Science.gov

Sample records for alignment partial alignment

  1. Partial Automated Alignment and Integration System

    NASA Technical Reports Server (NTRS)

    Kelley, Gary Wayne (Inventor)

    2014-01-01

    The present invention is a Partial Automated Alignment and Integration System (PAAIS) used to automate the alignment and integration of space vehicle components. A PAAIS includes ground support apparatuses, a track assembly with a plurality of energy-emitting components and an energy-receiving component containing a plurality of energy-receiving surfaces. Communication components and processors allow communication and feedback through PAAIS.

  2. Partial face recognition: alignment-free approach.

    PubMed

    Liao, Shengcai; Jain, Anil K; Li, Stan Z

    2013-05-01

    Numerous methods have been developed for holistic face recognition with impressive performance. However, few studies have tackled how to recognize an arbitrary patch of a face image. Partial faces frequently appear in unconstrained scenarios, with images captured by surveillance cameras or handheld devices (e.g., mobile phones) in particular. In this paper, we propose a general partial face recognition approach that does not require face alignment by eye coordinates or any other fiducial points. We develop an alignment-free face representation method based on Multi-Keypoint Descriptors (MKD), where the descriptor size of a face is determined by the actual content of the image. In this way, any probe face image, holistic or partial, can be sparsely represented by a large dictionary of gallery descriptors. A new keypoint descriptor called Gabor Ternary Pattern (GTP) is also developed for robust and discriminative face recognition. Experimental results are reported on four public domain face databases (FRGCv2.0, AR, LFW, and PubFig) under both the open-set identification and verification scenarios. Comparisons with two leading commercial face recognition SDKs (PittPatt and FaceVACS) and two baseline algorithms (PCA+LDA and LBP) show that the proposed method, overall, is superior in recognizing both holistic and partial faces without requiring alignment. PMID:23520259

  3. The partially aligned gradient instability in the ionosphere

    NASA Technical Reports Server (NTRS)

    Whitehead, J. D.

    1976-01-01

    Ionization irregularities which are almost but not exactly aligned along the magnetic field may grow much more rapidly than purely aligned irregularities in the presence of a background gradient of ionization and current flow. The stability of these irregularities is considered, taking into account the finite thickness of the gradient and shear in the ion motion. It is shown in particular that the normal E region of the ionosphere is usually stable, whereas sporadic E is often unstable, and this may limit the compression of metallic ions to form such layers. The F region may sometimes be unstable. Temperate zone conditions are considered throughout.

  4. Alignment validation

    SciTech Connect

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

    The four experiments, ALICE, ATLAS, CMS and LHCb are currently under constructionat CERN. They will study the products of proton-proton collisions at the Large Hadron Collider. All experiments are equipped with sophisticated tracking systems, unprecedented in size and complexity. Full exploitation of both the inner detector andthe muon system requires an accurate alignment of all detector elements. Alignmentinformation is deduced from dedicated hardware alignment systems and the reconstruction of charged particles. However, the system is degenerate which means the data is insufficient to constrain all alignment degrees of freedom, so the techniques are prone to converging on wrong geometries. This deficiency necessitates validation and monitoring of the alignment. An exhaustive discussion of means to validate is subject to this document, including examples and plans from all four LHC experiments, as well as other high energy experiments.

  5. Alignment fixture

    DOEpatents

    Bell, Grover C.; Gibson, O. Theodore

    1980-01-01

    A part alignment fixture is provided which may be used for precise variable lateral and tilt alignment relative to the fixture base of various shaped parts. The fixture may be used as a part holder for machining or inspection of parts or alignment of parts during assembly and the like. The fixture includes a precisely machined diameter disc-shaped hub adapted to receive the part to be aligned. The hub is nested in a guide plate which is adapted to carry two oppositely disposed pairs of positioning wedges so that the wedges may be reciprocatively positioned by means of respective micrometer screws. The sloping faces of the wedges contact the hub at respective quadrants of the hub periphery. The lateral position of the hub relative to the guide plate is adjusted by positioning the wedges with the associated micrometer screws. The tilt of the part is adjusted relative to a base plate, to which the guide plate is pivotally connected by means of a holding plate. Two pairs of oppositely disposed wedges are mounted for reciprocative lateral positioning by means of separate micrometer screws between flanges of the guide plate and the base plate. Once the wedges are positioned to achieve the proper tilt of the part or hub on which the part is mounted relative to the base plate, the fixture may be bolted to a machining, inspection, or assembly device.

  6. ALIGNING JIG

    DOEpatents

    Culver, J.S.; Tunnell, W.C.

    1958-08-01

    A jig or device is described for setting or aligning an opening in one member relative to another member or structure, with a predetermined offset, or it may be used for measuring the amount of offset with which the parts have previously been sct. This jig comprises two blocks rabbeted to each other, with means for securing thc upper block to the lower block. The upper block has fingers for contacting one of the members to be a1igmed, the lower block is designed to ride in grooves within the reference member, and calibration marks are provided to determine the amount of offset. This jig is specially designed to align the collimating slits of a mass spectrometer.

  7. 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,

  8. Image alignment

    DOEpatents

    Dowell, Larry Jonathan

    2014-04-22

    Disclosed is a method and device for aligning at least two digital images. An embodiment may use frequency-domain transforms of small tiles created from each image to identify substantially similar, "distinguishing" features within each of the images, and then align the images together based on the location of the distinguishing features. To accomplish this, an embodiment may create equal sized tile sub-images for each image. A "key" for each tile may be created by performing a frequency-domain transform calculation on each tile. A information-distance difference between each possible pair of tiles on each image may be calculated to identify distinguishing features. From analysis of the information-distance differences of the pairs of tiles, a subset of tiles with high discrimination metrics in relation to other tiles may be located for each image. The subset of distinguishing tiles for each image may then be compared to locate tiles with substantially similar keys and/or information-distance metrics to other tiles of other images. Once similar tiles are located for each image, the images may be aligned in relation to the identified similar tiles.

  9. Easy axis alignment of chemically partially ordered FePt nanoparticles

    SciTech Connect

    Kang, Shishou; Jia Zhiyong; Shi, Shifan; Nikles, David E.; Harrell, J.W.

    2005-02-07

    Partially ordered Fe{sub 53}Pt{sub 47} nanoparticles with size around 8 nm were prepared by the simultaneous decomposition of iron pentacarbonyl and platinum acetylacetonate. The high boiling point chemical, hexadecylamine, was used as a solvent, and 1-adamantanecarboxylic acid was used as a stabilizer. X-ray diffraction measurements reveal that as-made FePt particles were partially transformed into the ordered L1{sub 0} phase with some weak superlattice peaks. The room-temperature hysteresis loop and remanence curve suggest a broad distribution of anisotropies in the partially ordered particles. By coating the partially ordered FePt nanoparticles with a polyvinylchloride polymer binder, the particles could be re-dispersed in cyclohexanone. Furthermore, the easy axis of the particles coated with the polyvinylchloride polymer binder could be aligned under an external field. Easy axis alignment was confirmed from both alternating gradient magnetometer and x-ray diffraction measurements.

  10. Partial alignment and measurement of residual dipolar couplings of proteins under high hydrostatic pressure

    PubMed Central

    Fu, Yinan; Wand, A. Joshua

    2013-01-01

    High-pressure NMR spectroscopy has emerged as a complementary approach for investigating various structural and thermodynamic properties of macromolecules. Noticeably absent from the array of experimental restraints that have been employed to characterize protein structures at high hydrostatic pressure is the residual dipolar coupling, which requires the partial alignment of the macromolecule of interest. Here we examine five alignment media that are commonly used at ambient pressure for this purpose. We find that the spontaneous alignment of Pf1 phage, d(GpG) and a C12E5/n-hexnanol mixture in a magnetic field is preserved under high hydrostatic pressure. However, DMPC/ DHPC bicelles and collagen gel are found to be unsuitable. Evidence is presented to demonstrate that pressure-induced structural changes can be identified using the residual dipolar coupling. PMID:23807390

  11. 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.

  12. Investigation of Accelerated Partial Breast Patient Alignment and Treatment With Helical Tomotherapy Unit

    SciTech Connect

    Langen, Katja M. Buchholz, Daniel J.; Burch, Doug R. C.; Burkavage, Rob C.; Limaye, Arti U.; Meeks, Sanford L.; Kupelian, Patrick A.; Ruchala, Kenneth J.; Haimerl, Jason; Henderson, Doug; Olivera, Gustavo H.

    2008-03-15

    Purpose: To determine the precision of megavoltage computed tomography (MVCT)-based alignment of the seroma cavity for patients undergoing partial breast irradiation; and to determine whether accelerated partial breast irradiation (APBI) plans can be generated for TomoTherapy deliveries that meet the National Surgical Adjuvant Breast and Bowel Project (NSABP) B-39/Radiation Therapy Oncology Group (RTOG) 0413 protocol guidelines for target coverage and normal tissue dose limitations. Methods and Materials: We obtained 50 MVCT images from 10 patients. An interuser study was designed to assess the alignment precision. Using a standard helical and a fixed beam prototype ('topotherapy') optimizer, two APBI plans for each patient were developed. Results: The precision of the MVCT-based seroma cavity alignment was better than 2 mm if averaged over the patient population. Both treatment techniques could be used to generate acceptable APBI plans for patients that fulfilled the recommended NSABP B-39/RTOG-0413 selection criteria. For plans of comparable treatment time, the conformation of the prescription dose to the target was greater for helical deliveries, while the ipsilateral lung dose was significantly reduced for the topotherapy plans. Conclusions: The inherent volumetric imaging capabilities of a TomoTherapy Hi-Art unit allow for alignment of patients undergoing partial breast irradiation that is determined from the visibility of the seroma cavity on the MVCT image. The precision of the MVCT-based alignment was better than 2 mm ({+-} standard deviation) when averaged over the patient population. Using the NSABP B-39/RTOG-0413 guidelines, acceptable APBI treatment plans can be generated using helical- or topotherapy-based delivery techniques.

  13. Enhancing field emission performance of aligned Si nanowires via in situ partial oxidization.

    PubMed

    Qian, Zhongjian; Liu, Xianyun; Yang, Ye; Yin, Qiaoxia

    2014-08-01

    Partially oxidized Si nanowire (NW) arrays have been achieved via a combinatorial process of selectively etching Si wafer to obtain vertically aligned single crystalline Si NW arrays and subsequent in situ partially oxidizing the as-etched bare Si NWs. The resultant Si products are Si-SiOx nanocable-like structures consisting of single-crystalline Si NW inner cores and outer shells of insulating SiOx. Field emission measurements demonstrate that surface partial oxidization enhances the field emission current of the as-etched bare Si NWs effectively, which can be ascribed to the outer shell of insulating SiOx that has small electron affinity (0.6-0.8 eV) and can protect Si NW inner cores. The results indicate that the partially oxidized Si NW arrays would act as the excellent field emitters in the future vacuum micro- and nano-electronic devices. PMID:25936088

  14. DNA Align Editor: DNA Alignment Editor Tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The SNPAlignEditor is a DNA sequence alignment editor that runs on Windows platforms. The purpose of the program is to provide an intuitive, user-friendly tool for manual editing of multiple sequence alignments by providing functions for input, editing, and output of nucleotide sequence alignments....

  15. Implement of Digital Moire technique on DSP for alignment of partial compensation interferometer

    NASA Astrophysics Data System (ADS)

    Tian, Yuhan; QunHao; YaoHu; Wang, Shaopu; Li, Tengfei; Wang, Jingxian

    2016-01-01

    Digital Moiré technique is adopted in partial compensation interferometer (PCI) for high-precision testing of figure error of the aspheric surfaces. The figure error of the measured aspheric is obtained by a series of calculation with the real interferogram and ideal interferograms generated by computer. The dense interference fringes at the exit pupil make it difficult to align the PCI. On the contrary, digital Moire fringes composed from real and ideal interferograms are sparse and corresponding to the figure error of the measured aspheric, making it easier to align the PCI. Generally, digital Moire technique is processed on the computer, resulting in slow processing speed and difficult display in real time. Digital Signal Processor (DSP) can be used to implement digital Moire technique and display digital Moire fringes in real time with its powerful processing capacity. In this paper, digital Moire technique is implemented on the TMS320C6455 DSP. The hardware system consists of a DSP module, a CCD camera and a monitor. Finally we experimentally obtain the digital Moire image, and further analyze how to align the PCI theoretically.

  16. 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.

    2011-01-01

    The future space-based gravitational wave detector LISA will be able to measure parameters of coalescing massive black hole binaries, often to extremely high accuracy. Previous work has demonstrated that the black hole spins can have a strong impact on the accuracy of parameter measurement. Relativistic spin-induced precession modulates the waveform in a manner which can break degeneracies between parameters, in principle significantly improving how well they are measured. Recent studies have indicated, however, that spin precession may be weak for an important subset of astrophysical binary black holes: those in which the spins are aligned due to interactions with gas. In this paper, we examine how well a binary's parameters can be measured when its spins are partially aligned and compare results using waveforms that include higher post-Newtonian harmonics to those that are truncated at leading quadrupole order. We find that the weakened precession can substantially degrade parameter estimation, particularly for the "extrinsic" parameters sky position and distance. Absent higher harmonics, LISA typically localizes the sky position of a nearly aligned binary about an order of magnitude less accurately than one for which the spin orientations are random. Our knowledge of a source's sky position will thus be worst for the gas-rich systems which are most likely to produce electromagnetic counterparts. Fortunately, higher harmonics of the waveform can make up for this degradation. By including harmonics beyond the quadrupole in our waveform model, we find that the accuracy with which most of the binary's parameters are measured can be substantially improved. In some cases, the improvement is such that they are measured almost as well as when the binary spins are randomly aligned.

  17. Grain-scale alignment of melt in sheared partially molten rocks: implications for viscous anisotropy

    NASA Astrophysics Data System (ADS)

    Pec, Matej; Quintanilla-Terminel, Alejandra; Holtzman, Benjamin; Zimmerman, Mark; Kohlstedt, David

    2016-04-01

    Presence of melt significantly influences rheological properties of partially molten rocks by providing fast diffusional pathways. Under stress, melt aligns at the grain scale and this alignment induces viscous anisotropy in the deforming aggregate. One of the consequences of viscous anisotropy is melt segregation into melt-rich sheets oriented at low angle to the shear plane on much larger scales than the grain scale. The magnitude and orientation of viscous anisotropy with respect to the applied stress are important parameters for constitutive models (Takei and Holtzman 2009) that must be constrained by experimental studies. In this contribution, we analyze the shape preferred orientation (SPO) of individual grain-scale melt pockets in deformed partially molten mantle rocks. The starting materials were obtained by isostatically hot-pressing olivine + basalt and olivine + chromite + basalt powders. These partially molten rocks were deformed in general shear or torsion at a confining pressure, Pc = 300 MPa, temperature, T = 1200° - 1250° C, and strain rates of 10‑3 - 10‑5 s‑1to finite shear strains, γ, of 0.5 - 5. After the experiment, high resolution backscattered electron images were obtained using a SEM equipped with a field emission gun. Individual melt pockets were segmented and their SPO analyzed using the paror and surfor methods and Fourier transforms (Heilbronner and Barret 2014). Melt segregation into melt-rich sheets inclined at 15° -20° antithetic with respect to the shear plane occurs in three-phase system (olivine + chromite + basalt) and in two-phase systems (olivine + basalt) twisted to high strain. The SPO of individual melt pockets within the melt-rich bands is moderately strong (b/a ≈ 0.8) and is always steeper (20° -40°) than the average melt-rich band orientation. In the two-phase system (olivine + basalt) sheared to lower strains, no distinct melt-rich sheets are observed. Individual grain-scale melt pockets are oriented at 45

  18. Nearest Alignment Space Termination

    2006-07-13

    Near Alignment Space Termination (NAST) is the Greengenes algorithm that matches up submitted sequences with the Greengenes database to look for similarities and align the submitted sequences based on those similarities.

  19. Onorbit IMU alignment error budget

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

    The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

  20. Shiva automatic pinhole alignment

    SciTech Connect

    Suski, G.J.

    1980-09-05

    This paper describes a computer controlled closed loop alignment subsystem for Shiva, which represents the first use of video sensors for large laser alignment at LLNL. The techniques used on this now operational subsystem are serving as the basis for all closed loop alignment on Nova, the 200 terawatt successor to Shiva.

  1. Fast statistical alignment.

    PubMed

    Bradley, Robert K; Roberts, Adam; Smoot, Michael; Juvekar, Sudeep; Do, Jaeyoung; Dewey, Colin; Holmes, Ian; Pachter, Lior

    2009-05-01

    We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches--yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/. PMID:19478997

  2. Girder Alignment Plan

    SciTech Connect

    Wolf, Zackary; Ruland, Robert; LeCocq, Catherine; Lundahl, Eric; Levashov, Yurii; Reese, Ed; Rago, Carl; Poling, Ben; Schafer, Donald; Nuhn, Heinz-Dieter; Wienands, Uli; /SLAC

    2010-11-18

    The girders for the LCLS undulator system contain components which must be aligned with high accuracy relative to each other. The alignment is one of the last steps before the girders go into the tunnel, so the alignment must be done efficiently, on a tight schedule. This note documents the alignment plan which includes efficiency and high accuracy. The motivation for girder alignment involves the following considerations. Using beam based alignment, the girder position will be adjusted until the beam goes through the center of the quadrupole and beam finder wire. For the machine to work properly, the undulator axis must be on this line and the center of the undulator beam pipe must be on this line. The physics reasons for the undulator axis and undulator beam pipe axis to be centered on the beam are different, but the alignment tolerance for both are similar. In addition, the beam position monitor must be centered on the beam to preserve its calibration. Thus, the undulator, undulator beam pipe, quadrupole, beam finder wire, and beam position monitor axes must all be aligned to a common line. All relative alignments are equally important, not just, for example, between quadrupole and undulator. We begin by making the common axis the nominal beam axis in the girder coordinate system. All components will be initially aligned to this axis. A more accurate alignment will then position the components relative to each other, without incorporating the girder itself.

  3. Gold Alignment and Internal Dissipation

    NASA Astrophysics Data System (ADS)

    Lazarian, A.

    1997-07-01

    The measures of mechanical alignment are obtained for both prolate and oblate grains whose temperatures are comparable to the grain kinetic energy divided by k, the Boltzmann constant. For such grains, the alignment of angular momentum, J, with the axis of maximal inertia, a, is only partial, which substantially alters the mechanical alignment as compared with the results obtained by Lazarian and Roberge, Hanany, & Messinger under the assumption of perfect alignment. We also describe Gold alignment when the Barnett dissipation is suppressed and derive an analytical expression that relates the measure of alignment to the parameters of grain nonsphericity and the direction of the gas-grain drift. This solution provides the lower limit for the measure of alignment, while the upper limit is given by the method derived by Lazarian. Using the results of a recent study of incomplete internal relaxation by Lazarian & Roberge, we find measures of alignment for the whole range of ratios of grain rotational energy to kTs, where Ts is the grain temperature. To describe alignment for mildly supersonic drifts, we suggest an analytical approach that provides good correspondence with the results of direct numerical simulations by Roberge, Hanany, & Messinger. We also extend our approach to account for simultaneous action of the Gold and Davis-Greenstein mechanisms.

  4. Partial slip effect on non-aligned stagnation point nanofluid over a stretching convective surface

    NASA Astrophysics Data System (ADS)

    Nadeem, S.; Rashid, Mehmood; Noreen Sher, Akbar

    2015-01-01

    The present study inspects the non-aligned stagnation point nano fluid over a convective surface in the presence of partial slip.Two types of base fluids namely water and kerosene are selected with Cu nanoparticles. The governing physical problem is presented and transformed into a system of coupled nonlinear differential equations using suitable similarity transformations. These equations are then solved numerically using midpoint integration scheme along with Richardson extrapolation via Maple. Impact of relevant physical parameters on the dimensionless velocity and temperature profiles are portrayed through graphs. Physical quantities such as local skin frictions co-efficient and Nusselt numbers are tabularized. It is detected from numerical computations that kerosene-based nano fluids have better heat transfer capability compared with water-based nanofluids. Moreover it is found that water-based nanofluids offer less resistance in terms of skin friction than kerosene-based fluid. In order to authenticate our present study, the calculated results are compared with the prevailing literature and a considerable agreement is perceived for the limiting case.

  5. Horizontal carbon nanotube alignment.

    PubMed

    Cole, Matthew T; Cientanni, Vito; Milne, William I

    2016-09-21

    The production of horizontally aligned carbon nanotubes offers a rapid means of realizing a myriad of self-assembled near-atom-scale technologies - from novel photonic crystals to nanoscale transistors. The ability to reproducibly align anisotropic nanostructures has huge technological value. Here we review the present state-of-the-art in horizontal carbon nanotube alignment. For both in and ex situ approaches, we quantitatively assess the reported linear packing densities alongside the degree of alignment possible for each of these core methodologies. PMID:27546174

  6. Orthodontics and Aligners

    MedlinePlus

    ... Repairing Chipped Teeth Teeth Whitening Tooth-Colored Fillings Orthodontics and Aligners Straighten teeth for a healthier smile. Orthodontics When consumers think about orthodontics, braces are the ...

  7. Alignability of Optical Interconnects

    NASA Astrophysics Data System (ADS)

    Beech, Russell Scott

    With the continuing drive towards higher speed, density, and functionality in electronics, electrical interconnects become inadequate. Due to optics' high speed and bandwidth, freedom from capacitive loading effects, and freedom from crosstalk, optical interconnects can meet more stringent interconnect requirements. But, an optical interconnect requires additional components, such as an optical source and detector, lenses, holographic elements, etc. Fabrication and assembly of an optical interconnect requires precise alignment of these components. The successful development and deployment of optical interconnects depend on how easily the interconnect components can be aligned and/or how tolerant the interconnect is to misalignments. In this thesis, a method of quantitatively specifying the relative difficulty of properly aligning an optical interconnect is described. Ways of using this theory of alignment to obtain design and packaging guidelines for optical interconnects are examined. The measure of the ease with which an optical interconnect can be aligned, called the alignability, uses the efficiency of power transfer as a measure of alignment quality. The alignability is related to interconnect package design through the overall cost measure, which depends upon various physical parameters of the interconnect, such as the cost of the components and the time required for fabrication and alignment. Through a mutual dependence on detector size, the relationship between an interconnect's alignability and its bandwidth, signal-to-noise ratio, and bit-error -rate is examined. The results indicate that a range of device sizes exists for which given performance threshold values are satisfied. Next, the alignability of integrated planar-optic backplanes is analyzed in detail. The resulting data show that the alignability can be optimized by varying the substrate thickness or the angle of reflection. By including the effects of crosstalk, in a multi-channel backplane, the

  8. Tidal alignment of galaxies

    NASA Astrophysics Data System (ADS)

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    2015-08-01

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact of smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.

  9. SPEAR3 Construction Alignment

    SciTech Connect

    LeCocq, Catherine; Banuelos, Cristobal; Fuss, Brian; Gaudreault, Francis; Gaydosh, Michael; Griffin, Levirt; Imfeld, Hans; McDougal, John; Perry, Michael; Rogers, Michael; /SLAC

    2005-08-17

    An ambitious seven month shutdown of the existing SPEAR2 synchrotron radiation facility was successfully completed in March 2004 when the first synchrotron light was observed in the new SPEAR3 ring, SPEAR3 completely replaced SPEAR2 with new components aligned on a new highly-flat concrete floor. Devices such as magnets and vacuum chambers had to be fiducialized and later aligned on girder rafts that were then placed into the ring over pre-aligned support plates. Key to the success of aligning this new ring was to ensure that the new beam orbit matched the old SPEAR2 orbit so that existing experimental beamlines would not have to be reoriented. In this presentation a pictorial summary of the Alignment Engineering Group's surveying tasks for the construction of the SPEAR3 ring is provided. Details on the networking and analysis of various surveys throughout the project can be found in the accompanying paper.

  10. Extracting Electron-Ion Differential Scattering Cross Sections for Partially Aligned Molecules by Laser-Induced Rescattering Photoelectron Spectroscopy

    NASA Astrophysics Data System (ADS)

    Okunishi, Misaki; Niikura, Hiromichi; Lucchese, R. R.; Morishita, Toru; Ueda, Kiyoshi

    2011-02-01

    We extract large-angle elastic differential cross sections (DCSs) for electrons scattering from partially aligned O2+ and CO2+ molecules using rescattering photoelectrons generated by infrared laser pulses. The extracted DCSs are in good agreement with those calculated theoretically, demonstrating that accurate DCSs for electron-ion scattering can be extracted from the laser-induced rescattering spectra, thus paving the way for dynamic imaging of chemical reactions by rescattering photoelectron spectroscopy.

  11. Precision alignment device

    DOEpatents

    Jones, N.E.

    1988-03-10

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

  12. Precision alignment device

    DOEpatents

    Jones, Nelson E.

    1990-01-01

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam.

  13. Hybrid vehicle motor alignment

    DOEpatents

    Levin, Michael Benjamin

    2001-07-03

    A rotor of an electric motor for a motor vehicle is aligned to an axis of rotation for a crankshaft of an internal combustion engine having an internal combustion engine and an electric motor. A locator is provided on the crankshaft, a piloting tool is located radially by the first locator to the crankshaft. A stator of the electric motor is aligned to a second locator provided on the piloting tool. The stator is secured to the engine block. The rotor is aligned to the crankshaft and secured thereto.

  14. Antares alignment gimbal positioner

    SciTech Connect

    Day, R.D.; Viswanathan, V.K.; Saxman, A.C.; Lujan, R.E.; Woodfin, G.L.; Sweatt, W.C.

    1981-01-01

    Antares is a 24-beam 40-TW carbon-dioxide (CO/sub 2/) laser fusion system currently under construction at the Los Alamos National Laboratory. The Antares alignment gimbal positioner (AGP) is an optomechanical instrument that will be used for target alignment and alignment of the 24 laser beams, as well as beam quality assessments. The AGP will be capable of providing pointing, focusing, and wavefront optical path difference, as well as aberration information at both helium-neon (He-Ne) and CO/sub 2/ wavelengths. It is designed to allow the laser beams to be aligned to any position within a 1-cm cube to a tolerance of 10 ..mu..m.

  15. EINSTEIN Cluster Alignments Revisited

    NASA Astrophysics Data System (ADS)

    Chambers, S. W.; Melott, A. L.; Miller, C. J.

    2000-12-01

    We have examined whether the major axes of rich galaxy clusters tend to point (in projection) toward their nearest neighboring cluster. We used the data of Ulmer, McMillan and Kowalski, who used x-ray morphology to define position angles. Our cluster samples, with well measured redshifts and updated positions, were taken from the MX Northern Abell Cluster Survey. The usual Kolmogorov-Smirnov test shows no significant alignment signal for nonrandom angles for all separations less than 100 Mpc/h. Refining the null hypothesis, however, with the Wilcoxon rank-sum test, reveals a high confidence signal for alignment. This confidence is highest when we restrict our sample to small nearest neighbor separations. We conclude that we have identified a more powerful tool for testing cluster-cluster alignments. Moreover, there is a strong signal in the data for alignment, consistent with a picture of hierarchical cluster formation in which matter falls into clusters along large scale filamentary structures.

  16. Pairwise Sequence Alignment Library

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprintmore » that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

  17. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  18. PDV Probe Alignment Technique

    SciTech Connect

    Whitworth, T L; May, C M; Strand, O T

    2007-10-26

    This alignment technique was developed while performing heterodyne velocimetry measurements at LLNL. There are a few minor items needed, such as a white card with aperture in center, visible alignment laser, IR back reflection meter, and a microscope to view the bridge surface. The work was performed on KCP flyers that were 6 and 8 mils wide. The probes used were Oz Optics manufactured with focal distances of 42mm and 26mm. Both probes provide a spot size of approximately 80?m at 1550nm. The 42mm probes were specified to provide an internal back reflection of -35 to -40dB, and the probe back reflections were measured to be -37dB and -33dB. The 26mm probes were specified as -30dB and both measured -30.5dB. The probe is initially aligned normal to the flyer/bridge surface. This provides a very high return signal, up to -2dB, due to the bridge reflectivity. A white card with a hole in the center as an aperture can be used to check the reflected beam position relative to the probe and launch beam, and the alignment laser spot centered on the bridge, see Figure 1 and Figure 2. The IR back reflection meter is used to measure the dB return from the probe and surface, and a white card or similar object is inserted between the probe and surface to block surface reflection. It may take several iterations between the visible alignment laser and the IR back reflection meter to complete this alignment procedure. Once aligned normal to the surface, the probe should be tilted to position the visible alignment beam as shown in Figure 3, and the flyer should be translated in the X and Y axis to reposition the alignment beam onto the flyer as shown in Figure 4. This tilting of the probe minimizes the amount of light from the bridge reflection into the fiber within the probe while maintaining the alignment as near normal to the flyer surface as possible. When the back reflection is measured after the tilt adjustment, the level should be about -3dB to -6dB higher than the probes

  19. Curriculum Alignment Research Suggests that Alignment Can Improve Student Achievement

    ERIC Educational Resources Information Center

    Squires, David

    2012-01-01

    Curriculum alignment research has developed showing the relationship among three alignment categories: the taught curriculum, the tested curriculum and the written curriculum. Each pair (for example, the taught and the written curriculum) shows a positive impact for aligning those results. Following this, alignment results from the Third…

  20. FMIT alignment cart

    SciTech Connect

    Potter, R.C.; Dauelsberg, L.B.; Clark, D.C.; Grieggs, R.J.

    1981-01-01

    The Fusion Materials Irradiation Test (FMIT) Facility alignment cart must perform several functions. It must serve as a fixture to receive the drift-tube girder assembly when it is removed from the linac tank. It must transport the girder assembly from the linac vault to the area where alignment or disassembly is to take place. It must serve as a disassembly fixture to hold the girder while individual drift tubes are removed for repair. It must align the drift tube bores in a straight line parallel to the girder, using an optical system. These functions must be performed without violating any clearances found within the building. The bore tubes of the drift tubes will be irradiated, and shielding will be included in the system for easier maintenance.

  1. Barrel alignment fixture

    NASA Astrophysics Data System (ADS)

    Sheeley, J. D.

    1981-04-01

    Fabrication of slapper type detonator cables requires bonding of a thin barrel over a bridge. Location of the barrel hole with respect to the bridge is critical: the barrel hole must be centered over the bridge uniform spacing on each side. An alignment fixture which permits rapid adjustment of the barrel position with respect to the bridge is described. The barrel is manipulated by pincer-type fingers which are mounted on a small x-y table equipped with micrometer adjustments. Barrel positioning, performed under a binocular microscopy, is rapid and accurate. After alignment, the microscope is moved out of position and an infrared (IR) heat source is aimed at the barrel. A 5-second pulse of infrared heat flows the adhesive under the barrel and bonds it to the cable. Sapphire and Fotoform glass barrels were bonded successfully with the alignment fixture.

  2. 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.

  3. Optics Alignment Panel

    NASA Technical Reports Server (NTRS)

    Schroeder, Daniel J.

    1992-01-01

    The Optics Alignment Panel (OAP) was commissioned by the HST Science Working Group to determine the optimum alignment of the OTA optics. The goal was to find the position of the secondary mirror (SM) for which there is no coma or astigmatism in the camera images due to misaligned optics, either tilt or decenter. The despace position was reviewed of the SM and the optimum focus was sought. The results of these efforts are as follows: (1) the best estimate of the aligned position of the SM in the notation of HDOS is (DZ,DY,TZ,TY) = (+248 microns, +8 microns, +53 arcsec, -79 arcsec), and (2) the best focus, defined to be that despace which maximizes the fractional energy at 486 nm in a 0.1 arcsec radius of a stellar image, is 12.2 mm beyond paraxial focus. The data leading to these conclusions, and the estimated uncertainties in the final results, are presented.

  4. MUSE optical alignment procedure

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

    2012-09-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

  5. Orientation and Alignment Echoes

    NASA Astrophysics Data System (ADS)

    Karras, G.; Hertz, E.; Billard, F.; Lavorel, B.; Hartmann, J.-M.; Faucher, O.; Gershnabel, Erez; Prior, Yehiam; Averbukh, Ilya Sh.

    2015-04-01

    We present one of the simplest classical systems featuring the echo phenomenon—a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation or alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by the kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO2 molecules excited by a pair of femtosecond laser pulses.

  6. Segment alignment control system

    NASA Technical Reports Server (NTRS)

    Aubrun, JEAN-N.; Lorell, Ken R.

    1988-01-01

    The segmented primary mirror for the LDR will require a special segment alignment control system to precisely control the orientation of each of the segments so that the resulting composite reflector behaves like a monolith. The W.M. Keck Ten Meter Telescope will utilize a primary mirror made up of 36 actively controlled segments. Thus the primary mirror and its segment alignment control system are directly analogous to the LDR. The problems of controlling the segments in the face of disturbances and control/structures interaction, as analyzed for the TMT, are virtually identical to those for the LDR. The two systems are briefly compared.

  7. Vertical Alignment and Collaboration.

    ERIC Educational Resources Information Center

    Bergman, Donna; Calzada, Lucio; LaPointe, Nancy; Lee, Audra; Sullivan, Lynn

    This study investigated whether vertical (grade level sequence) alignment of the curriculum in conjunction with teacher collaboration would enhance student performance on the Texas Assessment of Academic Skills (TAAS) test in south Texas school districts of various sizes. Surveys were mailed to the office of the superintendent of 47 school…

  8. Curriculum Alignment: Establishing Coherence

    ERIC Educational Resources Information Center

    Gagné, Philippe; Dumont, Laurence; Brunet, Sabine; Boucher, Geneviève

    2013-01-01

    In this paper, we present a step-by-step guide to implement a curricular alignment project, directed at professional development and student support, and developed in a higher education French as a second language department. We outline best practices and preliminary results from our experience and provide ways to adapt our experience to other…

  9. Aligning brains and minds

    PubMed Central

    Tong, Frank

    2012-01-01

    In this issue of Neuron, Haxby and colleagues describe a new method for aligning functional brain activity patterns across participants. Their study demonstrates that objects are similarly represented across different brains, allowing for reliable classification of one person’s brain activity based on another’s. PMID:22017984

  10. Aligned-or Not?

    ERIC Educational Resources Information Center

    Roseman, Jo Ellen; Koppal, Mary

    2015-01-01

    When state leaders and national partners in the development of the Next Generation Science Standards met to consider implementation strategies, states and school districts wanted to know which materials were aligned to the new standards. The answer from the developers was short but not sweet: You won't find much now, and it's going to…

  11. Optically Aligned Drill Press

    NASA Technical Reports Server (NTRS)

    Adderholdt, Bruce M.

    1994-01-01

    Precise drill press equipped with rotary-indexing microscope. Microscope and drill exchange places when turret rotated. Microscope axis first aligned over future hole, then rotated out of way so drill axis assumes its precise position. New procedure takes less time to locate drilling positions and produces more accurate results. Apparatus adapted to such other machine tools as milling and measuring machines.

  12. MUSE alignment onto VLT

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dupuy, Christophe; Jarno, Aurélien; Lizon, Jean-Louis; Migniau, Jean-Emmanuel; Nicklas, Harald; Piqueras, Laure

    2014-07-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation Very Large Telescope (VLT) integral field spectrograph developed for the European Southern Observatory (ESO). It combines a 1' x 1' field of view sampled at 0.2 arcsec for its Wide Field Mode (WFM) and a 7.5"x7.5" field of view for its Narrow Field Mode (NFM). Both modes will operate with the improved spatial resolution provided by GALACSI (Ground Atmospheric Layer Adaptive Optics for Spectroscopic Imaging), that will use the VLT deformable secondary mirror and 4 Laser Guide Stars (LGS) foreseen in 2015. MUSE operates in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently commissioning MUSE in the Very Large Telescope for the Preliminary Acceptance in Chile, scheduled for September, 2014. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2012 and 2013, all MUSE subsystems were integrated, aligned and tested to the P.I. institute at Lyon. After successful PAE in September 2013, MUSE instrument was shipped to the Very Large Telescope in Chile where that was aligned and tested in ESO integration hall at Paranal. After, MUSE was directly transported, fully aligned and without any optomechanical dismounting, onto VLT telescope where the first light was overcame the 7th of February, 2014. This paper describes the alignment procedure of the whole MUSE instrument with respect to the Very Large Telescope (VLT). It describes how 6 tons could be move with accuracy better than 0.025mm and less than 0.25 arcmin in order to reach alignment requirements. The success

  13. Inflation by alignment

    SciTech Connect

    Burgess, C.P.; Roest, Diederik

    2015-06-08

    Pseudo-Goldstone bosons (pGBs) can provide technically natural inflatons, as has been comparatively well-explored in the simplest axion examples. Although inflationary success requires trans-Planckian decay constants, f≳M{sub p}, several mechanisms have been proposed to obtain this, relying on (mis-)alignments between potential and kinetic energies in multiple-field models. We extend these mechanisms to a broader class of inflationary models, including in particular the exponential potentials that arise for pGB potentials based on noncompact groups (and so which might apply to moduli in an extra-dimensional setting). The resulting potentials provide natural large-field inflationary models and can predict a larger primordial tensor signal than is true for simpler single-field versions of these models. In so doing we provide a unified treatment of several alignment mechanisms, showing how each emerges as a limit of the more general setup.

  14. Alignments of RNA structures.

    PubMed

    Blin, Guillaume; Denise, Alain; Dulucq, Serge; Herrbach, Claire; Touzet, Hélène

    2010-01-01

    We describe a theoretical unifying framework to express the comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences and encompasses the main existing models for RNA structure comparison based on trees and arc-annotated sequences with a variety of edit operations. It also gives rise to edit models that have not been studied yet. We provide a thorough analysis of the alignment hierarchy, including a new polynomial-time algorithm and an NP-completeness proof. The polynomial-time algorithm involves biologically relevant edit operations such as pairing or unpairing nucleotides. It has been implemented in a software, called gardenia, which is available at the Web server http://bioinfo.lifl.fr/RNA/gardenia. PMID:20431150

  15. On the alignment space.

    PubMed

    Shen, Shi-Yi; Wang, Kui; Hu, Gang; Chen, Lu-Sheng; Zhang, Hua; Xia, Shu-Tao

    2005-01-01

    Sequences with generalized errors which are called mutations in bioinformatics and generalized error-correcting codes are studied in this paper. In the areas of bioinformatics, computer science and information theory, sequences with generalized errors are discussed respectively for different aims. Firstly, we give the definitions of alignment distance and Levenshtein distance by expansion sequences and discuss their properties and relations. Then the modular structure theory is introduced for strictly describe the expansion sequences. We show that the expansion modular structures of sequences form a Boolean algebra. As applications of the modular structure theory, we give a new and more strict proof of triangle inequality for alignment distance. At last, the definition and construction of generalized error-correcting codes are studied, and some optimal codes with small length are listed. PMID:17282158

  16. Alignment reference device

    DOEpatents

    Patton, Gail Y.; Torgerson, Darrel D.

    1987-01-01

    An alignment reference device provides a collimated laser beam that minimizes angular deviations therein. A laser beam source outputs the beam into a single mode optical fiber. The output end of the optical fiber acts as a source of radiant energy and is positioned at the focal point of a lens system where the focal point is positioned within the lens. The output beam reflects off a mirror back to the lens that produces a collimated beam.

  17. Nuclear reactor alignment plate configuration

    DOEpatents

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

    2014-01-28

    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  18. Dynamic Alignment at SLS

    SciTech Connect

    Ruland, Robert E.

    2003-04-23

    The relative alignment of components in the storage ring of the Swiss Light Source (SLS) is guaranteed by mechanical means. The magnets are rigidly fixed to 48 girders by means of alignment rails with tolerances of less than {+-}15 {micro}m. The bending magnets, supported by 3 point ball bearings, overlap adjacent girders and thus establish virtual train links between the girders, located near the bending magnet centres. Keeping the distortion of the storage ring geometry within a tolerance of {+-}100 {micro}m in order to guarantee sufficient dynamic apertures, requires continuous monitoring and correction of the girder locations. Two monitoring systems for the horizontal and the vertical direction will be installed to measure displacements of the train link between girders, which are due to ground settings and temperature effects: The hydrostatic levelling system (HLS) gives an absolute vertical reference, while the horizontal positioning system (HPS), which employs low cost linear encoders with sub-micron resolution, measures relative horizontal movements. The girder mover system based on five DC motors per girder allows a dynamic realignment of the storage ring within a working window of more than {+-}1 mm for girder translations and {+-}1 mrad for rotations. We will describe both monitoring systems (HLS and HPS) as well as the applied correction scheme based on the girder movers. We also show simulations indicating that beam based girder alignment takes care of most of the static closed orbit correction.

  19. 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.

