and OSAC ray tracing code agree very well. This theory also provides a tool to predict how rigid body motions and surface errors of the mirrors compensate each other.

Pilot performance and workload using simulated GPS track angle error displays

DOT National Transportation Integrated Search

1995-01-01

The effect on simulated GPS instrument approach performance and workload resulting from the addition of Track Angle Error (TAE) information to cockpit RNAV receiver displays in explicit analog form was studied experimentally (S display formats, 6 pil...

An automatic alignment system for measuring optical path of transmissometer based on light beam scanning

NASA Astrophysics Data System (ADS)

Zhou, Shudao; Ma, Zhongliang; Wang, Min; Peng, Shuling

2018-05-01

This paper proposes a novel alignment system based on the measurement of optical path using a light beam scanning mode in a transmissometer. The system controls both the probe beam and the receiving field of view while scanning in two vertical directions. The system then calculates the azimuth angle of the transmitter and the receiver to determine the precise alignment of the optical path. Experiments show that this method can determine the alignment angles in less than 10 min with errors smaller than 66 μrad in the azimuth. This system also features high collimation precision, process automation and simple installation.

Effectiveness of Variable-Gain Kalman Filter Based on Angle Error Calculated from Acceleration Signals in Lower Limb Angle Measurement with Inertial Sensors

PubMed Central

Watanabe, Takashi

2013-01-01

The wearable sensor system developed by our group, which measured lower limb angles using Kalman-filtering-based method, was suggested to be useful in evaluation of gait function for rehabilitation support. However, it was expected to reduce variations of measurement errors. In this paper, a variable-Kalman-gain method based on angle error that was calculated from acceleration signals was proposed to improve measurement accuracy. The proposed method was tested comparing to fixed-gain Kalman filter and a variable-Kalman-gain method that was based on acceleration magnitude used in previous studies. First, in angle measurement in treadmill walking, the proposed method measured lower limb angles with the highest measurement accuracy and improved significantly foot inclination angle measurement, while it improved slightly shank and thigh inclination angles. The variable-gain method based on acceleration magnitude was not effective for our Kalman filter system. Then, in angle measurement of a rigid body model, it was shown that the proposed method had measurement accuracy similar to or higher than results seen in other studies that used markers of camera-based motion measurement system fixing on a rigid plate together with a sensor or on the sensor directly. The proposed method was found to be effective in angle measurement with inertial sensors. PMID:24282442

A line-source method for aligning on-board and other pinhole SPECT systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Susu; Bowsher, James; Yin, Fang-Fang

2013-12-15

Purpose: In order to achieve functional and molecular imaging as patients are in position for radiation therapy, a robotic multipinhole SPECT system is being developed. Alignment of the SPECT system—to the linear accelerator (LINAC) coordinate frame and to the coordinate frames of other on-board imaging systems such as cone-beam CT (CBCT)—is essential for target localization and image reconstruction. An alignment method that utilizes line sources and one pinhole projection is proposed and investigated to achieve this goal. Potentially, this method could also be applied to the calibration of the other pinhole SPECT systems.Methods: An alignment model consisting of multiple alignmentmore » parameters was developed which maps line sources in three-dimensional (3D) space to their two-dimensional (2D) projections on the SPECT detector. In a computer-simulation study, 3D coordinates of line-sources were defined in a reference room coordinate frame, such as the LINAC coordinate frame. Corresponding 2D line-source projections were generated by computer simulation that included SPECT blurring and noise effects. The Radon transform was utilized to detect angles (α) and offsets (ρ) of the line-source projections. Alignment parameters were then estimated by a nonlinear least squares method, based on the α and ρ values and the alignment model. Alignment performance was evaluated as a function of number of line sources, Radon transform accuracy, finite line-source width, intrinsic camera resolution, Poisson noise, and acquisition geometry. Experimental evaluations were performed using a physical line-source phantom and a pinhole-collimated gamma camera attached to a robot.Results: In computer-simulation studies, when there was no error in determining angles (α) and offsets (ρ) of the measured projections, six alignment parameters (three translational and three rotational) were estimated perfectly using three line sources. When angles (α) and offsets (ρ) were

Application of advanced shearing techniques to the calibration of autocollimators with small angle generators and investigation of error sources.

PubMed

Yandayan, T; Geckeler, R D; Aksulu, M; Akgoz, S A; Ozgur, B

2016-05-01

The application of advanced error-separating shearing techniques to the precise calibration of autocollimators with Small Angle Generators (SAGs) was carried out for the first time. The experimental realization was achieved using the High Precision Small Angle Generator (HPSAG) of TUBITAK UME under classical dimensional metrology laboratory environmental conditions. The standard uncertainty value of 5 mas (24.2 nrad) reached by classical calibration method was improved to the level of 1.38 mas (6.7 nrad). Shearing techniques, which offer a unique opportunity to separate the errors of devices without recourse to any external standard, were first adapted by Physikalisch-Technische Bundesanstalt (PTB) to the calibration of autocollimators with angle encoders. It has been demonstrated experimentally in a clean room environment using the primary angle standard of PTB (WMT 220). The application of the technique to a different type of angle measurement system extends the range of the shearing technique further and reveals other advantages. For example, the angular scales of the SAGs are based on linear measurement systems (e.g., capacitive nanosensors for the HPSAG). Therefore, SAGs show different systematic errors when compared to angle encoders. In addition to the error-separation of HPSAG and the autocollimator, detailed investigations on error sources were carried out. Apart from determination of the systematic errors of the capacitive sensor used in the HPSAG, it was also demonstrated that the shearing method enables the unique opportunity to characterize other error sources such as errors due to temperature drift in long term measurements. This proves that the shearing technique is a very powerful method for investigating angle measuring systems, for their improvement, and for specifying precautions to be taken during the measurements.

Heading error in an alignment-based magnetometer

NASA Astrophysics Data System (ADS)

Hovde, Chris; Patton, Brian; Versolato, Oscar; Corsini, Eric; Rochester, Simon; Budker, Dmitry

2011-06-01

A prototype magnetometer for anti-submarine warfare applications is being developed based on nonlinear magneto-optical rotation (NMOR) in atomic vapors. NMOR is an atomic spectroscopy technique that exploits coherences among magnetic sublevels of atoms such as cesium or rubidium to measure magnetic fields with high precision. NMOR uses stroboscopic optical pumping via frequency or amplitude modulation of a linearly polarized laser beam to create the alignment. An anti-relaxation coating on the walls of the atomic vapor cell can result in a long lifetime of 1 s or more for the coherence and enables precise measurement of the precession frequency. With proper feedback, the magnetometer can self-oscillate, resulting in accurate tracking and fast time response. The NMOR magnetic resonance spectrum of 87Rb has been measured as a function of heading in Earth's field. Optical pumping of alignment within the F=2 hyperfine manifold generates three resonances separated by the nonlinear Zeeman splitting. The spectra show a high degree of symmetry, consisting of a central peak and two side peaks of nearly equal intensity. As the heading changes, the ratio of the central peak to the average of the two side peaks changes. The amplitudes of the side peaks remain nearly equal. An analysis of the forced oscillation spectra indicates that, away from dead zones, heading error in self-oscillating mode should be less than 1 nT. A broader background is also observed in the spectra. While this background can be removed when fitting resonance spectra, understanding it will be important to achieving the small heading error in self-oscillating mode that is implied by the spectral measurements. Progress in miniaturizing the magnetometer is also reported. The new design is less than 10 cm across and includes fiber coupling of light to and from the magnetometer head. Initial tests show that the prototype has achieved a narrow spectral width and a strong polarization rotation signal.

Modeling of Geometric Error in Linear Guide Way to Improved the vertical three-axis CNC Milling machine’s accuracy

NASA Astrophysics Data System (ADS)

Kwintarini, Widiyanti; Wibowo, Agung; Arthaya, Bagus M.; Yuwana Martawirya, Yatna

2018-03-01

The purpose of this study was to improve the accuracy of three-axis CNC Milling Vertical engines with a general approach by using mathematical modeling methods of machine tool geometric errors. The inaccuracy of CNC machines can be caused by geometric errors that are an important factor during the manufacturing process and during the assembly phase, and are factors for being able to build machines with high-accuracy. To improve the accuracy of the three-axis vertical milling machine, by knowing geometric errors and identifying the error position parameters in the machine tool by arranging the mathematical modeling. The geometric error in the machine tool consists of twenty-one error parameters consisting of nine linear error parameters, nine angle error parameters and three perpendicular error parameters. The mathematical modeling approach of geometric error with the calculated alignment error and angle error in the supporting components of the machine motion is linear guide way and linear motion. The purpose of using this mathematical modeling approach is the identification of geometric errors that can be helpful as reference during the design, assembly and maintenance stages to improve the accuracy of CNC machines. Mathematically modeling geometric errors in CNC machine tools can illustrate the relationship between alignment error, position and angle on a linear guide way of three-axis vertical milling machines.

Predicting areas of sustainable error growth in quasigeostrophic flows using perturbation alignment properties

NASA Astrophysics Data System (ADS)

Rivière, G.; Hua, B. L.

2004-10-01

A new perturbation initialization method is used to quantify error growth due to inaccuracies of the forecast model initial conditions in a quasigeostrophic box ocean model describing a wind-driven double gyre circulation. This method is based on recent analytical results on Lagrangian alignment dynamics of the perturbation velocity vector in quasigeostrophic flows. More specifically, it consists in initializing a unique perturbation from the sole knowledge of the control flow properties at the initial time of the forecast and whose velocity vector orientation satisfies a Lagrangian equilibrium criterion. This Alignment-based Initialization method is hereafter denoted as the AI method.In terms of spatial distribution of the errors, we have compared favorably the AI error forecast with the mean error obtained with a Monte-Carlo ensemble prediction. It is shown that the AI forecast is on average as efficient as the error forecast initialized with the leading singular vector for the palenstrophy norm, and significantly more efficient than that for total energy and enstrophy norms. Furthermore, a more precise examination shows that the AI forecast is systematically relevant for all control flows whereas the palenstrophy singular vector forecast leads sometimes to very good scores and sometimes to very bad ones.A principal component analysis at the final time of the forecast shows that the AI mode spatial structure is comparable to that of the first eigenvector of the error covariance matrix for a "bred mode" ensemble. Furthermore, the kinetic energy of the AI mode grows at the same constant rate as that of the "bred modes" from the initial time to the final time of the forecast and is therefore characterized by a sustained phase of error growth. In this sense, the AI mode based on Lagrangian dynamics of the perturbation velocity orientation provides a rationale of the "bred mode" behavior.

Error analysis of speed of sound reconstruction in ultrasound limited angle transmission tomography.

PubMed

Jintamethasawat, Rungroj; Lee, Won-Mean; Carson, Paul L; Hooi, Fong Ming; Fowlkes, J Brian; Goodsitt, Mitchell M; Sampson, Richard; Wenisch, Thomas F; Wei, Siyuan; Zhou, Jian; Chakrabarti, Chaitali; Kripfgans, Oliver D

2018-04-07

We have investigated limited angle transmission tomography to estimate speed of sound (SOS) distributions for breast cancer detection. That requires both accurate delineations of major tissues, in this case by segmentation of prior B-mode images, and calibration of the relative positions of the opposed transducers. Experimental sensitivity evaluation of the reconstructions with respect to segmentation and calibration errors is difficult with our current system. Therefore, parametric studies of SOS errors in our bent-ray reconstructions were simulated. They included mis-segmentation of an object of interest or a nearby object, and miscalibration of relative transducer positions in 3D. Close correspondence of reconstruction accuracy was verified in the simplest case, a cylindrical object in homogeneous background with induced segmentation and calibration inaccuracies. Simulated mis-segmentation in object size and lateral location produced maximum SOS errors of 6.3% within 10 mm diameter change and 9.1% within 5 mm shift, respectively. Modest errors in assumed transducer separation produced the maximum SOS error from miscalibrations (57.3% within 5 mm shift), still, correction of this type of error can easily be achieved in the clinic. This study should aid in designing adequate transducer mounts and calibration procedures, and in specification of B-mode image quality and segmentation algorithms for limited angle transmission tomography relying on ray tracing algorithms. Copyright © 2018 Elsevier B.V. All rights reserved.

Aberration caused by the errors of alignment and adjustment in reflecting telescope

NASA Astrophysics Data System (ADS)

Tan, Hui-Song

The 2-mirror Cassegrain geometry has firmly become a standard tool for modern astronomical research. The alignment and adjustment of aplanatic (RC) Cassegrain telescope is therefore by far the most important aspect. The errors that arise in telescope through maladjustment are discussed and the aberrations are calculated for the 2.4 m telescope which will be mounted at Gaomeigu.

Wave-optical assessment of alignment tolerances in nano-focusing with ellipsoidal mirror

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yumoto, Hirokatsu, E-mail: yumoto@spring8.or.jp; Koyama, Takahisa; Matsuyama, Satoshi

2016-01-28

High-precision ellipsoidal mirrors, which can efficiently focus X-rays to the nanometer dimension with a mirror, have not been realized because of the difficulties in the fabrication process. The purpose of our study was to develop nano-focusing ellipsoidal mirrors in the hard X-ray region. We developed a wave-optical focusing simulator for investigating alignment tolerances in nano-focusing with a designed ellipsoidal mirror, which produce a diffraction-limited focus size of 30 × 35 nm{sup 2} in full width at half maximum at an X-ray energy of 7 keV. The simulator can calculate focusing intensity distributions around the focal point under conditions of misalignment. Themore » wave-optical simulator enabled the calculation of interference intensity distributions, which cannot be predicted by the conventional ray-trace method. The alignment conditions with a focal length error of ≲ ±10 µm, incident angle error of ≲ ±0.5 µrad, and in-plane rotation angle error of ≲ ±0.25 µrad must be satisfied for nano-focusing.« less

Alignment error of mirror modules of advanced telescope for high-energy astrophysics due to wavefront aberrations

NASA Astrophysics Data System (ADS)

Zocchi, Fabio E.

2017-10-01

One of the approaches that is being tested for the integration of the mirror modules of the advanced telescope for high-energy astrophysics x-ray mission of the European Space Agency consists in aligning each module on an optical bench operated at an ultraviolet wavelength. The mirror module is illuminated by a plane wave and, in order to overcome diffraction effects, the centroid of the image produced by the module is used as a reference to assess the accuracy of the optical alignment of the mirror module itself. Among other sources of uncertainty, the wave-front error of the plane wave also introduces an error in the position of the centroid, thus affecting the quality of the mirror module alignment. The power spectral density of the position of the point spread function centroid is here derived from the power spectral density of the wave-front error of the plane wave in the framework of the scalar theory of Fourier diffraction. This allows the defining of a specification on the collimator quality used for generating the plane wave starting from the contribution to the error budget allocated for the uncertainty of the centroid position. The theory generally applies whenever Fourier diffraction is a valid approximation, in which case the obtained result is identical to that derived by geometrical optics considerations.

Empirical Evaluation of Visual Fatigue from Display Alignment Errors Using Cerebral Hemodynamic Responses

PubMed Central

Wiyor, Hanniebey D.; Ntuen, Celestine A.

2013-01-01

The purpose of this study was to investigate the effect of stereoscopic display alignment errors on visual fatigue and prefrontal cortical tissue hemodynamic responses. We collected hemodynamic data and perceptual ratings of visual fatigue while participants performed visual display tasks on 8 ft × 6 ft NEC LT silver screen with NEC LT 245 DLP projectors. There was statistical significant difference between subjective measures of visual fatigue before air traffic control task (BATC) and after air traffic control task (ATC 3), (P < 0.05). Statistical significance was observed between left dorsolateral prefrontal cortex oxygenated hemoglobin (l DLPFC-HbO2), left dorsolateral prefrontal cortex deoxygenated hemoglobin (l DLPFC-Hbb), and right dorsolateral prefrontal cortex deoxygenated hemoglobin (r DLPFC-Hbb) on stereoscopic alignment errors (P < 0.05). Thus, cortical tissue oxygenation requirement in the left hemisphere indicates that the effect of visual fatigue is more pronounced in the left dorsolateral prefrontal cortex. PMID:27006917

Minimizing pulling geometry errors in atomic force microscope single molecule force spectroscopy.

PubMed

Rivera, Monica; Lee, Whasil; Ke, Changhong; Marszalek, Piotr E; Cole, Daniel G; Clark, Robert L

2008-10-01

In atomic force microscopy-based single molecule force spectroscopy (AFM-SMFS), it is assumed that the pulling angle is negligible and that the force applied to the molecule is equivalent to the force measured by the instrument. Recent studies, however, have indicated that the pulling geometry errors can drastically alter the measured force-extension relationship of molecules. Here we describe a software-based alignment method that repositions the cantilever such that it is located directly above the molecule's substrate attachment site. By aligning the applied force with the measurement axis, the molecule is no longer undergoing combined loading, and the full force can be measured by the cantilever. Simulations and experimental results verify the ability of the alignment program to minimize pulling geometry errors in AFM-SMFS studies.

Mineral crystal alignment in mineralized fracture callus determined by 3D small-angle X-ray scattering

NASA Astrophysics Data System (ADS)

Liu, Yifei; Manjubala, Inderchand; Roschger, Paul; Schell, Hanna; Duda, Georg N.; Fratzl, Peter

2010-10-01

Callus tissue formed during bone fracture healing is a mixture of different tissue types as revealed by histological analysis. But the structural characteristics of mineral crystals within the healing callus are not well known. Since two-dimensional (2D) scanning small-angle X-ray scattering (sSAXS) patterns showed that the size and orientation of callus crystals vary both spatially and temporally [1] and 2D electron microscopic analysis implies an anisotropic property of the callus morphology, the mineral crystals within the callus are also expected to vary in size and orientation in 3D. Three-dimensional small-angle X-ray scattering (3D SAXS), which combines 2D SAXS patterns collected at different angles of sample tilting, has been previously applied to investigate bone minerals in horse radius [2] and oim/oim mouse femur/tibia [3]. We implement a similar 3D SAXS method but with a different way of data analysis to gather information on the mineral alignment in fracture callus. With the proposed accurate yet fast assessment of 3D SAXS information, it was shown that the plate shaped mineral particles in the healing callus were aligned in groups with their predominant orientations occurring as a fiber texture.

Flight Test Results of an Angle of Attack and Angle of Sideslip Calibration Method Using Output-Error Optimization

NASA Technical Reports Server (NTRS)

Siu, Marie-Michele; Martos, Borja; Foster, John V.

2013-01-01

As part of a joint partnership between the NASA Aviation Safety Program (AvSP) and the University of Tennessee Space Institute (UTSI), research on advanced air data calibration methods has been in progress. This research was initiated to expand a novel pitot-static calibration method that was developed to allow rapid in-flight calibration for the NASA Airborne Subscale Transport Aircraft Research (AirSTAR) facility. This approach uses Global Positioning System (GPS) technology coupled with modern system identification methods that rapidly computes optimal pressure error models over a range of airspeed with defined confidence bounds. Subscale flight tests demonstrated small 2-s error bounds with significant reduction in test time compared to other methods. Recent UTSI full scale flight tests have shown airspeed calibrations with the same accuracy or better as the Federal Aviation Administration (FAA) accepted GPS 'four-leg' method in a smaller test area and in less time. The current research was motivated by the desire to extend this method for inflight calibration of angle of attack (AOA) and angle of sideslip (AOS) flow vanes. An instrumented Piper Saratoga research aircraft from the UTSI was used to collect the flight test data and evaluate flight test maneuvers. Results showed that the output-error approach produces good results for flow vane calibration. In addition, maneuvers for pitot-static and flow vane calibration can be integrated to enable simultaneous and efficient testing of each system.

Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sedlak, Steffen M.; Bruetzel, Linda K.; Lipfert, Jan

A new model is proposed for the measurement errors incurred in typical small-angle X-ray scattering (SAXS) experiments, which takes into account the setup geometry and physics of the measurement process. The model accurately captures the experimentally determined errors from a large range of synchrotron and in-house anode-based measurements. Its most general formulation gives for the variance of the buffer-subtracted SAXS intensity σ 2(q) = [I(q) + const.]/(kq), whereI(q) is the scattering intensity as a function of the momentum transferq;kand const. are fitting parameters that are characteristic of the experimental setup. The model gives a concrete procedure for calculating realistic measurementmore » errors for simulated SAXS profiles. In addition, the results provide guidelines for optimizing SAXS measurements, which are in line with established procedures for SAXS experiments, and enable a quantitative evaluation of measurement errors.« less

OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

PubMed

Verzotto, Davide; M Teo, Audrey S; Hillmer, Axel M; Nagarajan, Niranjan

2016-01-01

Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences. We introduce a novel seed-and-extend glocal (short for global-local) alignment method, OPTIMA (and a sliding-window extension for overlap alignment, OPTIMA-Overlap), which is the first to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic with respect to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests. We show that OPTIMA and OPTIMA-Overlap outperform other state-of-the-art approaches (1.6-2 times more sensitive) and are more efficient (170-200 %) and precise in their alignments (nearly 99 % precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust, provide improved sensitivity and guarantee high precision.

The deficit of joint position sense in the chronic unstable ankle as measured by inversion angle replication error.

PubMed

Nakasa, Tomoyuki; Fukuhara, Kohei; Adachi, Nobuo; Ochi, Mitsuo

2008-05-01

Functional instability is defined as a repeated ankle inversion sprain and a giving way sensation. Previous studies have described the damage of sensori-motor control in ankle sprain as being a possible cause of functional instability. The aim of this study was to evaluate the inversion angle replication errors in patients with functional instability after ankle sprain. The difference between the index angle and replication angle was measured in 12 subjects with functional instability, with the aim of evaluating the replication error. As a control group, the replication errors of 17 healthy volunteers were investigated. The side-to-side differences of the replication errors were compared between both the groups, and the relationship between the side-to-side differences of the replication errors and the mechanical instability were statistically analyzed in the unstable group. The side-to-side difference of the replication errors was 1.0 +/- 0.7 degrees in the unstable group and 0.2 +/- 0.7 degrees in the control group. There was a statistically significant difference between both the groups. The side-to-side differences of the replication errors in the unstable group did not statistically correlate to the anterior talar translation and talar tilt. The patients with functional instability had the deficit of joint position sense in comparison with healthy volunteers. The replication error did not correlate to the mechanical instability. The patients with functional instability should be treated appropriately in spite of having less mechanical instability.

Flow tilt angle measurements using lidar anemometry

NASA Astrophysics Data System (ADS)

Dellwik, Ebba; Mann, Jakob

2010-05-01

A new way of estimating near-surface mean flow tilt angles from ground based Doppler lidar measurements is presented. The results are compared with traditional mast based in-situ sonic anemometry. The tilt angle assessed with the lidar is based on 10 or 30 minute mean values of the velocity field from a conically scanning lidar. In this mode of measurement, the lidar beam is rotated in a circle by a prism with a fixed angle to the vertical at varying focus distances. By fitting a trigonometric function to the scans, the mean vertical velocity can be estimated. Lidar measurements from (1) a fetch-limited beech forest site taken at 48-175m above ground level, (2) a reference site in flat agricultural terrain and (3) a second reference site in very complex terrain are presented. The method to derive flow tilt angles and mean vertical velocities from lidar has several advantages compared to sonic anemometry; there is no flow distortion caused by the instrument itself, there are no temperature effects and the instrument misalignment can be corrected for by comparing tilt estimates at various heights. Contrary to mast-based instruments, the lidar measures the wind field with the exact same alignment error at a multitude of heights. Disadvantages with estimating vertical velocities from a lidar compared to mast-based measurements are slightly increased levels of statistical errors due to limited sampling time, because the sampling is disjunct and a requirement for homogeneous flow. The estimated mean vertical velocity is biased if the flow over the scanned circle is not homogeneous. However, the error on the mean vertical velocity due to flow inhomogeneity can be approximated by a function of the angle of the lidar beam to the vertical, the measurement height and the vertical gradient of the mean vertical velocity, whereas the error due to flow inhomogeneity on the horizontal mean wind speed is independent of the lidar beam angle. For the presented measurements over

The Use of Analog Track Angle Error Display for Improving Simulated GPS Approach Performance

DOT National Transportation Integrated Search

1995-08-01

The effect of adding track angle error (TAE) information to general aviation aircraft cockpit displays used for GPS : nonprecision instrument approaches was studied experimentally. Six pilots flew 120 approaches in a Frasca 242 light : twin aircraft ...

GPS measurement error gives rise to spurious 180 degree turning angles and strong directional biases in animal movement data.

PubMed

Hurford, Amy

2009-05-20

Movement data are frequently collected using Global Positioning System (GPS) receivers, but recorded GPS locations are subject to errors. While past studies have suggested methods to improve location accuracy, mechanistic movement models utilize distributions of turning angles and directional biases and these data present a new challenge in recognizing and reducing the effect of measurement error. I collected locations from a stationary GPS collar, analyzed a probabilistic model and used Monte Carlo simulations to understand how measurement error affects measured turning angles and directional biases. Results from each of the three methods were in complete agreement: measurement error gives rise to a systematic bias where a stationary animal is most likely to be measured as turning 180 degrees or moving towards a fixed point in space. These spurious effects occur in GPS data when the measured distance between locations is <20 meters. Measurement error must be considered as a possible cause of 180 degree turning angles in GPS data. Consequences of failing to account for measurement error are predicting overly tortuous movement, numerous returns to previously visited locations, inaccurately predicting species range, core areas, and the frequency of crossing linear features. By understanding the effect of GPS measurement error, ecologists are able to disregard false signals to more accurately design conservation plans for endangered wildlife.

Addressing refractive error visual impairment: volunteer organisations' alignment with Vision 2020 and public health principles.

PubMed

Pearce, Matthew G; Pearce, Nicole

2012-11-01

Eye care professionals have been making short visits to developing countries for decades in an effort to reduce visual impairment caused by refractive error. A 2006 survey revealed that volunteer organisations were not working within the Vision 2020 framework. Recommendations were made for volunteer organisations that would better align their work with accepted Vision 2020 and public health principles. This study re-evaluates the alignment of volunteer organisations with Vision 2020 and public health principles. To determine their philosophies and methods, a web-based survey was sent to 89 volunteer organisations identified from an internet search. The response rate was 48 per cent. Many (70.7 per cent) organisations exclusively mention direct service provision in their statement of purpose, often provided by student volunteers (75.6 per cent). A few (19.5 per cent) provide short training in refraction, not necessarily following best principles. The majority (82.1 per cent) dispenses recycled spectacles and many use medications not on national essential drug lists. Few attempt to follow aid effectiveness principles with only 26.8 per cent stating they follow Vision 2020 country plans. Overall, as in 2006, the work of these organisations is largely not in alignment with Vision 2020 and public health principles. Organisations interested in decreasing visual impairment due to refractive error in the developing world are encouraged to transition to organisations that not only recognise but also implement public health principles. This should include reprioritisation of their work to developing human resources and infrastructure, determining the burden and causes of disease, assisting in the training of mid-level personnel and providing professional and community education, collaborating via partnerships, discontinuing the use of recycled spectacles and inappropriate medications, and evaluating their outcomes. Following these recommendations as well as creating a better

SU-E-J-94: Positioning Errors Resulting From Using Bony Anatomy Alignment for Treating SBRT Lung Tumor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frame, C; Ding, G

Purpose: To quantify patient setups errors based on bony anatomy registration rather than 3D tumor alignment for SBRT lung treatments. Method: A retrospective study was performed for patients treated with lung SBRT and imaged with kV cone beam computed tomography (kV-CBCT) image-guidance. Daily CBCT images were registered to treatment planning CTs based on bony anatomy alignment and then inter-fraction tumor movement was evaluated by comparing shift in the tumor center in the medial-lateral, anterior-posterior, and superior-inferior directions. The PTV V100% was evaluated for each patient based on the average daily tumor displacement to assess the impact of the positioning errormore » on the target coverage when the registrations were based on bony anatomy. Of the 35 patients studied, 15 were free-breathing treatments, 10 used abdominal compression with a stereotactic body frame, and the remaining 10 were performed with BodyFIX vacuum bags. Results: For free-breathing treatments, the range of tumor displacement error is between 1–6 mm in the medial-lateral, 1–13 mm in the anterior-posterior, and 1–7 mm in the superior-inferior directions. These positioning errors lead to 6–22% underdose coverage for PTV - V100% . Patients treated with abdominal compression immobilization showed positional errors of 0–4mm mediallaterally, 0–3mm anterior-posteriorly, and 0–2 mm inferior-superiorly with PTV - V100% underdose ranging between 6–17%. For patients immobilized with the vacuum bags, the positional errors were found to be 0–1 mm medial-laterally, 0–1mm anterior-posteriorly, and 0–2 mm inferior-superiorly with PTV - V100% under dose ranging between 5–6% only. Conclusion: It is necessary to align the tumor target by using 3D image guidance to ensure adequate tumor coverage before performing SBRT lung treatments. The BodyFIX vacuum bag immobilization method has the least positioning errors among the three methods studied when bony anatomy is used for

Rotation of intramedullary alignment rods affects distal femoral cutting plane in total knee arthroplasty.

PubMed

Maderbacher, Günther; Matussek, Jan; Keshmiri, Armin; Greimel, Felix; Baier, Clemens; Grifka, Joachim; Maderbacher, Hermann

2018-02-17

Intramedullary rods are widely used to align the distal femoral cut in total knee arthroplasty. We hypothesised that both coronal (varus/valgus) and sagittal (extension/flexion) cutting plane are affected by rotational changes of intramedullary femoral alignment guides. Distal femoral cuts using intramedullary alignment rods were simulated by means of a computer-aided engineering software in 4°, 6°, 8°, 10°, and 12° of valgus in relation to the femoral anatomical axis and 4° extension, neutral, as well as 4°, 8°, and 12° of flexion in relation to the femoral mechanical axis. This reflects the different angles between anatomical and mechanical axis in coronal and sagittal planes. To assess the influence of rotation of the alignment guide on the effective distal femoral cutting plane, all combinations were simulated with the rod gradually aligned from 40° of external to 40° of internal rotation. Rotational changes of the distal femoral alignment guides affect both the coronal and sagittal cutting planes. When alignment rods are intruded neutrally with regards to sagittal alignment, external rotation causes flexion, while internal rotation causes extension of the sagittal cutting plane. Simultaneously the coronal effect (valgus) decreases resulting in an increased varus of the cutting plane. However, when alignment rods are intruded in extension or flexion partly contradictory effects are observed. Generally the effect increases with the degree of valgus preset, rotation and flexion. As incorrect rotation of intramedullary alignment guides for distal femoral cuts causes significant cutting errors, exact rotational alignment is crucial. Coronal cutting errors in the distal femoral plane might result in overall leg malalignment, asymmetric extension gaps and subsequent sagittal cutting errors.

Sagittal alignment after single cervical disc arthroplasty.

PubMed

Guérin, Patrick; Obeid, Ibrahim; Gille, Olivier; Bourghli, Anouar; Luc, Stéphane; Pointillart, Vincent; Vital, Jean-Marc

2012-02-01

Prospective study. To analyze the sagittal balance after single-level cervical disc replacement (CDR) and range of motion (ROM). To define clinical and radiologic parameters those have a significant correlation with segmental and overall cervical curvature after CDR. Clinical outcomes and ROM after CDR with Mobi-C (LDR, Troyes, France) prosthesis have been documented in few studies. No earlier report of this prosthesis has studied correlations between static and dynamic parameters or those between static parameters and clinical outcomes. Forty patients were evaluated. Clinical outcome was assessed using the Short Form-36 questionnaire, Neck Disability Index, and a Visual Analog Scale. Spineview software (Surgiview, Paris, France) was used to investigate sagittal balance parameters and ROM. The mean follow-up was 24.3 months (range: 12 to 36 mo). Clinical outcomes were satisfactory. There was a significant improvement of Short Form-36, Neck Disability Index, and Visual Analog Scale scores. Mean ROM was 8.3 degrees preoperatively and 11.0 degrees postoperatively (P=0.013). Mean preoperative C2C7 curvature was 12.8 and 16.0 degrees at last follow-up (P=0.001). Mean preoperative functional spinal unit (FSU) angle was 2.3 and 5.3 degrees postoperatively (P<0.0001). Mean postoperative shell angle was 5.5 degrees. There was a significant correlation between postoperative C2C7 alignment and preoperative C2C7 alignment, change of C2C7 alignment, preoperative and postoperative FSU angle, and prosthesis shell angle. There was also a significant correlation between postoperative FSU angle and preoperative C2C7 alignment, preoperative FSU angle, change of FSU angle, and prosthesis shell angle. Regression analysis showed that prosthesis shell angle and preoperative FSU angle contributed significantly to postoperative FSU angle. Moreover, preoperative C2C7 alignment, preoperative FSU angle, postoperative FSU angle, and prosthesis shell angle contributed significantly to

IUS prerelease alignment

NASA Technical Reports Server (NTRS)

Evans, F. A.

1978-01-01

Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

Omni-Directional Viewing-Angle Switching through Control of the Beam Divergence Angle in a Liquid Crystal Panel

NASA Astrophysics Data System (ADS)

Baek, Jong-In; Kim, Ki-Han; Kim, Jae Chang; Yoon, Tae-Hoon

2010-01-01

This paper proposes a method of omni-directional viewing-angle switching by controlling the beam diverging angle (BDA) in a liquid crystal (LC) panel. The LCs aligned randomly by in-cell polymer structures diffuse the collimated backlight for the bright state of the wide viewing-angle mode. We align the LCs homogeneously by applying an in-plane field for the narrow viewing-angle mode. By doing this the scattering is significantly reduced so that the small BDA is maintained as it passes through the LC layer. The dark state can be obtained by aligning the LCs homeotropically with a vertical electric field. We demonstrated experimentally the omni-directional switching of the viewing-angle, without an additional panel or backlighting system.

Characterisation of residual ionospheric errors in bending angles using GNSS RO end-to-end simulations

NASA Astrophysics Data System (ADS)

Liu, C. L.; Kirchengast, G.; Zhang, K. F.; Norman, R.; Li, Y.; Zhang, S. C.; Carter, B.; Fritzer, J.; Schwaerz, M.; Choy, S. L.; Wu, S. Q.; Tan, Z. X.

2013-09-01

Global Navigation Satellite System (GNSS) radio occultation (RO) is an innovative meteorological remote sensing technique for measuring atmospheric parameters such as refractivity, temperature, water vapour and pressure for the improvement of numerical weather prediction (NWP) and global climate monitoring (GCM). GNSS RO has many unique characteristics including global coverage, long-term stability of observations, as well as high accuracy and high vertical resolution of the derived atmospheric profiles. One of the main error sources in GNSS RO observations that significantly affect the accuracy of the derived atmospheric parameters in the stratosphere is the ionospheric error. In order to mitigate the effect of this error, the linear ionospheric correction approach for dual-frequency GNSS RO observations is commonly used. However, the residual ionospheric errors (RIEs) can be still significant, especially when large ionospheric disturbances occur and prevail such as during the periods of active space weather. In this study, the RIEs were investigated under different local time, propagation direction and solar activity conditions and their effects on RO bending angles are characterised using end-to-end simulations. A three-step simulation study was designed to investigate the characteristics of the RIEs through comparing the bending angles with and without the effects of the RIEs. This research forms an important step forward in improving the accuracy of the atmospheric profiles derived from the GNSS RO technique.

Application of round grating angle measurement composite error amendment in the online measurement accuracy improvement of large diameter

NASA Astrophysics Data System (ADS)

Wang, Biao; Yu, Xiaofen; Li, Qinzhao; Zheng, Yu

2008-10-01

The paper aiming at the influence factor of round grating dividing error, rolling-wheel produce eccentricity and surface shape errors provides an amendment method based on rolling-wheel to get the composite error model which includes all influence factors above, and then corrects the non-circle measurement angle error of the rolling-wheel. We make soft simulation verification and have experiment; the result indicates that the composite error amendment method can improve the diameter measurement accuracy with rolling-wheel theory. It has wide application prospect for the measurement accuracy higher than 5 μm/m.

Analysis of the influence of manufacturing and alignment related errors on an optical tweezer system

NASA Astrophysics Data System (ADS)

Kampmann, R.; Sinzinger, S.

2014-12-01

In this work we present the design process as well as experimental results of an optical system for trapping particles in air. For positioning applications of micro-sized objects onto a glass wafer we developed a highly efficient optical tweezer. The focus of this paper is the iterative design process where we combine classical optics design software with a ray optics based force simulation tool. Thus we can find the best compromise which matches the optical systems restrictions with stable trapping conditions. Furthermore we analyze the influence of manufacturing related tolerances and errors in the alignment process of the optical elements on the optical forces. We present the design procedure for the necessary optical elements as well as experimental results for the aligned system.

Omnidirectional anti-reflection properties of vertically align SiO2 nanorod films prepared by electron beam evaporation with glancing angle deposition

NASA Astrophysics Data System (ADS)

Prachachet, R.; Samransuksamer, B.; Horprathum, M.; Eiamchai, P.; Limwichean, S.; Chananonnawathorn, C.; Lertvanithphol, T.; Muthitamongkol, P.; Boonruang, S.; Buranasiri, P.

2018-03-01

Omnidirectional anti-reflection coating nanostructure film have attracted enormous attention for the developments of the optical coating, lenses, light emitting diode, display and photovoltaic. However, fabricated of the omnidirectional antireflection nanostructure film on glass substrate in large area was a challenge topic. In the past two decades, the invention of glancing angle deposition technique as a growth of well-controlled two and three-dimensional morphologies has gained significant attention because of it is simple, fast, cost-effective and high mass production capability. In this present work, the omnidirectional anti-reflection nanostructure coating namely silicon dioxide (SiO2) nanorods has been investigated for optimized high transparent layer at all light incident angle. The SiO2 nanorod films of an optimally low refractive index have been fabricated by electron beam evaporation with the glancing angle deposition technique. The morphological of the prepared sampled were characterized by field-emission scanning electron microscope (FE-SEM) and high-resolution transmission electron microscope (HRTEM). The optical transmission and omnidirectional property of the SiO2 nanorod films were investigated by UV-Vis-NIR spectrophotometer. The measurement were performed at normal incident angle and a full spectral range of 200 - 2000 nm. The angle dependent transmission measure were investigated by rotating the specimen, with incidence angle defined relative to the surface normal of the prepared samples. The morphological characterization results showed that when the glancing angle deposition technique was applied, the vertically align SiO2 nanorods with partially isolated columnar structure can be constructed due to the enhanced shadowing and limited addtom diffusion effect. The average transmission of the vertically align SiO2 nanorods were higher than the glass substrate reference sample over the visible wavelength range at all incident angle due to the

Mapping local orientation of aligned fibrous scatterers for cancerous tissues using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Liu, Shaoxiong; Guo, Yihong; Wu, Jian; He, Yonghong; Ma, Hui

2014-10-01

Polarization measurements are sensitive to the microstructure of tissues and can be used to detect pathological changes. Many tissues contain anisotropic fibrous structures. We obtain the local orientation of aligned fibrous scatterers using different groups of the backscattering Mueller matrix elements. Experiments on concentrically well-aligned silk fibers and unstained human papillary thyroid carcinoma tissues show that the m22, m33, m23, and m32 elements have better contrast but higher degeneracy for the extraction of orientation angles. The m12 and m13 elements show lower contrast, but allow us to determine the orientation angle for the fibrous scatterers along all directions. Moreover, Monte Carlo simulations based on the sphere-cylinder scattering model indicate that the oblique incidence of the illumination beam introduces some errors in the orientation angles obtained by both methods. Mapping the local orientation of anisotropic tissues may not only provide information on pathological changes, but can also give new leads to reduce the orientation dependence of polarization measurements.

Particle Filter with Novel Nonlinear Error Model for Miniature Gyroscope-Based Measurement While Drilling Navigation

PubMed Central

Li, Tao; Yuan, Gannan; Li, Wang

2016-01-01

The derivation of a conventional error model for the miniature gyroscope-based measurement while drilling (MGWD) system is based on the assumption that the errors of attitude are small enough so that the direction cosine matrix (DCM) can be approximated or simplified by the errors of small-angle attitude. However, the simplification of the DCM would introduce errors to the navigation solutions of the MGWD system if the initial alignment cannot provide precise attitude, especially for the low-cost microelectromechanical system (MEMS) sensors operated in harsh multilateral horizontal downhole drilling environments. This paper proposes a novel nonlinear error model (NNEM) by the introduction of the error of DCM, and the NNEM can reduce the propagated errors under large-angle attitude error conditions. The zero velocity and zero position are the reference points and the innovations in the states estimation of particle filter (PF) and Kalman filter (KF). The experimental results illustrate that the performance of PF is better than KF and the PF with NNEM can effectively restrain the errors of system states, especially for the azimuth, velocity, and height in the quasi-stationary condition. PMID:26999130

Particle Filter with Novel Nonlinear Error Model for Miniature Gyroscope-Based Measurement While Drilling Navigation.

PubMed

Li, Tao; Yuan, Gannan; Li, Wang

2016-03-15

The derivation of a conventional error model for the miniature gyroscope-based measurement while drilling (MGWD) system is based on the assumption that the errors of attitude are small enough so that the direction cosine matrix (DCM) can be approximated or simplified by the errors of small-angle attitude. However, the simplification of the DCM would introduce errors to the navigation solutions of the MGWD system if the initial alignment cannot provide precise attitude, especially for the low-cost microelectromechanical system (MEMS) sensors operated in harsh multilateral horizontal downhole drilling environments. This paper proposes a novel nonlinear error model (NNEM) by the introduction of the error of DCM, and the NNEM can reduce the propagated errors under large-angle attitude error conditions. The zero velocity and zero position are the reference points and the innovations in the states estimation of particle filter (PF) and Kalman filter (KF). The experimental results illustrate that the performance of PF is better than KF and the PF with NNEM can effectively restrain the errors of system states, especially for the azimuth, velocity, and height in the quasi-stationary condition.

Calculation of stochastic broadening due to noise and field errors in the simple map in action-angle coordinates

NASA Astrophysics Data System (ADS)

Hinton, Courtney; Punjabi, Alkesh; Ali, Halima

2008-11-01

The simple map is the simplest map that has topology of divertor tokamaks [1]. Recently, the action-angle coordinates for simple map are analytically calculated, and simple map is constructed in action-angle coordinates [2]. Action-angle coordinates for simple map can not be inverted to real space coordinates (R,Z). Because there is logarithmic singularity on the ideal separatrix, trajectories can not cross separatrix [2]. Simple map in action-angle coordinates is applied to calculate stochastic broadening due to magnetic noise and field errors. Mode numbers for noise + field errors from the DIII-D tokamak are used. Mode numbers are (m,n)=(3,1), (4,1), (6,2), (7,2), (8,2), (9,3), (10,3), (11,3), (12,3) [3]. The common amplitude δ is varied from 0.8X10-5 to 2.0X10-5. For this noise and field errors, the width of stochastic layer in simple map is calculated. This work is supported by US Department of Energy grants DE-FG02-07ER54937, DE-FG02-01ER54624 and DE-FG02-04ER54793 1. A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Let. A 364, 140--145 (2007). 2. O. Kerwin, A. Punjabi, and H. Ali, to appear in Physics of Plasmas. 3. A. Punjabi and H. Ali, P1.012, 35^th EPS Conference on Plasma Physics, June 9-13, 2008, Hersonissos, Crete, Greece.

Swing arm profilometer: analytical solutions of misalignment errors for testing axisymmetric optics

NASA Astrophysics Data System (ADS)

Xiong, Ling; Luo, Xiao; Liu, Zhenyu; Wang, Xiaokun; Hu, Haixiang; Zhang, Feng; Zheng, Ligong; Zhang, Xuejun

2016-07-01

The swing arm profilometer (SAP) has been playing a very important role in testing large aspheric optics. As one of most significant error sources that affects the test accuracy, misalignment error leads to low-order errors such as aspherical aberrations and coma apart from power. In order to analyze the effect of misalignment errors, the relation between alignment parameters and test results of axisymmetric optics is presented. Analytical solutions of SAP system errors from tested mirror misalignment, arm length L deviation, tilt-angle θ deviation, air-table spin error, and air-table misalignment are derived, respectively; and misalignment tolerance is given to guide surface measurement. In addition, experiments on a 2-m diameter parabolic mirror are demonstrated to verify the model; according to the error budget, we achieve the SAP test for low-order errors except power with accuracy of 0.1 μm root-mean-square.

Case-related factors affecting cutting errors of the proximal tibia in total knee arthroplasty assessed by computer navigation.

PubMed

Tsukeoka, Tadashi; Tsuneizumi, Yoshikazu; Yoshino, Kensuke; Suzuki, Mashiko

2018-05-01

The aim of this study was to determine factors that contribute to bone cutting errors of conventional instrumentation for tibial resection in total knee arthroplasty (TKA) as assessed by an image-free navigation system. The hypothesis is that preoperative varus alignment is a significant contributory factor to tibial bone cutting errors. This was a prospective study of a consecutive series of 72 TKAs. The amount of the tibial first-cut errors with reference to the planned cutting plane in both coronal and sagittal planes was measured by an image-free computer navigation system. Multiple regression models were developed with the amount of tibial cutting error in the coronal and sagittal planes as dependent variables and sex, age, disease, height, body mass index, preoperative alignment, patellar height (Insall-Salvati ratio) and preoperative flexion angle as independent variables. Multiple regression analysis showed that sex (male gender) (R = 0.25 p = 0.047) and preoperative varus alignment (R = 0.42, p = 0.001) were positively associated with varus tibial cutting errors in the coronal plane. In the sagittal plane, none of the independent variables was significant. When performing TKA in varus deformity, careful confirmation of the bone cutting surface should be performed to avoid varus alignment. The results of this study suggest technical considerations that can help a surgeon achieve more accurate component placement. IV.

Flow tilt angles near forest edges - Part 2: Lidar anemometry

NASA Astrophysics Data System (ADS)

Dellwik, E.; Mann, J.; Bingöl, F.

2010-05-01

A novel way of estimating near-surface mean flow tilt angles from ground based Doppler lidar measurements is presented. The results are compared with traditional mast based in-situ sonic anemometry. The tilt angle assessed with the lidar is based on 10 or 30 min mean values of the velocity field from a conically scanning lidar. In this mode of measurement, the lidar beam is rotated in a circle by a prism with a fixed angle to the vertical at varying focus distances. By fitting a trigonometric function to the scans, the mean vertical velocity can be estimated. Lidar measurements from (1) a fetch-limited beech forest site taken at 48-175 m a.g.l. (above ground level), (2) a reference site in flat agricultural terrain and (3) a second reference site in complex terrain are presented. The method to derive flow tilt angles and mean vertical velocities from lidar has several advantages compared to sonic anemometry; there is no flow distortion caused by the instrument itself, there are no temperature effects and the instrument misalignment can be corrected for by assuming zero tilt angle at high altitudes. Contrary to mast-based instruments, the lidar measures the wind field with the exact same alignment error at a multitude of heights. Disadvantages with estimating vertical velocities from a lidar compared to mast-based measurements are potentially slightly increased levels of statistical errors due to limited sampling time, because the sampling is disjunct, and a requirement for homogeneous flow. The estimated mean vertical velocity is biased if the flow over the scanned circle is not homogeneous. It is demonstrated that the error on the mean vertical velocity due to flow inhomogeneity can be approximated by a function of the angle of the lidar beam to the vertical and the vertical gradient of the mean vertical velocity, whereas the error due to flow inhomogeneity on the horizontal mean wind speed is independent of the lidar beam angle. For the presented measurements

Evaluation of joint position sense measured by inversion angle replication error in patients with an osteochondral lesion of the talus.

PubMed

Nakasa, Tomoyuki; Adachi, Nobuo; Shibuya, Hayatoshi; Okuhara, Atsushi; Ochi, Mitsuo

2013-01-01

The etiology of the osteochondral lesion of the talar dome (OLT) remains unclear. A joint position sense deficit of the ankle is reported to be a possible cause of ankle disorder. Repeated contact of the articular surface of the talar dome with the plafond during inversion might be a cause of OLT. The aim of the present study was to evaluate the joint position sense deficit by measuring the replication error of the inversion angle in patients with OLT. The replication error, which is the difference between the index angle and replication angle in inversion, was measured in 15 patients with OLT. The replication error in 15 healthy volunteers was evaluated as a control group. The side to side differences of the replication errors between the patients with OLT and healthy volunteers and the replication errors in each angle between the involved and uninvolved ankle in the patients with OLT were investigated. Finally, the side to side differences of the replication errors between the patients with OLT with a traumatic and nontraumatic history were compared. The side to side difference in the patients with OLT (1.3° ± 0.2°) was significantly greater than that in the healthy subjects (0.4° ± 0.7°) (p ≤ .05). Significant differences were found between the involved and uninvolved sides at 10°, 15°, 20°, and 25° in the patients with OLT. No significant difference (p > .05) was found between the patients with traumatic and nontraumatic OLT. The present study found that the patients with OLT have a joint position sense deficit during inversion movement, regardless of a traumatic history. Although various factors for the etiology of OLT have been reported, the joint position sense deficit in inversion might be a cause of OLT. Copyright © 2013 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Alignment methods: strategies, challenges, benchmarking, and comparative overview.

PubMed

Löytynoja, Ari

2012-01-01

Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.

Prism Window for Optical Alignment

NASA Technical Reports Server (NTRS)

Tang, Hong

2008-01-01

A prism window has been devised for use, with an autocollimator, in aligning optical components that are (1) required to be oriented parallel to each other and/or at a specified angle of incidence with respect to a common optical path and (2) mounted at different positions along the common optical path. The prism window can also be used to align a single optical component at a specified angle of incidence. Prism windows could be generally useful for orienting optical components in manufacture of optical instruments. "Prism window" denotes an application-specific unit comprising two beam-splitter windows that are bonded together at an angle chosen to obtain the specified angle of incidence.

Calculation of lens alignment errors using the ray transfer matrices for the lens assembly system with an autocollimator and a rotation stage

NASA Astrophysics Data System (ADS)

Chu, Jiyoung; Cho, Sungwhi; Joo, Won Don; Jang, Sangdon

2017-08-01

One of the most popular methods for high precision lens assembly of an optical system is using an autocollimator and a rotation stage. Some companies provide software for calculating the state of the lens along with their lens assembly systems, but the calculation algorithms used by the software are unknown. In this paper, we suggest a calculation method for lens alignment errors using ray transfer matrices. Alignment errors resulting from tilting and decentering of a lens element can be calculated from the tilts of the front and back surfaces of the lens. The tilt of each surface can be obtained from the position of the reticle image on the CCD camera of the autocollimator. Rays from a reticle of the autocollimator are reflected from the target surface of the lens, which rotates with the rotation stage, and are imaged on the CCD camera. To obtain a clear image, the distance between the autocollimator and the first lens surface should be adjusted according to the focusing lens of the autocollimator and the lens surfaces from the first to the target surface. Ray propagations for the autocollimator and the tilted lens surfaces can be expressed effectively by using ray transfer matrices and lens alignment errors can be derived from them. This method was compared with Zemax simulation for various lenses with spherical or flat surfaces and the error was less than a few percent.