  20. Polar cap arcs: Sun-aligned or cusp-aligned?

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Paxton, L. J.; Zhang, Qinghe; Xing, Zanyang

    2016-08-01

    Polar cap arcs are often called sun-aligned arcs. Satellite observations reveal that polar cap arcs join together at the cusp and are actually cusp aligned. Strong ionospheric plasma velocity shears, thus field aligned currents, were associated with polar arcs and they were likely caused by Kelvin-Helmholtz waves around the low-latitude magnetopause under a northward IMF Bz. The magnetic field lines around the magnetopause join together in the cusp region so are the field aligned currents and particle precipitation. This explains why polar arcs are cusp aligned.

  1. Alignment and alignment transition of bent core nematics

    NASA Astrophysics Data System (ADS)

    Elamain, Omaima; Hegde, Gurumurthy; Komitov, Lachezar

    2013-07-01

    We report on the alignment of nematics consisting of bimesogen bent core molecules of chlorine substituent of benzene derivative and their binary mixture with rod like nematics. It was found that the alignment layer made from polyimide material, which is usually used for promoting vertical (homeotropic) alignment of rod like nematics, promotes instead a planar alignment of the bent core nematic and its nematic mixtures. At higher concentration of the rod like nematic component in these mixtures, a temperature driven transition from vertical to planar alignment was found near the transition to isotropic phase.

  2. Alignment as a Teacher Variable

    ERIC Educational Resources Information Center

    Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

    2007-01-01

    With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

  3. Solar Alignments - Identification and Analysis

    NASA Astrophysics Data System (ADS)

    Belmonte, Juan Antonio

    The sun was such an important divinity in antiquity, and even today, that solar alignments should be expected within a large variety of places and cultures. These are probably the most conspicuous kind of astronomical alignments a field researcher can deal with. The need for a correct identification is thus evident. The different kind of solar phenomena susceptible of being determined by astronomical alignments will be scrutinized, following by the way in which such alignments can materialize in space. It will be shown that analyzing solar alignments is not always an easy task.

  4. TSGC and JSC Alignment

    NASA Technical Reports Server (NTRS)

    Sanchez, Humberto

    2013-01-01

    NASA and the SGCs are, by design, intended to work closely together and have synergistic Vision, Mission, and Goals. The TSGC affiliates and JSC have been working together, but not always in a concise, coordinated, nor strategic manner. Today we have a couple of simple ideas to present about how TSGC and JSC have started to work together in a more concise, coordinated, and strategic manner, and how JSC and non-TSG Jurisdiction members have started to collaborate: Idea I: TSGC and JSC Technical Alignment Idea II: Concept of Clusters.

  5. Conditional alignment random fields for multiple motion sequence alignment.

    PubMed

    Kim, Minyoung

    2013-11-01

    We consider the multiple time-series alignment problem, typically focusing on the task of synchronizing multiple motion videos of the same kind of human activity. Finding an optimal global alignment of multiple sequences is infeasible, while there have been several approximate solutions, including iterative pairwise warping algorithms and variants of hidden Markov models. In this paper, we propose a novel probabilistic model that represents the conditional densities of the latent target sequences which are aligned with the given observed sequences through the hidden alignment variables. By imposing certain constraints on the target sequences at the learning stage, we have a sensible model for multiple alignments that can be learned very efficiently by the EM algorithm. Compared to existing methods, our approach yields more accurate alignment while being more robust to local optima and initial configurations. We demonstrate its efficacy on both synthetic and real-world motion videos including facial emotions and human activities. PMID:24051737

  6. Fourier transform interferometer alignment method.

    PubMed

    Goldberg, Kenneth A; Naulleau, Patrick; Bokor, Jeffrey

    2002-08-01

    A rapid and convenient method has been developed to facilitate the alignment of the image-plane components of point-diffraction interferometers, including the phase-shifting point-diffraction interferometer. In real time, the Fourier transform of the detected image is used to calculate a pseudoimage of the electric field in the image plane of the test optic where thecritical alignment o f variousoptical components is performed. Reconstruction of the pseudoimage is similar to off-axis, Fourier transform holography. Intermediate steps in the alignment procedure are described. Fine alignment is aided by the introduction and optimization of a global-contrast parameter that is easily calculated from the Fourier transform. Additional applications include the alignment of image-plane apertures in general optical systems, the rapid identification of patterned image-plane alignment marks, and the probing of important image-plane field properties. PMID:12153074

  7. Nuclear reactor internals alignment configuration

    DOEpatents

    Gilmore, Charles B.; Singleton, Norman R.

    2009-11-10

    An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

  8. Aligned Defrosting Dunes

    NASA Technical Reports Server (NTRS)

    2004-01-01

    17 August 2004 This July 2004 Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a group of aligned barchan sand dunes in the martian north polar region. At the time, the dunes were covered with seasonal frost, but the frost had begun to sublime away, leaving dark spots and dark outlines around the dunes. The surrounding plains exhibit small, diffuse spots that are also the result of subliming seasonal frost. This northern spring image, acquired on a descending ground track (as MGS was moving north to south on the 'night' side of Mars) is located near 78.8oN, 34.8oW. The image covers an area about 3 km (1.9 mi) across and sunlight illuminates the scene from the upper left.

  9. Alignment system for encoders

    NASA Technical Reports Server (NTRS)

    Villani, Daniel D. (Inventor)

    1988-01-01

    An improved encoder alignment system is disclosed which provides an indication of the extent of misalignment and a measure of the rate at which the misalignment may be changing. The invention is adapted for use with a conventional encoder which provides a digital coarse word having at least significant bit and a digital fine word having a least significant bit and a most significant bit. The invention generates the exclusive or of the least significant bit of the coarse digital signal and the least significant bit of the fine digital signal to provide a first signal. The invention then generates the exclusive or of the first signal and the complement of the most significant bit of the fine digital signal to provide an output signal which represents the misalignment of the encoder.

  10. Lunar Alignments - Identification and Analysis

    NASA Astrophysics Data System (ADS)

    González-García, A. César

    Lunar alignments are difficult to establish given the apparent lack of written accounts clearly pointing toward lunar alignments for individual temples. While some individual cases are reviewed and highlighted, the weight of the proof must fall on statistical sampling. Some definitions for the lunar alignments are provided in order to clarify the targets, and thus, some new tools are provided to try to test the lunar hypothesis in several cases, especially in megalithic astronomy.

  11. Drive alignment pays maintenance dividends

    SciTech Connect

    Fedder, R.

    2008-12-15

    Proper alignment of the motor and gear drive on conveying and processing equipment will result in longer bearing and coupling life, along with lower maintenance costs. Selecting an alignment free drive package instead of a traditional foot mounted drive and motor is a major advancement toward these goals. 4 photos.

  12. Lexical alignment in triadic communication

    PubMed Central

    Foltz, Anouschka; Gaspers, Judith; Thiele, Kristina; Stenneken, Prisca; Cimiano, Philipp

    2015-01-01

    Lexical alignment refers to the adoption of one’s interlocutor’s lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants’ lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment. PMID:25762955

  13. Semiautomated improvement of RNA alignments

    PubMed Central

    Andersen, Ebbe S.; Lind-Thomsen, Allan; Knudsen, Bjarne; Kristensen, Susie E.; Havgaard, Jakob H.; Torarinsson, Elfar; Larsen, Niels; Zwieb, Christian; Sestoft, Peter; Kjems, Jørgen; Gorodkin, Jan

    2007-01-01

    We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture of the SARSE editor makes it a flexible tool to improve all RNA alignments with relatively little human intervention. Online documentation and software are available at http://sarse.ku.dk. PMID:17804647

  14. Well-pump alignment system

    DOEpatents

    Drumheller, Douglas S.

    1998-01-01

    An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping.

  15. On the alignment of quasars

    NASA Astrophysics Data System (ADS)

    Zhu, X.-F.

    1986-06-01

    Taking the two Savage-Bolton 5 deg x 5 deg regions of optical quasar patrol as samples, a systematic analysis of the number of aligned quasars was made and compared with the random data generated by Monte Carlo method. The statistical result is that, at least for these two samples, there is no clear evidence for alignment.

  16. On the alignment of quasars

    NASA Astrophysics Data System (ADS)

    Zhu, Xing-fen

    1986-06-01

    Taking the two Savage-Bolton 5° × 5° regions of optical quasar patrol as samples, I made a systematic analysis of the number of aligned quasars and compared with the random data generated by Monte Carlo method. The statistical result is that, at least for these two samples, there is no clear evidence for alignment.

  17. CATO: The Clone Alignment Tool.

    PubMed

    Henstock, Peter V; LaPan, Peter

    2016-01-01

    High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1) a top-level summary of the top candidate sequences aligned to each reference sequence, 2) a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3) a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow. PMID:27459605

  18. CATO: The Clone Alignment Tool

    PubMed Central

    Henstock, Peter V.; LaPan, Peter

    2016-01-01

    High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1) a top-level summary of the top candidate sequences aligned to each reference sequence, 2) a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3) a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow. PMID:27459605

  19. Space Mirror Alignment System

    NASA Technical Reports Server (NTRS)

    Jau, Bruno M.; McKinney, Colin; Smythe, Robert F.; Palmer, Dean L.

    2011-01-01

    An optical alignment mirror mechanism (AMM) has been developed with angular positioning accuracy of +/-0.2 arcsec. This requires the mirror s linear positioning actuators to have positioning resolutions of +/-112 nm to enable the mirror to meet the angular tip/tilt accuracy requirement. Demonstrated capabilities are 0.1 arc-sec angular mirror positioning accuracy, which translates into linear positioning resolutions at the actuator of 50 nm. The mechanism consists of a structure with sets of cross-directional flexures that enable the mirror s tip and tilt motion, a mirror with its kinematic mount, and two linear actuators. An actuator comprises a brushless DC motor, a linear ball screw, and a piezoelectric brake that holds the mirror s position while the unit is unpowered. An interferometric linear position sensor senses the actuator s position. The AMMs were developed for an Astrometric Beam Combiner (ABC) optical bench, which is part of an interferometer development. Custom electronics were also developed to accommodate the presence of multiple AMMs within the ABC and provide a compact, all-in-one solution to power and control the AMMs.

  20. Alignment positioning mechanism

    NASA Technical Reports Server (NTRS)

    Fantasia, Peter M. (Inventor)

    1991-01-01

    An alignment positioning mechanism for correcting and compensating for misalignment of structures to be coupled is disclosed. The mechanism comprises a power screw with a base portion and a threaded shank portion. A mounting fixture is provided for rigidly coupling said base portion to the mounting interface of a supporting structure with the axis of the screw perpendicular thereto. A traveling ball nut threaded on the power screw is formed with an external annular arcuate surface configured in the form of a spherical segment and enclosed by a ball nut housing with a conforming arcuate surface for permitting gimballed motion thereon. The ball nut housing is provided with a mounting surface which is positionable in cooperable engagement with the mounting interface of a primary structure to be coupled to the supporting structure. Cooperative means are provided on the ball nut and ball nut housing, respectively, for positioning the ball nut and ball nut housing in relative gimballed position within a predetermined range of relative angular relationship whereby severe structural stresses due to unequal loadings and undesirable bending moments on the mechanism are avoided.

  1. Alignment-Annotator web server: rendering and annotating sequence alignments

    PubMed Central

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-01-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

  2. Testing the tidal alignment model of galaxy intrinsic alignment

    SciTech Connect

    Blazek, Jonathan; Seljak, Uroš; McQuinn, Matthew E-mail: mmcquinn@berkeley.edu

    2011-05-01

    Weak gravitational lensing has become a powerful probe of large-scale structure and cosmological parameters. Precision weak lensing measurements require an understanding of the intrinsic alignment of galaxy ellipticities, which can in turn inform models of galaxy formation. It is hypothesized that elliptical galaxies align with the background tidal field and that this alignment mechanism dominates the correlation between ellipticities on cosmological scales (in the absence of lensing). We use recent large-scale structure measurements from the Sloan Digital Sky Survey to test this picture with several statistics: (1) the correlation between ellipticity and galaxy overdensity, w{sub g+}; (2) the intrinsic alignment auto-correlation functions; (3) the correlation functions of curl-free, E, and divergence-free, B, modes, the latter of which is zero in the linear tidal alignment theory; (4) the alignment correlation function, w{sub g}(r{sub p},θ), a recently developed statistic that generalizes the galaxy correlation function to account for the angle between the galaxy separation vector and the principle axis of ellipticity. We show that recent measurements are largely consistent with the tidal alignment model and discuss dependence on galaxy luminosity. In addition, we show that at linear order the tidal alignment model predicts that the angular dependence of w{sub g}(r{sub p},θ) is simply w{sub g+}(r{sub p})cos (2θ) and that this dependence is consistent with recent measurements. We also study how stochastic nonlinear contributions to galaxy ellipticity impact these statistics. We find that a significant fraction of the observed LRG ellipticity can be explained by alignment with the tidal field on scales ∼> 10 \\hMpc. These considerations are relevant to galaxy formation and evolution.

  3. Advanced Mask Aligner Lithography (AMALITH)

    NASA Astrophysics Data System (ADS)

    Voelkel, Reinhard; Vogler, Uwe; Bramati, Arianna

    2015-03-01

    Mask aligner lithography is very attractive for less-critical lithography layers and is widely used for LED, display, CMOS image sensor, micro-fluidics and MEMS manufacturing. Mask aligner lithography is also a preferred choice the semiconductor back-end for 3D-IC, TSV interconnects, advanced packaging (AdP) and wafer-level-packaging (WLP). Mask aligner lithography is a mature technique based on shadow printing and has not much changed since the 1980s. In shadow printing lithography a geometric pattern is transferred by free-space propagation from a photomask to a photosensitive layer on a wafer. The inherent simplicity of the pattern transfer offers ease of operation, low maintenance, moderate capital expenditure, high wafers-per-hour (WPH) throughput, and attractive cost-of-ownership (COO). Advanced mask aligner lithography (AMALITH) comprises different measures to improve shadow printing lithography beyond current limits. The key enabling technology for AMALITH is a novel light integrator systems, referred to as MO Exposure Optics® (MOEO). MOEO allows to fully control and shape the properties of the illumination light in a mask aligner. Full control is the base for accurate simulation and optimization of the shadow printing process (computational lithography). Now photolithography enhancement techniques like customized illumination, optical proximity correction (OPC), phase masks (AAPSM), half-tone lithography and Talbot lithography could be used in mask aligner lithography. We summarize the recent progress in advanced mask aligner lithography (AMALITH) and discuss possible measures to further improve shadow printing lithography.

  4. Aligning for Innovation - Alignment Strategy to Drive Innovation

    NASA Technical Reports Server (NTRS)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

    2010-01-01

    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  5. Fusion bonding and alignment fixture

    DOEpatents

    Ackler, Harold D.; Swierkowski, Stefan P.; Tarte, Lisa A.; Hicks, Randall K.

    2000-01-01

    An improved vacuum fusion bonding structure and process for aligned bonding of large area glass plates, patterned with microchannels and access holes and slots, for elevated glass fusion temperatures. Vacuum pumpout of all the components is through the bottom platform which yields an untouched, defect free top surface which greatly improves optical access through this smooth surface. Also, a completely non-adherent interlayer, such as graphite, with alignment and location features is located between the main steel platform and the glass plate pair, which makes large improvements in quality, yield, and ease of use, and enables aligned bonding of very large glass structures.

  6. Adaptive control of molecular alignment

    SciTech Connect

    Horn, C.; Wollenhaupt, M.; Krug, M.; Baumert, T.; Nalda, R. de; Banares, L.

    2006-03-15

    We demonstrate control on nonadiabatic molecular alignment by using a spectrally phase-shaped laser pulse. An evolutionary algorithm in a closed feedback loop has been used in order to find pulse shapes that maximize a given effect. In particular, this scheme has been applied to the optimization of total alignment, and to the control of the temporal structure of the alignment transient within a revival. Asymmetric temporal pulse shapes have been found to be very effective for the latter and have been studied separately in a single-parameter control scheme. Our experimental results are supported by numerical simulations.

  7. Laser beam alignment apparatus and method

    DOEpatents

    Gruhn, Charles R.; Hammond, Robert B.

    1981-01-01

    The disclosure relates to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

  8. Laser beam alignment apparatus and method

    DOEpatents

    Gruhn, C.R.; Hammond, R.B.

    The disclosure related to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

  9. Theory of grain alignment in molecular clouds

    NASA Technical Reports Server (NTRS)

    Roberge, Wayne G.

    1993-01-01

    Research accomplishments are presented and include the following: (1) mathematical theory of grain alignment; (2) super-paramagnetic alignment of molecular cloud grains; and (3) theory of grain alignment by ambipolar diffusion.

  10. Protein structure alignment beyond spatial proximity

    PubMed Central

    Wang, Sheng; Ma, Jianzhu; Peng, Jian; Xu, Jinbo

    2013-01-01

    Protein structure alignment is a fundamental problem in computational structure biology. Many programs have been developed for automatic protein structure alignment, but most of them align two protein structures purely based upon geometric similarity without considering evolutionary and functional relationship. As such, these programs may generate structure alignments which are not very biologically meaningful from the evolutionary perspective. This paper presents a novel method DeepAlign for automatic pairwise protein structure alignment. DeepAlign aligns two protein structures using not only spatial proximity of equivalent residues (after rigid-body superposition), but also evolutionary relationship and hydrogen-bonding similarity. Experimental results show that DeepAlign can generate structure alignments much more consistent with manually-curated alignments than other automatic tools especially when proteins under consideration are remote homologs. These results imply that in addition to geometric similarity, evolutionary information and hydrogen-bonding similarity are essential to aligning two protein structures. PMID:23486213

  11. Fixture for aligning motor assembly

    DOEpatents

    Shervington, Roger M.; Vaghani, Vallabh V.; Vanek, Laurence D.; Christensen, Scott A.

    2009-12-08

    An alignment fixture includes a rotor fixture, a stator fixture and a sensor system which measures a rotational displacement therebetween. The fixture precisely measures rotation of a generator stator assembly away from a NULL position referenced by a unique reference spline on the rotor shaft. By providing an adjustable location of the stator assembly within the housing, the magnetic axes within each generator shall be aligned to a predetermined and controlled tolerance between the generator interface mounting pin and the reference spline on the rotor shaft. Once magnetically aligned, each generator is essentially a line replaceable unit which may be readily mounted to any input of a multi-generator gearbox assembly with the assurance that the magnetic alignment will be within a predetermined tolerance.

  12. Well-pump alignment system

    DOEpatents

    Drumheller, D.S.

    1998-10-20

    An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump are disclosed, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping. 6 figs.

  13. Projection-Based Volume Alignment

    PubMed Central

    Yu, Lingbo; Snapp, Robert R.; Ruiz, Teresa; Radermacher, Michael

    2013-01-01

    When heterogeneous samples of macromolecular assemblies are being examined by 3D electron microscopy (3DEM), often multiple reconstructions are obtained. For example, subtomograms of individual particles can be acquired from tomography, or volumes of multiple 2D classes can be obtained by random conical tilt reconstruction. Of these, similar volumes can be averaged to achieve higher resolution. Volume alignment is an essential step before 3D classification and averaging. Here we present a projection-based volume alignment (PBVA) algorithm. We select a set of projections to represent the reference volume and align them to a second volume. Projection alignment is achieved by maximizing the cross-correlation function with respect to rotation and translation parameters. If data are missing, the cross-correlation functions are normalized accordingly. Accurate alignments are obtained by averaging and quadratic interpolation of the cross-correlation maximum. Comparisons of the computation time between PBVA and traditional 3D cross-correlation methods demonstrate that PBVA outperforms the traditional methods. Performance tests were carried out with different signal-to-noise ratios using modeled noise and with different percentages of missing data using a cryo-EM dataset. All tests show that the algorithm is robust and highly accurate. PBVA was applied to align the reconstructions of a subcomplex of the NADH: ubiquinone oxidoreductase (Complex I) from the yeast Yarrowia lipolytica, followed by classification and averaging. PMID:23410725

  14. Binocular collimation vs conditional alignment

    NASA Astrophysics Data System (ADS)

    Cook, William J.

    2012-10-01

    As binocular enthusiasts share their passion, topics related to collimation abound. Typically, we find how observers, armed only with a jeweler's screwdriver, can "perfectly collimate" his or her binocular, make it "spot on," or other verbiage of similar connotation. Unfortunately, what most are addressing is a form of pseudo-collimation I have referred to since the mid-1970s as "Conditional Alignment." Ignoring the importance of the mechanical axis (hinge) in the alignment process, this "condition," while having the potential to make alignment serviceable, or even outstanding—within a small range of IPD (Interpupillary Distance) settings relative to the user's spatial accommodation (the ability to accept small errors in parallelism of the optical axes)—may take the instrument farther from the 3-axis collimation conscientious manufacturers seek to implement. Becoming more optically savvy—and especially with so many mechanically inferior binoculars entering the marketplace— the consumer contemplating self-repair and alignment has a need to understand the difference between clinical, 3-axis "collimation" (meaning both optical axes are parallel with the axis of the hinge) and "conditional alignment," as differentiated in this paper. Furthermore, I believe there has been a long-standing need for the term "Conditional Alignment," or some equivalent, to be accepted as part of the vernacular of those who use binoculars extensively, whether for professional or recreational activities. Achieving that acceptance is the aim of this paper.

  15. BinAligner: a heuristic method to align biological networks.

    PubMed

    Yang, Jialiang; Li, Jun; Grünewald, Stefan; Wan, Xiu-Feng

    2013-01-01

    The advances in high throughput omics technologies have made it possible to characterize molecular interactions within and across various species. Alignments and comparison of molecular networks across species will help detect orthologs and conserved functional modules and provide insights on the evolutionary relationships of the compared species. However, such analyses are not trivial due to the complexity of network and high computational cost. Here we develop a mixture of global and local algorithm, BinAligner, for network alignments. Based on the hypotheses that the similarity between two vertices across networks would be context dependent and that the information from the edges and the structures of subnetworks can be more informative than vertices alone, two scoring schema, 1-neighborhood subnetwork and graphlet, were introduced to derive the scoring matrices between networks, besides the commonly used scoring scheme from vertices. Then the alignment problem is formulated as an assignment problem, which is solved by the combinatorial optimization algorithm, such as the Hungarian method. The proposed algorithm was applied and validated in aligning the protein-protein interaction network of Kaposi's sarcoma associated herpesvirus (KSHV) and that of varicella zoster virus (VZV). Interestingly, we identified several putative functional orthologous proteins with similar functions but very low sequence similarity between the two viruses. For example, KSHV open reading frame 56 (ORF56) and VZV ORF55 are helicase-primase subunits with sequence identity 14.6%, and KSHV ORF75 and VZV ORF44 are tegument proteins with sequence identity 15.3%. These functional pairs can not be identified if one restricts the alignment into orthologous protein pairs. In addition, BinAligner identified a conserved pathway between two viruses, which consists of 7 orthologous protein pairs and these proteins are connected by conserved links. This pathway might be crucial for virus packing and

  16. The partial space qualification of a vertically aligned carbon nanotube coating on aluminium substrates for EO applications.

    PubMed

    Theocharous, Evangelos; Chunnilall, Christopher J; Mole, Ryan; Gibbs, David; Fox, Nigel; Shang, Naigui; Howlett, Guy; Jensen, Ben; Taylor, Rosie; Reveles, Juan R; Harris, Oliver B; Ahmed, Naseer

    2014-03-24

    The fabrication of NanoTube Black, a Vertically Aligned carbon NanoTube Array (VANTA) on aluminium substrates is reported for the first time. The coating on aluminium was realised using a process that employs top down thermal radiation to assist growth, enabling deposition at temperatures below the substrate's melting point. The NanoTube Black coatings were shown to exhibit directional hemispherical reflectance values of typically less than 1% across wavelengths in the 2.5 µm to 15 µm range. VANTA-coated aluminium substrates were subjected to space qualification testing (mass loss, outgassing, shock, vibration and temperature cycling) before their optical properties were re-assessed. Within measurement uncertainty, no changes to hemispherical reflectance were detected, confirming that NanoTube Black coatings on aluminium are good candidates for Earth Observation (EO) applications. PMID:24664077

  17. A Nonlinear Observer for Gyro Alignment Estimation

    NASA Technical Reports Server (NTRS)

    Thienel, J.; Sanner, R. M.

    2003-01-01

    A nonlinear observer for gyro alignment estimation is presented. The observer is composed of two error terms, an attitude error and an alignment error. The observer is globally stable with exponential convergence of the attitude errors. The gyro alignment estimate converges to the true alignment when the system is completely observable.

  18. Global Alignment System for Large Genomic Sequencing

    2002-03-01

    AVID is a global alignment system tailored for the alignment of large genomic sequences up to megabases in length. Features include the possibility of one sequence being in draft form, fast alignment, robustness and accuracy. The method is an anchor based alignment using maximal matches derived from suffix trees.

  19. Mould insert fabrication of a single-mode fibre connector alignment structure optimized by justified partial metallization

    NASA Astrophysics Data System (ADS)

    Wissmann, Markus; Barié, Nicole; Guttmann, Markus; Schneider, Marc; Kolew, Alexander; Besser, Heino; Pfleging, Wilhelm; Hofmann, Andreas; Van Erps, Jürgen; Beri, Stefano; Watté, Jan

    2015-03-01

    For mass production of multiscale-optical components, microstructured moulding tools are needed. Metal tools are used for hot embossing or injection moulding of microcomponents made of a thermoplastic polymer. Microstructures with extremely tight specifications, e.g. low side wall roughness and high aspect ratios are generally made by lithographic procedures such as x-ray lithography or deep proton writing. However, these processes are unsuitable for low-cost mass production. An alternative manufacturing method of moulding tools has been developed at the Karlsruhe Institute of Technology (KIT). This article describes a mould insert fabrication and a new replication process for self-centring fibre alignment structures for low loss field installable single-mode fibre connectors, developed and fabricated by the Vrije Universiteit Brussel (VUB) in collaboration with TE Connectivity. These components are to be used in fibre-to-the-home networks and support the deployment and maintenance of fibre optic links. The special feature of this particular fibre connector is a self-centring fibre alignment, achieved by means of a through hole with deflectable cantilevers acting as micro-springs. The particular challenge is the electroforming of through holes with a centre hole diameter smaller than 125 µm. The fibre connector structure is prototyped by deep proton writing in polymethylmethacrylate and used as a sacrificial part. Using joining, physical vapour deposition and electroforming technology, a negative copy of the prototyped connector is transferred into nickel to be used as a moulding tool. The benefits of this replication technique are a rapid and economical fabrication of moulding tools with high-precision microstructures and a long tool life. With these moulding tools low-cost mass production is possible. We present the manufacturing chain we have established. Each individual manufacturing step of the mould insert fabrication will be shown in this report. The

  20. Combining Multiple Pairwise Structure-based Alignments

    SciTech Connect

    2014-11-12

    CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a new tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.

  1. Alignment method for parabolic trough solar concentrators

    DOEpatents

    Diver, Richard B.

    2010-02-23

    A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

  2. Grain Alignment in Starless Cores

    NASA Astrophysics Data System (ADS)

    Jones, T. J.; Bagley, M.; Krejny, M.; Andersson, B.-G.; Bastien, P.

    2015-01-01

    We present near-IR polarimetry data of background stars shining through a selection of starless cores taken in the K band, probing visual extinctions up to {{A}V}˜ 48. We find that {{P}K}/{{τ }K} continues to decline with increasing AV with a power law slope of roughly -0.5. Examination of published submillimeter (submm) polarimetry of starless cores suggests that by {{A}V}≳ 20 the slope for P versus τ becomes ˜-1, indicating no grain alignment at greater optical depths. Combining these two data sets, we find good evidence that, in the absence of a central illuminating source, the dust grains in dense molecular cloud cores with no internal radiation source cease to become aligned with the local magnetic field at optical depths greater than {{A}V}˜ 20. A simple model relating the alignment efficiency to the optical depth into the cloud reproduces the observations well.

  3. Alignment of the VISA Undulator

    SciTech Connect

    Ruland, Robert

    1999-04-15

    The Visible-Infrared SASE Amplifier (VISA) undulator consists of four 99cm long segments. Each undulator segment is set up on a pulsed-wire bench, to characterize the magnetic properties and to locate the magnetic axis of the FODO array. Subsequently, the location of the magnetic axis, as defined by the wire, is referenced to tooling balls on each magnet segment by means of a straightness interferometer. After installation in the vacuum chamber, the four magnet segments are aligned with respect to themselves and globally to the beam line reference laser. A specially designed alignment fixture is used to mount one straightness interferometer each in the horizontal and vertical plane of the beam. The goal of these procedures is to keep the combined rms trajectory error, due to magnetic and alignment errors, to 50{micro}m.

  4. Measurements of magnetic field alignment

    SciTech Connect

    Kuchnir, M.; Schmidt, E.E.

    1987-11-06

    The procedure for installing Superconducting Super Collider (SSC) dipoles in their respective cryostats involves aligning the average direction of their field with the vertical to an accuracy of 0.5 mrad. The equipment developed for carrying on these measurements is described and the measurements performed on the first few prototypes SSC magnets are presented. The field angle as a function of position in these 16.6 m long magnets is a characteristic of the individual magnet with possible feedback information to its manufacturing procedure. A comparison of this vertical alignment characteristic with a magnetic field intensity (by NMR) characteristic for one of the prototypes is also presented. 5 refs., 7 figs.

  5. XUV ionization of aligned molecules

    SciTech Connect

    Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  6. Alignment Tool For Inertia Welding

    NASA Technical Reports Server (NTRS)

    Snyder, Gary L.

    1991-01-01

    Compact, easy-to-use tool aligns drive bar of inertia welder over hole in stub. Ensures drive bar concentric to hole within 0.002 in. (0.051 mm.). Holds two batteries and light bulb. Electrical circuit completed, providing current to bulb when pin in contact with post. When pin centered in post hole, it does not touch post, and lamp turns off. Built for use in making repair welds on liquid-oxygen-injector posts in Space Shuttle main engine. Version having suitably modified dimensions used to facilitate alignment in other forests of post.

  7. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  8. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment-distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  9. Aligned natural inflation with modulations

    NASA Astrophysics Data System (ADS)

    Choi, Kiwoon; Kim, Hyungjin

    2016-08-01

    The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  10. Laser-Beam-Alignment Controller

    NASA Technical Reports Server (NTRS)

    Krasowski, M. J.; Dickens, D. E.

    1995-01-01

    In laser-beam-alignment controller, images from video camera compared to reference patterns by fuzzy-logic pattern comparator. Results processed by fuzzy-logic microcontroller, which sends control signals to motor driver adjusting lens and pinhole in spatial filter.

  11. Aligning Assessments for COSMA Accreditation

    ERIC Educational Resources Information Center

    Laird, Curt; Johnson, Dennis A.; Alderman, Heather

    2015-01-01

    Many higher education sport management programs are currently in the process of seeking accreditation from the Commission on Sport Management Accreditation (COSMA). This article provides a best-practice method for aligning student learning outcomes with a sport management program's mission and goals. Formative and summative assessment procedures…

  12. Support Vector Training of Protein Alignment Models

    PubMed Central

    Joachims, Thorsten; Elber, Ron; Pillardy, Jaroslaw

    2008-01-01

    Abstract Sequence to structure alignment is an important step in homology modeling of protein structures. Incorporation of features such as secondary structure, solvent accessibility, or evolutionary information improve sequence to structure alignment accuracy, but conventional generative estimation techniques for alignment models impose independence assumptions that make these features difficult to include in a principled way. In this paper, we overcome this problem using a Support Vector Machine (SVM) method that provides a well-founded way of estimating complex alignment models with hundred of thousands of parameters. Furthermore, we show that the method can be trained using a variety of loss functions. In a rigorous empirical evaluation, the SVM algorithm outperforms the generative alignment method SSALN, a highly accurate generative alignment model that incorporates structural information. The alignment model learned by the SVM aligns 50% of the residues correctly and aligns over 70% of the residues within a shift of four positions. PMID:18707536

  13. Instability of Ocular Alignment in Childhood Esotropia

    PubMed Central

    2008-01-01

    Objective Instability of ocular alignment may cause surgeons to delay surgical correction of childhood esotropia. We investigated the stability of ocular alignment over 18 weeks in children with infantile esotropia (IET), acquired non-accommodative esotropia (ANAET), or acquired partially-accommodative esotropia (APAET). Design Prospective observational study Participants Two hundred thirty-three children aged 2 months to <5 years with IET, ANAET, or APAET of less than 6 months duration Methods Ocular alignment was measured at baseline and at six-week intervals for 18 weeks. Main Outcome Measure 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) between any two of the four measurements, as ‘stable’ if all four measurements were within ≤ 5 PD of one another, or as ‘uncertain’ if neither criteria was met. Results Of those who completed all three 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 to 59%), 20% as stable (95% CI = 11 to 33%), and 34% as uncertain (95% CI = 22 to 47%). Thirteen (22%) of 60 subjects with ANAET had ocular alignment classified as unstable (95% confidence interval (CI) = 12 to 34%), 37% as stable (95% CI = 25 to 50%), and 42% as uncertain (95% CI = 29 to 55%). Six (15%) of 41 subjects with APAET had ocular alignment classified as unstable (95% CI = 6 to 29%), 39% as stable (95% CI = 24 to 56%), and 46% as uncertain (95% CI = 31 to 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 to 0.99). Conclusions Ocular alignment instability is common in children with IET, ANAET and APAET. The impact of this finding

  14. 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.

  15. Sequence alignment with tandem duplication

    SciTech Connect

    Benson, G.

    1997-12-01

    Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked farily well, it has long been apparent that other mutational events occur. In this paper, we introduce a new model, the DSI model which includes another common mutational event, tandem duplication. Tandem duplication produces tandem repeats which are common in DNA, making up perhaps 10% of the human genome. They are responsible for some human diseases and may serve a multitude of functions in DNA regulation and evolution. Using the DSI model, we develop new exact and heuristic algorithms for comparing and aligning DNA sequences when they contain tandem repeats. 30 refs., 3 figs.

  16. Alignment of the VISA Undulator

    SciTech Connect

    Ruland, Robert E.

    2000-02-09

    As part of the R and D program towards a fourth generation light source, a Self-Amplified Spontaneous Emission (SASE) demonstration is being prepared. The Visible-Infrared SASE Amplifier (VISA) undulator is being installed at Brookhaven National Laboratory. The VISA undulator is an in-vacuum, 4-meter long, 1.8 cm period, pure-permanent magnet device, with a novel, strong focusing, permanent magnet FODO array included within the fixed, 6 mm undulator gap. The undulator is constructed of 99 cm long segments. To attain maximum SASE gain requires establishing overlap of electron and photon beams to within 50 pm rms. This imposes challenging tolerances on mechanical fabrication and magnetic field quality, and necessitates use of laser straightness interferometry for calibration and alignment of the magnetic axes of the undulator segments. This paper describes the magnetic centerline determination, and the fiducialization and alignment processes, which were performed to meet the tolerance goal.

  17. Aligned mesoporous architectures and devices.

    SciTech Connect

    Brinker, C. Jeffrey; Lu, Yunfeng

    2011-03-01

    This is the final report for the Presidential Early Career Award for Science and Engineering - PECASE (LDRD projects 93369 and 118841) awarded to Professor Yunfeng Lu (Tulane University and University of California-Los Angeles). During the last decade, mesoporous materials with tunable periodic pores have been synthesized using surfactant liquid crystalline as templates, opening a new avenue for a wide spectrum of applications. However, the applications are somewhat limited by the unfavorabe pore orientation of these materials. Although substantial effort has been devoted to align the pore channels, fabrication of mesoporous materials with perpendicular pore channels remains challenging. This project focused on fabrication of mesoporous materials with perpendicularly aligned pore channels. We demonstrated structures for use in water purification, separation, sensors, templated synthesis, microelectronics, optics, controlled release, and highly selective catalysts.

  18. Fiber alignment apparatus and method

    DOEpatents

    Kravitz, Stanley H.; Warren, Mial Evans; Snipes, Jr., Morris Burton; Armendariz, Marcelino Guadalupe; Word, V., James Cole

    1997-01-01

    A fiber alignment apparatus includes a micro-machined nickel spring that captures and locks arrays of single mode fibers into position. The design consists of a movable nickel leaf shaped spring and a fixed pocket where fibers are held. The fiber is slid between the spring and a fixed block, which tensions the spring. When the fiber reaches the pocket, it automatically falls into the pocket and is held by the pressure of the leaf spring.

  19. Fiber alignment apparatus and method

    DOEpatents

    Kravitz, S.H.; Warren, M.E.; Snipes, M.B. Jr.; Armendariz, M.G.; Word, J.C. V

    1997-08-19

    A fiber alignment apparatus includes a micro-machined nickel spring that captures and locks arrays of single mode fibers into position. The design consists of a movable nickel leaf shaped spring and a fixed pocket where fibers are held. The fiber is slid between the spring and a fixed block, which tensions the spring. When the fiber reaches the pocket, it automatically falls into the pocket and is held by the pressure of the leaf spring. 8 figs.

  20. Alignment Tool For Welding Sensor

    NASA Technical Reports Server (NTRS)

    Gilbert, Jeffrey L.; Steffins, Alfred P.

    1992-01-01

    Alignment tool enables accurate positioning of optoelectronic sensor measuring weld penetration. Designed for use on tungsten/inert-gas welding apparatus, used to adjust position of sensor so photodiode puts out maximum signal. Tangs of slotted cap bent slightly inward to provide spring force holding cap snugly on sensor mount. Tool installed and removed without aid of other tools. Length of pointer adjusted with set-screws. Used with variety of gas cup and electrode lengths.

  1. NICMOS SM-2 SMOV Alignment Results

    NASA Astrophysics Data System (ADS)

    Lupie, O.; Lallo, M.; Cox, C.; Bergeron, E.

    1997-08-01

    This technical memo documents the alignment calibration, spreadsheet model modifications and the update of aperture tables using results from in-flight NICM alignment tests performed during the Second Servicing Mission Orbital Verification Phase.

  2. SIM Lite: ground alignment of the instrument

    NASA Astrophysics Data System (ADS)

    Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

    2010-07-01

    We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

  3. SIM Lite: Ground Alignment of the Instrument

    NASA Technical Reports Server (NTRS)

    Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

    2010-01-01

    We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

  4. Threaded pilot insures cutting tool alignment

    NASA Technical Reports Server (NTRS)

    Goldman, R.; Schneider, W. E.

    1966-01-01

    Threaded pilot allows machining of a port component, or boss, after the reciprocating hole has been threaded. It is used to align cutting surfaces with the boss threads, thus insuring precision alignment.

  5. Structural analysis of aligned RNAs.

    PubMed

    Voss, Björn

    2006-01-01

    The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de. PMID:17020924

  6. Grain alignment in starless cores

    SciTech Connect

    Jones, T. J.; Bagley, M.; Krejny, M.; Andersson, B.-G.; Bastien, P.

    2015-01-01

    We present near-IR polarimetry data of background stars shining through a selection of starless cores taken in the K band, probing visual extinctions up to A{sub V}∼48. We find that P{sub K}/τ{sub K} continues to decline with increasing A{sub V} with a power law slope of roughly −0.5. Examination of published submillimeter (submm) polarimetry of starless cores suggests that by A{sub V}≳20 the slope for P versus τ becomes ∼−1, indicating no grain alignment at greater optical depths. Combining these two data sets, we find good evidence that, in the absence of a central illuminating source, the dust grains in dense molecular cloud cores with no internal radiation source cease to become aligned with the local magnetic field at optical depths greater than A{sub V}∼20. A simple model relating the alignment efficiency to the optical depth into the cloud reproduces the observations well.

  7. Text-image alignment for historical handwritten documents

    NASA Astrophysics Data System (ADS)

    Zinger, S.; Nerbonne, J.; Schomaker, L.

    2009-01-01

    We describe our work on text-image alignment in context of building a historical document retrieval system. We aim at aligning images of words in handwritten lines with their text transcriptions. The images of handwritten lines are automatically segmented from the scanned pages of historical documents and then manually transcribed. To train automatic routines to detect words in an image of handwritten text, we need a training set - images of words with their transcriptions. We present our results on aligning words from the images of handwritten lines and their corresponding text transcriptions. Alignment based on the longest spaces between portions of handwriting is a baseline. We then show that relative lengths, i.e. proportions of words in their lines, can be used to improve the alignment results considerably. To take into account the relative word length, we define the expressions for the cost function that has to be minimized for aligning text words with their images. We apply right to left alignment as well as alignment based on exhaustive search. The quality assessment of these alignments shows correct results for 69% of words from 100 lines, or 90% of partially correct and correct alignments combined.

  8. Alignment mechanisms of paramagnetic grains revisited

    NASA Technical Reports Server (NTRS)

    Seki, Munezo

    1989-01-01

    Taking into account the tight coupling of grain axis with angular momentum due to effective dissipation of rotation energy, the alignment of spheroidal grains was investigated by paramagnetic relaxation. Alignment degree will be significantly improved in diffuse clouds. The inclusions of superparamagnetic (SPM) substances may play a key role in grain alignment in dark clouds as well as in diffuse clouds.

  9. Ultrafast electron diffraction from aligned molecules

    SciTech Connect

    Centurion, Martin

    2015-08-17

    The aim of this project was to record time-resolved electron diffraction patterns of aligned molecules and to reconstruct the 3D molecular structure. The molecules are aligned non-adiabatically using a femtosecond laser pulse. A femtosecond electron pulse then records a diffraction pattern while the molecules are aligned. The diffraction patterns are then be processed to obtain the molecular structure.

  10. Vertically aligned nanostructure scanning probe microscope tips

    SciTech Connect

    Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

    2006-12-19

    Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

  11. Physician-Hospital Alignment in Orthopedic Surgery.

    PubMed

    Bushnell, Brandon D

    2015-09-01

    The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. PMID:26375539

  12. Accelerator and transport line survey and alignment

    SciTech Connect

    Ruland, R.E.

    1991-10-01

    This paper summarizes the survey and alignment processes of accelerators and transport lines and discusses the propagation of errors associated with these processes. The major geodetic principles governing the survey and alignment measurement space are introduced and their relationship to a lattice coordinate system shown. The paper continues with a broad overview about the activities involved in the step sequence from initial absolute alignment to final smoothing. Emphasis is given to the relative alignment of components, in particular to the importance of incorporating methods to remove residual systematic effects in surveying and alignment operations. Various approaches to smoothing used at major laboratories are discussed. 47 refs., 19 figs., 1 tab.

  13. Statistical significance of normalized global alignment.

    PubMed

    Peris, Guillermo; Marzal, Andrés

    2014-03-01

    The comparison of homologous proteins from different species is a first step toward a function assignment and a reconstruction of the species evolution. Though local alignment is mostly used for this purpose, global alignment is important for constructing multiple alignments or phylogenetic trees. However, statistical significance of global alignments is not completely clear, lacking a specific statistical model to describe alignments or depending on computationally expensive methods like Z-score. Recently we presented a normalized global alignment, defined as the best compromise between global alignment cost and length, and showed that this new technique led to better classification results than Z-score at a much lower computational cost. However, it is necessary to analyze the statistical significance of the normalized global alignment in order to be considered a completely functional algorithm for protein alignment. Experiments with unrelated proteins extracted from the SCOP ASTRAL database showed that normalized global alignment scores can be fitted to a log-normal distribution. This fact, obtained without any theoretical support, can be used to derive statistical significance of normalized global alignments. Results are summarized in a table with fitted parameters for different scoring schemes. PMID:24400820

  14. Antares beam-alignment-system performance

    SciTech Connect

    Appert, Q.D.; Bender, S.C.

    1983-01-01

    The beam alignment system for the 24-beam-sector Antares CO/sub 2/ fusion laser automatically aligns more than 200 optical elements. A visible-wavelength alignment technique is employed which uses a telescope/TV system to view point-light sources appropriately located down the beamline. The centroids of the light spots are determined by a video tracker, which generates error signals used by the computer control system to move appropriate mirrors in a closed-loop system. Final touch-up alignment is accomplished by projecting a CO/sub 2/ alignment laser beam through the system and sensing its position at the target location. The techniques and control algorithms employed have resulted in alignment accuracies exceeding design requirements. By employing video processing to determine the centroids of diffraction images and by averaging over multiple TV frames, we achieve alignment accuracies better than 0.1 times system diffraction limits in the presence of air turbulence.

  15. Target alignment in the National Ignition Facility

    SciTech Connect

    Vann, C.S.; Bliss, E.S.; Murray, J.E.

    1994-06-06

    Accurate placement of hundreds of focused laser beams on target is necessary to achieve success in the National Ignition Facility (NIF). The current system requirement is {le}7 {mu}rad error in output pointing and {le}1 mm error in focusing. To accommodate several system shots per day, a target alignment system must be able to align the target to chamber center, inject an alignment beam to represent each shot beam, and point and focus the alignment beams onto the target in about one hour. At Lawrence Livermore National Laboratory, we have developed a target alignment concept and built a prototype to validate the approach. The concept comprises three systems: the chamber center reference, target alignment sensor, and target alignment beams.

  16. Combining Multiple Pairwise Structure-based Alignments

    2014-11-12

    CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a newmore » tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.« less

  17. Multiscale peak alignment for chromatographic datasets.

    PubMed

    Zhang, Zhi-Min; Liang, Yi-Zeng; Lu, Hong-Mei; Tan, Bin-Bin; Xu, Xiao-Na; Ferro, Miguel

    2012-02-01

    Chromatography has been extensively applied in many fields, such as metabolomics and quality control of herbal medicines. Preprocessing, especially peak alignment, is a time-consuming task prior to the extraction of useful information from the datasets by chemometrics and statistics. To accurately and rapidly align shift peaks among one-dimensional chromatograms, multiscale peak alignment (MSPA) is presented in this research. Peaks of each chromatogram were detected based on continuous wavelet transform (CWT) and aligned against a reference chromatogram from large to small scale gradually, and the aligning procedure is accelerated by fast Fourier transform cross correlation. The presented method was compared with two widely used alignment methods on chromatographic dataset, which demonstrates that MSPA can preserve the shapes of peaks and has an excellent speed during alignment. Furthermore, MSPA method is robust and not sensitive to noise and baseline. MSPA was implemented and is available at http://code.google.com/p/mspa. PMID:22222564

  18. 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.

  19. Pupil Alignment Measuring Technique and Alignment Reference for Instruments or Optical Systems

    NASA Technical Reports Server (NTRS)

    Hagopian, John G.

    2010-01-01

    A technique was created to measure the pupil alignment of instruments in situ by measuring calibrated pupil alignment references (PARs) in instruments. The PAR can also be measured using an alignment telescope or an imaging system. PAR allows the verification of the science instrument (SI) pupil alignment at the integrated science instrument module (ISIM) level of assembly at ambient and cryogenic operating temperature. This will allow verification of the ISIM+SI alignment, and provide feedback to realign the SI if necessary.

  20. Ridge effect and alignment phenomenon

    SciTech Connect

    Lokhtin, I. P. Managadze, A. K. Snigirev, A. M.

    2013-05-15

    It is assumed that the ridge effect observed by the CMS Collaboration in proton-proton collisions at the LHC and the phenomenon observed by the Pamir Collaboration in emulsion experiments with cosmic rays and characterized by the alignment of spots on a film is a manifestation of the same as-yet-unknown mechanism of the emergence of a coplanar structure of events. A large coplanar effect at the LHC in the region of forward rapidities is predicted on the basis of this hypothesis and an analysis of experimental data.

  1. Aligned interactions in cosmic rays

    NASA Astrophysics Data System (ADS)

    Kempa, J.

    2015-12-01

    The first clean Centauro was found in cosmic rays years many ago at Mt Chacaltaya experiment. Since that time, many people have tried to find this type of interaction, both in cosmic rays and at accelerators. But no one has found a clean cases of this type of interaction.It happened finally in the last exposure of emulsion at Mt Chacaltaya where the second clean Centauro has been found. The experimental data for both the Centauros and STRANA will be presented and discussed in this paper. We also present our comments to the intriguing question of the existence of a type of nuclear interactions at high energy with alignment.

  2. Aligned interactions in cosmic rays

    SciTech Connect

    Kempa, J.

    2015-12-15

    The first clean Centauro was found in cosmic rays years many ago at Mt Chacaltaya experiment. Since that time, many people have tried to find this type of interaction, both in cosmic rays and at accelerators. But no one has found a clean cases of this type of interaction.It happened finally in the last exposure of emulsion at Mt Chacaltaya where the second clean Centauro has been found. The experimental data for both the Centauros and STRANA will be presented and discussed in this paper. We also present our comments to the intriguing question of the existence of a type of nuclear interactions at high energy with alignment.

  3. MEANS FOR DETERMINING CENTRIFUGE ALIGNMENT

    DOEpatents

    Smith, W.Q.

    1958-08-26

    An apparatus is presented for remotely determining the alignment of a centrifuge. The centrifage shaft is provided with a shoulder, upon which two followers ride, one for detecting radial movements, and one upon the shoulder face for determining the axial motion. The followers are attached to separate liquid filled bellows, and a tube connects each bellows to its respective indicating gage at a remote location. Vibrations produced by misalignment of the centrifuge shaft are transmitted to the bellows, and tbence through the tubing to the indicator gage. This apparatus is particularly useful for operation in a hot cell where the materials handled are dangerous to the operating personnel.

  4. Method for protein structure alignment

    DOEpatents

    Blankenbecler, Richard; Ohlsson, Mattias; Peterson, Carsten; Ringner, Markus

    2005-02-22

    This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

  5. Strategies for active alignment of lenses

    NASA Astrophysics Data System (ADS)

    Langehanenberg, Patrik; Heinisch, Josef; Wilde, Chrisitan; Hahne, Felix; Lüerß, Bernd

    2015-10-01

    Today's optical systems require up-to-date assembly and joining technology. The trend of keeping dimensions as small as possible while maintaining or increasing optical imaging performance leaves little to no room for mechanical lens adjustment equipment that may remain in the final product. In this context active alignment of optical elements opens up possibilities for the fast and cost-economic manufacturing of lenses and lens assemblies with highest optical performance. Active alignment for lens manufacturing is the precise alignment of the optical axis of a lens with respect to an optical or mechanical reference axis (e.g. housing) including subsequent fixation by glue. In this contribution we will describe different approaches for active alignment and outline strengths and limitations of the different methods. Using the SmartAlign principle, highest quality cemented lenses can be manufactured without the need for high precision prealignment, while the reduction to a single alignment step greatly reduces the cycle time. The same strategies can also be applied to bonding processes. Lenses and lens groups can be aligned to both mechanical and optical axes to maximize the optical performance of a given assembly. In hybrid assemblies using both mechanical tolerances and active alignment, SmartAlign can be used to align critical lens elements anywhere inside the system for optimized total performance. Since all geometrical parameters are re-measured before each alignment, this process is especially suited for complex and time-consuming production processes where the stability of the reference axis would otherwise be critical. For highest performance, lenses can be actively aligned using up to five degrees of freedom. In this way, SmartAlign enables the production of ultra-precise mounted lenses with an alignment precision below 1 μm.

  6. Measuring alignment of loading fixture

    DOEpatents

    Scavone, Donald W.

    1989-01-01

    An apparatus and method for measuring the alignment of a clevis and pin type loading fixture for compact tension specimens include a pair of substantially identical flat loading ligaments. Each loading ligament has two apertures for the reception of a respective pin of the loading fixture and a thickness less than one-half of a width of the clevis opening. The pair of loading ligaments are mounted in the clevis openings at respective sides thereof. The loading ligaments are then loaded by the pins of the loading fixture and the strain in each loading ligament is measured. By comparing the relative strain of each loading ligament, the alignment of the loading fixture is determined. Preferably, a suitable strain gage device is located at each longitudinal edge of a respective loading ligament equidistant from the two apertures in order to determine the strain thereat and hence the strain of each ligament. The loading ligaments are made substantially identical by jig grinding the loading ligaments as a matched set. Each loading ligament can also be individually calibrated prior to the measurement.

  7. VISA undulator fiducialization and alignment

    SciTech Connect

    1999-12-13

    As part of the R and D program towards a fourth generation light source, a Self-Amplified Spontaneous Emission (SASE) demonstration is being prepared. The Visible-Infrared SASE Amplifier (VISA) undulator will be installed at Brookhaven National Laboratory by the end of the year. The VISA undulator is an in-vacuum, 4-meter long, 1.8 cm period, pure-permanent magnet device, with a novel, strong focusing, permanent magnet FODO array included within the fixed, 6 mm undulator gap. The undulator is constructed of 99 cm long segments. To attain maximum SASE gain requires establishing overlap of electron and photon beams to within 50 {micro}m rms. This imposes challenging tolerances on mechanical fabrication and magnetic field quality, and necessitates use of laser straightness interferometry for calibration and alignment of the magnetic axes of the undulator segments. This paper describes the magnetic centerline determination, and the fiducialization and alignment processes which were performed to meet the tolerance goal.

  8. ARYANA: Aligning Reads by Yet Another Approach

    PubMed Central

    2014-01-01

    Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

  9. Alignment of atmospheric mineral dust due to electric field

    NASA Astrophysics Data System (ADS)

    Ulanowski, Z.; Bailey, J.; Lucas, P. W.; Hough, J. H.; Hirst, E.

    2007-12-01

    Optical polarimetry observations on La Palma, Canary Islands, during a Saharan dust episode show dichroic extinction indicating the presence of vertically aligned particles in the atmosphere. Modelling of the extinction together with particle orientation indicates that the alignment could have been due to an electric field of the order of 2 kV/m. Two alternative mechanisms for the origin of the field are examined: the effect of reduced atmospheric conductivity and charging of the dust layer, the latter effect being a more likely candidate. It is concluded that partial alignment may be a common feature of Saharan dust layers. The modelling indicates that the alignment can significantly alter dust optical depth. This "Venetian blind effect" may have decreased optical thickness in the vertical direction by as much as 10% for the case reported here. It is also possible that the alignment and the electric field modify dust transport.

  10. Magnetic alignment and patterning of cellulose fibers

    NASA Astrophysics Data System (ADS)

    Kimura, Fumiko; Kimura, Tsunehisa

    2008-04-01

    The alignment and patterning of cellulose fibers under magnetic fields are reported. Static and rotating magnetic fields were used to align cellulose fibers with sizes ranging from millimeter to nanometer sizes. Cellulose fibers of the millimeter order, which were prepared for papermaking, and much smaller fibers with micrometer to nanometer sizes prepared by the acid hydrolysis of larger ones underwent magnetic alignment. Under a rotating field, a uniaxial alignment of fibers was achieved. The alignment was successfully fixed by the photopolymerization of a UV-curable resin precursor used as matrix. A monodomain chiral nematic film was prepared from an aqueous suspension of nanofibers. Using a field modulator inserted in a homogeneous magnetic field, simultaneous alignment and patterning were achieved.

  11. Innovative optical alignment technique for CMP wafers

    NASA Astrophysics Data System (ADS)

    Sugaya, Ayako; Kanaya, Yuho; Nakajima, Shinichi; Nagayama, Tadashi; Shiraishi, Naomasa

    2002-07-01

    Detecting position of the wafers such as after CMP process is critical theme of current and forthcoming IC manufacturing. The alignment system must be with high accuracy for any process. To satisfy such requirements, we have studied and analyzed factors that have made alignment difficult. From the result of the studies, we have developed new optical alignment techniques which improve the accuracy of FIA (alignment sensor of Nikon's NSR series) and examined them. The approaches are optimizing the focus position, developing an advanced algorithm for position detection, and selecting a suitable mark design. For experiment, we have developed the special wafers that make it possible to evaluate the influence of CMP processes. The experimental results show that the overlay errors decrease dramatically with the new alignment techniques. FIA with these new techniques will be much accurate and suitable alignment sensor for CMP and other processes of future generation ULSI production.

  12. Laminar silk scaffolds for aligned tissue fabrication

    PubMed Central

    Mandal, Biman B.; Gil, Eun Seok; Panilaitis, Bruce; Kaplan, David L.

    2013-01-01

    3D biomaterial scaffolds with aligned architecture are of vital importance in tissue regeneration to mimic native tissue hierarchy and hence function. We demonstrate a generic method to produce aligned biomaterial scaffolds using the physics of directional ice freezing. Homogeneously aligned 3D silk scaffold with high porosity and alignment was demonstrated. The method can be adapted to a wide range of polymers and is devoid of any chemical reactions, thus avoiding potential complications associated with by-products and purification procedures. Subsequently, the 3D aligned system was tested for mechanical properties and cellular responses with chondrocytes and bone marrow derived human mesenchymal stem cells, assessing survival, proliferation and differentiation. In vivo tests suggested biocompatibility of the matrices for future tissue engineering applications, specifically in areas where high cellular alignment is needed. PMID:23161731

  13. Multiple alignment using hidden Markov models

    SciTech Connect

    Eddy, S.R.

    1995-12-31

    A simulated annealing method is described for training hidden Markov models and producing multiple sequence alignments from initially unaligned protein or DNA sequences. Simulated annealing in turn uses a dynamic programming algorithm for correctly sampling suboptimal multiple alignments according to their probability and a Boltzmann temperature factor. The quality of simulated annealing alignments is evaluated on structural alignments of ten different protein families, and compared to the performance of other HMM training methods and the ClustalW program. Simulated annealing is better able to find near-global optima in the multiple alignment probability landscape than the other tested HMM training methods. Neither ClustalW nor simulated annealing produce consistently better alignments compared to each other. Examination of the specific cases in which ClustalW outperforms simulated annealing, and vice versa, provides insight into the strengths and weaknesses of current hidden Maxkov model approaches.

  14. 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.

  15. AIMFAST: Alignment Implementation for Manufacturing

    SciTech Connect

    2012-09-13

    AIMFAST is a software code used to align facets on a dish concentrator to a specific aimpoint strategy to minimize peak fluxes and maximize system optical performance. AIMFAST uses a large monitor or projections screen to display fringe patterns, and a machine vision camera to image the reflection of these patterns in the subject dish mirrors. From these images, a detailed map of surface normals can be generated and compared to design or fitted mirror shapes. This fitted comparison is then used to develop a single vector representing the orientation of the facets relative to the design orientation, and provide near-real-time adjustment information to a communicating computer. The communicating computer can display adjustments or directly interface with adjustment tools. The software for the communicating computer is specific to the implementation and is not a part of AIMFAST.

  16. The Alignment of Galaxy Structures

    NASA Astrophysics Data System (ADS)

    Biernacka, M.; Panko, E.; Bajan, K.; Godłowski, W.; Flin, P.

    2015-11-01

    We analyzed the orientation of the sample of ACO galaxy clusters. We examined the alignment in a subsample of 1056 galaxy structures taken from the Panko-Flin (2006) Catalog with known BM morphological types. We were looking for a correlation between the orientation of the cluster and the positions of neighboring clusters. The Binggeli effect (the excess of small values of the Δθ angles between the direction toward neighboring clusters and the cluster position angle) is observed, having a range up to about 45 h-1 Mpc. The strongest effect was found for elongated BM type I clusters. This is probably connected with the origins of the supergiant galaxy and with cluster formation along a long filament or plane in a supercluster.

  17. AIMFAST: Alignment Implementation for Manufacturing

    2012-09-13

    AIMFAST is a software code used to align facets on a dish concentrator to a specific aimpoint strategy to minimize peak fluxes and maximize system optical performance. AIMFAST uses a large monitor or projections screen to display fringe patterns, and a machine vision camera to image the reflection of these patterns in the subject dish mirrors. From these images, a detailed map of surface normals can be generated and compared to design or fitted mirrormore » shapes. This fitted comparison is then used to develop a single vector representing the orientation of the facets relative to the design orientation, and provide near-real-time adjustment information to a communicating computer. The communicating computer can display adjustments or directly interface with adjustment tools. The software for the communicating computer is specific to the implementation and is not a part of AIMFAST.« less

  18. IAIMFAST: Alignment Implementation for Manufacturing

    2013-08-29

    AIMFAST is a software code used to align facets on a dish concentrator to a specific aimpoint strategy to minimize peak fluxes and maximize system optical performance. AIM FAST uses a large monitor to display fringe patterns, and a machine vision camera to image the reflection of these patterns in the subject dish mirrors. From these images, a detailed map of surface normals can be generated and compared to design or fitted mirror shapes. Thismore » fitted comparison is then used to develop a single vector representing the orientation of the facets relative to the design orientation, and provide near-real-time adjustment information to a communicating computer. The communicating computer can display adjustments or directly interface with adjustment tools.« less

  19. Magnetic alignment of grains. [in interstellar space

    NASA Technical Reports Server (NTRS)

    Hildebrand, Roger H.

    1988-01-01

    This paper reviews mechanisms that have been proposed to account for alignment of dust grains in diffuse clouds and in dense clouds. The mechanisms that have proved inadequate are considered, including alignment by nonmagnetic and magnetic processes. The results thus far favor the Davis-Greenstein mechanism, in which paramagnetic relaxation of spinning grains removes components of rotation perpendicular to the magnetic field. Polarization measurements showing the alignment of grains in cool dense clouds are discussed.

  20. COS to FGS Alignment {NUV}

    NASA Astrophysics Data System (ADS)

    Hartig, George

    2009-07-01

    DESCRIPTION: In order to determine the location of the COS reference frame with respect to the FGS reference frames, NUV MIRRORA images will be obtained of an astrometric target and field. Astrometric guide stars and targets must be employed for this activity in order to facilitate the alignment wth the FGS. Images will be obtained at the initial pointing and at positions offset in V2 and in V3. Starting with the original blind pointing, obtain MIRRORA image exposures in a 5x5 POS-TARG grid centered on initial pointing; repeat the image sequence at two bracketing focus positions in same visit. Following completion of third pattern, return to nominal focus and perform 5x5 ACQ/SEARCH target acquisition and obtain one TIME-TAG MIRRORA image and one ACCUM verification exposure. Next perform an ACQ/IMAGE target acquisition followed by an ACCUM verification exposure. Also obtain ACCUM verification exposure for each of the two alternate focus positions used previously. Using MIRRORB obtain ACCUM confirmation image at nominal focus and ACCUM images at alternate focus positions and then perform an ACQ/IMAGE and confirming image at nominal focus. Analyze imagery, uplink pointing offset as offset 11469A and adjust nominal focus via patchable constant uplinked with subsequent visit of this program; update aperture locations via modified SIAF file uplinked with subsequent SMS. Use updated focus and offset pointing as input for COS 09 {program 11469 - NUV Optics Alignment and Focus} {note the SIAF update is not a prerequisite for COS 09 to proceed, but the pointing offset and focus update are}.

  1. Advancements of vertically aligned liquid crystal displays.

    PubMed

    Kumar, Pankaj; Jaggi, Chinky; Sharma, Vandna; Raina, Kuldeep Kumar

    2016-02-01

    This review describes the recent advancements in the field of the vertical aligned (VA) liquid crystal displays. The process and formation of different vertical alignment modes such as conventional VA, patterned VA, multi-domain VA, and polymer stabilised VA etc are widely discussed. Vertical alignment of liquid crystal due to nano particle dispersion in LC host, bifunctional PR-SAM formed by silane coupling reaction to oxide surfaces, azo dye etc., are also highlighted and discussed. Overall, the article highlights the advances in the research of vertical aligned liquid crystal in terms of their scientific and technological aspects. PMID:26800482

  2. DNAAlignEditor: DNA alignment editor tool

    PubMed Central

    Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

    2008-01-01

    Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism. PMID:18366684

  3. Anisotropic light emission from aligned luminophores

    NASA Astrophysics Data System (ADS)

    Verbunt, Paul P. C.; de Jong, Ties M.; de Boer, Dick K. G.; Broer, Dirk J.; Debije, Michael G.

    2014-07-01

    The emission of aligned dichroic dyes in a luminescent solar concentrator (LSC) illuminated from one side with collimated light results in a non-isotropic light distribution. We develop a model to describe emission profiles for dichroic dyes aligned at a general tilt angle with respect to a lightguide surface (including planar and homeotropic alignments) for various order parameters. We compare calculations with experimental results, demonstrating the dichroic nature of the dyes can have significant impact on the surface loss of luminescent solar concentrators. Including this dichroic nature is essential in correctly simulating the preferred edge emissions demonstrated experimentally in dyes aligned planarly on the surface of a lightguide.

  4. Liquid crystal alignment in cylindrical microcapillaries

    NASA Astrophysics Data System (ADS)

    Chychłowski, M.; Yaroshchuk, O.; Kravchuk, R.; Woliński, T.

    2011-09-01

    A variety of alignment configurations of liquid crystals (LCs) inside the glassy cylindrical capillaries is realized by using alignment materials providing different anchoring. The radial configuration with central disclination line is obtained for homeotropic boundary conditions. In turn, the axial, transversal and tilted alignment structures are realized by using materials for planar anchoring. The uniformity and controlling of the latter structures were provided by photoalignment method. This approach can be further used to control LC alignment in the photonic crystal fibers recognized as advanced elements for different optical devices.

  5. Liquid crystal alignment in cylindrical microcapillaries

    NASA Astrophysics Data System (ADS)

    Chychłowski, M.; Yaroshchuk, O.; Kravchuk, R.; Woliński, T.

    2012-03-01

    A variety of alignment configurations of liquid crystals (LCs) inside the glassy cylindrical capillaries is realized by using alignment materials providing different anchoring. The radial configuration with central disclination line is obtained for homeotropic boundary conditions. In turn, the axial, transversal and tilted alignment structures are realized by using materials for planar anchoring. The uniformity and controlling of the latter structures were provided by photoalignment method. This approach can be further used to control LC alignment in the photonic crystal fibers recognized as advanced elements for different optical devices.

  6. Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

    SciTech Connect

    Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.; Grama, Ananth

    2015-11-01

    Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.

  7. Alignments between galaxies, satellite systems and haloes

    NASA Astrophysics Data System (ADS)

    Shao, Shi; Cautun, Marius; Frenk, Carlos S.; Gao, Liang; Crain, Robert A.; Schaller, Matthieu; Schaye, Joop; Theuns, Tom

    2016-08-01

    The spatial distribution of the satellite populations of the Milky Way and Andromeda are puzzling in that they are nearly perpendicular to the disks of their central galaxies. To understand the origin of such configurations we study the alignment of the central galaxy, satellite system and dark matter halo in the largest of the "Evolution and Assembly of GaLaxies and their Environments" (EAGLE) simulation. We find that centrals and their satellite systems tend to be well aligned with their haloes, with a median misalignment angle of $33^{\\circ}$ in both cases. While the centrals are better aligned with the inner $10$ kpc halo, the satellite systems are better aligned with the entire halo indicating that satellites preferentially trace the outer halo. The central - satellite alignment is weak (median misalignment angle of $52^{\\circ}$) and we find that around $20\\%$ of systems have a misalignment angle larger than $78^{\\circ}$, which is the value for the Milky Way. The central - satellite alignment is a consequence of the tendency of both components to align with the dark matter halo. As a consequence, when the central is parallel to the satellite system, it also tends to be parallel to the halo. In contrast, if the central is perpendicular to the satellite system, as in the case of the Milky Way and Andromeda, then the central - halo alignment is much weaker. Dispersion-dominated (spheroidal) centrals have a stronger alignment with both their halo and their satellites than rotation-dominated (disk) centrals. We also found that the halo, the central galaxy and the satellite system tend to be aligned with the surrounding large-scale distribution of matter, with the halo being the better aligned of the three.

  8. Alignments between galaxies, satellite systems and haloes

    NASA Astrophysics Data System (ADS)

    Shao, Shi; Cautun, Marius; Frenk, Carlos S.; Gao, Liang; Crain, Robert A.; Schaller, Matthieu; Schaye, Joop; Theuns, Tom

    2016-08-01

    The spatial distribution of the satellite populations of the Milky Way and Andromeda are puzzling in that they are nearly perpendicular to the discs of their central galaxies. To understand the origin of such configurations we study the alignment of the central galaxy, satellite system and dark matter halo in the largest of the `Evolution and Assembly of GaLaxies and their Environments' (EAGLE) simulation. We find that centrals and their satellite systems tend to be well aligned with their haloes, with a median misalignment angle of 33° in both cases. While the centrals are better aligned with the inner 10 kpc halo, the satellite systems are better aligned with the entire halo indicating that satellites preferentially trace the outer halo. The central-satellite alignment is weak (median misalignment angle of 52°) and we find that around 20 per cent of systems have a misalignment angle larger than 78°, which is the value for the Milky Way. The central-satellite alignment is a consequence of the tendency of both components to align with the dark matter halo. As a consequence, when the central is parallel to the satellite system, it also tends to be parallel to the halo. In contrast, if the central is perpendicular to the satellite system, as in the case of the Milky Way and Andromeda, then the central-halo alignment is much weaker. Dispersion-dominated (spheroidal) centrals have a stronger alignment with both their halo and their satellites than rotation-dominated (disc) centrals. We also found that the halo, the central galaxy and the satellite system tend to be aligned with the surrounding large-scale distribution of matter, with the halo being the better aligned of the three.

  9. Implementation of two-state alignment system into CXrL aligner (Poster Paper)

    NASA Astrophysics Data System (ADS)

    Chen, Guan-Jye; Bodoh, D.; Wallace, John P.; Anderson, Paul D.; Reilly, Michael T.; Nachman, Ramez; Cerrina, Franco

    1992-07-01

    We describe the implementation of the two-state alignment system into the CXrL aligner, which is developed at our Center for X-ray Lithography. The CXrL aligner is designed to expose sub 0.25 μm feature size integrated circuits. The aligner consists of a three-axes two-state alignment system for alignment error detection and a piezo based precision mechanical stage for alignment error correction. The wafer is held by a precision vacuum chuck, while the mask is held by three vacuum suction cups located around the glass ring. In the prototype, the mask to wafer relative positioning is achieved by 3 motorized stages (for gap setting) and 3 piezo-actuators (for lateral alignment). Since the optical system is designed to be located outside of the synchrotron radiation path, alignment can be performed during exposure. We present the results of the alignment system performance, such as noise equivalent displacement and alignment signal response time. An alignment signal repeatibility of much better than 3σ = 0.07μm is achieved. We also briefly describe the future evaluation of the system, such as overlay measurement of the system using verniers and SEM inspection of some specially designed patterns.

  10. X-ray determination of parts alignment

    NASA Technical Reports Server (NTRS)

    Nelson, C. W.

    1985-01-01

    A method for determining the alignment of adjoining metal objects is provided. The method comprises producing an X-ray image of adjoining surfaces of the two metal objects. The X-ray beam is tangential to the point the surfaces are joined. The method is particularly applicable where the alignment of the two metal objects is not readily susceptible to visual inspection.

  11. Phylogenetic Inference From Conserved sites Alignments

    SciTech Connect

    grundy, W.N.; Naylor, G.J.P.

    1999-08-15

    Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly conserved, motif regions of the alignment. This work introduces two methods of producing multiple alignments that include only the conserved regions of the initial alignment. The first method retains conserved motifs, whereas the second retains individual conserved sites in the initial alignment. Using parsimony analysis on a mitochondrial data set containing 19 species among which the phylogenetic relationships are widely accepted, both conserved alignment methods produce better phylogenetic trees than the complete alignment. Unlike any of the 19 inference methods used before to analyze this data, both methods produce trees that are completely consistent with the known phylogeny. The motif-based method employs far fewer alignment sites for comparable error rates. For a larger data set containing mitochondrial sequences from 39 species, the site-based method produces a phylogenetic tree that is largely consistent with known phylogenetic relationships and suggests several novel placements.

  12. Achieving Organisational Change through Values Alignment

    ERIC Educational Resources Information Center

    Branson, Christopher M.

    2008-01-01

    Purpose: The purpose of this paper is to, first, establish the interdependency between the successful achievement of organisational change and the attainment of values alignment within an organisation's culture and then, second, to describe an effective means for attaining such values alignment. Design/methodology/approach: Literature from the…

  13. Evaluating Alignment between Curriculum, Assessment, and Instruction

    ERIC Educational Resources Information Center

    Martone, Andrea; Sireci, Stephen G.

    2009-01-01

    The authors (a) discuss the importance of alignment for facilitating proper assessment and instruction, (b) describe the three most common methods for evaluating the alignment between state content standards and assessments, (c) discuss the relative strengths and limitations of these methods, and (d) discuss examples of applications of each…

  14. Instructional Alignment under No Child Left Behind

    ERIC Educational Resources Information Center

    Polikoff, Morgan S.

    2012-01-01

    The alignment of instruction with the content of standards and assessments is the key mediating variable separating the policy of standards-based reform (SBR) from the outcome of improved student achievement. Few studies have investigated SBR's effects on instructional alignment, and most have serious methodological limitations. This research uses…

  15. Systematic Agreement: A Theory of Organizational Alignment.

    ERIC Educational Resources Information Center

    Semler, Steven W.

    1997-01-01

    The theory of organizational alignment considers the extent to which organizational strategy, structure, and culture create an environment that facilitates achievement of organizational objectives and development of high performance work organizations. Well-aligned organizations have systematic agreement among goals, tactics, reward systems, and…

  16. Precision aligned split V-block

    DOEpatents

    George, Irwin S.

    1984-01-01

    A precision aligned split V-block for holding a workpiece during a milling operation having an expandable frame for allowing various sized workpieces to be accommodated, is easily secured directly to the mill table and having key lugs in one base of the split V-block that assures constant alignment.

  17. Evaluating Content Alignment in Computerized Adaptive Testing

    ERIC Educational Resources Information Center

    Wise, Steven L.; Kingsbury, G. Gage; Webb, Norman L.

    2015-01-01

    The alignment between a test and the content domain it measures represents key evidence for the validation of test score inferences. Although procedures have been developed for evaluating the content alignment of linear tests, these procedures are not readily applicable to computerized adaptive tests (CATs), which require large item pools and do…

  18. On comparing two structured RNA multiple alignments.

    PubMed

    Patel, Vandanaben; Wang, Jason T L; Setia, Shefali; Verma, Anurag; Warden, Charles D; Zhang, Kaizhong

    2010-12-01

    We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at http://bioinformatics.njit.edu/blockmatch. A jar file of the program is also available for download from the web server. PMID:21121021

  19. Nonvisual Cues for Aligning to Cross Streets

    ERIC Educational Resources Information Center

    Scott, Alan C.; Barlow, Janet M.; Guth, David A.; Bentzen, Billie Louise; Cunningham, Christopher M.; Long, Richard

    2011-01-01

    Accurately aligning to a crosswalk is an important component of safe street crossing for pedestrians who are blind. Six alignment cues were evaluated in a simulated crosswalk environment in which the angle of the crosswalk was not always in line with the slope of the ramp. The effectiveness of each cue is reported and implications are discussed.…

  20. Aligning the μs-ALEX Setup.

    PubMed

    Kapanidis, Achillefs; Majumdar, Devdoot; Heilemann, Mike; Nir, Eyal; Weiss, Shimon

    2015-11-01

    To achieve single-molecule sensitivity and thus have the ability to detect single diffusing fluorophores, careful alignment of the microsecond-alternating laser excitation (μs-Alex) setup is crucial. The following protocol describes routine alignment for 2c-ALEX (532 nm/635 nm) with spectral windows G(550-620)R(650-750). PMID:26527766

  1. Probabilistic sequence alignment of stratigraphic records

    NASA Astrophysics Data System (ADS)

    Lin, Luan; Khider, Deborah; Lisiecki, Lorraine E.; Lawrence, Charles E.

    2014-10-01

    The assessment of age uncertainty in stratigraphically aligned records is a pressing need in paleoceanographic research. The alignment of ocean sediment cores is used to develop mutually consistent age models for climate proxies and is often based on the δ18O of calcite from benthic foraminifera, which records a global ice volume and deep water temperature signal. To date, δ18O alignment has been performed by manual, qualitative comparison or by deterministic algorithms. Here we present a hidden Markov model (HMM) probabilistic algorithm to find 95% confidence bands for δ18O alignment. This model considers the probability of every possible alignment based on its fit to the δ18O data and transition probabilities for sedimentation rate changes obtained from radiocarbon-based estimates for 37 cores. Uncertainty is assessed using a stochastic back trace recursion to sample alignments in exact proportion to their probability. We applied the algorithm to align 35 late Pleistocene records to a global benthic δ18O stack and found that the mean width of 95% confidence intervals varies between 3 and 23 kyr depending on the resolution and noisiness of the record's δ18O signal. Confidence bands within individual cores also vary greatly, ranging from ~0 to >40 kyr. These alignment uncertainty estimates will allow researchers to examine the robustness of their conclusions, including the statistical evaluation of lead-lag relationships between events observed in different cores.

  2. Galaxy Alignments: Observations and Impact on Cosmology

    NASA Astrophysics Data System (ADS)

    Kirk, Donnacha; Brown, Michael L.; Hoekstra, Henk; Joachimi, Benjamin; Kitching, Thomas D.; Mandelbaum, Rachel; Sifón, Cristóbal; Cacciato, Marcello; Choi, Ami; Kiessling, Alina; Leonard, Adrienne; Rassat, Anais; Schäfer, Björn Malte

    2015-11-01

    Galaxy shapes are not randomly oriented, rather they are statistically aligned in a way that can depend on formation environment, history and galaxy type. Studying the alignment of galaxies can therefore deliver important information about the physics of galaxy formation and evolution as well as the growth of structure in the Universe. In this review paper we summarise key measurements of galaxy alignments, divided by galaxy type, scale and environment. We also cover the statistics and formalism necessary to understand the observations in the literature. With the emergence of weak gravitational lensing as a precision probe of cosmology, galaxy alignments have taken on an added importance because they can mimic cosmic shear, the effect of gravitational lensing by large-scale structure on observed galaxy shapes. This makes galaxy alignments, commonly referred to as intrinsic alignments, an important systematic effect in weak lensing studies. We quantify the impact of intrinsic alignments on cosmic shear surveys and finish by reviewing practical mitigation techniques which attempt to remove contamination by intrinsic alignments.

  3. A theoretical model for whole genome alignment.

    PubMed

    Belal, Nahla A; Heath, Lenwood S

    2011-05-01

    We present a graph-based model for representing two aligned genomic sequences. An alignment graph is a mixed graph consisting of two sets of vertices, each representing one of the input sequences, and three sets of edges. These edges allow the model to represent a number of evolutionary events. This model is used to perform sequence alignment at the level of nucleotides. We define a scoring function for alignment graphs. We show that minimizing the score is NP-complete. However, we present a dynamic programming algorithm that solves the minimization problem optimally for a certain class of alignments, called breakable arrangements. Algorithms for analyzing breakable arrangements are presented. We also present a greedy algorithm that is capable of representing reversals. We present a dynamic programming algorithm that optimally aligns two genomic sequences, when one of the input sequences is a breakable arrangement of the other. Comparing what we define as breakable arrangements to alignments generated by other algorithms, it is seen that many already aligned genomes fall into the category of being breakable. Moreover, the greedy algorithm is shown to represent reversals, besides rearrangements, mutations, and other evolutionary events. PMID:21210739

  4. Compositions for directed alignment of conjugated polymers

    DOEpatents

    Kim, Jinsang; Kim, Bong-Gi; Jeong, Eun Jeong

    2016-04-19

    Conjugated polymers (CPs) achieve directed alignment along an applied flow field and a dichroic ratio of as high as 16.67 in emission from well-aligned thin films and fully realized anisotropic optoelectronic properties of CPs in field-effect transistor (FET).

  5. CARNA--alignment of RNA structure ensembles.

    PubMed

    Sorescu, Dragos Alexandru; Möhl, Mathias; Mann, Martin; Backofen, Rolf; Will, Sebastian

    2012-07-01

    Due to recent algorithmic progress, tools for the gold standard of comparative RNA analysis, namely Sankoff-style simultaneous alignment and folding, are now readily applicable. Such approaches, however, compare RNAs with respect to a simultaneously predicted, single, nested consensus structure. To make multiple alignment of RNAs available in cases, where this limitation of the standard approach is critical, we introduce a web server that provides a complete and convenient interface to the RNA structure alignment tool 'CARNA'. This tool uniquely supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically; these features are highly desirable for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots. We represent structural input and output information as base pair probability dot plots; this provides large flexibility in the input, ranging from fixed structures to structure ensembles, and enables immediate visual analysis of the results. In contrast to conventional Sankoff-style approaches, 'CARNA' optimizes all structural similarities in the input simultaneously, for example across an entire RNA structure ensemble. Even compared with already costly Sankoff-style alignment, 'CARNA' solves an intrinsically much harder problem by applying advanced, constraint-based, algorithmic techniques. Although 'CARNA' is specialized to the alignment of RNAs with several conserved structures, its performance on RNAs in general is on par with state-of-the-art general-purpose RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server is freely available at http://rna.informatik.uni-freiburg.de/CARNA. PMID:22689637

  6. Aligning Greek-English parallel texts

    NASA Astrophysics Data System (ADS)

    Galiotou, Eleni; Koronakis, George; Lazari, Vassiliki

    2015-02-01

    In this paper, we discuss issues concerning the alignment of parallel texts written in languages with different alphabets based on an experiment of aligning texts from the proceedings of the European Parliament in Greek and English. First, we describe our implementation of the k-vec algorithm and its application to the bilingual corpus. Then the output of the algorithm is used as a starting point for an alignment procedure at a sentence level which also takes into account mark-ups of meta-information. The results of the implementation are compared to those of the application of the Church and Gale alignment algorithm on the Europarl corpus. The conclusions of this comparison can give useful insights as for the efficiency of alignment algorithms when applied to the particular bilingual corpus.

  7. Vane segment support and alignment device

    DOEpatents

    McLaurin, Leroy Dixon; Sizemore, John Derek

    1999-01-01

    A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pin is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position.

  8. 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.

  9. Vane segment support and alignment device

    DOEpatents

    McLaurin, L.D.; Sizemore, J.D.