Multiobjective optimization of cartilage stress for non-invasive, patient-specific recommendations of high tibial osteotomy correction angle - a novel method to investigate alignment correction.

PubMed

Zheng, Keke; Scholes, Corey J; Chen, Junning; Parker, David; Li, Qing

2017-04-01

Medial opening wedge high tibial osteotomy (MOWHTO) is a surgical procedure to treat knee osteoarthritis associated with varus deformity. However, the ideal final alignment of the Hip-Knee-Ankle (HKA) angle in the frontal plane, that maximizes procedural success and post-operative knee function, remains controversial. Therefore, the purpose of this study was to introduce a subject-specific modeling procedure in determining the biomechanical effects of MOWHTO alignment on tibiofemoral cartilage stress distribution. A 3D finite element knee model derived from magnetic resonance imaging of a healthy participant was manipulated in-silico to simulate a range of final HKA angles (i.e. 0.2°, 2.7°, 3.9° and 6.6° valgus). Loading and boundary conditions were assigned based on subject-specific kinematic and kinetic data from gait analysis. Multiobjective optimization was used to identify the final alignment that balanced compressive and shear forces between medial and lateral knee compartments. Peak stresses decreased in the medial and increased in the lateral compartment as the HKA was shifted into valgus, with balanced loading occurring at angles of 4.3° and 2.9° valgus for the femoral and tibial cartilage respectively. The concept introduced here provides a platform for non-invasive, patient-specific preoperative planning of the osteotomy for medial compartment knee osteoarthritis. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

Effect of limbal marking prior to laser ablation on the magnitude of cyclotorsional error.

PubMed

Chen, Xiangjun; Stojanovic, Aleksandar; Stojanovic, Filip; Eidet, Jon Roger; Raeder, Sten; Øritsland, Haakon; Utheim, Tor Paaske

2012-05-01

To evaluate the residual registration error after limbal-marking-based manual adjustment in cyclotorsional tracker-controlled laser refractive surgery. Two hundred eyes undergoing custom surface ablation with the iVIS Suite (iVIS Technologies) were divided into limbal marked (marked) and non-limbal marked (unmarked) groups. Iris registration information was acquired preoperatively from all eyes. Preoperatively, the horizontal axis was recorded in the marked group for use in manual cyclotorsional alignment prior to surgical iris registration. During iris registration, the preoperative iris information was compared to the eye-tracker captured image. The magnitudes of the registration error angle and cyclotorsional movement during the subsequent laser ablation were recorded and analyzed. Mean magnitude of registration error angle (absolute value) was 1.82°±1.31° (range: 0.00° to 5.50°) and 2.90°±2.40° (range: 0.00° to 13.50°) for the marked and unmarked groups, respectively (P<.001). Mean magnitude of cyclotorsional movement during the laser ablation (absolute value) was 1.15°±1.34° (range: 0.00° to 7.00°) and 0.68°±0.97° (range: 0.00° to 6.00°) for the marked and unmarked groups, respectively (P=.005). Forty-six percent and 60% of eyes had registration error >2°, whereas 22% and 20% of eyes had cyclotorsional movement during ablation >2° in the marked and unmarked groups, respectively. Limbal-marking-based manual alignment prior to laser ablation significantly reduced cyclotorsional registration error. However, residual registration misalignment and cyclotorsional movements remained during ablation. Copyright 2012, SLACK Incorporated.

Large field distributed aperture laser semiactive angle measurement system design with imaging fiber bundles.

PubMed

Xu, Chunyun; Cheng, Haobo; Feng, Yunpeng; Jing, Xiaoli

2016-09-01

A type of laser semiactive angle measurement system is designed for target detecting and tracking. Only one detector is used to detect target location from four distributed aperture optical systems through a 4×1 imaging fiber bundle. A telecentric optical system in image space is designed to increase the efficiency of imaging fiber bundles. According to the working principle of a four-quadrant (4Q) detector, fiber diamond alignment is adopted between an optical system and a 4Q detector. The structure of the laser semiactive angle measurement system is, we believe, novel. Tolerance analysis is carried out to determine tolerance limits of manufacture and installation errors of the optical system. The performance of the proposed method is identified by computer simulations and experiments. It is demonstrated that the linear region of the system is ±12°, with measurement error of better than 0.2°. In general, this new system can be used with large field of view and high accuracy, providing an efficient, stable, and fast method for angle measurement in practical situations.

ϕ Meson Spin Alignment and the Azimuthal Angle Dependence of Λ (Λ) Polarization in Au+Au collisions at RHIC

NASA Astrophysics Data System (ADS)

Tu, Biao

2018-02-01

Initial large global angular momentum in non-central relativistic heavy-ion collisions can produce strong vorticity, and through the spin-orbit coupling, causes the spin of particles to align with the system's global angular momentum. We present the azimuthal angle dependent (relative to the reaction plane) polarization for Λ and Λ in mid-central Au+Au collisions at = 200 GeV. We also present the ϕ meson spin alignment parameter, ρ00 in Au+Au collisions at = 19.6, 27, 39, 62.4 and 200 GeV. The implications of the results are discussed.

Attitude algorithm and initial alignment method for SINS applied in short-range aircraft

NASA Astrophysics Data System (ADS)

Zhang, Rong-Hui; He, Zhao-Cheng; You, Feng; Chen, Bo

2017-07-01

This paper presents an attitude solution algorithm based on the Micro-Electro-Mechanical System and quaternion method. We completed the numerical calculation and engineering practice by adopting fourth-order Runge-Kutta algorithm in the digital signal processor. The state space mathematical model of initial alignment in static base was established, and the initial alignment method based on Kalman filter was proposed. Based on the hardware in the loop simulation platform, the short-range flight simulation test and the actual flight test were carried out. The results show that the error of pitch, yaw and roll angle is fast convergent, and the fitting rate between flight simulation and flight test is more than 85%.

Reliability of the Phi angle to assess rotational alignment of the talar component in total ankle replacement.

PubMed

Manzi, Luigi; Villafañe, Jorge Hugo; Indino, Cristian; Tamini, Jacopo; Berjano, Pedro; Usuelli, Federico Giuseppe

2017-11-08

The purpose of this study was to investigate the test-retest reliability of the Phi angle in patients undergoing total ankle replacement (TAR) for end stage ankle osteoarthritis (OA) to assess the rotational alignment of the talar component. Retrospective observational cross-sectional study of prospectively collected data. Post-operative anteroposterior radiographs of the foot of 170 patients who underwent TAR for the ankle OA were evaluated. Three physicians measured Phi on the 170 randomly sorted and anonymized radiographs on two occasions, one week apart (test and retest conditions), inter and intra-observer agreement were evaluated. Test-retest reliability of Phi angle measurement was excellent for patients with Hintegra TAR (ICC=0.995; p<0.001) and Zimmer TAR (ICC=0.995; p<0.001) on radiographs of subjects with ankle OA. There were no significant differences in the reliability of the Phi angle measurement between patients with Hintegra vs. Zimmer implants (p>0.05). Measurement of Phi angle on weight-bearing dorsoplantar radiograph showed an excellent reliability among orthopaedic surgeons in determining the position of the talar component in the axial plane. Level II, cross sectional study. Copyright © 2017 European Foot and Ankle Society. Published by Elsevier Ltd. All rights reserved.

An IMU-to-Body Alignment Method Applied to Human Gait Analysis

PubMed Central

Vargas-Valencia, Laura Susana; Elias, Arlindo; Rocon, Eduardo; Bastos-Filho, Teodiano; Frizera, Anselmo

2016-01-01

This paper presents a novel calibration procedure as a simple, yet powerful, method to place and align inertial sensors with body segments. The calibration can be easily replicated without the need of any additional tools. The proposed method is validated in three different applications: a computer mathematical simulation; a simplified joint composed of two semi-spheres interconnected by a universal goniometer; and a real gait test with five able-bodied subjects. Simulation results demonstrate that, after the calibration method is applied, the joint angles are correctly measured independently of previous sensor placement on the joint, thus validating the proposed procedure. In the cases of a simplified joint and a real gait test with human volunteers, the method also performs correctly, although secondary plane errors appear when compared with the simulation results. We believe that such errors are caused by limitations of the current inertial measurement unit (IMU) technology and fusion algorithms. In conclusion, the presented calibration procedure is an interesting option to solve the alignment problem when using IMUs for gait analysis. PMID:27973406

An IMU-to-Body Alignment Method Applied to Human Gait Analysis.

PubMed

Vargas-Valencia, Laura Susana; Elias, Arlindo; Rocon, Eduardo; Bastos-Filho, Teodiano; Frizera, Anselmo

2016-12-10

This paper presents a novel calibration procedure as a simple, yet powerful, method to place and align inertial sensors with body segments. The calibration can be easily replicated without the need of any additional tools. The proposed method is validated in three different applications: a computer mathematical simulation; a simplified joint composed of two semi-spheres interconnected by a universal goniometer; and a real gait test with five able-bodied subjects. Simulation results demonstrate that, after the calibration method is applied, the joint angles are correctly measured independently of previous sensor placement on the joint, thus validating the proposed procedure. In the cases of a simplified joint and a real gait test with human volunteers, the method also performs correctly, although secondary plane errors appear when compared with the simulation results. We believe that such errors are caused by limitations of the current inertial measurement unit (IMU) technology and fusion algorithms. In conclusion, the presented calibration procedure is an interesting option to solve the alignment problem when using IMUs for gait analysis.

Local alignment of two-base encoded DNA sequence

PubMed Central

Homer, Nils; Merriman, Barry; Nelson, Stanley F

2009-01-01

Background DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding considered here. In order to compare such data to a reference sequence, the data must be decoded into sequence. The decoding is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting alignments to achieve an optimal balance of fewer errors versus greater sequence similarity. Results We present an extension of the standard dynamic programming method for local alignment, which simultaneously decodes the data and performs the alignment, maximizing a similarity score based on a weighted combination of errors and edits, and allowing an affine gap penalty. We also present simulations that demonstrate the performance characteristics of our two base encoded alignment method and contrast those with standard DNA sequence alignment under the same conditions. Conclusion The new local alignment algorithm for two-base encoded data has substantial power to properly detect and correct measurement errors while identifying underlying sequence variants, and facilitating genome re-sequencing efforts based on this form of sequence data. PMID:19508732

Kinematically aligned TKA can align knee joint line to horizontal.

PubMed

Ji, Hyung-Min; Han, Jun; Jin, Dong San; Seo, Hyunseok; Won, Ye-Yeon

2016-08-01

The joint line of the native knee is horizontal to the floor and perpendicular to the vertical weight-bearing axis of the patient in a bipedal stance. The purposes of this study were as follows: (1) to find out the distribution of the native joint line in a population of normal patients with normal knees; (2) to compare the native joint line orientation between patients receiving conventional mechanically aligned total knee arthroplasty (TKA), navigated mechanically aligned TKA, and kinematically aligned TKA; and (3) to determine which of the three TKA methods aligns the postoperative knee joint perpendicular to the weight-bearing axis of the limb in bipedal stance. To determine the joint line orientation of a native knee, 50 full-length standing hip-to-ankle digital radiographs were obtained in 50 young, healthy individuals. The angle between knee joint line and the line parallel to the floor was measured and defined as joint line orientation angle (JLOA). JLOA was also measured prior to and after conventional mechanically aligned TKA (65 knees), mechanically aligned TKA using imageless navigation (65 knees), and kinematically aligned TKA (65 knees). The proportion of the knees similar to the native joint line was calculated for each group. The mean JLOA in healthy individuals was parallel to the floor (0.2° ± 1.1°). The pre-operative JLOA of all treatment groups slanted down to the lateral side. Postoperative JLOA slanted down to the lateral side in conventional mechanically aligned TKA (-3.3° ± 2.2°) and in navigation mechanically aligned TKA (-2.6° ± 1.8°), while it was horizontal to the floor in kinematically aligned TKA (0.6° ± 1.7°). Only 6.9 % of the conventional mechanically aligned TKA and 16.9 % of the navigation mechanically aligned TKA were within one SD of the mean JLOA of the native knee, while the proportion was significantly higher (50.8 %) in kinematically aligned TKA. The portion was statistically greater in mechanically

A Swiss cheese error detection method for real-time EPID-based quality assurance and error prevention.

PubMed

Passarge, Michelle; Fix, Michael K; Manser, Peter; Stampanoni, Marco F M; Siebers, Jeffrey V

2017-04-01

To develop a robust and efficient process that detects relevant dose errors (dose errors of ≥5%) in external beam radiation therapy and directly indicates the origin of the error. The process is illustrated in the context of electronic portal imaging device (EPID)-based angle-resolved volumetric-modulated arc therapy (VMAT) quality assurance (QA), particularly as would be implemented in a real-time monitoring program. A Swiss cheese error detection (SCED) method was created as a paradigm for a cine EPID-based during-treatment QA. For VMAT, the method compares a treatment plan-based reference set of EPID images with images acquired over each 2° gantry angle interval. The process utilizes a sequence of independent consecutively executed error detection tests: an aperture check that verifies in-field radiation delivery and ensures no out-of-field radiation; output normalization checks at two different stages; global image alignment check to examine if rotation, scaling, and translation are within tolerances; pixel intensity check containing the standard gamma evaluation (3%, 3 mm) and pixel intensity deviation checks including and excluding high dose gradient regions. Tolerances for each check were determined. To test the SCED method, 12 different types of errors were selected to modify the original plan. A series of angle-resolved predicted EPID images were artificially generated for each test case, resulting in a sequence of precalculated frames for each modified treatment plan. The SCED method was applied multiple times for each test case to assess the ability to detect introduced plan variations. To compare the performance of the SCED process with that of a standard gamma analysis, both error detection methods were applied to the generated test cases with realistic noise variations. Averaged over ten test runs, 95.1% of all plan variations that resulted in relevant patient dose errors were detected within 2° and 100% within 14° (<4% of patient dose delivery

Measuring Scale Errors in a Laser Tracker’s Horizontal Angle Encoder Through Simple Length Measurement and Two-Face System Tests

PubMed Central

Muralikrishnan, B.; Blackburn, C.; Sawyer, D.; Phillips, S.; Bridges, R.

2010-01-01

We describe a method to estimate the scale errors in the horizontal angle encoder of a laser tracker in this paper. The method does not require expensive instrumentation such as a rotary stage or even a calibrated artifact. An uncalibrated but stable length is realized between two targets mounted on stands that are at tracker height. The tracker measures the distance between these two targets from different azimuthal positions (say, in intervals of 20° over 360°). Each target is measured in both front face and back face. Low order harmonic scale errors can be estimated from this data and may then be used to correct the encoder’s error map to improve the tracker’s angle measurement accuracy. We have demonstrated this for the second order harmonic in this paper. It is important to compensate for even order harmonics as their influence cannot be removed by averaging front face and back face measurements whereas odd orders can be removed by averaging. We tested six trackers from three different manufacturers. Two of those trackers are newer models introduced at the time of writing of this paper. For older trackers from two manufacturers, the length errors in a 7.75 m horizontal length placed 7 m away from a tracker were of the order of ± 65 μm before correcting the error map. They reduced to less than ± 25 μm after correcting the error map for second order scale errors. Newer trackers from the same manufacturers did not show this error. An older tracker from a third manufacturer also did not show this error. PMID:27134789

SU-G-JeP3-02: Comparison of Magnitude and Frequency of Patient Positioning Errors in Breast Irradiation Using AlignRT 3D Optical Surface Imaging and Skin Mark Techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao, R; Chisela, W; Dorbu, G

2016-06-15

Purpose: To evaluate clinical usefulness of AlignRT (Vision RT Ltd., London, UK) in reducing patient positioning errors in breast irradiation. Methods: 60 patients undergoing whole breast irradiation were selected for this study. Patients were treated to the left or right breast lying on Qfix Access breast board (Qfix, Avondale, PA) in supine position for 28 fractions using tangential fields. 30 patients were aligned using AlignRT by aligning a breast surface region of interest (ROI) to the same area from a reference surface image extracted from planning CT. When the patient’s surface image deviated from the reference by more than 3mmmore » on one or more translational and rotational directions, a new reference was acquired using AlignRT in-room cameras. The other 30 patients were aligned to the skin marks with room lasers. On-Board MV portal images of medial field were taken daily and matched to the DRRs. The magnitude and frequency of positioning errors were determined from measured translational shifts. Kolmogorov-Smirnov test was used to evaluate statistical differences of positional accuracy and precision between AlignRT and non-AlignRT patients. Results: The percentage of port images with no shift required was 46.5% and 27.0% in vertical, 49.8% and 25.8% in longitudinal, 47.6% and 28.5% in lateral for AlignRT and non-AlignRT patients, respectively. The percentage of port images requiring more than 3mm shifts was 18.1% and 35.1% in vertical, 28.6% and 50.8% in longitudinal, 11.3% and 24.2% in lateral for AlignRT and non-AlignRT patients, respectively. Kolmogorov-Smirnov test showed that there were significant differences between the frequency distributions of AlignRT and non-AlignRT in vertical, longitudinal, and lateral shifts. Conclusion: As confirmed by port images, AlignRT-assisted patient positioning can significantly reduce the frequency and magnitude of patient setup errors in breast irradiation compared to the use of lasers and skin marks.« less

Analysis of naturalistic driving videos of fleet services drivers to estimate driver error and potentially distracting behaviors as risk factors for rear-end versus angle crashes.

PubMed

Harland, Karisa K; Carney, Cher; McGehee, Daniel

2016-07-03

The objective of this study was to estimate the prevalence and odds of fleet driver errors and potentially distracting behaviors just prior to rear-end versus angle crashes. Analysis of naturalistic driving videos among fleet services drivers for errors and potentially distracting behaviors occurring in the 6 s before crash impact. Categorical variables were examined using the Pearson's chi-square test, and continuous variables, such as eyes-off-road time, were compared using the Student's t-test. Multivariable logistic regression was used to estimate the odds of a driver error or potentially distracting behavior being present in the seconds before rear-end versus angle crashes. Of the 229 crashes analyzed, 101 (44%) were rear-end and 128 (56%) were angle crashes. Driver age, gender, and presence of passengers did not differ significantly by crash type. Over 95% of rear-end crashes involved inadequate surveillance compared to only 52% of angle crashes (P < .0001). Almost 65% of rear-end crashes involved a potentially distracting driver behavior, whereas less than 40% of angle crashes involved these behaviors (P < .01). On average, drivers spent 4.4 s with their eyes off the road while operating or manipulating their cell phone. Drivers in rear-end crashes were at 3.06 (95% confidence interval [CI], 1.73-5.44) times adjusted higher odds of being potentially distracted than those in angle crashes. Fleet driver driving errors and potentially distracting behaviors are frequent. This analysis provides data to inform safe driving interventions for fleet services drivers. Further research is needed in effective interventions to reduce the likelihood of drivers' distracting behaviors and errors that may potentially reducing crashes.

Does Assessing Eye Alignment along with Refractive Error or Visual Acuity Increase Sensitivity for Detection of Strabismus in Preschool Vision Screening?

PubMed Central

2007-01-01

Purpose Preschool vision screenings often include refractive error or visual acuity (VA) testing to detect amblyopia, as well as alignment testing to detect strabismus. The purpose of this study was to determine the effect of combining screening for eye alignment with screening for refractive error or reduced VA on sensitivity for detection of strabismus, with specificity set at 90% and 94%. Methods Over 3 years, 4040 preschool children were screened in the Vision in Preschoolers (VIP) Study, with different screening tests administered each year. Examinations were performed to identify children with strabismus. The best screening tests for detecting children with any targeted condition were noncycloplegic retinoscopy (NCR), Retinomax autorefractor (Right Manufacturing, Virginia Beach, VA), SureSight Vision Screener (Welch-Allyn, Inc., Skaneateles, NY), and Lea Symbols (Precision Vision, LaSalle, IL and Good-Lite Co., Elgin, IL) and HOTV optotypes VA tests. Analyses were conducted with these tests of refractive error or VA paired with the best tests for detecting strabismus (unilateral cover testing, Random Dot “E” [RDE] and Stereo Smile Test II [Stereo Optical, Inc., Chicago, IL]; and MTI PhotoScreener [PhotoScreener, Inc., Palm Beach, FL]). The change in sensitivity that resulted from combining a test of eye alignment with a test of refractive error or VA was determined with specificity set at 90% and 94%. Results Among the 4040 children, 157 were identified as having strabismus. For screening tests conducted by eye care professionals, the addition of a unilateral cover test to a test of refraction generally resulted in a statistically significant increase (range, 15%–25%) in detection of strabismus. For screening tests administered by trained lay screeners, the addition of Stereo Smile II to SureSight resulted in a statistically significant increase (21%) in sensitivity for detection of strabismus. Conclusions The most efficient and low-cost ways to achieve

On the Error State Selection for Stationary SINS Alignment and Calibration Kalman Filters—Part II: Observability/Estimability Analysis

PubMed Central

Silva, Felipe O.; Hemerly, Elder M.; Leite Filho, Waldemar C.

2017-01-01

This paper presents the second part of a study aiming at the error state selection in Kalman filters applied to the stationary self-alignment and calibration (SSAC) problem of strapdown inertial navigation systems (SINS). The observability properties of the system are systematically investigated, and the number of unobservable modes is established. Through the analytical manipulation of the full SINS error model, the unobservable modes of the system are determined, and the SSAC error states (except the velocity errors) are proven to be individually unobservable. The estimability of the system is determined through the examination of the major diagonal terms of the covariance matrix and their eigenvalues/eigenvectors. Filter order reduction based on observability analysis is shown to be inadequate, and several misconceptions regarding SSAC observability and estimability deficiencies are removed. As the main contributions of this paper, we demonstrate that, except for the position errors, all error states can be minimally estimated in the SSAC problem and, hence, should not be removed from the filter. Corroborating the conclusions of the first part of this study, a 12-state Kalman filter is found to be the optimal error state selection for SSAC purposes. Results from simulated and experimental tests support the outlined conclusions. PMID:28241494

Pupil Alignment Considerations for Large, Deployable Space Telescopes

NASA Technical Reports Server (NTRS)

Bos, Brent J.; Ohl, Raymond G.; Kubalak, Daivd A.

2011-01-01

For many optical systems the properties and alignment of the internal apertures and pupils are not critical or controlled with high precision during optical system design, fabrication or assembly. In wide angle imaging systems, for instance, the entrance pupil position and orientation is typically unconstrained and varies over the system s field of view in order to optimize image quality. Aperture tolerances usually do not receive the same amount of scrutiny as optical surface aberrations or throughput characteristics because performance degradation is typically graceful with misalignment, generally only causing a slight reduction in system sensitivity due to vignetting. But for a large deployable space-based observatory like the James Webb Space Telescope (JWST), we have found that pupil alignment is a key parameter. For in addition to vignetting, JWST pupil errors cause uncertainty in the wavefront sensing process that is used to construct the observatory on-orbit. Furthermore they also open stray light paths that degrade the science return from some of the telescope s instrument channels. In response to these consequences, we have developed several pupil measurement techniques for the cryogenic vacuum test where JWST science instrument pupil alignment is verified. These approaches use pupil alignment references within the JWST science instruments; pupil imaging lenses in three science instrument channels; and unique pupil characterization features in the optical test equipment. This will allow us to verify and crosscheck the lateral pupil alignment of the JWST science instruments to approximately 1-2% of their pupil diameters.

A comparison of cylindrical and row trenched cooling holes with alignment angle of 0 degree near the combustor endwall

NASA Astrophysics Data System (ADS)

Kianpour, E.; Nor Azwadi, C. S.; Golshokouh, I.

2013-12-01

We studied the effects of cylindrical and row trenched cooling holes with alignment angle of 0° at BR=3.18 on the film cooling performance near the endwall surface of a combustor simulator. In this research, a three-dimensional presentation of gas turbine engine was simulated and analyzed with a commercial finite volume package FLUENT 6.2.26 to gain fundamental data. The current study has been performed with Reynolds-averaged Navier-Stokes turbulence model (RANS) on internal cooling passages. This combustor simulator combined the interaction of two rows of dilution jets, which were staggered in the stream wise direction and aligned in the span wise direction. The entire findings of the study declared that with using the row trenched holes near the enwall surface; film cooling effectiveness is doubled compared to the cooling performance of baseline case.

In-motion initial alignment and positioning with INS/CNS/ODO integrated navigation system for lunar rovers

NASA Astrophysics Data System (ADS)

Lu, Jiazhen; Lei, Chaohua; Yang, Yanqiang; Liu, Ming

2017-06-01

Many countries have been paying great attention to space exploration, especially about the Moon and the Mars. Autonomous and high-accuracy navigation systems are needed for probers and rovers to accomplish missions. Inertial navigation system (INS)/celestial navigation system (CNS) based navigation system has been used widely on the lunar rovers. Initialization is a particularly important step for navigation. This paper presents an in-motion alignment and positioning method for lunar rovers by INS/CNS/odometer integrated navigation. The method can estimate not only the position and attitude errors, but also the biases of the accelerometers and gyros using the standard Kalman filter. The differences between the platform star azimuth, elevation angles and the computed star azimuth, elevation angles, and the difference between the velocity measured by odometer and the velocity measured by inertial sensors are taken as measurements. The semi-physical experiments are implemented to demonstrate that the position error can reduce to 10 m and attitude error is within 2″ during 5 min. The experiment results prove that it is an effective and attractive initialization approach for lunar rovers.

Self-Alignment MEMS IMU Method Based on the Rotation Modulation Technique on a Swing Base

PubMed Central

Chen, Zhiyong; Yang, Haotian; Wang, Chengbin; Lin, Zhihui; Guo, Meifeng

2018-01-01

The micro-electro-mechanical-system (MEMS) inertial measurement unit (IMU) has been widely used in the field of inertial navigation due to its small size, low cost, and light weight, but aligning MEMS IMUs remains a challenge for researchers. MEMS IMUs have been conventionally aligned on a static base, requiring other sensors, such as magnetometers or satellites, to provide auxiliary information, which limits its application range to some extent. Therefore, improving the alignment accuracy of MEMS IMU as much as possible under swing conditions is of considerable value. This paper proposes an alignment method based on the rotation modulation technique (RMT), which is completely self-aligned, unlike the existing alignment techniques. The effect of the inertial sensor errors is mitigated by rotating the IMU. Then, inertial frame-based alignment using the rotation modulation technique (RMT-IFBA) achieved coarse alignment on the swing base. The strong tracking filter (STF) further improved the alignment accuracy. The performance of the proposed method was validated with a physical experiment, and the results of the alignment showed that the standard deviations of pitch, roll, and heading angle were 0.0140°, 0.0097°, and 0.91°, respectively, which verified the practicality and efficacy of the proposed method for the self-alignment of the MEMS IMU on a swing base. PMID:29649150

Sensitivity of medial and lateral knee contact force predictions to frontal plane alignment and contact locations.

PubMed

Saliba, Christopher M; Brandon, Scott C E; Deluzio, Kevin J

2017-05-24

Musculoskeletal models are increasingly used to estimate medial and lateral knee contact forces, which are difficult to measure in vivo. The sensitivity of contact force predictions to modeling parameters is important to the interpretation and implication of results generated by the model. The purpose of this study was to quantify the sensitivity of knee contact force predictions to simultaneous errors in frontal plane knee alignment and contact locations under different dynamic conditions. We scaled a generic musculoskeletal model for N=23 subjects' stature and radiographic knee alignment, then perturbed frontal plane alignment and mediolateral contact locations within experimentally-possible ranges of 10° to -10° and 10 to -10mm, respectively. The sensitivity of first peak, second peak, and mean medial and lateral knee contact forces to knee adduction angle and contact locations was modeled using linear regression. Medial loads increased, and lateral loads decreased, by between 3% and 6% bodyweight for each degree of varus perturbation. Shifting the medial contact point medially increased medial loads and decreased lateral loads by between 1% and 4% bodyweight per millimeter. This study demonstrates that realistic measurement errors of 5mm (contact distance) or 5° (frontal plane alignment) could result in a combined 50% BW error in subject specific contact force estimates. We also show that model sensitivity varies between subjects as a result of differences in gait dynamics. These results demonstrate that predicted knee joint contact forces should be considered as a range of possible values determined by model uncertainty. Copyright © 2017 Elsevier Ltd. All rights reserved.

Alignment control study for the solar optical telescope

NASA Technical Reports Server (NTRS)

1976-01-01

Analysis of the alignment and focus errors than can be tolerated, methods of sensing such errors, and mechanisms to make the necessary corrections were addressed. Alternate approaches and their relative merits were considered. The results of this study indicate that adequate alignment control can be achieved.

Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection.

PubMed

Gürsoy, Doğa; Hong, Young P; He, Kuan; Hujsak, Karl; Yoo, Seunghwan; Chen, Si; Li, Yue; Ge, Mingyuan; Miller, Lisa M; Chu, Yong S; De Andrade, Vincent; He, Kai; Cossairt, Oliver; Katsaggelos, Aggelos K; Jacobsen, Chris

2017-09-18

As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the same error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.

Apparatus and method for variable angle slant hole collimator

DOEpatents

Lee, Seung Joon; Kross, Brian J.; McKisson, John E.

2017-07-18

A variable angle slant hole (VASH) collimator for providing collimation of high energy photons such as gamma rays during radiological imaging of humans. The VASH collimator includes a stack of multiple collimator leaves and a means of quickly aligning each leaf to provide various projection angles. Rather than rotate the detector around the subject, the VASH collimator enables the detector to remain stationary while the projection angle of the collimator is varied for tomographic acquisition. High collimator efficiency is achieved by maintaining the leaves in accurate alignment through the various projection angles. Individual leaves include unique angled cuts to maintain a precise target collimation angle. Matching wedge blocks driven by two actuators with twin-lead screws accurately position each leaf in the stack resulting in the precise target collimation angle. A computer interface with the actuators enables precise control of the projection angle of the collimator.

Alignment of a vector magnetometer to an optical prism

NASA Astrophysics Data System (ADS)

Dietrich, M. R.; Bailey, K. G.; O'Connor, T. P.

2017-05-01

A method for alignment of a vector magnetometer to a rigidly attached prism is presented. This enables optical comparison of the magnetometer axes to physical surfaces in the apparatus, and thus an absolute determination of the magnetic field direction in space. This is in contrast with more common techniques, which focus on precise determination of the relative angles between magnetometer axes, and so are more suited to measuring differences in the direction of magnetic fields. Here we demonstrate precision better than 500 μrad on a fluxgate magnetometer, which also gives the coil orthogonality errors to a similar precision. The relative sensitivity of the three axes is also determined, with a precision of about 5 ×10 -4 .

Alignment of a vector magnetometer to an optical prism.

PubMed

Dietrich, M R; Bailey, K G; O'Connor, T P

2017-05-01

A method for alignment of a vector magnetometer to a rigidly attached prism is presented. This enables optical comparison of the magnetometer axes to physical surfaces in the apparatus, and thus an absolute determination of the magnetic field direction in space. This is in contrast with more common techniques, which focus on precise determination of the relative angles between magnetometer axes, and so are more suited to measuring differences in the direction of magnetic fields. Here we demonstrate precision better than 500 μrad on a fluxgate magnetometer, which also gives the coil orthogonality errors to a similar precision. The relative sensitivity of the three axes is also determined, with a precision of about 5 × 10 -4 .

Biomechanical influence of pin placement and elbow angle on joint distraction and hinge alignment for an arthrodiatasis elbow-pin-fixator construct.

PubMed

Lee, Wei-Shiun; Linz, Shang-Chih; Shih, Kao-Shang; Chao, Ching-Kong; Chen, Yeung-Jen; Fan, Chang-Yuan

2012-10-01

Stiffness and contracture of the periarticular tissues are common complications of a post-traumatic elbow. Arthrodiatasis is a surgical technique that uses an external fixator for initial immobilization and subsequent distraction. The two prerequisites for an ideal arthrodiatasis are concentric distraction (avoiding bony contact) and hinge alignment (reducing internal stress). This study used the finite element (FE) method to clarify the relationship between these two prerequisites and the initial conditions (pin placement, elbow angle, and distraction mode). A total of 12 variations of the initial conditions were symmetrically arranged to evaluate their biomechanical influence on concentric distraction and hinge alignment. The humeroulnar surface was hypothesized to be ideally distracted orthogonal to the line joining the tips of the olecranon and the coronoid. The eccentric separation of the humeroulnar surfaces is a response to the non-orthogonality of the distracting force and joining line. Pin placement significantly affects the effective moment arm of the fixing pins to distract the bridged elbow. Both elbow angle and distraction mode directly alter the direction of the distracting force at the elbow center. In general, the hinges misalignment occurs in a direction opposite to the distraction-activated site. After joint distraction, the elastic deflection of the fixing pins inevitably makes both elbow and fixator hinges to misalign. This indicates that both joint distraction and hinge alignment are the interactive mechanisms. The humeroulnar separation is more concentric in the situation of the 120 degrees humeral distraction by using stiffer pins with convergent placement. Even so, the eccentric displacement of the elbow hinge is a crucial consideration in the initial placement of the guiding pin to compensate for hinge misalignment.

Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection

DOE PAGES

Gürsoy, Doğa; Hong, Young P.; He, Kuan; ...

2017-09-18

As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the samemore » error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.« less

Self-Noise of the STS-2 and sensitivity of its computation to errors in alignment of sensors

NASA Astrophysics Data System (ADS)

Gerner, Andreas; Sleeman, Reinoud; Grasemann, Bernhard; Lenhardt, Wolfgang

2016-04-01

The assessment of a seismometer's self-noise is an important part of establishing its health, quality, and suitability. A spectral coherence technique proposed by Sleeman et al. (2006) using synchronously recorded data of triples of collocated and co-aligned seismometers has shown to be a very robust and reliable way to estimate the self-noise of modern broadband seismic sensors. It has been demonstrated in previous works that the resulting self-noise spectra, primarily in the frequency range of Earth's microseisms, are considerably affected by small errors in the alignment of sensors. Further, due to the sensitivity of the 3-channel correlation technique to misalignment, numerical rotation of the recorded traces prior to self-noise computation can be performed to find best possible alignment by searching for minimum self-noise values. In this study we focus on the sensitivity of the 3-channel correlation technique to misalignment, and investigate the possibility of complete removal of the microseism signal from self-noise estimates for the sensors' three components separately. Data from a long-term installation of four STS-2 sensors, specifically intended for self-noise studies, at the Conrad Observatory (Austria) in a collaboration between the KNMI (Netherlands) and the ZAMG (Austria) provides a reliable basis for an accurate sensitivity analysis and self-noise assessment. Our work resulted in undisturbed self-noise estimates for the vertical components, and our current focus is on improving alignment of horizontal axes, and verification of the manufacturer's specification regarding orthogonality of all three components. The tools and methods developed within this research can help to quickly establish consistent self-noise models, including estimates of orthogonality and alignment, which facilitates comparison of different models and provides us with a means to test quality and accuracy of a seismic sensor over its life span.

Comparison of Lumbosacral Alignment in Geriatric and Non-Geriatric patients suffering low back pain.

PubMed

Kocyigit, Burhan Fatih; Berk, Ejder

2018-01-01

Lumbosacral alignment is a crucial factor for an appropriate spinal function. Changes in spinal alignment lead to diminished body biomechanics. Additionally, lumbosacral alignment may affect quality of life, sagittal balance and fall risk in elderly. In this study, we aimed to compare lumbosacral alignment in geriatric and non-geriatric patients suffering from low back pain. A total of 202 (120 male and 82 female) patients who visited to physical medicine and rehabilitation clinic with low back pain between January 2017 and August 2017 were enrolled in this study. Standing lateral lumbar radiographs were obtained from the electronic hospital database. Lumbar lordosis angle, sacral tilt, lumbosacral angle and lumbosacral disc angle were calculated on lateral standing lumbar radiographs. The mean age of the non-geriatric group was 43.02 ± 13.20 years, the geriatric group was 71.61 ± 6.42 years. In geriatric patients, lumbar lordosis angle, sacral tilt and lumbosacral disc angle were significantly smaller (p = 0.042, p = 0.017 and p = 0.017). No significant differences were observed in lumbosacral angle between the groups (p = 0.508). Our study indicates the specific changes in lumbosacral alignment with aging. Identifying these changes in lumbosacral alignment in the geriatric population will enable to create proper rehabilitation strategies.

System alignment using the Talbot effect

NASA Astrophysics Data System (ADS)

Chevallier, Raymond; Le Falher, Eric; Heggarty, Kevin

1990-08-01

The Talbot effect is utilized to correct an alignment problem related to a neural network used for image recognition, which required the alignment of a spatial light modulator (SLM) with the input module. A mathematical model which employs the Fresnel diffraction theory is presented to describe the method. The calculation of the diffracted amplitude describes the wavefront sphericity and the original object transmittance function in order to qualify the lateral shift of the Talbot image. Another explanation is set forth in terms of plane-wave illumination in the neural network. Using a Fourier series and by describing planes where all the harmonics are in phase, the reconstruction of Talbot images is explained. The alignment is effective when the lenslet array is aligned on the even Talbot images of the SLM pixels and the incident wave is a plane wave. The alignment is evaluated in terms of source and periodicity errors, tilt of the incident plane waves, and finite object dimensions. The effects of the error sources are concluded to be negligible, the lenslet array is shown to be successfully aligned with the SLM, and other alignment applications are shown to be possible.

A New Continuous Rotation IMU Alignment Algorithm Based on Stochastic Modeling for Cost Effective North-Finding Applications

PubMed Central

Li, Yun; Wu, Wenqi; Jiang, Qingan; Wang, Jinling

2016-01-01

Based on stochastic modeling of Coriolis vibration gyros by the Allan variance technique, this paper discusses Angle Random Walk (ARW), Rate Random Walk (RRW) and Markov process gyroscope noises which have significant impacts on the North-finding accuracy. A new continuous rotation alignment algorithm for a Coriolis vibration gyroscope Inertial Measurement Unit (IMU) is proposed in this paper, in which the extended observation equations are used for the Kalman filter to enhance the estimation of gyro drift errors, thus improving the north-finding accuracy. Theoretical and numerical comparisons between the proposed algorithm and the traditional ones are presented. The experimental results show that the new continuous rotation alignment algorithm using the extended observation equations in the Kalman filter is more efficient than the traditional two-position alignment method. Using Coriolis vibration gyros with bias instability of 0.1°/h, a north-finding accuracy of 0.1° (1σ) is achieved by the new continuous rotation alignment algorithm, compared with 0.6° (1σ) north-finding accuracy for the two-position alignment and 1° (1σ) for the fixed-position alignment. PMID:27983585

Effect of Transducer Orientation on Errors in Ultrasound Image-Based Measurements of Human Medial Gastrocnemius Muscle Fascicle Length and Pennation

PubMed Central

Gandevia, Simon C.; Herbert, Robert D.

2016-01-01

Ultrasound imaging is often used to measure muscle fascicle lengths and pennation angles in human muscles in vivo. Theoretically the most accurate measurements are made when the transducer is oriented so that the image plane aligns with muscle fascicles and, for measurements of pennation, when the image plane also intersects the aponeuroses perpendicularly. However this orientation is difficult to achieve and usually there is some degree of misalignment. Here, we used simulated ultrasound images based on three-dimensional models of the human medial gastrocnemius, derived from magnetic resonance and diffusion tensor images, to describe the relationship between transducer orientation and measurement errors. With the transducer oriented perpendicular to the surface of the leg, the error in measurement of fascicle lengths was about 0.4 mm per degree of misalignment of the ultrasound image with the muscle fascicles. If the transducer is then tipped by 20°, the error increases to 1.1 mm per degree of misalignment. For a given degree of misalignment of muscle fascicles with the image plane, the smallest absolute error in fascicle length measurements occurs when the transducer is held perpendicular to the surface of the leg. Misalignment of the transducer with the fascicles may cause fascicle length measurements to be underestimated or overestimated. Contrary to widely held beliefs, it is shown that pennation angles are always overestimated if the image is not perpendicular to the aponeurosis, even when the image is perfectly aligned with the fascicles. An analytical explanation is provided for this finding. PMID:27294280

Effect of Transducer Orientation on Errors in Ultrasound Image-Based Measurements of Human Medial Gastrocnemius Muscle Fascicle Length and Pennation.

PubMed

Bolsterlee, Bart; Gandevia, Simon C; Herbert, Robert D

2016-01-01

Ultrasound imaging is often used to measure muscle fascicle lengths and pennation angles in human muscles in vivo. Theoretically the most accurate measurements are made when the transducer is oriented so that the image plane aligns with muscle fascicles and, for measurements of pennation, when the image plane also intersects the aponeuroses perpendicularly. However this orientation is difficult to achieve and usually there is some degree of misalignment. Here, we used simulated ultrasound images based on three-dimensional models of the human medial gastrocnemius, derived from magnetic resonance and diffusion tensor images, to describe the relationship between transducer orientation and measurement errors. With the transducer oriented perpendicular to the surface of the leg, the error in measurement of fascicle lengths was about 0.4 mm per degree of misalignment of the ultrasound image with the muscle fascicles. If the transducer is then tipped by 20°, the error increases to 1.1 mm per degree of misalignment. For a given degree of misalignment of muscle fascicles with the image plane, the smallest absolute error in fascicle length measurements occurs when the transducer is held perpendicular to the surface of the leg. Misalignment of the transducer with the fascicles may cause fascicle length measurements to be underestimated or overestimated. Contrary to widely held beliefs, it is shown that pennation angles are always overestimated if the image is not perpendicular to the aponeurosis, even when the image is perfectly aligned with the fascicles. An analytical explanation is provided for this finding.

Alignment and Performance of the Infrared Multi-Object Spectrometer

NASA Technical Reports Server (NTRS)

Connelly, Joseph A.; Ohl, Raymond G.; Mentzell, J. Eric; Madison, Timothy J.; Hylan, Jason E.; Mink, Ronald G.; Saha, Timo T.; Tveekrem, June L.; Sparr, Leroy M.; Chambers, V. John;

Measuring Alignments between Galaxies and the Cosmic Web at z ˜ 2-3 Using IGM Tomography

NASA Astrophysics Data System (ADS)

Krolewski, Alex; Lee, Khee-Gan; Lukić, Zarija; White, Martin

2017-03-01

Many galaxy formation models predict alignments between galaxy spin and the cosmic web (I.e., directions of filaments and sheets), leading to an intrinsic alignment between galaxies that creates a systematic error in weak-lensing measurements. These effects are often predicted to be stronger at high redshifts (z ≳ 1) that are inaccessible to massive galaxy surveys on foreseeable instrumentation, but IGM tomography of the Lyα forest from closely spaced quasars and galaxies is starting to measure the z ˜ 2-3 cosmic web with requisite fidelity. Using mock surveys from hydrodynamical simulations, we examine the utility of this technique, in conjunction with coeval galaxy samples, to measure alignment between galaxies and the cosmic web at z ˜ 2.5. We show that IGM tomography surveys with ≲5 h -1 Mpc sightline spacing can accurately recover the eigenvectors of the tidal tensor, which we use to define the directions of the cosmic web. For galaxy spins and shapes, we use a model parameterized by the alignment strength, {{Δ }}< \\cos θ > , with respect to the tidal tensor eigenvectors from the underlying density field, and also consider observational effects such as errors in the galaxy position angle, inclination, and redshift. Measurements using the upcoming ˜1 deg2 CLAMATO tomographic survey and 600 coeval zCOSMOS-Deep galaxies should place 3σ limits on extreme alignment models with {{Δ }}< \\cos θ > ˜ 0.1, but much larger surveys encompassing >10,000 galaxies, such as Subaru PFS, will be required to constrain models with {{Δ }}< \\cos θ > ˜ 0.03. These measurements will constrain models of galaxy-cosmic web alignment and test tidal torque theory at z ˜ 2, improving our understanding of the physics of intrinsic alignments.

Measuring Alignments between Galaxies and the Cosmic Web at z ~ 2–3 Using IGM Tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krolewski, Alex; Lee, Khee-Gan; Luki?, Zarija

Many galaxy formation models predict alignments between galaxy spin and the cosmic web (i.e., directions of filaments and sheets), leading to an intrinsic alignment between galaxies that creates a systematic error in weak-lensing measurements. These effects are often predicted to be stronger at high redshifts (z ≳ 1) that are inaccessible to massive galaxy surveys on foreseeable instrumentation, but IGM tomography of the Lyα forest from closely spaced quasars and galaxies is starting to measure the z ~ 2-3 cosmic web with requisite fidelity. Using mock surveys from hydrodynamical simulations, we examine the utility of this technique, in conjunction withmore » coeval galaxy samples, to measure alignment between galaxies and the cosmic web at z ~ 2.5. We show that IGM tomography surveys with ≲ 5 h -1 Mpc sightline spacing can accurately recover the eigenvectors of the tidal tensor, which we use to define the directions of the cosmic web. For galaxy spins and shapes, we use a model parameterized by the alignment strength, Δ (cos θ), with respect to the tidal tensor eigenvectors from the underlying density field, and also consider observational effects such as errors in the galaxy position angle, inclination, and redshift. Measurements using the upcoming ~ 1 deg 2 CLAMATO tomographic survey and 600 coeval zCOSMOS-Deep galaxies should place 3σ limits on extreme alignment models with Δ (cos θ) ~ 0.1, but much larger surveys encompassing > 10,000 galaxies, such as Subaru PFS, will be required to constrain models with Δ (cos θ) ~ 0.3. These measurements will constrain models of galaxy-cosmic web alignment and test tidal torque theory at z ~ 2, improving our understanding of the physics of intrinsic alignments.« less

Measuring Alignments between Galaxies and the Cosmic Web at z ~ 2–3 Using IGM Tomography

DOE PAGES

Krolewski, Alex; Lee, Khee-Gan; Luki?, Zarija; ...

2017-02-28

Many galaxy formation models predict alignments between galaxy spin and the cosmic web (i.e., directions of filaments and sheets), leading to an intrinsic alignment between galaxies that creates a systematic error in weak-lensing measurements. These effects are often predicted to be stronger at high redshifts (z ≳ 1) that are inaccessible to massive galaxy surveys on foreseeable instrumentation, but IGM tomography of the Lyα forest from closely spaced quasars and galaxies is starting to measure the z ~ 2-3 cosmic web with requisite fidelity. Using mock surveys from hydrodynamical simulations, we examine the utility of this technique, in conjunction withmore » coeval galaxy samples, to measure alignment between galaxies and the cosmic web at z ~ 2.5. We show that IGM tomography surveys with ≲ 5 h -1 Mpc sightline spacing can accurately recover the eigenvectors of the tidal tensor, which we use to define the directions of the cosmic web. For galaxy spins and shapes, we use a model parameterized by the alignment strength, Δ (cos θ), with respect to the tidal tensor eigenvectors from the underlying density field, and also consider observational effects such as errors in the galaxy position angle, inclination, and redshift. Measurements using the upcoming ~ 1 deg 2 CLAMATO tomographic survey and 600 coeval zCOSMOS-Deep galaxies should place 3σ limits on extreme alignment models with Δ (cos θ) ~ 0.1, but much larger surveys encompassing > 10,000 galaxies, such as Subaru PFS, will be required to constrain models with Δ (cos θ) ~ 0.3. These measurements will constrain models of galaxy-cosmic web alignment and test tidal torque theory at z ~ 2, improving our understanding of the physics of intrinsic alignments.« less

Angle-domain common-image gathers from anisotropic Gaussian beam migration and its application to anisotropy-induced imaging errors analysis

NASA Astrophysics Data System (ADS)

Han, Jianguang; Wang, Yun; Yu, Changqing; Chen, Peng

2017-02-01

An approach for extracting angle-domain common-image gathers (ADCIGs) from anisotropic Gaussian beam prestack depth migration (GB-PSDM) is presented in this paper. The propagation angle is calculated in the process of migration using the real-value traveltime information of Gaussian beam. Based on the above, we further investigate the effects of anisotropy on GB-PSDM, where the corresponding ADCIGs are extracted to assess the quality of migration images. The test results of the VTI syncline model and the TTI thrust sheet model show that anisotropic parameters ɛ, δ, and tilt angle 𝜃, have a great influence on the accuracy of the migrated image in anisotropic media, and ignoring any one of them will cause obvious imaging errors. The anisotropic GB-PSDM with the true anisotropic parameters can obtain more accurate seismic images of subsurface structures in anisotropic media.

Design of an all-attitude flight control system to execute commanded bank angles and angles of attack

NASA Technical Reports Server (NTRS)

Burgin, G. H.; Eggleston, D. M.

1976-01-01

A flight control system for use in air-to-air combat simulation was designed. The input to the flight control system are commanded bank angle and angle of attack, the output are commands to the control surface actuators such that the commanded values will be achieved in near minimum time and sideslip is controlled to remain small. For the longitudinal direction, a conventional linear control system with gains scheduled as a function of dynamic pressure is employed. For the lateral direction, a novel control system, consisting of a linear portion for small bank angle errors and a bang-bang control system for large errors and error rates is employed.

Evaluation of Eight Methods for Aligning Orientation of Two Coordinate Systems.

PubMed

Mecheri, Hakim; Robert-Lachaine, Xavier; Larue, Christian; Plamondon, André

2016-08-01

The aim of this study was to evaluate eight methods for aligning the orientation of two different local coordinate systems. Alignment is very important when combining two different systems of motion analysis. Two of the methods were developed specifically for biomechanical studies, and because there have been at least three decades of algorithm development in robotics, it was decided to include six methods from this field. To compare these methods, an Xsens sensor and two Optotrak clusters were attached to a Plexiglas plate. The first optical marker cluster was fixed on the sensor and 20 trials were recorded. The error of alignment was calculated for each trial, and the mean, the standard deviation, and the maximum values of this error over all trials were reported. One-way repeated measures analysis of variance revealed that the alignment error differed significantly across the eight methods. Post-hoc tests showed that the alignment error from the methods based on angular velocities was significantly lower than for the other methods. The method using angular velocities performed the best, with an average error of 0.17 ± 0.08 deg. We therefore recommend this method, which is easy to perform and provides accurate alignment.

Telescope and mirrors development for the monolithic silicon carbide instrument of the osiris narrow angle camera

NASA Astrophysics Data System (ADS)

Calvel, Bertrand; Castel, Didier; Standarovski, Eric; Rousset, Gérard; Bougoin, Michel

2017-11-01

The international Rosetta mission, now planned by ESA to be launched in January 2003, will provide a unique opportunity to directly study the nucleus of comet 46P/Wirtanen and its activity in 2013. We describe here the design, the development and the performances of the telescope of the Narrow Angle Camera of the OSIRIS experiment et its Silicon Carbide telescope which will give high resolution images of the cometary nucleus in the visible spectrum. The development of the mirrors has been specifically detailed. The SiC parts have been manufactured by BOOSTEC, polished by STIGMA OPTIQUE and ion figured by IOM under the prime contractorship of ASTRIUM. ASTRIUM was also in charge of the alignment. The final optical quality of the aligned telescope is 30 nm rms wavefront error.

Comparison of two on-orbit attitude sensor alignment methods

NASA Technical Reports Server (NTRS)

Krack, Kenneth; Lambertson, Michael; Markley, F. Landis

1990-01-01

Compared here are two methods of on-orbit alignment of vector attitude sensors. The first method uses the angular difference between simultaneous measurements from two or more sensors. These angles are compared to the angular differences between the respective reference positions of the sensed objects. The alignments of the sensors are adjusted to minimize the difference between the two sets of angles. In the second method, the sensor alignment is part of a state vector that includes the attitude. The alignments are adjusted along with the attitude to minimize all observation residuals. It is shown that the latter method can result in much less alignment uncertainty when gyroscopes are used for attitude propagation during the alignment estimation. The additional information for this increased accuracy comes from knowledge of relative attitude obtained from the spacecraft gyroscopes. The theoretical calculations of this difference in accuracy are presented. Also presented are numerical estimates of the alignment uncertainties of the fixed-head star trackers on the Extreme Ultraviolet Explorer spacecraft using both methods.

Alignment of a vector magnetometer to an optical prism

DOE PAGES

Dietrich, M. R.; Bailey, K. G.; O’Connor, T. P.

2017-05-12

A method for alignment of a vector magnetometer to a rigidly attached prism is presented. This enables optical comparison of the magnetometer axes to physical surfaces in the apparatus, and thus an absolute determination of the magnetic field direction in space. This is in contrast with more common techniques, which focus on precise determination of the relative angles between magnetometer axes, and so are more suited to measuring differences in the direction of magnetic fields. Here we demonstrate precision better than 500 μrad on a fluxgate magnetometer, which also gives the coil orthogonality errors to a similar precision. As amore » result, the relative sensitivity of the three axes is also determined, with a precision of about 5 ×10 –4.« less

Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

PubMed Central

Pightling, Arthur W.; Petronella, Nicholas; Pagotto, Franco

2014-01-01

The wide availability of whole-genome sequencing (WGS) and an abundance of open-source software have made detection of single-nucleotide polymorphisms (SNPs) in bacterial genomes an increasingly accessible and effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between genomes (i.e., true SNPs) are detected at high rates and that the influences of errors (such as false positive SNPs, ambiguously called sites, and gaps) are mitigated is of utmost importance. The choices researchers make regarding the generation and analysis of WGS data can greatly influence the accuracy of short-read sequence alignments and, therefore, the efficacy of such experiments. We studied the effects of some of these choices, including: i) depth of sequencing coverage, ii) choice of reference-guided short-read sequence assembler, iii) choice of reference genome, and iv) whether to perform read-quality filtering and trimming, on our ability to detect true SNPs and on the frequencies of errors. We performed benchmarking experiments, during which we assembled simulated and real Listeria monocytogenes strain 08-5578 short-read sequence datasets of varying quality with four commonly used assemblers (BWA, MOSAIK, Novoalign, and SMALT), using reference genomes of varying genetic distances, and with or without read pre-processing (i.e., quality filtering and trimming). We found that assemblies of at least 50-fold coverage provided the most accurate results. In addition, MOSAIK yielded the fewest errors when reads were aligned to a nearly identical reference genome, while using SMALT to align reads against a reference sequence that is ∼0.82% distant from 08-5578 at the nucleotide level resulted in the detection of the greatest numbers of true SNPs and the fewest errors. Finally, we show that whether read pre-processing improves SNP detection depends upon the choice of reference sequence and assembler. In total, this study demonstrates that researchers should

Attenuation-emission alignment in cardiac PET∕CT based on consistency conditions

PubMed Central

Alessio, Adam M.; Kinahan, Paul E.; Champley, Kyle M.; Caldwell, James H.

2010-01-01

Purpose: In cardiac PET and PET∕CT imaging, misaligned transmission and emission images are a common problem due to respiratory and cardiac motion. This misalignment leads to erroneous attenuation correction and can cause errors in perfusion mapping and quantification. This study develops and tests a method for automated alignment of attenuation and emission data. Methods: The CT-based attenuation map is iteratively transformed until the attenuation corrected emission data minimize an objective function based on the Radon consistency conditions. The alignment process is derived from previous work by Welch et al. [“Attenuation correction in PET using consistency information,” IEEE Trans. Nucl. Sci. 45, 3134–3141 (1998)] for stand-alone PET imaging. The process was evaluated with the simulated data and measured patient data from multiple cardiac ammonia PET∕CT exams. The alignment procedure was applied to simulations of five different noise levels with three different initial attenuation maps. For the measured patient data, the alignment procedure was applied to eight attenuation-emission combinations with initially acceptable alignment and eight combinations with unacceptable alignment. The initially acceptable alignment studies were forced out of alignment a known amount and quantitatively evaluated for alignment and perfusion accuracy. The initially unacceptable studies were compared to the proposed aligned images in a blinded side-by-side review. Results: The proposed automatic alignment procedure reduced errors in the simulated data and iteratively approaches global minimum solutions with the patient data. In simulations, the alignment procedure reduced the root mean square error to less than 5 mm and reduces the axial translation error to less than 1 mm. In patient studies, the procedure reduced the translation error by >50% and resolved perfusion artifacts after a known misalignment for the eight initially acceptable patient combinations. The side

Coherent errors in quantum error correction

NASA Astrophysics Data System (ADS)

Greenbaum, Daniel; Dutton, Zachary

Analysis of quantum error correcting (QEC) codes is typically done using a stochastic, Pauli channel error model for describing the noise on physical qubits. However, it was recently found that coherent errors (systematic rotations) on physical data qubits result in both physical and logical error rates that differ significantly from those predicted by a Pauli model. We present analytic results for the logical error as a function of concatenation level and code distance for coherent errors under the repetition code. For data-only coherent errors, we find that the logical error is partially coherent and therefore non-Pauli. However, the coherent part of the error is negligible after two or more concatenation levels or at fewer than ɛ - (d - 1) error correction cycles. Here ɛ << 1 is the rotation angle error per cycle for a single physical qubit and d is the code distance. These results support the validity of modeling coherent errors using a Pauli channel under some minimum requirements for code distance and/or concatenation. We discuss extensions to imperfect syndrome extraction and implications for general QEC.

Achieving diffraction-limited nanometer-scale X-ray point focus with two crossed multilayer Laue lenses: alignment challenges

DOE PAGES

Yan, Hanfei; Huang, Xiaojing; Bouet, Nathalie; ...

2017-10-16

In this article, we discuss misalignment-induced aberrations in a pair of crossed multilayer Laue lenses used for achieving a nanometer-scale x-ray point focus. We thoroughly investigate the impacts of two most important contributions, the orthogonality and the separation distance between two lenses. We find that misalignment in the orthogonality results in astigmatism at 45º and other inclination angles when coupled with a separation distance error. Theoretical explanation and experimental verification are provided. We show that to achieve a diffraction-limited point focus, accurate alignment of the azimuthal angle is required to ensure orthogonality between two lenses, and the required accuracy ismore » scaled with the ratio of the focus size to the aperture size.« less

Alignment between Protostellar Outflows and Filamentary Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.

2017-09-01

We present new Submillimeter Array (SMA) observations of CO(2–1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mixmore » of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ∼3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.« less

Alignment between Protostellar Outflows and Filamentary Structure

NASA Astrophysics Data System (ADS)

Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.; Pokhrel, Riwaj; Sadavoy, Sarah I.; Vorobyov, Eduard I.; Tobin, John J.; Pineda, Jaime E.; Offner, Stella S. R.; Lee, Katherine I.; Kristensen, Lars E.; Jørgensen, Jes K.; Goodman, Alyssa A.; Bourke, Tyler L.; Arce, Héctor G.; Plunkett, Adele L.

2017-09-01

We present new Submillimeter Array (SMA) observations of CO(2-1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mix of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ˜3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.

Telemetry location error in a forested habitat

USGS Publications Warehouse

Chu, D.S.; Hoover, B.A.; Fuller, M.R.; Geissler, P.H.; Amlaner, Charles J.

1989-01-01

The error associated with locations estimated by radio-telemetry triangulation can be large and variable in a hardwood forest. We assessed the magnitude and cause of telemetry location errors in a mature hardwood forest by using a 4-element Yagi antenna and compass bearings toward four transmitters, from 21 receiving sites. The distance error from the azimuth intersection to known transmitter locations ranged from 0 to 9251 meters. Ninety-five percent of the estimated locations were within 16 to 1963 meters, and 50% were within 99 to 416 meters of actual locations. Angles with 20o of parallel had larger distance errors than other angles. While angle appeared most important, greater distances and the amount of vegetation between receivers and transmitters also contributed to distance error.

Roll and pitch set-up errors during volumetric modulated arc delivery: can adapting gantry and collimator angles compensate?

PubMed

Hoffmans-Holtzer, Nienke A; Hoffmans, Daan; Dahele, Max; Slotman, Ben J; Verbakel, Wilko F A R

2015-03-01

The purpose of this work was to investigate whether adapting gantry and collimator angles can compensate for roll and pitch setup errors during volumetric modulated arc therapy (VMAT) delivery. Previously delivered clinical plans for locally advanced head-and-neck (H&N) cancer (n = 5), localized prostate cancer (n = 2), and whole brain with simultaneous integrated boost to 5 metastases (WB + 5M, n = 1) were used for this study. Known rigid rotations were introduced in the planning CT scans. To compensate for these, in-house software was used to adapt gantry and collimator angles in the plan. Doses to planning target volumes (PTV) and critical organs at risk (OAR) were calculated with and without compensation and compared with the original clinical plan. Measurements in the sagittal plane in a polystyrene phantom using radiochromic film were compared by gamma (γ) evaluation for 2 H&N cancer patients. For H&N plans, the introduction of 2°-roll and 3°-pitch rotations reduced mean PTV coverage from 98.7 to 96.3%. This improved to 98.1% with gantry and collimator compensation. For prostate plans respective figures were 98.4, 97.5, and 98.4%. For WB + 5M, compensation worked less well, especially for smaller volumes and volumes farther from the isocenter. Mean comparative γ evaluation (3%, 1 mm) between original and pitched plans resulted in 86% γ < 1. The corrected plan restored the mean comparison to 96% γ < 1. Preliminary data suggest that adapting gantry and collimator angles is a promising way to correct roll and pitch set-up errors of < 3° during VMAT for H&N and prostate cancer.

RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning.

PubMed

Gao, Yujuan; Wang, Sheng; Deng, Minghua; Xu, Jinbo

2018-05-08

Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly, thus aiding protein tertiary structure prediction. However, direct angle prediction from sequence alone is challenging. In this article, we present a novel method (named RaptorX-Angle) to predict real-valued angles by combining clustering and deep learning. Tested on a subset of PDB25 and the targets in the latest two Critical Assessment of protein Structure Prediction (CASP), our method outperforms the existing state-of-art method SPIDER2 in terms of Pearson Correlation Coefficient (PCC) and Mean Absolute Error (MAE). Our result also shows approximately linear relationship between the real prediction errors and our estimated bounds. That is, the real prediction error can be well approximated by our estimated bounds. Our study provides an alternative and more accurate prediction of dihedral angles, which may facilitate protein structure prediction and functional study.

Controlled alignment of carbon nanofibers in a large-scale synthesis process

NASA Astrophysics Data System (ADS)

Merkulov, Vladimir I.; Melechko, A. V.; Guillorn, M. A.; Simpson, M. L.; Lowndes, D. H.; Whealton, J. H.; Raridon, R. J.

2002-06-01

Controlled alignment of catalytically grown carbon nanofibers (CNFs) at a variable angle to the substrate during a plasma-enhanced chemical vapor deposition process is achieved. The CNF alignment is controlled by the direction of the electric field lines during the synthesis process. Off normal CNF orientations are achieved by positioning the sample in the vicinity of geometrical features of the sample holder, where bending of the electric field lines occurs. The controlled growth of kinked CNFs that consist of two parts aligned at different angles to the substrate normal also is demonstrated.

Dual-mode switching of a liquid crystal panel for viewing angle control

NASA Astrophysics Data System (ADS)

Baek, Jong-In; Kwon, Yong-Hoan; Kim, Jae Chang; Yoon, Tae-Hoon

2007-03-01

The authors propose a method to control the viewing angle of a liquid crystal (LC) panel using dual-mode switching. To realize both wide viewing angle (WVA) characteristics and narrow viewing angle (NVA) characteristics with a single LC panel, the authors use two different dark states. The LC layer can be aligned homogeneously parallel to the transmission axis of the bottom polarizer for WVA dark state operation, while it can be aligned vertically for NVA dark state operation. The authors demonstrated that viewing angle control can be achieved with a single panel without any loss of contrast at the front.

Homogeneous alignment of nematic liquid crystals by ion beam etched surfaces

NASA Technical Reports Server (NTRS)

Wintucky, E. G.; Mahmood, R.; Johnson, D. L.

1979-01-01

A wide range of ion beam etch parameters capable of producing uniform homogeneous alignment of nematic liquid crystals on SiO2 films are discussed. The alignment surfaces were generated by obliquely incident (angles of 5 to 25 deg) argon ions with energies in the range of 0.5 to 2.0 KeV, ion current densities of 0.1 to 0.6 mA sq cm and etch times of 1 to 9 min. A smaller range of ion beam parameters (2.0 KeV, 0.2 mA sq cm, 5 to 10 deg and 1 to 5 min.) were also investigated with ZrO2 films and found suitable for homogeneous alignment. Extinction ratios were very high (1000), twist angles were small ( or = 3 deg) and tilt-bias angles very small ( or = 1 deg). Preliminary scanning electron microscopy results indicate a parallel oriented surface structure on the ion beam etched surfaces which may determine alignment.

Do small changes in rotation affect measurements of lower extremity limb alignment?

PubMed

Jamali, Amir A; Meehan, John P; Moroski, Nathan M; Anderson, Matthew J; Lamba, Ramit; Parise, Carol

2017-05-22

The alignment of the lower extremity has important implications in the development of knee arthritis. The effect of incremental rotations of the limb on common parameters of alignment has not been studied. The purpose of the study was to (1) determine the standardized neutral position measurements of alignment and (2) determine the effect of rotation on commonly used measurements of alignment. Eighty-seven full length CT angiography studies (49 males and 38 females, average age 66 years old) were included. Three-dimensional models were created using a rendering software program and placed on a virtual plane. An image of the extremity was obtained. Thirty scans were randomly selected, and those models were rotated in 3° intervals around the longitudinal axis and additional images were obtained. In the neutral position, the mechanical lateral distal femoral articular angle (mLDFA) was 85.6 ± 2.3°, medial proximal tibial angle (MPTA) was 86.1 ± 2.8°, and mechanical tibiofemoral angle (mTFA) was -0.7 ± 3.1°. Females had a more valgus alignment with a mTFA of 0.5 ± 2.9° while males had a more varus alignment with a mTFA of -1.7 ± 2.9°. The anatomic tibiofemoral angle (aTFA) was 4.8 ± 2.6°, the anatomic lateral distal femoral angle (aLDFA) measured 80.2 ± 2.2°, and the anatomical-mechanical angle (AMA) was 5.4 ± 0.7°. The prevalence of constitutional varus was 18%. The effect of rotation on the rotated scans led to statistically significant differences relative to the 0° measurement for all measurements. These effects may be small, and their clinical importance is unknown. This study provides new information on standardized measures of lower extremity alignment and the relationship between discreet axial rotations of the entire lower extremity and these parameters.

Precision lens assembly with alignment turning system

NASA Astrophysics Data System (ADS)

Ho, Cheng-Fang; Huang, Chien-Yao; Lin, Yi-Hao; Kuo, Hui-Jean; Kuo, Ching-Hsiang; Hsu, Wei-Yao; Chen, Fong-Zhi

2017-10-01

The poker chip assembly with high precision lens barrels is widely applied to ultra-high performance optical system. ITRC applies the poker chip assembly technology to the high numerical aperture objective lenses and lithography projection lenses because of its high efficiency assembly process. In order to achieve high precision lens cell for poker chip assembly, an alignment turning system (ATS) is developed. The ATS includes measurement, alignment and turning modules. The measurement module is equipped with a non-contact displacement sensor (NCDS) and an autocollimator (ACM). The NCDS and ACM are used to measure centration errors of the top and the bottom surface of a lens respectively; then the amount of adjustment of displacement and tilt with respect to the rotational axis of the turning machine for the alignment module can be determined. After measurement, alignment and turning processes on the ATS, the centration error of a lens cell with 200 mm in diameter can be controlled within 10 arcsec. Furthermore, a poker chip assembly lens cell with three sub-cells is demonstrated, each sub-cells are measured and accomplished with alignment and turning processes. The lens assembly test for five times by each three technicians; the average transmission centration error of assembly lens is 12.45 arcsec. The results show that ATS can achieve high assembly efficiency for precision optical systems.

Optimal reconstruction angles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook, G.O. Jr.; Knight, L.

1979-07-01

The question of optimal projection angles has recently become of interest in the field of reconstruction from projections. Here, studies are concentrated on the n x n pixel space, where literative algorithms such as ART and direct matrix techniques due to Katz are considered. The best angles are determined in a Gauss--Markov statistical sense as well as with respect to a function-theoretical error bound. The possibility of making photon intensity a function of angle is also examined. Finally, the best angles to use in an ART-like algorithm are studied. A certain set of unequally spaced angles was found to bemore » preferred in several contexts. 15 figures, 6 tables.« less

Navigated total knee arthroplasty: is it error-free?

PubMed

Chua, Kerk Hsiang Zackary; Chen, Yongsheng; Lingaraj, Krishna

2014-03-01

The aim of this study was to determine whether errors do occur in navigated total knee arthroplasty (TKAs) and to study whether errors in bone resection or implantation contribute to these errors. A series of 20 TKAs was studied using computer navigation. The coronal and sagittal alignments of the femoral and tibial cutting guides, the coronal and sagittal alignments of the final tibial implant and the coronal alignment of the final femoral implant were compared with that of the respective bone resections. To determine the post-implantation mechanical alignment of the limb, the coronal alignment of the femoral and tibial implants was combined. The median deviation between the femoral cutting guide and bone resection was 0° (range -0.5° to +0.5°) in the coronal plane and 1.0° (range -2.0° to +1.0°) in the sagittal plane. The median deviation between the tibial cutting guide and bone resection was 0.5° (range -1.0° to +1.5°) in the coronal plane and 1.0° (range -1.0° to +3.5°) in the sagittal plane. The median deviation between the femoral bone resection and the final implant was 0.25° (range -2.0° to 3.0°) in the coronal plane. The median deviation between the tibial bone resection and the final implant was 0.75° (range -3.0° to +1.5°) in the coronal plane and 1.75° (range -4.0° to +2.0°) in the sagittal plane. The median post-implantation mechanical alignment of the limb was 0.25° (range -3.0° to +2.0°). When navigation is used only to guide the positioning of the cutting jig, errors may arise in the manual, non-navigated steps of the procedure. Our study showed increased cutting errors in the sagittal plane for both the femur and the tibia, and following implantation, the greatest error was seen in the sagittal alignment of the tibial component. Computer navigation should be used not only to guide the positioning of the cutting jig, but also to check the bone resection and implant position during TKA. IV.

Downwind pre-aligned rotors for extreme-scale wind turbines

DOE PAGES

Loth, Eric; Steele, Adam; Qin, Chao; ...

2017-03-08

Downwind force angles are small for current turbines systems (1-5 MW) such that they may be readily accommodated by conventional upwind configurations. However, analysis indicates that extreme-scale systems (10-20 MW) will have larger angles that may benefit from downwind-aligned configurations. To examine potential rotor mass reduction, the pre-alignment concept was investigated a two-bladed configuration by keeping the structural and aerodynamic characteristics of each blade fixed (to avoids a complete blade re-design). Simulations for a 13.2 MW rated rotor at steady-state conditions show that this concept-level two-bladed design may yield 25% rotor mass savings while also reducing average blade stress overmore » all wind speeds. These results employed a pre-alignment on the basis of a wind speed of 1.25 times the rated wind speed. The downwind pre-aligned concept may also reduce damage equivalent loads on the blades by 60% for steady rated wind conditions. Even higher mass and damage equivalent load savings (relative to conventional upwind designs) may be possible for larger systems (15-20 MW) for which load-alignment angles become even larger. Furthermore, much more work is needed to determine whether this concept can be translated into a practical design that must meet a wide myriad of other criteria.« less

Downwind pre-aligned rotors for extreme-scale wind turbines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loth, Eric; Steele, Adam; Qin, Chao

Downwind force angles are small for current turbines systems (1-5 MW) such that they may be readily accommodated by conventional upwind configurations. However, analysis indicates that extreme-scale systems (10-20 MW) will have larger angles that may benefit from downwind-aligned configurations. To examine potential rotor mass reduction, the pre-alignment concept was investigated a two-bladed configuration by keeping the structural and aerodynamic characteristics of each blade fixed (to avoids a complete blade re-design). Simulations for a 13.2 MW rated rotor at steady-state conditions show that this concept-level two-bladed design may yield 25% rotor mass savings while also reducing average blade stress overmore » all wind speeds. These results employed a pre-alignment on the basis of a wind speed of 1.25 times the rated wind speed. The downwind pre-aligned concept may also reduce damage equivalent loads on the blades by 60% for steady rated wind conditions. Even higher mass and damage equivalent load savings (relative to conventional upwind designs) may be possible for larger systems (15-20 MW) for which load-alignment angles become even larger. Furthermore, much more work is needed to determine whether this concept can be translated into a practical design that must meet a wide myriad of other criteria.« less

Orbit Alignment in Triple Stars

NASA Astrophysics Data System (ADS)

Tokovinin, Andrei

2017-08-01

The statistics of the angle Φ between orbital angular momenta in hierarchical triple systems with known inner visual or astrometric orbits are studied. A correlation between apparent revolution directions proves the partial orbit alignment known from earlier works. The alignment is strong in triples with outer projected separation less than ˜50 au, where the average Φ is about 20^\\circ . In contrast, outer orbits wider than 1000 au are not aligned with the inner orbits. It is established that the orbit alignment decreases with the increasing mass of the primary component. The average eccentricity of inner orbits in well-aligned triples is smaller than in randomly aligned ones. These findings highlight the role of dissipative interactions with gas in defining the orbital architecture of low-mass triple systems. On the other hand, chaotic dynamics apparently played a role in shaping more massive hierarchies. The analysis of projected configurations and triples with known inner and outer orbits indicates that the distribution of Φ is likely bimodal, where 80% of triples have {{Φ }}< 70^\\circ and the remaining ones are randomly aligned.

The Alignment of the Mean Wind and Stress Vectors in the Unstable Surface Layer

NASA Astrophysics Data System (ADS)

Bernardes, M.; Dias, N. L.

2010-01-01

A significant non-alignment between the mean horizontal wind vector and the stress vector was observed for turbulence measurements both above the water surface of a large lake, and over a land surface (soybean crop). Possible causes for this discrepancy such as flow distortion, averaging times and the procedure used for extracting the turbulent fluctuations (low-pass filtering and filter widths etc.), were dismissed after a detailed analysis. Minimum averaging times always less than 30 min were established by calculating ogives, and error bounds for the turbulent stresses were derived with three different approaches, based on integral time scales (first-crossing and lag-window estimates) and on a bootstrap technique. It was found that the mean absolute value of the angle between the mean wind and stress vectors is highly related to atmospheric stability, with the non-alignment increasing distinctively with increasing instability. Given a coordinate rotation that aligns the mean wind with the x direction, this behaviour can be explained by the growth of the relative error of the u- w component with instability. As a result, under more unstable conditions the u- w and the v- w components become of the same order of magnitude, and the local stress vector gives the impression of being non-aligned with the mean wind vector. The relative error of the v- w component is large enough to make it undistinguishable from zero throughout the range of stabilities. Therefore, the standard assumptions of Monin-Obukhov similarity theory hold: it is fair to assume that the v- w stress component is actually zero, and that the non-alignment is a purely statistical effect. An analysis of the dimensionless budgets of the u- w and the v- w components confirms this interpretation, with both shear and buoyant production of u- w decreasing with increasing instability. In the v- w budget, shear production is zero by definition, while buoyancy displays very low-intensity fluctuations around

Alignment of chirped-pulse compressor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yakovlev, I V

2012-11-30

An original method of alignment of grating compressors for ultrahigh-power CPA laser systems is proposed. The use of this method for adjustment of the grating compressor of a PEARL subpetawatt laser complex made it possible to align the diffraction gratings with a second accuracy in all three angular degrees of freedom, including alignment of the grooves, and to adjust the angles of beam incidence on the grating with a high accuracy. A simple method for measuring the difference in the groove densities of gratings with accuracy better than 0.005 lines mm{sup -1} is proposed and tested. (control of laser radiationmore » parameters)« less

Experimental observation of water saturation effects on shear wave splitting in synthetic rock with fractures aligned at oblique angles

NASA Astrophysics Data System (ADS)

Amalokwu, Kelvin; Chapman, Mark; Best, Angus I.; Sothcott, Jeremy; Minshull, Timothy A.; Li, Xiang-Yang

2015-01-01

Fractured rocks are known to exhibit seismic anisotropy and shear wave splitting (SWS). SWS is commonly used for fractured rock characterization and has been shown to be sensitive to fluid type. The presence of partial liquid/gas saturation is also known to affect the elastic properties of rocks. The combined effect of both fractures and partial liquid/gas saturation is still unknown. Using synthetic, silica-cemented sandstones with aligned penny-shaped voids, we conducted laboratory ultrasonic experiments to investigate the effect fractures aligned at an oblique angle to wave propagation would have on SWS under partial liquid/gas saturation conditions. The result for the fractured rock shows a saturation dependence which can be explained by combining a fractured rock model and a partial saturation model. At high to full water saturation values, SWS decreases as a result of the fluid bulk modulus effect on the quasi-shear wave. This bulk modulus effect is frequency dependent as a result of wave-induced fluid flow mechanisms, which would in turn lead to frequency dependent SWS. This result suggests the possible use of SWS for discriminating between full liquid saturation and partial liquid/gas saturation.

Ambient and Cryogenic Alignment Verification and Performance of the Infrared Multi-Object Spectrometer

NASA Technical Reports Server (NTRS)

Connelly, Joseph A.; Ohl, Raymond G.; Mink, Ronald G.; Mentzell, J. Eric; Saha, Timo T.; Tveekrem, June L.; Hylan, Jason E.; Sparr, Leroy M.; Chambers, V. John; Hagopian, John G.

2003-01-01

The Infrared Multi-Object Spectrometer (IRMOS) is a facility instrument for the Kitt Peak National Observatory 4 and 2.1 meter telescopes. IRMOS is a near-IR (0.8 - 2.5 micron) spectrometer with low- to mid-resolving power (R = 300 - 3000). IRMOS produces simultaneous spectra of approximately 100 objects in its 2.8 x 2.0 arc-min field of view using a commercial Micro Electro-Mechanical Systems (MEMS) Digital Micro-mirror Device (DMD) from Texas Instruments. The IRMOS optical design consists of two imaging subsystems. The focal reducer images the focal plane of the telescope onto the DMD field stop, and the spectrograph images the DMD onto the detector. We describe ambient breadboard subsystem alignment and imaging performance of each stage independently, and the ambient and cryogenic imaging performance of the fully assembled instrument. Interferometric measurements of subsystem wavefront error serve to venfy alignment, and are accomplished using a commercial, modified Twyman-Green laser unequal path interferometer. Image testing provides further verification of the optomechanical alignment method and a measurement of near-angle scattered light due to mirror small-scale surface error. Image testing is performed at multiple field points. A mercury-argon pencil lamp provides spectral lines at 546.1 nm and 1550 nm, and a CCD camera and IR camera are used as detectors. We use commercial optical modeling software to predict the point-spread function and its effect on instrument slit transmission and resolution. Our breadboard test results validate this prediction. We conclude with an instrument performance prediction for first light.

Implant alignment in total elbow arthroplasty: conventional vs. navigated techniques

NASA Astrophysics Data System (ADS)

McDonald, Colin P.; Johnson, James A.; King, Graham J. W.; Peters, Terry M.

2009-02-01

Incorrect selection of the native flexion-extension axis during implant alignment in elbow replacement surgery is likely a significant contributor to failure of the prosthesis. Computer and image-assisted surgery is emerging as a useful surgical tool in terms of improving the accuracy of orthopaedic procedures. This study evaluated the accuracy of implant alignment using an image-based navigation technique compared against a conventional non-navigated approach. Implant alignment error was 0.8 +/- 0.3 mm in translation and 1.1 +/- 0.4° in rotation for the navigated alignment, compared with 3.1 +/- 1.3 mm and 5.0 +/- 3.8° for the non-navigated alignment. Five (5) of the 11 non-navigated alignments were malaligned greater than 5° while none of the navigated alignments were placed with an error of greater than 2.0°. It is likely that improved implant positioning will lead to reduced implant loading and wear, resulting in fewer implantrelated complications and revision surgeries.

IMU-to-Segment Assignment and Orientation Alignment for the Lower Body Using Deep Learning

PubMed Central

2018-01-01

approaches and final models we achieved 98.57% average accuracy over all segments for the I2S assignment task (100% when excluding left/right switches) and an average median angle error over all segments and axes of 2.91° for the I2S alignment task. PMID:29351262

Fabrication and material properties of fibrous PHBV scaffolds depending on the cross-ply angle for tissue engineering.

PubMed

Kim, Yang-Hee; Min, Young-Ki; Lee, Byong-Taek

2012-11-01

Fibrous PHBV cross-ply scaffolds were fabricated using the electrospinning technique. The electrospun fibers were arranged depending on angles of alignment, which were 180°, 90°, 60°, and 45°. The stress and strain values of the fibrous PHBV cross-ply scaffolds increased as the cross-ply angle increased. At 180°, the strength and strain values of the fibers depended on tensile loading directions. At an alignment of 90°, the PHBV scaffolds had a stress value of 3.5 MPa, which was more than two times higher than the random structure. The cell morphology and proliferation of L-929 cells was strongly dependant on the fiber alignment and the best results were observed when the angle alignment was high. The results of this study showed that the cross-ply structure of the PHBV scaffold affected not only the cell adhesion and spreading properties but also dictated the mechanical properties, which were dependent on the angles of alignment.

Accuracy of estimating Unicondylar Knee Replacement implant varus/valgus angles from antero-posterior radiographs.

PubMed

Khare, Rahul; Jaramaz, Branislav

2016-12-01

Unicondylar Knee Replacement (UKR) is an orthopedic surgical procedure to reduce pain and improve function in the knee. Load-bearing long-standing antero-posterior (AP) radiographs are typically used postoperatively to measure the leg alignment and assess the varus/valgus implant orientation. However, implant out-of-plane rotations, user variability, and X-ray acquisition parameters introduce errors in the estimation of the implant varus/valgus estimation. Previous work has explored the accuracy of various imaging modalities in this estimation. In this work, we explored the impact of out-of-plane rotations and X-ray acquisition parameters on the estimation of implant component varus/valgus angles. For our study, we used a single CT scan and positioned femoral and tibial implants under varying orientations within the CT volume. Then, a custom software application was used to obtain digitally reconstructed radiographs from the CT scan with implants under varying orientations. Two users were then asked to manually estimate the varus/valgus angles for the implants. We found that there was significant inter-user variability (p < 0.05) in the varus/valgus estimates for the two users. However, the 'ideal' measurements, obtained using actual implant orientations, showed small errors due to variations in implant orientation. We also found that variation in the projection center does not have a statistically significant impact (p < 0.01) on the estimation of implant varus/valgus angles. We conclude that manual estimates of UKR implant varus/valgus orientations are unreliable.

The effect of dimple error on the horizontal launch angle and side spin of the golf ball during putting.

PubMed

Richardson, Ashley K; Mitchell, Andrew C S; Hughes, Gerwyn

2017-02-01

This study aimed to examine the effect of the impact point on the golf ball on the horizontal launch angle and side spin during putting with a mechanical putting arm and human participants. Putts of 3.2 m were completed with a mechanical putting arm (four putter-ball combinations, total of 160 trials) and human participants (two putter-ball combinations, total of 337 trials). The centre of the dimple pattern (centroid) was located and the following variables were measured: distance and angle of the impact point from the centroid and surface area of the impact zone. Multiple regression analysis was conducted to identify whether impact variables had significant associations with ball roll variables, horizontal launch angle and side spin. Significant associations were identified between impact variables and horizontal launch angle with the mechanical putting arm but this was not replicated with human participants. The variability caused by "dimple error" was minimal with the mechanical putting arm and not evident with human participants. Differences between the mechanical putting arm and human participants may be due to the way impulse is imparted on the ball. Therefore it is concluded that variability of impact point on the golf ball has a minimal effect on putting performance.

Alignment method for solar collector arrays

DOEpatents

Driver, Jr., Richard B

2012-10-23

The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

Cervical spine alignment in the pediatric population: a radiographic normative study of 150 asymptomatic patients.

PubMed

Abelin-Genevois, K; Idjerouidene, A; Roussouly, P; Vital, J M; Garin, C

2014-07-01

To describe the normal cervical sagittal alignment of the pediatric spine in a normal population and to identify the changes during growth period. We randomly selected in PACS database 150 full-spine standing views. Exclusion criteria were: age >18 years, spinal deformity and any disease affecting the spine (medical charts reviewing). For cervical alignment we measured: OC-angle according to Mc Gregor, C1C7 angle, upper cervical angle, inferior cervical angle and C7 tilt. Spino pelvic parameters were analyzed: T1 tilt, thoracic kyphosis, lumbar lordosis, pelvic incidence, sacral slope and pelvic tilt. We compared two age subgroups (juvenile and adolescent). Differences between age groups and gender were tested using Student's t test. Correlations between sagittal spinal parameters were evaluated using Pearson's test. Cervical spine shape was correlated to cranio cervical orientation to maintain horizontal gaze (r = 0.60) and to thoracic kyphosis (r = -0.46). Cervical spine alignment was significantly different between the two age groups except for the global C1C7 cervical lordosis, which remained stable. A significant gender difference was found for all the cervical sagittal angles (p < 0.01) whereas no differences were demonstrated for the spino pelvic parameters, except the lumbar lordosis (p = 0.047). This study is the first to report the cervical spinal alignment in a normal pediatric Caucasian population. Even though cervical lordosis is the common shape, our results showed variability in cervical sagittal alignment. Cervical spine is a junctional area that adjusts its alignment to the head position and to the underlying spinal alignment.

Relay telescope for high power laser alignment system

DOEpatents

Dane, C. Brent; Hackel, Lloyd; Harris, Fritz B.

2006-09-19

A laser system includes an optical path having an intracavity relay telescope with a telescope focal point for imaging an output of the gain medium between an image location at or near the gain medium and an image location at or near an output coupler for the laser system. A kinematic mount is provided within a vacuum chamber, and adapted to secure beam baffles near the telescope focal point. An access port on the vacuum chamber is adapted for allowing insertion and removal of the beam baffles. A first baffle formed using an alignment pinhole aperture is used during alignment of the laser system. A second tapered baffle replaces the alignment aperture during operation and acts as a far-field baffle in which off angle beams strike the baffle a grazing angle of incidence, reducing fluence levels at the impact areas.

Accounting for optical errors in microtensiometry.

PubMed

Hinton, Zachary R; Alvarez, Nicolas J

2018-09-15

Drop shape analysis (DSA) techniques measure interfacial tension subject to error in image analysis and the optical system. While considerable efforts have been made to minimize image analysis errors, very little work has treated optical errors. There are two main sources of error when considering the optical system: the angle of misalignment and the choice of focal plane. Due to the convoluted nature of these sources, small angles of misalignment can lead to large errors in measured curvature. We demonstrate using microtensiometry the contributions of these sources to measured errors in radius, and, more importantly, deconvolute the effects of misalignment and focal plane. Our findings are expected to have broad implications on all optical techniques measuring interfacial curvature. A geometric model is developed to analytically determine the contributions of misalignment angle and choice of focal plane on measurement error for spherical cap interfaces. This work utilizes a microtensiometer to validate the geometric model and to quantify the effect of both sources of error. For the case of a microtensiometer, an empirical calibration is demonstrated that corrects for optical errors and drastically simplifies implementation. The combination of geometric modeling and experimental results reveal a convoluted relationship between the true and measured interfacial radius as a function of the misalignment angle and choice of focal plane. The validated geometric model produces a full operating window that is strongly dependent on the capillary radius and spherical cap height. In all cases, the contribution of optical errors is minimized when the height of the spherical cap is equivalent to the capillary radius, i.e. a hemispherical interface. The understanding of these errors allow for correct measure of interfacial curvature and interfacial tension regardless of experimental setup. For the case of microtensiometry, this greatly decreases the time for experimental setup

Multi-Angle Snowflake Camera Instrument Handbook

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stuefer, Martin; Bailey, J.

2016-07-01

The Multi-Angle Snowflake Camera (MASC) takes 9- to 37-micron resolution stereographic photographs of free-falling hydrometers from three angles, while simultaneously measuring their fall speed. Information about hydrometeor size, shape orientation, and aspect ratio is derived from MASC photographs. The instrument consists of three commercial cameras separated by angles of 36º. Each camera field of view is aligned to have a common single focus point about 10 cm distant from the cameras. Two near-infrared emitter pairs are aligned with the camera’s field of view within a 10-angular ring and detect hydrometeor passage, with the lower emitters configured to trigger the MASCmore » cameras. The sensitive IR motion sensors are designed to filter out slow variations in ambient light. Fall speed is derived from successive triggers along the fall path. The camera exposure times are extremely short, in the range of 1/25,000th of a second, enabling the MASC to capture snowflake sizes ranging from 30 micrometers to 3 cm.« less

Some Alignment Considerations for the Next Linear Collider

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruland, R

Next Linear Collider type accelerators require a new level of alignment quality. The relative alignment of these machines is to be maintained in an error envelope dimensioned in micrometers and for certain parts in nanometers. In the nanometer domain our terra firma cannot be considered monolithic but compares closer to jelly. Since conventional optical alignment methods cannot deal with the dynamics and cannot approach the level of accuracy, special alignment and monitoring techniques must be pursued.

A single camera photogrammetry system for multi-angle fast localization of EEG electrodes.

PubMed

Qian, Shuo; Sheng, Yang

2011-11-01

Photogrammetry has become an effective method for the determination of electroencephalography (EEG) electrode positions in three dimensions (3D). Capturing multi-angle images of the electrodes on the head is a fundamental objective in the design of photogrammetry system for EEG localization. Methods in previous studies are all based on the use of either a rotating camera or multiple cameras, which are time-consuming or not cost-effective. This study aims to present a novel photogrammetry system that can realize simultaneous acquisition of multi-angle head images in a single camera position. Aligning two planar mirrors with the angle of 51.4°, seven views of the head with 25 electrodes are captured simultaneously by the digital camera placed in front of them. A complete set of algorithms for electrode recognition, matching, and 3D reconstruction is developed. It is found that the elapsed time of the whole localization procedure is about 3 min, and camera calibration computation takes about 1 min, after the measurement of calibration points. The positioning accuracy with the maximum error of 1.19 mm is acceptable. Experimental results demonstrate that the proposed system provides a fast and cost-effective method for the EEG positioning.

Modeling coherent errors in quantum error correction

NASA Astrophysics Data System (ADS)

Greenbaum, Daniel; Dutton, Zachary

2018-01-01

Analysis of quantum error correcting codes is typically done using a stochastic, Pauli channel error model for describing the noise on physical qubits. However, it was recently found that coherent errors (systematic rotations) on physical data qubits result in both physical and logical error rates that differ significantly from those predicted by a Pauli model. Here we examine the accuracy of the Pauli approximation for noise containing coherent errors (characterized by a rotation angle ɛ) under the repetition code. We derive an analytic expression for the logical error channel as a function of arbitrary code distance d and concatenation level n, in the small error limit. We find that coherent physical errors result in logical errors that are partially coherent and therefore non-Pauli. However, the coherent part of the logical error is negligible at fewer than {ε }-({dn-1)} error correction cycles when the decoder is optimized for independent Pauli errors, thus providing a regime of validity for the Pauli approximation. Above this number of correction cycles, the persistent coherent logical error will cause logical failure more quickly than the Pauli model would predict, and this may need to be combated with coherent suppression methods at the physical level or larger codes.

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

PubMed Central

Satija, Rahul; Novák, Ádám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-01-01

Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the α-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from PMID:19715598

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

PubMed

Satija, Rahul; Novák, Adám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-08-28

We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the alpha-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from http://www.stats.ox.ac.uk/~satija/BigFoot/

RF Jitter Modulation Alignment Sensing

NASA Astrophysics Data System (ADS)

Ortega, L. F.; Fulda, P.; Diaz-Ortiz, M.; Perez Sanchez, G.; Ciani, G.; Voss, D.; Mueller, G.; Tanner, D. B.

2017-01-01

We will present the numerical and experimental results of a new alignment sensing scheme which can reduce the complexity of alignment sensing systems currently used, while maintaining the same shot noise limited sensitivity. This scheme relies on the ability of electro-optic beam deflectors to create angular modulation sidebands in radio frequency, and needs only a single-element photodiode and IQ demodulation to generate error signals for tilt and translation degrees of freedom in one dimension. It distances itself from current techniques by eliminating the need for beam centering servo systems, quadrant photodetectors and Gouy phase telescopes. RF Jitter alignment sensing can be used to reduce the complexity in the alignment systems of many laser optical experiments, including LIGO and the ALPS experiment.

Postoperative limb alignment and its determinants after minimally invasive Oxford medial unicompartmental knee arthroplasty.

PubMed

Mullaji, Arun B; Shetty, Gautam M; Kanna, Raj

2011-09-01

One hundred twenty-two consecutive minimally invasive Oxford phase 3 medial unicompartmental knee arthroplasties in 109 patients were evaluated for postoperative limb alignment and the influence of factors such as preoperative limb alignment, age, body mass index, sex, insert thickness, and surgeon's experience. The mean mechanical preoperative hip-knee-ankle (HKA) angle of 172.2° ± 3.1° improved to 177.1° ± 2.9° postoperatively. In 75% of the limbs, the HKA angle was restored to within an acceptable alignment of 177° ± 3°, 14% of the limbs were in excessive varus (<174°), and 11% were in valgus (>180°). Only preoperative HKA angle was predictive of postoperative HKA angle. Although most of the limbs had acceptable limb alignment after unicompartmental knee arthroplasty, limbs with more severe preoperative varus deformity had a tendency to remain in excessive varus, and limbs with lesser preoperative varus deformity had a greater tendency to go into valgus postoperatively. Copyright © 2011 Elsevier Inc. All rights reserved.

Computation of misalignment and primary mirror astigmatism figure error of two-mirror telescopes

NASA Astrophysics Data System (ADS)

Gu, Zhiyuan; Wang, Yang; Ju, Guohao; Yan, Changxiang

2018-01-01

Active optics usually uses the computation models based on numerical methods to correct misalignments and figure errors at present. These methods can hardly lead to any insight into the aberration field dependencies that arise in the presence of the misalignments. An analytical alignment model based on third-order nodal aberration theory is presented for this problem, which can be utilized to compute the primary mirror astigmatic figure error and misalignments for two-mirror telescopes. Alignment simulations are conducted for an R-C telescope based on this analytical alignment model. It is shown that in the absence of wavefront measurement errors, wavefront measurements at only two field points are enough, and the correction process can be completed with only one alignment action. In the presence of wavefront measurement errors, increasing the number of field points for wavefront measurements can enhance the robustness of the alignment model. Monte Carlo simulation shows that, when -2 mm ≤ linear misalignment ≤ 2 mm, -0.1 deg ≤ angular misalignment ≤ 0.1 deg, and -0.2 λ ≤ astigmatism figure error (expressed as fringe Zernike coefficients C5 / C6, λ = 632.8 nm) ≤0.2 λ, the misaligned systems can be corrected to be close to nominal state without wavefront testing error. In addition, the root mean square deviation of RMS wavefront error of all the misaligned samples after being corrected is linearly related to wavefront testing error.

Wafer scale oblique angle plasma etching

DOEpatents

Burckel, David Bruce; Jarecki, Jr., Robert L.; Finnegan, Patrick Sean

2017-05-23

Wafer scale oblique angle etching of a semiconductor substrate is performed in a conventional plasma etch chamber by using a fixture that supports a multiple number of separate Faraday cages. Each cage is formed to include an angled grid surface and is positioned such that it will be positioned over a separate one of the die locations on the wafer surface when the fixture is placed over the wafer. The presence of the Faraday cages influences the local electric field surrounding each wafer die, re-shaping the local field to be disposed in alignment with the angled grid surface. The re-shaped plasma causes the reactive ions to follow a linear trajectory through the plasma sheath and angled grid surface, ultimately impinging the wafer surface at an angle. The selected geometry of the Faraday cage angled grid surface thus determines the angle at with the reactive ions will impinge the wafer.

Evaluation of lens distortion errors in video-based motion analysis

NASA Technical Reports Server (NTRS)

Poliner, Jeffrey; Wilmington, Robert; Klute, Glenn K.; Micocci, Angelo

1993-01-01

In an effort to study lens distortion errors, a grid of points of known dimensions was constructed and videotaped using a standard and a wide-angle lens. Recorded images were played back on a VCR and stored on a personal computer. Using these stored images, two experiments were conducted. Errors were calculated as the difference in distance from the known coordinates of the points to the calculated coordinates. The purposes of this project were as follows: (1) to develop the methodology to evaluate errors introduced by lens distortion; (2) to quantify and compare errors introduced by use of both a 'standard' and a wide-angle lens; (3) to investigate techniques to minimize lens-induced errors; and (4) to determine the most effective use of calibration points when using a wide-angle lens with a significant amount of distortion. It was seen that when using a wide-angle lens, errors from lens distortion could be as high as 10 percent of the size of the entire field of view. Even with a standard lens, there was a small amount of lens distortion. It was also found that the choice of calibration points influenced the lens distortion error. By properly selecting the calibration points and avoidance of the outermost regions of a wide-angle lens, the error from lens distortion can be kept below approximately 0.5 percent with a standard lens and 1.5 percent with a wide-angle lens.

Wave drag reduction with a self-aligning aerodisk on a missile configuration

NASA Astrophysics Data System (ADS)

Schnepf, C.; Wysocki, O.; Schülein, E.

2017-06-01

A self-aligning aerodisk to reduce the wave drag on a pitching missile is numerically investigated. The motion and the Mach number were chosen to match a maneuver flight of an actual missile: pitching frequency f = 7.5 Hz, Mach number M = 2.2, and range of angle of attack 0° < < 21° . The self-alignment was realized with a coupling of the §ow solver with a 6DoF (6 degrees of freedom) tool. In the entire range of angle of attack, the drag could be reduced with the self-aligning aerodisk. A comparison with experimental data showed in parts a quite good agreement in the aerodynamic coe©cients, in the shock structure, and in the alignment of the aerodisk.

Automatic Alignment of Displacement-Measuring Interferometer

NASA Technical Reports Server (NTRS)

Halverson, Peter; Regehr, Martin; Spero, Robert; Alvarez-Salazar, Oscar; Loya, Frank; Logan, Jennifer

2006-01-01

A control system strives to maintain the correct alignment of a laser beam in an interferometer dedicated to measuring the displacement or distance between two fiducial corner-cube reflectors. The correct alignment of the laser beam is parallel to the line between the corner points of the corner-cube reflectors: Any deviation from parallelism changes the length of the optical path between the reflectors, thereby introducing a displacement or distance measurement error. On the basis of the geometrical optics of corner-cube reflectors, the length of the optical path can be shown to be L = L(sub 0)cos theta, where L(sub 0) is the distance between the corner points and theta is the misalignment angle. Therefore, the measurement error is given by DeltaL = L(sub 0)(cos theta - 1). In the usual case in which the misalignment is small, this error can be approximated as DeltaL approximately equal to -L(sub 0)theta sup 2/2. The control system (see figure) is implemented partly in hardware and partly in software. The control system includes three piezoelectric actuators for rapid, fine adjustment of the direction of the laser beam. The voltages applied to the piezoelectric actuators include components designed to scan the beam in a circular pattern so that the beam traces out a narrow cone (60 microradians wide in the initial application) about the direction in which it is nominally aimed. This scan is performed at a frequency (2.5 Hz in the initial application) well below the resonance frequency of any vibration of the interferometer. The laser beam makes a round trip to both corner-cube reflectors and then interferes with the launched beam. The interference is detected on a photodiode. The length of the optical path is measured by a heterodyne technique: A 100- kHz frequency shift between the launched beam and a reference beam imposes, on the detected signal, an interferometric phase shift proportional to the length of the optical path. A phase meter comprising analog

Effects of Lordotic Angle of a Cage on Sagittal Alignment and Clinical Outcome in One Level Posterior Lumbar Interbody Fusion with Pedicle Screw Fixation

PubMed Central

Lee, Ji-Ho; Lee, Dong-Oh; Lee, Jae Hyup; Shim, Hee Jong

2015-01-01

This study aims to assess the differences in the radiological and clinical results depending on the lordotic angles of the cage in posterior lumbar interbody fusion (PLIF). We reviewed 185 segments which underwent PLIF using two different lordotic angles of 4° and 8° of a polyetheretherketone (PEEK) cage. The segmental lordosis and total lumbar lordosis of the 4° and 8° cage groups were compared preoperatively, as well as on the first postoperative day, 6th and 12th months postoperatively. Clinical assessment was performed using the ODI and the VAS of low back pain. The pre- and immediate postoperative segmental lordosis angles were 12.9° and 12.6° in the 4° group and 12° and 12.0° in the 8° group. Both groups exhibited no significant different segmental lordosis angle and total lumbar lordosis over period and time. However, the total lumbar lordosis significantly increased from six months postoperatively compared with the immediate postoperative day in the 8° group. The ODI and the VAS in both groups had no differences. Cages with different lordotic angles of 4° and 8° showed insignificant results clinically and radiologically in short-level PLIF surgery. Clinical improvements and sagittal alignment recovery were significantly observed in both groups. PMID:25685795

The effect of tibiotalar alignment on coronal plane mechanics following total ankle replacement.

PubMed

Grier, A Jordan; Schmitt, Abigail C; Adams, Samuel B; Queen, Robin M

2016-07-01

Gait mechanics following total ankle replacement (TAR) have reported improved ankle motion following surgery. However, no studies have addressed the impact of preoperative radiographic tibiotalar alignment on post-TAR gait mechanics. We therefore investigated whether preoperative tibiotalar alignment (varus, valgus, or neutral) resulted in significantly different coronal plane mechanics or ground reaction forces post-TAR. We conducted a non-randomized study of 93 consecutive end-stage ankle arthritis patients. Standard weight-bearing radiographs were obtained preoperatively to categorize patients as having neutral (±4°), varus (≥5° of varus), or valgus (≥5° of valgus) coronal plane tibiotalar alignment. All patients underwent a standard walking assessment including three-dimensional lower extremity kinetics and kinematics preoperatively, 12 and 24 months postoperatively. A significant group by time interaction was observed for the propulsive vertical ground reaction force (vGRF), coronal plane hip range of motion (ROM) and the peak hip abduction moment. The valgus group demonstrated an increase in the peak knee adduction angle and knee adduction angle at heel strike when compared to the other groups. Coronal plane ankle ROM, knee and hip angles at heel strike, and the peak hip angle exhibited significant increases across time. Peak ankle inversion moment, peak knee abduction moment and the weight acceptance vGRF also exhibited significant increases across time. Neutral ankle alignment was achieved for all patients by 2 years following TAR. Restoration of neutral ankle alignment at the time of TAR in patients with preoperative varus or valgus tibiotalar alignment resulted in biomechanics similar to those of patients with neutral preoperative tibiotalar alignment by 24-month follow-up. Copyright © 2016 Elsevier B.V. All rights reserved.