    1999-07-13

    A support and alignment assembly for supporting and aligning a vane segment is provided. The support and alignment assembly comprises a torque plate which defines an opening for receiving an eccentric pin and a locking end member for receiving a lock socket member. An eccentric pin adjustably supported by the torque plate opening for supporting and aligning a vane segment is provided. A lock socket member adapted to securely receive the eccentric pin and rotated therewith, and adjustably engage the torque plate locking end is provided. The lock socket member receives the eccentric pin, such that when the eccentric pin is adjusted to align the vane segment, the lock socket member engages the torque plate locking end to secure the vane segment in the desired position. 5 figs.

  10. Array tomography: semiautomated image alignment.

    PubMed

    Micheva, Kristina D; O'Rourke, Nancy; Busse, Brad; Smith, Stephen J

    2010-11-01

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. Successful array tomography requires that the captured images be properly stacked and aligned, and the software to achieve these ends is freely available. This protocol describes the construction of volumetric image stacks from images of fluorescently labeled arrays for three-dimensional image visualization, analysis, and archiving. PMID:21041400

  11. Structural Alignment Sensor Feasibility Demonstration

    NASA Technical Reports Server (NTRS)

    Anderson, R. H.; Huang, C. C.; Hodor, J. R.

    1978-01-01

    A structural alignment sensor (SAS) was developed for use with large deployable antenna systems for contour measurement and/or active control. The SAS is a laser ranging system using frequency modulation and accurate phase measurement to determine distance. Work was done with a CO2 and HeNe laser. The capability of the SAS to measure antenna rib contours was studied over ranges of 50 meters to a resolution of 100 microns. Initial resolution data was taken with the CO2 system. This data shows that it will indeed meet the SAS requirements. The development of the HeNe system was initiated because it offers substantial improvement in size, weight, and power over the CO2 system. The final demonstration was made with the HeNe system and it too showed that the SAS requirements could be met with this alternate approach. The projection of these results to a conceptual design for a flight system and its application are described.

  12. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

    PubMed Central

    Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  13. Algorithms for Automatic Alignment of Arrays

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Oliker, Leonid; Schreiber, Robert; Sheffler, Thomas J.

    1996-01-01

    Aggregate data objects (such as arrays) are distributed across the processor memories when compiling a data-parallel language for a distributed-memory machine. The mapping determines the amount of communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: an alignment that maps all the objects to an abstract template, followed by a distribution that maps the template to the processors. This paper describes algorithms for solving the various facets of the alignment problem: axis and stride alignment, static and mobile offset alignment, and replication labeling. We show that optimal axis and stride alignment is NP-complete for general program graphs, and give a heuristic method that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. We also show how local graph contractions can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. We show how to model the static offset alignment problem using linear programming, and we show that loop-dependent mobile offset alignment is sometimes necessary for optimum performance. We describe an algorithm with for determining mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself or can be used to improve performance. We describe an algorithm based on network flow that replicates objects so as to minimize the total amount of broadcast communication in replication.

  14. Recursive dynamic programming for adaptive sequence and structure alignment

    SciTech Connect

    Thiele, R.; Zimmer, R.; Lengauer, T.

    1995-12-31

    We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method.

  15. An Improved Inertial Frame Alignment Algorithm Based on Horizontal Alignment Information for Marine SINS.

    PubMed

    Che, Yanting; Wang, Qiuying; Gao, Wei; Yu, Fei

    2015-01-01

    In this paper, an improved inertial frame alignment algorithm for a marine SINS under mooring conditions is proposed, which significantly improves accuracy. Since the horizontal alignment is easy to complete, and a characteristic of gravity is that its component in the horizontal plane is zero, we use a clever method to improve the conventional inertial alignment algorithm. Firstly, a large misalignment angle model and a dimensionality reduction Gauss-Hermite filter are employed to establish the fine horizontal reference frame. Based on this, the projection of the gravity in the body inertial coordinate frame can be calculated easily. Then, the initial alignment algorithm is accomplished through an inertial frame alignment algorithm. The simulation and experiment results show that the improved initial alignment algorithm performs better than the conventional inertial alignment algorithm, and meets the accuracy requirements of a medium-accuracy marine SINS. PMID:26445048

  16. An Improved Inertial Frame Alignment Algorithm Based on Horizontal Alignment Information for Marine SINS

    PubMed Central

    Che, Yanting; Wang, Qiuying; Gao, Wei; Yu, Fei

    2015-01-01

    In this paper, an improved inertial frame alignment algorithm for a marine SINS under mooring conditions is proposed, which significantly improves accuracy. Since the horizontal alignment is easy to complete, and a characteristic of gravity is that its component in the horizontal plane is zero, we use a clever method to improve the conventional inertial alignment algorithm. Firstly, a large misalignment angle model and a dimensionality reduction Gauss-Hermite filter are employed to establish the fine horizontal reference frame. Based on this, the projection of the gravity in the body inertial coordinate frame can be calculated easily. Then, the initial alignment algorithm is accomplished through an inertial frame alignment algorithm. The simulation and experiment results show that the improved initial alignment algorithm performs better than the conventional inertial alignment algorithm, and meets the accuracy requirements of a medium-accuracy marine SINS. PMID:26445048

  17. Proper alignment of the microscope.

    PubMed

    Rottenfusser, Rudi

    2013-01-01

    The light microscope is merely the first element of an imaging system in a research facility. Such a system may include high-speed and/or high-resolution image acquisition capabilities, confocal technologies, and super-resolution methods of various types. Yet more than ever, the proverb "garbage in-garbage out" remains a fact. Image manipulations may be used to conceal a suboptimal microscope setup, but an artifact-free image can only be obtained when the microscope is optimally aligned, both mechanically and optically. Something else is often overlooked in the quest to get the best image out of the microscope: Proper sample preparation! The microscope optics can only do its job when its design criteria are matched to the specimen or vice versa. The specimen itself, the mounting medium, the cover slip, and the type of immersion medium (if applicable) are all part of the total optical makeup. To get the best results out of a microscope, understanding the functions of all of its variable components is important. Only then one knows how to optimize these components for the intended application. Different approaches might be chosen to discuss all of the microscope's components. We decided to follow the light path which starts with the light source and ends at the camera or the eyepieces. To add more transparency to this sequence, the section up to the microscope stage was called the "Illuminating Section", to be followed by the "Imaging Section" which starts with the microscope objective. After understanding the various components, we can start "working with the microscope." To get the best resolution and contrast from the microscope, the practice of "Koehler Illumination" should be understood and followed by every serious microscopist. Step-by-step instructions as well as illustrations of the beam path in an upright and inverted microscope are included in this chapter. A few practical considerations are listed in Section 3. PMID:23931502

  18. Daily Bone Alignment With Limited Repeat CT Correction Rivals Daily Ultrasound Alignment for Prostate Radiotherapy

    SciTech Connect

    O'Daniel, Jennifer C.; Dong Lei Zhang Lifei; Wang He; Tucker, Susan L.; Kudchadker, Rajat J.; Lee, Andrew K.; Cheung, Rex; Cox, James D.; Kuban, Deborah A.; Mohan, Radhe

    2008-05-01

    Purpose: To compare the effectiveness of daily ultrasound (US)- and computed tomography (CT)-guided alignments with an off-line correction protocol using daily bone alignment plus a correction factor for systematic internal prostate displacement (CF{sub ID}). Methods and Materials: Ten prostate cancer patients underwent CT scans three times weekly using an integrated CT-linear accelerator system, followed by alignment using US for daily radiotherapy. Intensity-modulated radiotherapy plans were designed with our current clinical margins. The treatment plan was copied onto the repeat CT images and aligned using several methods: (1) bone alignment plus CF{sub ID} after three off-line CT scans (bone+3CT), (2) bone alignment plus CF{sub ID} after six off-line CT scans (bone+6CT), (3) US alignment, and (4) CT alignment. The accuracy of the repeated US and CT measurements to determine the CF{sub ID} was compared. The target dosimetric effect was quantified. Results: The CF{sub ID} for internal systematic prostate displacements was more accurately measured with limited repeat CT scans than with US (residual error, 0.0 {+-} 0.7 mm vs. 2.0 {+-} 3.2 mm). Bone+3CT, bone+6CT, and US provided equivalent prostate and seminal vesicle dose coverage, but bone+3CT and bone+6CT produced more precise daily alignments. Daily CT alignment provided the greatest target dose coverage. Conclusion: Daily bone alignment plus CF{sub ID} for internal systematic prostate displacement provided better daily alignment precision and equivalent dose coverage compared with daily US alignment. The CF{sub ID} should be based on at least three repeat CT scans, which could be collected before the start of treatment or during the first 3 treatment days. Daily bone alignment plus CF{sub ID} provides another option for accurate prostate cancer patient positioning.

  19. Protein alignment: Exact versus approximate. An illustration.

    PubMed

    Randić, Milan; Pisanski, Tomaž

    2015-05-30

    We illustrate solving the protein alignment problem exactly using the algorithm VESPA (very efficient search for protein alignment). We have compared our result with the approximate solution obtained with BLAST (basic local alignment search tool) software, which is currently the most widely used for searching for protein alignment. We have selected human and mouse proteins having around 170 amino acids for comparison. The exact solution has found 78 pairs of amino acids, to which one should add 17 individual amino acid alignments giving a total of 95 aligned amino acids. BLAST has identified 64 aligned amino acids which involve pairs of more than two adjacent amino acids. However, the difference between the two outputs is not as large as it may appear, because a number of amino acids that are adjacent have been reported by BLAST as single amino acids. So if one counts all amino acids, whether isolated (single) or in a group of two and more amino acids, then the count for BLAST is 89 and for VESPA is 95, a difference of only six. PMID:25800773

  20. Sparse alignment for robust tensor learning.

    PubMed

    Lai, Zhihui; Wong, Wai Keung; Xu, Yong; Zhao, Cairong; Sun, Mingming

    2014-10-01

    Multilinear/tensor extensions of manifold learning based algorithms have been widely used in computer vision and pattern recognition. This paper first provides a systematic analysis of the multilinear extensions for the most popular methods by using alignment techniques, thereby obtaining a general tensor alignment framework. From this framework, it is easy to show that the manifold learning based tensor learning methods are intrinsically different from the alignment techniques. Based on the alignment framework, a robust tensor learning method called sparse tensor alignment (STA) is then proposed for unsupervised tensor feature extraction. Different from the existing tensor learning methods, L1- and L2-norms are introduced to enhance the robustness in the alignment step of the STA. The advantage of the proposed technique is that the difficulty in selecting the size of the local neighborhood can be avoided in the manifold learning based tensor feature extraction algorithms. Although STA is an unsupervised learning method, the sparsity encodes the discriminative information in the alignment step and provides the robustness of STA. Extensive experiments on the well-known image databases as well as action and hand gesture databases by encoding object images as tensors demonstrate that the proposed STA algorithm gives the most competitive performance when compared with the tensor-based unsupervised learning methods. PMID:25291733

  1. Alignment of atmospheric mineral dust due to electric field

    NASA Astrophysics Data System (ADS)

    Ulanowski, Z.; Bailey, J.; Lucas, P. W.; Hough, J. H.; Hirst, E.

    2007-09-01

    Optical polarimetry observations on La Palma, Canary Islands, during a Saharan dust episode show dichroic extinction consistent with the presence of vertically aligned particles in the atmosphere. Modelling of the extinction together with particle orientation indicates that the alignment could have been due to an electric field of the order of 2 kV/m. Two alternative mechanisms for the origin of the field are examined: the effect of reduced atmospheric conductivity and charging of the dust layer, the latter effect being a more likely candidate. It is concluded that partial alignment may be a common feature of Saharan dust layers. The modelling also indicates that the alignment can significantly alter dust optical depth. This "Venetian blind effect" may have decreased optical thickness in the vertical direction by as much as 10% for the case reported here.

  2. Alignment Cube with One Diffractive Face

    NASA Technical Reports Server (NTRS)

    Ohl, Raymond G.; Sampler, Henry P.; Strojny, Carl R.; Hagopian, John G.; McMann, Joseph C.

    2006-01-01

    An enhanced alignment cube has been invented for use in a confined setting (e.g., a cryogenic chamber) in which optical access may be limited to a single line of sight. Whereas traditional alignment-cube practice entails the use of two theodolites aimed along two lines of sight, the enhanced alignment cube yields complete alignment information through use of a single theodolite aimed along a single line of sight. Typically, an alignment cube is placed in contact with a datum surface or other reference feature on a scientific instrument during assembly or testing of the instrument. The alignment cube is then used in measuring a small angular deviation of the feature from a precise required orientation. Commonly, the deviation is expressed in terms of rotations (Rx,Ry,Rz) of the cube about the corresponding Cartesian axes (x,y,z). In traditional practice, in order to measure all three rotations, it is necessary to use two theodolites aimed at two orthogonal faces of the alignment cube, as shown in the upper part of the figure. To be able to perform such a measurement, one needs optical access to these two faces. In the case of an alignment cube inside a cryogenic chamber or other enclosed space, the optical-access requirement translates to a requirement for two windows located along the corresponding two orthogonal lines of sight into the chamber. In a typical application, it is difficult or impossible to provide two windows. The present enhanced version of the alignment cube makes it possible to measure all three rotations by use of a single line of sight, thereby obviating a second window.

  3. 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.

  4. Self-aligning biaxial load frame

    DOEpatents

    Ward, M.B.; Epstein, J.S.; Lloyd, W.R.

    1994-01-18

    An self-aligning biaxial loading apparatus for use in testing the strength of specimens while maintaining a constant specimen centroid during the loading operation. The self-aligning biaxial loading apparatus consists of a load frame and two load assemblies for imparting two independent perpendicular forces upon a test specimen. The constant test specimen centroid is maintained by providing elements for linear motion of the load frame relative to a fixed cross head, and by alignment and linear motion elements of one load assembly relative to the load frame. 3 figures.

  5. Self-aligning biaxial load frame

    DOEpatents

    Ward, Michael B.; Epstein, Jonathan S.; Lloyd, W. Randolph

    1994-01-01

    An self-aligning biaxial loading apparatus for use in testing the strength of specimens while maintaining a constant specimen centroid during the loading operation. The self-aligning biaxial loading apparatus consists of a load frame and two load assemblies for imparting two independent perpendicular forces upon a test specimen. The constant test specimen centroid is maintained by providing elements for linear motion of the load frame relative to a fixed crosshead, and by alignment and linear motion elements of one load assembly relative to the load frame.

  6. Alignment strategy for the ATLAS tracker

    SciTech Connect

    ATLAS; Golling, T.

    2007-09-23

    The ATLAS experiment is a multi-purpose particle detector that will study high-energy particle collisions produced by the Large Hadron Collider. For the reconstruction of charged particles, and their production and their decay vertices, ATLAS is equipped with a sophisticated tracking system, unprecedented in size and complexity. Full exploitation of both the Inner Detector and the muon spectrometer requires an accurate alignment. The challenge of aligning the ATLAS tracking devices is discussed, and the ATLAS alignment strategy is presented and illustrated with both data and Monte Carlo results.

  7. Optical Alignment Device For Laser Communication

    NASA Technical Reports Server (NTRS)

    Casey, William L.

    1988-01-01

    Optical alignment device under development enables continuous tracking and coalignment of two beams of light. Intended primarily for laser-communication station, in which transmitted beam must be aligned with received beam to ensure transmitted beam falls on receiver at other station. Expected to consume less power and be smaller and less complicated than alignment shutter and drive previously used. Prism and filter separate two overlapping collimated light beams of different wavelength or polarization. Coordinates of two beams tracked on charge-coupled device to determine degree of directional misalignment between two beams.

  8. Global multiple protein-protein interaction network alignment by combining pairwise network alignments

    PubMed Central

    2015-01-01

    Background A wealth of protein interaction data has become available in recent years, creating an urgent need for powerful analysis techniques. In this context, the problem of finding biologically meaningful correspondences between different protein-protein interaction networks (PPIN) is of particular interest. The PPIN of a species can be compared with that of other species through the process of PPIN alignment. Such an alignment can provide insight into basic problems like species evolution and network component function determination, as well as translational problems such as target identification and elucidation of mechanisms of disease spread. Furthermore, multiple PPINs can be aligned simultaneously, expanding the analytical implications of the result. While there are several pairwise network alignment algorithms, few methods are capable of multiple network alignment. Results We propose SMAL, a MNA algorithm based on the philosophy of scaffold-based alignment. SMAL is capable of converting results from any global pairwise alignment algorithms into a MNA in linear time. Using this method, we have built multiple network alignments based on combining pairwise alignments from a number of publicly available (pairwise) network aligners. We tested SMAL using PPINs of eight species derived from the IntAct repository and employed a number of measures to evaluate performance. Additionally, as part of our experimental investigations, we compared the effectiveness of SMAL while aligning up to eight input PPINs, and examined the effect of scaffold network choice on the alignments. Conclusions A key advantage of SMAL lies in its ability to create MNAs through the use of pairwise network aligners for which native MNA implementations do not exist. Experiments indicate that the performance of SMAL was comparable to that of the native MNA implementation of established methods such as IsoRankN and SMETANA. However, in terms of computational time, SMAL was significantly faster

  9. Computing posterior probabilities for score-based alignments using ppALIGN.

    PubMed

    Wolfsheimer, Stefan; Hartmann, Alexander; Rabus, Ralf; Nuel, Gregory

    2012-01-01

    Score-based pairwise alignments are widely used in bioinformatics in particular with molecular database search tools, such as the BLAST family. Due to sophisticated heuristics, such algorithms are usually fast but the underlying scoring model unfortunately lacks a statistical description of the reliability of the reported alignments. In particular, close to gaps, in low-score or low-complexity regions, a huge number of alternative alignments arise which results in a decrease of the certainty of the alignment. ppALIGN is a software package that uses hidden Markov Model techniques to compute position-wise reliability of score-based pairwise alignments of DNA or protein sequences. The design of the model allows for a direct connection between the scoring function and the parameters of the probabilistic model. For this reason it is suitable to analyze the outcomes of popular score based aligners and search tools without having to choose a complicated set of parameters. By contrast, our program only requires the classical score parameters (the scoring function and gap costs). The package comes along with a library written in C++, a standalone program for user defined alignments (ppALIGN) and another program (ppBLAST) which can process a complete result set of BLAST. The main algorithms essentially exhibit a linear time complexity (in the alignment lengths), and they are hence suitable for on-line computations. We have also included alternative decoding algorithms to provide alternative alignments. ppALIGN is a fast program/library that helps detect and quantify questionable regions in pairwise alignments. Due to its structure, the input/output interface it can to be connected to other post-processing tools. Empirically, we illustrate its usefulness in terms of correctly predicted reliable regions for sequences generated using the ROSE model for sequence evolution, and identify sensor-specific regions in the denitrifying betaproteobacterium Aromatoleum aromaticum. PMID

  10. Aligning parallel arrays to reduce communication

    NASA Technical Reports Server (NTRS)

    Sheffler, Thomas J.; Schreiber, Robert; Gilbert, John R.; Chatterjee, Siddhartha

    1994-01-01

    Axis and stride alignment is an important optimization in compiling data-parallel programs for distributed-memory machines. We previously developed an optimal algorithm for aligning array expressions. Here, we examine alignment for more general program graphs. We show that optimal alignment is NP-complete in this setting, so we study heuristic methods. This paper makes two contributions. First, we show how local graph transformations can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. Second, we give a heuristic that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. Our algorithms have been implemented; we present experimental results showing their effect on the performance of some example programs running on the CM-5.

  11. Magnetic alignment of the Tara tandem mirror

    SciTech Connect

    Post, R.S.; Coleman, J.W.; Irby, J.H.; Olmstead, M.M.; Torti, R.P.

    1985-06-01

    Techniques developed for the alignment of high-energy accelerators have been applied to the alignment of the Tara tandem mirror magnetic confinement device. Tools used were: a transit/laser surveyor's system for establishing an invariant reference; optical scattering from ferromagnetic crystallites for establishing magnetic centers in the quadrupole anchor/transition modules; an electron-optical circle-generating wand for alignment of the solenoidal plug and central cell modules; and four differently configured electron emissive probes, including a 40-beam flux mapping e gun, for testing the alignment of the coils under vacuum. Procedures are outlined, and results are given which show that the magnetic axes of the individual coils in the Tara set have been made colinear with each other and with the reference to within +- 1.0 mm over the length of the machine between the anchor midplanes.

  12. Automatic alignment method for calibration of hydrometers

    NASA Astrophysics Data System (ADS)

    Lee, Y. J.; Chang, K. H.; Chon, J. C.; Oh, C. Y.

    2004-04-01

    This paper presents a new method to automatically align specific scale-marks for the calibration of hydrometers. A hydrometer calibration system adopting the new method consists of a vision system, a stepping motor, and software to control the system. The vision system is composed of a CCD camera and a frame grabber, and is used to acquire images. The stepping motor moves the camera, which is attached to the vessel containing a reference liquid, along the hydrometer. The operating program has two main functions: to process images from the camera to find the position of the horizontal plane and to control the stepping motor for the alignment of the horizontal plane with a particular scale-mark. Any system adopting this automatic alignment method is a convenient and precise means of calibrating a hydrometer. The performance of the proposed method is illustrated by comparing the calibration results using the automatic alignment method with those obtained using the manual method.

  13. MAST YAG Thomson scattering upgrade alignment system

    SciTech Connect

    Figueiredo, J.; Serra, F.; Naylor, G.; Walsh, M.; Dunstan, M.; Scannell, R.

    2010-10-15

    The recent upgrade to the MAST YAG Thomson scattering while enhancing the diagnostic capabilities increased the complexity of the system. There are eight YAG lasers now operational, doubling the number from the previous setup. This means alignment between each laser individually and reference points is essential to guarantee data quality and diagnostic reliability. To address this issue an alignment system was recently installed. It mimics the beams alignment in MAST by sampling 1% of the laser beam that is sent into a telescope which demagnifies by a factor of 8. The demagnified beam is viewed with a CCD camera. By scanning the camera the profile and position of the beams in the scattering zone and in a range of several meters inside MAST can be determined. Therefore alignment is checked along the beam path without having to sample it inside the vessel. The experimental apparatus and test procedures are described.

  14. Alignment Stage for a Cryogenic Dilatometer

    NASA Technical Reports Server (NTRS)

    Dudik, Matthew; Moore, Donald

    2005-01-01

    A three-degree-of-freedom alignment stage has been designed and built for use in a cryogenic dilatometer that is used to measure thermal strains. The alignment stage enables precise adjustments of the positions and orientations of optical components to be used in the measurements and, once adjustments have been completed, keeps the components precisely aligned during cryogenic-dilatometer operations that can last as long as several days. The alignment stage includes a case, a circular tilt/tip platform, and a variety of flexural couplings between the case and the platform, all machined from a single block of the low-thermal-expansion iron/nickel alloy Invar, in order to minimize effects of temperature gradients and to obtain couplings that are free of stiction and friction. There are three sets of flexural couplings clocked at equal angles of 120 degrees around the platform, constituting a three-point kinematic support system.

  15. Aligner for Elastic Collisions of Dropped Balls.

    ERIC Educational Resources Information Center

    Mellen, Walter Roy

    1995-01-01

    Discusses an aligner that permits dropping a stack of any number of balls of different sizes, elasticities, hardnesses, or types to observe the rebound of the top ball. Experimental results allow a reasonable comparison with theory. (MVL)

  16. Little solar impact from planets' alignment

    NASA Astrophysics Data System (ADS)

    Bell, Peter M.

    Contrary to some projections, planetary alignments of the type that have begun recently (when the sun, Venus, Earth, Jupiter, and Saturn move into almost perfect alignment) should have no perceptible effect on solar flare activity. Some researchers have postulated that the increased gravitational attraction exerted on the sun by the aligned planets could produce massive eruptions near sunspots. The radiation and particles directed earthward by the sun, according to this hypothesis, would change the atmosphere in a way that would slow the earth's rotation; and this change in rotation rate would cause the large plates which constitute the earth's crust to grind together more vigorously and cause major earthquakes. Because Jupiter is the largest of the planets, and so exerts the most gravitational attraction, this geophysical domino theory is sometimes referred to as the Jupiter Effect. But, at least at the solar end of this theory, one would not expect much change in solar activity from planetary alignments of this type.

  17. Short Read Alignment Using SOAP2.

    PubMed

    Hurgobin, Bhavna

    2016-01-01

    Next-generation sequencing (NGS) technologies have rapidly evolved in the last 5 years, leading to the generation of millions of short reads in a single run. Consequently, various sequence alignment algorithms have been developed to compare these reads to an appropriate reference in order to perform important downstream analysis. SOAP2 from the SOAP series is one of the most commonly used alignment programs to handle NGS data, and it efficiently does so using low computer memory usage and fast alignment speed. This chapter describes the protocol used to align short reads to a reference genome using SOAP2, and highlights the significance of using the in-built command-line options to tune the behavior of the algorithm according to the inputs and the desired results. PMID:26519410

  18. GRAT--genome-scale rapid alignment tool.

    PubMed

    Kindlund, Ellen; Tammi, Martti T; Arner, Erik; Nilsson, Daniel; Andersson, Björn

    2007-04-01

    Modern alignment methods designed to work rapidly and efficiently with large datasets often do so at the cost of method sensitivity. To overcome this, we have developed a novel alignment program, GRAT, built to accurately align short, highly similar DNA sequences. The program runs rapidly and requires no more memory and CPU power than a desktop computer. In addition, specificity is ensured by statistically separating the true alignments from spurious matches using phred quality values. An efficient separation is especially important when searching large datasets and whenever there are repeats present in the dataset. Results are superior in comparison to widely used existing software, and analysis of two large genomic datasets show the usefulness and scalability of the algorithm. PMID:17292508

  19. Intense laser ionization of transiently aligned CO

    SciTech Connect

    Pinkham, D.; Jones, R.R.

    2005-08-15

    We have measured the ionization rate for CO molecules exposed to intense 30 fsec 780 nm laser pulses as a function of the angle between the molecular and laser polarization axes. Nonionizing, 70 fsec laser pulses are used to coherently prepare the molecules, preferentially aligning them for the strong-field ionization experiments. We find a 2:1 ionization-rate ratio for molecules aligned parallel or perpendicular to the ionizing field.

  20. 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.

  1. Technology Alignment and Portfolio Prioritization (TAPP)

    NASA Technical Reports Server (NTRS)

    Funaro, Gregory V.; Alexander, Reginald A.

    2015-01-01

    Technology Alignment and Portfolio Prioritization (TAPP) is a method being developed by the Advanced Concepts Office, at NASA Marshall Space Flight Center. The TAPP method expands on current technology assessment methods by incorporating the technological structure underlying technology development, e.g., organizational structures and resources, institutional policy and strategy, and the factors that motivate technological change. This paper discusses the methods ACO is currently developing to better perform technology assessments while taking into consideration Strategic Alignment, Technology Forecasting, and Long Term Planning.

  2. Total overlay analysis for designing future aligner

    NASA Astrophysics Data System (ADS)

    Magome, Nobutaka; Kawai, Hidemi

    1995-05-01

    We found total overlay with respect to optical lithography using an approach similar to quality control technique employed at a semiconductor factory. This approach involves an aligner performance, process quality, reticle error and overlay measurement. This paper further describes new ides for the number of machines to be used for matching and data collection period. Lastly, improvement on total overlay and a prospective view for a future aligner and its usage are also described.

  3. Dynamic alignment and selective decay in MHD

    NASA Technical Reports Server (NTRS)

    Matthaeus, W. H.; Montgomery, D.

    1983-01-01

    Under some circumstances, incompressible magnetohydrodynamic turbulence will evolve toward a state in which the velocity fields and magnetic fields are aligned or anti-aligned. We propose a mechanism for this effect and illustrate with numerical computations. Under some other circumstances, the energy appears to decay selectively toward a minimum energy state in which the kinetic energy has disappeared. It has not been possible so far to identify a boundary in the phase space which divides the two regimes.

  4. Smart and precise alignment of optical systems

    NASA Astrophysics Data System (ADS)

    Langehanenberg, Patrik; Heinisch, Josef; Stickler, Daniel

    2013-09-01

    For the assembly of any kind of optical systems the precise centration of every single element is of particular importance. Classically the precise alignment of optical components is based on the precise centering of all components to an external axis (usually a high-precision rotary spindle axis). Main drawback of this timeconsuming process is that it is significantly sensitive to misalignments of the reference (e.g. the housing) axis. In order to facilitate process in this contribution we present a novel alignment strategy for the TRIOPTICS OptiCentric® instrument family that directly aligns two elements with respect to each other by measuring the first element's axis and using this axis as alignment reference without the detour of considering an external reference. According to the optical design any axis in the system can be chosen as target axis. In case of the alignment to a barrel this axis is measured by using a distance sensor (e.g., the classically used dial indicator). Instead of fine alignment the obtained data is used for the calculation of its orientation within the setup. Alternatively, the axis of an optical element (single lens or group of lenses) whose orientation is measured with the standard OptiCentric MultiLens concept can be used as a reference. In the instrument's software the decentering of the adjusting element to the calculated axis is displayed in realtime and indicated by a target mark that can be used for the manual alignment. In addition, the obtained information can also be applied for active and fully automated alignment of lens assemblies with the help of motorized actuators.

  5. CARNA—alignment of RNA structure ensembles

    PubMed Central

    Sorescu, Dragoş Alexandru; Möhl, Mathias; Mann, Martin; Backofen, Rolf; Will, Sebastian

    2012-01-01

    Due to recent algorithmic progress, tools for the gold standard of comparative RNA analysis, namely Sankoff-style simultaneous alignment and folding, are now readily applicable. Such approaches, however, compare RNAs with respect to a simultaneously predicted, single, nested consensus structure. To make multiple alignment of RNAs available in cases, where this limitation of the standard approach is critical, we introduce a web server that provides a complete and convenient interface to the RNA structure alignment tool ‘CARNA’. This tool uniquely supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically; these features are highly desirable for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots. We represent structural input and output information as base pair probability dot plots; this provides large flexibility in the input, ranging from fixed structures to structure ensembles, and enables immediate visual analysis of the results. In contrast to conventional Sankoff-style approaches, ‘CARNA’ optimizes all structural similarities in the input simultaneously, for example across an entire RNA structure ensemble. Even compared with already costly Sankoff-style alignment, ‘CARNA’ solves an intrinsically much harder problem by applying advanced, constraint-based, algorithmic techniques. Although ‘CARNA’ is specialized to the alignment of RNAs with several conserved structures, its performance on RNAs in general is on par with state-of-the-art general-purpose RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server is freely available at http://rna.informatik.uni-freiburg.de/CARNA. PMID:22689637

  6. STAR: ultrafast universal RNA-seq aligner

    PubMed Central

    Dobin, Alexander; Davis, Carrie A.; Schlesinger, Felix; Drenkow, Jorg; Zaleski, Chris; Jha, Sonali; Batut, Philippe; Chaisson, Mark; Gingeras, Thomas R.

    2013-01-01

    Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. Results: To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80–90% success rate, corroborating the high precision of the STAR mapping strategy. Availability and implementation: STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/. Contact: dobin@cshl.edu. PMID:23104886

  7. An implicit spatial memory alignment effect.

    PubMed

    Cerles, Mélanie; Gomez, Alice; Rousset, Stéphane

    2015-09-01

    The memory alignment effect is the advantage of reasoning from a perspective which is aligned with the frame of reference used to encode an environment in memory. It usually occurs when participants have to consciously take a perspective to perform a spatial memory task. The present experiment assesses whether the memory alignment effect can occur without requiring to consciously take a given perspective, when the misaligned perspective is only perceptively provided. In others words, does the memory alignment effect still arise when it is only implicitly prompted? Thirty participants learned a sequence of four objects' positions in a room from a north-as-up survey perspective. During the testing phase, they had to point to the direction of a target object from another object ('the reference') with a fixed north-up orientation. The background behind the reference object displayed either a uniform color (control condition) or a misaligned ground-level perspective. The latter displayed a reference object's position information which was either congruent with the studied environment (congruent misaligned condition) or incongruent (incongruent misaligned condition). Mean pointing errors were higher in the congruent misaligned condition than in the control condition, whereas the incongruent misaligned condition did not differ from the control one. The present study shows that the memory alignment effect can arise without requiring a conscious misaligned perspective taking. Moreover, the perceived misaligned perspective must share the same spatial content as the memorized spatial representation in order to induce an alignment effect. PMID:26233526

  8. New Attitude Sensor Alignment Calibration Algorithms

    NASA Technical Reports Server (NTRS)

    Hashmall, Joseph A.; Sedlak, Joseph E.; Harman, Richard (Technical Monitor)

    2002-01-01

    Accurate spacecraft attitudes may only be obtained if the primary attitude sensors are well calibrated. Launch shock, relaxation of gravitational stresses and similar effects often produce large enough alignment shifts so that on-orbit alignment calibration is necessary if attitude accuracy requirements are to be met. A variety of attitude sensor alignment algorithms have been developed to meet the need for on-orbit calibration. Two new algorithms are presented here: ALICAL and ALIQUEST. Each of these has advantages in particular circumstances. ALICAL is an attitude independent algorithm that uses near simultaneous measurements from two or more sensors to produce accurate sensor alignments. For each set of simultaneous observations the attitude is overdetermined. The information content of the extra degrees of freedom can be combined over numerous sets to provide the sensor alignments. ALIQUEST is an attitude dependent algorithm that combines sensor and attitude data into a loss function that has the same mathematical form as the Wahba problem. Alignments can then be determined using any of the algorithms (such as the QUEST quaternion estimator) that have been developed to solve the Wahba problem for attitude. Results from the use of these methods on active missions are presented.

  9. Aligning Biomolecular Networks Using Modular Graph Kernels

    NASA Astrophysics Data System (ADS)

    Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

    Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

  10. Silicon oxides as alignment surfaces for vertically-aligned nematics in photonic devices

    NASA Astrophysics Data System (ADS)

    Oton, E.; López-Andrés, S.; Bennis, N.; Otón, J. M.; Geday, M. A.

    2014-06-01

    A comparative study on alignment performance and microstructure of inorganic layers used for liquid crystal cell conditioning has been carried out. The study has focused on two specific materials, SiOx and SiO2, deposited under different conditions. The purpose was to establish a relationship between layer microstructure and liquid crystal alignment. The surface morphology has been studied by FESEM and AFM. An analysis on liquid crystal alignment, pretilt angle, response time, contrast ratio and the conditions to develop backflow effect (significant rise time increase due to pure homeotropic alignment) on vertically-aligned nematic cells has been carried out. A technique to overcome the presence of backflow has been identified. The full comparative study of SiOx and SiO2 layer properties and their influence over liquid crystal alignment and electrooptic response is presented.

  11. PSAR: measuring multiple sequence alignment reliability by probabilistic sampling

    PubMed Central

    Kim, Jaebum; Ma, Jian

    2011-01-01

    Multiple sequence alignment, which is of fundamental importance for comparative genomics, is a difficult problem and error-prone. Therefore, it is essential to measure the reliability of the alignments and incorporate it into downstream analyses. We propose a new probabilistic sampling-based alignment reliability (PSAR) score. Instead of relying on heuristic assumptions, such as the correlation between alignment quality and guide tree uncertainty in progressive alignment methods, we directly generate suboptimal alignments from an input multiple sequence alignment by a probabilistic sampling method, and compute the agreement of the input alignment with the suboptimal alignments as the alignment reliability score. We construct the suboptimal alignments by an approximate method that is based on pairwise comparisons between each single sequence and the sub-alignment of the input alignment where the chosen sequence is left out. By using simulation-based benchmarks, we find that our approach is superior to existing ones, supporting that the suboptimal alignments are highly informative source for assessing alignment reliability. We apply the PSAR method to the alignments in the UCSC Genome Browser to measure the reliability of alignments in different types of regions, such as coding exons and conserved non-coding regions, and use it to guide cross-species conservation study. PMID:21576232

  12. Multiple structure alignment with msTALI

    PubMed Central

    2012-01-01

    Background Multiple structure alignments have received increasing attention in recent years as an alternative to multiple sequence alignments. Although multiple structure alignment algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification. A method that is capable of solving a variety of problems using structure comparison is still absent. Here we introduce a program msTALI for aligning multiple protein structures. Our algorithm uses several informative features to guide its alignments: torsion angles, backbone Cα atom positions, secondary structure, residue type, surface accessibility, and properties of nearby atoms. The algorithm allows the user to weight the types of information used to generate the alignment, which expands its utility to a wide variety of problems. Results msTALI exhibits competitive results on 824 families from the Homstrad and SABmark databases when compared to Matt and Mustang. We also demonstrate success at building a database of protein cores using 341 randomly selected CATH domains and highlight the contribution of msTALI compared to the CATH classifications. Finally, we present an example applying msTALI to the problem of detecting hinges in a protein undergoing rigid-body motion. Conclusions msTALI is an effective algorithm for multiple structure alignment. In addition to its performance on standard comparison databases, it utilizes clear, informative features, allowing further customization for domain-specific applications. The C++ source code for msTALI is available for Linux on the web at http://ifestos.cse.sc.edu/mstali. PMID:22607234

  13. Using Quasi-Horizontal Alignment in the absence of the actual alignment.

    PubMed

    Banihashemi, Mohamadreza

    2016-10-01

    Horizontal alignment is a major roadway characteristic used in safety and operational evaluations of many facility types. The Highway Safety Manual (HSM) uses this characteristic in crash prediction models for rural two-lane highways, freeway segments, and freeway ramps/C-D roads. Traffic simulation models use this characteristic in their processes on almost all types of facilities. However, a good portion of roadway databases do not include horizontal alignment data; instead, many contain point coordinate data along the roadways. SHRP 2 Roadway Information Database (RID) is a good example of this type of data. Only about 5% of this geodatabase contains alignment information and for the rest, point data can easily be produced. Even though the point data can be used to extract actual horizontal alignment data but, extracting horizontal alignment is a cumbersome and costly process, especially for a database of miles and miles of highways. This research introduces a so called "Quasi-Horizontal Alignment" that can be produced easily and automatically from point coordinate data and can be used in the safety and operational evaluations of highways. SHRP 2 RID for rural two-lane highways in Washington State is used in this study. This paper presents a process through which Quasi-Horizontal Alignments are produced from point coordinates along highways by using spreadsheet software such as MS EXCEL. It is shown that the safety and operational evaluations of the highways with Quasi-Horizontal Alignments are almost identical to the ones with the actual alignments. In the absence of actual alignment the Quasi-Horizontal Alignment can easily be produced from any type of databases that contain highway coordinates such geodatabases and digital maps. PMID:27391796

  14. Parameterized BLOSUM Matrices for Protein Alignment.

    PubMed

    Song, Dandan; Chen, Jiaxing; Chen, Guang; Li, Ning; Li, Jin; Fan, Jun; Bu, Dongbo; Li, Shuai Cheng

    2015-01-01

    Protein alignment is a basic step for many molecular biology researches. The BLOSUM matrices, especially BLOSUM62, are the de facto standard matrices for protein alignments. However, after widely utilization of the matrices for 15 years, programming errors were surprisingly found in the initial version of source codes for their generation. And amazingly, after bug correction, the "intended" BLOSUM62 matrix performs consistently worse than the "miscalculated" one. In this paper, we find linear relationships among the eigenvalues of the matrices and propose an algorithm to find optimal unified eigenvectors. With them, we can parameterize matrix BLOSUMx for any given variable x that could change continuously. We compare the effectiveness of our parameterized isentropic matrix with BLOSUM62. Furthermore, an iterative alignment and matrix selection process is proposed to adaptively find the best parameter and globally align two sequences. Experiments are conducted on aligning 13,667 families of Pfam database and on clustering MHC II protein sequences, whose improved accuracy demonstrates the effectiveness of our proposed method. PMID:26357279

  15. LCLS Undulator Commissioning, Alignment, and Performance

    SciTech Connect

    Nuhn, Heinz-Dieter

    2009-10-30

    The LCLS x-ray FEL has recently achieved its 1.5-Angstrom lasing and saturation goals upon first trial. This was achieved as a result of a thorough pre-beam checkout, both traditional and beam-based component alignment techniques, and high electron beam brightness. The x-ray FEL process demands very tight tolerances on the straightness of the electron beam trajectory (<5 {micro}m) through the LCLS undulator system. Tight, but less stringent tolerances of {approx}100 {micro}m rms were met for the transverse placement of the individual undulator segments with respect to the beam axis. The tolerances for electron beam straightness can only be met through a beam-based alignment (BBA) method, which is implemented using large electron energy variations and sub-micron resolution cavity beam position monitors (BPM), with precise conventional alignment used to set the starting conditions. Precision-fiducialization of components mounted on remotely adjustable girders, and special beam-finder wires (BFW) at each girder have been used to meet these challenging alignment tolerances. Longer-term girder movement due to ground motion and temperature changes are being monitored, continuously, by a unique stretched wire and hydrostatic level Alignment Diagnostics System (ADS).