Docking alignment system

NASA Technical Reports Server (NTRS)

Monford, Leo G. (Inventor)

1990-01-01

Improved techniques are provided for alignment of two objects. The present invention is particularly suited for three-dimensional translation and three-dimensional rotational alignment of objects in outer space. A camera 18 is fixedly mounted to one object, such as a remote manipulator arm 10 of the spacecraft, while the planar reflective surface 30 is fixed to the other object, such as a grapple fixture 20. A monitor 50 displays in real-time images from the camera, such that the monitor displays both the reflected image of the camera and visible markings on the planar reflective surface when the objects are in proper alignment. The monitor may thus be viewed by the operator and the arm 10 manipulated so that the reflective surface is perpendicular to the optical axis of the camera, the roll of the reflective surface is at a selected angle with respect to the camera, and the camera is spaced a pre-selected distance from the reflective surface.

Optimized mirror shape tuning using beam weightings based on distance, angle of incidence, reflectivity, and power.

PubMed

Goldberg, Kenneth A; Yashchuk, Valeriy V

2016-05-01

For glancing-incidence optical systems, such as short-wavelength optics used for nano-focusing, incorporating physical factors in the calculations used for shape optimization can improve performance. Wavefront metrology, including the measurement of a mirror's shape or slope, is routinely used as input for mirror figure optimization on mirrors that can be bent, actuated, positioned, or aligned. Modeling shows that when the incident power distribution, distance from focus, angle of incidence, and the spatially varying reflectivity are included in the optimization, higher Strehl ratios can be achieved. Following the works of Maréchal and Mahajan, optimization of the Strehl ratio (for peak intensity with a coherently illuminated system) occurs when the expectation value of the phase error's variance is minimized. We describe an optimization procedure based on regression analysis that incorporates these physical parameters. This approach is suitable for coherently illuminated systems of nearly diffraction-limited quality. Mathematically, this work is an enhancement of the methods commonly applied for ex situ alignment based on uniform weighting of all points on the surface (or a sub-region of the surface). It follows a similar approach to the optimization of apodized and non-uniformly illuminated optical systems. Significantly, it reaches a different conclusion than a more recent approach based on minimization of focal plane ray errors.

The dynamic nature of alignment and variations in normal knees.

PubMed

Deep, K; Eachempati, K K; Apsingi, S

2015-04-01

The restoration of knee alignment is an important goal during total knee arthroplasty (TKA). In the past surgeons aimed to restore neutral limb alignment during surgery. However, previous studies have demonstrated alignment to be dynamic, varying depending on the position of the limb and the degree of weight-bearing, and between patients. We used a validated computer navigation system to measure the femorotibial mechanical angle (FTMA) in 264 knees in 77 male and 55 female healthy volunteers aged 18 to 35 years (mean 26.2). We found the mean supine alignment to be a varus angle of 1.2° (standard deviation (sd) 4), with few patients having neutral alignment. FTMA differs significantly between males and females (with a mean varus of 1.7° (sd 4) and 0.4° (sd 3.9), respectively; p = 0.008). It changes significantly with posture, the knee hyperextending by a mean of 5.6°, and coronal plane alignment becoming more varus by 2.2° (sd 3.6) on standing compared with supine. Knee alignment is different in different individuals and is dynamic in nature, changing with different postures. This may have implications for the assessment of alignment in TKA, which is achieved in non-weight-bearing conditions and which may not represent the situation observed during weight-bearing. ©2015 The British Editorial Society of Bone & Joint Surgery.

Can a surgeon drill accurately at a specified angle?

PubMed Central

Brioschi, Valentina; Cook, Jodie; Arthurs, Gareth I

2016-01-01

Objectives To investigate whether a surgeon can drill accurately a specified angle and whether surgeon experience, task repetition, drill bit size and perceived difficulty influence drilling angle accuracy. Methods The sample population consisted of final-year students (n=25), non-specialist veterinarians (n=22) and board-certified orthopaedic surgeons (n=8). Each participant drilled a hole twice in a horizontal oak plank at 30°, 45°, 60°, 80°, 85° and 90° angles with either a 2.5  or a 3.5 mm drill bit. Participants then rated the perceived difficulty to drill each angle. The true angle of each hole was measured using a digital goniometer. Results Greater drilling accuracy was achieved at angles closer to 90°. An error of ≤±4° was achieved by 84.5 per cent of participants drilling a 90° angle compared with approximately 20 per cent of participants drilling a 30–45° angle. There was no effect of surgeon experience, task repetition or drill bit size on the mean error for intended versus achieved angle. Increased perception of difficulty was associated with the more acute angles and decreased accuracy, but not experience level. Clinical significance This study shows that surgeon ability to drill accurately (within ±4° error) is limited, particularly at angles ≤60°. In situations where drill angle is critical, use of computer-assisted navigation or custom-made drill guides may be preferable. PMID:27547423

A method to align a bent crystal for channeling experiments by using quasichanneling oscillations

NASA Astrophysics Data System (ADS)

Sytov, A. I.; Guidi, V.; Tikhomirov, V. V.; Bandiera, L.; Bagli, E.; Germogli, G.; Mazzolari, A.; Romagnoni, M.

2018-04-01

A method to calculate both the bent crystal angle of alignment and radius of curvature by using only one distribution of deflection angles has been developed. The method is based on measuring of the angular position of recently predicted and observed quasichanneling oscillations in the deflection angle distribution and consequent fitting of both the radius and angular alignment by analytic formulae. In this paper this method is applied on the example of simulated angular distributions over a wide range of values of both radius and alignment for electrons. It is carried out through the example of (111) nonequidistant planes though this technique is general and could be applied to any kind of planes. In addition, the method application constraints are also discussed. It is shown by simulations that this method, being in fact a sort of beam diagnostics, allows one in a certain case to increase the crystal alignment accuracy as well as to control precisely the radius of curvature inside an accelerator tube without vacuum breaking. In addition, it speeds up the procedure of crystal alignment in channeling experiments, reducing beamtime consuming.

Solar cell angle of incidence corrections

NASA Technical Reports Server (NTRS)

Burger, Dale R.; Mueller, Robert L.

1995-01-01

Literature on solar array angle of incidence corrections was found to be sparse and contained no tabular data for support. This lack along with recent data on 27 GaAs/Ge 4 cm by 4 cm cells initiated the analysis presented in this paper. The literature cites seven possible contributors to angle of incidence effects: cosine, optical front surface, edge, shadowing, UV degradation, particulate soiling, and background color. Only the first three are covered in this paper due to lack of sufficient data. The cosine correction is commonly used but is not sufficient when the incident angle is large. Fresnel reflection calculations require knowledge of the index of refraction of the coverglass front surface. The absolute index of refraction for the coverglass front surface was not known nor was it measured due to lack of funds. However, a value for the index of refraction was obtained by examining how the prediction errors varied with different assumed indices and selecting the best fit to the set of measured values. Corrections using front surface Fresnel reflection along with the cosine correction give very good predictive results when compared to measured data, except there is a definite trend away from predicted values at the larger incident angles. This trend could be related to edge effects and is illustrated by a use of a box plot of the errors and by plotting the deviation of the mean against incidence angle. The trend is for larger deviations at larger incidence angles and there may be a fourth order effect involved in the trend. A chi-squared test was used to determine if the measurement errors were normally distributed. At 10 degrees the chi-squared test failed, probably due to the very small numbers involved or a bias from the measurement procedure. All other angles showed a good fit to the normal distribution with increasing goodness-of-fit as the angles increased which reinforces the very small numbers hypothesis. The contributed data only went to 65 degrees

Lateral displacement, sulcus angle and trochlear angle are associated with early patellofemoral osteoarthritis following anterior cruciate ligament reconstruction.

PubMed

Macri, Erin M; Culvenor, Adam G; Morris, Hayden G; Whitehead, Timothy S; Russell, Trevor G; Khan, Karim M; Crossley, Kay M

2017-05-09

Patellofemoral osteoarthritis (PFOA) occurs in approximately half of anterior cruciate ligament (ACL)-injured knees within 10-15 years of trauma. Risk factors for post-traumatic PFOA are poorly understood. Patellofemoral alignment and trochlear morphology may be associated with PFOA following ACL reconstruction (ACLR), and understanding these relationships, particularly early in the post-surgical time period, may guide effective early intervention strategies. In this study, patellofemoral alignment and trochlear morphology were investigated in relation to radiographic features of early PFOA 1-year post-ACLR. Participants (aged 18-50 years) had undergone ACLR approximately 1 year prior to being assessed. Early PFOA was defined as presence of a definite patellofemoral osteophyte on lateral or skyline radiograph. Sagittal and axial plane alignment and trochlear morphology were estimated using MRI. Using logistic regression, the relationship between alignment or morphology and presence of osteophytes was evaluated. Of 111 participants [age 30 ± 8.5; 41 (37%) women], 19 (17%) had definite osteophytes, only two of whom had had patellofemoral chondral lesions noted intra-operatively. One measure of patellar alignment (bisect offset OR 1.1 [95% confidence interval 1.0, 1.2]) and two measures of trochlear morphology (sulcus angle OR 1.1 [1.0, 1.2], trochlear angle OR 1.2 [1.0, 1.5]) were associated with patellofemoral osteophytes. Patellofemoral malalignment and/or altered trochlear morphology were associated with PFOA 1 year following ACLR compared to individuals post-ACLR without these features. Clarifying the role of alignment and morphology in post-traumatic PFOA may contribute to improving early intervention strategies aimed at secondary prevention. IV.

Intraoperative panoramic image using alignment grid, is it accurate?

PubMed

Apivatthakakul, T; Duanghakrung, M; Luevitoonvechkit, S; Patumasutra, S

2013-07-01

Minimally invasive orthopedic trauma surgery relies heavily on intraoperative fluoroscopic images to evaluate the quality of fracture reduction and fixation. However, fluoroscopic images have a narrow field of view and often cannot visualize the entire long bone axis. To compare the coronal femoral alignment between conventional X-rays to that achieved with a new method of acquiring a panoramic intraoperative image. Twenty-four cadaveric femurs with simple diaphyseal fractures were fixed with an angulated broad DCP to create coronal plane malalignment. An intraoperative alignment grid was used to help stitch different fluoroscopic images together to produce a panoramic image. A conventional X-ray of the entire femur was then performed. The coronal plane angulation in the panoramic images was then compared to the conventional X-rays using a Wilcoxon signed rank test. The mean angle measured from the panoramic view was 173.9° (range 169.3°-178.0°) with median of 173.2°. The mean angle measured from the conventional X-ray was 173.4° (range 167.7°-178.7°) with a median angle of 173.5°. There was no significant difference between both methods of measurement (P = 0.48). Panoramic images produced by stitching fluoroscopic images together with help of an alignment grid demonstrated the same accuracy at evaluating the coronal plane alignment of femur fractures as conventional X-rays.

Feed-forward alignment correction for advanced overlay process control using a standalone alignment station "Litho Booster"

NASA Astrophysics Data System (ADS)

Yahiro, Takehisa; Sawamura, Junpei; Dosho, Tomonori; Shiba, Yuji; Ando, Satoshi; Ishikawa, Jun; Morita, Masahiro; Shibazaki, Yuichi

2018-03-01

One of the main components of an On-Product Overlay (OPO) error budget is the process induced wafer error. This necessitates wafer-to-wafer correction in order to optimize overlay accuracy. This paper introduces the Litho Booster (LB), standalone alignment station as a solution to improving OPO. LB can execute high speed alignment measurements without throughput (THP) loss. LB can be installed in any lithography process control loop as a metrology tool, and is then able to provide feed-forward (FF) corrections to the scanners. In this paper, the detailed LB design is described and basic LB performance and OPO improvement is demonstrated. Litho Booster's extendibility and applicability as a solution for next generation manufacturing accuracy and productivity challenges are also outlined

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

PubMed Central

Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

2013-01-01

Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

Simulations in site error estimation for direction finders

NASA Astrophysics Data System (ADS)

López, Raúl E.; Passi, Ranjit M.

1991-08-01

The performance of an algorithm for the recovery of site-specific errors of direction finder (DF) networks is tested under controlled simulated conditions. The simulations show that the algorithm has some inherent shortcomings for the recovery of site errors from the measured azimuth data. These limitations are fundamental to the problem of site error estimation using azimuth information. Several ways for resolving or ameliorating these basic complications are tested by means of simulations. From these it appears that for the effective implementation of the site error determination algorithm, one should design the networks with at least four DFs, improve the alignment of the antennas, and increase the gain of the DFs as much as it is compatible with other operational requirements. The use of a nonzero initial estimate of the site errors when working with data from networks of four or more DFs also improves the accuracy of the site error recovery. Even for networks of three DFs, reasonable site error corrections could be obtained if the antennas could be well aligned.

Fiber optics welder having movable aligning mirror

DOEpatents

Higgins, Robert W.; Robichaud, Roger E.

1981-01-01

A system for welding fiber optic waveguides together. The ends of the two fibers to be joined together are accurately, collinearly aligned in a vertical orientation and subjected to a controlled, diffuse arc to effect welding and thermal conditioning. A front-surfaced mirror mounted at a 45.degree. angle to the optical axis of a stereomicroscope mounted for viewing the junction of the ends provides two orthogonal views of the interface during the alignment operation.

A highly accurate dynamic contact angle algorithm for drops on inclined surface based on ellipse-fitting.

PubMed

Xu, Z N; Wang, S Y

2015-02-01

To improve the accuracy in the calculation of dynamic contact angle for drops on the inclined surface, a significant number of numerical drop profiles on the inclined surface with different inclination angles, drop volumes, and contact angles are generated based on the finite difference method, a least-squares ellipse-fitting algorithm is used to calculate the dynamic contact angle. The influences of the above three factors are systematically investigated. The results reveal that the dynamic contact angle errors, including the errors of the left and right contact angles, evaluated by the ellipse-fitting algorithm tend to increase with inclination angle/drop volume/contact angle. If the drop volume and the solid substrate are fixed, the errors of the left and right contact angles increase with inclination angle. After performing a tremendous amount of computation, the critical dimensionless drop volumes corresponding to the critical contact angle error are obtained. Based on the values of the critical volumes, a highly accurate dynamic contact angle algorithm is proposed and fully validated. Within nearly the whole hydrophobicity range, it can decrease the dynamic contact angle error in the inclined plane method to less than a certain value even for different types of liquids.

Northwest Angle, Minnesota

NASA Image and Video Library

2017-10-02

Minnesota's Northwest Angle is the northernmost point of the continental United States. The Angle became part of the US due to a map error during the 1783 Treaty of Paris. Located in the Lake of the Woods, driving there requires crossing the US-Canada border twice. The image was acquired September 22, 2013, covers an area of 40 by 55 km, and is located at 49.2 degrees north, 95.1 degrees west. https://photojournal.jpl.nasa.gov/catalog/PIA21997

Alignment of cD-galaxies with their surroundings

NASA Technical Reports Server (NTRS)

Vankampen, Eelco; Rhee, George

1990-01-01

For a sample of 122 rich Abell clusters the authors find a strong correlation of the position angle (orientation) of the first-ranked galaxy and its parent cluster. This alignment effect is strongest for cD-galaxies. Formation scenarios for cD galaxies, like the merging scenario, must produce such a strong alignment effect. The authors show some N-body simulations done for this purpose.

Non-contact measurement of rotation angle with solo camera

NASA Astrophysics Data System (ADS)

Gan, Xiaochuan; Sun, Anbin; Ye, Xin; Ma, Liqun

2015-02-01

For the purpose to measure a rotation angle around the axis of an object, a non-contact rotation angle measurement method based on solo camera was promoted. The intrinsic parameters of camera were calibrated using chessboard on principle of plane calibration theory. The translation matrix and rotation matrix between the object coordinate and the camera coordinate were calculated according to the relationship between the corners' position on object and their coordinates on image. Then the rotation angle between the measured object and the camera could be resolved from the rotation matrix. A precise angle dividing table (PADT) was chosen as the reference to verify the angle measurement error of this method. Test results indicated that the rotation angle measurement error of this method did not exceed +/- 0.01 degree.

Model benchmarking and reference signals for angled-beam shear wave ultrasonic nondestructive evaluation (NDE) inspections

NASA Astrophysics Data System (ADS)

Aldrin, John C.; Hopkins, Deborah; Datuin, Marvin; Warchol, Mark; Warchol, Lyudmila; Forsyth, David S.; Buynak, Charlie; Lindgren, Eric A.

2017-02-01

For model benchmark studies, the accuracy of the model is typically evaluated based on the change in response relative to a selected reference signal. The use of a side drilled hole (SDH) in a plate was investigated as a reference signal for angled beam shear wave inspection for aircraft structure inspections of fastener sites. Systematic studies were performed with varying SDH depth and size, and varying the ultrasonic probe frequency, focal depth, and probe height. Increased error was observed with the simulation of angled shear wave beams in the near-field. Even more significant, asymmetry in real probes and the inherent sensitivity of signals in the near-field to subtle test conditions were found to provide a greater challenge with achieving model agreement. To achieve quality model benchmark results for this problem, it is critical to carefully align the probe with the part geometry, to verify symmetry in probe response, and ideally avoid using reference signals from the near-field response. Suggested reference signals for angled beam shear wave inspections include using the `through hole' corner specular reflection signal and the full skip' signal off of the far wall from the side drilled hole.

Study on temperature measurement of gas turbine blade based on analysis of error caused by the reflected radiation and emission angle

NASA Astrophysics Data System (ADS)

Li, Dong; Feng, Chi; Gao, Shan; Chen, Liwei; Daniel, Ketui

2018-06-01

Accurate measurement of gas turbine blade temperature is of great significance as far as blade health monitoring is concerned. An important method for measuring this temperature is the use of a radiation pyrometer. In this research, error of the pyrometer caused by reflected radiation from the surfaces surrounding the target and the emission angle of the target was analyzed. Important parameters for this analysis were the view factor between interacting surfaces, spectral directional emissivity, pyrometer operating wavelength and the surface temperature distribution on the blades and the vanes. The interacting surface of the rotor blade and the vane models used were discretized using triangular surface elements from which contour integral was used to calculate the view factor between the surface elements. Spectral directional emissivities were obtained from an experimental setup of Ni based alloy samples. A pyrometer operating wavelength of 1.6 μm was chosen. Computational fluid dynamics software was used to simulate the temperature distribution of the rotor blade and the guide vane based on the actual gas turbine input parameters. Results obtained in this analysis show that temperature error introduced by reflected radiation and emission angle ranges from  ‑23 K to 49 K.

Effect of prosthetic alignment changes on socket reaction moment impulse during walking in transtibial amputees

PubMed Central

Kobayashi, Toshiki; Orendurff, Michael S.; Arabian, Adam K.; Rosenbaum-Chou, Teri G.; Boone, David A.

2014-01-01

The alignment of a lower limb prosthesis affects the way load is transferred to the residual limb through the socket, and this load is critically important for the comfort and function of the prosthesis. Both magnitude and duration of the moment are important factors that may affect the residual limb health. Moment impulse is a well-accepted measurement that incorporates both factors via moment–time integrals. The aim of this study was to investigate the effect of alignment changes on the socket reaction moment impulse in transtibial prostheses. Ten amputees with transtibial prostheses participated in this study. The socket reaction moment impulse was measured at a self-selected walking speed using a Smart Pyramid™ in 25 alignment conditions, including a nominal alignment (clinically aligned by a prosthetist), as well as angle malalignments of 2°, 4° and 6° (abduction, adduction, extension and flexion) and translation malalignments of 5 mm, 10 mm and 15 mm (lateral, medial, anterior and posterior). The socket reaction moment impulse of the nominal alignment was compared for each condition. The relationship between the alignment and the socket reaction moment impulse was clearly observed in the coronal angle, coronal translation and sagittal translation alignment changes. However, this relationship was not evident in the sagittal angle alignment changes. The results of this study suggested that the socket reaction moment impulse could potentially serve as a valuable parameter to assist the alignment tuning process for transtibial prostheses. Further study is needed to investigate the influence of the socket reaction moment impulse on the residual limb health. PMID:24612718

Error and Error Mitigation in Low-Coverage Genome Assemblies

PubMed Central

Hubisz, Melissa J.; Lin, Michael F.; Kellis, Manolis; Siepel, Adam

2011-01-01

The recent release of twenty-two new genome sequences has dramatically increased the data available for mammalian comparative genomics, but twenty of these new sequences are currently limited to ∼2× coverage. Here we examine the extent of sequencing error in these 2× assemblies, and its potential impact in downstream analyses. By comparing 2× assemblies with high-quality sequences from the ENCODE regions, we estimate the rate of sequencing error to be 1–4 errors per kilobase. While this error rate is fairly modest, sequencing error can still have surprising effects. For example, an apparent lineage-specific insertion in a coding region is more likely to reflect sequencing error than a true biological event, and the length distribution of coding indels is strongly distorted by error. We find that most errors are contributed by a small fraction of bases with low quality scores, in particular, by the ends of reads in regions of single-read coverage in the assembly. We explore several approaches for automatic sequencing error mitigation (SEM), making use of the localized nature of sequencing error, the fact that it is well predicted by quality scores, and information about errors that comes from comparisons across species. Our automatic methods for error mitigation cannot replace the need for additional sequencing, but they do allow substantial fractions of errors to be masked or eliminated at the cost of modest amounts of over-correction, and they can reduce the impact of error in downstream phylogenomic analyses. Our error-mitigated alignments are available for download. PMID:21340033

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

Rotational Alignment Altered by Source Position Correlations

NASA Technical Reports Server (NTRS)

Jacobs, Chris S.; Heflin, M. B.; Lanyi, G. E.; Sovers, O. J.; Steppe, J. A.

2010-01-01

In the construction of modern Celestial Reference Frames (CRFs) the overall rotational alignment is only weakly constrained by the data. Therefore, common practice has been to apply a 3-dimensional No-Net-Rotation (NNR) constraint in order to align an under-construction frame to the ICRF. We present evidence that correlations amongst source position parameters must be accounted for in order to properly align a CRF at the 5-10 (mu)as level of uncertainty found in current work. Failure to do so creates errors at the 10-40 (mu)as level.

A UNIFIED MODEL OF GRAIN ALIGNMENT: RADIATIVE ALIGNMENT OF INTERSTELLAR GRAINS WITH MAGNETIC INCLUSIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoang, Thiem; Lazarian, A.

The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by earlier studies. The alignment of such grains depends on the so-called RAT parameter q {sup max}, which is determined by the grain shape. In this paper, we elaborate on our model of RAT alignment for grains with enhanced magnetic susceptibility due to iron inclusions, such that RAT alignment is magnetically enhanced, which we term the MRAT mechanism. Such grains can be aligned with high angular momentum at the so-called high- J attractor points, achieving a high degree of alignment. Using our analytical model ofmore » RATs, we derive the critical value of the magnetic relaxation parameter δ {sub m} to produce high- J attractor points as functions of q {sup max} and the anisotropic radiation angle relative to the magnetic field ψ . We find that if about 10% of the total iron abundance present in silicate grains is forming iron clusters, this is sufficient to produce high- J attractor points for all reasonable values of q {sup max}. To calculate the degree of grain alignment, we carry out numerical simulations of MRAT alignment by including stochastic excitations from gas collisions and magnetic fluctuations. We show that large grains can achieve perfect alignment when the high- J attractor point is present, regardless of the values of q {sup max}. Our obtained results pave the way for the physical modeling of polarized thermal dust emission as well as magnetic dipole emission. We also find that millimeter-sized grains in accretion disks may be aligned with the magnetic field if they are incorporated with iron nanoparticles.« less

Research on calibration error of carrier phase against antenna arraying

NASA Astrophysics Data System (ADS)

Sun, Ke; Hou, Xiaomin

2016-11-01

It is the technical difficulty of uplink antenna arraying that signals from various quarters can not be automatically aligned at the target in deep space. The size of the far-field power combining gain is directly determined by the accuracy of carrier phase calibration. It is necessary to analyze the entire arraying system in order to improve the accuracy of the phase calibration. This paper analyzes the factors affecting the calibration error of carrier phase of uplink antenna arraying system including the error of phase measurement and equipment, the error of the uplink channel phase shift, the position error of ground antenna, calibration receiver and target spacecraft, the error of the atmospheric turbulence disturbance. Discuss the spatial and temporal autocorrelation model of atmospheric disturbances. Each antenna of the uplink antenna arraying is no common reference signal for continuous calibration. So it must be a system of the periodic calibration. Calibration is refered to communication of one or more spacecrafts in a certain period. Because the deep space targets are not automatically aligned to multiplexing received signal. Therefore the aligned signal should be done in advance on the ground. Data is shown that the error can be controlled within the range of demand by the use of existing technology to meet the accuracy of carrier phase calibration. The total error can be controlled within a reasonable range.

Alignment system for SGII-Up laser facility

NASA Astrophysics Data System (ADS)

Gao, Yanqi; Cui, Yong; Li, Hong; Gong, Lei; Lin, Qiang; Liu, Daizhong; Zhu, Baoqiang; Ma, Weixin; Zhu, Jian; Lin, Zunqi

2018-03-01

The SGII-Up laser facility in Shanghai is one of the most important high-power laser facilities in China. It is designed to obtain 24 kJ (3ω) of energy with a square pulse of 3 ns using eight laser beams (two bundles). To satisfy the requirements for the safety, efficiency, and quality, an alignment system is developed for this facility. This alignment system can perform automatic alignment of the preamplifier system, main amplifier system, and harmonic conversion system within 30 min before every shot during the routine operation of the facility. In this article, an overview of the alignment system is first presented. Then, its alignment characteristics are discussed, along with the alignment process. Finally, experimental results, including the alignment results and the facility performance, are reported. The results show that the far-field beam pointing alignment accuracy is better than 3 μrad, and the alignment error of the near-field beam centering is no larger than 1 mm. These satisfy the design requirements very well.

Alignment of the femoral component in a mobile-bearing unicompartmental knee arthroplasty: a study in 10 cadaver femora.

PubMed

Kort, N P; van Raay, J J A M; Thomassen, B J W

2007-08-01

Use of an intramedullary rod is advised for the alignment of the femoral component of an Oxford phase-III prosthesis. There are users moving toward extramedullary alignment, which is merely an indicator of frustration with accuracy of intramedullary alignment. The results of our study with 10 cadaver femora demonstrate that use of a short and long intramedullary femoral rod may result in excessive flexion alignment error of the femoral component. Understanding of the extramedullary alignment possibility and experience with the visual alignment of the femoral drill guide is essential toward minimizing potential errors in the alignment of the femoral component.

Enhanced critical-current in P-doped BaFe2As2 thin films on metal substrates arising from poorly aligned grain boundaries.

PubMed

Sato, Hikaru; Hiramatsu, Hidenori; Kamiya, Toshio; Hosono, Hideo

2016-11-11

Thin films of the iron-based superconductor BaFe 2 (As 1-x P x ) 2 (Ba122:P) were fabricated on polycrystalline metal-tape substrates with two kinds of in-plane grain boundary alignments (well aligned (4°) and poorly aligned (8°)) by pulsed laser deposition. The poorly aligned substrate is not applicable to cuprate-coated conductors because the in-plane alignment >4° results in exponential decay of the critical current density (J c ). The Ba122:P film exhibited higher J c at 4 K when grown on the poorly aligned substrate than on the well-aligned substrate even though the crystallinity was poorer. It was revealed that the misorientation angles of the poorly aligned samples were less than 6°, which are less than the critical angle of an iron-based superconductor, cobalt-doped BaFe 2 As 2 (~9°), and the observed strong pinning in the Ba122:P is attributed to the high-density grain boundaries with the misorientation angles smaller than the critical angle. This result reveals a distinct advantage over cuprate-coated conductors because well-aligned metal-tape substrates are not necessary for practical applications of the iron-based superconductors.

STELLAR: fast and exact local alignments

PubMed Central

2011-01-01

Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de. PMID:22151882

Right-Angle Mechanized Electrical Connector

NASA Technical Reports Server (NTRS)

Collins, Clint A.; Blackler, David T.

1996-01-01

Right-angle electrical connector embedded in mechanism accommodates some initial misalignment and aligns itself. Connection and disconnection effected with relatively small forces and torques and simple movements. Actuated by one gloved hand or by robotic manipulator. Useful in underwater, nuclear, hot, cold, or toxic environments in which connections made or broken by heavily clothed technicians or by robots.

Effects of interfacial alignments on the stability of graphene on Ru(0001) substrate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Lei; Liu, Yanmin; Ma, Tianbao, E-mail: mtb@mail.tsinghua.edu.cn

2016-06-27

Structure and electronic properties of two-dimensional materials could be tuned by interfacial misfit or orientation angles. However, graphene grown on Ru(0001) substrate usually shows stable moiré superlattice with a periodicity of 3.0 nm indicating an aligned geometry. The reason for the absence of misaligned structure is still unknown. We have performed first-principles calculation to investigate the microstructure and morphology of graphene on Ru(0001) substrate in both aligned and misaligned geometries with rotation angles of 0°, 7.6°, and 23.4°, respectively. Our results indicate that both the graphene corrugation and moiré superlattice periodicity decrease as the rotation angle increases. Meanwhile the interaction energymore » between graphene and Ru(0001) substrate also becomes weakened with the rotation angle, as the decrease and discretization of intense charge transfer sites at the graphene/Ru interface, which is closely related to the interface stacking structure. Counterintuitively, the strain energy in graphene also increases anomalously with the rotation angle, which is attributed to the highly distorted local deformation of graphene due to the strong but discrete covalent bonding with Ru substrate. The simultaneous increase in both the interaction energy and strain energy in graphene/Ru(0001) heterostructure with rotation angle contributes to the preferred configuration in the aligned state.« less

Association of the canine guidance angle with maxillary and mandibular intercanine widths and anterior alignment relapse: Extraction vs nonextraction treatment.

PubMed

Heiser, Wolfgang; Richter, Martin; Niederwanger, Andreas; Neunteufel, Nikolaus; Kulmer, Siegfried

2008-05-01

Long-term stability is an important measure of the success of orthodontic treatment. Research in the 1970s suggested that premolar extraction treatment had poor stability over the long term. The purpose of this prospective follow-up study was to investigate changes in intercanine widths and the irregularity index during the postretention phase in patients treated with and without extractions. Associations between the maxillary canine guidance angle and the mandibular intercanine widths and the mandibular irregularity index were also examined. Two groups of 30 patients each, with and without premolar extractions, were studied and the results compared. Records were taken at pretreatment, at bracket removal, at the end of retention, and out of retention. The times out of retention were 6.3 years for the nonextraction group and 6.5 years for the extraction group. Stone casts were mounted on an articulator with an anatomical facebow and a central wax record. The measurements were made with a 3-dimensional digitizer. Maxillary and mandibular intercanine distances behaved differently. The mandibular intercanine distance showed a net decrease between pretreatment and follow-up, whereas the maxillary arch had a net increase. The maxillary canine guidance angle at the end of retention, measured to the axis-orbital plane, was highly associated with relapse of mandibular anterior alignment and change of the mandibular intercanine distance. Methods are needed that consider the anatomical configuration of the teeth for bracket selection before treatment. Individualized brackets (torque) should then be coordinated with the guidance angle of the maxillary teeth.

Improved docking alignment system

NASA Technical Reports Server (NTRS)

Monford, Leo G. (Inventor)

1988-01-01

Improved techniques are provided for the alignment of two objects. The present invention is particularly suited for 3-D translation and 3-D rotational alignment of objects in outer space. A camera is affixed to one object, such as a remote manipulator arm of the spacecraft, while the planar reflective surface is affixed to the other object, such as a grapple fixture. A monitor displays in real-time images from the camera such that the monitor displays both the reflected image of the camera and visible marking on the planar reflective surface when the objects are in proper alignment. The monitor may thus be viewed by the operator and the arm manipulated so that the reflective surface is perpendicular to the optical axis of the camera, the roll of the reflective surface is at a selected angle with respect to the camera, and the camera is spaced a pre-selected distance from the reflective surface.

Vector correlation between the alignment of reactant N2 (A 3Σu+) and the alignment of product NO (A 2Σ+) rotation in the energy transfer reaction of aligned N2 (A 3Σu+) + NO (X 2Π) → NO (A 2Σ+) + N2 (X 1Σg+).

PubMed

Ohoyama, H

2013-12-21

The vector correlation between the alignment of reactant N2 (A (3)Σu(+)) and the alignment of product NO (A (2)Σ(+)) rotation has been studied in the energy transfer reaction of aligned N2 (A (3)Σu(+)) + NO (X (2)Π) → NO (A (2)Σ(+)) + N2 (X (1)Σg(+)) under the crossed beam condition at a collision energy of ~0.07 eV. NO (A (2)Σ(+)) emission in the two linear polarization directions (i.e., parallel and perpendicular with respect to the relative velocity vector v(R)) has been measured as a function of the alignment of N2 (A (3)Σu(+)) along its molecular axis in the collision frame. The degree of polarization of NO (A (2)Σ(+)) emission is found to depend on the alignment angle (θ(v(R))) of N2 (A (3)Σu(+)) in the collision frame. The shape of the steric opacity function at the two polarization conditions turns out to be extremely different from each other: The steric opacity function at the parallel polarization condition is more favorable for the oblique configuration of N2 (A (3)Σu(+)) at an alignment angle of θ(v(R)) ~ 45° as compared with that at the perpendicular polarization condition. The alignment of N2 (A (3)Σu(+)) is found to give a significant effect on the alignment of NO (A (2)Σ(+)) rotation in the collision frame: The N2 (A (3)Σu(+)) configuration at an oblique alignment angle θ(v(R)) ~ 45° leads to a parallel alignment of NO (A (2)Σ(+)) rotation (J-vector) with respect to v(R), while the axial and sideways configurations of N2 (A (3)Σu(+)) lead to a perpendicular alignment of NO (A (2)Σ(+)) rotation with respect to vR. These stereocorrelated alignments of the product rotation have a good correlation with the stereocorrelated reactivity observed in the multi-dimensional steric opacity function [H. Ohoyama and S. Maruyama, J. Chem. Phys. 137, 064311 (2012)].

Deep learning methods for protein torsion angle prediction.

PubMed

Li, Haiou; Hou, Jie; Adhikari, Badri; Lyu, Qiang; Cheng, Jianlin

2017-09-18

Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012, it has achieved success in a number of areas such as protein residue-residue contact prediction, secondary structure prediction, and fold recognition. In this work, we developed deep learning methods to improve the prediction of torsion (dihedral) angles of proteins. We design four different deep learning architectures to predict protein torsion angles. The architectures including deep neural network (DNN) and deep restricted Boltzmann machine (DRBN), deep recurrent neural network (DRNN) and deep recurrent restricted Boltzmann machine (DReRBM) since the protein torsion angle prediction is a sequence related problem. In addition to existing protein features, two new features (predicted residue contact number and the error distribution of torsion angles extracted from sequence fragments) are used as input to each of the four deep learning architectures to predict phi and psi angles of protein backbone. The mean absolute error (MAE) of phi and psi angles predicted by DRNN, DReRBM, DRBM and DNN is about 20-21° and 29-30° on an independent dataset. The MAE of phi angle is comparable to the existing methods, but the MAE of psi angle is 29°, 2° lower than the existing methods. On the latest CASP12 targets, our methods also achieved the performance better than or comparable to a state-of-the art method. Our experiment demonstrates that deep learning is a valuable method for predicting protein torsion angles. The deep recurrent network architecture performs slightly better than deep feed-forward architecture, and the predicted residue contact number and the error distribution of torsion angles extracted from sequence fragments are useful features for improving prediction accuracy.

Tilted Liquid Crystal Alignment on Asymmetrically Grooved Porous Alumina Film

NASA Astrophysics Data System (ADS)

Maeda, Tsuyoshi; Hiroshima, Kohki

2005-06-01

This paper reports the achievement of tilted liquid crystal (LC) alignment on an anodic porous alumina (APA) film using microgrooves with asymmetric shapes and dozens of minute pores. The microgrooves with asymmetric shapes were formed by a rubbing technique. The minute pores were then produced by anodization. The LC pretilt angle was controlled by the shapes of the microgrooves and pores. The LC director was orientated in the same inclining direction as that of a rubbed polyimide (PI) film. The pretilt angle was in the range of 20 to 90°. This tilted LC alignment remains very stable against external forces such as thermal shock and intense light.

Multispectral optical telescope alignment testing for a cryogenic space environment

NASA Astrophysics Data System (ADS)

Newswander, Trent; Hooser, Preston; Champagne, James

2016-09-01

Multispectral space telescopes with visible to long wave infrared spectral bands provide difficult alignment challenges. The visible channels require precision in alignment and stability to provide good image quality in short wavelengths. This is most often accomplished by choosing materials with near zero thermal expansion glass or ceramic mirrors metered with carbon fiber reinforced polymer (CFRP) that are designed to have a matching thermal expansion. The IR channels are less sensitive to alignment but they often require cryogenic cooling for improved sensitivity with the reduced radiometric background. Finding efficient solutions to this difficult problem of maintaining good visible image quality at cryogenic temperatures has been explored with the building and testing of a telescope simulator. The telescope simulator is an onaxis ZERODUR® mirror, CFRP metered set of optics. Testing has been completed to accurately measure telescope optical element alignment and mirror figure changes in a cryogenic space simulated environment. Measured alignment error and mirror figure error test results are reported with a discussion of their impact on system optical performance.

Effect of prosthetic alignment changes on socket reaction moment impulse during walking in transtibial amputees.

PubMed

Kobayashi, Toshiki; Orendurff, Michael S; Arabian, Adam K; Rosenbaum-Chou, Teri G; Boone, David A

2014-04-11

The alignment of a lower limb prosthesis affects the way load is transferred to the residual limb through the socket, and this load is critically important for the comfort and function of the prosthesis. Both magnitude and duration of the moment are important factors that may affect the residual limb health. Moment impulse is a well-accepted measurement that incorporates both factors via moment-time integrals. The aim of this study was to investigate the effect of alignment changes on the socket reaction moment impulse in transtibial prostheses. Ten amputees with transtibial prostheses participated in this study. The socket reaction moment impulse was measured at a self-selected walking speed using a Smart Pyramid in 25 alignment conditions, including a nominal alignment (clinically aligned by a prosthetist), as well as angle malalignments of 2°, 4° and 6° (abduction, adduction, extension and flexion) and translation malalignments of 5 mm, 10 mm and 15 mm (lateral, medial, anterior and posterior). The socket reaction moment impulse of the nominal alignment was compared for each condition. The relationship between the alignment and the socket reaction moment impulse was clearly observed in the coronal angle, coronal translation and sagittal translation alignment changes. However, this relationship was not evident in the sagittal angle alignment changes. The results of this study suggested that the socket reaction moment impulse could potentially serve as a valuable parameter to assist the alignment tuning process for transtibial prostheses. Further study is needed to investigate the influence of the socket reaction moment impulse on the residual limb health. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative modeling without implicit sequence alignments.

PubMed

Kolinski, Andrzej; Gront, Dominik

2007-10-01

The number of known protein sequences is about thousand times larger than the number of experimentally solved 3D structures. For more than half of the protein sequences a close or distant structural analog could be identified. The key starting point in a classical comparative modeling is to generate the best possible sequence alignment with a template or templates. With decreasing sequence similarity, the number of errors in the alignments increases and these errors are the main causes of the decreasing accuracy of the molecular models generated. Here we propose a new approach to comparative modeling, which does not require the implicit alignment - the model building phase explores geometric, evolutionary and physical properties of a template (or templates). The proposed method requires prior identification of a template, although the initial sequence alignment is ignored. The model is built using a very efficient reduced representation search engine CABS to find the best possible superposition of the query protein onto the template represented as a 3D multi-featured scaffold. The criteria used include: sequence similarity, predicted secondary structure consistency, local geometric features and hydrophobicity profile. For more difficult cases, the new method qualitatively outperforms existing schemes of comparative modeling. The algorithm unifies de novo modeling, 3D threading and sequence-based methods. The main idea is general and could be easily combined with other efficient modeling tools as Rosetta, UNRES and others.

Effect of EMIC Wave Normal Angle Distribution on Relativistic Electron Scattering in Outer RB

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Gamayunov, K. V.

2007-01-01

We present the equatorial and bounce average pitch angle diffusion coefficients for scattering of relativistic electrons by the H+ mode of EMIC waves. Both the model (prescribed) and self consistent distributions over the wave normal angle are considered. The main results of our calculation can be summarized as follows: First, in comparison with field aligned waves, the intermediate and highly oblique waves reduce the pitch angle range subject to diffusion, and strongly suppress the scattering rate for low energy electrons (E less than 2 MeV). Second, for electron energies greater than 5 MeV, the |n| = 1 resonances operate only in a narrow region at large pitch-angles, and despite their greatest contribution in case of field aligned waves, cannot cause electron diffusion into the loss cone. For those energies, oblique waves at |n| greater than 1 resonances are more effective, extending the range of pitch angle diffusion down to the loss cone boundary, and increasing diffusion at small pitch angles by orders of magnitude.

Effect of limb rotation on radiographic alignment in total knee arthroplasties.

PubMed

Radtke, Kerstin; Becher, Christoph; Noll, Yvonne; Ostermeier, Sven

2010-04-01

Even in a well-aligned total knee arthroplasty (TKA), limb rotation at the time of radiographic assessment will alter the measurement of alignment. This could influence the radiographic outcome of TKA. The purpose of this study was to evaluate the effect of limb rotation on radiographic alignment after TKA and to establish a re-calculation of this rotation by using existing radiographic landmarks. Synthetic femur and tibia (Sawbones), Inc. Vashon Island, WA) were used to create a TKA of the Triathlon knee prosthesis system (Stryker), Limerick, Ireland). The femoral alignment was 6.5 degrees valgus. The model was fixed in an upright stand. Five series of nine anteroposterior (AP) long leg radiographs were taken on a 30 cm x 120 cm plates in full extension with the limb rotated, in 5 degrees increments, from 20 degrees external rotation to 20 degrees internal rotation. After digitizing each radiograph (Scanner Hewlett Packard XJ 527), an observer measured the anatomic mechanical angle of the femur [AMA ( degrees )], the mechanical lateral proximal femur angle [mLPFA ( degrees )], the mechanical lateral distal femur angle [mLDFA ( degrees )], the mechanical medial proximal tibia angle [mMPTA ( degrees )] and the mechanical lateral distal tibia angle [mLDTA ( degrees )] using a digital measurement software (MediCAD, Hectec, Altfraunhofen, Germany). Besides, the observer measured the geometrical distances of the femoral component figured on the long leg radiograph. A ratio of one distance to another was measured (called femoral component distance ratio). The average radiographic anatomic alignment ranged from 6.827 degrees AMA (SD = 0.22 degrees ) in 20 degrees internal rotation to 4.627 degrees AMA (SD = 0.22 degrees ) in 20 degrees external rotation. Average mLPFA ( degrees ) ranged from 101.63 degrees (SD = 0.63) in 20 degrees internal rotation to 93.60 degrees (SD = 0.74 degrees ) in 20 degrees external rotation. Average mLDFA ( degrees ) ranged from 90.59 degrees

Only marginal alignment of disc galaxies

NASA Astrophysics Data System (ADS)

Andrae, René; Jahnke, Knud

2011-12-01

Testing theories of angular-momentum acquisition of rotationally supported disc galaxies is the key to understanding the formation of this type of galaxies. The tidal-torque theory aims to explain this acquisition process in a cosmological framework and predicts positive autocorrelations of angular-momentum orientation and spiral-arm handedness, i.e. alignment of disc galaxies, on short distance scales of 1 Mpc h-1. This disc alignment can also cause systematic effects in weak-lensing measurements. Previous observations claimed discovering these correlations but are overly optimistic in the reported level of statistical significance of the detections. Errors in redshift, ellipticity and morphological classifications were not taken into account, although they have a significant impact. We explain how to rigorously propagate all the important errors through the estimation process. Analysing disc galaxies in the Sloan Digital Sky Survey (SDSS) data base, we find that positive autocorrelations of spiral-arm handedness and angular-momentum orientations on distance scales of 1 Mpc h-1 are plausible but not statistically significant. Current data appear not good enough to constrain parameters of theory. This result agrees with a simple hypothesis test in the Local Group, where we also find no evidence for disc alignment. Moreover, we demonstrate that ellipticity estimates based on second moments are strongly biased by galactic bulges even for Scd galaxies, thereby corrupting correlation estimates and overestimating the impact of disc alignment on weak-lensing studies. Finally, we discuss the potential of future sky surveys. We argue that photometric redshifts have too large errors, i.e. PanSTARRS and LSST cannot be used. Conversely, the EUCLID project will not cover the relevant redshift regime. We also discuss the potentials and problems of front-edge classifications of galaxy discs in order to improve the autocorrelation estimates of angular-momentum orientation.

Improved astigmatic focus error detection method

NASA Technical Reports Server (NTRS)

Bernacki, Bruce E.

1992-01-01

All easy-to-implement focus- and track-error detection methods presently used in magneto-optical (MO) disk drives using pre-grooved media suffer from a side effect known as feedthrough. Feedthrough is the unwanted focus error signal (FES) produced when the optical head is seeking a new track, and light refracted from the pre-grooved disk produces an erroneous FES. Some focus and track-error detection methods are more resistant to feedthrough, but tend to be complicated and/or difficult to keep in alignment as a result of environmental insults. The astigmatic focus/push-pull tracking method is an elegant, easy-to-align focus- and track-error detection method. Unfortunately, it is also highly susceptible to feedthrough when astigmatism is present, with the worst effects caused by astigmatism oriented such that the tangential and sagittal foci are at 45 deg to the track direction. This disclosure outlines a method to nearly completely eliminate the worst-case form of feedthrough due to astigmatism oriented 45 deg to the track direction. Feedthrough due to other primary aberrations is not improved, but performance is identical to the unimproved astigmatic method.

Ocular Biometrics of Myopic Eyes With Narrow Angles.

PubMed

Chong, Gabriel T; Wen, Joanne C; Su, Daniel Hsien-Wen; Stinnett, Sandra; Asrani, Sanjay

2016-02-01

The purpose of this study was to compare the ocular biometrics between myopic patients with and without narrow angles. Patients with a stable myopic refraction (myopia worse than -1.00 D spherical equivalent) were prospectively recruited. Angle status was assessed using gonioscopy and biometric measurements were performed using an anterior segment optical coherence tomography and an IOLMaster. A total of 29 patients (58 eyes) were enrolled with 13 patients (26 eyes) classified as having narrow angles and 16 patients (32 eyes) classified as having open angles. Baseline demographics of age, sex, and ethnicity did not differ significantly between the 2 groups. The patients with narrow angles were on average older than those with open angles but the difference did not reach statistical significance (P=0.12). The central anterior chamber depth was significantly less in the eyes with narrow angles (P=0.05). However, the average lens thickness, although greater in the eyes with narrow angles, did not reach statistical significance (P=0.10). Refractive error, axial lengths, and iris thicknesses did not differ significantly between the 2 groups (P=0.32, 0.47, 0.15). Narrow angles can occur in myopic eyes. Routine gonioscopy is therefore recommended for all patients regardless of refractive error.

Precision alignment and calibration of optical systems using computer generated holograms

NASA Astrophysics Data System (ADS)

Coyle, Laura Elizabeth

As techniques for manufacturing and metrology advance, optical systems are being designed with more complexity than ever before. Given these prescriptions, alignment and calibration can be a limiting factor in their final performance. Computer generated holograms (CGHs) have several unique properties that make them powerful tools for meeting these demanding tolerances. This work will present three novel methods for alignment and calibration of optical systems using computer generated holograms. Alignment methods using CGHs require that the optical wavefront created by the CGH be related to a mechanical datum to locate it space. An overview of existing methods is provided as background, then two new alignment methods are discussed in detail. In the first method, the CGH contact Ball Alignment Tool (CBAT) is used to align a ball or sphere mounted retroreflector (SMR) to a Fresnel zone plate pattern with micron level accuracy. The ball is bonded directly onto the CGH substrate and provides permanent, accurate registration between the optical wavefront and a mechanical reference to locate the CGH in space. A prototype CBAT was built and used to align and bond an SMR to a CGH. In the second method, CGH references are used to align axi-symmetric optics in four degrees of freedom with low uncertainty and real time feedback. The CGHs create simultaneous 3D optical references where the zero order reflection sets tilt and the first diffracted order sets centration. The flexibility of the CGH design can be used to accommodate a wide variety of optical systems and maximize sensitivity to misalignments. A 2-CGH prototype system was aligned multiplied times and the alignment uncertainty was quantified and compared to an error model. Finally, an enhanced calibration method is presented. It uses multiple perturbed measurements of a master sphere to improve the calibration of CGH-based Fizeau interferometers ultimately measuring aspheric test surfaces. The improvement in the

The twilight zone of cis element alignments.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-02-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

Initial Navigation Alignment of Optical Instruments on GOES-R

NASA Astrophysics Data System (ADS)

Isaacson, P.; DeLuccia, F.; Reth, A. D.; Igli, D. A.; Carter, D.

2016-12-01

The GOES-R satellite is the first in NOAA's next-generation series of geostationary weather satellites. In addition to a number of space weather sensors, it will carry two principal optical earth-observing instruments, the Advanced Baseline Imager (ABI) and the Geostationary Lightning Mapper (GLM). During launch, currently scheduled for November of 2016, the alignment of these optical instruments is anticipated to shift from that measured during pre-launch characterization. While both instruments have image navigation and registration (INR) processing algorithms to enable automated geolocation of the collected data, the launch-derived misalignment may be too large for these approaches to function without an initial adjustment to calibration parameters. The parameters that may require adjustment are for Line of Sight Motion Compensation (LMC), and the adjustments will be estimated on orbit during the post-launch test (PLT) phase. We have developed approaches to estimate the initial alignment errors for both ABI and GLM image products. Our approaches involve comparison of ABI and GLM images collected during PLT to a set of reference ("truth") images using custom image processing tools and other software (the INR Performance Assessment Tool Set, or "IPATS") being developed for other INR assessments of ABI and GLM data. IPATS is based on image correlation approaches to determine offsets between input and reference images, and these offsets are the fundamental input to our estimate of the initial alignment errors. Initial testing of our alignment algorithms on proxy datasets lends high confidence that their application will determine the initial alignment errors to within sufficient accuracy to enable the operational INR processing approaches to proceed in a nominal fashion. We will report on the algorithms, implementation approach, and status of these initial alignment tools being developed for the GOES-R ABI and GLM instruments.