  16. Multiple network alignment on quantum computers

    NASA Astrophysics Data System (ADS)

    Daskin, Anmer; Grama, Ananth; Kais, Sabre

    2014-12-01

    Comparative analyses of graph-structured datasets underly diverse problems. Examples of these problems include identification of conserved functional components (biochemical interactions) across species, structural similarity of large biomolecules, and recurring patterns of interactions in social networks. A large class of such analyses methods quantify the topological similarity of nodes across networks. The resulting correspondence of nodes across networks, also called node alignment, can be used to identify invariant subgraphs across the input graphs. Given graphs as input, alignment algorithms use topological information to assign a similarity score to each -tuple of nodes, with elements (nodes) drawn from each of the input graphs. Nodes are considered similar if their neighbors are also similar. An alternate, equivalent view of these network alignment algorithms is to consider the Kronecker product of the input graphs and to identify high-ranked nodes in the Kronecker product graph. Conventional methods such as PageRank and HITS (Hypertext-Induced Topic Selection) can be used for this purpose. These methods typically require computation of the principal eigenvector of a suitably modified Kronecker product matrix of the input graphs. We adopt this alternate view of the problem to address the problem of multiple network alignment. Using the phase estimation algorithm, we show that the multiple network alignment problem can be efficiently solved on quantum computers. We characterize the accuracy and performance of our method and show that it can deliver exponential speedups over conventional (non-quantum) methods.

  17. Alignment and Integration of Lightweight Mirror Segments

    NASA Technical Reports Server (NTRS)

    Evans, Tyler; Biskach, Michael; Mazzarella, Jim; McClelland, Ryan; Saha, Timo; Zhang, Will; Chan, Kai-Wing

    2011-01-01

    The optics for the International X-Ray Observatory (IXO) require alignment and integration of about fourteen thousand thin mirror segments to achieve the mission goal of 3.0 square meters of effective area at 1.25 keV with an angular resolution of five arc-seconds. These mirror segments are 0.4 mm thick, and 200 to 400 mm in size, which makes it difficult not to impart distortion at the sub-arc-second level. This paper outlines the precise alignment, permanent bonding, and verification testing techniques developed at NASA's Goddard Space Flight Center (GSFC). Improvements in alignment include new hardware and automation software. Improvements in bonding include two module new simulators to bond mirrors into, a glass housing for proving single pair bonding, and a Kovar module for bonding multiple pairs of mirrors. Three separate bonding trials were x-ray tested producing results meeting the requirement of sub ten arc-second alignment. This paper will highlight these recent advances in alignment, testing, and bonding techniques and the exciting developments in thin x-ray optic technology development.

  18. Evolution of shiva laser alignment systems

    SciTech Connect

    Boyd, R.D.

    1980-07-01

    The Shiva oscillator pulse is preamplified and divided into twenty beams. Each beam is then amplified, spatially filtered, directed, and focused onto a target a few hundred micrometers in size producing optical intensities up to 10/sup 16/W/cm/sup 2/. The laser was designed and built with three automatic alignment systems: the oscillator alignment system, which aligns each of the laser's three oscillators to a reference beamline; the chain input pointing system, which points each beam into its respective chain; and the chain output pointing, focusing and centering system which points, centers and focuses the beam onto the target. Recently the alignment of the laser's one hundred twenty spatial filter pinholes was also automated. This system uses digitized video images of back-illuminated pinholes and computer analysis to determine current positions. The offset of each current position from a desired center point is then translated into stepper motor commands and the pinhole is moved the proper distance. While motors for one pinhole are moving, the system can digitize, analyze, and send commands to other motors, allowing the system to efficiently align several pinholes in parallel.

  19. Large Telescope Segmented Primary Mirror Alignment

    NASA Technical Reports Server (NTRS)

    Rud, Mayer

    2010-01-01

    A document discusses a broadband (white light) point source, located at the telescope Cassegrain focus, which generates a cone of light limited by the hole in the secondary mirror (SM). It propagates to the aspheric null-mirror, which is optimized to make all the reflected rays to be normal to the primary mirror (PM) upon reflection. PM retro-reflects the rays back through the system for wavefront analysis. The point source and the wavefront analysis subsystems are all located behind the PM. The PM phasing is absolute (white light) and does not involve the SM. A relatively small, aspheric null-mirror located near the PM center of curvature has been designed to deliver the high level of optical wavefront correction. The phasing of the segments is absolute due to the use of a broadband source. The segmented PM is optically aligned independently and separately from the SM alignment. The separation of the PM segments alignment from the PM to the SM, and other telescope optics alignments, may be a significant advantage, eliminating the errors coupling. The point source of this concept is fully cooperative, unlike a star or laser-generated guide-star, providing the necessary brightness for the optimal S/N ratio, the spectral content, and the stable on-axis position. This concept can be implemented in the lab for the PM initial alignment, or made to be a permanent feature of the space-based or groundbased telescope.

  20. Multiple network alignment on quantum computers

    NASA Astrophysics Data System (ADS)

    Daskin, Anmer; Grama, Ananth; Kais, Sabre

    2014-09-01

    Comparative analyses of graph structured datasets underly diverse problems. Examples of these problems include identification of conserved functional components (biochemical interactions) across species, structural similarity of large biomolecules, and recurring patterns of interactions in social networks. A large class of such analyses methods quantify the topological similarity of nodes across networks. The resulting correspondence of nodes across networks, also called node alignment, can be used to identify invariant subgraphs across the input graphs. Given $k$ graphs as input, alignment algorithms use topological information to assign a similarity score to each $k$-tuple of nodes, with elements (nodes) drawn from each of the input graphs. Nodes are considered similar if their neighbors are also similar. An alternate, equivalent view of these network alignment algorithms is to consider the Kronecker product of the input graphs, and to identify high-ranked nodes in the Kronecker product graph. Conventional methods such as PageRank and HITS (Hypertext Induced Topic Selection) can be used for this purpose. These methods typically require computation of the principal eigenvector of a suitably modified Kronecker product matrix of the input graphs. We adopt this alternate view of the problem to address the problem of multiple network alignment. Using the phase estimation algorithm, we show that the multiple network alignment problem can be efficiently solved on quantum computers. We characterize the accuracy and performance of our method, and show that it can deliver exponential speedups over conventional (non-quantum) methods.

  1. Knee alignment in professional tennis players.

    PubMed

    Maquirriain, Javier

    2002-01-01

    This study determined lower-limb alignment and knee geometry in professional tennis players and compared the data with those from nonathletic individuals. Twenty-four radiographs from 12 asymptomatic players (mean age: 23.4+/-3.8 years) were prospectively studied. The three angles most useful for describing limb alignment and knee geometry in the coronal plane were measured: hip-knee-ankle, condylar-hip, and plateau-ankle. The condylar-plateau angle, frontal foot rotation angle, and the relationship between the mechanical axis and tibial plateau also were calculated. Varus limb alignment was predominant and the mechanical axis passed medially through the knee center; there was increased valgus inclination of the distal femur, varus angulation of the tibial plateau, near parallel alignment of the joint, and exaggerated external foot rotation. Hip-knee-ankle, condylar-hip, plateau-ankle, and frontal foot rotation angles were significantly different (P<.05, two-tailed t test) from previously reported angles of nonathletic individuals. Variations, probably due to repetitive dynamic demands imposed on lower limbs from an early age, seem to involve both femoral condyles and proximal tibial metaphyses, maintaining normal parallel joint alignment. PMID:11829331

  2. DoSA: Database of Structural Alignments.

    PubMed

    Mahajan, Swapnil; Agarwal, Garima; Iftekhar, Mohammed; Offmann, Bernard; de Brevern, Alexandre G; Srinivasan, Narayanaswamy

    2013-01-01

    Protein structure alignment is a crucial step in protein structure-function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159,780 conformationally similar and 56,140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function. Database URL: http://bo-protscience.fr/dosa/ PMID:23846594

  3. DoSA: Database of Structural Alignments

    PubMed Central

    Mahajan, Swapnil; Agarwal, Garima; Iftekhar, Mohammed; Offmann, Bernard; de Brevern, Alexandre G.; Srinivasan, Narayanaswamy

    2013-01-01

    Protein structure alignment is a crucial step in protein structure–function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159 780 conformationally similar and 56 140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function. Database URL: http://bo-protscience.fr/dosa/ PMID:23846594

  4. New alignment marks for improved measurement maturity

    NASA Astrophysics Data System (ADS)

    Weidenmueller, U.; Alves, H.; Schnabel, B.; Icard, B.; Pain, L.; Le Denmat, J.-C.; Manakli, S.; Pradelles, J.

    2008-04-01

    With shrinking dimensions in the semiconductor industry the lithographic demands are exceeding the parameters of the standard optical lithography. Electron beam direct write (EBDW) presents a good solution to overcome these limits and to successfully use this technology in R&D as well as in prototyping and some niche applications. For the industrial application of EBDW an alignment strategy adapted to the industrial standards is required to be compatible with optical lithography. In this context the crucial factor is the overlay performance, i.e. the maturity of the alignment strategy under different process conditions. New alignment marks improve the alignment repeatability and increase the window of the signal-to-noise ratio towards smaller or noisier signals. Particularly the latter has proved to be a major contribution to a higher maturity of the alignment. A comparison between the double cross and the new Barker mark type is presented in this paper. Furthermore, the mark reading repeatability and the final overlay results achieved are discussed.

  5. Galaxy pairs align with Galactic filaments

    NASA Astrophysics Data System (ADS)

    Tempel, E.; Tamm, A.

    2015-04-01

    Context. Gravitational collapse theory and numerical simulations suggest that the velocity field within large-scale galaxy filaments is dominated by motions along the filaments. Aims: Our aim is to check whether observational data reveal any preferred orientation of galaxy pairs with respect to the underlying filaments as a result of the expectedly anisotropic velocity field. Methods: We use galaxy pairs and galaxy filaments identified from Sloan Digital Sky Survey data. For filament extraction, we use the Bisous model that is based on the marked point process technique. During the filament detection, we use the centre point of each pair instead of the positions of galaxies to avoid a built-in influence of pair orientation on the filament construction. For pairs lying within filaments (3012 cases), we calculate the angle between the line connecting the galaxies of each pair and their host filaments. To avoid redshift-space distortions, the angle is measured in the plane of the sky. Results: The alignment analysis shows that the orientation of galaxy pairs correlates strongly with their host filaments. The alignment signal is stronger for loose pairs, with at least 25% excess of aligned pairs compared to a random distribution. The alignment of galaxy pairs and filaments measured from the observational data is in good agreement with the alignment in the Millennium simulation and thus provides support to the ΛCDM formalism.

  6. Business-IT Alignment: A Current-State Evaluation of Strategic Alignment within the Hospital Organization

    ERIC Educational Resources Information Center

    Evers, Kevin W.

    2010-01-01

    More than thirty years of research has shown that the practical value of business-IT alignment is significant and that its importance derives from strategic impact on business outcomes. The purpose of this exploratory study is to identify the current-state of business-IT alignment maturity within the hospital organization. Data for this study was…

  7. Alignment of Standards and Assessment: A Theoretical and Empirical Study of Methods for Alignment

    ERIC Educational Resources Information Center

    Nasstrom, Gunilla; Henriksson, Widar

    2008-01-01

    Introduction: In a standards-based school-system alignment of policy documents with standards and assessment is important. To be able to evaluate whether schools and students have reached the standards, the assessment should focus on the standards. Different models and methods can be used for measuring alignment, i.e. the correspondence between…

  8. What Are We Aligning Tests to When We Report Test Alignment to the CEFR?

    ERIC Educational Resources Information Center

    Harsch, Claudia; Hartig, Johannes

    2015-01-01

    The study reported here investigates the validity of judgments made when aligning tests to the "Common European Framework of Reference" (CEFR). Listening tests operationalizing pre-defined difficulty-determining characteristics were to be aligned to CEFR levels. We employed a modified version of the item-descriptor-matching-method. Ten…

  9. Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have developed Look-Align, an interactive web-based viewer to display pre-computed multiple sequence alignments. Although initially developed to support the visualization needs of the maize diversity website Panzea (http://www.panzea.org), the viewer is a generic stand-alone tool that can be easi...

  10. An active alignment method for post launch co-alignment of laser beam combiner systems

    NASA Technical Reports Server (NTRS)

    Yu, A. W.; Green, J. W.; Maynard, W. L.; Minott, P. O.; Krainak, M. A.

    1992-01-01

    A laser transmitter for high bandwidth geosynchronous satellite communications is described. High optical power is achieved by combining semiconductor laser diodes. An active alignment scheme is proposed for achieving the +/- 20 microrad post launch multiple laser angular co-alignment requirement.

  11. A simple method to control over-alignment in the MAFFT multiple sequence alignment program

    PubMed Central

    Katoh, Kazutaka; Standley, Daron M.

    2016-01-01

    Motivation: We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction. Results: The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, the effect of the proposed method is slightly negative in real protein-based benchmarks, and mostly neutral in simulation-based benchmarks. This approach is based on natural biological reasoning and should be compatible with many methods based on dynamic programming for multiple sequence alignment. Availability and implementation: The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/ Contact: katoh@ifrec.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153688

  12. 33 CFR 101.205 - Department of Homeland Security alignment.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... alignment. 101.205 Section 101.205 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... Department of Homeland Security alignment. The MARSEC Levels are aligned with the Department of Homeland... alignment. Table 101.205—Relation Between HSAS and MARSEC Levels Homeland security advisory system...

  13. 33 CFR 101.205 - Department of Homeland Security alignment.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... alignment. 101.205 Section 101.205 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... Department of Homeland Security alignment. The MARSEC Levels are aligned with the Department of Homeland... alignment. Table 101.205—Relation Between HSAS and MARSEC Levels Homeland security advisory system...

  14. Comparison of Beam-Based Alignment Algorithms for the ILC

    SciTech Connect

    Smith, J.C.; Gibbons, L.; Patterson, J.R.; Rubin, D.L.; Sagan, D.; Tenenbaum, P.; /SLAC

    2006-03-15

    The main linac of the International Linear Collider (ILC) requires more sophisticated alignment techniques than those provided by survey alone. Various Beam-Based Alignment (BBA) algorithms have been proposed to achieve the desired low emittance preservation. Dispersion Free Steering, Ballistic Alignment and the Kubo method are compared. Alignment algorithms are also tested in the presence of an Earth-like stray field.

  15. Alignment issues of the SLC linac accelerating structure

    SciTech Connect

    Seeman, J.T.; Adolphsen, C.; Decker, F.J.; Fischer, G.; Hodgson, J.; Pennacchi, R.; Perkins, C.; Pietryka, M.

    1991-05-01

    The accelerating structure of the Stanford Linear Collider (SLC) is required to be aligned to 100--200 {mu}m rms. Alignment at such a level will reduce transverse wakefield effects sufficiently so that only a small emittance enlargement of the beam is expected during acceleration to 50 GeV with up to 7 {times} 10{sup 10} particles per bunch. This report describes many aspects of the alignment including global alignment, local alignment, construction of the accelerating cavities, active controls of the structure alignment, external constraints, temperature and airflow effects, and alignment stability. 9 refs., 8 figs.

  16. Spent fuel container alignment device and method

    DOEpatents

    Jones, Stewart D.; Chapek, George V.

    1996-01-01

    An alignment device is used with a spent fuel shipping container including a plurality of fuel pockets for spent fuel arranged in an annular array and having a rotatable cover including an access opening therein. The alignment device includes a lightweight plate which is installed over the access opening of the cover. A laser device is mounted on the plate so as to emit a laser beam through a laser admittance window in the cover into the container in the direction of a pre-established target associated with a particular fuel pocket. An indexing arrangement on the container provides an indication of the angular position of the rotatable cover when the laser beam produced by the laser is brought into alignment with the target of the associated fuel pocket.

  17. Prosody and alignment: a sequential perspective

    NASA Astrophysics Data System (ADS)

    Szczepek Reed, Beatrice

    2010-12-01

    In their analysis of a corpus of classroom interactions in an inner city high school, Roth and Tobin describe how teachers and students accomplish interactional alignment by prosodically matching each other's turns. Prosodic matching, and specific prosodic patterns are interpreted as signs of, and contributions to successful interactional outcomes and positive emotions. Lack of prosodic matching, and other specific prosodic patterns are interpreted as features of unsuccessful interactions, and negative emotions. This forum focuses on the article's analysis of the relation between interpersonal alignment, emotion and prosody. It argues that prosodic matching, and other prosodic linking practices, play a primarily sequential role, i.e. one that displays the way in which participants place and design their turns in relation to other participants' turns. Prosodic matching, rather than being a conversational action in itself, is argued to be an interactional practice (Schegloff 1997), which is not always employed for the accomplishment of `positive', or aligning actions.

  18. Making Macroscopic Assemblies of Aligned Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Smalley, Richard E.; Colbert, Daniel T.; Smith, Ken A.; Walters, Deron A.; Casavant, Michael J.; Qin, Xiaochuan; Yakobson, Boris; Hauge, Robert H.; Saini, Rajesh Kumar; Chiung, Wan-Ting; Huffman, Charles B.

    2005-01-01

    A method of aligning and assembling single-wall carbon nanotubes (SWNTs) to fabricate macroscopic structures has been invented. The method entails suspending SWNTs in a fluid, orienting the SWNTs by use of a magnetic and/or electric field, and then removing the aligned SWNTs from suspension in such a way as to assemble them while maintaining the alignment. SWNTs are essentially tubular extensions of fullerene molecules. It is desirable to assemble aligned SWNTs into macroscopic structures because the common alignment of the SWNTs in such a structure makes it possible to exploit, on a macroscopic scale, the unique mechanical, chemical, and electrical properties that individual oriented SWNTs exhibit at the molecular level. Because of their small size and high electrical conductivity, carbon nanotubes, and especially SWNTs, are useful for making electrical connectors in integrated circuits. Carbon nanotubes can be used as antennas at optical frequencies, and as probes in scanning tunneling microscopes, atomic-force microscopes, and the like. Carbon nanotubes can be used with or instead of carbon black in tires. Carbon nanotubes are useful as supports for catalysts. Ropes of SWNTs are metallic and, as such, are potentially useful in some applications in which electrical conductors are needed - for example, they could be used as additives in formulating electrically conductive paints. Finally, macroscopic assemblies of aligned SWNTs can serve as templates for the growth of more and larger structures of the same type. The great variety of tubular fullerene molecules and of the structures that could be formed by assembling them in various ways precludes a complete description of the present method within the limits of this article. It must suffice to present a typical example of the use of one of many possible variants of the method to form a membrane comprising SWNTs aligned substantially parallel to each other in the membrane plane. The apparatus used in this variant

  19. Purification process for vertically aligned carbon nanofibers

    NASA Technical Reports Server (NTRS)

    Nguyen, Cattien V.; Delziet, Lance; Matthews, Kristopher; Chen, Bin; Meyyappan, M.

    2003-01-01

    Individual, free-standing, vertically aligned multiwall carbon nanotubes or nanofibers are ideal for sensor and electrode applications. Our plasma-enhanced chemical vapor deposition techniques for producing free-standing and vertically aligned carbon nanofibers use catalyst particles at the tip of the fiber. Here we present a simple purification process for the removal of iron catalyst particles at the tip of vertically aligned carbon nanofibers derived by plasma-enhanced chemical vapor deposition. The first step involves thermal oxidation in air, at temperatures of 200-400 degrees C, resulting in the physical swelling of the iron particles from the formation of iron oxide. Subsequently, the complete removal of the iron oxide particles is achieved with diluted acid (12% HCl). The purification process appears to be very efficient at removing all of the iron catalyst particles. Electron microscopy images and Raman spectroscopy data indicate that the purification process does not damage the graphitic structure of the nanotubes.

  20. The relationship between pelvic alignment and dysmenorrhea

    PubMed Central

    Kim, Moon-jeong; Baek, Il-hun; Goo, Bong-oh

    2016-01-01

    [Purpose] The purpose of this study was to investigate the relationship between pelvic alignment and dysmenorrhea in general women. [Subjects and Methods] One hundred two females participated in this study. They were divided into a dysmenorrhea group and a normal group based on the results of a Visual Analogue Scale (VAS) assessment of pain and the Menstrual Distress Questionnaire (MDQ). The survey data was collecting from 5th July to 20th September, 2014. Formetric 4D was used to measure the pelvic alignment, including the values of Trunk Imbalance, Pelvic Tilt, Surface Rotation, Lateral Deviation, Kyphosis Angle, Lordosis Angle. [Results] There was a difference in the spine alignments of each group. The value of pelvic torsion was 2.4 ± 1.8 degree in those with dysmenorrhea, while it was 1.7 ± 1.1 degree in those without. [Conclusion] In conclusion, the results suggest that there is a relationship between menstrual pain and pelvic torsion. PMID:27134354

  1. Active alignment/contact verification system

    DOEpatents

    Greenbaum, William M.

    2000-01-01

    A system involving an active (i.e. electrical) technique for the verification of: 1) close tolerance mechanical alignment between two component, and 2) electrical contact between mating through an elastomeric interface. For example, the two components may be an alumina carrier and a printed circuit board, two mating parts that are extremely small, high density parts and require alignment within a fraction of a mil, as well as a specified interface point of engagement between the parts. The system comprises pairs of conductive structures defined in the surfaces layers of the alumina carrier and the printed circuit board, for example. The first pair of conductive structures relate to item (1) above and permit alignment verification between mating parts. The second pair of conductive structures relate to item (2) above and permit verification of electrical contact between mating parts.

  2. System and method for 2D workpiece alignment

    SciTech Connect

    Weaver, William T.; Carlson, Charles T.; Smith, Scott A.; Beck, Michael A.; Webb, Aaron P.; Strassner, James D.; Gravell, Lawrence R.; Simmons, Michael C.

    2015-07-14

    A carrier capable of holding one or more workpieces is disclosed. The carrier includes movable projections located along the sides of each cell in the carrier. This carrier, in conjunction with a separate alignment apparatus, aligns each workpiece within its respective cell against several alignment pins, using a multiple step alignment process to guarantee proper positioning of the workpiece in the cell. First, the workpieces are moved toward one side of the cell. Once the workpieces have been aligned against this side, the workpieces are then moved toward an adjacent orthogonal side such that the workpieces are aligned to two sides of the cell. Once aligned, the workpiece is held in place by the projections located along each side of each cell. In addition, the alignment pins are also used to align the associated mask, thereby guaranteeing that the mask is properly aligned to the workpiece.

  3. Backup Alignment Devices on Shuttle: Heads-Up Display or Crew Optical Alignment Sight

    NASA Technical Reports Server (NTRS)

    Chavez, Melissa A.

    2011-01-01

    NASA s Space Shuttle was built to withstand multiple failures while still keeping the crew and vehicle safe. Although the design of the Space Shuttle had a great deal of redundancy built into each system, there were often additional ways to keep systems in the best configuration if a failure were to occur. One such method was to use select pieces of hardware in a way for which they were not primarily intended. The primary function of the Heads-Up Display (HUD) was to provide the crew with a display of flight critical information during the entry phase. The primary function of the Crew Optical Alignment Sight (COAS) was to provide the crew an optical alignment capability for rendezvous and docking phases. An alignment device was required to keep the Inertial Measurement Units (IMUs) well aligned for a safe Entry; nominally this alignment device would be the two on-board Star Trackers. However, in the event of a Star Tracker failure, the HUD or COAS could also be used as a backup alignment device, but only if the device had been calibrated beforehand. Once the HUD or COAS was calibrated and verified then it was considered an adequate backup to the Star Trackers for entry IMU alignment. There were procedures in place and the astronauts were trained on how to accurately calibrate the HUD or COAS and how to use them as an alignment device. The calibration procedure for the HUD and COAS had been performed on many Shuttle missions. Many of the first calibrations performed were for data gathering purposes to determine which device was more accurate as a backup alignment device, HUD or COAS. Once this was determined, the following missions would frequently calibrate the HUD in order to be one step closer to having the device ready in case it was needed as a backup alignment device.

  4. Robust optical alignment systems using geometric invariants

    NASA Astrophysics Data System (ADS)

    Ho, Tzung-Hsien; Rzasa, John; Milner, Stuart D.; Davis, Christopher C.

    2007-09-01

    Traditional coarse pointing, acquisition, and tracking (CPAT) systems are pre-calibrated to have the center pixel of the camera aligned to the laser pointing vector and the center pixel is manually moved to the target of interest to complete the alignment process. Such a system has previously demonstrated its capability in aligning with distant targets and the pointing accuracy is on the order of sensor resolution. However, aligning with targets at medium range where the distance between angular sensor and transceiver is not negligible is its Achilles Heel. This limitation can be resolved by imposing constraints, such as the trifocal tensor (TT), which is deduced from the geometrical dependence between cameras and transceivers. Two autonomous CPAT systems are introduced for FSO transceiver alignment in mid- and long-range scenarios. This work focuses on experimental results that validate the pointing performance for targets at different distances, backed up by the theoretical derivations. A mid-range CPAT system, applying a trifocal tensor as its geometric invariant, includes two perspective cameras as sensors to perceive target distances. The long-range CPAT system, applying linear mapping as the invariant, requires only one camera to determine the pointing angle. Calibration procedures for both systems are robust to measurement noise and the resulting system can autonomously point to a target of interest with a high accuracy, which is also on the order of sensor resolution. The results of this work are not only beneficial to the design of CPAT systems for FSO transceiver alignment, but also in new applications such as surveillance and navigation.

  5. Experimental and simulation studies of alignment marks

    NASA Astrophysics Data System (ADS)

    Wong, Alfred K. K.; Doi, Takeshi; Dunn, Diana D.; Neureuther, Andrew R.

    1991-07-01

    The roles of alignment mark structure, geometry, film materials and scanned illumination image on dark-field alignment signal quality are investigated through simulation interpreted experiments. The illumination of the alignment system consists of a low numerical aperture 1.0 micrometers image of a slit at 488.0 and 514.5 nm which is scanned across the alignment mark. The light scattered into a dark-band protected cone is collected. The structures consist of 0.5 to 1.2 micrometers wide features including trenches in silicon coated with 1.34 micrometers of photoresist, and trenches in nitride coated silicon with 1.00 micrometers of photoresist. For simulation, the illumination image is calculated using SAMPLE and input to a massively parallel finite-difference time-domain scattering analysis program called TEMPEST at various lateral shifts to simulate scanning. The diffracted orders output from TEMPEST are used to calculate total diffracted energy in various angular bands and to view dark field instantaneous images. Studied of depth, width, thin-film stack and coating thickness are used to identify key phenomena such as the role of interference between reflection from the alignment mark and substrate surfaces. Simulations are used to interpret the experimental observations and provide guidelines for topography control, and illumination and collection optics. The alignment signal is shown to be a strong function of trench depth, and only a weak function of trench width. An order of magnitude signal strength reduction occurs when the effective optical depth of the trench is a multiple of (lambda) resist/2 compared to the surrounding area.

  6. Time-Resolved Electron Diffraction from Selectively Aligned Molecules

    SciTech Connect

    Reckenthaeler, Peter; Krausz, Ferenc; Centurion, Martin; Fuss, Werner; Trushin, Sergei A.; Fill, Ernst E.

    2009-05-29

    We experimentally demonstrate ultrafast electron diffraction from transiently aligned molecules in the absence of external (aligning) fields. A sample of aligned molecules is generated through photodissociation with femtosecond laser pulses, and the diffraction pattern is captured by probing the sample with picosecond electron pulses shortly after dissociation - before molecular rotation causes the alignment to vanish. In our experiments the alignment decays with a time constant of 2.6{+-}1.2 ps.

  7. Survey and Alignment of SLAC's B Factory

    SciTech Connect

    Pietryka, Matthew J.; Gaydosh, Michael L.; /SLAC

    2011-09-08

    The survey and alignment of SLAC's B-factory injector and high energy ring will be complete in March 1997. Modern digital electronic surveying tools are contributing to new, efficient alignment procedures. A laser tracker was used to fiducialize almost 300 quadrupole magnets. Digital levels were used to pre-set base plate elevations. Theodolites with very accurate co-axial distance meters were used for everything from layout to 3D magnet positioning to network surveys, all in free stationing mode. A number of procedures and measurement results are outlined.

  8. Fine alignment of a large segmented mirror

    NASA Technical Reports Server (NTRS)

    Dey, Thomas William (Inventor)

    2010-01-01

    A system for aligning a segmented mirror includes a source of radiation directed along a first axis to the segmented mirror and a beamsplitter removably inserted along the first axis for redirecting radiation from the first axis to a second axis, substantially perpendicular to the first axis. An imaging array is positioned along the second axis for imaging the redirected radiation, and a knife-edge configured for cutting the redirected radiation is serially positioned to occlude and not occlude the redirected radiation, effectively providing a variable radiation pattern detected by the imaging array for aligning the segmented mirror.

  9. Alignment Pins for Assembling and Disassembling Structures

    NASA Technical Reports Server (NTRS)

    Campbell, Oliver C.

    2008-01-01

    Simple, easy-to-use, highly effective tooling has been devised for maintaining alignment of bolt holes in mating structures during assembly and disassembly of the structures. The tooling was originally used during removal of a body flap from the space shuttle Atlantis, in which misalignments during removal of the last few bolts could cause the bolts to bind in their holes. By suitably modifying the dimensions of the tooling components, the basic design of the tooling can readily be adapted to other structures that must be maintained in alignment. The tooling includes tapered, internally threaded alignment pins designed to fit in the bolt holes in one of the mating structures, plus a draw bolt and a cup that are used to install or remove each alignment pin. In preparation for disassembly of two mating structures, external supports are provided to prevent unintended movement of the structures. During disassembly of the structures, as each bolt that joins the structures is removed, an alignment pin is installed in its place. Once all the bolts have been removed and replaced with pins, the pins maintain alignment as the structures are gently pushed or pulled apart on the supports. In assembling the two structures, one reverses the procedure described above: pins are installed in the bolt holes, the structures are pulled or pushed together on the supports, then the pins are removed and replaced with bolts. The figure depicts the tooling and its use. To install an alignment pin in a bolt hole in a structural panel, the tapered end of the pin is inserted from one side of the panel, the cup is placed over the pin on the opposite side of the panel, the draw bolt is inserted through the cup and threaded into the pin, the draw bolt is tightened to pull the pin until the pin is seated firmly in the hole, then the draw bolt and cup are removed, leaving the pin in place. To remove an alignment pin, the cup is placed over the pin on the first-mentioned side of the panel, the draw

  10. Drift Chamber Alignment using Cosmic Rays

    SciTech Connect

    Kotwal, Ashutosh V.; Hays, Christopher P.

    2014-05-07

    The Collider Detector at Fermilab (CDF) is a general-purpose experimental apparatus with an inner tracking detector for measuring charged particles, surrounded by a calorimeter for measurements of electromagnetic and hadronic showers, and a muon detector system. We present a technique for, and results of, a precise relative alignment of the drift chamber wires of the CDF tracker. This alignment has been an important component of the track momentum calibration, which is the basis for the charged-lepton calibration for the measurement of the W boson mass at CDF.

  11. Review of Alignment Activities at Jefferson Laboratory

    SciTech Connect

    Christopher Curtis

    2002-12-01

    The Thomas Jefferson National Accelerator Facility (Jefferson Lab) comprises a 5 GeV continuous electron beam accelerator (CEBAF) delivering beam to three experimental halls, and a kilowatt range tunable free electron laser (FEL), currently being upgraded to a 10 kW machine. The progression into steady state experimental runs at the facility has allowed the alignment group the opportunity to incorporate new developments into the alignment system. Two of these are discussed, together with some of the more unusual (e.g. gyrotheodolite survey) and the more routine surveys performed at the lab over the last three years.

  12. Laboratory simulation of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Wessel, Frank J.; Rostoker, Norman

    1993-01-01

    A summary of progress during the period Apr. 1992 to Mar. 1993 is provided. Objectives of the research are (1) to simulate, via laboratory experiments, the three terms of the field-aligned current equation; (2) to simulate auroral-arc formation processes by configuring the boundary conditions of the experimental chamber and plasma parameters to produce highly localized return currents at the end of a field-aligned current system; and (3) to extrapolate these results, using theoretical and computational techniques, to the problem of magnetospheric-ionospheric coupling and to compare them with published literature signatures of auroral-arc phenomena.

  13. Advanced alignment of the ATLAS inner detector

    NASA Astrophysics Data System (ADS)

    Stahlman, Jonathan M.; Atlas Collaboration

    2013-08-01

    The primary goal of the ATLAS inner detector (ID) is to accurately measure the trajectories of charged particles in the high particle density environment of the large hadron collider (LHC) collisions. This is achieved using a combination of different technologies, including silicon pixels, silicon microstrips, and gaseous drift-tubes, all immersed in a 2 Tesla magnetic field. With nearly 750 k alignable degrees of freedom, it is crucial that an accurate model of the detector positions be produced using an automated and robust algorithm in order to achieve good tracking performance. This has been accomplished using a variety of alignment techniques resulting in near optimal hit and momentum resolutions.

  14. Cell Alignment Driven by Mechanically Induced Collagen Fiber Alignment in Collagen/Alginate Coatings.

    PubMed

    Chaubaroux, Christophe; Perrin-Schmitt, Fabienne; Senger, Bernard; Vidal, Loïc; Voegel, Jean-Claude; Schaaf, Pierre; Haikel, Youssef; Boulmedais, Fouzia; Lavalle, Philippe; Hemmerlé, Joseph

    2015-09-01

    For many years it has been a major challenge to regenerate damaged tissues using synthetic or natural materials. To favor the healing processes after tendon, cornea, muscle, or brain injuries, aligned collagen-based architectures are of utmost interest. In this study, we define a novel aligned coating based on a collagen/alginate (COL/ALG) multilayer film. The coating exhibiting a nanofibrillar structure is cross-linked with genipin for stability in physiological conditions. By stretching COL/ALG-coated polydimethylsiloxane substrates, we developed a versatile method to align the collagen fibrils of the polymeric coating. Assays on cell morphology and alignment were performed to investigate the properties of these films. Microscopic assessments revealed that cells align with the stretched collagen fibrils of the coating. The degree of alignment is tuned by the stretching rate (i.e., the strain) of the COL/ALG-coated elastic substrate. Such coatings are of great interest for strategies that require aligned nanofibrillar biological material as a substrate for tissue engineering. PMID:25658028

  15. 'Skullduggery': Lions Align and Their Mandibles Rock!

    PubMed

    Williams, Vivienne L; Loveridge, Andrew J; Newton, David J; Macdonald, David W

    2015-01-01

    South Africa has legally exported substantial quantities of lion bones to Southeast Asia and China since 2008, apparently as part of the multinational trade substituting bones and body parts of other large cats for those of the tiger in wine and other health tonics. The legal sale of lion bones may mask an illegal trade, the size of which is only partially known. An observed component of the illegal trade is that quantities of skeletons are sometimes declared falsely/fraudulently on CITES export permits. Furthermore, there are emerging concerns that bones from tigers reared in captivity in South Africa and elsewhere are being laundered as lion bones using CITES Appendix II permits. There is therefore a need for tools to monitor the trade in lion body parts and to distinguish between lions and tigers. Our research indicates that it is possible to use skeletons, skulls and cranial sutures to detect misdeclarations in the lion bone trade. It is also possible to use the average mass of a lion skeleton to corroborate the numbers of skeletons declared on CITES permits, relative to the weight of the consolidated consignments stated on the air waybills. When the mass of consolidated consignments of skeletons destined for export was regressed against the number of skeletons in that consignment, there was a strong correlation between the variables (r2 = 0.992) that can be used as a predictor of the accuracy of a declaration on a CITES permit. Additionally, the skulls of lions and tigers differ: two cranial sutures of lions align and their mandibles rock when placed on a flat surface, whereas the cranial sutures of tigers are not aligned and their mandibles rest naturally on two contact points. These two morphological differences between the skulls of tigers and lions are easy to observe at a glance and provide a method for distinguishing between the species if illegal trade in the bones is suspected and the skulls are present. These identifications should ideally be

  16. Bokeh mirror alignment for Cherenkov telescopes

    NASA Astrophysics Data System (ADS)

    Ahnen, M. L.; Baack, D.; Balbo, M.; Bergmann, M.; Biland, A.; Blank, M.; Bretz, T.; Bruegge, K. A.; Buss, J.; Domke, M.; Dorner, D.; Einecke, S.; Hempfling, C.; Hildebrand, D.; Hughes, G.; Lustermann, W.; Mannheim, K.; Mueller, S. A.; Neise, D.; Neronov, A.; Noethe, M.; Overkemping, A.-K.; Paravac, A.; Pauss, F.; Rhode, W.; Shukla, A.; Temme, F.; Thaele, J.; Toscano, S.; Vogler, P.; Walter, R.; Wilbert, A.

    2016-09-01

    Imaging Atmospheric Cherenkov Telescopes (IACTs) need imaging optics with large apertures and high image intensities to map the faint Cherenkov light emitted from cosmic ray air showers onto their image sensors. Segmented reflectors fulfill these needs, and composed from mass production mirror facets they are inexpensive and lightweight. However, as the overall image is a superposition of the individual facet images, alignment remains a challenge. Here we present a simple, yet extendable method, to align a segmented reflector using its Bokeh. Bokeh alig nment does not need a star or good weather nights but can be done even during daytime. Bokeh alignment optimizes the facet orientations by comparing the segmented reflectors Bokeh to a predefined template. The optimal Bokeh template is highly constricted by the reflector's aperture and is easy accessible. The Bokeh is observed using the out of focus image of a near by point like light source in a distance of about 10 focal lengths. We introduce Bokeh alignment on segmented reflectors and demonstrate it on the First Geiger-mode Avalanche Cherenkov Telescope (FACT) on La Palma, Spain.

  17. Efficient alignment-free DNA barcode analytics

    PubMed Central

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-01-01

    Background In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. Results New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Conclusion Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding. PMID:19900305

  18. Further solar alignments of Greek Byzantine churches

    NASA Astrophysics Data System (ADS)

    Liritzis, I.; Vasiliou, H.

    Following the recent work on the solar alignment of Greek byzantine churches (Liritzis and Vassiliou 2006 a,b,c) the solar orientations of twenty one more churches are presented. The question examined is if the day of solar rise across the eastern direction of the church is related with the feast day of Patron Saint. Measurements were carried out with magnetic compass, inclinometer, portable GPS and appropriate corrections for the solar declination. The alignments towards eastern sunrise were examined for various angular altitudes of the perceptible horizon. At least for all Rhodean churches the patron's day is met when sun oblique path crosses horizon a few degrees beyond the intersection of extrapolated eastern axis of the church with horizons skyline. Therefore, taken the orientation as the glitter of first sunrays -early dawn- correlation of thirteen present churches are aligned near the autumnal equinox, three have relation with the feast of patron saint, four are related to the other important feast of Christianity and one seem orientated randomly. However accounting for a due east sun position a few degrees above horizon in early liturgy hours (6:30 - 9:30 am) all the Rhodean alignments coincides with Saint's name day.

  19. General Education Reform: Opportunities for Institutional Alignment

    ERIC Educational Resources Information Center

    Fuess, Scott M., Jr.; Mitchell, Nancy D.

    2011-01-01

    General education reform provides strategic opportunities for departments. This article analyzes reform at the University of Nebraska-Lincoln, illustrating how departments could use the reform process to clarify their strategic planning, align with institutional goals, and steer the university closer to departmental objectives. (Contains 1 table.)

  20. Aligning Student Support with Achievement Goals. Perspective

    ERIC Educational Resources Information Center

    Wallace Foundation, The, 2006

    2006-01-01

    This Wallace Perspective paper summarizes key findings of a newly-published book, "Aligning Student Support with Achievement Goals: The Secondary Principal's Guide," that argues that school counselors could be much more active players in improving student learning. The book, which bases its conclusions heavily on Wallace's Transforming School…

  1. Quasiparticle Level Alignment for Photocatalytic Interfaces.

    PubMed

    Migani, Annapaoala; Mowbray, Duncan J; Zhao, Jin; Petek, Hrvoje; Rubio, Angel

    2014-05-13

    Electronic level alignment at the interface between an adsorbed molecular layer and a semiconducting substrate determines the activity and efficiency of many photocatalytic materials. Standard density functional theory (DFT)-based methods have proven unable to provide a quantitative description of this level alignment. This requires a proper treatment of the anisotropic screening, necessitating the use of quasiparticle (QP) techniques. However, the computational complexity of QP algorithms has meant a quantitative description of interfacial levels has remained elusive. We provide a systematic study of a prototypical interface, bare and methanol-covered rutile TiO2(110) surfaces, to determine the type of many-body theory required to obtain an accurate description of the level alignment. This is accomplished via a direct comparison with metastable impact electron spectroscopy (MIES), ultraviolet photoelectron spectroscopy (UPS), and two-photon photoemission (2PP) spectroscopy. We consider GGA DFT, hybrid DFT, and G0W0, scQPGW1, scQPGW0, and scQPGW QP calculations. Our results demonstrate that G0W0, or our recently introduced scQPGW1 approach, are required to obtain the correct alignment of both the highest occupied and lowest unoccupied interfacial molecular levels (HOMO/LUMO). These calculations set a new standard in the interpretation of electronic structure probe experiments of complex organic molecule/semiconductor interfaces. PMID:26580537

  2. Thematic Roles, Markedness Alignment and Processing Complexity

    ERIC Educational Resources Information Center

    Lee, Yoonhyoung; Kwon, Youan; Gordon, Peter C.

    2015-01-01

    Two experiments used eye-tracking during reading to investigate the role of the consistency of the relative markedness alignment of noun phrases (NPs) in the processing of complex sentences in Korean. To do so, the animacy of the first NP was varied in both experiments to manipulate the relative markedness of NPs. In addition, case markings of the…

  3. Survey and alignment at the ALS

    SciTech Connect

    Krebs, G.F.; Lauritzen, T.; Thur, W.

    1995-11-01

    This paper describes survey and alignment at the Lawrence Berkeley National Laboratory`s Advanced Light Source (ALS) accelerators from 1993 to 1995. The ALS is a 1.0 - 1.9 GeV electron accelerator producing extremely bright synchrotron light in the UV and soft-X-ray wavelengths. At the ALS, electrons are accelerated in a LINAC to 50 MeV, injected into a booster ring for further acceleration and finally injected into the storage ring. This is shown schematically in Figure 1. The storage ring, some 200 m in circumference, has been run with electron currents above 400 mA with lifetimes as high as 24 hours. The ALS is a third generation light source and requires for efficient storage ring operation, magnets aligned to within 150 mm of their ideal position. To accomplish this a network of monuments was established and their positions measured with respect to one another. The data was reduced using GEONET`` and STAR*NET`` software. Using the monuments as reference points, magnet positions were measured and alignment confirmed using the Kem Electronic Coordinate Determination System (ECDS``). A number of other papers dealing with survey and alignment (S&A) at the ALS have been written that may further elucidate some details of the methods and systems described in this paper.

  4. Recombination-aware alignment of diploid individuals

    PubMed Central

    2014-01-01

    Background Traditionally biological similarity search has been studied under the abstraction of a single string to represent each genome. The more realistic representation of diploid genomes, with two strings defining the genome, has so far been largely omitted in this context. With the development of sequencing techniques and better phasing routines through haplotype assembly algorithms, we are not far from the situation when individual diploid genomes could be represented in their full complexity with a pair-wise alignment defining the genome. Results We propose a generalization of global alignment that is designed to measure similarity between phased predictions of individual diploid genomes. This generalization takes into account that individual diploid genomes evolve through a mutation and recombination process, and that predictions may be erroneous in both dimensions. Even though our model is generic, we focus on the case where one wants to measure only the similarity of genome content allowing free recombination. This results into efficient algorithms for direct application in (i) evaluation of variation calling predictions and (ii) progressive multiple alignments based on labeled directed acyclic graphs (DAGs) to represent profiles. The latter may be of more general interest, in connection to covering alignment of DAGs. Extensions of our model and algorithms can be foreseen to have applications in evaluating phasing algorithms, as well as more fundamental role in phasing child genome based on parent genomes. PMID:25572943

  5. Graph-based molecular alignment (GMA).

    PubMed

    Marialke, J; Körner, R; Tietze, S; Apostolakis, Joannis

    2007-01-01

    We describe a combined 2D/3D approach for the superposition of flexible chemical structures, which is based on recent progress in the efficient identification of common subgraphs and a gradient-based torsion space optimization algorithm. The simplicity of the approach is reflected in its generality and computational efficiency: the suggested approach neither requires precalculated statistics on the conformations of the molecules nor does it make simplifying assumptions on the topology of the molecules being compared. Furthermore, graph-based molecular alignment produces alignments that are consistent with the chemistry of the molecules as well as their general structure, as it depends on both the local connectivities between atoms and the overall topology of the molecules. We validate this approach on benchmark sets taken from the literature and show that it leads to good results compared to computationally and algorithmically more involved methods. The results suggest that, for most practical purposes, graph-based molecular alignment is a viable alternative to molecular field alignment with respect to structural superposition and leads to structures of comparable quality in a fraction of the time. PMID:17381175

  6. Methodological Alignment in Design-Based Research

    ERIC Educational Resources Information Center

    Hoadley, Christopher M.

    2004-01-01

    Empirical research is all about trying to model and predict the world. In this article, I discuss how design-based research methods can help do this effectively. In particular, design-based research methods can help with the problem of methodological alignment: ensuring that the research methods we use actually test what we think they are testing.…

  7. Aligning Technology Education Teaching with Brain Development

    ERIC Educational Resources Information Center

    Katsioloudis, Petros

    2015-01-01

    This exploratory study was designed to determine if there is a level of alignment between technology education curriculum and theories of intellectual development. The researcher compared Epstein's Brain Growth Theory and Piaget's Status of Intellectual Development with technology education curriculum from Australia, England, and the United…

  8. Aligning Standards and Curriculum for Classroom Success.

    ERIC Educational Resources Information Center

    Perna, Daniel M.; Davis, James R.

    This book provides classroom teachers at every grade level and subject the tools and background to effectively work with standards as a guide in their planning. It explains the process by which educators can rearticulate state standards and align the locally rearticulated standards to their curriculum and student performance. Six chapters include:…

  9. Constructing Aligned Assessments Using Automated Test Construction

    ERIC Educational Resources Information Center

    Porter, Andrew; Polikoff, Morgan S.; Barghaus, Katherine M.; Yang, Rui

    2013-01-01

    We describe an innovative automated test construction algorithm for building aligned achievement tests. By incorporating the algorithm into the test construction process, along with other test construction procedures for building reliable and unbiased assessments, the result is much more valid tests than result from current test construction…

  10. Aligning risk management with patient safety.

    PubMed

    McCormick, Timothy; Hern, Warren

    2009-07-01

    There are four key components to the success of HCCI, a captive insurance company formed by five healthcare systems: Common and aligned goals. A commitment to ongoing education. Open and honest dialogue among member-owners. Easy-to-use technology to support information flow and decision making. PMID:19588814

  11. Rounding And Aligning Tubes For Butt Welding

    NASA Technical Reports Server (NTRS)

    Burley, Richard H.; Burow, Glenn H.

    1990-01-01

    Easy-to-use tool helps to ensure solid, reliable joint. Tool similar to automobile-tailpipe expander corrects out-of-roundness in tubes before butt-welded and holds tubes in position during welding. Two tubes rounded and aligned with each other by expansion shoes. After use, shoes retracted so tool withdrawn, even through tube narrower than its mate.

  12. Molecular mechanism of viscoelasticity in aligned polyethylene

    NASA Astrophysics Data System (ADS)

    Hammad, Ali; Hasan, Hikmatyar; Swinburne, Thomas; Del Rosso, Stefano; Iannucci, Lorenzo; Sutton, Adrian

    2014-03-01

    Aligned polyethylene is used in industrial and medical applications due to its low density and high tensile strength. Extensive experimental work has been done to determine its mechanical properties, notably its viscoelasticity. However, the molecular processes that underlie these macroscopic properties are poorly understood. We develop a united atom model of aligned chains, in which intermolecular interactions are modelled by a Lennard-Jones potential, and the elastic energy within chains is modelled with harmonic springs. Using this simple model, we demonstrate the nucleation of solitons from chain ends, as one molecular chain is stretched with respect to another, and how load is transferred between chains in disregistry by intermolecular interactions. We develop an equation of motion for the movement of solitons along molecular chains, allowing us to replace a collection of aligned chains with a gas of solitons. Although solitons have been invoked to account for dielectric relaxation in crystalline regions of polyethylene, we believe this may be the first time they are discussed in the context of mechanical properties of aligned polyethylene.

  13. Quasiparticle Level Alignment for Photocatalytic Interfaces

    SciTech Connect

    Migani, Annapaola; Mowbray, Duncan J.; Zhao, Jin; Petek, Hrvoje; Rubio, Angel

    2014-05-13

    Electronic level alignment at the interface between an adsorbed molecular layer and a semiconducting substrate determines the activity and efficiency of many photocatalytic materials. Standard density functional theory (DFT)-based methods have proven unable to provide a quantitative description of this level alignment. This requires a proper treatment of the anisotropic screening, necessitating the use of quasiparticle (QP) techniques. However, the computational complexity of QP algorithms has meant a quantitative description of interfacial levels has remained elusive. We provide a systematic study of a prototypical interface, bare and methanol-covered rutile TiO2(110) surfaces, to determine the type of many-body theory required to obtain an accurate description of the level alignment. This is accomplished via a direct comparison with metastable impact electron spectroscopy (MIES), ultraviolet photoelectron spectroscopy (UPS), and two-photon photoemission (2PP) spectroscopy. We consider GGA DFT, hybrid DFT, and G0W0, scQPGW1, scQPGW0, and scQPGW QP calculations. Our results demonstrate that G0W0, or our recently introduced scQPGW1 approach, are required to obtain the correct alignment of both the highest occupied and lowest unoccupied interfacial molecular levels (HOMO/LUMO). These calculations set a new standard in the interpretation of electronic structure probe experiments of complex organic molecule/semiconductor interfaces.

  14. Prosody and Alignment: A Sequential Perspective

    ERIC Educational Resources Information Center

    Reed, Beatrice Szczepek

    2010-01-01

    In their analysis of a corpus of classroom interactions in an inner city high school, Roth and Tobin describe how teachers and students accomplish interactional alignment by prosodically matching each other's turns. Prosodic matching, and specific prosodic patterns are interpreted as signs of, and contributions to successful interactional outcomes…

  15. Bringing COM Technology to Alignment Software

    SciTech Connect

    Langer, Lothar

    2002-11-19

    Software tools for alignment purposes should be versatile and flexible handling data in various formats. Microsoft's Component Object Model is the base for an appropriate software architecture to be built upon. COM-components comply with different programming environments like web applications, C++, Visual Basic, and MATLAB. The benefits for the user and the program developer are discussed.

  16. Aligning English Language Testing with Curriculum

    ERIC Educational Resources Information Center

    Palacio, Marcela; Gaviria, Sandra; Brown, James Dean

    2016-01-01

    Frustrations with traditional testing led a group of teachers at the English for adults program at Universidad EAFIT (Colombia) to design tests aligned with the institutional teaching philosophy and classroom practices. This article reports on a study of an item-by-item evaluation of a series of English exams for validity and reliability in an…

  17. Alignment modification for pencil eye shields

    SciTech Connect

    Evans, M.D.; Pla, M.; Podgorsak, E.B. )

    1989-01-01

    Accurate alignment of pencil beam eye shields to protect the lens of the eye may be made easier by means of a simple modification of existing apparatus. This involves drilling a small hole through the center of the shield to isolate the rayline directed to the lens and fabricating a suitable plug for this hole.

  18. Interstellar Silicate Dust: Modeling and Grain Alignment

    NASA Astrophysics Data System (ADS)

    Das, Indrajit

    We examine some aspects of the alignment of silicate dust grains with respect to the interstellar magnetic field. First, we consider possible observational constraints on the magnetic properties of the grains. Second, we investigate the role of collisions with gas atoms and the production of H2 molecules on the grain surface in the alignment process when the grain is drifting in the gaseous medium. Paramagnetism associated with Fe content in the dust is thought to play a critical role in alignment. Min et al (2007) claimed that the Fe content of the silicate dust can be constrained by the shape of the 10 μm extinction feature. They found low Fe abundances, potentially posing problems for grain alignment theories. We revisit this analysis modeling the grains with irregularly shaped Gaussian Random Sphere (GRS). We give a comprehensive review of all the relevant constraints researchers apply and discuss their effects on the inferred mineralogy. Also, we extend this analysis to examine whether constraints can be placed on the presence of Fe-rich inclusions which could yield "super-paramagnetism". This possibility has long been speculated, but so far observational constraints are lacking. Every time a gas atom collides with a grain, the grain's angular momentum is slightly modified. Likewise when an H2 molecule forms on the surface and is ejected. Here also we model the grain with GRS shape and considered various scenarios about how the colliding gas particles depart the grain. We develop theoretical and computational tools to estimate the torques associated with these aforementioned events for a range of grain drift speeds---from low subsonic to high supersonic speeds. Code results were verified with spherical grain for which analytical results were available. Finally, the above torque results were used to study the grain rotational dynamics. Solving dynamical equations we examine how these torques influence the grain alignment process. Our analysis suggests that

  19. Kernel Manifold Alignment for Domain Adaptation.

    PubMed

    Tuia, Devis; Camps-Valls, Gustau

    2016-01-01

    The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors' knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational

  20. Kernel Manifold Alignment for Domain Adaptation

    PubMed Central

    Tuia, Devis; Camps-Valls, Gustau

    2016-01-01

    The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors’ knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational

  1. To develop a geometric matching method for precision mold alignment

    NASA Astrophysics Data System (ADS)

    Chen, Chun-Jen; Chang, Chun-Li; Jywe, Wenyuh

    2014-09-01

    In order to develop a high accuracy optical alignment system for precision molding machine, a geometric matching method was developed in this paper. The alignment system includes 4 high magnification lenses, 4 CCD cameras and 4 LED light sources. In the precision molding machine, a bottom metal mold and a top glass mold are used to produce a micro lens. The two molds combination does not use any pin or alignment part. They only use the optical alignment system to alignment. In this optical alignment system, the off-axis alignment method was used. The alignment accuracy of the alignment system is about 0.5 μm. There are 2 cross marks on the top glass mold and 2 cross marks on the bottom metal mod. In this paper did not use edge detection to recognize the mask center because the mask easy wears when the combination times increased. Therefore, this paper develops a geometric matching method to recognize mask center.

  2. Primordial alignment of elliptical galaxies in intermediate redshift clusters

    NASA Astrophysics Data System (ADS)

    Rong, Yu; Zhang, Shuang-Nan; Liao, Jin-Yuan

    2015-10-01

    We measure primordial alignments for the red galaxies in the sample of eight massive galaxy clusters in the southern sky from the Cluster Lensing And Supernova survey with Hubble-Very Large Telescope (CLASH-VLT) Large Programme, at a median redshift of 0.375. We find primordial alignment with about 3σ significance in the four dynamically young clusters, but null detection of primordial alignment in the four highly relaxed clusters. The observed primordial alignment is not dominated by any single one of the four dynamically young clusters, and is primarily due to a population of bright galaxies (Mr < -20.5)residing in the region 300-810 kpc from the cluster centres. For the first time, we point out that the combination of radial alignment and halo alignment can cause fake primordial alignment. Finally, we find that the detected alignment for the dynamically young clusters is real rather than fake primordial alignment.

  3. Robust temporal alignment of multimodal cardiac sequences

    NASA Astrophysics Data System (ADS)

    Perissinotto, Andrea; Queirós, Sandro; Morais, Pedro; Baptista, Maria J.; Monaghan, Mark; Rodrigues, Nuno F.; D'hooge, Jan; Vilaça, João. L.; Barbosa, Daniel

    2015-03-01

    Given the dynamic nature of cardiac function, correct temporal alignment of pre-operative models and intraoperative images is crucial for augmented reality in cardiac image-guided interventions. As such, the current study focuses on the development of an image-based strategy for temporal alignment of multimodal cardiac imaging sequences, such as cine Magnetic Resonance Imaging (MRI) or 3D Ultrasound (US). First, we derive a robust, modality-independent signal from the image sequences, estimated by computing the normalized cross-correlation between each frame in the temporal sequence and the end-diastolic frame. This signal is a resembler for the left-ventricle (LV) volume curve over time, whose variation indicates different temporal landmarks of the cardiac cycle. We then perform the temporal alignment of these surrogate signals derived from MRI and US sequences of the same patient through Dynamic Time Warping (DTW), allowing to synchronize both sequences. The proposed framework was evaluated in 98 patients, which have undergone both 3D+t MRI and US scans. The end-systolic frame could be accurately estimated as the minimum of the image-derived surrogate signal, presenting a relative error of 1.6 +/- 1.9% and 4.0 +/- 4.2% for the MRI and US sequences, respectively, thus supporting its association with key temporal instants of the cardiac cycle. The use of DTW reduces the desynchronization of the cardiac events in MRI and US sequences, allowing to temporally align multimodal cardiac imaging sequences. Overall, a generic, fast and accurate method for temporal synchronization of MRI and US sequences of the same patient was introduced. This approach could be straightforwardly used for the correct temporal alignment of pre-operative MRI information and intra-operative US images.

  4. Explaining compact groups as change alignments

    NASA Technical Reports Server (NTRS)

    Mamon, Gary A.

    1990-01-01

    The physical nature of the apparently densest groups of galaxies, known as compact groups is a topic of some recent controversy, despite the detailed observations of a well-defined catalog of 100 isolated compact groups compiled by Hickson (1982). Whereas many authors have espoused the view that compact groups are bound systems, typically as dense as they appear in projection on the sky (e.g., Williams & Rood 1987; Sulentic 1987; Hickson & Rood 1988), others see them as the result of chance configurations within larger systems, either in 1D (chance alignments: Mamon 1986; Walke & Mamon 1989), or in 3D (transient cores: Rose 1979). As outlined in the companion review to this contribution (Mamon, in these proceedings), the implication of Hickson's compact groups (HCGs) being dense bound systems is that they would then constitute the densest isolated systems of galaxies in the Universe and the privileged site for galaxy interactions. In a previous paper (Mamon 1986), the author reviewed the arguments given for the different theories of compact groups. Since then, a dozen papers have been published on the subject, including a thorough and perceptive review by White (1990), thus more than doubling the amount written on the subject. Here, the author first enumerates the arguments that he brought up in 1986 substantiating the chance alignment hypothesis, then he reviews the current status of the numerous recent arguments arguing against chance alignments and/or for the bound dense group hypothesis (both for the majority of HCGs but not all of them), and finally he reconsiders each one of these anti-chance alignment arguments and shows that, rather than being discredited, the chance alignment hypothesis remains a fully consistent explanation for the nature of compact groups.

  5. Image correlation method for DNA sequence alignment.

    PubMed

    Curilem Saldías, Millaray; Villarroel Sassarini, Felipe; Muñoz Poblete, Carlos; Vargas Vásquez, Asticio; Maureira Butler, Iván

    2012-01-01

    The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment. PMID:22761742

  6. Multiple Whole Genome Alignments Without a Reference Organism

    SciTech Connect

    Dubchak, Inna; Poliakov, Alexander; Kislyuk, Andrey; Brudno, Michael

    2009-01-16

    Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and sixDrosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families?perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.

  7. Two Influential Primate Classifications Logically Aligned

    PubMed Central

    Franz, Nico M.; Pier, Naomi M.; Reeder, Deeann M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

    2016-01-01

    Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2–317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3–483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across

  8. Tool for Inspecting Alignment of Twinaxial Connectors

    NASA Technical Reports Server (NTRS)

    Smith, Christopher R.

    2008-01-01

    A proposed tool would be used to inspect alignments of mating twinaxial-connector assemblies on interconnecting wiring harnesses. More specifically, the tool would be used to inspect the alignment of each contact pin of each connector on one assembly with the corresponding socket in the corresponding connector on the other assembly. It is necessary to inspect the alignment because if mating of the assemblies is attempted when any pin/socket pair is misaligned beyond tolerance, the connection will not be completed and the dielectric material in the socket will be damaged (see Figure 1). Although the basic principle of the tool is applicable to almost any type of mating connector assemblies, the specific geometry of the tool must match the pin-and-socket geometry of the specific mating assemblies to be inspected. In the original application for which the tool was conceived, each of the mating assemblies contains eight twinaxial connectors; the pin diameter is 0.014 in. (.0.35 mm), and the maximum allowable pin/socket misalignment is 0.007 in. (.0.18 mm). Incomplete connections can result in loss of flight data within the functional path to the space shuttle crew cockpit displays. The tool (see Figure 2) would consist mainly of a transparent disk with alignment clocking tabs that can be fitted onto either connector assembly. Sets of circles or equivalent reference markings are affixed to the face of the tool, located at the desired positions of the mating contact pairs. An inspector would simply fit the tool onto a connector assembly, engaging the clocking tabs until the tool fits tightly. The inspector would then align one set of circles positioning a line of sight perpendicular to one contact within the connector assembly. Mis alignments would be evidenced by the tip of a pin contact straying past the inner edge of the circle. Socket contact misalignments would be evidenced by a crescent-shaped portion of the white dielectric appearing within the circle. The tool

  9. Two Influential Primate Classifications Logically Aligned.

    PubMed

    Franz, Nico M; Pier, Naomi M; Reeder, Deeann M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

    2016-07-01

    Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments

  10. Assembly and alignment of infrared refractive system

    NASA Astrophysics Data System (ADS)

    Yang, Lin; Lin, Jian-chun; Wang, Ya-jing; Chen, Fan-sheng

    2013-09-01

    Optical systems for scientific instrumentation frequently include lens or mirrors with critical mechanical requirements. Position issues of those components are inextricably bound to the efficiency of the instrument. The position referring to the lens system mainly means spacer and rotation of all elements concerned. Instrument could not be completed without the accuracy assembly even the previous design was top one. The alignment of infrared optical system always is a tough thing due to the IR material being opaque to visible light which hardly effect on the imaging ability of the system. In this paper a large-aperture IR refractive system was described in details and the alignment of this system was presented. The brief work describes the assembly and integration of the camera barrel in lab. First of all, all the mechanical elements must be manufactured with high accuracy requirements to meet alignment tolerances and minimum errors mostly could be ignored. The rotations relative to the optical axis were hardy restricted by the space between barrel and cells. The lens vertex displacements were determined through high accuracy titanium alloy spacer. So the actual shape data of the optical lenses were obtained by coordinate measuring machining (CMM) to calculate the real space between lenses after alignment1 done. All the measured results were critical for instruction of the practical assemble. Based on the properties and tolerances of the system, the camera barrel includes sets of six lenses with their respective supports and cells which are composed of two parts: the flied lens group and the relay lenses group. The first one was aligned by the geometry centering used CMM. And the relay lenses were integrated one by one after centered individually with a classical centering instrument. Then the two separate components were assembled under the monitor of the CMM with micron precision. Three parameters on the opti-mechanical elements which include decenter, tilt and

  11. Far-field detection system for laser beams alignment and crystals alignment

    NASA Astrophysics Data System (ADS)

    Liu, D.; Qin, H.; Zhu, B.

    2015-08-01

    Laser beams far-field alignment is very important for the high power laser facility as well as the frequency doubling crystals adjustment. Traditional beams alignment system and crystals alignment system are separated. That means, they use different optical image systems and CCD cameras, which will occupy larger space and use more money. A new farfield detection system of laser beams is presented with a big diffraction grating (37mm*37mm), a set of optical imaging components and a high resolution CCD camera. This detection system, which is fully demonstrated on the National Laser Facility of Israel, can align high power laser facility beams' direction as well as the frequency doubling crystals. The new system occupies small space in the spatial filter through off-axial grating sampling. The experimental results indicate that the average far-field alignment error is less than 5% of spatial filter pinhole diameter, and the average crystals' matching angle error is less than 10urad, which meet the alignment system requirements for beams and crystals.

  12. Using automatic alignment to analyze endangered language data: testing the viability of untrained alignment.

    PubMed

    DiCanio, Christian; Nam, Hosung; Whalen, Douglas H; Bunnell, H Timothy; Amith, Jonathan D; García, Rey Castillo

    2013-09-01

    While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones. PMID:23967953

  13. Quantifying the Displacement of Mismatches in Multiple Sequence Alignment Benchmarks

    PubMed Central

    Bawono, Punto; van der Velde, Arjan; Abeln, Sanne; Heringa, Jaap

    2015-01-01

    Multiple Sequence Alignment (MSA) methods are typically benchmarked on sets of reference alignments. The quality of the alignment can then be represented by the sum-of-pairs (SP) or column (CS) scores, which measure the agreement between a reference and corresponding query alignment. Both the SP and CS scores treat mismatches between a query and reference alignment as equally bad, and do not take the separation into account between two amino acids in the query alignment, that should have been matched according to the reference alignment. This is significant since the magnitude of alignment shifts is often of relevance in biological analyses, including homology modeling and MSA refinement/manual alignment editing. In this study we develop a new alignment benchmark scoring scheme, SPdist, that takes the degree of discordance of mismatches into account by measuring the sequence distance between mismatched residue pairs in the query alignment. Using this new score along with the standard SP score, we investigate the discriminatory behavior of the new score by assessing how well six different MSA methods perform with respect to BAliBASE reference alignments. The SP score and the SPdist score yield very similar outcomes when the reference and query alignments are close. However, for more divergent reference alignments the SPdist score is able to distinguish between methods that keep alignments approximately close to the reference and those exhibiting larger shifts. We observed that by using SPdist together with SP scoring we were able to better delineate the alignment quality difference between alternative MSA methods. With a case study we exemplify why it is important, from a biological perspective, to consider the separation of mismatches. The SPdist scoring scheme has been implemented in the VerAlign web server (http://www.ibi.vu.nl/programs/veralignwww/). The code for calculating SPdist score is also available upon request. PMID:25993129

  14. Algorithms, applications, and challenges of protein structure alignment.

    PubMed

    Ma, Jianzhu; Wang, Sheng

    2014-01-01

    As a fundamental problem in computational structure biology, protein structure alignment has attracted the focus of the community for more than 20 years. While the pairwise structure alignment could be applied to measure the similarity between two proteins, which is a first step for homology search and fold space construction, the multiple structure alignment could be used to understand evolutionary conservation and divergence from a family of protein structures. Structure alignment is an NP-hard problem, which is only computationally tractable by using heuristics. Three levels of heuristics for pairwise structure alignment have been proposed, from the representations of protein structure, the perspectives of viewing protein as a rigid-body or flexible, to the scoring functions as well as the search algorithms for the alignment. For multiple structure alignment, the fourth level of heuristics is applied on how to merge all input structures to a multiple structure alignment. In this review, we first present a small survey of current methods for protein pairwise and multiple alignment, focusing on those that are publicly available as web servers. In more detail, we also discuss the advancements on the development of the new approaches to increase the pairwise alignment accuracy, to efficiently and reliably merge input structures to the multiple structure alignment. Finally, besides broadening the spectrum of the applications of structure alignment for protein template-based prediction, we also list several open problems that need to be solved in the future, such as the large complex alignment and the fast database search. PMID:24629187

  15. Tevatron alignment issues 2003-2004

    SciTech Connect

    Volk, J.T.; Annala, J.; Elementi, L.; Gelfand, N.; Gollwitzer, K.E.; Greenwood, J.; Martens, M.; Moore, Craig D.; Nobrega, A.; Russell, A.D.; Shiltsev, V.; Stefanski, R.; Sager, T.; Syphers, M.J.; Wojcik, G.; /Fermilab

    2005-01-01

    It was observed during the early part of Run II that dipole corrector currents in the Tevatron were changing over time. Measurement of the roll for dipoles and quadrupoles confirmed that there was a slow and systematic movement of the magnets from their ideal position. A simple system using a digital protractor and laptop computer was developed to allow roll measurements of all dipoles and quadrupoles. These measurements showed that many magnets in the Tevatron had rolled more than 1 milliradian. To aid in magnet alignment a new survey network was built in the Tevatron tunnel. This network is based on the use of free centering laser tracker. During the measurement of the network coordinates for all dipole, quadrupole and corrector magnets were obtained. This paper discusses roll measurement techniques and data, the old and new Tevatron alignment network.

  16. Internal Alignment of the SLD Vertex Detector

    SciTech Connect

    Jackson, D.J.; Wickens, F.J.; Su, D.; /SLAC

    2007-12-03

    The tracking resolution and vertex finding capabilities of the SLD experiment depended upon a precise knowledge of the location and orientation of the elements of the SLD pixel vertex detector (VXD3) in 3D space. At the heart of the procedure described here to align the 96 CCDs is the matrix inversion technique of singular value decomposition (SVD). This tool was employed to unfold the detector geometry corrections from the track data in the VXD3. The algorithm was adapted to perform an optimal {chi}{sup 2} minimization by careful treatment of the track hit residual measurement errors. The tracking resolution obtained with the aligned geometry achieved the design performance. Comments are given on how this method could be used for other trackers.

  17. Aligning Astronomical Telescopes via Identification of Stars

    NASA Technical Reports Server (NTRS)

    Whorton, Mark

    2010-01-01

    A proposed method of automated, precise alignment of a ground-based astronomical telescope would eliminate the need for initial manual alignment. The method, based on automated identification of known stars and other celestial objects in the telescope field of view, would also eliminate the need for an initial estimate of the aiming direction. The method does not require any equipment other than a digital imaging device such as a charge-coupled-device digital imaging camera and control computers of the telescope and camera, all of which are standard components in professional astronomical telescope systems and in high-end amateur astronomical telescope systems. The method could be implemented in software running in the telescope or camera control computer or in an external computer communicating with the telescope pointing mount and camera control computers.

  18. Thematic roles, markedness alignment and processing complexity.

    PubMed

    Lee, Yoonhyoung; Kwon, Youan; Gordon, Peter C

    2015-06-01

    Two experiments used eye-tracking during reading to investigate the role of the consistency of the relative markedness alignment of noun phrases (NPs) in the processing of complex sentences in Korean. To do so, the animacy of the first NP was varied in both experiments to manipulate the relative markedness of NPs. In addition, case markings of the second NP (nominative vs. accusative) were manipulated in the first experiment and the markings of the first NP (nominative vs. topic) were manipulated in the second experiment. Results revealed that the animacy manipulation and the nominative-topicality manipulation showed measurable influence on the participants' reading of the complex sentences. Also, the effect of the prominence misalignment caused by animacy seems to have a stronger effect on reading than the effect caused by the nominative-topicality manipulation. The experiments suggested that on-line processing of Korean complex sentences are affected by the consistency of the relative markedness alignment of NPs. PMID:25341491

  19. An Alignment Model for Collaborative Value Networks

    NASA Astrophysics Data System (ADS)

    Bremer, Carlos; Azevedo, Rodrigo Cambiaghi; Klen, Alexandra Pereira

    This paper presents parts of the work carried out in several global organizations through the development of strategic projects with high tactical and operational complexity. By investing in long-term relationships, strongly operating in the transformation of the competitive model and focusing on the value chain management, the main aim of these projects was the alignment of multiple value chains. The projects were led by the Axia Transformation Methodology as well as by its Management Model and following the principles of Project Management. As a concrete result of the efforts made in the last years in the Brazilian market this work also introduces the Alignment Model which supports the transformation process that the companies undergo.

  20. Advanced mask aligner lithography: new illumination system.

    PubMed

    Voelkel, Reinhard; Vogler, Uwe; Bich, Andreas; Pernet, Pascal; Weible, Kenneth J; Hornung, Michael; Zoberbier, Ralph; Cullmann, Elmar; Stuerzebecher, Lorenz; Harzendorf, Torsten; Zeitner, Uwe D

    2010-09-27

    A new illumination system for mask aligner lithography is presented. The illumination system uses two subsequent microlens-based Köhler integrators. The second Köhler integrator is located in the Fourier plane of the first. The new illumination system uncouples the illumination light from the light source and provides excellent uniformity of the light irradiance and the angular spectrum. Spatial filtering allows to freely shape the angular spectrum to minimize diffraction effects in contact and proximity lithography. Telecentric illumination and ability to precisely control the illumination light allows to introduce resolution enhancement technologies (RET) like customized illumination, optical proximity correction (OPC) and source-mask optimization (SMO) in mask aligner lithography. PMID:20940992

  1. Aligning a reflection cavity by Anderson's method.

    PubMed

    Reasenberg, Robert D

    2012-06-01

    The sounding rocket principle of equivalence measurement uses a set of four laser gauges operating in Fabry-Perot cavities to determine the relative acceleration of two test masses that are chemically different. One end of each cavity is a flat mirror on a test mass. Because the test masses are unconstrained and thus expected to rotate slightly during measurement, and because the distance measurements are made at the sub-picometer level, it is essential to have real-time alignment of the beam entering the cavity. However, the cavity must be used in reflection and space is limited. We show that Anderson's alignment method can be used in reflection, but that it requires that the Fabry-Perot cavity have mirrors with significantly unequal reflectivities. PMID:22695543

  2. Strategies and tools for whole genome alignments

    SciTech Connect

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  3. Mutual Alignment Comparison Facilitates Abstraction and Transfer of a Complex Scientific Concept

    ERIC Educational Resources Information Center

    Orton, Judy M.; Anggoro, Florencia K.; Jee, Benjamin D.

    2012-01-01

    Learning about a scientific concept often occurs in the context of unfamiliar examples. Mutual alignment analogy--a type of analogical comparison in which the analogues are only partially understood--has been shown to facilitate learning from unfamiliar examples . In the present study, we examined the role of mutual alignment analogy in the…

  4. Controlled Deposition and Alignment of Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Smits, Jan M. (Inventor); Wincheski, Russell A. (Inventor); Ingram, JoAnne L. (Inventor); Watkins, Anthony Neal (Inventor); Jordan, Jeffrey D. (Inventor)

    2009-01-01

    A carbon nanotube (CNT) attraction material is deposited on a substrate in the gap region between two electrodes on the . substrate. An electric potential is applied to the two electrodes. The CNT attraction material is wetted with a solution defined by a carver liquid having carbon nanotubes (CNTs) suspended therein. A portion of the CNTs align with the electric field and adhere to The CNT attraction material. The carrier liquid and any CNTs not adhered to the CNT attraction material are then removed.

  5. Mounting and Alignment of IXO Mirror Segments

    NASA Technical Reports Server (NTRS)

    Chan, Kai-Wing; Zhang, William; Evans, Tyler; McClelland, Ryan; Hong, Melinda; Mazzarella, James; Saha, Timo; Jalota, Lalit; Olsen, Lawrence; Byron, Glenn

    2010-01-01

    A suspension-mounting scheme is developed for the IXO (International X-ray Observatory) mirror segments in which the figure of the mirror segment is preserved in each stage of mounting. The mirror, first fixed on a thermally compatible strongback, is subsequently transported, aligned and transferred onto its mirror housing. In this paper, we shall outline the requirement, approaches, and recent progress of the suspension mount processes.

  6. Improved pen alignment for bidirectional printing

    NASA Astrophysics Data System (ADS)

    Bernal, Edgar; Allebach, Jan P.; Pizlo, Zygmunt

    2006-01-01

    The quality of the prints produced by an inkjet printer is highly dependent on the characteristics of the dots produced by the inkjet pens. While some literature discusses metrics for the objective evaluation of print quality, few of the efforts have combined automated quality tests with subjective assessment. We develop an algorithm for analyzing printed dots and study the effects of the dot characteristics on the perceived print alignment. We establish the perceptual preferences of human observers via a set of psychophysical experiments.

  7. Experience report with the Alignment Diagnostic System

    SciTech Connect

    Gassner, Georg; /SLAC

    2011-03-03

    Since 2009 an Alignment Diagnostic System (ADS) has been operating at the undulator of the new Linac Coherent Light Source at SLAC National Accelerator Laboratory. The undulator spans a distance of 132 meters and is structured into 33 segments. Each segment is equipped with four hydrostatic leveling sensors and four wire position monitors. This report describes the set up and reflects the experience gained with the ADS.

  8. Alignment Mirror Mechanisms for Space Use

    NASA Technical Reports Server (NTRS)

    Jau, Bruno M.; McKinney, Colin M.; Smythe, Robert F.; Palmer, Dean

    2011-01-01

    The paper describes an optical Alignment Mirror Mechanism (AMM), and discusses its control scheme. The mirror's angular positioning accuracy requirement is +/- 0.2 arc-sec. This requires the mirror's linear positioning actuators to have a positioning accuracy of +/- 109 nm to enable the mirror to meet the angular tip/tilt accuracy requirement. Demonstrated capabilities are +/- 35 nm linear positioning capability at the actuator, which translates into +/- 0.07 arc-sec angular mirror positioning accuracy.

  9. Ion Implantation with Scanning Probe Alignment

    SciTech Connect

    Persaud, A.; Liddle, J.A.; Schenkel, T.; Bokor, J.; Ivanov, Tzv.; Rangelow, I.W.

    2005-07-12

    We describe a scanning probe instrument which integrates ion beams with the imaging and alignment function of a piezo-resistive scanning probe in high vacuum. The beam passes through several apertures and is finally collimated by a hole in the cantilever of the scanning probe. The ion beam spot size is limited by the size of the last aperture. Highly charged ions are used to show hits of single ions in resist, and we discuss the issues for implantation of single ions.

  10. Controlled Deposition and Alignment of Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Smits, Jan M. (Inventor); Wincheski, Russell A. (Inventor); Patry, JoAnne L. (Inventor); Watkins, Anthony Neal (Inventor); Jordan, Jeffrey D. (Inventor)

    2012-01-01

    A carbon nanotube (CNT) attraction material is deposited on a substrate in the gap region between two electrodes on the substrate. An electric potential is applied to the two electrodes. The CNT attraction material is wetted with a solution defined by a carrier liquid having carbon nanotubes (CNTs) suspended therein. A portion of the CNTs align with the electric field and adhere to the CNT attraction material. The carrier liquid and any CNTs not adhered to the CNT attraction material are then removed.

  11. Vertical bounce of two vertically aligned balls

    NASA Astrophysics Data System (ADS)

    Cross, Rod

    2007-11-01

    When a tennis ball rests on top of a basketball and both drop to the floor together, the tennis ball is projected vertically at high speed. A mass-spring model of the impact, as well as air track data, suggest that the tennis ball should be projected at relatively low speed. Measurements of the forces on each ball and the bounce of vertically aligned superballs are used to resolve the discrepancy.

  12. System Would Keep Telescope Reflector Segments Aligned

    NASA Technical Reports Server (NTRS)

    Mettler, Edward; Eldred, Daniel B.; Briggs, Hugh C.; Agronin, Michael L.; Kiceniuk, Taras

    1991-01-01

    Proposed actuation system maintains alignments of reflector segments of large telescope. Sensors measure positions and orientations of segments. Figure-control computer calculates orientation and figure of overall reflector surface from sensor data. Responding to computer output, servocontroller for each actuator corrects piston and tilt errors of each segment. Actuators adjust segments in response to sensed positions. Concept applicable to such large segmented space-based reflectors as those used in communication and in collection of solar energy.

  13. Capacitive Sensors And Targets Would Measure Alignments

    NASA Technical Reports Server (NTRS)

    Jenstrom, Del T.

    1994-01-01

    Multiple capacitive sensors and active targets used to measure distance between, and relative orientation of, two objects. Sensed target signals processed and used by control systems to align objects to be joined. Shapes, sizes, and layouts of sensors and targets optimized for specific application. Particular layout of targets and sensors enables determination of relative position and orientation of two objects in all six degrees of freedom.

  14. 2. DETAIL OF THEODOLITE PYLON NORTH OF AZIMUTH ALIGNMENT SHED ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. DETAIL OF THEODOLITE PYLON NORTH OF AZIMUTH ALIGNMENT SHED (BLDG. 775). - Vandenberg Air Force Base, Space Launch Complex 3, Azimuth Alignment Shed, Napa & Alden Roads, Lompoc, Santa Barbara County, CA

  15. Implementation of a parallel protein structure alignment service on cloud.

    PubMed

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

  16. Implementation of a Parallel Protein Structure Alignment Service on Cloud

    PubMed Central

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

  17. Blasting and Zipping: Sequence Alignment and Mutual Information

    NASA Astrophysics Data System (ADS)

    Penner, Orion; Grassberger, Peter; Paczuski, Maya

    2009-03-01

    Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. While the accomplishments of sequence alignment algorithms are undeniable the fact remains that these algorithms are based upon heuristic scoring schemes. Therefore, these algorithms do not provide model independent and objective measures for how similar two (or more) sequences actually are. Although information theory provides such a similarity measure - the mutual information (MI) - numerous previous attempts to connect sequence alignment and information have not produced realistic estimates for the MI from a given alignment. We report on a simple and flexible approach to get robust estimates of MI from global alignments. The presented results may help establish MI as a reliable tool for evaluating the quality of global alignments, judging the relative merits of different alignment algorithms, and estimating the significance of specific alignments.