Solar Tracking Error Analysis of Fresnel Reflector

PubMed Central

Zheng, Jiantao; Yan, Junjie; Pei, Jie; Liu, Guanjie

2014-01-01

Depending on the rotational structure of Fresnel reflector, the rotation angle of the mirror was deduced under the eccentric condition. By analyzing the influence of the sun tracking rotation angle error caused by main factors, the change rule and extent of the influence were revealed. It is concluded that the tracking errors caused by the difference between the rotation axis and true north meridian, at noon, were maximum under certain conditions and reduced at morning and afternoon gradually. The tracking error caused by other deviations such as rotating eccentric, latitude, and solar altitude was positive at morning, negative at afternoon, and zero at a certain moment of noon. PMID:24895664

Automated interferometric alignment system for paraboloidal mirrors

DOEpatents

Maxey, L.C.

1993-09-28

A method is described for a systematic method of interpreting interference fringes obtained by using a corner cube retroreflector as an alignment aid when aligning a paraboloid to a spherical wavefront. This is applicable to any general case where such alignment is required, but is specifically applicable in the case of aligning an autocollimating test using a diverging beam wavefront. In addition, the method provides information which can be systematically interpreted such that independent information about pitch, yaw and focus errors can be obtained. Thus, the system lends itself readily to automation. Finally, although the method is developed specifically for paraboloids, it can be seen to be applicable to a variety of other aspheric optics when applied in combination with a wavefront corrector that produces a wavefront which, when reflected from the correctly aligned aspheric surface will produce a collimated wavefront like that obtained from the paraboloid when it is correctly aligned to a spherical wavefront. 14 figures.

Hartman Testing of X-Ray Telescopes

NASA Technical Reports Server (NTRS)

Saha, Timo T.; Biskasch, Michael; Zhang, William W.

2013-01-01

Hartmann testing of x-ray telescopes is a simple test method to retrieve and analyze alignment errors and low-order circumferential errors of x-ray telescopes and their components. A narrow slit is scanned along the circumference of the telescope in front of the mirror and the centroids of the images are calculated. From the centroid data, alignment errors, radius variation errors, and cone-angle variation errors can be calculated. Mean cone angle, mean radial height (average radius), and the focal length of the telescope can also be estimated if the centroid data is measured at multiple focal plane locations. In this paper we present the basic equations that are used in the analysis process. These equations can be applied to full circumference or segmented x-ray telescopes. We use the Optical Surface Analysis Code (OSAC) to model a segmented x-ray telescope and show that the derived equations and accompanying analysis retrieves the alignment errors and low order circumferential errors accurately.

Various methods for assessing static lower extremity alignment: implications for prospective risk-factor screenings.

PubMed

Nguyen, Anh-Dung; Boling, Michelle C; Slye, Carrie A; Hartley, Emily M; Parisi, Gina L

2013-01-01

Accurate, efficient, and reliable measurement methods are essential to prospectively identify risk factors for knee injuries in large cohorts. To determine tester reliability using digital photographs for the measurement of static lower extremity alignment (LEA) and whether values quantified with an electromagnetic motion-tracking system are in agreement with those quantified with clinical methods and digital photographs. Descriptive laboratory study. Laboratory. Thirty-three individuals participated and included 17 (10 women, 7 men; age = 21.7 ± 2.7 years, height = 163.4 ± 6.4 cm, mass = 59.7 ± 7.8 kg, body mass index = 23.7 ± 2.6 kg/m2) in study 1, in which we examined the reliability between clinical measures and digital photographs in 1 trained and 1 novice investigator, and 16 (11 women, 5 men; age = 22.3 ± 1.6 years, height = 170.3 ± 6.9 cm, mass = 72.9 ± 16.4 kg, body mass index = 25.2 ± 5.4 kg/m2) in study 2, in which we examined the agreement among clinical measures, digital photographs, and an electromagnetic tracking system. We evaluated measures of pelvic angle, quadriceps angle, tibiofemoral angle, genu recurvatum, femur length, and tibia length. Clinical measures were assessed using clinically accepted methods. Frontal- and sagittal-plane digital images were captured and imported into a computer software program. Anatomic landmarks were digitized using an electromagnetic tracking system to calculate static LEA. Intraclass correlation coefficients and standard errors of measurement were calculated to examine tester reliability. We calculated 95% limits of agreement and used Bland-Altman plots to examine agreement among clinical measures, digital photographs, and an electromagnetic tracking system. Using digital photographs, fair to excellent intratester (intraclass correlation coefficient range = 0.70-0.99) and intertester (intraclass correlation coefficient range = 0.75-0.97) reliability were observed for static knee alignment and limb

Statistical Significance of Optical Map Alignments

PubMed Central

Sarkar, Deepayan; Goldstein, Steve; Schwartz, David C.

2012-01-01

Abstract The Optical Mapping System constructs ordered restriction maps spanning entire genomes through the assembly and analysis of large datasets comprising individually analyzed genomic DNA molecules. Such restriction maps uniquely reveal mammalian genome structure and variation, but also raise computational and statistical questions beyond those that have been solved in the analysis of smaller, microbial genomes. We address the problem of how to filter maps that align poorly to a reference genome. We obtain map-specific thresholds that control errors and improve iterative assembly. We also show how an optimal self-alignment score provides an accurate approximation to the probability of alignment, which is useful in applications seeking to identify structural genomic abnormalities. PMID:22506568

Ametropia, retinal anatomy, and OCT abnormality patterns in glaucoma. 1. Impacts of refractive error and interartery angle

NASA Astrophysics Data System (ADS)

Elze, Tobias; Baniasadi, Neda; Jin, Qingying; Wang, Hui; Wang, Mengyu

2017-12-01

Retinal nerve fiber layer thickness (RNFLT) measured by optical coherence tomography (OCT) is widely used in clinical practice to support glaucoma diagnosis. Clinicians frequently interpret peripapillary RNFLT areas marked as abnormal by OCT machines. However, presently, clinical OCT machines do not take individual retinal anatomy variation into account, and according diagnostic biases have been shown particularly for patients with ametropia. The angle between the two major temporal retinal arteries (interartery angle, IAA) is considered a fundamental retinal ametropia marker. Here, we analyze peripapillary spectral domain OCT RNFLT scans of 691 glaucoma patients and apply multivariate logistic regression to quantitatively compare the diagnostic bias of spherical equivalent (SE) of refractive error and IAA and to identify the precise retinal locations of false-positive/negative abnormality marks. Independent of glaucoma severity (visual field mean deviation), IAA/SE variations biased abnormality marks on OCT RNFLT printouts at 36.7%/22.9% of the peripapillary area, respectively. 17.2% of the biases due to SE are not explained by IAA variation, particularly in inferonasal areas. To conclude, the inclusion of SE and IAA in OCT RNFLT norms would help to increase diagnostic accuracy. Our detailed location maps may help clinicians to reduce diagnostic bias while interpreting retinal OCT scans.

Measuring Parameters of Massive Black Hole Binaries with Partially-Aligned Spins

NASA Technical Reports Server (NTRS)

Lang, Ryan N.; Hughes, Scott A.; Cornish, Neil J.

2010-01-01

It is important to understand how well the gravitational-wave observatory LISA can measure parameters of massive black hole binaries. It has been shown that including spin precession in the waveform breaks degeneracies and produces smaller expected parameter errors than a simpler, precession-free analysis. However, recent work has shown that gas in binaries can partially align the spins with the orbital angular momentum, thus reducing the precession effect. We show how this degrades the earlier results, producing more pessimistic errors in gaseous mergers. However, we then add higher harmonics to the signal model; these also break degeneracies, but they are not affected by the presence of gas. The harmonics often restore the errors in partially-aligned binaries to the same as, or better than/ those that are obtained for fully precessing binaries with no harmonics. Finally, we investigate what LISA measurements of spin alignment can tell us about the nature of gas around a binary,

High-resolution scanning precession electron diffraction: Alignment and spatial resolution.

PubMed

Barnard, Jonathan S; Johnstone, Duncan N; Midgley, Paul A

2017-03-01

Methods are presented for aligning the pivot point of a precessing electron probe in the scanning transmission electron microscope (STEM) and for assessing the spatial resolution in scanning precession electron diffraction (SPED) experiments. The alignment procedure is performed entirely in diffraction mode, minimising probe wander within the bright-field (BF) convergent beam electron diffraction (CBED) disk and is used to obtain high spatial resolution SPED maps. Through analysis of the power spectra of virtual bright-field images extracted from the SPED data, the precession-induced blur was measured as a function of precession angle. At low precession angles, SPED spatial resolution was limited by electronic noise in the scan coils; whereas at high precession angles SPED spatial resolution was limited by tilt-induced two-fold astigmatism caused by the positive spherical aberration of the probe-forming lens. Copyright © 2016 Elsevier B.V. All rights reserved.

Aperture alignment in autocollimator-based deflectometric profilometers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geckeler, R. D., E-mail: Ralf.Geckeler@ptb.de; Just, A.; Kranz, O.

2016-05-15

During the last ten years, deflectometric profilometers have become indispensable tools for the precision form measurement of optical surfaces. They have proven to be especially suitable for characterizing beam-shaping optical surfaces for x-ray beamline applications at synchrotrons and free electron lasers. Deflectometric profilometers use surface slope (angle) to assess topography and utilize commercial autocollimators for the contactless slope measurement. To this purpose, the autocollimator beam is deflected by a movable optical square (or pentaprism) towards the surface where a co-moving aperture limits and defines the beam footprint. In this paper, we focus on the precise and reproducible alignment of themore » aperture relative to the autocollimator’s optical axis. Its alignment needs to be maintained while it is scanned across the surface under test. The reproducibility of the autocollimator’s measuring conditions during calibration and during its use in the profilometer is of crucial importance to providing precise and traceable angle metrology. In the first part of the paper, we present the aperture alignment procedure developed at the Advanced Light Source, Lawrence Berkeley National Laboratory, USA, for the use of their deflectometric profilometers. In the second part, we investigate the topic further by providing extensive ray tracing simulations and calibrations of a commercial autocollimator performed at the Physikalisch-Technische Bundesanstalt, Germany, for evaluating the effects of the positioning of the aperture on the autocollimator’s angle response. The investigations which we performed are crucial for reaching fundamental metrological limits in deflectometric profilometry.« less

The development of alignment turning system for precision len cells

NASA Astrophysics Data System (ADS)

Huang, Chien-Yao; Ho, Cheng-Fang; Wang, Jung-Hsing; Chung, Chien-Kai; Chen, Jun-Cheng; Chang, Keng-Shou; Kuo, Ching-Hsiang; Hsu, Wei-Yao; Chen, Fong-Zhi

2017-08-01

In general, the drop-in and cell-mounted assembly are used for standard and high performance optical system respectively. The optical performance is limited by the residual centration error and position accuracy of the conventional assembly. Recently, the poker chip assembly with high precision lens barrels that can overcome the limitation of conventional assembly is widely applied to ultra-high performance optical system. ITRC also develops the poker chip assembly solution for high numerical aperture objective lenses and lithography projection lenses. In order to achieve high precision lens cell for poker chip assembly, an alignment turning system (ATS) is developed. The ATS includes measurement, alignment and turning modules. The measurement module including a non-contact displacement sensor and an autocollimator can measure centration errors of the top and the bottom surface of a lens respectively. The alignment module comprising tilt and translation stages can align the optical axis of the lens to the rotating axis of the vertical lathe. The key specifications of the ATS are maximum lens diameter, 400mm, and radial and axial runout of the rotary table < 2 μm. The cutting performances of the ATS are surface roughness Ra < 1 μm, flatness < 2 μm, and parallelism < 5 μm. After measurement, alignment and turning processes on our ATS, the centration error of a lens cell with 200mm in diameter can be controlled in 10 arcsec. This paper also presents the thermal expansion of the hydrostatic rotating table. A poker chip assembly lens cell with three sub-cells is accomplished with average transmission centration error in 12.45 arcsec by fresh technicians. The results show that ATS can achieve high assembly efficiency for precision optical systems.

Iterative refinement of structure-based sequence alignments by Seed Extension

PubMed Central

Kim, Changhoon; Tai, Chin-Hsien; Lee, Byungkook

2009-01-01

Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct such errors, we previously explored the possibility of replacing the residue-based dynamic programming algorithm in structure alignment procedures with the Seed Extension algorithm, which does not use a gap penalty. Here, we describe a new procedure called RSE (Refinement with Seed Extension) that iteratively refines a structure-based sequence alignment. Results RSE uses SE (Seed Extension) in its core, which is an algorithm that we reported recently for obtaining a sequence alignment from two superimposed structures. The RSE procedure was evaluated by comparing the correctly aligned fractions of residues before and after the refinement of the structure-based sequence alignments produced by popular programs. CE, DaliLite, FAST, LOCK2, MATRAS, MATT, TM-align, SHEBA and VAST were included in this analysis and the NCBI's CDD root node set was used as the reference alignments. RSE improved the average accuracy of sequence alignments for all programs tested when no shift error was allowed. The amount of improvement varied depending on the program. The average improvements were small for DaliLite and MATRAS but about 5% for CE and VAST. More substantial improvements have been seen in many individual cases. The additional computation times required for the refinements were negligible compared to the times taken by the structure alignment programs. Conclusion RSE is a computationally inexpensive way of improving the accuracy of a structure-based sequence alignment. It can be used as a standalone procedure following a regular structure-based sequence alignment or to replace the traditional

Slope Error Measurement Tool for Solar Parabolic Trough Collectors: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stynes, J. K.; Ihas, B.

2012-04-01

The National Renewable Energy Laboratory (NREL) has developed an optical measurement tool for parabolic solar collectors that measures the combined errors due to absorber misalignment and reflector slope error. The combined absorber alignment and reflector slope errors are measured using a digital camera to photograph the reflected image of the absorber in the collector. Previous work using the image of the reflection of the absorber finds the reflector slope errors from the reflection of the absorber and an independent measurement of the absorber location. The accuracy of the reflector slope error measurement is thus dependent on the accuracy of themore » absorber location measurement. By measuring the combined reflector-absorber errors, the uncertainty in the absorber location measurement is eliminated. The related performance merit, the intercept factor, depends on the combined effects of the absorber alignment and reflector slope errors. Measuring the combined effect provides a simpler measurement and a more accurate input to the intercept factor estimate. The minimal equipment and setup required for this measurement technique make it ideal for field measurements.« less

Patterning control strategies for minimum edge placement error in logic devices

NASA Astrophysics Data System (ADS)

Mulkens, Jan; Hanna, Michael; Slachter, Bram; Tel, Wim; Kubis, Michael; Maslow, Mark; Spence, Chris; Timoshkov, Vadim

2017-03-01

In this paper we discuss the edge placement error (EPE) for multi-patterning semiconductor manufacturing. In a multi-patterning scheme the creation of the final pattern is the result of a sequence of lithography and etching steps, and consequently the contour of the final pattern contains error sources of the different process steps. We describe the fidelity of the final pattern in terms of EPE, which is defined as the relative displacement of the edges of two features from their intended target position. We discuss our holistic patterning optimization approach to understand and minimize the EPE of the final pattern. As an experimental test vehicle we use the 7-nm logic device patterning process flow as developed by IMEC. This patterning process is based on Self-Aligned-Quadruple-Patterning (SAQP) using ArF lithography, combined with line cut exposures using EUV lithography. The computational metrology method to determine EPE is explained. It will be shown that ArF to EUV overlay, CDU from the individual process steps, and local CD and placement of the individual pattern features, are the important contributors. Based on the error budget, we developed an optimization strategy for each individual step and for the final pattern. Solutions include overlay and CD metrology based on angle resolved scatterometry, scanner actuator control to enable high order overlay corrections and computational lithography optimization to minimize imaging induced pattern placement errors of devices and metrology targets.

Estimating IMU heading error from SAR images.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doerry, Armin Walter

Angular orientation errors of the real antenna for Synthetic Aperture Radar (SAR) will manifest as undesired illumination gradients in SAR images. These gradients can be measured, and the pointing error can be calculated. This can be done for single images, but done more robustly using multi-image methods. Several methods are provided in this report. The pointing error can then be fed back to the navigation Kalman filter to correct for problematic heading (yaw) error drift. This can mitigate the need for uncomfortable and undesired IMU alignment maneuvers such as S-turns.

Modified alignment CGHs for aspheric surface test

NASA Astrophysics Data System (ADS)

Song, Jae-Bong; Yang, Ho-Soon; Rhee, Hyug-Gyo; Lee, Yun-Woo

2009-08-01

Computer Generated Holograms (CGH) for optical test are commonly consisted of one main pattern for testing aspheric surface and some alignment patterns for aligning the interferometer, CGH, and the test optics. To align the CGH plate and the test optics, we designed the alignment CGHs modified from the cat's eye alignment method, which are consisted of a couple of CGH patterns. The incident beam passed through the one part of the alignment CGH pattern is focused onto the one radius position of the test aspheric surface, and is reflected to the other part, and vice versa. This method has several merits compared to the conventional cat's eye alignment method. First, this method can be used in testing optics with a center hole, and the center part of CGH plate can be assigned to the alignment pattern. Second, the alignment pattern becomes a concentric circular arc pattern. The whole CGH patterns including the main pattern and alignment patterns are consisted of only concentric circular fringes. This concentric circular pattern can be easily made by the polar coordinated writer with circular scanning. The required diffraction angle becomes relatively small, so the 1st order diffraction beams instead of the 3rd order diffraction beam can be used as alignment beams, and the visibility can be improved. This alignment method also is more sensitive to the tilt and the lateral shift of the test aspheric surface. Using this alignment pattern, a 200 mm diameter F/0.5 aspheric mirror and a 600 mm diameter F/0.9 mirror were tested.

Robustly Aligning a Shape Model and Its Application to Car Alignment of Unknown Pose.

PubMed

Li, Yan; Gu, Leon; Kanade, Takeo

2011-09-01

Precisely localizing in an image a set of feature points that form a shape of an object, such as car or face, is called alignment. Previous shape alignment methods attempted to fit a whole shape model to the observed data, based on the assumption of Gaussian observation noise and the associated regularization process. However, such an approach, though able to deal with Gaussian noise in feature detection, turns out not to be robust or precise because it is vulnerable to gross feature detection errors or outliers resulting from partial occlusions or spurious features from the background or neighboring objects. We address this problem by adopting a randomized hypothesis-and-test approach. First, a Bayesian inference algorithm is developed to generate a shape-and-pose hypothesis of the object from a partial shape or a subset of feature points. For alignment, a large number of hypotheses are generated by randomly sampling subsets of feature points, and then evaluated to find the one that minimizes the shape prediction error. This method of randomized subset-based matching can effectively handle outliers and recover the correct object shape. We apply this approach on a challenging data set of over 5,000 different-posed car images, spanning a wide variety of car types, lighting, background scenes, and partial occlusions. Experimental results demonstrate favorable improvements over previous methods on both accuracy and robustness.

Retention-error patterns in complex alphanumeric serial-recall tasks.

PubMed

Mathy, Fabien; Varré, Jean-Stéphane

2013-01-01

We propose a new method based on an algorithm usually dedicated to DNA sequence alignment in order to both reliably score short-term memory performance on immediate serial-recall tasks and analyse retention-error patterns. There can be considerable confusion on how performance on immediate serial list recall tasks is scored, especially when the to-be-remembered items are sampled with replacement. We discuss the utility of sequence-alignment algorithms to compare the stimuli to the participants' responses. The idea is that deletion, substitution, translocation, and insertion errors, which are typical in DNA, are also typical putative errors in short-term memory (respectively omission, confusion, permutation, and intrusion errors). We analyse four data sets in which alphanumeric lists included a few (or many) repetitions. After examining the method on two simple data sets, we show that sequence alignment offers 1) a compelling method for measuring capacity in terms of chunks when many regularities are introduced in the material (third data set) and 2) a reliable estimator of individual differences in short-term memory capacity. This study illustrates the difficulty of arriving at a good measure of short-term memory performance, and also attempts to characterise the primary factors underpinning remembering and forgetting.

Angular dependent anisotropic terahertz response of vertically aligned multi-walled carbon nanotube arrays with spatial dispersion.

PubMed

Zhou, Yixuan; E, Yiwen; Xu, Xinlong; Li, Weilong; Wang, Huan; Zhu, Lipeng; Bai, Jintao; Ren, Zhaoyu; Wang, Li

2016-12-14

Spatial dispersion effect of aligned carbon nanotubes (CNTs) in the terahertz (THz) region has significance for both theoretical and applied consideration due to the unique intrinsically anisotropic physical properties of CNTs. Herein, we report the angular dependent reflection of p-polarized THz wave from vertically aligned multi-walled CNT arrays in both experiment and theory. The spectra indicate that the reflection depends on the film thickness of vertically aligned CNTs, the incident angle, and the frequency. The calculation model is based on the spatial dispersion effect of aligned CNTs and performed with effective impedance method and the Maxwell-Garnett approximation. The results fit well with the experiment when the thickness of CNT film is thin, which reveals a coherent superposition mechanism of the CNT surface reflection and CNTs/Si interface reflection. For thick CNT films, the CNTs/Si interface response determines the reflection at small incident angles, while the CNTs surface effect dominates at large incident angles. This work investigates the spatial dispersion effect of vertically aligned CNT arrays in the THz region, and paves a way for potential anisotropic THz applications based on CNTs with oblique incidence requirements.

Angular dependent anisotropic terahertz response of vertically aligned multi-walled carbon nanotube arrays with spatial dispersion

NASA Astrophysics Data System (ADS)

Zhou, Yixuan; Yiwen, E.; Xu, Xinlong; Li, Weilong; Wang, Huan; Zhu, Lipeng; Bai, Jintao; Ren, Zhaoyu; Wang, Li

2016-12-01

Spatial dispersion effect of aligned carbon nanotubes (CNTs) in the terahertz (THz) region has significance for both theoretical and applied consideration due to the unique intrinsically anisotropic physical properties of CNTs. Herein, we report the angular dependent reflection of p-polarized THz wave from vertically aligned multi-walled CNT arrays in both experiment and theory. The spectra indicate that the reflection depends on the film thickness of vertically aligned CNTs, the incident angle, and the frequency. The calculation model is based on the spatial dispersion effect of aligned CNTs and performed with effective impedance method and the Maxwell-Garnett approximation. The results fit well with the experiment when the thickness of CNT film is thin, which reveals a coherent superposition mechanism of the CNT surface reflection and CNTs/Si interface reflection. For thick CNT films, the CNTs/Si interface response determines the reflection at small incident angles, while the CNTs surface effect dominates at large incident angles. This work investigates the spatial dispersion effect of vertically aligned CNT arrays in the THz region, and paves a way for potential anisotropic THz applications based on CNTs with oblique incidence requirements.

Automation of the targeting and reflective alignment concept

NASA Technical Reports Server (NTRS)

Redfield, Robin C.

1992-01-01

The automated alignment system, described herein, employs a reflective, passive (requiring no power) target and includes a PC-based imaging system and one camera mounted on a six degree of freedom robot manipulator. The system detects and corrects for manipulator misalignment in three translational and three rotational directions by employing the Targeting and Reflective Alignment Concept (TRAC), which simplifies alignment by decoupling translational and rotational alignment control. The concept uses information on the camera and the target's relative position based on video feedback from the camera. These relative positions are converted into alignment errors and minimized by motions of the robot. The system is robust to exogenous lighting by virtue of a subtraction algorithm which enables the camera to only see the target. These capabilities are realized with relatively minimal complexity and expense.

Piezoelectric Response of Aligned Electrospun Polyvinylidene Fluoride/Carbon Nanotube Nanofibrous Membranes.

PubMed

Wu, Chang-Mou; Chou, Min-Hui; Zeng, Wun-Yuan

2018-06-10

Polyvinylidene fluoride (PVDF) shows piezoelectricity related to its β-phase content and mechanical and electrical properties influenced by its morphology and crystallinity. Electrospinning (ES) can produce ultrafine and well-aligned PVDF nanofibers. In this study, the effects of the presence of carbon nanotubes (CNT) and optimized ES parameters on the crystal structures and piezoelectric properties of aligned PVDF/CNT nanofibrous membranes were examined. The optimal β content and piezoelectric coefficient (d 33 ) of the aligned electrospun PVDF reached 88% and 27.4 pC/N; CNT addition increased the β-phase content to 89% and d 33 to 31.3 pC/N. The output voltages of piezoelectric units with aligned electrospun PVDF/CNT membranes increased linearly with applied loading and showed good stability during cyclic dynamic compression and tension. The sensitivities of the piezoelectric units with the membranes under dynamic compression and tension were 2.26 mV/N and 4.29 mV/%, respectively. In bending tests, the output voltage increased nonlinearly with bending angle because complicated forces were involved. The output of the aligned membrane-based piezoelectric unit with CNT was 1.89 V at the bending angle of 100°. The high electric outputs indicate that the aligned electrospun PVDF/CNT membranes are potentially effective for flexible wearable sensor application with high sensitivity.

Angles-centroids fitting calibration and the centroid algorithm applied to reverse Hartmann test

NASA Astrophysics Data System (ADS)

Zhao, Zhu; Hui, Mei; Xia, Zhengzheng; Dong, Liquan; Liu, Ming; Liu, Xiaohua; Kong, Lingqin; Zhao, Yuejin

2017-02-01

In this paper, we develop an angles-centroids fitting (ACF) system and the centroid algorithm to calibrate the reverse Hartmann test (RHT) with sufficient precision. The essence of ACF calibration is to establish the relationship between ray angles and detector coordinates. Centroids computation is used to find correspondences between the rays of datum marks and detector pixels. Here, the point spread function of RHT is classified as circle of confusion (CoC), and the fitting of a CoC spot with 2D Gaussian profile to identify the centroid forms the basis of the centroid algorithm. Theoretical and experimental results of centroids computation demonstrate that the Gaussian fitting method has a less centroid shift or the shift grows at a slower pace when the quality of the image is reduced. In ACF tests, the optical instrumental alignments reach an overall accuracy of 0.1 pixel with the application of laser spot centroids tracking program. Locating the crystal at different positions, the feasibility and accuracy of ACF calibration are further validated to 10-6-10-4 rad root-mean-square error of the calibrations differences.

Automatic alignment of double optical paths in excimer laser amplifier

NASA Astrophysics Data System (ADS)

Wang, Dahui; Zhao, Xueqing; Hua, Hengqi; Zhang, Yongsheng; Hu, Yun; Yi, Aiping; Zhao, Jun

2013-05-01

A kind of beam automatic alignment method used for double paths amplification in the electron pumped excimer laser system is demonstrated. In this way, the beams from the amplifiers can be transferred along the designated direction and accordingly irradiate on the target with high stabilization and accuracy. However, owing to nonexistence of natural alignment references in excimer laser amplifiers, two cross-hairs structure is used to align the beams. Here, one crosshair put into the input beam is regarded as the near-field reference while the other put into output beam is regarded as the far-field reference. The two cross-hairs are transmitted onto Charge Coupled Devices (CCD) by image-relaying structures separately. The errors between intersection points of two cross-talk images and centroid coordinates of actual beam are recorded automatically and sent to closed loop feedback control mechanism. Negative feedback keeps running until preset accuracy is reached. On the basis of above-mentioned design, the alignment optical path is built and the software is compiled, whereafter the experiment of double paths automatic alignment in electron pumped excimer laser amplifier is carried through. Meanwhile, the related influencing factors and the alignment precision are analyzed. Experimental results indicate that the alignment system can achieve the aiming direction of automatic aligning beams in short time. The analysis shows that the accuracy of alignment system is 0.63μrad and the beam maximum restoration error is 13.75μm. Furthermore, the bigger distance between the two cross-hairs, the higher precision of the system is. Therefore, the automatic alignment system has been used in angular multiplexing excimer Main Oscillation Power Amplification (MOPA) system and can satisfy the requirement of beam alignment precision on the whole.

The twilight zone of cis element alignments

PubMed Central

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-01-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein–DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein–DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments. PMID:23268451

Note: O-ring stack system for electron gun alignment.

PubMed

Park, In-Yong; Cho, Boklae; Han, Cheolsu; Shin, Seungmin; Lee, Dongjun; Ahn, Sang Jung

2015-01-01

We present a reliable method for aligning an electron gun which consists of an electron source and lenses by controlling a stack of rubber O-rings in a vacuum condition. The beam direction angle is precisely tilted along two axes by adjusting the height difference of a stack of O-rings. In addition, the source position is shifted in each of three orthogonal directions. We show that the tilting angle and linear shift along the x and y axes as obtained from ten stacked O-rings are ±2.55° and ±2 mm, respectively. This study can easily be adapted to charged particle gun alignment and adjustments of the flange position in a vacuum, ensuring that its results can be useful with regard to electrical insulation between flanges with slight modifications.

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly

PubMed Central

Wala, Jeremiah; Beroukhim, Rameen

2017-01-01

Abstract We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. Availability and Implementation: SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. Contact: jwala@broadinstitue.org; rameen@broadinstitute.org PMID:28011768

Alignment of galaxies relative to their local environment in SDSS-DR8

NASA Astrophysics Data System (ADS)

Hirv, A.; Pelt, J.; Saar, E.; Tago, E.; Tamm, A.; Tempel, E.; Einasto, M.

2017-03-01

Aims: We study the alignment of galaxies relative to their local environment in SDSS-DR8 and, using these data, we discuss evolution scenarios for different types of galaxies. Methods: We defined a vector field of the direction of anisotropy of the local environment of galaxies. We summed the unit direction vectors of all close neighbours of a given galaxy in a particular way to estimate this field. We found the alignment angles between the spin axes of disc galaxies, or the minor axes of elliptical galaxies, and the direction of anisotropy. The distributions of cosines of these angles are compared to the random distributions to analyse the alignment of galaxies. Results: Sab galaxies show perpendicular alignment relative to the direction of anisotropy in a sparse environment, for single galaxies and galaxies of low luminosity. Most of the parallel alignment of Scd galaxies comes from dense regions, from 2...3 member groups and from galaxies with low luminosity. The perpendicular alignment of S0 galaxies does not depend strongly on environmental density nor luminosity; it is detected for single and 2...3 member group galaxies, and for main galaxies of 4...10 member groups. The perpendicular alignment of elliptical galaxies is clearly detected for single galaxies and for members of ≤10 member groups; the alignment increases with environmental density and luminosity. Conclusions: We confirm the existence of fossil tidally induced alignment of Sab galaxies at low z. The alignment of Scd galaxies can be explained via the infall of matter to filaments. S0 galaxies may have encountered relatively massive mergers along the direction of anisotropy. Major mergers along this direction can explain the alignment of elliptical galaxies. Less massive, but repeated mergers are possibly responsible for the formation of elliptical galaxies in sparser areas and for less luminous elliptical galaxies.

Development of a method of alignment between various SOLAR MAXIMUM MISSION experiments

NASA Technical Reports Server (NTRS)

1977-01-01

Results of an engineering study of the methods of alignment between various experiments for the solar maximum mission are described. The configuration studied consists of the instruments, mounts and instrument support platform located within the experiment module. Hardware design, fabrication methods and alignment techniques were studied with regard to optimizing the coalignment between the experiments and the fine sun sensor. The proposed hardware design was reviewed with regard to loads, stress, thermal distortion, alignment error budgets, fabrication techniques, alignment techniques and producibility. Methods of achieving comparable alignment accuracies on previous projects were also reviewed.

Automated interferometric alignment system for paraboloidal mirrors

DOEpatents

Maxey, L. Curtis

1993-01-01

A method is described for a systematic method of interpreting interference fringes obtained by using a corner cube retroreflector as an alignment aid when aigning a paraboloid to a spherical wavefront. This is applicable to any general case where such alignment is required, but is specifically applicable in the case of aligning an autocollimating test using a diverging beam wavefront. In addition, the method provides information which can be systematically interpreted such that independent information about pitch, yaw and focus errors can be obtained. Thus, the system lends itself readily to automation. Finally, although the method is developed specifically for paraboloids, it can be seen to be applicable to a variety of other aspheric optics when applied in combination with a wavefront corrector that produces a wavefront which, when reflected from the correctly aligned aspheric surface will produce a collimated wavefront like that obtained from the paraboloid when it is correctly aligned to a spherical wavefront.

Effect of soft tissue laxity of the knee joint on limb alignment correction in open-wedge high tibial osteotomy.

PubMed

Lee, Dae-Hee; Park, Sung-Chul; Park, Hyung-Joon; Han, Seung-Beom

2016-12-01

Open-wedge high tibial osteotomy (HTO) cannot always accurately correct limb alignment, resulting in under- or over-correction. This study assessed the relationship between soft tissue laxity of the knee joint and alignment correction in open-wedge HTO. This prospective study involved 85 patients (86 knees) undergoing open-wedge HTO for primary medial osteoarthritis. The mechanical axis (MA), weight-bearing line (WBL) ratio, and joint line convergence angle (JLCA) were measured on radiographs preoperatively and after 6 months, and the differences between the pre- and post-surgery values were calculated. Post-operative WBL ratios of 57-67 % were classified as acceptable correction. WBL ratios <57 and >67 % were classified as under- and over-corrections, respectively. Preoperative JLCA correlated positively with differences in MA (r = 0.358, P = 0.001) and WBL ratio (P = 0.003). Difference in JLCA showed a stronger correlation than preoperative JLCA with differences in MA (P < 0.001) and WBL ratio (P < 0.001). Difference in JLCA was the only predictor of both difference in MA (P < 0.001) and difference in WBL ratio (P < 0.001). The difference between pre- and post-operative JLCA differed significantly between the under-correction, acceptable-correction, and over-correction groups (P = 0.033). Preoperative JLCA, however, did not differ significantly between the three groups. Neither preoperative JLCA nor difference in JLCA correlated with change in posterior slope. Preoperative degree of soft tissue laxity in the knee joint was related to the degree of alignment correction, but not to alignment correction error, in open-wedge HTO. Change in soft tissue laxity around the knee from before to after open-wedge HTO correlated with both correction amount and correction error. Therefore, a too large change in JLCA from before to after open-wedge osteotomy may be due to an overly large reduction in JLCA following osteotomy, suggesting alignment over

The Effect of Sliding Humeral Osteotomy (SHO) on Frontal Plane Thoracic Limb Alignment: An Ex Vivo Canine Cadaveric Study.

PubMed

Breiteneicher, Adam H; Norby, Bo; Schulz, Kurt S; Kerwin, Sharon C; Hulse, Don A; Fox, Derek B; Saunders, W Brian

2016-11-01

To determine the effect of sliding humeral osteotomy (SHO) on frontal plane thoracic limb alignment in standing and recumbent limb positions. Canine cadaveric study. Canine thoracic limbs (n=15 limb pairs). Limbs acquired from healthy Labrador Retrievers euthanatized for reasons unrelated to this study were mounted in a limb press and aligned in a standing position followed by axial loading at 30% body weight. Frontal plane radiography was performed in standing and recumbent positions pre- and post-SHO. In the standing position, lateralization of the foot was measured pre- and post-SHO using a textured grid secured to the limb press base plate. Twelve thoracic limb alignment values (mean ± SD and 95% CI) were determined using the center of rotation of angulation (CORA) method were compared using linear mixed models to determine if significant differences existed between limb alignment values pre- or post-SHO, controlling for dog, limb, and limb position. Six of 12 standing or recumbent alignment values were significantly different pre- and post-SHO. SHO resulted in decreased mechanical lateral distal humeral angle and movement of the mechanical humeral radio-ulnar angle, radio-ulnar metacarpal angle, thoracic humeral angle, and elbow mechanical axis deviation toward coaxial limb alignment. In the standing position, the foot underwent significant lateralization post-SHO. SHO resulted in significant alteration in frontal plane thoracic limb alignment. Additional studies are necessary to determine if the changes reported using our ex vivo model occur following SHO in vivo. © Copyright 2016 by The American College of Veterinary Surgeons.

Field Aligned Currents Derived from Pressure Profiles Obtained from TWINS ENA Images

NASA Astrophysics Data System (ADS)

Wood, K.; Perez, J. D.; McComas, D. J.; Goldstein, J.; Valek, P. W.

2015-12-01

Field aligned currents (FACs) that flow from the Earth's magnetosphere into the ionosphere are an important coupling mechanism in the interaction of the solar wind with the Earth's magnetosphere. Assuming pressure balance along with charge conservation yields an expression for the FACs in terms of plasma pressure gradients and pressure anisotropy. The Two Wide-Angle Imaging Neutral Atom Spectrometers (TWINS) mission, the first stereoscopic ENA magnetospheric imager, provides global images of the inner magnetosphere from which ion pressure distributions and pressure anisotropies can be obtained. Following the formulations in Heineman [1990] and using results from TWINS observations, we calculate the distribution of field aligned currents for the 17-18 March 2015 geomagnetic storm in which extended ionospheric precipitation was observed. Initial results for the field aligned currents will be generated assuming an isotropic pitch angle distribution. Global maps of field aligned currents during the main and recovery phase of the storm will be presented. Heinemann, H. (1990), Representations of Currents and Magnetic Fields in Anisotropic Magnetohydrostatic Plasma, J. Geophys. Res., 95, 7789.

Measurement method of rotation angle and clearance in intelligent spherical hinge

NASA Astrophysics Data System (ADS)

Hu, Penghao; Lu, Yichang; Chen, Shiyi; Hu, Yi; Zhu, Lianqing

2018-06-01

Precision ball hinges are widely applied in parallel mechanisms, robotics, and other areas, but their rotation orientation and angle cannot be obtained during passive motion. The simultaneous clearance error in a precision ball hinge’s motion also can not be determined. In this paper we propose an intelligent ball hinge (IBH) that can detect the rotation angle and moving clearance, based on our previous research results. The measurement model was optimized to promote measurement accuracy and resolution, and an optimal design for the IBH’s structure was determined. The experimental data showed that the measurement accuracy and resolution of the modified scheme were improved. Within  ±10° and  ±  20°, the average errors of the uniaxial measurements were 0.29° and 0.42°, respectively. The resolution of the measurements was 15″. The source of the measurement errors was analyzed through theory and experimental data and several key error sources were determined. A point capacitance model for measuring the clearance error is proposed, which is useful not only in compensating for the angle measurement error but also in realizing the motion clearance of an IBH in real-time.

Alignment of Irregular Grains by Mechanical Torques

NASA Astrophysics Data System (ADS)

Hoang, Thiem; Cho, Jungyeon; Lazarian, A.

2018-01-01

We study the alignment of irregular dust grains by mechanical torques due to the drift of grains through the ambient gas. We first calculate mechanical alignment torques (MATs) resulting from specular reflection of gas atoms for seven irregular shapes: one shape of mirror symmetry, three highly irregular shapes (HIS), and three weakly irregular shapes (WIS). We find that the grain with mirror symmetry experiences negligible MATs due to its mirror-symmetry geometry. Three HIS can produce strong MATs, which exhibit some generic properties as radiative torques (RATs), while three WIS produce less efficient MATs. We then study grain alignment by MATs for the different angles between the drift velocity and the ambient magnetic field, for paramagnetic and superparamagnetic grains assuming efficient internal relaxation. We find that for HIS grains, MATs can align subsonically drifting grains in the same way as RATs, with low-J and high-J attractors. For supersonic drift, MATs can align grains with low-J and high-J attractors, analogous to RAT alignment by anisotropic radiation. We also show that the joint action of MATs and magnetic torques in grains with iron inclusions can lead to perfect MAT alignment. Our results point out the potential importance of MAT alignment for HIS grains predicted by the analytical model of Lazarian & Hoang, although more theoretical and observational studies are required due to uncertainty in the shape of interstellar grains. We outline astrophysical environments where MAT alignment is potentially important.

Note: high precision angle generator using multiple ultrasonic motors and a self-calibratable encoder.

PubMed

Kim, Jong-Ahn; Kim, Jae Wan; Kang, Chu-Shik; Jin, Jonghan; Eom, Tae Bong

2011-11-01

We present an angle generator with high resolution and accuracy, which uses multiple ultrasonic motors and a self-calibratable encoder. A cylindrical air bearing guides a rotational motion, and the ultrasonic motors achieve high resolution over the full circle range with a simple configuration. The self-calibratable encoder can compensate the scale error of a divided circle (signal period: 20") effectively by applying the equal-division-averaged method. The angle generator configures a position feedback control loop using the readout of the encoder. By combining the ac and dc operation mode, the angle generator produced stepwise angular motion with 0.005" resolution. We also evaluated the performance of the angle generator using a precision angle encoder and an autocollimator. The expanded uncertainty (k = 2) in the angle generation was estimated less than 0.03", which included the calibrated scale error and the nonlinearity error. © 2011 American Institute of Physics

Estimation of daily interfractional larynx residual setup error after isocentric alignment for head and neck radiotherapy: Quality-assurance implications for target volume and organ-at-risk margination using daily CT-on-rails imaging

PubMed Central

Baron, Charles A.; Awan, Musaddiq J.; Mohamed, Abdallah S. R.; Akel, Imad; Rosenthal, David I.; Gunn, G. Brandon; Garden, Adam S.; Dyer, Brandon A.; Court, Laurence; Sevak, Parag R; Kocak-Uzel, Esengul; Fuller, Clifton D.

2016-01-01

Larynx may alternatively serve as a target or organ-at-risk (OAR) in head and neck cancer (HNC) image-guided radiotherapy (IGRT). The objective of this study was to estimate IGRT parameters required for larynx positional error independent of isocentric alignment and suggest population–based compensatory margins. Ten HNC patients receiving radiotherapy (RT) with daily CT-on-rails imaging were assessed. Seven landmark points were placed on each daily scan. Taking the most superior anterior point of the C5 vertebra as a reference isocenter for each scan, residual displacement vectors to the other 6 points were calculated post-isocentric alignment. Subsequently, using the first scan as a reference, the magnitude of vector differences for all 6 points for all scans over the course of treatment were calculated. Residual systematic and random error, and the necessary compensatory CTV-to-PTV and OAR-to-PRV margins were calculated, using both observational cohort data and a bootstrap-resampled population estimator. The grand mean displacements for all anatomical points was 5.07mm, with mean systematic error of 1.1mm and mean random setup error of 2.63mm, while bootstrapped POIs grand mean displacement was 5.09mm, with mean systematic error of 1.23mm and mean random setup error of 2.61mm. Required margin for CTV-PTV expansion was 4.6mm for all cohort points, while the bootstrap estimator of the equivalent margin was 4.9mm. The calculated OAR-to-PRV expansion for the observed residual set-up error was 2.7mm, and bootstrap estimated expansion of 2.9mm. We conclude that the interfractional larynx setup error is a significant source of RT set-up/delivery error in HNC both when the larynx is considered as a CTV or OAR. We estimate the need for a uniform expansion of 5mm to compensate for set up error if the larynx is a target or 3mm if the larynx is an OAR when using a non-laryngeal bony isocenter. PMID:25679151

Estimation of daily interfractional larynx residual setup error after isocentric alignment for head and neck radiotherapy: quality assurance implications for target volume and organs‐at‐risk margination using daily CT on‐rails imaging

PubMed Central

Baron, Charles A.; Awan, Musaddiq J.; Mohamed, Abdallah S.R.; Akel, Imad; Rosenthal, David I.; Gunn, G. Brandon; Garden, Adam S.; Dyer, Brandon A.; Court, Laurence; Sevak, Parag R.; Kocak‐Uzel, Esengul

2014-01-01

Larynx may alternatively serve as a target or organs at risk (OAR) in head and neck cancer (HNC) image‐guided radiotherapy (IGRT). The objective of this study was to estimate IGRT parameters required for larynx positional error independent of isocentric alignment and suggest population‐based compensatory margins. Ten HNC patients receiving radiotherapy (RT) with daily CT on‐rails imaging were assessed. Seven landmark points were placed on each daily scan. Taking the most superior‐anterior point of the C5 vertebra as a reference isocenter for each scan, residual displacement vectors to the other six points were calculated postisocentric alignment. Subsequently, using the first scan as a reference, the magnitude of vector differences for all six points for all scans over the course of treatment was calculated. Residual systematic and random error and the necessary compensatory CTV‐to‐PTV and OAR‐to‐PRV margins were calculated, using both observational cohort data and a bootstrap‐resampled population estimator. The grand mean displacements for all anatomical points was 5.07 mm, with mean systematic error of 1.1 mm and mean random setup error of 2.63 mm, while bootstrapped POIs grand mean displacement was 5.09 mm, with mean systematic error of 1.23 mm and mean random setup error of 2.61 mm. Required margin for CTV‐PTV expansion was 4.6 mm for all cohort points, while the bootstrap estimator of the equivalent margin was 4.9 mm. The calculated OAR‐to‐PRV expansion for the observed residual setup error was 2.7 mm and bootstrap estimated expansion of 2.9 mm. We conclude that the interfractional larynx setup error is a significant source of RT setup/delivery error in HNC, both when the larynx is considered as a CTV or OAR. We estimate the need for a uniform expansion of 5 mm to compensate for setup error if the larynx is a target, or 3 mm if the larynx is an OAR, when using a nonlaryngeal bony isocenter. PACS numbers: 87.55.D‐, 87.55.Qr

Calibration Errors in Interferometric Radio Polarimetry

NASA Astrophysics Data System (ADS)

Hales, Christopher A.

2017-08-01

Residual calibration errors are difficult to predict in interferometric radio polarimetry because they depend on the observational calibration strategy employed, encompassing the Stokes vector of the calibrator and parallactic angle coverage. This work presents analytic derivations and simulations that enable examination of residual on-axis instrumental leakage and position-angle errors for a suite of calibration strategies. The focus is on arrays comprising alt-azimuth antennas with common feeds over which parallactic angle is approximately uniform. The results indicate that calibration schemes requiring parallactic angle coverage in the linear feed basis (e.g., the Atacama Large Millimeter/submillimeter Array) need only observe over 30°, beyond which no significant improvements in calibration accuracy are obtained. In the circular feed basis (e.g., the Very Large Array above 1 GHz), 30° is also appropriate when the Stokes vector of the leakage calibrator is known a priori, but this rises to 90° when the Stokes vector is unknown. These findings illustrate and quantify concepts that were previously obscure rules of thumb.

Wavefront error sensing for LDR

NASA Technical Reports Server (NTRS)

Tubbs, Eldred F.; Glavich, T. A.

1988-01-01

Wavefront sensing is a significant aspect of the LDR control problem and requires attention at an early stage of the control system definition and design. A combination of a Hartmann test for wavefront slope measurement and an interference test for piston errors of the segments was examined and is presented as a point of departure for further discussion. The assumption is made that the wavefront sensor will be used for initial alignment and periodic alignment checks but that it will not be used during scientific observations. The Hartmann test and the interferometric test are briefly examined.

Kinematic alignment is a possible alternative to mechanical alignment in total knee arthroplasty.

PubMed

Lee, Yong Seuk; Howell, Stephen M; Won, Ye-Yeon; Lee, O-Sung; Lee, Seung Hoon; Vahedi, Hamed; Teo, Seow Hui

2017-11-01

A systematic review was conducted to answer the following questions: (1) Does kinematically aligned (KA) total knee arthroplasty (TKA) achieve clinical outcomes comparable to those of mechanically aligned (MA) TKA? (2) How do the limb, knee, and component alignments differ between KA and MA TKA? (3) How is joint line orientation angle (JLOA) changed from the native knee in KA TKA compared to that in MA TKA? Nine full-text articles in English that reported the clinical and radiological outcomes of KA TKA were included. Five studies had a control group of patients who underwent MA TKA. Data on patient demographics, clinical scores, and radiological results were extracted. There were two level I, one level II, three level III, and three level IV studies. Six of the nine studies used patient-specific instrumentation, one study used computer navigation, and two studies used manual instrumentation. The clinical outcomes of KA TKA were comparable or superior to those of MA TKA with a minimum 2-year follow-up. Limb and knee alignment in KA TKA was similar to those in MA TKA, and component alignment showed slightly more varus in the tibial component and slightly more valgus in the femoral component. The JLOA in KA TKA was relatively parallel to the floor compared to that in the native knee and not oblique (medial side up and lateral side down) compared to that in MA TKA. The implant survivorship and complication rate of the KA TKA were similar to those of the MA TKA. Similar or better clinical outcomes were produced by using a KA TKA at early-term follow-up and the component alignment differed from that of MA TKA. KA TKA seemed to restore function without catastrophic failure regardless of the alignment category up to midterm follow-up. The JLOA in KA TKA was relatively parallel to the floor similar to the native knee compared to that in MA TKA. The present review of nine published studies suggests that relatively new kinematic alignment is an acceptable and alternative

Effect of alignment changes on socket reaction moments while walking in transtibial prostheses with energy storage and return feet

PubMed Central

Kobayashi, Toshiki; Arabian, Adam K.; Orendurff, Michael S.; Rosenbaum-Chou, Teri G.; Boone, David A.

2014-01-01

Background Energy storage and return feet are designed for active amputees. However, little is known about the socket reaction moments in transtibial prostheses with energy storage and return feet. The aim of this study was to investigate the effect of alignment changes on the socket reaction moments during gait while using the energy storage and return feet. Methods A Smart Pyramid™ was used to measure the socket reaction moments in 10 subjects with transtibial prostheses while walking under 25 alignment conditions, including a nominal alignment (as defined by conventional clinical methods), as well as angle malalignments of 2°, 4° and 6° (flexion, extension, abduction, and adduction) and translation malalignments of 5mm, 10mm and 15mm (anterior, posterior, lateral, and medial) referenced from the nominal alignment. The socket reaction moments of the nominal alignment were compared with each malalignment. Findings Both coronal and sagittal alignment changes demonstrated systematic effects on the socket reaction moments. In the sagittal plane, angle and translation alignment changes demonstrated significant differences (P<0.05) in the minimum moment, the moment at 45% of stance and the maximum moment for some comparisons. In the coronal plane, angle and translation alignment changes demonstrated significant differences (P<0.05) in the moment at 30% and 75% of stance for all comparisons. Interpretation The alignment may have systematic effects on the socket reaction moments in transtibial prostheses with energy storage and return feet. The socket reaction moments could potentially be a useful biomechanical parameter to evaluate the alignment of the transtibial prostheses. PMID:24315709

Effect of alignment changes on socket reaction moments while walking in transtibial prostheses with energy storage and return feet.