  18. Surface Dipole Control of Liquid Crystal Alignment.

    PubMed

    Schwartz, Jeffrey J; Mendoza, Alexandra M; Wattanatorn, Natcha; Zhao, Yuxi; Nguyen, Vinh T; Spokoyny, Alexander M; Mirkin, Chad A; Baše, Tomáš; Weiss, Paul S

    2016-05-11

    Detailed understanding and control of the intermolecular forces that govern molecular assembly are necessary to engineer structure and function at the nanoscale. Liquid crystal (LC) assembly is exceptionally sensitive to surface properties, capable of transducing nanoscale intermolecular interactions into a macroscopic optical readout. Self-assembled monolayers (SAMs) modify surface interactions and are known to influence LC alignment. Here, we exploit the different dipole magnitudes and orientations of carboranethiol and -dithiol positional isomers to deconvolve the influence of SAM-LC dipolar coupling from variations in molecular geometry, tilt, and order. Director orientations and anchoring energies are measured for LC cells employing various carboranethiol and -dithiol isomer alignment layers. The normal component of the molecular dipole in the SAM, toward or away from the underlying substrate, was found to determine the in-plane LC director orientation relative to the anisotropy axis of the surface. By using LC alignment as a probe of interaction strength, we elucidate the role of dipolar coupling of molecular monolayers to their environment in determining molecular orientations. We apply this understanding to advance the engineering of molecular interactions at the nanoscale. PMID:27090503

  19. Regular language constrained sequence alignment revisited.

    PubMed

    Kucherov, Gregory; Pinhas, Tamar; Ziv-Ukelson, Michal

    2011-05-01

    Imposing constraints in the form of a finite automaton or a regular expression is an effective way to incorporate additional a priori knowledge into sequence alignment procedures. With this motivation, the Regular Expression Constrained Sequence Alignment Problem was introduced, which proposed an O(n²t⁴) time and O(n²t²) space algorithm for solving it, where n is the length of the input strings and t is the number of states in the input non-deterministic automaton. A faster O(n²t³) time algorithm for the same problem was subsequently proposed. In this article, we further speed up the algorithms for Regular Language Constrained Sequence Alignment by reducing their worst case time complexity bound to O(n²t³)/log t). This is done by establishing an optimal bound on the size of Straight-Line Programs solving the maxima computation subproblem of the basic dynamic programming algorithm. We also study another solution based on a Steiner Tree computation. While it does not improve the worst case, our simulations show that both approaches are efficient in practice, especially when the input automata are dense. PMID:21554020

  20. Polymeric templating and alignment of fullerenes

    NASA Astrophysics Data System (ADS)

    Kincer, Matthew Ryan

    Fullerene research has advanced to elevated levels in a short period of time due to the unique chemical and physical properties of the caged molecule that have been utilized in numerous applications. Due to the spherical shape of the fullerene molecule which allows for a hollow cavity, encapsulation of atoms or small molecules can occur within the ball structure. This encapsulation creates an endohedral component that is limited from interacting with other molecules which creates potential of control over electronic information of the isolated molecule. Endohedral fullerenes have the potential as serving as the base unit in a quantum computer if control over global alignment is attained. Thus, by using the inherent self-assembling capabilities of some organic materials, ordered endohedral fullerenes can be achieved. This dissertation investigates the ability to use self-assembling strategies to obtain alignment which include ordering within a morphologically controlled copolymer matrix, forming a supramolecular polymer complex with cyclodextrin, and encapsulation within the helical wrap of polymer chains. The ultimate goal is to understand the dynamics that control association and orientation of varying fullerene-based molecules in each strategy in order to maximize control over the final alignment of endohedral elements.

  1. Sentence alignment using feed forward neural network.

    PubMed

    Fattah, Mohamed Abdel; Ren, Fuji; Kuroiwa, Shingo

    2006-12-01

    Parallel corpora have become an essential resource for work in multi lingual natural language processing. However, sentence aligned parallel corpora are more efficient than non-aligned parallel corpora for cross language information retrieval and machine translation applications. In this paper, we present a new approach to align sentences in bilingual parallel corpora based on feed forward neural network classifier. A feature parameter vector is extracted from the text pair under consideration. This vector contains text features such as length, punctuate score, and cognate score values. A set of manually prepared training data has been assigned to train the feed forward neural network. Another set of data was used for testing. Using this new approach, we could achieve an error reduction of 60% over length based approach when applied on English-Arabic parallel documents. Moreover this new approach is valid for any language pair and it is quite flexible approach since the feature parameter vector may contain more/less or different features than that we used in our system such as lexical match feature. PMID:17285688

  2. Alignement automatise de fibres optiques amorces monomodes

    NASA Astrophysics Data System (ADS)

    St-Amant, Yves

    Cette these jette les bases necessaires au developpement d'algorithmes a base de modele pour l'automatisation de l'alignement de fibres amorces monomodes. A partir de la methode de l'integrale de recouvrement et de deux solutions approximatives existantes, un modele analytique d'efficacite de couplage optique permettant d'estimer la puissance transmise entre un composant et une fibre amorce monomode est d'abord formule. Avec celui-ci, sept proprietes pouvant etre utiles au developpement d'algorithmes a base de modele sont ensuite identifiees et validees. Enfin, a l'aide de ces proprietes, une strategie d'alignement a base de modele est developpee et validee experimentalement. Les resultats obtenus demontrent clairement la repetitivite, la robustesse, la precision et la rapidite de la strategie proposee. Ils demontrent aussi qu'il est possible de realiser un alignement complet sans l'utilisation de systemes auxiliaires tels des systemes de vision, des cameras infrarouges, des capteurs de contact ou des systemes de fixation hautement precis.

  3. Mask-to-wafer alignment system

    DOEpatents

    Sweatt, William C.; Tichenor, Daniel A.; Haney, Steven J.

    2003-11-04

    A modified beam splitter that has a hole pattern that is symmetric in one axis and anti-symmetric in the other can be employed in a mask-to-wafer alignment device. The device is particularly suited for rough alignment using visible light. The modified beam splitter transmits and reflects light from a source of electromagnetic radiation and it includes a substrate that has a first surface facing the source of electromagnetic radiation and second surface that is reflective of said electromagnetic radiation. The substrate defines a hole pattern about a central line of the substrate. In operation, an input beam from a camera is directed toward the modified beam splitter and the light from the camera that passes through the holes illuminates the reticle on the wafer. The light beam from the camera also projects an image of a corresponding reticle pattern that is formed on the mask surface of the that is positioned downstream from the camera. Alignment can be accomplished by detecting the radiation that is reflected from the second surface of the modified beam splitter since the reflected radiation contains both the image of the pattern from the mask and a corresponding pattern on the wafer.

  4. Energy-level alignment at organic heterointerfaces

    PubMed Central

    Oehzelt, Martin; Akaike, Kouki; Koch, Norbert; Heimel, Georg

    2015-01-01

    Today’s champion organic (opto-)electronic devices comprise an ever-increasing number of different organic-semiconductor layers. The functionality of these complex heterostructures largely derives from the relative alignment of the frontier molecular-orbital energies in each layer with respect to those in all others. Despite the technological relevance of the energy-level alignment at organic heterointerfaces, and despite continued scientific interest, a reliable model that can quantitatively predict the full range of phenomena observed at such interfaces is notably absent. We identify the limitations of previous attempts to formulate such a model and highlight inconsistencies in the interpretation of the experimental data they were based on. We then develop a theoretical framework, which we demonstrate to accurately reproduce experiment. Applying this theory, a comprehensive overview of all possible energy-level alignment scenarios that can be encountered at organic heterojunctions is finally given. These results will help focus future efforts on developing functional organic interfaces for superior device performance. PMID:26702447

  5. Evaluation of microRNA alignment techniques.

    PubMed

    Ziemann, Mark; Kaspi, Antony; El-Osta, Assam

    2016-08-01

    Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing. PMID:27284164

  6. Aligning genomes with inversions and swaps

    SciTech Connect

    Holloway, J.L.; Cull, P.

    1994-12-31

    The decision about what operators to allow and how to charge for these operations when aligning strings that arise in a biological context is the decision about what model of evolution to assume. Frequently the operators used to construct an alignment between biological sequences axe limited to deletion, insertion, or replacement of a character or block of characters, but there is biological evidence for the evolutionary operations of exchanging the positions of two segments in a sequence and the replacement of a segment by its reversed complement. In this paper we describe a family of heuristics designed to compute alignments of biological sequences assuming a model of evolution with swaps and inversions. The heuristics will necessarily be approximate since the appropriate way to charge for the evolutionary events (delete, insert, substitute, swap, and invert) is not known. The paper concludes with a pair-wise comparison of 20 Picornavirus genomes, and a detailed comparison of the hepatitis delta virus with the citrus exocortis viroid.

  7. Efficient visual grasping alignment for cylinders

    NASA Technical Reports Server (NTRS)

    Nicewarner, Keith E.; Kelley, Robert B.

    1991-01-01

    Monocular information from a gripper-mounted camera is used to servo the robot gripper to grasp a cylinder. The fundamental concept for rapid pose estimation is to reduce the amount of information that needs to be processed during each vision update interval. The grasping procedure is divided into four phases: learn, recognition, alignment, and approach. In the learn phase, a cylinder is placed in the gripper and the pose estimate is stored and later used as the servo target. This is performed once as a calibration step. The recognition phase verifies the presence of a cylinder in the camera field of view. An initial pose estimate is computed and uncluttered scan regions are selected. The radius of the cylinder is estimated by moving the robot a fixed distance toward the cylinder and observing the change in the image. The alignment phase processes only the scan regions obtained previously. Rapid pose estimates are used to align the robot with the cylinder at a fixed distance from it. The relative motion of the cylinder is used to generate an extrapolated pose-based trajectory for the robot controller. The approach phase guides the robot gripper to a grasping position. The cylinder can be grasped with a minimal reaction force and torque when only rough global pose information is initially available.

  8. Alignment limit of the NMSSM Higgs sector

    NASA Astrophysics Data System (ADS)

    Carena, Marcela; Haber, Howard E.; Low, Ian; Shah, Nausheen R.; Wagner, Carlos E. M.

    2016-02-01

    The next-to-minimal supersymmetric extension of the Standard Model (NMSSM) with a Higgs boson of mass 125 GeV can be compatible with stop masses of order of the electroweak scale, thereby reducing the degree of fine-tuning necessary to achieve electroweak symmetry breaking. Moreover, in an attractive region of the NMSSM parameter space, corresponding to the "alignment limit" in which one of the neutral Higgs fields lies approximately in the same direction in field space as the doublet Higgs vacuum expectation value, the observed Higgs boson is predicted to have Standard-Model-like properties. We derive analytical expressions for the alignment conditions and show that they point toward a more natural region of parameter space for electroweak symmetry breaking, while allowing for perturbativity of the theory up to the Planck scale. Moreover, the alignment limit in the NMSSM leads to a well-defined spectrum in the Higgs and Higgsino sectors and yields a rich and interesting Higgs boson phenomenology that can be tested at the LHC. We discuss the most promising channels for discovery and present several benchmark points for further study.

  9. Functionalization of vertically aligned carbon nanotubes

    PubMed Central

    Snyders, Rony; Colomer, Jean-François

    2013-01-01

    Summary This review focuses and summarizes recent studies on the functionalization of carbon nanotubes oriented perpendicularly to their substrate, so-called vertically aligned carbon nanotubes (VA-CNTs). The intrinsic properties of individual nanotubes make the VA-CNTs ideal candidates for integration in a wide range of devices, and many potential applications have been envisaged. These applications can benefit from the unidirectional alignment of the nanotubes, the large surface area, the high carbon purity, the outstanding electrical conductivity, and the uniformly long length. However, practical uses of VA-CNTs are limited by their surface characteristics, which must be often modified in order to meet the specificity of each particular application. The proposed approaches are based on the chemical modifications of the surface by functionalization (grafting of functional chemical groups, decoration with metal particles or wrapping of polymers) to bring new properties or to improve the interactions between the VA-CNTs and their environment while maintaining the alignment of CNTs. PMID:23504581

  10. Alignment limit of the NMSSM Higgs sector

    DOE PAGESBeta

    Carena, Marcela; Haber, Howard E.; Low, Ian; Shah, Nausheen R.; Wagner, Carlos E. M.

    2016-02-17

    The Next-to-Minimal Supersymmetric extension of the Standard Model (NMSSM) with a Higgs boson of mass 125 GeV can be compatible with stop masses of order of the electroweak scale, thereby reducing the degree of fine-tuning necessary to achieve electroweak symmetry breaking. Moreover, in an attractive region of the NMSSM parameter space, corresponding to the \\alignment limit" in which one of the neutral Higgs fields lies approximately in the same direction in field space as the doublet Higgs vacuum expectation value, the observed Higgs boson is predicted to have Standard- Model-like properties. We derive analytical expressions for the alignment conditions andmore » show that they point toward a more natural region of parameter space for electroweak symmetry breaking, while allowing for perturbativity of the theory up to the Planck scale. Additionally, the alignment limit in the NMSSM leads to a well defined spectrum in the Higgs and Higgsino sectors, and yields a rich and interesting Higgs boson phenomenology that can be tested at the LHC. Here, we discuss the most promising channels for discovery and present several benchmark points for further study.« less

  11. The Spontaneous Alignment of Microtubules in Vitro.

    NASA Astrophysics Data System (ADS)

    Hitt, Anne Louise

    Microtubules assembled at 37^circ C in vitro from tubulin, with or without microtubule associated proteins (MAPs), spontaneously form macroscopic domains of intense birefringence. Because the intrinsic birefringence of microtubules is small, the observed effect must be due to form birefringence, caused by a mutually parallel disposition of microtubules. The observed birefringence cannot be accounted for by multiple light scattering. Birefringence and microtubule polymerization are observed to be temporally coupled. The development of multiple macroscopic birefringent domains is mirrored by the formation of large domains which scatter light strongly. Because these solutions are not homogeneous, Beer's law may not apply. These turbid domains may account for the turbidity overshoot observed by several laboratories. Electron micrographs of sections of gluteraldehyde -fixed microtubule solutions which exhibited birefringence before and after fixation displayed a directionality. This confirms that microtubules in solution are aligned with respect to each other. Centrifugation of birefringent microtubule solutions yields an isotropic supernatant and an intensely birefringent pellet, suggesting that the birefringent domains are dense and sediment intact. If MAPs are present, the birefringent domains can be observed in dilute solution after more than 20 hours at 37^circ C. Polymerization conditions which result in oscillations in microtubule assembly due to dynamic instability also result in oscillations in microtubule alignment. These observations, taken together, indicate that microtubule solutions become nematic liquid crystals exhibiting a polydomain schlieren texture upon polymerization in vitro. These domains appear to be stable, dense constructs of microtubules, which are liquid-crystalline in character. Assembly of microtubules initially results in the formation of many small microtubules; with time, however, fewer but longer microtubules are observed. Recently, two

  12. SPA: A Probabilistic Algorithm for Spliced Alignment

    PubMed Central

    van Nimwegen, Erik; Paul, Nicodeme; Sheridan, Robert; Zavolan, Mihaela

    2006-01-01

    Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of the repertoire of splice variants, and to gain insight into the mechanisms of alternative splicing, it is essential that cDNAs are very accurately mapped to their respective genomes. Currently available algorithms for cDNA-to-genome alignment do not reach the necessary level of accuracy because they use ad hoc scoring models that cannot correctly trade off the likelihoods of various sequencing errors against the probabilities of different gene structures. Here we develop a Bayesian probabilistic approach to cDNA-to-genome alignment. Gene structures are assigned prior probabilities based on the lengths of their introns and exons, and based on the sequences at their splice boundaries. A likelihood model for sequencing errors takes into account the rates at which misincorporation, as well as insertions and deletions of different lengths, occurs during sequencing. The parameters of both the prior and likelihood model can be automatically estimated from a set of cDNAs, thus enabling our method to adapt itself to different organisms and experimental procedures. We implemented our method in a fast cDNA-to-genome alignment program, SPA, and applied it to the FANTOM3 dataset of over 100,000 full-length mouse cDNAs and a dataset of over 20,000 full-length human cDNAs. Comparison with the results of four other mapping programs shows that SPA produces alignments of significantly higher quality. In particular, the quality of the SPA alignments near splice boundaries and SPA's mapping of the 5′ and 3′ ends of the cDNAs are highly improved, allowing for more accurate identification of transcript starts and ends, and accurate identification of subtle splice variations. Finally, our splice boundary analysis on the human dataset suggests the existence of a novel non-canonical splice

  13. Rotational alignment of the femoral component in total knee arthroplasty

    PubMed Central

    Falvo, Daniele Antonio; Iapicca, Mario Luigi; Gotti, Valerio

    2016-01-01

    We describe here various surgical options to obtain a correct rotational alignment of femoral component in total knee arthroplasty (TKA). The correct rotational alignment is the key point to obtain a rectangular balanced flexion gap as well to have a good patellar tracking. For that reason, rotation alignment largely affects postoperative kinematic results particularly during flexion. PMID:26855940

  14. Technology of alignment mark in electron beam lithography

    NASA Astrophysics Data System (ADS)

    Zhao, Min; Xu, Tang; Chen, Baoqin; Niu, Jiebin

    2014-08-01

    Electron beam direct wring lithography has been an indispensable approach by which all sorts of novel nano-scale devices include many kinds optical devices can be fabricated. Alignment accuracy is a key factor especially to those devices which need multi-level lithography. In addition to electron beam lithography system itself the quality of alignment mark directly influences alignment accuracy. This paper introduces fundamental of alignment mark detection and discusses some techniques of alignment mark fabrication along with considerations for obtaining highly accurate alignment taking JBX5000LS and JBX6300FS e-beam lithography systems for example. The fundamental of alignment mark detection is expounded first. Many kinds of factors which can impact on the quality of alignment mark are analyzed including mark materials, depth of mark groove and influence of multi-channel process. It has been proved from experiments that material used as metal mark with higher average atomic number is better beneficial for getting high alignment accuracy. Depth of mark groove is required to 1.5~5 μm on our experience. The more process steps alignment mark must pass through, the more probability of being damaged there will be. So the compatibility of alignment mark fabrication with the whole device process and the protection of alignment mark are both need to be considered in advance.

  15. Qualitative Variation in Constructive Alignment in Curriculum Design

    ERIC Educational Resources Information Center

    Trigwell, Keith; Prosser, Michael

    2014-01-01

    Constructive alignment has emerged as a powerful curriculum design idea, but little is known of the extent to which the effectiveness of this idea is a function of qualitative variation. This article introduces a model of qualitative variation in constructive alignment, and uses the results from known alignment studies to test the model. The…

  16. Adjustable cutting guide aligns and positions stacks of material

    NASA Technical Reports Server (NTRS)

    Thiel, A. M.

    1966-01-01

    Adjustable guide tool aligns and positions stacks of material for cutting at various angles. The device adapts its shape to stacks of any corner angle, adjusts to any cutting angle, and quickly aligns the stacks for repeated cutting. With this device, an operator need not place his hands under the knife during alignment.

  17. Mirror device aligns machine surface perpendicular to sight lines

    NASA Technical Reports Server (NTRS)

    Kissler, H. R.

    1964-01-01

    A sight alignment device is used to align two machines so that an axis of the first machine is parallel to a flat surface on the second. This sighting device depends on the reflection of a light beam from the surface to be aligned.

  18. Refining Methods for Estimating Critical Values for an Alignment Index

    ERIC Educational Resources Information Center

    Polikoff, Morgan S.; Fulmer, Gavin W.

    2013-01-01

    The alignment among standards, assessments, and teachers' instruction is an essential element of standards-based educational reforms. The Surveys of Enacted Curriculum (SEC) is the only common tool that can be used to measure the alignment among all three of these sources (Martone & Sireci, 2009). Prior SEC alignment work has been limited…

  19. Sensitive Technique For Detecting Alignment Of Seed Laser

    NASA Technical Reports Server (NTRS)

    Barnes, Norman P.

    1994-01-01

    Frequency response near resonance measured. Improved technique for detection and quantification of alignment of injection-seeding laser with associated power-oscillator laser proposed. Particularly useful in indicating alignment at spectral purity greater than 98 percent because it becomes more sensitive as perfect alignment approached. In addition, implemented relatively easily, without turning on power-oscillator laser.

  20. Aligning an Early Childhood Assessment to State Kindergarten Content Standards: Application of a Nationally Recognized Alignment Framework

    ERIC Educational Resources Information Center

    Roach, Andrew T.; McGrath, Dawn; Wixson, Corinne; Talapatra, Devadrita

    2010-01-01

    This article describes an alignment study conducted to evaluate the alignment between Indiana's Kindergarten content standards and items on the Indiana Standards Tool for Alternate Reporting. Alignment is the extent to which standards and assessments are in agreement, working together to guide educators' efforts to support children's learning and…

  1. HubAlign: an accurate and efficient method for global alignment of protein–protein interaction networks

    PubMed Central

    Hashemifar, Somaye; Xu, Jinbo

    2014-01-01

    Motivation: High-throughput experimental techniques have produced a large amount of protein–protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. Results: This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. Availability: HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip Contact: jinboxu@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161231

  2. Optical alignments of the Cosmic Background Explorer (COBE) observatory

    NASA Technical Reports Server (NTRS)

    Sampler, Henry P.

    1990-01-01

    The angular alignments and stabilities of multiple components in a single coordinate system were determined using various alignment tooling techniques. These techniques use autocollimation measurements with a first order theodolite and transformation of coordinates to determine the relative alignment between various components with respect to a common set of COBE spacecraft coordinate axes. Optical-mechanical alignment techniques were also used to integrate the flight COBE observatory attitude control system module that consists of gyros, reaction wheels, and a momentum wheel. Particular attention is given to the techniques for alignments and stabilities of the earth scanners, sun sensors, far IR absolute spectrophotometer, Diffuse Infrared Background Experiment, and differential microwave radiometer antenna horn boresights.

  3. On Quantum Algorithm for Multiple Alignment of Amino Acid Sequences

    NASA Astrophysics Data System (ADS)

    Iriyama, Satoshi; Ohya, Masanori

    2009-02-01

    The alignment of genome sequences or amino acid sequences is one of fundamental operations for the study of life. Usual computational complexity for the multiple alignment of N sequences with common length L by dynamic programming is O(LN). This alignment is considered as one of the NP problems, so that it is desirable to find a nice algorithm of the multiple alignment. Thus in this paper we propose the quantum algorithm for the multiple alignment based on the works12,1,2 in which the NP complete problem was shown to be the P problem by means of quantum algorithm and chaos information dynamics.

  4. Business-IT Alignment in Trade Facilitation: A Case Study

    NASA Astrophysics Data System (ADS)

    Adaba, Godfried; Rusu, Lazar; El-Mekawy, Mohamed

    In the information age, no organization can thrive without harnessing the power of IT. The effective deployment of IT to achieve business goals and gain competitive advantage requires the alignment of business and IT strategies of organizations. Using the Strategic Alignment Maturity model, this paper evaluates strategic alignment maturity of Customs Excise Preventive service, a frontline public organization charged with trade facilitation in Ghana. Strategic alignment maturity is at level 3; which implies the existence of an established process to leverage IT for efficiency and effectiveness. Efforts are required to strengthen alignment and fully harness the potential of IT to facilitate trade in Ghana.

  5. PROMALS web server for accurate multiple protein sequence alignments.

    PubMed

    Pei, Jimin; Kim, Bong-Hyun; Tang, Ming; Grishin, Nick V

    2007-07-01

    Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS shows higher alignment accuracy than other advanced methods, such as MUMMALS, ProbCons, MAFFT and SPEM. The PROMALS web server takes FASTA format protein sequences as input. The output includes a colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS web server is available at: http://prodata.swmed.edu/promals/ PMID:17452345

  6. Alignment and focus of mirrored facets of a heliosat

    SciTech Connect

    Yellowhair, Julius E; Ho, Clifford Kuofei; Diver, Richard B; Moss, Timothy A

    2013-11-12

    Various technologies pertaining to aligning and focusing mirrored facets of a heliostat are described herein. Updating alignment and/or focus of mirrored facets is undertaken through generation of a theoretical image, wherein the theoretical image is indicative of a reflection of the target via the mirrored facets when the mirrored facets are properly aligned. This theoretical image includes reference points that are overlaid on an image of the target as reflected by the mirrored facets of the heliostat. A technician adjusts alignment/focus of a mirrored facet by causing reflected reference markings to become aligned with the reference points in the theoretical image.

  7. Aligned, short-fiber composites by novel flow processing methods

    SciTech Connect

    Guell, D.C.; Graham, A.L.; Papathanasiou, T.; Petrovic, J.J.

    1993-01-01

    A hydrodynamic method has been employed to align short, reinforcing fibers in polymer matrix composite materials. Samples of composite materials were prepared and tested two at a time (one with randomly oriented fibers and the other with aligned fibers) to isolate and directly measure the effect on mechanical properties of aligning the fibers. Data were collected for the ultimate tensile strength, modulus of elasticity, and ultimate tensile strain of the composite samples prepared. Results show that the aligned fibers were approximately twice as effective (as randomly oriented fibers) at stiffening and strengthening the composite in the alignment direction. 5 figs, 20 refs.

  8. Aligned, short-fiber composites by novel flow processing methods

    SciTech Connect

    Guell, D.C.; Graham, A.L.; Papathanasiou, T.; Petrovic, J.J.

    1993-03-01

    A hydrodynamic method has been employed to align short, reinforcing fibers in polymer matrix composite materials. Samples of composite materials were prepared and tested two at a time (one with randomly oriented fibers and the other with aligned fibers) to isolate and directly measure the effect on mechanical properties of aligning the fibers. Data were collected for the ultimate tensile strength, modulus of elasticity, and ultimate tensile strain of the composite samples prepared. Results show that the aligned fibers were approximately twice as effective (as randomly oriented fibers) at stiffening and strengthening the composite in the alignment direction. 5 figs, 20 refs.

  9. STS-51 orange launch/entry garments aligned on middeck prior to landing

    NASA Technical Reports Server (NTRS)

    1993-01-01

    The orange partial pressure garments used for launch and entry for the STS-51 crew members are neatly aligned on the middeck for the five crew members prior to the second and successful preparation for landing.

  10. Desktop aligner for fabrication of multilayer microfluidic devices

    PubMed Central

    Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

    2015-01-01

    Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

  11. INTRINSIC ALIGNMENT OF CLUSTER GALAXIES: THE REDSHIFT EVOLUTION

    SciTech Connect

    Hao Jiangang; Kubo, Jeffrey M.; Feldmann, Robert; Annis, James; Johnston, David E.; Lin Huan; McKay, Timothy A.

    2011-10-10

    We present measurements of two types of cluster galaxy alignments based on a volume limited and highly pure ({>=}90%) sample of clusters from the GMBCG catalog derived from Data Release 7 of the Sloan Digital Sky Survey (SDSS DR7). We detect a clear brightest cluster galaxy (BCG) alignment (the alignment of major axis of the BCG toward the distribution of cluster satellite galaxies). We find that the BCG alignment signal becomes stronger as the redshift and BCG absolute magnitude decrease and becomes weaker as BCG stellar mass decreases. No dependence of the BCG alignment on cluster richness is found. We can detect a statistically significant ({>=}3{sigma}) satellite alignment (the alignment of the major axes of the cluster satellite galaxies toward the BCG) only when we use the isophotal fit position angles (P.A.s), and the satellite alignment depends on the apparent magnitudes rather than the absolute magnitudes of the BCGs. This suggests that the detected satellite alignment based on isophotal P.A.s from the SDSS pipeline is possibly due to the contamination from the diffuse light of nearby BCGs. We caution that this should not be simply interpreted as non-existence of the satellite alignment, but rather that we cannot detect them with our current photometric SDSS data. We perform our measurements on both SDSS r-band and i-band data, but do not observe a passband dependence of the alignments.

  12. Desktop aligner for fabrication of multilayer microfluidic devices

    NASA Astrophysics Data System (ADS)

    Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

    2015-07-01

    Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm-1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

  13. SUMONA: A supervised method for optimizing network alignment.

    PubMed

    Tuncay, Erhun Giray; Can, Tolga

    2016-08-01

    This study focuses on improving the multi-objective memetic algorithm for protein-protein interaction (PPI) network alignment, Optimizing Network Aligner - OptNetAlign, via integration with other existing network alignment methods such as SPINAL, NETAL and HubAlign. The output of this algorithm is an elite set of aligned networks all of which are optimal with respect to multiple user-defined criteria. However, OptNetAlign is an unsupervised genetic algorithm that initiates its search with completely random solutions and it requires substantial running times to generate an elite set of solutions that have high scores with respect to the given criteria. In order to improve running time, the search space of the algorithm can be narrowed down by focusing on remarkably qualified alignments and trying to optimize the most desired criteria on a more limited set of solutions. The method presented in this study improves OptNetAlign in a supervised fashion by utilizing the alignment results of different network alignment algorithms with varying parameters that depend upon user preferences. Therefore, the user can prioritize certain objectives upon others and achieve better running time performance while optimizing the secondary objectives. PMID:27177812

  14. Corrective optics space telescope axial replacement alignment system

    NASA Astrophysics Data System (ADS)

    Slusher, Robert B.; Satter, Michael J.; Kaplan, Michael L.; Martella, Mark A.; Freymiller, Ed D.; Buzzetta, Victor

    1993-10-01

    To facilitate the accurate placement and alignment of the corrective optics space telescope axial replacement (COSTAR) structure, mechanisms, and optics, the COSTAR Alignment System (CAS) has been designed and assembled. It consists of a 20-foot optical bench, support structures for holding and aligning the COSTAR instrument at various stages of assembly, a focal plane target fixture (FPTF) providing an accurate reference to the as-built Hubble Space Telescope (HST) focal plane, two alignment translation stages with interchangeable alignment telescopes and alignment lasers, and a Zygo Mark IV interferometer with a reference sphere custom designed to allow accurate double-pass operation of the COSTAR correction optics. The system is used to align the fixed optical bench (FOB), the track, the deployable optical bench (DOB), the mechanisms, and the optics to ensure that the correction mirrors are all located in the required positions and orientations on-orbit after deployment. In this paper, the layout of the CAS is presented and the various alignment operations are listed along with the relevant alignment requirements. In addition, calibration of the necessary support structure elements and alignment aids is described, including the two-axis translation stages, the latch positions, the FPTF, and the COSTAR-mounted alignment cubes.

  15. Multipoint Observations of Oval-aligned Transpolar Arc Formation

    NASA Astrophysics Data System (ADS)

    Cumnock, J. A.; Le, G.; Zhang, Y.; Slavin, J. A.

    2013-12-01

    We analyze changes in field-aligned currents associated with auroral oval-aligned transpolar arc formation during quiet times on time scales of a few minutes. This is accomplished using observations from the highly accurate multipoint magnetic field measurements provided by the Space Technology 5 mission which consists of three micro-satellites in low Earth orbit. Simultaneous measurements of precipitating particles are provided by three DMSP satellites. We analyze field-aligned currents associated with the dusk oval. For the first time we observe the field-aligned currents associated with the formation of an oval-aligned transpolar arc poleward of the auroral oval which in one case are large compared with the field-aligned currents associated with the auroral oval measured 10 minutes earlier. These events clearly illustrate the dynamic nature of oval-aligned arc formation.

  16. DAPS: Database of Aligned Protein Structures

    DOE Data Explorer

    Mallick, Parag; Rice, Danny; Eisenberg, David

    DAPS is based on the FSSP, DSSP, PDB and CATH databases. There also exists a subset of DAPS known as DDAPS (also pronounced DAPS) - Database of Distant Aligned Protein Structures. It is a database of structures that have low sequence similarity but share a similar fold. There are a number of filters used to make the DDAPS list more useful. The algorithm requires that an FSSP file exists for one of the members of a pair and that the other member is listed in that FSSP file. It requires that each member of the pair be within the CATH database and share a common CAT classification. It also requires that the secondary structure can be determined by DSSP. How is DAPS constructed? We begin with the set of all chains from the current release of the PDB. An all on all search is done on the list to find pairs that have the same fold acoording to both the FSSP and CATH databases and clustered into groups by a representative structure (representative structures have less than 25% sequence identity to each other). For each protein pair, regions aligned by the DALI program are extracted from the corresponding FSSP file, or recomputed using DALI-lite. In domain DAPS, only regions that are called "domains" by CATH are included in the alignment. The amino acid type, secondary structure type, and solvent accessibility are extracted from the DSSP file and written pairwise into the database. DAPS is updated with updates of CATH.[Taken from http://nihserver.mbi.ucla.edu/DAPS/daps_help.html

  17. Shear adhesion strength of aligned electrospun nanofibers.

    PubMed

    Najem, Johnny F; Wong, Shing-Chung; Ji, Guang

    2014-09-01

    Inspiration from nature such as insects' foot hairs motivates scientists to fabricate nanoscale cylindrical solids that allow tens of millions of contact points per unit area with material substrates. In this paper, we present a simple yet robust method for fabricating directionally sensitive shear adhesive laminates. By using aligned electrospun nylon-6, we create dry adhesives, as a succession of our previous work on measuring adhesion energies between two single free-standing electrospun polymer fibers in cross-cylinder geometry, randomly oriented membranes and substrate, and peel forces between aligned fibers and substrate. The synthetic aligned cylindrical solids in this study are electrically insulating and show a maximal Mode II shear adhesion strength of 27 N/cm(2) on a glass slide. This measured value, for the purpose of comparison, is 270% of that reported from gecko feet. The Mode II shear adhesion strength, based on a commonly known "dead-weight" test, is 97-fold greater than the Mode I (normal) adhesion strength of the same. The data indicate a strong shear binding on and easy normal lifting off. Anisotropic adhesion (Mode II/Mode I) is pronounced. The size and surface boundary effects, crystallinity, and bending stiffness of fibers are used to understand these electrospun nanofibers, which vastly differ from otherwise known adhesive technologies. The anisotropic strength distribution is attributed to a decreasing fiber diameter and an optimized laminate thickness, which, in turn, influences the bending stiffness and solid-state "wettability" of points of contact between nanofibers and surface asperities. PMID:25105533

  18. Fabrication of Dense Horizontally Aligned Arrays of Single-Wall Carbon Nanotubes from Vertically Aligned Arrays

    NASA Astrophysics Data System (ADS)

    Zheng, Gang; Wang, Xueshen; Li, Qunqing; Xie, Jing; Zhu, Zhendong; Zou, Yuan; Liu, Junku; Jiang, Kaili; Fan, Shoushan

    2011-01-01

    The as-grown vertically aligned single-wall carbon nanotube (SWNT) arrays are transferred from the original silicon substrate to a poly(ethylene terephthalate) (PET) substrate, which acts as a stamp. Thin SWNT films can be applied from the stamp to the target substrate and subsequently treated by an ultrasonic process to reduce their thickness to 6.6 nm. The transferred SWNT thin film retains the advantageous super-alignment and high-density properties of the vertical SWNT arrays. The linear density, transmittance, and square resistance of the thin film are as high as 15 tubes per micrometer, 99% at 550 nm, and 16 kΩ, respectively.

  19. Conceptual Alignment: How Brains Achieve Mutual Understanding.

    PubMed

    Stolk, Arjen; Verhagen, Lennart; Toni, Ivan

    2016-03-01

    We share our thoughts with other minds, but we do not understand how. Having a common language certainly helps, but infants' and tourists' communicative success clearly illustrates that sharing thoughts does not require signals with a pre-assigned meaning. In fact, human communicators jointly build a fleeting conceptual space in which signals are a means to seek and provide evidence for mutual understanding. Recent work has started to capture the neural mechanisms supporting those fleeting conceptual alignments. The evidence suggests that communicators and addressees achieve mutual understanding by using the same computational procedures, implemented in the same neuronal substrate, and operating over temporal scales independent from the signals' occurrences. PMID:26792458

  20. Linear and angular retroreflecting interferometric alignment target

    DOEpatents

    Maxey, L. Curtis

    2001-01-01

    The present invention provides a method and apparatus for measuring both the linear displacement and angular displacement of an object using a linear interferometer system and an optical target comprising a lens, a reflective surface and a retroreflector. The lens, reflecting surface and retroreflector are specifically aligned and fixed in optical connection with one another, creating a single optical target which moves as a unit that provides multi-axis displacement information for the object with which it is associated. This displacement information is useful in many applications including machine tool control systems and laser tracker systems, among others.

  1. Anisotropic fiber alignment in composite structures

    DOEpatents

    Graham, A.L.; Mondy, L.A.; Guell, D.C.

    1993-11-16

    High strength material composite structures are formed with oriented fibers to provide controlled anisotropic fibers. Fibers suspended in non-dilute concentrations (e.g., up to 20 volume percent for fibers having an aspect ratio of 20) in a selected medium are oriented by moving an axially spaced array of elements in the direction of desired fiber alignment. The array elements are generally perpendicular to the desired orientation. The suspension medium may also include sphere-like particles where the resulting material is a ceramic. 5 figures.

  2. Anisotropic fiber alignment in composite structures

    DOEpatents

    Graham, Alan L.; Mondy, Lisa A.; Guell, David C.

    1993-01-01

    High strength material composite structures are formed with oriented fibers to provide controlled anisotropic fibers. Fibers suspended in non-dilute concentrations (e.g., up to 20 volume percent for fibers having an aspect ratio of 20) in a selected medium are oriented by moving an axially spaced array of elements in the direction of desired fiber alignment. The array elements are generally perpendicular to the desired orientation. The suspension medium may also include sphere-like particles where the resulting material is a ceramic.

  3. Datum definition problems in accelerator alignment

    SciTech Connect

    Bell, B.; Friedsam, H.; Oren, W.; Ruland, R.

    1990-04-01

    Any measurement task requires a fixed reference base (the datum) from which measurements can be made and calculated. The linac was the datum to which all SLC components were aligned; although this reference existed as a physical object, the actual establishment of the datum and its transferral to datums that were more useful for the SLC installation challenged the technology and computational ability of the survey group. Once established, the maintenance of datums is not to be taken for granted, as demonstrated by the 1989 earthquake which destroyed all SLAC's survey datums. 7 refs., 6 figs.

  4. Alignment and nonlinear elasticity in biopolymer gels

    NASA Astrophysics Data System (ADS)

    Feng, Jingchen; Levine, Herbert; Mao, Xiaoming; Sander, Leonard M.

    2015-04-01

    We present a Landau-type theory for the nonlinear elasticity of biopolymer gels with a part of the order parameter describing induced nematic order of fibers in the gel. We attribute the nonlinear elastic behavior of these materials to fiber alignment induced by strain. We suggest an application to contact guidance of cell motility in tissue. We compare our theory to simulation of a disordered lattice model for biopolymers. We treat homogeneous deformations such as simple shear, hydrostatic expansion, and simple extension, and obtain good agreement between theory and simulation. We also consider a localized perturbation which is a simple model for a contracting cell in a medium.

  5. Aligned natural inflation in string theory

    NASA Astrophysics Data System (ADS)

    Long, Cody; McAllister, Liam; McGuirk, Paul

    2014-07-01

    We propose a scenario for realizing super-Planckian axion decay constants in Calabi-Yau orientifolds of type IIB string theory, leading to large-field inflation. Our construction is a simple embedding in string theory of the mechanism of Kim, Nilles, and Peloso, in which a large effective decay constant arises from alignment of two smaller decay constants. The key ingredient is gaugino condensation on magnetized or multiply-wound D7-branes. We argue that, under very mild assumptions about the topology of the Calabi-Yau, there are controllable points in moduli space with large effective decay constants.

  6. Multiple Sequence Alignment Based on Chaotic PSO

    NASA Astrophysics Data System (ADS)

    Lei, Xiu-Juan; Sun, Jing-Jing; Ma, Qian-Zhi

    This paper introduces a new improved algorithm called chaotic PSO (CPSO) based on the thought of chaos optimization to solve multiple sequence alignment. For one thing, the chaotic variables are generated between 0 and 1 when initializing the population so that the particles are distributed uniformly in the solution space. For another thing, the chaotic sequences are generated using the Logistic mapping function in order to make chaotic search and strengthen the diversity of the population. The simulation results of several benchmark data sets of BAliBase show that the improved algorithm is effective and has good performances for the data sets with different similarity.

  7. Silicon on insulator self-aligned transistors

    DOEpatents

    McCarthy, Anthony M.

    2003-11-18

    A method for fabricating thin-film single-crystal silicon-on-insulator (SOI) self-aligned transistors. Standard processing of silicon substrates is used to fabricate the transistors. Physical spaces, between the source and gate, and the drain and gate, introduced by etching the polysilicon gate material, are used to provide connecting implants (bridges) which allow the transistor to perform normally. After completion of the silicon substrate processing, the silicon wafer is bonded to an insulator (glass) substrate, and the silicon substrate is removed leaving the transistors on the insulator (glass) substrate. Transistors fabricated by this method may be utilized, for example, in flat panel displays, etc.

  8. QUADRUPOLE BEAM-BASED ALIGNMENT AT RHIC.

    SciTech Connect

    NIEDZIELA, J.; MONTAG, C.; SATOGATA, T.

    2005-05-16

    Successful implementation of a beam-based alignment algorithm, tailored to different types of quadrupoles at RHIC, provides significant benefits to machine operations for heavy ions and polarized protons. This algorithm was used to calibrate beam position monitor centers relative to interaction region quadrupoles to maximize aperture. This approach was also used to determine the optimal orbit through transition jump quadrupoles to minimize orbit changes during the transition jump for heavy ion acceleration. This paper provides background discussion and results from first measurements during the RHIC 2005 run.

  9. Computational studies of the x-ray scattering properties of laser aligned stilbene

    SciTech Connect

    Debnarova, Andrea; Techert, Simone; Schmatz, Stefan

    2011-02-07

    The enhancement of the x-ray scattering signal from partially aligned molecular samples is investigated. The alignment properties of the studied molecular system are modeled based on the method of laser alignment. With the advances in the area of laser alignment of molecules, the application of this sample manipulation technique promises a great potential for x-ray scattering measurements. Preferential alignment of molecules in an otherwise amorphous sample leads to constructive interference and thus increases the scattering intensity. This enhances the structural information encoded in the scattering images and enables improved resolution in studies of reaction dynamics, as in this work is shown for the example of the photo-isomerization of stilbene. We demonstrate that the scattering signal is strongly influenced by the alignment axis. Even the most basic one-dimensional alignment offers significant improvement compared to the structural information provided by a randomly oriented sample. Although the signal is sensitive to the uncertainty in the alignment angle, it offers encouraging results even at realistic alignment uncertainties.