PubMed

Kobayashi, Toshiki; Arabian, Adam K; Orendurff, Michael S; Rosenbaum-Chou, Teri G; Boone, David A

2014-01-01

Energy storage and return feet are designed for active amputees. However, little is known about the socket reaction moments in transtibial prostheses with energy storage and return feet. The aim of this study was to investigate the effect of alignment changes on the socket reaction moments during gait while using the energy storage and return feet. A Smart Pyramid™ was used to measure the socket reaction moments in 10 subjects with transtibial prostheses while walking under 25 alignment conditions, including a nominal alignment (as defined by conventional clinical methods), as well as angle malalignments of 2°, 4° and 6° (flexion, extension, abduction, and adduction) and translation malalignments of 5mm, 10mm and 15mm (anterior, posterior, lateral, and medial) referenced from the nominal alignment. The socket reaction moments of the nominal alignment were compared with each malalignment. Both coronal and sagittal alignment changes demonstrated systematic effects on the socket reaction moments. In the sagittal plane, angle and translation alignment changes demonstrated significant differences (P<0.05) in the minimum moment, the moment at 45% of stance and the maximum moment for some comparisons. In the coronal plane, angle and translation alignment changes demonstrated significant differences (P<0.05) in the moment at 30% and 75% of stance for all comparisons. The alignment may have systematic effects on the socket reaction moments in transtibial prostheses with energy storage and return feet. The socket reaction moments could potentially be a useful biomechanical parameter to evaluate the alignment of the transtibial prostheses. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bounded-Angle Iterative Decoding of LDPC Codes

NASA Technical Reports Server (NTRS)

Dolinar, Samuel; Andrews, Kenneth; Pollara, Fabrizio; Divsalar, Dariush

2009-01-01

Bounded-angle iterative decoding is a modified version of conventional iterative decoding, conceived as a means of reducing undetected-error rates for short low-density parity-check (LDPC) codes. For a given code, bounded-angle iterative decoding can be implemented by means of a simple modification of the decoder algorithm, without redesigning the code. Bounded-angle iterative decoding is based on a representation of received words and code words as vectors in an n-dimensional Euclidean space (where n is an integer).

Comparison of Friction Characteristics on TN and VA Mode Alignment Films with Friction Force Microscopy

NASA Astrophysics Data System (ADS)

Kwak, Musun; Chung, Hanrok; Kwon, Hyukmin; Kim, Jehyun; Han, Daekyung; Yi, Yoonseon; Lee, Sangmun; Lee, Chulgu; Cha, Sooyoul

Using frictional force microscopy (FFM), the friction surface characteristics were compared between twisted nematic (TN) mode and vertical alignment (VA) mode alignment films (AFs). The friction asymmetry was detected depending on temperature conditions on TN mode AF, but not on VA mode AF. The difference between two modes was explained by leaning intermolecular repulsion caused by the pre-tilt angle uniformity and the density of side chain. No level difference according to temperature conditions appeared when the pre-tilt angle were measured after liquid crystal (LC) injection.

Lower limb alignment characteristics are not associated with running injuries in runners: Prospective cohort study.

PubMed

Hespanhol Junior, Luiz Carlos; de Carvalho, Aline Carla Araújo; Costa, Leonardo Oliveira Pena; Lopes, Alexandre Dias

2016-11-01

There is conflicting evidence on the association between lower limb alignment characteristics and the incidence of running-related injury (RRI). Therefore, the primary aim of this study was to investigate the association between lower limb alignment characteristics and the incidence proportion of RRI in a convenience sample of recreational runners. A total of 89 recreational runners were included in this prospective cohort study. These participants had been running for at least six months and were injury-free at baseline. Lower limb alignment measurements were conducted in order to calculate lower limb discrepancy, Q-angle, subtalar angle and plantar index. All participants also answered a baseline and biweekly online surveys about their running routine, history of RRI and newly developed RRI over a period of 12 weeks. The prevalence of previous RRI and the 12-week incidence proportion of new RRI were calculated. Logistic regression analysis was performed to estimate the association between lower limb length discrepancy, Q-angle, subtalar angle and plantar ach index with the incidence proportion of RRI. The prevalence of previous RRI was 55.1% (n = 49). The 12-week incidence proportion of new RRI was 27.0% (n = 24). Muscle injuries and tendinopathies were the main types of RRI identified. The lower leg and the knee were the main anatomical regions affected. We did not find significant associations between lower limb length discrepancy, Q-angle, subtalar angle and plantar arch index and injury occurrence.

A spin-orbit alignment for the hot Jupiter HATS-3b

DOE Office of Scientific and Technical Information (OSTI.GOV)

Addison, B. C.; Tinney, C. G.; Wright, D. J.

We have measured the alignment between the orbit of HATS-3b (a recently discovered, slightly inflated Hot Jupiter) and the spin axis of its host star. Data were obtained using the CYCLOPS2 optical-fiber bundle and its simultaneous calibration system feeding the UCLES spectrograph on the Anglo-Australian Telescope. The sky-projected spin-orbit angle of λ = 3° ± 25° was determined from spectroscopic measurements of the Rossiter-McLaughlin effect. This is the first exoplanet discovered through the HATSouth transit survey to have its spin-orbit angle measured. Our results indicate that the orbital plane of HATS-3b is consistent with being aligned to the spin axismore » of its host star. The low obliquity of the HATS-3 system, which has a relatively hot mid F-type host star, agrees with the general trend observed for Hot Jupiter host stars with effective temperatures >6250 K to have randomly distributed spin-orbit angles.« less

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.

PubMed

Wala, Jeremiah; Beroukhim, Rameen

2017-03-01

We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. jwala@broadinstitue.org ; rameen@broadinstitute.org. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Error Modeling of Multi-baseline Optical Truss. Part II; Application to SIM Metrology Truss Field Dependent Error

NASA Technical Reports Server (NTRS)

Zhang, Liwei Dennis; Milman, Mark; Korechoff, Robert

2004-01-01

The current design of the Space Interferometry Mission (SIM) employs a 19 laser-metrology-beam system (also called L19 external metrology truss) to monitor changes of distances between the fiducials of the flight system's multiple baselines. The function of the external metrology truss is to aid in the determination of the time-variations of the interferometer baseline. The largest contributor to truss error occurs in SIM wide-angle observations when the articulation of the siderostat mirrors (in order to gather starlight from different sky coordinates) brings to light systematic errors due to offsets at levels of instrument components (which include comer cube retro-reflectors, etc.). This error is labeled external metrology wide-angle field-dependent error. Physics-based model of field-dependent error at single metrology gauge level is developed and linearly propagated to errors in interferometer delay. In this manner delay error sensitivity to various error parameters or their combination can be studied using eigenvalue/eigenvector analysis. Also validation of physics-based field-dependent model on SIM testbed lends support to the present approach. As a first example, dihedral error model is developed for the comer cubes (CC) attached to the siderostat mirrors. Then the delay errors due to this effect can be characterized using the eigenvectors of composite CC dihedral error. The essence of the linear error model is contained in an error-mapping matrix. A corresponding Zernike component matrix approach is developed in parallel, first for convenience of describing the RMS of errors across the field-of-regard (FOR), and second for convenience of combining with additional models. Average and worst case residual errors are computed when various orders of field-dependent terms are removed from the delay error. Results of the residual errors are important in arriving at external metrology system component requirements. Double CCs with ideally co-incident vertices

Analysis of ionospheric structure influences on residual ionospheric errors in GNSS radio occultation bending angles based on ray tracing simulations

NASA Astrophysics Data System (ADS)

Liu, Congliang; Kirchengast, Gottfried; Sun, Yueqiang; Zhang, Kefei; Norman, Robert; Schwaerz, Marc; Bai, Weihua; Du, Qifei; Li, Ying

2018-04-01

The Global Navigation Satellite System (GNSS) radio occultation (RO) technique is widely used to observe the atmosphere for applications such as numerical weather prediction and global climate monitoring. The ionosphere is a major error source to RO at upper stratospheric altitudes, and a linear dual-frequency bending angle correction is commonly used to remove the first-order ionospheric effect. However, the higher-order residual ionospheric error (RIE) can still be significant, so it needs to be further mitigated for high-accuracy applications, especially from 35 km altitude upward, where the RIE is most relevant compared to the decreasing magnitude of the atmospheric bending angle. In a previous study we quantified RIEs using an ensemble of about 700 quasi-realistic end-to-end simulated RO events, finding typical RIEs at the 0.1 to 0.5 µrad noise level, but were left with 26 exceptional events with anomalous RIEs at the 1 to 10 µrad level that remained unexplained. In this study, we focused on investigating the causes of the high RIE of these exceptional events, employing detailed along-ray-path analyses of atmospheric and ionospheric refractivities, impact parameter changes, and bending angles and RIEs under asymmetric and symmetric ionospheric structures. We found that the main causes of the high RIEs are a combination of physics-based effects - where asymmetric ionospheric conditions play the primary role, more than the ionization level driven by solar activity - and technical ray tracer effects due to occasions of imperfect smoothness in ionospheric refractivity model derivatives. We also found that along-ray impact parameter variations of more than 10 to 20 m are possible due to ionospheric asymmetries and, depending on prevailing horizontal refractivity gradients, are positive or negative relative to the initial impact parameter at the GNSS transmitter. Furthermore, mesospheric RIEs are found generally higher than upper-stratospheric ones, likely due to

Deflection angle detecting system for the large-angle and high-linearity fast steering mirror using quadrant detector

NASA Astrophysics Data System (ADS)

Ni, Yingxue; Wu, Jiabin; San, Xiaogang; Gao, Shijie; Ding, Shaohang; Wang, Jing; Wang, Tao

2018-02-01

A deflection angle detecting system (DADS) using a quadrant detector (QD) is developed to achieve the large deflection angle and high linearity for the fast steering mirror (FSM). The mathematical model of the DADS is established by analyzing the principle of position detecting and error characteristics of the QD. Based on this mathematical model, the method of optimizing deflection angle and linearity of FSM is demonstrated, which is proved feasible by simulation and experimental results. Finally, a QD-based FSM is designed and tested. The results show that it achieves 0.72% nonlinearity, ±2.0 deg deflection angle, and 1.11-μrad resolution. Therefore, the application of this method will be beneficial to design the FSM.

Spirality: A Noval Way to Measure Spiral Arm Pitch Angle

NASA Astrophysics Data System (ADS)

Shields, Douglas W.; Boe, Benjamin; Henderson, Casey L.; Hartley, Matthew; Davis, Benjamin L.; Pour Imani, Hamed; Kennefick, Daniel; Kennefick, Julia D.

2015-01-01

We present the MATLAB code Spirality, a novel method for measuring spiral arm pitch angles by fitting galaxy images to spiral templates of known pitch. For a given pitch angle template, the mean pixel value is found along each of typically 1000 spiral axes. The fitting function, which shows a local maximum at the best-fit pitch angle, is the variance of these means. Error bars are found by varying the inner radius of the measurement annulus and finding the standard deviation of the best-fit pitches. Computation time is typically on the order of 2 minutes per galaxy, assuming at least 8 GB of working memory. We tested the code using 128 synthetic spiral images of known pitch. These spirals varied in the number of spiral arms, pitch angle, degree of logarithmicity, radius, SNR, inclination angle, bar length, and bulge radius. A correct result is defined as a result that matches the true pitch within the error bars, with error bars no greater than ±7°. For the non-logarithmic spiral sample, the correct answer is similarly defined, with the mean pitch as function of radius in place of the true pitch. For all synthetic spirals, correct results were obtained so long as SNR > 0.25, the bar length was no more than 60% of the spiral's diameter (when the bar was included in the measurement), the input center of the spiral was no more than 6% of the spiral radius away from the true center, and the inclination angle was no more than 30°. The synthetic spirals were not deprojected prior to measurement. The code produced the correct result for all barred spirals when the measurement annulus was placed outside the bar. Additionally, we compared the code's results against 2DFFT results for 203 visually selected spiral galaxies in GOODS North and South. Among the entire sample, Spirality's error bars overlapped 2DFFT's error bars 64% of the time. For those galaxies in which Source code is available by email request from the primary author.

Study on verifying the angle measurement performance of the rotary-laser system

NASA Astrophysics Data System (ADS)

Zhao, Jin; Ren, Yongjie; Lin, Jiarui; Yin, Shibin; Zhu, Jigui

2018-04-01

An angle verification method to verify the angle measurement performance of the rotary-laser system was developed. Angle measurement performance has a great impact on measuring accuracy. Although there is some previous research on the verification of angle measuring uncertainty for the rotary-laser system, there are still some limitations. High-precision reference angles are used in the study of the method, and an integrated verification platform is set up to evaluate the performance of the system. This paper also probes the error that has biggest influence on the verification system. Some errors of the verification system are avoided via the experimental method, and some are compensated through the computational formula and curve fitting. Experimental results show that the angle measurement performance meets the requirement for coordinate measurement. The verification platform can evaluate the uncertainty of angle measurement for the rotary-laser system efficiently.

Radiographic assessment of knee-ankle alignment after total knee arthroplasty for varus and valgus knee osteoarthritis.

PubMed

Gao, Fuqiang; Ma, Jinhui; Sun, Wei; Guo, Wanshou; Li, Zirong; Wang, Weiguo

2017-01-01

There are unanswered questions about knee-ankle alignment after total knee arthroplasty (TKA) for varus and valgus osteoarthritis (OA) of the knee. The aim of this retrospective study was to assess knee-ankle alignment after TKA. The study consisted of 149 patients who had undergone TKA due to varus and valgus knee OA. The alignment and angles in the selected knees and ankles were measured on full-length standing anteroposterior radiographs, both pre-operatively and post-operatively. The paired t-test and Pearson's correlation tests were used for statistical analysis. The results showed that ankle alignment correlated with knee alignment both pre-operatively and postoperatively (P<0.05). The pre-operative malalignment of the knee was corrected (P<0.05), and the ankle tilt angle was accordingly improved in the operative side after TKA (P<0.05). In addition, TKA had little effect on knee-ankle alignment on the non-operative side (P>0.05). These findings indicated that routine TKA could correct the varus or valgus deformity of a knee, and improve the tilt of the ankle. Ankle alignment correlated with knee alignment both pre-operatively and postoperatively. Both pre-operative knee and ankle malalignment can be simultaneously corrected following TKA. Level III. Copyright © 2016 Elsevier B.V. All rights reserved.

Development and preliminary evaluation of a new anatomically based prosthetic alignment method for below-knee prosthesis.

PubMed

Tafti, Nahid; Karimlou, Masoud; Mardani, Mohammad Ali; Jafarpisheh, Amir Salar; Aminian, Gholam Reza; Safari, Reza

2018-04-20

The objectives of current study were to a) assess similarities and relationships between anatomical landmark-based angles and distances of lower limbs in unilateral transtibial amputees and b) develop and evaluate a new anatomically based static prosthetic alignment method. First sub-study assessed the anthropometrical differences and relationships between the lower limbs in the photographs taken from amputees. Data were analysed via paired t-test and regression analysis. Results show no significant differences in frontal and transverse planes. In the sagittal plane, the anthropometric parameters of the amputated limb were significantly correlated to the corresponding variables of the sound limb. The results served as bases for the development of a new prosthetic alignment method. The method was evaluated on a single subject study. Prosthetic alignment carried out by an experienced prosthetist was compared with such alignment adjusted by an inexperienced prosthetist but with the use of the developed method. In sagittal and frontal planes, the socket angle was tuned with respect to the shin angle, and the position of the prosthetic foot was tuned in relation to the pelvic landmarks. Further study is needed to assess the proposed method on a larger sample of amputees and prosthetists.

An interpretation of radiosonde errors in the atmospheric boundary layer

Treesearch

Bernadette H. Connell; David R. Miller

1995-01-01

The authors review sources of error in radiosonde measurements in the atmospheric boundary layer and analyze errors of two radiosonde models manufactured by Atmospheric Instrumentation Research, Inc. The authors focus on temperature and humidity lag errors and wind errors. Errors in measurement of azimuth and elevation angles and pressure over short time intervals and...

Minimap2: pairwise alignment for nucleotide sequences.

PubMed

Li, Heng

2018-05-10

Recent advances in sequencing technologies promise ultra-long reads of ∼100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥ 100bp in length, ≥1kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads, and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions (INDELs) and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. https://github.com/lh3/minimap2. hengli@broadinstitute.org.

Moments of inclination error distribution computer program

NASA Technical Reports Server (NTRS)

Myler, T. R.

1981-01-01

A FORTRAN coded computer program is described which calculates orbital inclination error statistics using a closed-form solution. This solution uses a data base of trajectory errors from actual flights to predict the orbital inclination error statistics. The Scott flight history data base consists of orbit insertion errors in the trajectory parameters - altitude, velocity, flight path angle, flight azimuth, latitude and longitude. The methods used to generate the error statistics are of general interest since they have other applications. Program theory, user instructions, output definitions, subroutine descriptions and detailed FORTRAN coding information are included.

Theory of electrical conductivity and dielectric permittivity of highly aligned graphene-based nanocomposites.

PubMed

Xia, Xiaodong; Hao, Jia; Wang, Yang; Zhong, Zheng; Weng, George J

2017-05-24

Highly aligned graphene-based nanocomposites are of great interest due to their excellent electrical properties along the aligned direction. Graphene fillers in these composites are not necessarily perfectly aligned, but their orientations are highly confined to a certain angle, [Formula: see text] with 90° giving rise to the randomly oriented state and 0° to the perfectly aligned one. Recent experiments have shown that electrical conductivity and dielectric permittivity of highly aligned graphene-polymer nanocomposites are strongly dependent on this distribution angle, but at present no theory seems to exist to address this issue. In this work we present a new effective-medium theory that is derived from the underlying physical process including the effects of graphene orientation, filler loading, aspect ratio, percolation threshold, interfacial tunneling, and Maxwell-Wagner-Sillars polarization, to determine these two properties. The theory is formulated in the context of preferred orientational average. We highlight this new theory with an application to rGO/epoxy nanocomposites, and demonstrate that the calculated in-plane and out-of-plane conductivity and permittivity are in agreement with the experimental data as the range of graphene orientations changes from the randomly oriented to the highly aligned state. We also show that the percolation thresholds of highly aligned graphene nanocomposites are in general different along the planar and the normal directions, but they converge into a single one when the statistical distribution of graphene fillers is spherically symmetric.

Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques

PubMed Central

Wang, Hsin-Wei; Hsu, Yen-Chu; Hwang, Jenn-Kang; Lyu, Ping-Chiang; Pai, Tun-Wen; Tang, Chuan Yi

2010-01-01

This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had “opened” their “closed” structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge

Field-aligned current sources in the high-latitude ionosphere

NASA Technical Reports Server (NTRS)

Barbosa, D. D.

1979-01-01

The paper determines the electric potential in a plane which is fed current from a pair of field-aligned current sheets. The ionospheric conductivity is modelled as a constant with an enhanced conductivity annular ring. It is shown that field-aligned current distributions are arbitrary functions of azimuth angle (MLT) and thus allow for asymmetric potential configurations over the pole cap. In addition, ionospheric surface currents are computed by means of stream functions. Finally, the discussion relates these methods to the electrical characteristics of the magnetosphere.

DE 1 observations of type 1 counterstreaming electrons and field-aligned currents

NASA Technical Reports Server (NTRS)

Lin, C. S.; Burch, J. L.; Barfield, J. N.; Sugiura, M.; Nielsen, E.

1984-01-01

Dynamics Explorer 1 satellite observations of plasma and magnetic fields during type one counterstreaming electron events are presented. Counterstreaming electrons are observed at high altitudes in the region of field-aligned current. The total current density computed from the plasma data in the 18-10,000 eV energy range is generally about 1-2 micro-A/sq m. For the downward current, low-energy electrons contribute more than 40 percent of the total plasma current density integrated above 18 eV. For the upward current, such electrons contribute less than 50 percent of that current density. Electron beams in the field-aligned direction are occasionally detected. The pitch angle distributions of counterstreaming electrons are generally enhanced at both small and large pitch angles. STARE simultaneous observations for one DE 1 pass indicated that the field-aligned current was closed through Pedersen currents in the ionosphere. The directions of the ionospheric current systems are consistent with the DE 1 observations at high altitudes.

Space-Borne Laser Altimeter Geolocation Error Analysis

NASA Astrophysics Data System (ADS)

Wang, Y.; Fang, J.; Ai, Y.

2018-05-01

This paper reviews the development of space-borne laser altimetry technology over the past 40 years. Taking the ICESAT satellite as an example, a rigorous space-borne laser altimeter geolocation model is studied, and an error propagation equation is derived. The influence of the main error sources, such as the platform positioning error, attitude measurement error, pointing angle measurement error and range measurement error, on the geolocation accuracy of the laser spot are analysed by simulated experiments. The reasons for the different influences on geolocation accuracy in different directions are discussed, and to satisfy the accuracy of the laser control point, a design index for each error source is put forward.

Optical Enhancement of Exoskeleton-Based Estimation of Glenohumeral Angles

PubMed Central

Cortés, Camilo; Unzueta, Luis; de los Reyes-Guzmán, Ana; Ruiz, Oscar E.; Flórez, Julián

2016-01-01

In Robot-Assisted Rehabilitation (RAR) the accurate estimation of the patient limb joint angles is critical for assessing therapy efficacy. In RAR, the use of classic motion capture systems (MOCAPs) (e.g., optical and electromagnetic) to estimate the Glenohumeral (GH) joint angles is hindered by the exoskeleton body, which causes occlusions and magnetic disturbances. Moreover, the exoskeleton posture does not accurately reflect limb posture, as their kinematic models differ. To address the said limitations in posture estimation, we propose installing the cameras of an optical marker-based MOCAP in the rehabilitation exoskeleton. Then, the GH joint angles are estimated by combining the estimated marker poses and exoskeleton Forward Kinematics. Such hybrid system prevents problems related to marker occlusions, reduced camera detection volume, and imprecise joint angle estimation due to the kinematic mismatch of the patient and exoskeleton models. This paper presents the formulation, simulation, and accuracy quantification of the proposed method with simulated human movements. In addition, a sensitivity analysis of the method accuracy to marker position estimation errors, due to system calibration errors and marker drifts, has been carried out. The results show that, even with significant errors in the marker position estimation, method accuracy is adequate for RAR. PMID:27403044

The Effect of Suture Anchor Insertion Angle on Calcaneus Pullout Strength: Challenging the Deadman's Angle.

PubMed

Weiss, William M; Saucedo, Ramon P; Robinson, John D; Lo, Chung-Chieh Jason; Morris, Randal P; Panchbhavi, Vinod K

2017-10-01

Refractory cases of Achilles tendinopathy amenable to surgery may include reattachment of the tendon using suture anchors. However, there is paucity of information describing the optimal insertion angle to maximize the tendon footprint and anchor stability in the calcaneus. The purpose of this investigation is to compare the fixation strength of suture anchors inserted at 90° and 45° (the Deadman's angle) relative to the primary compressive trabeculae of the calcaneus. A total of 12 matched pairs of adult cadaveric calcanei were excised and potted to approximate their alignment in vivo. Each pair was implanted with 5.5-mm bioabsorbable suture anchors placed either perpendicular (90°) or oblique (45°) to the primary compressive trabeculae. A tensile load was applied until failure of anchor fixation. Differences in failure load and stiffness between anchor fixation angles were determined by paired t-tests. No significant differences were detected between perpendicular and oblique suture anchor insertion relative to primary compressive trabeculae in terms of load to failure or stiffness. This investigation suggests that the fixation strength of suture anchors inserted perpendicular to the primary compression trabeculae and at the Deadman's angle are possibly comparable. Biomechanical comparison study.

COACH: profile-profile alignment of protein families using hidden Markov models.

PubMed

Edgar, Robert C; Sjölander, Kimmen

2004-05-22

Alignments of two multiple-sequence alignments, or statistical models of such alignments (profiles), have important applications in computational biology. The increased amount of information in a profile versus a single sequence can lead to more accurate alignments and more sensitive homolog detection in database searches. Several profile-profile alignment methods have been proposed and have been shown to improve sensitivity and alignment quality compared with sequence-sequence methods (such as BLAST) and profile-sequence methods (e.g. PSI-BLAST). Here we present a new approach to profile-profile alignment we call Comparison of Alignments by Constructing Hidden Markov Models (HMMs) (COACH). COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM. We compare the alignment accuracy of COACH with two recently published methods: Yona and Levitt's prof_sim and Sadreyev and Grishin's COMPASS. On two sets of reference alignments selected from the FSSP database, we find that COACH is able, on average, to produce alignments giving the best coverage or the fewest errors, depending on the chosen parameter settings. COACH is freely available from www.drive5.com/lobster

Influence of incident angle on the decoding in laser polarization encoding guidance

NASA Astrophysics Data System (ADS)

Zhou, Muchun; Chen, Yanru; Zhao, Qi; Xin, Yu; Wen, Hongyuan

2009-07-01

Dynamic detection of polarization states is very important for laser polarization coding guidance systems. In this paper, a set of dynamic polarization decoding and detection system used in laser polarization coding guidance was designed. Detection process of the normal incident polarized light is analyzed with Jones Matrix; the system can effectively detect changes in polarization. Influence of non-normal incident light on performance of polarization decoding and detection system is studied; analysis showed that changes in incident angle will have a negative impact on measure results, the non-normal incident influence is mainly caused by second-order birefringence and polarization sensitivity effect generated in the phase delay and beam splitter prism. Combined with Fresnel formula, decoding errors of linearly polarized light, elliptically polarized light and circularly polarized light with different incident angles into the detector are calculated respectively, the results show that the decoding errors increase with increase of incident angle. Decoding errors have relations with geometry parameters, material refractive index of wave plate, polarization beam splitting prism. Decoding error can be reduced by using thin low-order wave-plate. Simulation of detection of polarized light with different incident angle confirmed the corresponding conclusions.

Improved model for correcting the ionospheric impact on bending angle in radio occultation measurements

NASA Astrophysics Data System (ADS)

Angling, Matthew J.; Elvidge, Sean; Healy, Sean B.

2018-04-01

The standard approach to remove the effects of the ionosphere from neutral atmosphere GPS radio occultation measurements is to estimate a corrected bending angle from a combination of the L1 and L2 bending angles. This approach is known to result in systematic errors and an extension has been proposed to the standard ionospheric correction that is dependent on the squared L1 / L2 bending angle difference and a scaling term (κ). The variation of κ with height, time, season, location and solar activity (i.e. the F10.7 flux) has been investigated by applying a 1-D bending angle operator to electron density profiles provided by a monthly median ionospheric climatology model. As expected, the residual bending angle is well correlated (negatively) with the vertical total electron content (TEC). κ is more strongly dependent on the solar zenith angle, indicating that the TEC-dependent component of the residual error is effectively modelled by the squared L1 / L2 bending angle difference term in the correction. The residual error from the ionospheric correction is likely to be a major contributor to the overall error budget of neutral atmosphere retrievals between 40 and 80 km. Over this height range κ is approximately linear with height. A simple κ model has also been developed. It is independent of ionospheric measurements, but incorporates geophysical dependencies (i.e. solar zenith angle, solar flux, altitude). The global mean error (i.e. bias) and the standard deviation of the residual errors are reduced from -1.3×10-8 and 2.2×10-8 for the uncorrected case to -2.2×10-10 rad and 2.0×10-9 rad, respectively, for the corrections using the κ model. Although a fixed scalar κ also reduces bias for the global average, the selected value of κ (14 rad-1) is only appropriate for a small band of locations around the solar terminator. In the daytime, the scalar κ is consistently too high and this results in an overcorrection of the bending angles and a positive bending

Accuracy of the Heidelberg Spectralis in the alignment between near-infrared image and tomographic scan in a model eye: a multicenter study.

PubMed

Barteselli, Giulio; Bartsch, Dirk-Uwe; Viola, Francesco; Mojana, Francesca; Pellegrini, Marco; Hartmann, Kathrin I; Benatti, Eleonora; Leicht, Simon; Ratiglia, Roberto; Staurenghi, Giovanni; Weinreb, Robert N; Freeman, William R

2013-09-01

To evaluate temporal changes and predictors of accuracy in the alignment between simultaneous near-infrared image and optical coherence tomography (OCT) scan on the Heidelberg Spectralis using a model eye. Laboratory investigation. After calibrating the device, 6 sites performed weekly testing of the alignment for 12 weeks using a model eye. The maximum error was compared with multiple variables to evaluate predictors of inaccurate alignment. Variables included the number of weekly scanned patients, total number of OCT scans and B-scans performed, room temperature and its variation, and working time of the scanning laser. A 4-week extension study was subsequently performed to analyze short-term changes in the alignment. The average maximum error in the alignment was 15 ± 6 μm; the greatest error was 35 μm. The error increased significantly at week 1 (P = .01), specifically after the second imaging study (P < .05); reached a maximum after the eighth patient (P < .001); and then varied randomly over time. Predictors for inaccurate alignment were temperature variation and scans per patient (P < .001). For each 1 unit of increase in temperature variation, the estimated increase in maximum error was 1.26 μm. For the average number of scans per patient, each increase of 1 unit increased the error by 0.34 μm. Overall, the accuracy of the Heidelberg Spectralis was excellent. The greatest error happened in the first week after calibration, and specifically after the second imaging study. To improve the accuracy, room temperature should be kept stable and unnecessary scans should be avoided. The alignment of the device does not need to be checked on a regular basis in the clinical setting, but it should be checked after every other patient for more precise research purposes. Published by Elsevier Inc.

An Emprical Point Error Model for Tls Derived Point Clouds

NASA Astrophysics Data System (ADS)

Ozendi, Mustafa; Akca, Devrim; Topan, Hüseyin

2016-06-01

The random error pattern of point clouds has significant effect on the quality of final 3D model. The magnitude and distribution of random errors should be modelled numerically. This work aims at developing such an anisotropic point error model, specifically for the terrestrial laser scanner (TLS) acquired 3D point clouds. A priori precisions of basic TLS observations, which are the range, horizontal angle and vertical angle, are determined by predefined and practical measurement configurations, performed at real-world test environments. A priori precision of horizontal (𝜎𝜃) and vertical (𝜎𝛼) angles are constant for each point of a data set, and can directly be determined through the repetitive scanning of the same environment. In our practical tests, precisions of the horizontal and vertical angles were found as 𝜎𝜃=±36.6𝑐𝑐 and 𝜎𝛼=±17.8𝑐𝑐, respectively. On the other hand, a priori precision of the range observation (𝜎𝜌) is assumed to be a function of range, incidence angle of the incoming laser ray, and reflectivity of object surface. Hence, it is a variable, and computed for each point individually by employing an empirically developed formula varying as 𝜎𝜌=±2-12 𝑚𝑚 for a FARO Focus X330 laser scanner. This procedure was followed by the computation of error ellipsoids of each point using the law of variance-covariance propagation. The direction and size of the error ellipsoids were computed by the principal components transformation. The usability and feasibility of the model was investigated in real world scenarios. These investigations validated the suitability and practicality of the proposed method.

Angle performance on optima MDxt

DOE Office of Scientific and Technical Information (OSTI.GOV)

David, Jonathan; Kamenitsa, Dennis

2012-11-06

Angle control on medium current implanters is important due to the high angle-sensitivity of typical medium current implants, such as halo implants. On the Optima MDxt, beam-to-wafer angles are controlled in both the horizontal and vertical directions. In the horizontal direction, the beam angle is measured through six narrow slits, and any angle adjustment is made by electrostatically steering the beam, while cross-wafer beam parallelism is adjusted by changing the focus of the electrostatic parallelizing lens (P-lens). In the vertical direction, the beam angle is measured through a high aspect ratio mask, and any angle adjustment is made by slightlymore » tilting the wafer platen prior to implant. A variety of tests were run to measure the accuracy and repeatability of Optima MDxt's angle control. SIMS profiles of a high energy, channeling sensitive condition show both the cross-wafer angle uniformity, along with the small-angle resolution of the system. Angle repeatability was quantified by running a channeling sensitive implant as a regular monitor over a seven month period and measuring the sheet resistance-to-angle sensitivity. Even though crystal cut error was not controlled for in this case, when attributing all Rs variation to angle changes, the overall angle repeatability was measured as 0.16 Degree-Sign (1{sigma}). A separate angle repeatability test involved running a series of V-curves tests over a four month period using low crystal cut wafers selected from the same boule. The results of this test showed the angle repeatability to be <0.1 Degree-Sign (1{sigma}).« less

Genome alignment with graph data structures: a comparison

PubMed Central

2014-01-01

Background Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. Results We compare the structures of commonly used graphs in terms of their abilities to represent alignment information. We describe how the graphs can be transformed into each other, and identify and classify graph substructures common to one or more graphs. Based on previous approaches, we compile a list of modifications that remove these substructures. Conclusion We show that crucial pieces of alignment information, associated with inversions and duplications, are not visible in the structure of all graphs. If we neglect vertex or edge labels, the graphs differ in their information content. Still, many ideas are shared among all graph-based approaches. Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools. PMID:24712884

Outcome of corneal and laser astigmatic axis alignment in photoastigmatic refractive keratectomy.

PubMed

Farah, S G; Olafsson, E; Gwynn, D G; Azar, D T; Brightbill, F S

2000-12-01

To compare the refractive results of laser astigmatic treatment in eyes in which the astigmatic axes of the eye and laser are aligned by limbal marking at the 6 o'clock position and in eyes that are not marked. University Hospital and Clinics, Madison, Wisconsin, USA. This retrospective study comprised 143 eyes that had photoastigmatic refractive keratectomy with the VISX Star excimer laser. The eyes were divided into marked (G1) and unmarked (G2) groups. Based on the preoperative astigmatism, each group was subdivided into low astigmatism (/=1.25 D). Early postoperative manifest refractions (1.0 to 2.5 months) were analyzed. The Alpins vector analysis method was used to calculate the target induced astigmatism, surgically induced astigmatism, difference vector (DV), magnitude of error (ME), angle of error (AE), and index of success (IS). There was no significant difference between the groups in DV, ME, and IS. When the subgroups were analyzed, the DV and ME were comparable; the IS in the G1 high astigmatism subgroup was significantly better than that in the G2 high astigmatism subgroup (0.22 +/- 0.08 and 0.29 +/- 0.04, respectively; P <.0001). There was comparable scatter of AE values; 30% and 36% in G1 and G2, respectively, had an AE of 0. Similar scatter was observed in the subgroups. Of the eyes that had an AE of 0, 90% and 43% in the high astigmatism subgroups of G1 and G2, respectively (P <.05), had full correction of astigmatism. Limbal marking and subsequent eye and laser astigmatic axis alignment improved the refractive outcome of laser astigmatic treatment of >/=1.25 D. A preliminary report of an ongoing prospective randomized study of eyes that had laser in situ keratomileusis is included.

Multiple nodes transfer alignment for airborne missiles based on inertial sensor network

NASA Astrophysics Data System (ADS)

Si, Fan; Zhao, Yan

2017-09-01

Transfer alignment is an important initialization method for airborne missiles because the alignment accuracy largely determines the performance of the missile. However, traditional alignment methods are limited by complicated and unknown flexure angle, and cannot meet the actual requirement when wing flexure deformation occurs. To address this problem, we propose a new method that uses the relative navigation parameters between the weapons and fighter to achieve transfer alignment. First, in the relative inertial navigation algorithm, the relative attitudes and positions are constantly computed in wing flexure deformation situations. Secondly, the alignment results of each weapon are processed using a data fusion algorithm to improve the overall performance. Finally, the feasibility and performance of the proposed method were evaluated under two typical types of deformation, and the simulation results demonstrated that the new transfer alignment method is practical and has high-precision.

The effects of window shape and reticle presence on performance in a vertical alignment task

NASA Technical Reports Server (NTRS)

Rosenberg, Erika L.; Haines, Richard F.; Jordan, Kevin

1989-01-01

This study was conducted to evaluate the effect of selected interior work-station orientational cuing upon the ability to align a target image with local vertical in the frontal plane. Angular error from gravitational vertical in an alignment task was measured for 20 observers viewing through two window shapes (square, round), two initial orientations of a computer-generated space shuttle image, and the presence or absence of a stabilized optical alignment reticle. In terms of overall accuracy, it was found that observer error was significantly smaller for the square window and reticle-present conditions than for the round window and reticle-absent conditions. Response bias data reflected an overall tendency to undershoot and greater variability of response in the round window/no reticle condition. These results suggest that environmental cuing information, such as that provided by square window frames and alignment reticles, may aid in subjective orientation and increase accuracy of response in a Space Station proximity operations alignment task.

A Survey of Exoplanetary Spin-Orbit Angles

NASA Astrophysics Data System (ADS)

Winn, Josh

2010-02-01

Are the orbits of exoplanets aligned with the spin axes of their parent stars? One might expect a close alignment, but some of the proposed migration mechanisms predict otherwise. Indeed at least 4 planets with strongly tilted orbits are now known, including the first case of a retrograde or polar orbit. This raises the questions of how commonly misalignments occur, and which types of planets have them. We request 10 half-nights with Keck/HIRES spread over 2010A and 2010B, to measure spin-orbit angles for 9 exoplanets spanning a range of masses, periods, and eccentricities. Our measurement is based on the Rossiter-McLaughlin effect: the anomalous Doppler shift observed during planetary transits.

A Survey of Exoplanetary Spin-Orbit Angles

NASA Astrophysics Data System (ADS)

Winn, Josh

2010-08-01

Are the orbits of exoplanets aligned with the spin axes of their parent stars? One might expect a close alignment, but some of the proposed migration mechanisms predict otherwise. Indeed at least 4 planets with strongly tilted orbits are now known, including the first case of a retrograde or polar orbit. This raises the questions of how commonly misalignments occur, and which types of planets have them. We request 4 half-nights with Keck/HIRES spread over the 2010B semester, to measure spin-orbit angles for 4 exoplanets spanning a range of masses, periods, and eccentricities. Our measurement is based on the Rossiter-McLaughlin effect: the anomalous Doppler shift observed during planetary transits.

Directed branch growth in aligned nanowire arrays.

PubMed

Beaudry, Allan L; LaForge, Joshua M; Tucker, Ryan T; Sorge, Jason B; Adamski, Nicholas L; Li, Peng; Taschuk, Michael T; Brett, Michael J

2014-01-01

Branch growth is directed along two, three, or four in-plane directions in vertically aligned nanowire arrays using vapor-liquid-solid glancing angle deposition (VLS-GLAD) flux engineering. In this work, a dynamically controlled collimated vapor flux guides branch placement during the self-catalyzed epitaxial growth of branched indium tin oxide nanowire arrays. The flux is positioned to grow branches on select nanowire facets, enabling fabrication of aligned nanotree arrays with L-, T-, or X-branching. In addition, a flux motion algorithm is designed to selectively elongate branches along one in-plane axis. Nanotrees are found to be aligned across large areas by X-ray diffraction pole figure analysis and through branch length and orientation measurements collected over 140 μm(2) from scanning electron microscopy images for each array. The pathway to guided assembly of nanowire architectures with controlled interconnectivity in three-dimensions using VLS-GLAD is discussed.

Structure, rheology and shear alignment of Pluronic block copolymer mixtures.

PubMed

Newby, Gemma E; Hamley, Ian W; King, Stephen M; Martin, Christopher M; Terrill, Nicholas J

2009-01-01

The structure and flow behaviour of binary mixtures of Pluronic block copolymers P85 and P123 is investigated by small-angle scattering, rheometry and mobility tests. Micelle dimensions are probed by dynamic light scattering. The micelle hydrodynamic radius for the 50/50 mixture is larger than that for either P85 or P123 alone, due to the formation of mixed micelles with a higher association number. The phase diagram for 50/50 mixtures contains regions of cubic and hexagonal phases similar to those for the parent homopolymers, however the region of stability of the cubic phase is enhanced at low temperature and concentrations above 40 wt%. This is ascribed to favourable packing of the mixed micelles containing core blocks with two different chain lengths, but similar corona chain lengths. The shear flow alignment of face-centred cubic and hexagonal phases is probed by in situ small-angle X-ray or neutron scattering with simultaneous rheology. The hexagonal phase can be aligned using steady shear in a Couette geometry, however the high modulus cubic phase cannot be aligned well in this way. This requires the application of oscillatory shear or compression.

Clustering of reads with alignment-free measures and quality values.

PubMed

Comin, Matteo; Leoni, Andrea; Schimd, Michele

2015-01-01

The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers counts, have been used to cluster reads. Quality scores produced by NGS platforms are fundamental for various analysis of NGS data like reads mapping and error detection. Moreover future-generation sequencing platforms will produce long reads but with a large number of erroneous bases (up to 15 %). In this scenario it will be fundamental to exploit quality value information within the alignment-free framework. To the best of our knowledge this is the first study that incorporates quality value information and k-mers counts, in the context of alignment-free measures, for the comparison of reads data. Based on this principles, in this paper we present a family of alignment-free measures called D (q) -type. A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered. Also results on de novo assembly and metagenomic reads classification show that the introduction of quality values improves over standard alignment-free measures. These statistics are implemented in a software called QCluster (http://www.dei.unipd.it/~ciompin/main/qcluster.html).

Angle and Base of Gait Long Leg Axial and Intraoperative Simulated Weightbearing Long Leg Axial Imaging to Capture True Frontal Plane Tibia to Calcaneus Alignment in Valgus and Varus Deformities of the Rearfoot and Ankle.

PubMed

Boffeli, Troy J; Waverly, Brett J

2016-01-01

The long leg axial view is primarily used to evaluate the frontal plane alignment of the calcaneus in relation to the long axis of the tibia when standing. This view allows both angular measurement and assessment for the apex of varus and valgus deformity of the rearfoot and ankle with clinical utility in the preoperative, intraoperative, and postoperative settings. The frontal plane alignment of the calcaneus to the long axis of the tibia is rarely fixed in the varus or valgus position because of the inherent flexibility of the foot and ankle, which makes patient positioning critical to obtain accurate and reproducible images. Inconsistent patient positioning and imaging techniques are commonly encountered with the long leg axial view for a variety of reasons, including the lack of a standardized or validated protocol. This angle and base of gait imaging protocol involves positioning the patient to align the tibia with the long axis of the foot, which is represented by the second metatarsal. Non-weightbearing long leg axial imaging is commonly performed intraoperatively, which requires a modified patient positioning technique to capture simulated weightbearing long leg axial images. A case series is presented to demonstrate our angle and base of gait long leg axial and intraoperative simulated weightbearing long leg axial imaging protocols that can be applied throughout all phases of patient care for various foot and ankle conditions. Copyright © 2015 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Investigation on the interfacial chemical state and band alignment for the sputtering-deposited CaF2/p-GaN heterojunction by angle-resolved X-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Kexiong; Liao, Meiyong; Sumiya, Masatomo; Koide, Yasuo; Sang, Liwen

2016-11-01

The interfacial chemical state and the band alignment of the sputtering-deposited CaF2/p-GaN hetero-structure were investigated by angle-resolved X-ray photoelectron spectroscopy. The dependence of Ga 3p core-level positions on the collection angles proves that the downward band bending of p-GaN is reduced from 1.51 to 0.85 eV after the deposition of CaF2, which may be due to the reduction of Mg-Ga-O-related interface states by the oxygen-free deposition of CaF2. The band gap of sputtering-deposited CaF2 is estimated to be about 7.97 eV with a potential gradient of 0.48 eV obtained by the variation of the Ca 2p3/2 position on different collection angles. By taking into account the p-GaN surface band bending and potential gradient in the CaF2 layer, large valence and conduction band offsets of 2.66 ± 0.20 and 1.92 ± 0.20 eV between CaF2 and p-GaN are obtained. These results indicate that CaF2 is a promising gate dielectric layer on the p-GaN for the application of metal-insulator-semiconductor devices.

Face Alignment via Regressing Local Binary Features.

PubMed

Ren, Shaoqing; Cao, Xudong; Wei, Yichen; Sun, Jian

2016-03-01

This paper presents a highly efficient and accurate regression approach for face alignment. Our approach has two novel components: 1) a set of local binary features and 2) a locality principle for learning those features. The locality principle guides us to learn a set of highly discriminative local binary features for each facial landmark independently. The obtained local binary features are used to jointly learn a linear regression for the final output. This approach achieves the state-of-the-art results when tested on the most challenging benchmarks to date. Furthermore, because extracting and regressing local binary features are computationally very cheap, our system is much faster than previous methods. It achieves over 3000 frames per second (FPS) on a desktop or 300 FPS on a mobile phone for locating a few dozens of landmarks. We also study a key issue that is important but has received little attention in the previous research, which is the face detector used to initialize alignment. We investigate several face detectors and perform quantitative evaluation on how they affect alignment accuracy. We find that an alignment friendly detector can further greatly boost the accuracy of our alignment method, reducing the error up to 16% relatively. To facilitate practical usage of face detection/alignment methods, we also propose a convenient metric to measure how good a detector is for alignment initialization.

Relative range error evaluation of terrestrial laser scanners using a plate, a sphere, and a novel dual-sphere-plate target.

PubMed

Muralikrishnan, Bala; Rachakonda, Prem; Lee, Vincent; Shilling, Meghan; Sawyer, Daniel; Cheok, Geraldine; Cournoyer, Luc

2017-12-01

Terrestrial laser scanners (TLS) are a class of 3D imaging systems that produce a 3D point cloud by measuring the range and two angles to a point. The fundamental measurement of a TLS is range. Relative range error is one component of the overall range error of TLS and its estimation is therefore an important aspect in establishing metrological traceability of measurements performed using these systems. Target geometry is an important aspect to consider when realizing the relative range tests. The recently published ASTM E2938-15 mandates the use of a plate target for the relative range tests. While a plate target may reasonably be expected to produce distortion free data even at far distances, the target itself needs careful alignment at each of the relative range test positions. In this paper, we discuss relative range experiments performed using a plate target and then address the advantages and limitations of using a sphere target. We then present a novel dual-sphere-plate target that draws from the advantages of the sphere and the plate without the associated limitations. The spheres in the dual-sphere-plate target are used simply as fiducials to identify a point on the surface of the plate that is common to both the scanner and the reference instrument, thus overcoming the need to carefully align the target.

Error of the slanted edge method for measuring the modulation transfer function of imaging systems.

PubMed

Xie, Xufen; Fan, Hongda; Wang, Hongyuan; Wang, Zebin; Zou, Nianyu

2018-03-01

The slanted edge method is a basic approach for measuring the modulation transfer function (MTF) of imaging systems; however, its measurement accuracy is limited in practice. Theoretical analysis of the slanted edge MTF measurement method performed in this paper reveals that inappropriate edge angles and random noise reduce this accuracy. The error caused by edge angles is analyzed using sampling and reconstruction theory. Furthermore, an error model combining noise and edge angles is proposed. We verify the analyses and model with respect to (i) the edge angle, (ii) a statistical analysis of the measurement error, (iii) the full width at half-maximum of a point spread function, and (iv) the error model. The experimental results verify the theoretical findings. This research can be referential for applications of the slanted edge MTF measurement method.

An optimal beam alignment method for large-scale distributed space surveillance radar system

NASA Astrophysics Data System (ADS)

Huang, Jian; Wang, Dongya; Xia, Shuangzhi

2018-06-01

Large-scale distributed space surveillance radar is a very important ground-based equipment to maintain a complete catalogue for Low Earth Orbit (LEO) space debris. However, due to the thousands of kilometers distance between each sites of the distributed radar system, how to optimally implement the Transmitting/Receiving (T/R) beams alignment in a great space using the narrow beam, which proposed a special and considerable technical challenge in the space surveillance area. According to the common coordinate transformation model and the radar beam space model, we presented a two dimensional projection algorithm for T/R beam using the direction angles, which could visually describe and assess the beam alignment performance. Subsequently, the optimal mathematical models for the orientation angle of the antenna array, the site location and the T/R beam coverage are constructed, and also the beam alignment parameters are precisely solved. At last, we conducted the optimal beam alignment experiments base on the site parameters of Air Force Space Surveillance System (AFSSS). The simulation results demonstrate the correctness and effectiveness of our novel method, which can significantly stimulate the construction for the LEO space debris surveillance equipment.

Three dimensional thermal stresses in angle-ply composite laminates

NASA Technical Reports Server (NTRS)

Griffin, O. Hayden, Jr.

1988-01-01

The room temperature stress distributions and shapes of a family of angle ply graphite/epoxy laminates have been obtained using a three-dimensional linear finite element analysis. The sensitivity of the corners to fiber angle variations is examined, in addition to the errors introduced by assuming planes of symmetry which do not exist in angle-ply laminates. The results show that angle ply laminates with 'clustered' plies will tend to delaminate at diagonally opposite corners, and that matrix cracks in this family of laminates will be initiated in the laminate interior.

Evaluation of an image-based tracking workflow using a passive marker and resonant micro-coil fiducials for automatic image plane alignment in interventional MRI.

PubMed

Neumann, M; Breton, E; Cuvillon, L; Pan, L; Lorenz, C H; de Mathelin, M

2012-01-01

In this paper, an original workflow is presented for MR image plane alignment based on tracking in real-time MR images. A test device consisting of two resonant micro-coils and a passive marker is proposed for detection using image-based algorithms. Micro-coils allow for automated initialization of the object detection in dedicated low flip angle projection images; then the passive marker is tracked in clinical real-time MR images, with alternation between two oblique orthogonal image planes along the test device axis; in case the passive marker is lost in real-time images, the workflow is reinitialized. The proposed workflow was designed to minimize dedicated acquisition time to a single dedicated acquisition in the ideal case (no reinitialization required). First experiments have shown promising results for test-device tracking precision, with a mean position error of 0.79 mm and a mean orientation error of 0.24°.

Reduction of deviation angle during occlusion therapy: in partially accommodative esotropia with moderate amblyopia.

PubMed

Chun, Bo Young; Kwon, Soon Jae; Chae, Sun Hwa; Kwon, Jung Yoon

2007-09-01

To evaluate changes in ocular alignment in partially accommodative esotropic children age ranged from 3 to 8 years during occlusion therapy for amblyopia. Angle measurements of twenty-two partially accommodative esotropic patients with moderate amblyopia were evaluated before and at 2 years after occlusion therapy. Mean deviation angle with glasses at the start of occlusion treatment was 19.45+/-5.97 PD and decreased to 12.14+/-12.96 PD at 2 years after occlusion therapy (p<0.01). After occlusion therapy, 9 (41%) cases were indications of surgery for residual deviation but if we had planned surgery before occlusion treatment, 18 (82%) of patients would have had surgery. There was a statistical relationship between increase of visual acuity ratio and decrease of deviation angle (r=-0.479, p=0.024). There was a significant reduction of deviation angle of partially accommodative esotropic patients at 2 years after occlusion therapy. Our results suggest that occlusion therapy has an influence on ocular alignment in partially accommodative esotropic patients with amblyopia.

Reduction of Deviation Angle During Occlusion Therapy: In Partially Accommodative Esotropia with Moderate Amblyopia

PubMed Central

Chun, Bo Young; Kwon, Soon Jae; Chae, Sun Hwa

2007-01-01

Purpose To evaluate changes in ocular alignment in partially accommodative esotropic children age ranged from 3 to 8 years during occlusion therapy for amblyopia. Methods Angle measurements of twenty-two partially accommodative esotropic patients with moderate amblyopia were evaluated before and at 2 years after occlusion therapy. Results Mean deviation angle with glasses at the start of occlusion treatment was 19.45±5.97 PD and decreased to 12.14±12.96 PD at 2 years after occlusion therapy (p<0.01). After occlusion therapy, 9 (41%) cases were indications of surgery for residual deviation but if we had planned surgery before occlusion treatment, 18 (82%) of patients would have had surgery. There was a statistical relationship between increase of visual acuity ratio and decrease of deviation angle (r=-0.479, p=0.024). Conclusions There was a significant reduction of deviation angle of partially accommodative esotropic patients at 2 years after occlusion therapy. Our results suggest that occlusion therapy has an influence on ocular alignment in partially accommodative esotropic patients with amblyopia. PMID:17804922

Automated tilt series alignment and tomographic reconstruction in IMOD.

PubMed

Mastronarde, David N; Held, Susannah R

2017-02-01

Automated tomographic reconstruction is now possible in the IMOD software package, including the merging of tomograms taken around two orthogonal axes. Several developments enable the production of high-quality tomograms. When using fiducial markers for alignment, the markers to be tracked through the series are chosen automatically; if there is an excess of markers available, a well-distributed subset is selected that is most likely to track well. Marker positions are refined by applying an edge-enhancing Sobel filter, which results in a 20% improvement in alignment error for plastic-embedded samples and 10% for frozen-hydrated samples. Robust fitting, in which outlying points are given less or no weight in computing the fitting error, is used to obtain an alignment solution, so that aberrant points from the automated tracking can have little effect on the alignment. When merging two dual-axis tomograms, the alignment between them is refined from correlations between local patches; a measure of structure was developed so that patches with insufficient structure to give accurate correlations can now be excluded automatically. We have also developed a script for running all steps in the reconstruction process with a flexible mechanism for setting parameters, and we have added a user interface for batch processing of tilt series to the Etomo program in IMOD. Batch processing is fully compatible with interactive processing and can increase efficiency even when the automation is not fully successful, because users can focus their effort on the steps that require manual intervention. Copyright © 2016 Elsevier Inc. All rights reserved.

Diffractive optics for precision alignment of Euclid space telescope optics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Asfour, Jean-Michel; Weidner, Frank; Bodendorf, Christof; Bode, Andreas; Poleshchuk, Alexander G.; Nasyrov, Ruslan K.; Grupp, Frank; Bender, Ralf

2017-09-01

We present a method for precise alignment of lens elements using specific Computer Generated Hologram (CGH) with an integrated Fizeau reference flat surface and a Fizeau interferometer. The method is used for aligning the so called Camera Lens Assembly for ESAs Euclid telescope. Each lens has a corresponding annular area on the diffractive optics, which is used to control the position of each lens. The lenses are subsequently positioned using individual annular rings of the CGH. The overall alignment accuracy is below 1 µm, the alignment sensitivity is in the range of 0.1 µm. The achieved alignment accuracy of the lenses relative to each other is mainly depending on the stability in time of the alignment tower. Error budgets when using computer generated holograms and physical limitations are explained. Calibration measurements of the alignment system and the typically reached alignment accuracies will be shown and discussed.

Physically motivated global alignment method for electron tomography

DOE PAGES

Sanders, Toby; Prange, Micah; Akatay, Cem; ...

2015-04-08

Electron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop amore » new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.« less

Rectifying calibration error of Goldmann applanation tonometer is easy!

PubMed

Choudhari, Nikhil S; Moorthy, Krishna P; Tungikar, Vinod B; Kumar, Mohan; George, Ronnie; Rao, Harsha L; Senthil, Sirisha; Vijaya, Lingam; Garudadri, Chandra Sekhar

2014-11-01

Purpose: Goldmann applanation tonometer (GAT) is the current Gold standard tonometer. However, its calibration error is common and can go unnoticed in clinics. Its company repair has limitations. The purpose of this report is to describe a self-taught technique of rectifying calibration error of GAT. Materials and Methods: Twenty-nine slit-lamp-mounted Haag-Streit Goldmann tonometers (Model AT 900 C/M; Haag-Streit, Switzerland) were included in this cross-sectional interventional pilot study. The technique of rectification of calibration error of the tonometer involved cleaning and lubrication of the instrument followed by alignment of weights when lubrication alone didn't suffice. We followed the South East Asia Glaucoma Interest Group's definition of calibration error tolerance (acceptable GAT calibration error within ±2, ±3 and ±4 mm Hg at the 0, 20 and 60-mm Hg testing levels, respectively). Results: Twelve out of 29 (41.3%) GATs were out of calibration. The range of positive and negative calibration error at the clinically most important 20-mm Hg testing level was 0.5 to 20 mm Hg and -0.5 to -18 mm Hg, respectively. Cleaning and lubrication alone sufficed to rectify calibration error of 11 (91.6%) faulty instruments. Only one (8.3%) faulty GAT required alignment of the counter-weight. Conclusions: Rectification of calibration error of GAT is possible in-house. Cleaning and lubrication of GAT can be carried out even by eye care professionals and may suffice to rectify calibration error in the majority of faulty instruments. Such an exercise may drastically reduce the downtime of the Gold standard tonometer.

Analog track angle error displays improve simulated GPS approach performance

DOT National Transportation Integrated Search

1996-01-01

Pilots flying non-precision instrument approaches traditionally rely on a course deviation indicator (CDI) analog display of cross track error (XTE) information. THe new generation of GPS based area navigation (RNAV) receivers can also compute accura...

FEAST: sensitive local alignment with multiple rates of evolution.

PubMed

Hudek, Alexander K; Brown, Daniel G

2011-01-01

We present a pairwise local aligner, FEAST, which uses two new techniques: a sensitive extension algorithm for identifying homologous subsequences, and a descriptive probabilistic alignment model. We also present a new procedure for training alignment parameters and apply it to the human and mouse genomes, producing a better parameter set for these sequences. Our extension algorithm identifies homologous subsequences by considering all evolutionary histories. It has higher maximum sensitivity than Viterbi extensions, and better balances specificity. We model alignments with several submodels, each with unique statistical properties, describing strongly similar and weakly similar regions of homologous DNA. Training parameters using two submodels produces superior alignments, even when we align with only the parameters from the weaker submodel. Our extension algorithm combined with our new parameter set achieves sensitivity 0.59 on synthetic tests. In contrast, LASTZ with default settings achieves sensitivity 0.35 with the same false positive rate. Using the weak submodel as parameters for LASTZ increases its sensitivity to 0.59 with high error. FEAST is available at http://monod.uwaterloo.ca/feast/.

Utilizing field-aligned current profiles derived from Swarm to estimate the peak emission height of 630 nm auroral arcs: a comparison of methods and discussion of associated error estimates in the ASI data.

NASA Astrophysics Data System (ADS)

Gillies, D. M.; Knudsen, D. J.; Donovan, E.; Jackel, B. J.; Gillies, R.; Spanswick, E.

2017-12-01

We compare field-aligned currents (FACs) measured by the Swarm constellation of satellites with the location of red-line (630 nm) auroral arcs observed by all-sky imagers (ASIs) to derive a characteristic emission height for the optical emissions. In our 10 events we find that an altitude of 200 km applied to the ASI maps gives optimal agreement between the two observations. We also compare the new FAC method against the traditional triangulation method using pairs of all-sky imagers (ASIs), and against electron density profiles obtained from the Resolute Bay Incoherent Scatter Radar-Canadian radar (RISR-C), both of which are consistent with a characteristic emission height of 200 km. We also present the spatial error associated with georeferencing REdline Geospace Observatory (REGO) and THEMIS all-sky imagers (ASIs) and how it applies to altitude projections of the mapped image. Utilizing this error we validate the estimated altitude of redline aurora using two methods: triangulation between ASIs and field-aligned current profiles derived from magnetometers on-board the Swarm satellites.

Effects of Patellofemoral Taping on Patellofemoral Joint Alignment and Contact Area During Weight Bearing.

PubMed

Ho, Kai-Yu; Epstein, Ryan; Garcia, Ron; Riley, Nicole; Lee, Szu-Ping

2017-02-01

Study Design Controlled laboratory study. Background Although it has been theorized that patellofemoral joint (PFJ) taping can correct patellar malalignment, the effects of PFJ taping techniques on patellar alignment and contact area have not yet been studied during weight bearing. Objective To examine the effects of 2 taping approaches (Kinesio and McConnell) on PFJ alignment and contact area. Methods Fourteen female subjects with patellofemoral pain and PFJ malalignment participated. Each subject underwent a pretaping magnetic resonance imaging (MRI) scan session and 2 MRI scan sessions after the application of the 2 taping techniques, which aimed to correct lateral patellar displacement. Subjects were asked to report their pain level prior to each scan session. During MRI assessment, subjects were loaded with 25% of body weight on their involved/more symptomatic leg at 0°, 20°, and 40° of knee flexion. The outcome measures included patellar lateral displacement (bisect-offset [BSO] index), mediolateral patellar tilt angle, patellar height (Insall-Salvati ratio), contact area, and pain. Patellofemoral joint alignment and contact area were compared among the 3 conditions (no tape, Kinesio, and McConnell) at 3 knee angles using a 2-factor, repeated-measures analysis of variance. Pain was compared among the 3 conditions using the Friedman test and post hoc Wilcoxon signed-rank tests. Results Our data did not reveal any significant effects of either McConnell or Kinesio taping on the BSO index, patellar tilt angle, Insall-Salvati ratio, or contact area across the 3 knee angles, whereas knee angle had a significant effect on the BSO index and contact area. A reduction in pain was observed after the application of the Kinesio taping technique. Conclusion In a weight-bearing condition, this preliminary study did not support the use of PFJ taping as a medial correction technique to alter the PFJ contact area or alignment of the patella. J Orthop Sports Phys Ther 2017

Simulator for beam-based LHC collimator alignment

NASA Astrophysics Data System (ADS)

Valentino, Gianluca; Aßmann, Ralph; Redaelli, Stefano; Sammut, Nicholas

2014-02-01

In the CERN Large Hadron Collider, collimators need to be set up to form a multistage hierarchy to ensure efficient multiturn cleaning of halo particles. Automatic algorithms were introduced during the first run to reduce the beam time required for beam-based setup, improve the alignment accuracy, and reduce the risk of human errors. Simulating the alignment procedure would allow for off-line tests of alignment policies and algorithms. A simulator was developed based on a diffusion beam model to generate the characteristic beam loss signal spike and decay produced when a collimator jaw touches the beam, which is observed in a beam loss monitor (BLM). Empirical models derived from the available measurement data are used to simulate the steady-state beam loss and crosstalk between multiple BLMs. The simulator design is presented, together with simulation results and comparison to measurement data.

Age, Gender, Biometry, Refractive Error, and the Anterior Chamber Angle among Alaskan Eskimos

PubMed Central

Wojciechowski, Robert; Congdon, Nathan; Anninger, William; Broman, Aimee Teo

2011-01-01

Background The prevalence of angle-closure glaucoma (ACG) is greater for Eskimos/Inuit than it is for any other ethnic group in the world. Although it has been suggested that this prevalence may be due to a population tendency toward shallower anterior chamber angles, available evidence for other populations such as Chinese with high rates of ACG has not consistently demonstrated such a tendency. Methods A reticule, slit-lamp, and standard Goldmann one-mirror goniolens were used to make measurements in the anterior chamber (AC) angle according to a previously reported protocol for biometric gonioscopy (BG) (Ophthalmology 1999;106:2161–7). Measurements were made in all four quadrants of one eye among 133 phakic Alaskan Eskimos aged 40 years and older. Automatic refraction, dilated examination of the anterior segment and optic nerve, and A-scan measurements of AC depth, lens thickness, and axial length were also carried out for all subjects. Results Both central and peripheral AC measurements for the Eskimo subjects were significantly lower than those previously reported by us for Chinese, blacks, and whites under the identical protocol. Eskimos also seemed to have somewhat more hyperopia. There were no differences in biometric measurements between men and women in this Eskimo population. Angle measurements by BG seemed to decline more rapidly over life among Eskimos and Chinese than blacks or whites. Although there was a significant apparent decrease in AC depth, increase in lens thickness, and increase in hyperopia with age among Eskimos, all of these trends seemed to reverse in the seventh decade and beyond. Conclusions Eskimos do seem to have shallower ACs than do other racial groups. Measurements of the AC angle seem to decline more rapidly over life among Eskimos than among blacks or whites, a phenomenon also observed by us among Chinese, another group with high ACG prevalence. This apparent more rapid decline may be due to a cohort effect with higher

A comparison of registration errors with imageless computer navigation during MIS total knee arthroplasty versus standard incision total knee arthroplasty: a cadaveric study.

PubMed

Davis, Edward T; Pagkalos, Joseph; Gallie, Price A M; Macgroarty, Kelly; Waddell, James P; Schemitsch, Emil H

2015-01-01

Optimal component alignment in total knee arthroplasty has been associated with better functional outcome as well as improved implant longevity. The ability to align components optimally during minimally invasive (MIS) total knee replacement (TKR) has been a cause of concern. Computer navigation is a useful aid in achieving the desired alignment although it is limited by the error during the manual registration of landmarks. Our study aims to compare the registration process error between a standard and a MIS surgical approach. We hypothesized that performing the registration error via an MIS approach would increase the registration process error. Five fresh frozen lower limbs were routinely prepared and draped. The registration process was performed through an MIS approach. This was then extended to the standard approach and the registration was performed again. Two surgeons performed the registration process five times with each approach. Performing the registration process through the MIS approach was not associated with higher error compared to the standard approach in the alignment parameters of interest. This rejects our hypothesis. Image-free navigated MIS TKR does not appear to carry higher risk of component malalignment due to the registration process error. Navigation can be used during MIS TKR to improve alignment without reduced accuracy due to the approach.

Using doppler radar images to estimate aircraft navigational heading error

DOEpatents

Doerry, Armin W [Albuquerque, NM; Jordan, Jay D [Albuquerque, NM; Kim, Theodore J [Albuquerque, NM

2012-07-03

A yaw angle error of a motion measurement system carried on an aircraft for navigation is estimated from Doppler radar images captured using the aircraft. At least two radar pulses aimed at respectively different physical locations in a targeted area are transmitted from a radar antenna carried on the aircraft. At least two Doppler radar images that respectively correspond to the at least two transmitted radar pulses are produced. These images are used to produce an estimate of the yaw angle error.

An a-posteriori finite element error estimator for adaptive grid computation of viscous incompressible flows

NASA Astrophysics Data System (ADS)

Wu, Heng

2000-10-01

In this thesis, an a-posteriori error estimator is presented and employed for solving viscous incompressible flow problems. In an effort to detect local flow features, such as vortices and separation, and to resolve flow details precisely, a velocity angle error estimator e theta which is based on the spatial derivative of velocity direction fields is designed and constructed. The a-posteriori error estimator corresponds to the antisymmetric part of the deformation-rate-tensor, and it is sensitive to the second derivative of the velocity angle field. Rationality discussions reveal that the velocity angle error estimator is a curvature error estimator, and its value reflects the accuracy of streamline curves. It is also found that the velocity angle error estimator contains the nonlinear convective term of the Navier-Stokes equations, and it identifies and computes the direction difference when the convective acceleration direction and the flow velocity direction have a disparity. Through benchmarking computed variables with the analytic solution of Kovasznay flow or the finest grid of cavity flow, it is demonstrated that the velocity angle error estimator has a better performance than the strain error estimator. The benchmarking work also shows that the computed profile obtained by using etheta can achieve the best matching outcome with the true theta field, and that it is asymptotic to the true theta variation field, with a promise of fewer unknowns. Unstructured grids are adapted by employing local cell division as well as unrefinement of transition cells. Using element class and node class can efficiently construct a hierarchical data structure which provides cell and node inter-reference at each adaptive level. Employing element pointers and node pointers can dynamically maintain the connection of adjacent elements and adjacent nodes, and thus avoids time-consuming search processes. The adaptive scheme is applied to viscous incompressible flow at different

The effect of instrument alignment on peripheral refraction measurements by automated optometer.

PubMed

Ehsaei, Asieh; Chisholm, Catharine M; Mallen, Edward A H; Pacey, Ian E

2011-07-01

Interest in peripheral refraction measurement has grown in recent years in response to the insight it may provide into myopia development. In light of the likely increase in the clinical use of open-field autorefractors for peripheral refraction measurements, the question of instrument alignment and its impact on the accuracy of refraction measurements is raised. The aim of this study was to investigate the accuracy and precision when an open-field device was moved away from alignment with the corneal reflex towards the pupil margins, and to determine the optimum alignment position for peripheral refraction measurements. Autorefractions were performed on the right eyes of 10 healthy participants using the Shin-Nippon NVision-K 5001 autorefractor. At least five measurements were taken with the subject fixating a distance target in the primary position of gaze, and then four peripheral fixation targets located along the horizontal meridian (10° and 20° eccentricities in the nasal and temporal retina). Measurements were taken at seven alignment positions across the pupil for each fixation angle. Refraction was recorded as the spherical and cylindrical power. The central objective refraction achieved under cycloplegia based on the autorefraction result for the whole sample, ranged between -5.62 D and +1.85 D for the value of sphere, with a maximum astigmatism of -1.00 D. Acceptable alignment position range varied with fixation angle but was -1.0 to +1.0 mm in width across the pupil. Peripheral refraction measurements centred on the entrance pupil were as reliable as those centred on the corneal reflex. Our data suggest that for peripheral refraction measurements, there is a range of acceptable positions and operators can be confident of the validity of results obtained if aligned half way between the pupil centre and corneal reflex. The alignment becomes more critical at greater eccentricities. Ophthalmic & Physiological Optics © 2011 The College of Optometrists.

Computational split-field finite-difference time-domain evaluation of simplified tilt-angle models for parallel-aligned liquid-crystal devices

NASA Astrophysics Data System (ADS)

Márquez, Andrés; Francés, Jorge; Martínez, Francisco J.; Gallego, Sergi; Álvarez, Mariela L.; Calzado, Eva M.; Pascual, Inmaculada; Beléndez, Augusto

2018-03-01

Simplified analytical models with predictive capability enable simpler and faster optimization of the performance in applications of complex photonic devices. We recently demonstrated the most simplified analytical model still showing predictive capability for parallel-aligned liquid crystal on silicon (PA-LCoS) devices, which provides the voltage-dependent retardance for a very wide range of incidence angles and any wavelength in the visible. We further show that the proposed model is not only phenomenological but also physically meaningful, since two of its parameters provide the correct values for important internal properties of these devices related to the birefringence, cell gap, and director profile. Therefore, the proposed model can be used as a means to inspect internal physical properties of the cell. As an innovation, we also show the applicability of the split-field finite-difference time-domain (SF-FDTD) technique for phase-shift and retardance evaluation of PA-LCoS devices under oblique incidence. As a simplified model for PA-LCoS devices, we also consider the exact description of homogeneous birefringent slabs. However, we show that, despite its higher degree of simplification, the proposed model is more robust, providing unambiguous and physically meaningful solutions when fitting its parameters.

Association between measures of patella height, morphologic features of the trochlea, and patellofemoral joint alignment: the MOST study.

PubMed

Stefanik, Joshua J; Zumwalt, Ann C; Segal, Neil A; Lynch, John A; Powers, Christopher M

2013-08-01

Patellofemoral joint (PFJ) malalignment (lateral patella displacement and tilt) has been proposed as a cause of patellofemoral pain. Patella height and/or the morphologic features of the femoral trochlea may predispose one to patella malalignment. The purposes of our study were to assess the associations among patella height, morphologic features of the trochlea, and measures of PFJ alignment and to determine which measures of patella height and morphologic features of the trochlea were the best predictors of PFJ alignment. Measures of patella height (Insall-Salvati ratio and modified Insall-Salvati ratio), morphologic features of the trochlea (sulcus angle, trochlear angle, lateral trochlear inclination, medial trochlear inclination), and PFJ alignment (bisect offset and patella tilt angle) were assessed in 566 knees from the Multicenter Osteoarthritis Study. Bisect offset was correlated with the Insall-Salvati ratio (r = 0.25) and lateral trochlear inclination (r = -0.38). Patella tilt angle correlated with the trochlear angle (-0.27) and lateral trochlear inclination (-0.32). Linear regression models including the Insall-Salvati ratio and lateral trochlear inclination explained 20% and 11% of the variance in bisect offset and patella tilt angle, respectively. Of the variables measured in the current study, the Insall-Salvati ratio and lateral trochlear inclination were the best predictors of lateral patella displacement and lateral tilt. This knowledge will aid clinicians in the identification of anatomic risk factors for PFJ malalignment and/or PFJ dysfunction.

Effects of clear aligners on sleep bruxism: randomized controlled trial.

PubMed

Castroflorio, T; Bargellini, A; Lucchese, A; Manuelli, M; Casasco, F; Cugliari, G; Cioffi, I; Deregibus, A

2018-01-01

The possible effects on sleep bruxism (SB) of clear aligners in orthodontics are unknown. This study was conducted to analyze the effects of clear aligners on SB. Sixty subjects needing orthodontic treatment and affected by SB (33 m, 27 f, 20±;5 years) were enrolled in the study and randomly assigned to one of the following three groups: 20 were given clear aligners (CAT) (12 m, 8 f, 19±5 years), 20 occlusal splint (MOS) (9 m, 11 f, 22±5 years) and 20 a placebo splint (PMS) (12 m, 8 f, 24±3 years). All groups were followed for 6 consecutive months and monitored for SB with a portable electromyographic-electrocardiographic (EMG-ECG) device (Bruxoff®, OT Bioelettronica, Torino, Italy). MOS subjects reduced masseter contractions after 6 months of treatment (t3) (MD=-29.11, std. error 11.74, p=0.017) but increased phasic contractions related to SB after 3 months of treatment (t2) (MD=4.73, std. error 2.36, p=0.048) and tonic contractions related to SB during all the six months of treatment (t1, t2, t3) when compared to PMS. CAT subjects increased phasic contractions related to SB during the first (t1) (MD=3.94, std. error 2.27, p=0.04) and the third month (t2) of treatment (MD=4.62, std. error 2.36, p=0.046) when compared to PMS. No significant differences were found for SB index at any time for all the three groups. Although MOS and CAT affected EMG signals during sleep time differently, they did not influence the overall SB index.

The impact of acquisition angle differences on three-dimensional quantitative coronary angiography.

PubMed

Tu, Shengxian; Holm, Niels R; Koning, Gerhard; Maeng, Michael; Reiber, Johan H C

2011-08-01

Three-dimensional (3D) quantitative coronary angiography (QCA) requires two angiographic views to restore vessel dimensions. This study investigated the impact of acquisition angle differences (AADs) of the two angiographic views on the assessed dimensions by 3D QCA. X-ray angiograms of an assembled brass phantom with different types of straight lesions were recorded at multiple angiographic projections. The projections were randomly matched as pairs and 3D QCA was performed in those pairs with AAD larger than 25°. The lesion length and diameter stenosis in three different lesions, a circular concentric severe lesion (A), a circular concentric moderate lesion (B), and a circular eccentric moderate lesion (C), were measured by 3D QCA. The acquisition protocol was repeated for a silicone bifurcation phantom, and the bifurcation angles and bifurcation core volume were measured by 3D QCA. The measurements were compared with the true dimensions if applicable and their correlation with AAD was studied. 50 matched pairs of angiographic views were analyzed for the brass phantom. The average value of AAD was 48.0 ± 14.1°. The percent diameter stenosis was slightly overestimated by 3D QCA for all lesions: A (error 1.2 ± 0.9%, P < 0.001); B (error 0.6 ± 0.5%, P < 0.001); C (error 1.1 ± 0.6%, P < 0.001). The correlation of the measurements with AAD was only significant for lesion A (R(2) = 0.151, P = 0.005). The lesion length was slightly overestimated by 3D QCA for lesion A (error 0.06 ± 0.18 mm, P = 0.026), but well assessed for lesion B (error -0.00 ± 0.16 mm, P = 0.950) and lesion C (error -0.01 ± 0.18 mm, P = 0.585). The correlation of the measurements with AAD was not significant for any lesion. Forty matched pairs of angiographic views were analyzed for the bifurcation phantom. The average value of AAD was 49.1 ± 15.4°. 3D QCA slightly overestimated the proximal angle (error 0.4 ± 1.1°, P = 0.046) and the distal angle (error 1.5 ± 1.3°, P < 0.001). The

Rapid Transfer Alignment of MEMS SINS Based on Adaptive Incremental Kalman Filter.

PubMed

Chu, Hairong; Sun, Tingting; Zhang, Baiqiang; Zhang, Hongwei; Chen, Yang

2017-01-14

In airborne MEMS SINS transfer alignment, the error of MEMS IMU is highly environment-dependent and the parameters of the system model are also uncertain, which may lead to large error and bad convergence of the Kalman filter. In order to solve this problem, an improved adaptive incremental Kalman filter (AIKF) algorithm is proposed. First, the model of SINS transfer alignment is defined based on the "Velocity and Attitude" matching method. Then the detailed algorithm progress of AIKF and its recurrence formulas are presented. The performance and calculation amount of AKF and AIKF are also compared. Finally, a simulation test is designed to verify the accuracy and the rapidity of the AIKF algorithm by comparing it with KF and AKF. The results show that the AIKF algorithm has better estimation accuracy and shorter convergence time, especially for the bias of the gyroscope and the accelerometer, which can meet the accuracy and rapidity requirement of transfer alignment.

Rapid Transfer Alignment of MEMS SINS Based on Adaptive Incremental Kalman Filter

PubMed Central

Chu, Hairong; Sun, Tingting; Zhang, Baiqiang; Zhang, Hongwei; Chen, Yang

2017-01-01

In airborne MEMS SINS transfer alignment, the error of MEMS IMU is highly environment-dependent and the parameters of the system model are also uncertain, which may lead to large error and bad convergence of the Kalman filter. In order to solve this problem, an improved adaptive incremental Kalman filter (AIKF) algorithm is proposed. First, the model of SINS transfer alignment is defined based on the “Velocity and Attitude” matching method. Then the detailed algorithm progress of AIKF and its recurrence formulas are presented. The performance and calculation amount of AKF and AIKF are also compared. Finally, a simulation test is designed to verify the accuracy and the rapidity of the AIKF algorithm by comparing it with KF and AKF. The results show that the AIKF algorithm has better estimation accuracy and shorter convergence time, especially for the bias of the gyroscope and the accelerometer, which can meet the accuracy and rapidity requirement of transfer alignment. PMID:28098829

Coordinate alignment of combined measurement systems using a modified common points method

NASA Astrophysics Data System (ADS)

Zhao, G.; Zhang, P.; Xiao, W.

2018-03-01

The co-ordinate metrology has been extensively researched for its outstanding advantages in measurement range and accuracy. The alignment of different measurement systems is usually achieved by integrating local coordinates via common points before measurement. The alignment errors would accumulate and significantly reduce the global accuracy, thus need to be minimized. In this thesis, a modified common points method (MCPM) is proposed to combine different traceable system errors of the cooperating machines, and optimize the global accuracy by introducing mutual geometric constraints. The geometric constraints, obtained by measuring the common points in individual local coordinate systems, provide the possibility to reduce the local measuring uncertainty whereby enhance the global measuring certainty. A simulation system is developed in Matlab to analyze the feature of MCPM using the Monto-Carlo method. An exemplary setup is constructed to verify the feasibility and efficiency of the proposed method associated with laser tracker and indoor iGPS systems. Experimental results show that MCPM could significantly improve the alignment accuracy.

The Dual-Angle Method for Fast, Sensitive T1 Measurement in Vivo with Low-Angle Adiabatic Pulses

NASA Astrophysics Data System (ADS)

Bottomley, P. A.; Ouwerkerk, R.

A new method for measuring T1 based on a measurement of the ratio, R, of the steady-state partially saturated NMR signals acquired at two fixed low flip angles (<90°) and a single sequence-repetition period, TR, is presented, The flip angles are chosen to optimize both the signal-to-noise ratio per unit time relative to the best possible Ernst-angle performance and the sensitivity with which a measurement of R can resolve differences in T1. A flip-angle pair at of around (60°, 15°) yields 70-79% of the maximum achievable Ernst-angle signal-to-noise ratio and a near-linear dependence of R on TR/ T1 with gradient of about 2:1 over the range 0.1 ≤ TR/ T1 ≤ 1. Errors in hip-angle and excitation-field ( B1) inhomogeneity result in roughly proportionate errors in the apparent T1. The method is best implemented with adiabatic low-angle pulses such as B1-independent rotation (BIR-4) or BIR-4 phase-cycled (BIRP) pulses, which permit measurements with surface coils. Experimental validation was obtained at 2 T by comparison of unlocalized inversion-recovery and dual-angle proton ( 1H) and phosphorus ( 31P) measurements from vials containing doped water with 0.04 ≤ T1 ≤ 2.8 s and from the metabolites in the calf muscles of eight human volunteers. Calf muscle values of 6 ± 0.5 s for phosphocreatine and around 3.7 ± 0.8 s for the adenosine triphosphates (ATP) were in good agreement with inversion-recovery T1 values and values from the literature. Use of the dual-angle method accelerated T1 measurement time by about fivefold over inversion recovery. The dual-angle method was implemented in a one-dimensional localized surface-coil 31P spectroscopy sequence, producing consistent T1 measurements from phantoms, the calf muscle, and the human liver. 31P T1 values of ATP in the livers of six volunteers were about 0.5 ± 0.1 to 0.6 ± 0.2 s: the total exam times were about 35 minutes per subject. The method is ideally suited to low-sensitivity and/or low

Modeling of Field-Aligned Guided Echoes in the Plasmasphere

NASA Technical Reports Server (NTRS)

Fung, Shing F.; Green, James L.

2004-01-01

The conditions under which high frequency (f>>f(sub uh)) long-range extraordinary-mode discrete field-aligned echoes observed by the Radio Plasma Imager (RPI) on board the Imager for Magnetopause-to-Aurora Global Exploration (IMAGE) satellite in the plasmasphere are investigated by ray tracing modeling. Field-aligned discrete echoes are most commonly observed by RPI in the plasmasphere although they are also observed over the polar cap region. The plasmasphere field-aligned echoes appearing as multiple echo traces at different virtual ranges are attributed to signals reflected successively between conjugate hemispheres that propagate along or nearly along closed geomagnetic field lines. The ray tracing simulations show that field-aligned ducts with as little as 1% density perturbations (depletions) and less than 10 wavelengths wide can guide nearly field-aligned propagating high frequency X mode waves. Effective guidance of wave at a given frequency and wave normal angle (Psi) depends on the cross-field density scale of the duct, such that ducts with stronger density depletions need to be wider in order to maintain the same gradient of refractive index across the magnetic field. While signal guidance by field aligned density gradient without ducting is possible only over the polar region, conjugate field-aligned echoes that have traversed through the equatorial region are most likely guided by ducting.

Contact angle distribution of particles at fluid interfaces.

PubMed

Snoeyink, Craig; Barman, Sourav; Christopher, Gordon F

2015-01-27

Recent measurements have implied a distribution of interfacially adsorbed particles' contact angles; however, it has been impossible to measure statistically significant numbers for these contact angles noninvasively in situ. Using a new microscopy method that allows nanometer-scale resolution of particle's 3D positions on an interface, we have measured the contact angles for thousands of latex particles at an oil/water interface. Furthermore, these measurements are dynamic, allowing the observation of the particle contact angle with high temporal resolution, resulting in hundreds of thousands of individual contact angle measurements. The contact angle has been found to fit a normal distribution with a standard deviation of 19.3°, which is much larger than previously recorded. Furthermore, the technique used allows the effect of measurement error, constrained interfacial diffusion, and particle property variation on the contact angle distribution to be individually evaluated. Because of the ability to measure the contact angle noninvasively, the results provide previously unobtainable, unique data on the dynamics and distribution of the adsorbed particles' contact angle.

Impact angle constrained three-dimensional integrated guidance and control for STT missile in the presence of input saturation.

PubMed

Wang, Sen; Wang, Weihong; Xiong, Shaofeng

2016-09-01

Considering a class of skid-to-turn (STT) missile with fixed target and constrained terminal impact angles, a novel three-dimensional (3D) integrated guidance and control (IGC) scheme is proposed in this paper. Based on coriolis theorem, the fully nonlinear IGC model without the assumption that the missile flies heading to the target at initial time is established in the three-dimensional space. For this strict-feedback form of multi-variable system, dynamic surface control algorithm is implemented combining with extended observer (ESO) to complete the preliminary design. Then, in order to deal with the problems of the input constraints, a hyperbolic tangent function is introduced to approximate the saturation function and auxiliary system including a Nussbaum function established to compensate for the approximation error. The stability of the closed-loop system is proven based on Lyapunov theory. Numerical simulations results show that the proposed integrated guidance and control algorithm can ensure the accuracy of target interception with initial alignment angle deviation and the input saturation is suppressed with smooth deflection curves. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Pennation angle dependency in skeletal muscle tissue doppler strain in dynamic contractions.

PubMed

Lindberg, Frida; Öhberg, Fredrik; Granåsen, Gabriel; Brodin, Lars-Åke; Grönlund, Christer

2011-07-01

Tissue velocity imaging (TVI) is a Doppler based ultrasound technique that can be used to study regional deformation in skeletal muscle tissue. The aim of this study was to develop a biomechanical model to describe the TVI strain's dependency on the pennation angle. We demonstrate its impact as the subsequent strain measurement error using dynamic elbow contractions from the medial and the lateral part of biceps brachii at two different loadings; 5% and 25% of maximum voluntary contraction (MVC). The estimated pennation angles were on average about 4° in extended position and increased to a maximal of 13° in flexed elbow position. The corresponding relative angular error spread from around 7% up to around 40%. To accurately apply TVI on skeletal muscles, the error due to angle changes should be compensated for. As a suggestion, this could be done according to the presented model. Copyright © 2011 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Renal artery origins: best angiographic projection angles.

PubMed

Verschuyl, E J; Kaatee, R; Beek, F J; Patel, N H; Fontaine, A B; Daly, C P; Coldwell, D M; Bush, W H; Mali, W P

1997-10-01

To determine the best projection angles for imaging the renal artery origins in profile. A mathematical model of the anatomy at the renal artery origins in the transverse plane was used to analyze the amount of aortic lumen that projects over the renal artery origins at various projection angles. Computed tomographic (CT) angiographic data about the location of 400 renal artery origins in 200 patients were statistically analyzed. In patients with an abdominal aortic diameter no larger than 3.0 cm, approximately 0.5 mm of the proximal part of the renal artery and origin may be hidden from view if there is a projection error of +/-10 degrees from the ideal image. A combination of anteroposterior and 20 degrees and 40 degrees left anterior oblique projections resulted in a 92% yield of images that adequately profiled the renal artery origins. Right anterior oblique projections resulted in the least useful images. An error in projection angle of +/-10 degrees is acceptable for angiographic imaging of the renal artery origins. Patients sex, site of interest (left or right artery), and local diameter of the abdominal aorta are important factors to consider.

Error Correcting Optical Mapping Data.

PubMed

Mukherjee, Kingshuk; Washimkar, Darshan; Muggli, Martin D; Salmela, Leena; Boucher, Christina

2018-05-26

Optical mapping is a unique system that is capable of producing high-resolution, high-throughput genomic map data that gives information about the structure of a genome [21]. Recently it has been used for scaffolding contigs and assembly validation for large-scale sequencing projects, including the maize [32], goat [6], and amborella [4] genomes. However, a major impediment in the use of this data is the variety and quantity of errors in the raw optical mapping data, which are called Rmaps. The challenges associated with using Rmap data are analogous to dealing with insertions and deletions in the alignment of long reads. Moreover, they are arguably harder to tackle since the data is numerical and susceptible to inaccuracy. We develop cOMET to error correct Rmap data, which to the best of our knowledge is the only optical mapping error correction method. Our experimental results demonstrate that cOMET has high prevision and corrects 82.49% of insertion errors and 77.38% of deletion errors in Rmap data generated from the E. coli K-12 reference genome. Out of the deletion errors corrected, 98.26% are true errors. Similarly, out of the insertion errors corrected, 82.19% are true errors. It also successfully scales to large genomes, improving the quality of 78% and 99% of the Rmaps in the plum and goat genomes, respectively. Lastly, we show the utility of error correction by demonstrating how it improves the assembly of Rmap data. Error corrected Rmap data results in an assembly that is more contiguous, and covers a larger fraction of the genome.

An algorithm for selecting the most accurate protocol for contact angle measurement by drop shape analysis.

PubMed

Xu, Z N

2014-12-01

In this study, an error analysis is performed to study real water drop images and the corresponding numerically generated water drop profiles for three widely used static contact angle algorithms: the circle- and ellipse-fitting algorithms and the axisymmetric drop shape analysis-profile (ADSA-P) algorithm. The results demonstrate the accuracy of the numerically generated drop profiles based on the Laplace equation. A significant number of water drop profiles with different volumes, contact angles, and noise levels are generated, and the influences of the three factors on the accuracies of the three algorithms are systematically investigated. The results reveal that the above-mentioned three algorithms are complementary. In fact, the circle- and ellipse-fitting algorithms show low errors and are highly resistant to noise for water drops with small/medium volumes and contact angles, while for water drop with large volumes and contact angles just the ADSA-P algorithm can meet accuracy requirement. However, this algorithm introduces significant errors in the case of small volumes and contact angles because of its high sensitivity to noise. The critical water drop volumes of the circle- and ellipse-fitting algorithms corresponding to a certain contact angle error are obtained through a significant amount of computation. To improve the precision of the static contact angle measurement, a more accurate algorithm based on a combination of the three algorithms is proposed. Following a systematic investigation, the algorithm selection rule is described in detail, while maintaining the advantages of the three algorithms and overcoming their deficiencies. In general, static contact angles over the entire hydrophobicity range can be accurately evaluated using the proposed algorithm. The ease of erroneous judgment in static contact angle measurements is avoided. The proposed algorithm is validated by a static contact angle evaluation of real and numerically generated water drop

A novel mechanism important for the alignment of microtubules.

PubMed

Wightman, Raymond; Turner, Simon R

2008-04-01

Using a live-cell imaging approach to study individual micro-tubules, we have compared microtubule behavior between net-like and aligned cortical arrays. In contrast to previous studies, a steep angled collision between the growing end of a microtubule and a preexisting microtubule was found to favor crossover. Frequencies of microtubule crossovers, bundling and catastrophes are similar regardless of whether the cell exhibited a net-like or aligned microtubule array. In the predominantly aligned array of petiole cells, severing occurs at the sites of microtubule crossovers and serves to remove unaligned microtubules and to increase microtubule density. Severing was observed to be rare in net-like arrays. Microtubule severing is carried out by the katanin enzyme. In this addendum, we present new insights into the possible mechanism of crossing over and preliminary data looking at organization of the array in a katanin mutant.

Multiscale registration algorithm for alignment of meshes

NASA Astrophysics Data System (ADS)

Vadde, Srikanth; Kamarthi, Sagar V.; Gupta, Surendra M.

2004-03-01

Taking a multi-resolution approach, this research work proposes an effective algorithm for aligning a pair of scans obtained by scanning an object's surface from two adjacent views. This algorithm first encases each scan in the pair with an array of cubes of equal and fixed size. For each scan in the pair a surrogate scan is created by the centroids of the cubes that encase the scan. The Gaussian curvatures of points across the surrogate scan pair are compared to find the surrogate corresponding points. If the difference between the Gaussian curvatures of any two points on the surrogate scan pair is less than a predetermined threshold, then those two points are accepted as a pair of surrogate corresponding points. The rotation and translation values between the surrogate scan pair are determined by using a set of surrogate corresponding points. Using the same rotation and translation values the original scan pairs are aligned. The resulting registration (or alignment) error is computed to check the accuracy of the scan alignment. When the registration error becomes acceptably small, the algorithm is terminated. Otherwise the above process is continued with cubes of smaller and smaller sizes until the algorithm is terminated. However at each finer resolution the search space for finding the surrogate corresponding points is restricted to the regions in the neighborhood of the surrogate points that were at found at the preceding coarser level. The surrogate corresponding points, as the resolution becomes finer and finer, converge to the true corresponding points on the original scans. This approach offers three main benefits: it improves the chances of finding the true corresponding points on the scans, minimize the adverse effects of noise in the scans, and reduce the computational load for finding the corresponding points.

Galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation

NASA Astrophysics Data System (ADS)

Chisari, N. E.; Koukoufilippas, N.; Jindal, A.; Peirani, S.; Beckmann, R. S.; Codis, S.; Devriendt, J.; Miller, L.; Dubois, Y.; Laigle, C.; Slyz, A.; Pichon, C.

2017-11-01

Intrinsic alignments of galaxies are a significant astrophysical systematic affecting cosmological constraints from weak gravitational lensing. Obtaining numerical predictions from hydrodynamical simulations of expected survey volumes is expensive, and a cheaper alternative relies on populating large dark matter-only simulations with accurate models of alignments calibrated on smaller hydrodynamical runs. This requires connecting the shapes and orientations of galaxies to those of dark matter haloes and to the large-scale structure. In this paper, we characterize galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation. We compare the shapes and orientations of galaxies in the redshift range of 0 < z < 3 to those of their embedding dark matter haloes, and to the matching haloes of a twin dark-matter only run with identical initial conditions. We find that galaxy ellipticities, in general, cannot be predicted directly from halo ellipticities. The mean misalignment angle between the minor axis of a galaxy and its embedding halo is a function of halo mass, with residuals arising from the dependence of alignment on galaxy type, but not on environment. Haloes are much more strongly aligned among themselves than galaxies, and they decrease their alignment towards low redshift. Galaxy alignments compete with this effect, as galaxies tend to increase their alignment with haloes towards low redshift. We discuss the implications of these results for current halo models of intrinsic alignments and suggest several avenues for improvement.

Impact of Measurement Error on Synchrophasor Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yilu; Gracia, Jose R.; Ewing, Paul D.

2015-07-01

Phasor measurement units (PMUs), a type of synchrophasor, are powerful diagnostic tools that can help avert catastrophic failures in the power grid. Because of this, PMU measurement errors are particularly worrisome. This report examines the internal and external factors contributing to PMU phase angle and frequency measurement errors and gives a reasonable explanation for them. It also analyzes the impact of those measurement errors on several synchrophasor applications: event location detection, oscillation detection, islanding detection, and dynamic line rating. The primary finding is that dynamic line rating is more likely to be influenced by measurement error. Other findings include themore » possibility of reporting nonoscillatory activity as an oscillation as the result of error, failing to detect oscillations submerged by error, and the unlikely impact of error on event location and islanding detection.« less

Geometry calibration for x-ray equipment in radiation treatment devices and estimation of remaining patient alignment errors

NASA Astrophysics Data System (ADS)

Selby, Boris P.; Sakas, Georgios; Walter, Stefan; Stilla, Uwe

2008-03-01

Positioning a patient accurately in treatment devices is crucial for radiological treatment, especially if accuracy vantages of particle beam treatment are exploited. To avoid sub-millimeter misalignments, X-ray images acquired from within the device are compared to a CT to compute respective alignment corrections. Unfortunately, deviations of the underlying geometry model for the imaging system degrade the achievable accuracy. We propose an automatic calibration routine, which bases on the geometry of a phantom and its automatic detection in digital radiographs acquired for various geometric device settings during the calibration. The results from the registration of the phantom's X-ray projections and its known geometry are used to update the model of the respective beamlines, which is used to compute the patient alignment correction. The geometric calibration of a beamline takes all nine relevant degrees of freedom into account, including detector translations in three directions, detector tilt by three axes and three possible translations for the X-ray tube. Introducing a stochastic model for the calibration we are able to predict the patient alignment deviations resulting from inaccuracies inherent to the phantom design and the calibration. Comparisons of the alignment results for a treatment device without calibrated imaging systems and a calibrated device show that an accurate calibration can enhance alignment accuracy.

ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection

PubMed Central

Alachiotis, Nikolaos; Vogiatzi, Emmanouella; Pavlidis, Pavlos; Stamatakis, Alexandros

2013-01-01

Automated DNA sequencers generate chromatograms that contain raw sequencing data. They also generate data that translates the chromatograms into molecular sequences of A, C, G, T, or N (undetermined) characters. Since chromatogram translation programs frequently introduce errors, a manual inspection of the generated sequence data is required. As sequence numbers and lengths increase, visual inspection and manual correction of chromatograms and corresponding sequences on a per-peak and per-nucleotide basis becomes an error-prone, time-consuming, and tedious process. Here, we introduce ChromatoGate (CG), an open-source software that accelerates and partially automates the inspection of chromatograms and the detection of sequencing errors for bidirectional sequencing runs. To provide users full control over the error correction process, a fully automated error correction algorithm has not been implemented. Initially, the program scans a given multiple sequence alignment (MSA) for potential sequencing errors, assuming that each polymorphic site in the alignment may be attributed to a sequencing error with a certain probability. The guided MSA assembly procedure in ChromatoGate detects chromatogram peaks of all characters in an alignment that lead to polymorphic sites, given a user-defined threshold. The threshold value represents the sensitivity of the sequencing error detection mechanism. After this pre-filtering, the user only needs to inspect a small number of peaks in every chromatogram to correct sequencing errors. Finally, we show that correcting sequencing errors is important, because population genetic and phylogenetic inferences can be misled by MSAs with uncorrected mis-calls. Our experiments indicate that estimates of population mutation rates can be affected two- to three-fold by uncorrected errors. PMID:24688709

ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection.

PubMed

Alachiotis, Nikolaos; Vogiatzi, Emmanouella; Pavlidis, Pavlos; Stamatakis, Alexandros

2013-01-01

Automated DNA sequencers generate chromatograms that contain raw sequencing data. They also generate data that translates the chromatograms into molecular sequences of A, C, G, T, or N (undetermined) characters. Since chromatogram translation programs frequently introduce errors, a manual inspection of the generated sequence data is required. As sequence numbers and lengths increase, visual inspection and manual correction of chromatograms and corresponding sequences on a per-peak and per-nucleotide basis becomes an error-prone, time-consuming, and tedious process. Here, we introduce ChromatoGate (CG), an open-source software that accelerates and partially automates the inspection of chromatograms and the detection of sequencing errors for bidirectional sequencing runs. To provide users full control over the error correction process, a fully automated error correction algorithm has not been implemented. Initially, the program scans a given multiple sequence alignment (MSA) for potential sequencing errors, assuming that each polymorphic site in the alignment may be attributed to a sequencing error with a certain probability. The guided MSA assembly procedure in ChromatoGate detects chromatogram peaks of all characters in an alignment that lead to polymorphic sites, given a user-defined threshold. The threshold value represents the sensitivity of the sequencing error detection mechanism. After this pre-filtering, the user only needs to inspect a small number of peaks in every chromatogram to correct sequencing errors. Finally, we show that correcting sequencing errors is important, because population genetic and phylogenetic inferences can be misled by MSAs with uncorrected mis-calls. Our experiments indicate that estimates of population mutation rates can be affected two- to three-fold by uncorrected errors.

The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

NASA Astrophysics Data System (ADS)

Livingston, Ken

2009-05-01

This paper describes a technique for the alignment of crystal radiators used to produce high energy, linearly polarized photons via coherent bremsstrahlung scattering at electron beam facilities. In these experiments the crystal is mounted on a goniometer which is used to adjust its orientation relative to the electron beam. The angles and equations which relate the crystal lattice, goniometer and electron beam direction are presented here, and the method of alignment is illustrated with data taken at MAMI (the Mainz microtron). A practical guide to setting up a coherent bremsstrahlung facility and installing new crystals using this technique is also included.

Global distortion of GPS networks associated with satellite antenna model errors

NASA Astrophysics Data System (ADS)

Cardellach, E.; Elósegui, P.; Davis, J. L.

2007-07-01

Recent studies of the GPS satellite phase center offsets (PCOs) suggest that these have been in error by ˜1 m. Previous studies had shown that PCO errors are absorbed mainly by parameters representing satellite clock and the radial components of site position. On the basis of the assumption that the radial errors are equal, PCO errors will therefore introduce an error in network scale. However, PCO errors also introduce distortions, or apparent deformations, within the network, primarily in the radial (vertical) component of site position that cannot be corrected via a Helmert transformation. Using numerical simulations to quantify the effects of PCO errors, we found that these PCO errors lead to a vertical network distortion of 6-12 mm per meter of PCO error. The network distortion depends on the minimum elevation angle used in the analysis of the GPS phase observables, becoming larger as the minimum elevation angle increases. The steady evolution of the GPS constellation as new satellites are launched, age, and are decommissioned, leads to the effects of PCO errors varying with time that introduce an apparent global-scale rate change. We demonstrate here that current estimates for PCO errors result in a geographically variable error in the vertical rate at the 1-2 mm yr-1 level, which will impact high-precision crustal deformation studies.

Global Distortion of GPS Networks Associated with Satellite Antenna Model Errors

NASA Technical Reports Server (NTRS)

Cardellach, E.; Elosequi, P.; Davis, J. L.

2007-01-01

Recent studies of the GPS satellite phase center offsets (PCOs) suggest that these have been in error by approx.1 m. Previous studies had shown that PCO errors are absorbed mainly by parameters representing satellite clock and the radial components of site position. On the basis of the assumption that the radial errors are equal, PCO errors will therefore introduce an error in network scale. However, PCO errors also introduce distortions, or apparent deformations, within the network, primarily in the radial (vertical) component of site position that cannot be corrected via a Helmert transformation. Using numerical simulations to quantify the effects of PC0 errors, we found that these PCO errors lead to a vertical network distortion of 6-12 mm per meter of PCO error. The network distortion depends on the minimum elevation angle used in the analysis of the GPS phase observables, becoming larger as the minimum elevation angle increases. The steady evolution of the GPS constellation as new satellites are launched, age, and are decommissioned, leads to the effects of PCO errors varying with time that introduce an apparent global-scale rate change. We demonstrate here that current estimates for PCO errors result in a geographically variable error in the vertical rate at the 1-2 mm/yr level, which will impact high-precision crustal deformation studies.

The Shank-to-Vertical-Angle as a parameter to evaluate tuning of Ankle-Foot Orthoses.

PubMed

Kerkum, Yvette L; Houdijk, Han; Brehm, Merel-Anne; Buizer, Annemieke I; Kessels, Manon L C; Sterk, Arjan; van den Noort, Josien C; Harlaar, Jaap

2015-09-01

The effectiveness of an Ankle-Foot Orthosis footwear combination (AFO-FC) may be partly dependent on the alignment of the ground reaction force with respect to lower limb joint rotation centers, reflected by joint angles and moments. Adjusting (i.e. tuning) the AFO-FC's properties could affect this alignment, which may be guided by monitoring the Shank-to-Vertical-Angle. This study aimed to investigate whether the Shank-to-Vertical-Angle during walking responds to variations in heel height and footplate stiffness, and if this would reflect changes in joint angles and net moments in healthy adults. Ten subjects walked on an instrumented treadmill and performed six trials while walking with bilateral rigid Ankle-Foot Orthoses. The AFO-FC heel height was increased, aiming to impose a Shank-to-Vertical-Angle of 5°, 11° and 20°, and combined with a flexible or stiff footplate. For each trial, the Shank-to-Vertical-Angle, joint flexion-extension angles and net joint moments of the right leg at midstance were averaged over 25 gait cycles. The Shank-to-Vertical-Angle significantly increased with increasing heel height (p<0.001), resulting in an increase in knee flexion angle and internal knee extensor moment (p<0.001). The stiff footplate reduced the effect of heel height on the internal knee extensor moment (p=0.030), while the internal ankle plantar flexion moment increased (p=0.035). Effects of heel height and footplate stiffness on the hip joint were limited. Our results support the potential to use the Shank-to-Vertical-Angle as a parameter to evaluate AFO-FC tuning, as it is responsive to changes in heel height and reflects concomitant changes in the lower limb angles and moments. Copyright © 2015 Elsevier B.V. All rights reserved.

Sagittal Vertical Axias, Spinosacral Angle, Spinopelvic Angle, and T1 Pelvic Angle: Which Parameters May Effectively Predict the Quality of Life in Ankylosing Spondylitis Patients With Thoracolumbar Kyphosis?

PubMed

Zhang, Yun-Peng; Qian, Bang-Ping; Qiu, Yong; Qu, Zhe; Mao, Sai-Hu; Jiang, Jun; Zhu, Ze-Zhang

2017-08-01

This is a retrospective study. To identify the relationship between global sagittal alignment and health-related quality of life (HRQoL) in ankylosing spondylitis (AS) patients with thoracolumbar kyphosis. Little data are available on correlation between global sagittal alignment and HRQoL in AS. A total of 107 AS patients were included in this study. The radiographic parameters were measured on lateral radiographs of the whole spine, including sagittal vertical axias (SVA), spinosacral angle (SSA), spinopelvic angle (SPA), and T1 pelvic angle (TPA). HRQoL was assessed using the oswestry disability index questionnaire, the bath ankylosing spondylitis disease activity index, the bath ankylosing spondylitis functional index, and short form-36 questionnaire. The patients were divided into 2 groups: group A (n=76, global kyphosis≤70 degrees), group B (n=31, global kyphosis>70 degrees). Statistical analysis was performed to identify significant differences between these 2 groups. In addition, correlation analysis and multiple regression analysis between radiologic parameters and clinical questionnaires were conducted. With respect to SVA, SSA, SPA, TPA, and HRQoL scores, significant differences were observed between 2 groups (P<0.05). Also, SVA, SSA, SPA, and TPA were significantly related to HRQoL. Multiple regression analysis revealed that SVA, SSA, SPA, and TPA were significant parameters in the prediction of HRQoL in AS patients with thoracolumbar kyphosis. Of note, HRQoL related much more to SSA and SPA than SVA and TPA. AS patients with moderate and severe deformity were demonstrated to be significantly different in terms of SVA, SSA, SPA, TPA, and HRQoL. Moreover, SVA, SSA, SPA, and TPA correlated with HRQoL significantly. In particular, SSA and SPA could better predict HRQoL than SVA and TPA in AS patients with thoracolumbar kyphosis.

GNSS Clock Error Impacts on Radio Occultation Retrievals

NASA Astrophysics Data System (ADS)

Weiss, Jan; Sokolovskiy, Sergey; Schreiner, Bill; Yoon, Yoke

2017-04-01

We assess the impacts of GPS and GLONASS clock errors on radio occultation retrieval of bending angle, refractivity, and temperature from low Earth orbit. The major contributing factor is the interpretation of GNSS clock offsets sampled at 30 sec or longer intervals. Using 1 Hz GNSS clock estimates as truth we apply several interpolation and fitting schemes to evaluate how they affect the accuracy of atmospheric retrieval products. The results are organized by GPS and GLONASS space vehicle and the GNSS clock interpolation/fitting scheme. We find that bending angle error is roughly similar for all current GPS transmitters (about 0.7 mcrad) but note some differences related to the type of atomic oscillator onboard the transmitter satellite. GLONASS bending angle errors show more variation over the constellation and are approximately two times larger than GPS. An investigation of the transmitter clock spectra reveals this is due to more power in periods between 2-10 sec. Retrieved refractivity and temperature products show clear differences between GNSS satellite generations, and indicate that GNSS clocks sampled at intervals smaller than 5 sec significantly improve accuracy, particularly for GLONASS. We conclude by summarizing the tested GNSS clock estimation and application strategies in the context of current and future radio occultation missions.

Stochastic Integration H∞ Filter for Rapid Transfer Alignment of INS.

PubMed

Zhou, Dapeng; Guo, Lei

2017-11-18

The performance of an inertial navigation system (INS) operated on a moving base greatly depends on the accuracy of rapid transfer alignment (RTA). However, in practice, the coexistence of large initial attitude errors and uncertain observation noise statistics poses a great challenge for the estimation accuracy of misalignment angles. This study aims to develop a novel robust nonlinear filter, namely the stochastic integration H ∞ filter (SIH ∞ F) for improving both the accuracy and robustness of RTA. In this new nonlinear H ∞ filter, the stochastic spherical-radial integration rule is incorporated with the framework of the derivative-free H ∞ filter for the first time, and the resulting SIH ∞ F simultaneously attenuates the negative effect in estimations caused by significant nonlinearity and large uncertainty. Comparisons between the SIH ∞ F and previously well-known methodologies are carried out by means of numerical simulation and a van test. The results demonstrate that the newly-proposed method outperforms the cubature H ∞ filter. Moreover, the SIH ∞ F inherits the benefit of the traditional stochastic integration filter, but with more robustness in the presence of uncertainty.

Photometric theory for wide-angle phenomena

NASA Technical Reports Server (NTRS)

Usher, Peter D.

1990-01-01

An examination is made of the problem posed by wide-angle photographic photometry, in order to extract a photometric-morphological history of Comet P/Halley. Photometric solutions are presently achieved over wide angles through a generalization of an assumption-free moment-sum method. Standard stars in the field allow a complete solution to be obtained for extinction, sky brightness, and the characteristic curve. After formulating Newton's method for the solution of the general nonlinear least-square problem, an implementation is undertaken for a canonical data set. Attention is given to the problem of random and systematic photometric errors.

Reflective properties of randomly rough surfaces under large incidence angles.

PubMed

Qiu, J; Zhang, W J; Liu, L H; Hsu, P-f; Liu, L J

2014-06-01

The reflective properties of randomly rough surfaces at large incidence angles have been reported due to their potential applications in some of the radiative heat transfer research areas. The main purpose of this work is to investigate the formation mechanism of the specular reflection peak of rough surfaces at large incidence angles. The bidirectional reflectance distribution function (BRDF) of rough aluminum surfaces with different roughnesses at different incident angles is measured by a three-axis automated scatterometer. This study used a validated and accurate computational model, the rigorous coupled-wave analysis (RCWA) method, to compare and analyze the measurement BRDF results. It is found that the RCWA results show the same trend of specular peak as the measurement. This paper mainly focuses on the relative roughness at the range of 0.16<σ/λ<5.35. As the relative roughness decreases, the specular peak enhancement dramatically increases and the scattering region significantly reduces, especially under large incidence angles. The RCWA and the Rayleigh criterion results have been compared, showing that the relative error of the total integrated scatter increases as the roughness of the surface increases at large incidence angles. In addition, the zero-order diffractive power calculated by RCWA and the reflectance calculated by Fresnel equations are compared. The comparison shows that the relative error declines sharply when the incident angle is large and the roughness is small.

Spatio-temporal alignment of pedobarographic image sequences.

PubMed

Oliveira, Francisco P M; Sousa, Andreia; Santos, Rubim; Tavares, João Manuel R S

2011-07-01

This article presents a methodology to align plantar pressure image sequences simultaneously in time and space. The spatial position and orientation of a foot in a sequence are changed to match the foot represented in a second sequence. Simultaneously with the spatial alignment, the temporal scale of the first sequence is transformed with the aim of synchronizing the two input footsteps. Consequently, the spatial correspondence of the foot regions along the sequences as well as the temporal synchronizing is automatically attained, making the study easier and more straightforward. In terms of spatial alignment, the methodology can use one of four possible geometric transformation models: rigid, similarity, affine, or projective. In the temporal alignment, a polynomial transformation up to the 4th degree can be adopted in order to model linear and curved time behaviors. Suitable geometric and temporal transformations are found by minimizing the mean squared error (MSE) between the input sequences. The methodology was tested on a set of real image sequences acquired from a common pedobarographic device. When used in experimental cases generated by applying geometric and temporal control transformations, the methodology revealed high accuracy. In addition, the intra-subject alignment tests from real plantar pressure image sequences showed that the curved temporal models produced better MSE results (P < 0.001) than the linear temporal model. This article represents an important step forward in the alignment of pedobarographic image data, since previous methods can only be applied on static images.

Moment expansion for ionospheric range error

NASA Technical Reports Server (NTRS)

Mallinckrodt, A.; Reich, R.; Parker, H.; Berbert, J.

1972-01-01

On a plane earth, the ionospheric or tropospheric range error depends only on the total refractivity content or zeroth moment of the refracting layer and the elevation angle. On a spherical earth, however, the dependence is more complex; so for more accurate results it has been necessary to resort to complex ray-tracing calculations. A simple, high-accuracy alternative to the ray-tracing calculation is presented. By appropriate expansion of the angular dependence in the ray-tracing integral in a power series in height, an expression is obtained for the range error in terms of a simple function of elevation angle, E, at the expansion height and of the mth moment of the refractivity, N, distribution about the expansion height. The rapidity of convergence is heavily dependent on the choice of expansion height. For expansion heights in the neighborhood of the centroid of the layer (300-490 km), the expansion to N = 2 (three terms) gives results accurate to about 0.4% at E = 10 deg. As an analytic tool, the expansion affords some insight on the influence of layer shape on range errors in special problems.

Traveltime inversion and error analysis for layered anisotropy

NASA Astrophysics Data System (ADS)

Jiang, Fan; Zhou, Hua-wei

2011-02-01

While tilted transverse isotropy (TTI) is a good approximation of the velocity structure for many dipping and fractured strata, it is still challenging to estimate anisotropic depth models even when the tilted angle is known. With the assumption of weak anisotropy, we present a TTI traveltime inversion approach for models consisting of several thickness-varying layers where the anisotropic parameters are constant for each layer. For each model layer the inversion variables consist of the anisotropic parameters ɛ and δ, the tilted angle φ of its symmetry axis, layer velocity along the symmetry axis, and thickness variation of the layer. Using this method and synthetic data, we evaluate the effects of errors in some of the model parameters on the inverted values of the other parameters in crosswell and Vertical Seismic Profile (VSP) acquisition geometry. The analyses show that the errors in the layer symmetry axes sensitively affect the inverted values of other parameters, especially δ. However, the impact of errors in δ on the inversion of other parameters is much less than the impact on δ from the errors in other parameters. Hence, a practical strategy is first to invert for the most error-tolerant parameter layer velocity, then progressively invert for ɛ in crosswell geometry or δ in VSP geometry.

High-speed reference-beam-angle control technique for holographic memory drive

NASA Astrophysics Data System (ADS)

Yamada, Ken-ichiro; Ogata, Takeshi; Hosaka, Makoto; Fujita, Koji; Okuyama, Atsushi

2016-09-01

We developed a holographic memory drive for next-generation optical memory. In this study, we present the key technology for achieving a high-speed transfer rate for reproduction, that is, a high-speed control technique for the reference beam angle. In reproduction in a holographic memory drive, there is the issue that the optimum reference beam angle during reproduction varies owing to distortion of the medium. The distortion is caused by, for example, temperature variation, beam irradiation, and moisture absorption. Therefore, a reference-beam-angle control technique to position the reference beam at the optimum angle is crucial. We developed a new optical system that generates an angle-error-signal to detect the optimum reference beam angle. To achieve the high-speed control technique using the new optical system, we developed a new control technique called adaptive final-state control (AFSC) that adds a second control input to the first one derived from conventional final-state control (FSC) at the time of angle-error-signal detection. We established an actual experimental system employing AFSC to achieve moving control between each page (Page Seek) within 300 µs. In sequential multiple Page Seeks, we were able to realize positioning to the optimum angles of the reference beam that maximize the diffracted beam intensity. We expect that applying the new control technique to the holographic memory drive will enable a giga-bit/s-class transfer rate.

Refinement procedure for the image alignment in high-resolution electron tomography.

PubMed

Houben, L; Bar Sadan, M

2011-01-01

High-resolution electron tomography from a tilt series of transmission electron microscopy images requires an accurate image alignment procedure in order to maximise the resolution of the tomogram. This is the case in particular for ultra-high resolution where even very small misalignments between individual images can dramatically reduce the fidelity of the resultant reconstruction. A tomographic-reconstruction based and marker-free method is proposed, which uses an iterative optimisation of the tomogram resolution. The method utilises a search algorithm that maximises the contrast in tomogram sub-volumes. Unlike conventional cross-correlation analysis it provides the required correlation over a large tilt angle separation and guarantees a consistent alignment of images for the full range of object tilt angles. An assessment based on experimental reconstructions shows that the marker-free procedure is competitive to the reference of marker-based procedures at lower resolution and yields sub-pixel accuracy even for simulated high-resolution data. Copyright © 2011 Elsevier B.V. All rights reserved.

Parallel alignment of bacteria using near-field optical force array for cell sorting

NASA Astrophysics Data System (ADS)

Zhao, H. T.; Zhang, Y.; Chin, L. K.; Yap, P. H.; Wang, K.; Ser, W.; Liu, A. Q.

2017-08-01

This paper presents a near-field approach to align multiple rod-shaped bacteria based on the interference pattern in silicon nano-waveguide arrays. The bacteria in the optical field will be first trapped by the gradient force and then rotated by the scattering force to the equilibrium position. In the experiment, the Shigella bacteria is rotated 90 deg and aligned to horizontal direction in 9.4 s. Meanwhile, 150 Shigella is trapped on the surface in 5 min and 86% is aligned with angle < 5 deg. This method is a promising toolbox for the research of parallel single-cell biophysical characterization, cell-cell interaction, etc.

Tilt Error in Cryospheric Surface Radiation Measurements at High Latitudes: A Model Study

NASA Astrophysics Data System (ADS)

Bogren, W.; Kylling, A.; Burkhart, J. F.

2015-12-01

We have evaluated the magnitude and makeup of error in cryospheric radiation observations due to small sensor misalignment in in-situ measurements of solar irradiance. This error is examined through simulation of diffuse and direct irradiance arriving at a detector with a cosine-response foreoptic. Emphasis is placed on assessing total error over the solar shortwave spectrum from 250nm to 4500nm, as well as supporting investigation over other relevant shortwave spectral ranges. The total measurement error introduced by sensor tilt is dominated by the direct component. For a typical high latitude albedo measurement with a solar zenith angle of 60◦, a sensor tilted by 1, 3, and 5◦ can respectively introduce up to 2.6, 7.7, and 12.8% error into the measured irradiance and similar errors in the derived albedo. Depending on the daily range of solar azimuth and zenith angles, significant measurement error can persist also in integrated daily irradiance and albedo.

Kinematic error magnitude in the single-mass inverted pendulum model of human standing posture.

PubMed

Fok, Kai Lon; Lee, Jae; Vette, Albert H; Masani, Kei

2018-06-01

Many postural control studies employ a single-mass inverted pendulum model (IPM) to represent the body during standing. However, it is not known to what degree and for what conditions the model's kinematic assumptions are valid. Our first objective was to quantify the IPM error, corresponding to a distance change between the ankle joint and center of mass (COM) during unrestricted, natural, unperturbed standing. A second objective was to quantify the error of having the ankle joint angle represent the COM angle. Eleven young participants completed five standing conditions: quiet standing with eyes open (EO) and closed (EC), voluntarily swaying forward (VSf) and backward (VSb), and freely moving (FR). The modified Helen-Hayes marker model was used to capture the body kinematics. The COM distance changed <0.1% during EO and EC, <0.25% during VSf and VSb, and <1.5% during FR. The ankle angle moderately and positively correlated with the COM angle for EO, EC, and VSf, indicating that temporal features of the ankle angle moderately represent those of the COM angle. However, a considerable offset between the two existed, which needs to be considered when estimating the COM angle using the ankle angle. For VSb and FR, the correlation coefficients were low and/or negative, suggesting that a large error would result from using the ankle angle as an estimate of the COM angle. Insights from this study will be critical for deciding when to use the IPM in postural control research and for interpreting associated results. Copyright © 2018 Elsevier B.V. All rights reserved.

Modeling of field-aligned guided echoes in the plasmasphere

NASA Astrophysics Data System (ADS)

Fung, Shing F.; Green, James L.

2005-01-01

Ray tracing modeling is used to investigate the plasma conditions under which high-frequency (f ≫ fuh) extraordinary mode waves can be guided along geomagnetic field lines. These guided signals have often been observed as long-range discrete echoes in the plasmasphere by the Radio Plasma Imager (RPI) onboard the Imager for Magnetopause-to-Aurora Global Exploration satellite. Field-aligned discrete echoes are most commonly observed by RPI in the plasmasphere, although they are also observed over the polar cap region. The plasmasphere field-aligned echoes appearing as multiple echo traces at different virtual ranges are attributed to signals reflected successively between conjugate hemispheres that propagate along or nearly along closed geomagnetic field lines. The ray tracing simulations show that field-aligned ducts with as little as 1% density perturbations (depletions) and <10 wavelengths wide can guide nearly field-aligned propagating high-frequency X mode waves. Effective guidance of a wave at a given frequency and wave normal angle (Ψ) depends on the cross-field density scale of the duct, such that ducts with stronger density depletions need to be wider in order to maintain the same gradient of refractive index across the magnetic field. While signal guidance by field aligned density gradient without ducting is possible only over the polar region, conjugate field-aligned echoes that have traversed through the equatorial region are most likely guided by ducting.

A low-cost GPS/INS integrated vehicle heading angle measurement system

NASA Astrophysics Data System (ADS)

Wu, Ye; Gao, Tongyue; Ding, Yi

2018-04-01

GPS can provide continuous heading information, but the accuracy is easily affected by the velocity and shelter from buildings or trees. For vehicle systems, we propose a low-cost heading angle update algorithm. Based on the GPS/INS integrated navigation kalman filter, we add the GPS heading angle to the measurement vector, and establish its error model. The experiment results show that this algorithm can effectively improve the accuracy of GPS heading angle.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

PubMed

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

Estimation Filter for Alignment of the Spitzer Space Telescope

NASA Technical Reports Server (NTRS)

Bayard, David

2007-01-01

A document presents a summary of an onboard estimation algorithm now being used to calibrate the alignment of the Spitzer Space Telescope (formerly known as the Space Infrared Telescope Facility). The algorithm, denoted the S2P calibration filter, recursively generates estimates of the alignment angles between a telescope reference frame and a star-tracker reference frame. At several discrete times during the day, the filter accepts, as input, attitude estimates from the star tracker and observations taken by the Pointing Control Reference Sensor (a sensor in the field of view of the telescope). The output of the filter is a calibrated quaternion that represents the best current mean-square estimate of the alignment angles between the telescope and the star tracker. The S2P calibration filter incorporates a Kalman filter that tracks six states - two for each of three orthogonal coordinate axes. Although, in principle, one state per axis is sufficient, the use of two states per axis makes it possible to model both short- and long-term behaviors. Specifically, the filter properly models transient learning, characteristic times and bounds of thermomechanical drift, and long-term steady-state statistics, whether calibration measurements are taken frequently or infrequently. These properties ensure that the S2P filter performance is optimal over a broad range of flight conditions, and can be confidently run autonomously over several years of in-flight operation without human intervention.

Static knee alignment and its association with radiographic knee osteoarthritis.

PubMed

Teichtahl, A J; Cicuttini, F M; Janakiramanan, N; Davis, S R; Wluka, A E

2006-09-01

Although knee alignment is associated with the progression of knee osteoarthritis (OA), it is unclear which features that characterize radiographic OA are related to alignment. The aim of this study was to examine the relationship between static knee joint alignment (measured as a continuous variable) and the radiographic features of knee OA (joint space narrowing and osteophytes). One hundred and twenty one adults with symptomatic knee OA were recruited using a combined strategy including referral from specialist centres, arthritis support groups and media advertising. X-rays were performed to classify the severity of disease and to determine static knee alignment. Increasing varus knee alignment was associated with increasing risk of medial compartment joint space narrowing (P < 0.001) and osteophytes (P = 0.005). Increasing valgus knee alignment was associated with an increased risk for lateral compartment joint space narrowing (P < 0.001) and osteophytes (P = 0.002). This study has demonstrated that the static knee angle, measured as a continuous variable, is an important determinant of the compartment-specific features of radiographic knee OA. Further work is required to determine whether interventions aimed at correcting these relatively minor levels of varus and valgus angulation will have an effect on the risk of tibiofemoral OA.

Beam alignment based on two-dimensional power spectral density of a near-field image.

PubMed

Wang, Shenzhen; Yuan, Qiang; Zeng, Fa; Zhang, Xin; Zhao, Junpu; Li, Kehong; Zhang, Xiaolu; Xue, Qiao; Yang, Ying; Dai, Wanjun; Zhou, Wei; Wang, Yuanchen; Zheng, Kuixing; Su, Jingqin; Hu, Dongxia; Zhu, Qihua

2017-10-30

Beam alignment is crucial to high-power laser facilities and is used to adjust the laser beams quickly and accurately to meet stringent requirements of pointing and centering. In this paper, a novel alignment method is presented, which employs data processing of the two-dimensional power spectral density (2D-PSD) for a near-field image and resolves the beam pointing error relative to the spatial filter pinhole directly. Combining this with a near-field fiducial mark, the operation of beam alignment is achieved. It is experimentally demonstrated that this scheme realizes a far-field alignment precision of approximately 3% of the pinhole size. This scheme adopts only one near-field camera to construct the alignment system, which provides a simple, efficient, and low-cost way to align lasers.

Large format focal plane array integration with precision alignment, metrology and accuracy capabilities

NASA Astrophysics Data System (ADS)

Neumann, Jay; Parlato, Russell; Tracy, Gregory; Randolph, Max

2015-09-01

Focal plane alignment for large format arrays and faster optical systems require enhanced precision methodology and stability over temperature. The increase in focal plane array size continues to drive the alignment capability. Depending on the optical system, the focal plane flatness of less than 25μm (.001") is required over transition temperatures from ambient to cooled operating temperatures. The focal plane flatness requirement must also be maintained in airborne or launch vibration environments. This paper addresses the challenge of the detector integration into the focal plane module and housing assemblies, the methodology to reduce error terms during integration and the evaluation of thermal effects. The driving factors influencing the alignment accuracy include: datum transfers, material effects over temperature, alignment stability over test, adjustment precision and traceability to NIST standard. The FPA module design and alignment methodology reduces the error terms by minimizing the measurement transfers to the housing. In the design, the proper material selection requires matched coefficient of expansion materials minimizes both the physical shift over temperature as well as lowering the stress induced into the detector. When required, the co-registration of focal planes and filters can achieve submicron relative positioning by applying precision equipment, interferometry and piezoelectric positioning stages. All measurements and characterizations maintain traceability to NIST standards. The metrology characterizes the equipment's accuracy, repeatability and precision of the measurements.

Gaze and viewing angle influence visual stabilization of upright posture

PubMed Central

Ustinova, KI; Perkins, J

2011-01-01

Focusing gaze on a target helps stabilize upright posture. We investigated how this visual stabilization can be affected by observing a target presented under different gaze and viewing angles. In a series of 10-second trials, participants (N = 20, 29.3 ± 9 years of age) stood on a force plate and fixed their gaze on a figure presented on a screen at a distance of 1 m. The figure changed position (gaze angle: eye level (0°), 25° up or down), vertical body orientation (viewing angle: at eye level but rotated 25° as if leaning toward or away from the participant), or both (gaze and viewing angle: 25° up or down with the rotation equivalent of a natural visual perspective). Amplitude of participants’ sagittal displacement, surface area, and angular position of the center of gravity (COG) were compared. Results showed decreased COG velocity and amplitude for up and down gaze angles. Changes in viewing angles resulted in altered body alignment and increased amplitude of COG displacement. No significant changes in postural stability were observed when both gaze and viewing angles were altered. Results suggest that both the gaze angle and viewing perspective may be essential variables of the visuomotor system modulating postural responses. PMID:22398978

Cervical Alignment Variations in Different Postures and Predictors of Normal Cervical Kyphosis: A New Understanding.

PubMed

Hey, Hwee Weng Dennis; Lau, Eugene Tze-Chun; Wong, Gordon Chengyuan; Tan, Kimberly-Anne; Liu, Gabriel Ka-Po; Wong, Hee-Kit

2017-11-01

Comparative study of prospectively collected radiographic data. To predict physiological alignment of the cervical spine and study its morphology in different postures. There is increasing evidence that normal cervical spinal alignment may vary from lordosis to neutral to kyphosis, or form S-shaped or reverse S-shaped curves. Standing, erect sitting, and natural sitting whole-spine radiographs were obtained from 26 consecutive patients without cervical spine pathology. Sagittal vertical axis (SVA), global cervical lordosis, lower cervical alignment C4-T1, C0-C2 angle, T1 slope, C0-C7 SVA and C2-7SVA, SVA, thoracic kyphosis, thoracolumbar junctional angle, lumbar lordosis, sacral slope, pelvic tilt, and pelvic incidence were measured. Statistical analysis was performed to elucidate differences in cervical alignment for all postures. Predictive values of T1 slope and SVA for cervical kyphosis were evaluated. Most patients (73.0%) do not have lordotic cervical alignment (C2-C7) upon standing (mean -0.6, standard deviation 11.1°). Lordosis increases significantly when transitioning from standing to erect sitting, as well as from erect to natural sitting (mean -17.2, standard deviation 12.1°). Transition from standing to natural sitting also produces concomitant increases in SVA (-8.8-65.2 mm) and T1-slope (17.4°-30.2°). T1 slope and SVA measured during standing significantly predicts angular cervical spine alignment in the same position. SVA < 10 mm significantly predicts C4-C7 kyphosis (P < 0.001), and to a lesser extent, C2-C7 kyphosis (P = 0.02). T1 slope <20° is both predictive of C2-C7 and C4-7 kyphosis (P = 0.001 and P = 0.023, respectively). For global cervical Cobb angle, T1 slope seems to be a more significant predictor of kyphosis than SVA (odds ratio 17.33, P = 0.001 vs odds ratio 11.67, P = 0.02, respectively). The cervical spine has variable normal morphology. Key determinants of its alignment include SVA and T1 slope

In-Flight Alignment Using H ∞ Filter for Strapdown INS on Aircraft

PubMed Central

Pei, Fu-Jun; Liu, Xuan; Zhu, Li

2014-01-01

In-flight alignment is an effective way to improve the accuracy and speed of initial alignment for strapdown inertial navigation system (INS). During the aircraft flight, strapdown INS alignment was disturbed by lineal and angular movements of the aircraft. To deal with the disturbances in dynamic initial alignment, a novel alignment method for SINS is investigated in this paper. In this method, an initial alignment error model of SINS in the inertial frame is established. The observability of the system is discussed by piece-wise constant system (PWCS) theory and observable degree is computed by the singular value decomposition (SVD) theory. It is demonstrated that the system is completely observable, and all the system state parameters can be estimated by optimal filter. Then a H ∞ filter was designed to resolve the uncertainty of measurement noise. The simulation results demonstrate that the proposed algorithm can reach a better accuracy under the dynamic disturbance condition. PMID:24511300

In-flight alignment using H ∞ filter for strapdown INS on aircraft.

PubMed

Pei, Fu-Jun; Liu, Xuan; Zhu, Li

2014-01-01

In-flight alignment is an effective way to improve the accuracy and speed of initial alignment for strapdown inertial navigation system (INS). During the aircraft flight, strapdown INS alignment was disturbed by lineal and angular movements of the aircraft. To deal with the disturbances in dynamic initial alignment, a novel alignment method for SINS is investigated in this paper. In this method, an initial alignment error model of SINS in the inertial frame is established. The observability of the system is discussed by piece-wise constant system (PWCS) theory and observable degree is computed by the singular value decomposition (SVD) theory. It is demonstrated that the system is completely observable, and all the system state parameters can be estimated by optimal filter. Then a H ∞ filter was designed to resolve the uncertainty of measurement noise. The simulation results demonstrate that the proposed algorithm can reach a better accuracy under the dynamic disturbance condition.

Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

NASA Astrophysics Data System (ADS)

Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

2016-03-01

Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

Wavefront error sensing

NASA Technical Reports Server (NTRS)

Tubbs, Eldred F.

1986-01-01

A two-step approach to wavefront sensing for the Large Deployable Reflector (LDR) was examined as part of an effort to define wavefront-sensing requirements and to determine particular areas for more detailed study. A Hartmann test for coarse alignment, particularly segment tilt, seems feasible if LDR can operate at 5 microns or less. The direct measurement of the point spread function in the diffraction limited region may be a way to determine piston error, but this can only be answered by a detailed software model of the optical system. The question of suitable astronomical sources for either test must also be addressed.

Occipital and external acoustic meatus to axis angle as a predictor of the oropharyngeal space in healthy volunteers: a novel parameter for craniocervical junction alignment.

PubMed

Morizane, Kazuaki; Takemoto, Mitsuru; Neo, Masashi; Fujibayashi, Shunsuke; Otsuki, Bungo; Kawata, Tomotoshi; Matsuda, Shuichi

2018-05-01

The occipito-C2 angle (O-C2a) influences the oropharyngeal space. However, O-C2a has several limitations. There is no normal value of O-C2a because of the wide individual variations, and O-C2a does not reflect translation of the cranium to the axis, another factor influencing the oropharyngeal space in patients with atlantoaxial subluxation. The objective of this study was to propose a novel parameter that accounts for craniocervical junction alignment (CJA) and the oropharyngeal space. This is a post hoc analysis of craniocervical radiological parameters from another study. Forty healthy volunteers were included in the study. Craniocervical measurement parameters included the occipital and external acoustic meatus to axis angle (O-EAa), the C2 tilting angle (C2Ta), O-C2a, and the anterior-posterior distance of the narrowest oropharyngeal airway space (nPAS). We collected 40 healthy volunteers' lateral cervical radiographs in neutral, flexion, extension, protrusion, and retraction positions. We measured O-C2a, C2Ta (formed by the inferior end plate of C2 and a line connecting the external acoustic meatus and the midpoint of the inferior end plate of C2 [EA-line]), O-EAa (formed by the McGregor line and the EA-line), and nPAS. We evaluated the inter-rater and intrarater reliability of O-EAa and C2Ta, and the associations between each of the measured parameters. The inter-rater and intrarater reliabilities of measuring O-EAa and C2Ta were excellent. The neutral position O-EAa values remained in a narrower range (mean±standard deviation, 90.0°±5.0°) than O-C2a (15.6°±6.7°) (Levene test of equality of variances, p=.044). In the linear mixed-effects models, sex, O-C2a, C2Ta, and O-EAa were significantly associated with nPAS. The marginal R 2 values for the mixed-effect models, which express the variance explained by fixed effects, were 0.605 and 0.632 for the O-C2a and O-EAa models, respectively. In all models, the subaxial alignment (C2-C6a) had no significant

North error estimation based on solar elevation errors in the third step of sky-polarimetric Viking navigation.

PubMed

Száz, Dénes; Farkas, Alexandra; Barta, András; Kretzer, Balázs; Egri, Ádám; Horváth, Gábor

2016-07-01

The theory of sky-polarimetric Viking navigation has been widely accepted for decades without any information about the accuracy of this method. Previously, we have measured the accuracy of the first and second steps of this navigation method in psychophysical laboratory and planetarium experiments. Now, we have tested the accuracy of the third step in a planetarium experiment, assuming that the first and second steps are errorless. Using the fists of their outstretched arms, 10 test persons had to estimate the elevation angles (measured in numbers of fists and fingers) of black dots (representing the position of the occluded Sun) projected onto the planetarium dome. The test persons performed 2400 elevation estimations, 48% of which were more accurate than ±1°. We selected three test persons with the (i) largest and (ii) smallest elevation errors and (iii) highest standard deviation of the elevation error. From the errors of these three persons, we calculated their error function, from which the North errors (the angles with which they deviated from the geographical North) were determined for summer solstice and spring equinox, two specific dates of the Viking sailing period. The range of possible North errors Δ ω N was the lowest and highest at low and high solar elevations, respectively. At high elevations, the maximal Δ ω N was 35.6° and 73.7° at summer solstice and 23.8° and 43.9° at spring equinox for the best and worst test person (navigator), respectively. Thus, the best navigator was twice as good as the worst one. At solstice and equinox, high elevations occur the most frequently during the day, thus high North errors could occur more frequently than expected before. According to our findings, the ideal periods for sky-polarimetric Viking navigation are immediately after sunrise and before sunset, because the North errors are the lowest at low solar elevations.

North error estimation based on solar elevation errors in the third step of sky-polarimetric Viking navigation

PubMed Central

Száz, Dénes; Farkas, Alexandra; Barta, András; Kretzer, Balázs; Egri, Ádám

2016-01-01

The theory of sky-polarimetric Viking navigation has been widely accepted for decades without any information about the accuracy of this method. Previously, we have measured the accuracy of the first and second steps of this navigation method in psychophysical laboratory and planetarium experiments. Now, we have tested the accuracy of the third step in a planetarium experiment, assuming that the first and second steps are errorless. Using the fists of their outstretched arms, 10 test persons had to estimate the elevation angles (measured in numbers of fists and fingers) of black dots (representing the position of the occluded Sun) projected onto the planetarium dome. The test persons performed 2400 elevation estimations, 48% of which were more accurate than ±1°. We selected three test persons with the (i) largest and (ii) smallest elevation errors and (iii) highest standard deviation of the elevation error. From the errors of these three persons, we calculated their error function, from which the North errors (the angles with which they deviated from the geographical North) were determined for summer solstice and spring equinox, two specific dates of the Viking sailing period. The range of possible North errors ΔωN was the lowest and highest at low and high solar elevations, respectively. At high elevations, the maximal ΔωN was 35.6° and 73.7° at summer solstice and 23.8° and 43.9° at spring equinox for the best and worst test person (navigator), respectively. Thus, the best navigator was twice as good as the worst one. At solstice and equinox, high elevations occur the most frequently during the day, thus high North errors could occur more frequently than expected before. According to our findings, the ideal periods for sky-polarimetric Viking navigation are immediately after sunrise and before sunset, because the North errors are the lowest at low solar elevations. PMID:27493566

Error analysis and corrections to pupil diameter measurements with Langley Research Center's oculometer

NASA Technical Reports Server (NTRS)

Fulton, C. L.; Harris, R. L., Jr.

1980-01-01

Factors that can affect oculometer measurements of pupil diameter are: horizontal (azimuth) and vertical (elevation) viewing angle of the pilot; refraction of the eye and cornea; changes in distance of eye to camera; illumination intensity of light on the eye; and counting sensitivity of scan lines used to measure diameter, and output voltage. To estimate the accuracy of the measurements, an artificial eye was designed and a series of runs performed with the oculometer system. When refraction effects are included, results show that pupil diameter is a parabolic function of the azimuth angle similar to the cosine function predicted by theory: this error can be accounted for by using a correction equation, reducing the error from 6% to 1.5% of the actual diameter. Elevation angle and illumination effects were found to be negligible. The effects of counting sensitivity and output voltage can be calculated directly from system documentation. The overall accuracy of the unmodified system is about 6%. After correcting for the azimuth angle errors, the overall accuracy is approximately 2%.

Unique patellofemoral alignment in a patient with a symptomatic bipartite patella.

PubMed

Ishikawa, Masakazu; Adachi, Nobuo; Deie, Masataka; Nakamae, Atsuo; Nakasa, Tomoyuki; Kamei, Goki; Takazawa, Kobun; Ochi, Mitsuo

2016-01-01

A symptomatic bipartite patella is rarely seen in athletic adolescents or young adults in daily clinical practice. To date, only a limited number of studies have focused on patellofemoral alignment. The current study revealed a unique patellofemoral alignment in a patient with a symptomatic bipartite patella. Twelve patients with 12 symptomatic bipartite patellae who underwent arthroscopic vastus lateralis release (VLR) were investigated (10 males and two females, age: 15.7±4.4years). The radiographic data of contralateral intact and affected knees were reviewed retrospectively. From the lateral- and skyline-view imaging, the following parameters were measured: the congruence angle (CA), the lateral patellofemoral angle (LPA), and the Caton-Deschamps index (CDI). As an additional parameter, the bipartite fragment angle (BFA) was evaluated against the main part of the patella in the skyline view. Compared with the contralateral side, the affected patellae were significantly medialized and laterally tilted (CA: P=0.019; LPA: P=0.016), although there was no significant difference in CDI (P=0.877). This patellar malalignment was found to significantly change after VLR (CA: P=0.001; LPA: P=0.003) and the patellar height was significantly lower than in the preoperative condition (P=0.016). In addition, the BFA significantly shifted to a higher degree after operation (P=0.001). Patients with symptomatic bipartite patellae presented significantly medialized and laterally tilted patellae compared with the contralateral intact side. This malalignment was corrected by VLR, and the alignment of the bipartite fragment was also significantly changed. Level IV, case series. Copyright © 2015 Elsevier B.V. All rights reserved.

First-order approximation error analysis of Risley-prism-based beam directing system.

PubMed

Zhao, Yanyan; Yuan, Yan

2014-12-01

To improve the performance of a Risley-prism system for optical detection and measuring applications, it is necessary to be able to determine the direction of the outgoing beam with high accuracy. In previous works, error sources and their impact on the performance of the Risley-prism system have been analyzed, but their numerical approximation accuracy was not high. Besides, pointing error analysis of the Risley-prism system has provided results for the case when the component errors, prism orientation errors, and assembly errors are certain. In this work, the prototype of a Risley-prism system was designed. The first-order approximations of the error analysis were derived and compared with the exact results. The directing errors of a Risley-prism system associated with wedge-angle errors, prism mounting errors, and bearing assembly errors were analyzed based on the exact formula and the first-order approximation. The comparisons indicated that our first-order approximation is accurate. In addition, the combined errors produced by the wedge-angle errors and mounting errors of the two prisms together were derived and in both cases were proved to be the sum of errors caused by the first and the second prism separately. Based on these results, the system error of our prototype was estimated. The derived formulas can be implemented to evaluate beam directing errors of any Risley-prism beam directing system with a similar configuration.

Tilt error in cryospheric surface radiation measurements at high latitudes: a model study

NASA Astrophysics Data System (ADS)

Bogren, Wiley Steven; Faulkner Burkhart, John; Kylling, Arve

2016-03-01

We have evaluated the magnitude and makeup of error in cryospheric radiation observations due to small sensor misalignment in in situ measurements of solar irradiance. This error is examined through simulation of diffuse and direct irradiance arriving at a detector with a cosine-response fore optic. Emphasis is placed on assessing total error over the solar shortwave spectrum from 250 to 4500 nm, as well as supporting investigation over other relevant shortwave spectral ranges. The total measurement error introduced by sensor tilt is dominated by the direct component. For a typical high-latitude albedo measurement with a solar zenith angle of 60°, a sensor tilted by 1, 3, and 5° can, respectively introduce up to 2.7, 8.1, and 13.5 % error into the measured irradiance and similar errors in the derived albedo. Depending on the daily range of solar azimuth and zenith angles, significant measurement error can persist also in integrated daily irradiance and albedo. Simulations including a cloud layer demonstrate decreasing tilt error with increasing cloud optical depth.

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

PubMed

Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

2009-07-01

The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

Design and fabrication of a self-aligned parallel-plate-type silicon micromirror minimizing the effect of misalignment

NASA Astrophysics Data System (ADS)

Yoo, Byung-Wook; Park, Jae-Hyoung; Jin, Joo-Young; Jang, Yun-Ho; Kim, Yong-Kweon

2009-05-01

This paper describes a self-alignment method whereby a mirror actuation voltage, corresponding to a specific tilting angle, is unvarying in terms of misalignment during fabrication. A deep silicon etching process is proposed to penetrate the top silicon layer (the micromirror layer) and an amorphous silicon layer (the addressing electrode layer) together, through an aluminum mask pattern, in order to minimize the misalignment effect on the micromirror actuation. The size of a fabricated mirror plate is 250 × 250 × 4 µm3. A pair of amorphous silicon electrodes under the mirror plate is about half the size of the mirror plate individually. Numerical analysis associated with calculating the pull-in voltage and the bonding misalignment is performed to verify the self-alignment concepts focused upon in this paper. Curves of the applied voltage versus the tilt angle of the self-aligned micromirror are observed using a position sensing detector in order to compare the measurement results with MATLAB analysis of the expected static deflections. Although a 3.7 µm misalignment is found between the mirror plate and the electrodes, in the direction perpendicular to the shallow trench of the electrodes, before the self-alignment process, the measured pull-in voltage has been found to be 103.4 V on average; this differs from the pull-in voltage of a perfectly aligned micromirror by only 0.67%. Regardless of the unpredictable misalignments in repetitive photolithography and bonding, the tilting angles corresponding to the driving voltages are proved to be uniform along the single axis as well as conform to the results of analytical analysis.

Measuring contact angle and meniscus shape with a reflected laser beam.

PubMed

Eibach, T F; Fell, D; Nguyen, H; Butt, H J; Auernhammer, G K

2014-01-01

Side-view imaging of the contact angle between an extended planar solid surface and a liquid is problematic. Even when aligning the view perfectly parallel to the contact line, focusing one point of the contact line is not possible. We describe a new measurement technique for determining contact angles with the reflection of a widened laser sheet on a moving contact line. We verified this new technique measuring the contact angle on a cylinder, rotating partially immersed in a liquid. A laser sheet is inclined under an angle φ to the unperturbed liquid surface and is reflected off the meniscus. Collected on a screen, the reflection image contains information to determine the contact angle. When dividing the laser sheet into an array of laser rays by placing a mesh into the beam path, the shape of the meniscus can be reconstructed from the reflection image. We verified the method by measuring the receding contact angle versus speed for aqueous cetyltrimethyl ammonium bromide solutions on a smooth hydrophobized as well as on a rough polystyrene surface.

Measuring contact angle and meniscus shape with a reflected laser beam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eibach, T. F.; Nguyen, H.; Butt, H. J.

2014-01-15

Side-view imaging of the contact angle between an extended planar solid surface and a liquid is problematic. Even when aligning the view perfectly parallel to the contact line, focusing one point of the contact line is not possible. We describe a new measurement technique for determining contact angles with the reflection of a widened laser sheet on a moving contact line. We verified this new technique measuring the contact angle on a cylinder, rotating partially immersed in a liquid. A laser sheet is inclined under an angle φ to the unperturbed liquid surface and is reflected off the meniscus. Collectedmore » on a screen, the reflection image contains information to determine the contact angle. When dividing the laser sheet into an array of laser rays by placing a mesh into the beam path, the shape of the meniscus can be reconstructed from the reflection image. We verified the method by measuring the receding contact angle versus speed for aqueous cetyltrimethyl ammonium bromide solutions on a smooth hydrophobized as well as on a rough polystyrene surface.« less

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

PubMed

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. Copyright © 2015 Elsevier Inc. All rights reserved.

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law

PubMed Central

Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

2015-01-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment

PubMed Central

DeBlasio, Dan

2013-01-01

Abstract We develop a novel and general approach to estimating the accuracy of multiple sequence alignments without knowledge of a reference alignment, and use our approach to address a new task that we call parameter advising: the problem of choosing values for alignment scoring function parameters from a given set of choices to maximize the accuracy of a computed alignment. For protein alignments, we consider twelve independent features that contribute to a quality alignment. An accuracy estimator is learned that is a polynomial function of these features; its coefficients are determined by minimizing its error with respect to true accuracy using mathematical optimization. Compared to prior approaches for estimating accuracy, our new approach (a) introduces novel feature functions that measure nonlocal properties of an alignment yet are fast to evaluate, (b) considers more general classes of estimators beyond linear combinations of features, and (c) develops new regression formulations for learning an estimator from examples; in addition, for parameter advising, we (d) determine the optimal parameter set of a given cardinality, which specifies the best parameter values from which to choose. Our estimator, which we call Facet (for “feature-based accuracy estimator”), yields a parameter advisor that on the hardest benchmarks provides more than a 27% improvement in accuracy over the best default parameter choice, and for parameter advising significantly outperforms the best prior approaches to assessing alignment quality. PMID:23489379

THE BANANA PROJECT. IV. TWO ALIGNED STELLAR ROTATION AXES IN THE YOUNG ECCENTRIC BINARY SYSTEM EP CRUCIS: PRIMORDIAL ORIENTATION AND TIDAL ALIGNMENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Albrecht, Simon; Winn, Joshua N.; Setiawan, Johny

With observations of the EP Cru system, we continue our series of measurements of spin-orbit angles in eclipsing binary star systems, the BANANA project (Binaries Are Not Always Neatly Aligned). We find a close alignment between the sky projections of the rotational and orbital angular momentum vectors for both stars ({beta}{sub p} = -1. Degree-Sign 8 {+-} 1. Degree-Sign 6 and |{beta}{sub s}| < 17 Degree-Sign ). We also derive precise absolute dimensions and stellar ages for this system. The EP Cru and DI Her systems provide an interesting comparison: they have similar stellar types and orbital properties, but DImore » Her is younger and has major spin-orbit misalignments, raising the question of whether EP Cru also had a large misalignment at an earlier phase of evolution. We show that tidal dissipation is an unlikely explanation for the good alignment observed today, because realignment happens on the same timescale as spin-orbit synchronization, and the stars in EP Cru are far from synchronization (they are spinning nine times too quickly). Therefore it seems that some binaries form with aligned axes, while other superficially similar binaries are formed with misaligned axes.« less

Control of Angular Intervals for Angle-Multiplexed Holographic Memory

NASA Astrophysics Data System (ADS)

Kinoshita, Nobuhiro; Muroi, Tetsuhiko; Ishii, Norihiko; Kamijo, Koji; Shimidzu, Naoki

2009-03-01

In angle-multiplexed holographic memory, the full width at half maximum of the Bragg selectivity curves is dependent on the angle formed between the medium and incident laser beams. This indicates the possibility of high density and high multiplexing number by varying the angular intervals between adjacent holograms. We propose an angular interval scheduling for closely stacking holograms into medium even when the angle range is limited. We obtained bit error rates of the order of 10-4 under the following conditions: medium thickness of 1 mm, laser beam wavelength of 532 nm, and angular multiplexing number of 300.

Discovery of the Kinematic Alignment of Early-type Galaxies in the Virgo Cluster

NASA Astrophysics Data System (ADS)

Kim, Suk; Jeong, Hyunjin; Lee, Jaehyun; Lee, Youngdae; Joo, Seok-Joo; Kim, Hak-Sub; Rey, Soo-Chang

2018-06-01

Using the kinematic position angles (PAkin), an accurate indicator for the spin axis of a galaxy, obtained from the ATLAS3D integral-field-unit (IFU) spectroscopic data, we discovered that 57 Virgo early-type galaxies tend to prefer the specific PAkin values of 20° and 100°, suggesting that they are kinematically aligned with each other. These kinematic alignment angles are further associated with the directions of the two distinct axes of the Virgo cluster extending east–west and north–south, strongly suggesting that the two distinct axes are the filamentary structures within the cluster as a trace of infall patterns of galaxies. Given that the spin axis of a massive early-type galaxy does not change easily even in clusters from the hydrodynamic simulations, Virgo early-type galaxies are likely to fall into the cluster along the filamentary structures while maintaining their angular momentum. This implies that many early-type galaxies in clusters are formed in filaments via major mergers before subsequently falling into the cluster. Investigating the kinematic alignment in other clusters will allow us to understand the formation of galaxy clusters and early-type galaxies.

Instability of ocular alignment in childhood esotropia.

PubMed

Christiansen, Stephen P; Chandler, Danielle L; Holmes, Jonathan M; Arnold, Robert W; Birch, Eileen; Dagi, Linda R; Hoover, Darren L; Klimek, Deborah L; Melia, B Michele; Paysse, Evelyn; Repka, Michael X; Suh, Donny W; Ticho, Benjamin H; Wallace, David K; Weaver, Richard Grey

2008-12-01

Instability of ocular alignment may cause surgeons to delay surgical correction of childhood esotropia. The authors investigated the stability of ocular alignment over 18 weeks in children with infantile esotropia (IET), acquired nonaccommodative esotropia (ANAET), or acquired partially accommodative esotropia (APAET). Prospective, observational study. Two hundred thirty-three children aged 2 months to less than 5 years with IET, ANAET, or APAET of less than 6 months' duration. Ocular alignment was measured at baseline and at 6-week intervals for 18 weeks. Using definitions derived from a nested test-retest study and computer simulation modeling, ocular alignment was classified as unstable if there was a change of 15 prism diopters (PD) or more between any 2 of the 4 measurements, as stable if all 4 measurements were within 5 PD or less of one another, or as uncertain if neither criteria was met. Of those who completed all 3 follow-up visits within time windows for analysis, 27 (46%) of 59 subjects with IET had ocular alignment classified as unstable (95% confidence interval [CI], 33%-59%), 20% as stable (95% CI, 11%-33%), and 34% as uncertain (95% CI, 22%-47%). Thirteen (22%) of 60 subjects with ANAET had ocular alignment classified as unstable (95% CI, 12%-34%), 37% as stable (95% CI, 25%-50%), and 42% as uncertain (95% CI, 29%-55%). Six (15%) of 41 subjects with APAET had ocular alignment classified as unstable (95% CI, 6%-29%), 39% as stable (95% CI, 24%-56%), and 46% as uncertain (95% CI, 31%-63%). For IET, subjects who were older at presentation were less likely to have unstable angles than subjects who were younger at presentation (risk ratio for unstable vs stable per additional month of age, 0.85; 99% CI, 0.74-0.99). Ocular alignment instability is common in children with IET, ANAET, and APAET. The impact of this finding on the optimal timing for strabismus surgery in childhood esotropia awaits further study. The author(s) have no proprietary or commercial

An Incidence Loss Model for Wave Rotors with Axially Aligned Passages

NASA Technical Reports Server (NTRS)

Paxson, Daniel E.

1998-01-01

A simple mathematical model is described to account for the losses incurred when the flow in the duct (port) of a wave rotor is not aligned with the passages. The model, specifically for wave rotors with axially aligned passages, describes a loss mechanism which is sensitive to incident flow angle and Mach number. Implementation of the model in a one-dimensional CFD based wave rotor simulation is presented. Comparisons with limited experimental results are consistent with the model. Sensitivity studies are presented which highlight the significance of the incidence loss relative to other loss mechanisms in the wave rotor.

The effects of transverse rotation angle on compression and effective lever arm of prosthetic feet during simulated stance.

PubMed

Major, Matthew J; Howard, David; Jones, Rebecca; Twiste, Martin

2012-06-01

Unlike sagittal plane prosthesis alignment, few studies have observed the effects of transverse plane alignment on gait and prosthesis behaviour. Changes in transverse plane rotation angle will rotate the points of loading on the prosthesis during stance and may alter its mechanical behaviour. This study observed the effects of increasing the external transverse plane rotation angle, or toe-out, on foot compression and effective lever arm of three commonly prescribed prosthetic feet. The roll-over shape of a SACH, Flex and single-axis foot was measured at four external rotation angle conditions (0°, 5°, 7° and 12° relative to neutral). Differences in foot compression between conditions were measured as average distance between roll-over shapes. Increasing the transverse plane rotation angle did not affect foot compression. However, it did affect the effective lever arm, which was maximized with the 5° condition, although differences between conditions were small. Increasing the transverse plane rotation angle of prosthetic feet by up to 12° beyond neutral has minimal effects on their mechanical behaviour in the plane of walking progression during weight-bearing.