  10. Product Grammars for Alignment and Folding.

    PubMed

    Höner Zu Siederdissen, Christian; Hofacker, Ivo L; Stadler, Peter F

    2015-01-01

    We develop a theory of algebraic operations over linear and context-free grammars that makes it possible to combine simple "atomic" grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search spaces of complex alignment problems on multiple input sequences explicitly as algebraic expressions of very simple one-dimensional grammars. In particular, we provide a fully worked frameshift-aware, semiglobal DNA-protein alignment algorithm whose grammar is composed of products of small, atomic grammars. The compiler accompanying our theory makes it easy to experiment with the combination of multiple grammars and different operations. Composite grammars can be written out in L(A)T(E)X for documentation and as a guide to implementation of dynamic programming algorithms. An embedding in Haskell as a domain-specific language makes the theory directly accessible to writing and using grammar products without the detour of an external compiler. Software and supplemental files available here: http://www.bioinf. uni-leipzig.de/Software/gramprod/. PMID:26357262

  11. Theory of the deformation of aligned polyethylene

    PubMed Central

    Hammad, A.; Swinburne, T. D.; Hasan, H.; Del Rosso, S.; Iannucci, L.; Sutton, A. P.

    2015-01-01

    Solitons are proposed as the agents of plastic and viscoelastic deformation in aligned polyethylene. Interactions between straight, parallel molecules are mapped rigorously onto the Frenkel–Kontorova model. It is shown that these molecular interactions distribute an applied load between molecules, with a characteristic transfer length equal to the soliton width. Load transfer leads to the introduction of tensile and compressive solitons at the chain ends to mark the onset of plasticity at a well-defined yield stress, which is much less than the theoretical pull-out stress. Interaction energies between solitons and an equation of motion for solitons are derived. The equation of motion is based on Langevin dynamics and the fluctuation–dissipation theorem and it leads to the rigorous definition of an effective mass for solitons. It forms the basis of a soliton dynamics in direct analogy to dislocation dynamics. Close parallels are drawn between solitons in aligned polymers and dislocations in crystals, including the configurational force on a soliton. The origins of the strain rate and temperature dependencies of the viscoelastic behaviour are discussed in terms of the formation energy of solitons. A failure mechanism is proposed involving soliton condensation under a tensile load. PMID:26339196

  12. Optical alignment of Centaur's inertial guidance system

    NASA Technical Reports Server (NTRS)

    Gordan, Andrew L.

    1987-01-01

    During Centaur launch operations the launch azimuth of the inertial platform's U-accelerometer input axis must be accurately established and maintained. This is accomplished by using an optically closed loop system with a long-range autotheodolite whose line of sight was established by a first-order survey. A collimated light beam from the autotheodolite intercepts a reflecting Porro prism mounted on the platform azimuth gimbal. Thus, any deviation of the Porro prism from its predetermined heading is optically detected by the autotheodolite. The error signal produced is used to torque the azimuth gimbal back to its required launch azimuth. The heading of the U-accelerometer input axis is therefore maintained automatically. Previously, the autotheodolite system could not distinguish between vehicle sway and rotational motion of the inertial platform unless at least three prisms were used. One prism was mounted on the inertial platform to maintain azimuth alignment, and two prisms were mounted externally on the vehicle to track sway. For example, the automatic azimuth-laying theodolite (AALT-SV-M2) on the Saturn vehilce used three prisms. The results of testing and modifying the AALT-SV-M2 autotheodolite to simultaneously monitor and maintain alignment of the inertial platform and track the sway of the vehicle from a single Porro prism.

  13. Dipole Alignment in Rotating MHD Turbulence

    NASA Technical Reports Server (NTRS)

    Shebalin, John V.; Fu, Terry; Morin, Lee

    2012-01-01

    We present numerical results from long-term CPU and GPU simulations of rotating, homogeneous, magnetohydrodynamic (MHD) turbulence, and discuss their connection to the spherically bounded case. We compare our numerical results with a statistical theory of geodynamo action that has evolved from the absolute equilibrium ensemble theory of ideal MHD turbulence, which is based on the ideal MHD invariants are energy, cross helicity and magnetic helicity. However, for rotating MHD turbulence, the cross helicity is no longer an exact invariant, although rms cross helicity becomes quasistationary during an ideal MHD simulation. This and the anisotropy imposed by rotation suggests an ansatz in which an effective, nonzero value of cross helicity is assigned to axisymmetric modes and zero cross helicity to non-axisymmetric modes. This hybrid statistics predicts a large-scale quasistationary magnetic field due to broken ergodicity , as well as dipole vector alignment with the rotation axis, both of which are observed numerically. We find that only a relatively small value of effective cross helicity leads to the prediction of a dipole moment vector that is closely aligned (less than 10 degrees) with the rotation axis. We also discuss the effect of initial conditions, dissipation and grid size on the numerical simulations and statistical theory.

  14. Cloverleaf microgyroscope with electrostatic alignment and tuning

    NASA Technical Reports Server (NTRS)

    Challoner, A. Dorian (Inventor); Gutierrez, Roman C. (Inventor); Tang, Tony K. (Inventor)

    2007-01-01

    A micro-gyroscope (10) having closed loop output operation by a control voltage (V.sub.ty), that is demodulated by a drive axis (x-axis) signal V.sub.thx of the sense electrodes (S1, S2), providing Coriolis torque rebalance to prevent displacement of the micro-gyroscope (10) on the output axis (y-axis) V.sub.thy.about.0. Closed loop drive axis torque, V.sub.tx maintains a constant drive axis amplitude signal, V.sub.thx. The present invention provides independent alignment and tuning of the micro-gyroscope by using separate electrodes and electrostatic bias voltages to adjust alignment and tuning. A quadrature amplitude signal, or cross-axis transfer function peak amplitude is used to detect misalignment that is corrected to zero by an electrostatic bias voltage adjustment. The cross-axis transfer function is either V.sub.thy/V.sub.ty or V.sub.tnx/V.sub.tx. A quadrature signal noise level, or difference in natural frequencies estimated from measurements of the transfer functions is used to detect residual mistuning, that is corrected to zero by a second electrostatic bias voltage adjustment.

  15. Aligning Paramecium caudatum with static magnetic fields.

    PubMed

    Guevorkian, Karine; Valles, James M

    2006-04-15

    As they negotiate their environs, unicellular organisms adjust their swimming in response to various physical fields such as temperature, chemical gradients, and electric fields. Because of the weak magnetic properties of most biological materials, however, they do not respond to the earth's magnetic field (5 x 10(-5) Tesla) except in rare cases. Here, we show that the trajectories of Paramecium caudatum align with intense static magnetic fields >3 Tesla. Otherwise straight trajectories curve in magnetic fields and eventually orient parallel or antiparallel to the applied field direction. Neutrally buoyant immobilized paramecia also align with their long axis in the direction of the field. We model this magneto-orientation as a strictly passive, nonphysiological response to a magnetic torque exerted on the diamagnetically anisotropic components of the paramecia. We have determined the average net anisotropy of the diamagnetic susceptibility, Deltachi(p), of a whole Paramecium: Deltachi(p) = (6.7+/- 0.7) x 10(-23) m(3). We show how the measured Deltachi(p) compares to the anisotropy of the diamagnetic susceptibilities of the components in the cell. We suggest that magnetic fields can be exploited as a novel, noninvasive, quantitative means to manipulate swimming populations of unicellular organisms. PMID:16461406

  16. Vertically aligned biaxially textured molybdenum thin films

    SciTech Connect

    Krishnan, Rahul; Riley, Michael; Lee, Sabrina; Lu, Toh-Ming

    2011-09-15

    Vertically aligned, biaxially textured molybdenum nanorods were deposited using dc magnetron sputtering with glancing flux incidence (alpha = 85 degrees with respect to the substrate normal) and a two-step substrate-rotation mode. These nanorods were identified with a body-centered cubic crystal structure. The formation of a vertically aligned biaxial texture with a [110] out-of-plane orientation was combined with a [-110] in-plane orientation. The kinetics of the growth process was found to be highly sensitive to an optimum rest time of 35 seconds for the two-step substrate rotation mode. At all other rest times, the nanorods possessed two separate biaxial textures each tilted toward one flux direction. While the in-plane texture for the vertical nanorods maintains maximum flux capture area, inclined Mo nanorods deposited at alpha = 85 degrees without substrate rotation display a [-1-1-4] in-plane texture that does not comply with the maximum flux capture area argument. Finally, an in situ capping film was deposited with normal flux incidence over the biaxially textured vertical nanorods resulting in a thin film over the porous nanorods. This capping film possessed the same biaxial texture as the nanorods and could serve as an effective substrate for the epitaxial growth of other functional materials.

  17. DNA Sequence Alignment during Homologous Recombination.

    PubMed

    Greene, Eric C

    2016-05-27

    Homologous recombination allows for the regulated exchange of genetic information between two different DNA molecules of identical or nearly identical sequence composition, and is a major pathway for the repair of double-stranded DNA breaks. A key facet of homologous recombination is the ability of recombination proteins to perfectly align the damaged DNA with homologous sequence located elsewhere in the genome. This reaction is referred to as the homology search and is akin to the target searches conducted by many different DNA-binding proteins. Here I briefly highlight early investigations into the homology search mechanism, and then describe more recent research. Based on these studies, I summarize a model that includes a combination of intersegmental transfer, short-distance one-dimensional sliding, and length-specific microhomology recognition to efficiently align DNA sequences during the homology search. I also suggest some future directions to help further our understanding of the homology search. Where appropriate, I direct the reader to other recent reviews describing various issues related to homologous recombination. PMID:27129270

  18. Coordinate measurement machines as an alignment tool

    SciTech Connect

    Wand, B.T.

    1991-03-01

    In February of 1990 the Stanford Linear Accelerator Center (SLAC) purchased a LEITZ PM 12-10-6 CMM (Coordinate measurement machine). The machine is shared by the Quality Control Team and the Alignment Team. One of the alignment tasks in positioning beamline components in a particle accelerator is to define the component's magnetic centerline relative to external fiducials. This procedure, called fiducialization, is critical to the overall positioning tolerance of a magnet. It involves the definition of the magnetic center line with respect to the mechanical centerline and the transfer of the mechanical centerline to the external fiducials. To perform the latter a magnet coordinate system has to be established. This means defining an origin and the three rotation angles of the magnet. The datum definition can be done by either optical tooling techniques or with a CMM. As optical tooling measurements are very time consuming, not automated and are prone to errors, it is desirable to use the CMM fiducialization method instead. The establishment of a magnet coordinate system based on the mechanical center and the transfer to external fiducials will be discussed and presented with 2 examples from the Stanford Linear Collider (SLC). 7 figs.

  19. Rigorous electromagnetic simulation applied to alignment systems

    NASA Astrophysics Data System (ADS)

    Deng, Yunfei; Pistor, Thomas V.; Neureuther, Andrew R.

    2001-09-01

    Rigorous electromagnetic simulation with TEMPEST is used to provide benchmark data and understanding of key parameters in the design of topographical features of alignment marks. Periodic large silicon trenches are analyzed as a function of wavelength (530-800 nm), duty cycle, depth, slope and angle of incidence. The signals are well behaved except when the trench width becomes about 1 micrometers or smaller. Segmentation of the trenches to form 3D marks shows that a segmentation period of 2-5 wavelengths makes the diffraction in the (1,1) direction about 1/3 to 1/2 of that in the main first order (1,0). Transmission alignment marks nanoimprint lithography using the difference between the +1 and -1 reflected orders showed a sensitivity of the difference signal to misalignment of 0.7%/nm for rigorous simulation and 0.5%/nm for simple ray-tracing. The sensitivity to a slanted substrate indentation was 10 nm off-set per degree of tilt from horizontal.

  20. High precision beam alignment of electromagnetic wigglers

    SciTech Connect

    Ben-Zvi, I.; Qiu, X.Z.

    1993-01-01

    The performance of Free-Electron Lasers depends critically on the quality of the alignment of the electron beam to the wiggler's magnetic axis and the deviation of this axis from a straight fine. The measurement of the electron beam position requires numerous beam position monitors in the wiggler, where space is at premium. The beam position measurement is used to set beam steerers for an orbit correction in the wiggler. The authors propose an alternative high precision alignment method in which one or two external Beam Position Monitors (BPM) are used. In this technique, the field in the electro-wiggler is modulated section by section and the beam position movement at the external BPM is detected in synchronism with the modulation. A beam offset at the modulated beam section will produce a modulation of the beam position at the detector that is a function of the of the beam offset and the absolute value of the modulation current. The wiggler errors produce a modulation that is a function of the modulation current. It will be shown that this method allows the detection and correction of the beam position at each section in the presence of wiggler errors with a good resolution. Furthermore, it allows one to measure the first and second integrals of the wiggler error over each wiggler section. Lastly, provided that wiggler sections can be degaussed effectively, one can test the deviation of the wiggler's magnetic axis from a straight line.

  1. A New Analytic Alignment Method for a SINS

    PubMed Central

    Tan, Caiming; Zhu, Xinhua; Su, Yan; Wang, Yu; Wu, Zhiqiang; Gu, Dongbing

    2015-01-01

    Analytic alignment is a type of self-alignment for a Strapdown inertial navigation system (SINS) that is based solely on two non-collinear vectors, which are the gravity and rotational velocity vectors of the Earth at a stationary base on the ground. The attitude of the SINS with respect to the Earth can be obtained directly using the TRIAD algorithm given two vector measurements. For a traditional analytic coarse alignment, all six outputs from the inertial measurement unit (IMU) are used to compute the attitude. In this study, a novel analytic alignment method called selective alignment is presented. This method uses only three outputs of the IMU and a few properties from the remaining outputs such as the sign and the approximate value to calculate the attitude. Simulations and experimental results demonstrate the validity of this method, and the precision of yaw is improved using the selective alignment method compared to the traditional analytic coarse alignment method in the vehicle experiment. The selective alignment principle provides an accurate relationship between the outputs and the attitude of the SINS relative to the Earth for a stationary base, and it is an extension of the TRIAD algorithm. The selective alignment approach has potential uses in applications such as self-alignment, fault detection, and self-calibration. PMID:26556353

  2. Refinement by shifting secondary structure elements improves sequence alignments.

    PubMed

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V

    2015-03-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  3. Refinement by shifting secondary structure elements improves sequence alignments

    PubMed Central

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V.

    2015-01-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  4. Laser induced alignment of molecules dissolved in Helium nanodroplets

    NASA Astrophysics Data System (ADS)

    Stapelfeldt, Henrik

    2013-05-01

    Laser induced alignment, the method to confine the principal axes of molecules along axes fixed in the laboratory frame, is now used in a range of applications in physics and chemistry. With a few exceptions all studies have focused on isolated molecules in the gas phase. In this talk we present experimental studies of laser induced alignment of molecules embedded in the solvent of a superfluid helium nanodroplet. Alignment is conducted in both the adiabatic and the nonadiabtic regime where the alignment pulse is much longer or shorter, respectively, than the rotational period of the molecules. In the nonadiabatic limit, induced by a few-hundred femtosecond long laser pulse, we show that methyliodide molecules reach an alignment maximum 20 ps after the alignment pulse and gradually loose the alignment completely in another 60 ps. This dynamics is completely different from that of isolated methyliodide molecules where alignment occurs in regularly spaced (by 33.3 ps), narrow time windows, termed revivals. Adiabatic alignment, induced by 10 ns laser pulses, resembles the gas phase behavior although the observed degree of alignment falls below that of isolated molecules. Work done in collaboration with Dominik Pentkehner, Department of Chemistry, Aarhus University; Jens Hedegaard Nielsen, Department of Physics, Aarhus University; Alkwin Slenczka, Department of Chemistry, Regensburg University; and Klaus Mølmer, Department of Physics, Aarhus University.

  5. 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

  6. A New Analytic Alignment Method for a SINS.

    PubMed

    Tan, Caiming; Zhu, Xinhua; Su, Yan; Wang, Yu; Wu, Zhiqiang; Gu, Dongbing

    2015-01-01

    Analytic alignment is a type of self-alignment for a Strapdown inertial navigation system (SINS) that is based solely on two non-collinear vectors, which are the gravity and rotational velocity vectors of the Earth at a stationary base on the ground. The attitude of the SINS with respect to the Earth can be obtained directly using the TRIAD algorithm given two vector measurements. For a traditional analytic coarse alignment, all six outputs from the inertial measurement unit (IMU) are used to compute the attitude. In this study, a novel analytic alignment method called selective alignment is presented. This method uses only three outputs of the IMU and a few properties from the remaining outputs such as the sign and the approximate value to calculate the attitude. Simulations and experimental results demonstrate the validity of this method, and the precision of yaw is improved using the selective alignment method compared to the traditional analytic coarse alignment method in the vehicle experiment. The selective alignment principle provides an accurate relationship between the outputs and the attitude of the SINS relative to the Earth for a stationary base, and it is an extension of the TRIAD algorithm. The selective alignment approach has potential uses in applications such as self-alignment, fault detection, and self-calibration. PMID:26556353

  7. Aligned and Electrospun Piezoelectric Polymer Fiber Assembly and Scaffold

    NASA Technical Reports Server (NTRS)

    Scott-Carnell, Lisa A. (Inventor); Siochi, Emilie J. (Inventor); Holloway, Nancy M. (Inventor); Leong, Kam W. (Inventor); Kulangara, Karina (Inventor)

    2015-01-01

    A scaffold assembly and related methods of manufacturing and/or using the scaffold for stem cell culture and tissue engineering applications are disclosed which at least partially mimic a native biological environment by providing biochemical, topographical, mechanical and electrical cues by using an electroactive material. The assembly includes at least one layer of substantially aligned, electrospun polymer fiber having an operative connection for individual voltage application. A method of cell tissue engineering and/or stem cell differentiation uses the assembly seeded with a sample of cells suspended in cell culture media, incubates and applies voltage to one or more layers, and thus produces cells and/or a tissue construct. In another aspect, the invention provides a method of manufacturing the assembly including the steps of providing a first pre-electroded substrate surface; electrospinning a first substantially aligned polymer fiber layer onto the first surface; providing a second pre-electroded substrate surface; electrospinning a second substantially aligned polymer fiber layer onto the second surface; and, retaining together the layered surfaces with a clamp and/or an adhesive compound.

  8. Apse-Alignment of the Uranian Rings

    NASA Technical Reports Server (NTRS)

    Mosqueira, I.; Estrada, P. R.

    2000-01-01

    An explanation of the dynamical mechanism for apse-alignment of the eccentric Uranian rings is necessary before observations can be used to determine properties such as ring masses, particle sizes, and elasticities. The leading model relies on the ring self-gravity to accomplish this task, yet it yields equilibrium masses which are not in accord with Voyager radio measurements. We explore possible solutions such that the self-gravity and the collisional terms are both involved in the process of apse-alignment. We consider limits that correspond to a hot and a cold ring, and show that pressure terms may play a significant role in the equilibrium conditions for the narrow Uranian rings. In the cold ring case, where the scale height of the ring near periapse is comparable to the ring particle size, we introduce a new pressure correction pertaining to a region of the ring where the particles are locked in their relative positions and jammed against their neighbors, and the velocity dispersion is so low that the collisions are nearly elastic. In this case, we find a solution such that the ring self-gravity maintains apse-alignment against both differential precession (m = 1 mode) and the fluid pressure. We apply this model to the Uranian alpha ring, and show that, compared to the previous self-gravity model, the mass estimate for this ring increases by an order of magnitude. In the case of a hot ring, where the scale height can reach a value as much as fifty times larger than a particle size, we find velocity dispersion profiles that result in pressure forces which act in such a way as to alter the ring equilibrium conditions, again leading to a ring mass increase of an order of magnitude; however, such a velocity dispersion profile would require a different mechanism than is currently envisioned for establishing heating/cooling balance in a finite-sized, inelastic particle ring. Finally, we introduce an important correction to the model of Chiang and Goldreich.

  9. Alignment of the CMS silicon strip tracker during stand-alone commissioning

    SciTech Connect

    Adam, W.; et al.

    2009-07-01

    The results of the CMS tracker alignment analysis are presented using the data from cosmic tracks, optical survey information, and the laser alignment system at the Tracker Integration Facility at CERN. During several months of operation in the spring and summer of 2007, about five million cosmic track events were collected with a partially active CMS Tracker. This allowed us to perform first alignment of the active silicon modules with the cosmic tracks using three different statistical approaches; validate the survey and laser alignment system performance; and test the stability of Tracker structures under various stresses and temperatures ranging from +15C to -15C. Comparison with simulation shows that the achieved alignment precision in the barrel part of the tracker leads to residual distributions similar to those obtained with a random misalignment of 50 (80) microns in the outer (inner) part of the barrel.

  10. Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

    NASA Technical Reports Server (NTRS)

    Wheeler, Ward C.

    2003-01-01

    A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

  11. Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search.

    PubMed

    Wheeler, Ward C

    2003-06-01

    A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. PMID:12901383

  12. Homeotropic alignment of lyotropic chromonic liquid crystals using noncovalent interactions.

    PubMed

    Jeong, Joonwoo; Han, Ganghee; Johnson, A T Charlie; Collings, Peter J; Lubensky, Tom C; Yodh, Arjun G

    2014-03-18

    We report on the homeotropic alignment of lyotropic chromonic liquid crystals (LCLCs). Homeotropic anchoring of LCLCs is difficult to achieve, and this challenge has limited development of applications for LCLCs. In this work, homeotropic alignment is achieved using noncovalent interactions between the LCLC molecules and various alignment layers including graphene, parylene films, poly(methyl methacrylate) films, and fluoropolymer films. The LCLC molecules are unique in that they self-assemble via noncovalent interactions in water into elongated aggregates which, in turn, form nematic and columnar liquid crystal (LC) phases. Here we exploit these same noncovalent interactions to induce homeotropic anchoring of the nematic LCLC. Homeotropic alignment is confirmed by polarized optical microscopy and conoscopy. We also report on novel transient stripe textures that occur when an initial flow-induced planar alignment transforms into the equilibrium homeotropic alignment required by boundary conditions. An understanding of this behavior could be important for switching applications. PMID:24559290

  13. Snapshot imaging of postpulse transient molecular alignment revivals

    NASA Astrophysics Data System (ADS)

    Loriot, V.; Tehini, R.; Hertz, E.; Lavorel, B.; Faucher, O.

    2008-07-01

    Laser induced field-free alignment of linear molecules is investigated by using a single-shot spatial imaging technique. The measurements are achieved by femtosecond time-resolved optical polarigraphy (FTOP). Individual alignment revivals recorded at high resolution in CO2 , as well as simultaneous observation of several alignment revivals produced within the rotational period of the O2 molecule are reported. The data are analyzed with a theoretical model describing the alignment experienced by each molecule standing within the interaction region observed by the detector. The temporal dynamics, intensity dependence, and degree of alignment are measured and compared with the awaited results. The technique is simple and can be easily implemented in a large class of molecular samples. Improvement to extend the performance of the method is discussed. The reported study is a decisive step toward feedback optimization and optimal control of field-free molecular alignment.

  14. Local Structural Alignment of RNA with Affine Gap Model

    NASA Astrophysics Data System (ADS)

    Wong, Thomas K. F.; Cheung, Brenda W. Y.; Lam, T. W.; Yiu, S. M.

    Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.

  15. BBMap: A Fast, Accurate, Splice-Aware Aligner

    SciTech Connect

    Bushnell, Brian

    2014-03-17

    Alignment of reads is one of the primary computational tasks in bioinformatics. Of paramount importance to resequencing, alignment is also crucial to other areas - quality control, scaffolding, string-graph assembly, homology detection, assembly evaluation, error-correction, expression quantification, and even as a tool to evaluate other tools. An optimal aligner would greatly improve virtually any sequencing process, but optimal alignment is prohibitively expensive for gigabases of data. Here, we will present BBMap [1], a fast splice-aware aligner for short and long reads. We will demonstrate that BBMap has superior speed, sensitivity, and specificity to alternative high-throughput aligners bowtie2 [2], bwa [3], smalt, [4] GSNAP [5], and BLASR [6].

  16. Alignment of the magnet and a positioning method

    NASA Astrophysics Data System (ADS)

    Kim, Dae-Il

    2015-10-01

    The 100-MeV proton linac and magnets for the KOMAC (Korea Multi-purpose Accelerator Complex) were installed in the tunnel and the beamlines. The fiducialization process was accomplished with the measurement of mechanical shape and the transfer of the coordinates to the fiducial points that are used in two laser-trackers based alignments. The reference points called the alignment network were set up on the wall inside tunnel. The linac and the beam transport magnets were aligned based on the survey results of the alignment networks. In this paper, the alignment procedure and the alignment results are presented, and an algorithm that was developed to manipulate the adjusters of the magnetsis introduced.

  17. Subwavelength alignment mark signal analysis of advanced memory products

    NASA Astrophysics Data System (ADS)

    Yin, Xiaoming; Wong, Alfred K. K.; Wheeler, Donald C.; Williams, Gary; Lehner, Eric A.; Zach, Franz X.; Kim, Byeong Y.; Fukuzaki, Yuzo; Lu, Zhijian G.; Credendino, Santo; Wiltshire, Timothy J.

    2000-06-01

    The impact of alignment mark structure, mark geometry, and stepper alignment optical system on mark signal contrast was investigated using computer simulation. Several sub-wavelength poly silicon recessed film stack alignment targets of advanced memory products were studied. Stimulated alignment mark signals for both dark-field and bright-field systems using the rigorous electromagnetic simulation program TEMPEST showed excellent agreement with experimental data. For a dark-field alignment system, the critical parameters affecting signal contrast were found to be mark size and mark recess depth below silicon surface. On the other hand, film stack thickness and mark recess depth below/above silicon surface are the important parameters for a bright-field alignment system. From observed simulation results optimal process parameters are determined. Based on the simulation results some signal enhancement techniques will be discussed.

  18. Dimensionality reduction via locally reconstructive patch alignment

    NASA Astrophysics Data System (ADS)

    Chen, Yi; Yin, Jun; Zhu, Jie; Jin, Zhong

    2012-07-01

    Based on the local patch concept, we proposed locally reconstructive patch alignment (LRPA) for dimensionality reduction. For each patch, LRPA aims to find the low-dimensional subspace in which the reconstruction error of the within-class nearest neighbors is minimized and the reconstruction error of the between-class nearest neighbors is maximized. LRPA preserves the local structure hidden in the high-dimensional space. More importantly, LRPA has natural connections with linear regression classification (LRC). While LRC uses reconstruction errors as the classification rule, a sample can be classified correctly when the within-class reconstruction error is minimal. The goal of LRPA makes it cooperate well with LRC. The experimental results on the extended Yale B (YALE-B), AR, PolyU finger knuckle print, and the palm print databases demonstrate LRPA plus LRC is an effective and robust pattern-recognition system.

  19. A robust, automated alignment concept for robotics

    SciTech Connect

    Everett, L.J.; Redfield, R.C. . Dept. of Mechanical Engineering)

    1994-08-01

    A video-based pose sensor is presented that overcomes some of the common problems with typical robotic pose sensors. The Targeting and Reflective Alignment Concept (TRAC) sensor operates using the optics of reflection. TRAC is a robust sensor capable of both continuous and discrete pose sensing in the presence of a class of disturbance inputs (extraneous lighting). Key features of the sensor are its high sensitivity to orientation error, its decoupled handling of orientation and translation (without calibration transformations), and its ability to provide intuitive feedback to a human operator for tele-operation. The sensor has been shown successful at target tracking with a PUMA manipulator in the laboratory and in automatic positioning of NASA-JSC's Manipulator Development Facility (MDF) telemanipulator arm used for shuttle astronaut training.

  20. Bedform alignment in directionally varying flows

    USGS Publications Warehouse

    Rubin, D.M.; Hunter, R.E.

    1987-01-01

    Many kinds of sediment bedforms are presumed to trend either normal or parallel to the direction of sediment transport. For this reason, the trend of bedforms observed by remote sensing or by field observations is commonly used as an indicator of the direction of sediment transport. Such presumptions regarding bedform trend were tested experimentally in bidirectional flows by rotating a sand-covered board in steady winds. Transverse, oblique, and longitudinal bedforms were created by changing only two parameters: the angle between the two winds and the proportions of sand transported in the two directions. Regardless of whether the experimental bedforms were transverse, oblique, or longitudinal (as defined by the bedform trend relative to the resultant transport direction), they all had trends that yielded the maximum gross transport across the bedforms. The fact that many of the experimental bedforms were neither transverse nor parallel to the resultant transport direction suggests that transport directions cannot be accurately determined by presuming such alignment.

  1. Sensitivity of double-resonance alignment magnetometers

    SciTech Connect

    Di Domenico, Gianni; Saudan, Herve; Bison, Georg; Knowles, Paul; Weis, Antoine

    2007-08-15

    We present an experimental study of the intrinsic magnetometric sensitivity of an optical or rf-frequency double-resonance magnetometer in which linearly polarized laser light is used in the optical pumping and detection processes. We show that a semiempirical model of the magnetometer can be used to describe the magnetic resonance spectra. Then, we present an efficient method to predict the optimum operating point of the magnetometer, i.e., the light power and rf Rabi frequency providing maximum magnetometric sensitivity. Finally, we apply the method to investigate the evolution of the optimum operating point with temperature. The method is very efficient to determine relaxation rates and thus allowed us to determine the three collisional disalignment cross sections for the components of the alignment tensor. Both first and second harmonic signals from the magnetometer are considered and compared.

  2. MAGSAT: Vector magnetometer absolute sensor alignment determination

    NASA Technical Reports Server (NTRS)

    Acuna, M. H.

    1981-01-01

    A procedure is described for accurately determining the absolute alignment of the magnetic axes of a triaxial magnetometer sensor with respect to an external, fixed, reference coordinate system. The method does not require that the magnetic field vector orientation, as generated by a triaxial calibration coil system, be known to better than a few degrees from its true position, and minimizes the number of positions through which a sensor assembly must be rotated to obtain a solution. Computer simulations show that accuracies of better than 0.4 seconds of arc can be achieved under typical test conditions associated with existing magnetic test facilities. The basic approach is similar in nature to that presented by McPherron and Snare (1978) except that only three sensor positions are required and the system of equations to be solved is considerably simplified. Applications of the method to the case of the MAGSAT Vector Magnetometer are presented and the problems encountered discussed.

  3. Cover song identification by sequence alignment algorithms

    NASA Astrophysics Data System (ADS)

    Wang, Chih-Li; Zhong, Qian; Wang, Szu-Ying; Roychowdhury, Vwani

    2011-10-01

    Content-based music analysis has drawn much attention due to the rapidly growing digital music market. This paper describes a method that can be used to effectively identify cover songs. A cover song is a song that preserves only the crucial melody of its reference song but different in some other acoustic properties. Hence, the beat/chroma-synchronous chromagram, which is insensitive to the variation of the timber or rhythm of songs but sensitive to the melody, is chosen. The key transposition is achieved by cyclically shifting the chromatic domain of the chromagram. By using the Hidden Markov Model (HMM) to obtain the time sequences of songs, the system is made even more robust. Similar structure or length between the cover songs and its reference are not necessary by the Smith-Waterman Alignment Algorithm.

  4. Effective Electrocardiogram Steganography Based on Coefficient Alignment.

    PubMed

    Yang, Ching-Yu; Wang, Wen-Fong

    2016-03-01

    This study presents two types of data hiding methods based on coefficient alignment for electrocardiogram (ECG) signals, namely, lossy and reversible ECG steganographys. The lossy method is divided into high-quality and high-capacity ECG steganography, both of which are capable of hiding confidential patient data in ECG signals. The reversible data hiding method can not only hide secret messages but also completely restore the original ECG signal after bit extraction. Simulations confirmed that the perceived quality generated by the lossy ECG steganography methods was good, while hiding capacity was acceptable. In addition, these methods have a certain degree of robustness, which is rare in conventional ECG stegangraphy schemes. Moreover, the proposed reversible ECG steganography method can not only successfully extract hidden messages but also completely recover the original ECG data. PMID:26711443

  5. First-order aggregation models with alignment

    NASA Astrophysics Data System (ADS)

    Fetecau, Razvan C.; Sun, Weiran; Tan, Changhui

    2016-06-01

    We include alignment interactions in a well-studied first-order attractive-repulsive macroscopic model for aggregation. The distinctive feature of the extended model is that the equation that specifies the velocity in terms of the population density, becomes implicit, and can have non-unique solutions. We investigate the well-posedness of the model and show rigorously how it can be obtained as a macroscopic limit of a second-order kinetic equation. We work within the space of probability measures with compact support and use mass transportation ideas and the characteristic method as essential tools in the analysis. A discretization procedure that parallels the analysis is formulated and implemented numerically in one and two dimensions.

  6. Transition to capitation. Aligning incentives for success.

    PubMed

    Koeppen, L; Mess, M A; Trott, K J; Yazvac, L S

    1997-01-01

    Horror stories abound about providers that have failed to modify their incentive systems and have exhausted their annual capitation budget in the first six months of the plan year. Aligning the business strategy and financial incentives in advance is the best way to ensure that your integrated delivery system's transition to capitation is a success story. Rarely are physicians or hospitals with experience limited to the fee-for-service arena prepared to jump into a managed care or capitated compensation system. The transition can be eased by implementing a "shadow" capitation or similar arrangement that will test physician performance under a risk arrangement in advance. The information can be used to restructure the compensation system to ensure that the behaviors being encouraged will promote successful care and fiscal management. PMID:10164283

  7. Generating nonclassical correlations without fully aligning measurements

    SciTech Connect

    Wallman, Joel J.; Bartlett, Stephen D.; Liang, Yeong-Cherng

    2011-02-15

    We investigate the scenario where spatially separated parties perform measurements in randomly chosen bases on an N-partite Greenberger-Horne-Zeilinger state. We show that without any alignment of the measurements, the observers will obtain correlations that violate a Bell inequality with a probability that rapidly approaches 1 as N increases and that this probability is robust against noise. We also prove that restricting these randomly chosen measurements to a plane perpendicular to a common direction will always generate correlations that violate some Bell inequality. Specifically, if each observer chooses their two measurements to be locally orthogonal, then the N observers will violate one of two Bell inequalities by an amount that increases exponentially with N. These results are also robust against noise and perturbations of each observer's reference direction from the common direction.

  8. Portable weighing system with alignment features

    DOEpatents

    Abercrombie, Robert Knox; Richardson, Gregory David; Scudiere, Matthew Bligh; Sheldon, Frederick T.

    2012-11-06

    A system for weighing a load is disclosed. The weighing system includes a pad having at least one transducer for weighing a load disposed on the pad. In some embodiments the pad has a plurality of foot members and the weighing system may include a plate that disposed underneath the pad for receiving the plurality of foot member and for aligning the foot members when the weighing system is installed. The weighing system may include a spacer disposed adjacent the pad and in some embodiments, a spacer anchor operatively secures the spacer to a support surface, such as a plate, a railway bed, or a roadway. In some embodiments the spacer anchor operatively secures both the spacer and the pad to a roadway.

  9. Aligning self-assembled gelators by drying under shear.

    PubMed

    Draper, Emily R; Mykhaylyk, Oleksandr O; Adams, Dave J

    2016-05-25

    We show how drying under shear can be used to prepare aligned fibres and worm-like micelles from low molecular weight gelators. Shearing followed by drying leads to the dealignment before the water can be removed; continuous shear whilst drying is required to maintain the alignment. Combining a slow pH change with continuous shear allows alignment of the gelling fibres, which can then be dried. PMID:27146964

  10. A new initial alignment method of MIMU based on CCD

    NASA Astrophysics Data System (ADS)

    Ma, Kai; Ding, Quanxin; Zhang, Qiuzhi; Chen, Shaodong; Wang, Yongsheng

    2014-09-01

    A new initial alignment of MIMU based on CCD is proposed in this article to overcome problems of time consuming and low accuracy of the traditional HMS. By utilize the attitude information provided by CCD, MIMU can achieve initial alignment process and output real-time head attitude to compute line of sight. Simulation results indicated that the CCD measurement system can effectively reduce the wasting time of initial alignment and improve attitude measurement precision.

  11. Manipulation of plasma grating by impulsive molecular alignment

    SciTech Connect

    Lu, Peifen; Wu, Jian; Zeng, Heping

    2013-11-25

    We experimentally demonstrated that multiphoton-ionization-induced plasma grating in air could be precisely manipulated by impulsive molecular alignment. In the linear region, the impulsively aligned molecules modulated the diffraction efficiency of the plasma grating for a time-delayed femtosecond laser pulse. In the nonlinear region, the third harmonic generation from the plasma grating was either enhanced or suppressed by following the alignment of the molecules.

  12. Accurate Alignment of Plasma Channels Based on Laser Centroid Oscillations

    SciTech Connect

    Gonsalves, Anthony; Nakamura, Kei; Lin, Chen; Osterhoff, Jens; Shiraishi, Satomi; Schroeder, Carl; Geddes, Cameron; Toth, Csaba; Esarey, Eric; Leemans, Wim

    2011-03-23

    A technique has been developed to accurately align a laser beam through a plasma channel by minimizing the shift in laser centroid and angle at the channel outptut. If only the shift in centroid or angle is measured, then accurate alignment is provided by minimizing laser centroid motion at the channel exit as the channel properties are scanned. The improvement in alignment accuracy provided by this technique is important for minimizing electron beam pointing errors in laser plasma accelerators.

  13. MULTAN: a program to align multiple DNA sequences.

    PubMed Central

    Bains, W

    1986-01-01

    I describe a computer program which can align a large number of nucleic acid sequences with one another. The program uses an heuristic, iterative algorithm which has been tested extensively, and is found to produce useful alignments of a variety of sequence families. The algorithm is fast enough to be practical for the analysis of large number of sequences, and is implemented in a program which contains a variety of other functions to facilitate the analysis of the aligned result. PMID:3003672

  14. Consideratons Regarding the Alignment of Diffractometers for Residual stress Analysis

    SciTech Connect

    Watkins, Thomas R; Cavin, Odis Burl; Matlock, Beth

    2006-01-01

    Proper alignment of an X-ray diffractometer is critical to performing credible measurements, particularly for residual stress determinations. This article will emphasize practical aspects of diffractometer alignment and standards usage with regards to residual strain measurement. Essentially, what to do when one is confronted with a residual stress problem and an unfamiliar goniometer. Various alignment techniques, use of standards, and related issues will be discussed.

  15. Rapid alignment of velocity and magnetic field in magnetohydrodynamic turbulence.

    PubMed

    Matthaeus, W H; Pouquet, A; Mininni, P D; Dmitruk, P; Breech, B

    2008-02-29

    We show that local directional alignment of the velocity and magnetic field fluctuations occurs rapidly in magnetohydrodynamics for a variety of parameters and is seen both in direct numerical simulations and in solar wind data. The phenomenon is due to an alignment between magnetic field and gradients of either pressure or kinetic energy, and is similar to alignment of velocity and vorticity in Navier-Stokes turbulence. This rapid and robust relaxation process leads to a local weakening of nonlinear terms. PMID:18352632

  16. CSA: An efficient algorithm to improve circular DNA multiple alignment

    PubMed Central

    Fernandes, Francisco; Pereira, Luísa; Freitas, Ana T

    2009-01-01

    Background The comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes. Several complete mitochondrial and nuclear genomes are now available, increasing the importance of using multiple sequence alignment algorithms in comparative genomics. MtDNA has long been used in phylogenetic analysis and errors in the alignments can lead to errors in the interpretation of evolutionary information. Although a large number of multiple sequence alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an essentially manual process, before they can use multiple sequence alignment tools. Results In this paper we propose an efficient algorithm that identifies the most interesting region to cut circular genomes in order to improve phylogenetic analysis when using standard multiple sequence alignment algorithms. This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences. All the sequences are then rotated and made linear for multiple alignment purposes. To evaluate the effectiveness of this new tool, three different sets of mitochondrial DNA sequences were considered. Other tests considering randomly rotated sequences were also performed. The software package Arlequin was used to evaluate the standard genetic measures of the alignments obtained with and without the use of the CSA algorithm with two well known multiple alignment algorithms, the CLUSTALW and the MAVID tools, and also the visualization tool SinicView. Conclusion The results show that a circularization and rotation pre-processing step significantly improves the efficiency of public available multiple sequence alignment algorithms when used in the

  17. Simultaneous alignment of short reads against multiple genomes

    PubMed Central

    Schneeberger, Korbinian; Hagmann, Jörg; Ossowski, Stephan; Warthmann, Norman; Gesing, Sandra; Kohlbacher, Oliver; Weigel, Detlef

    2009-01-01

    Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be identified by alignments against the reference alone. Download GenomeMapper at . PMID:19761611

  18. Keeping speed and distance for aligned motion

    NASA Astrophysics Data System (ADS)

    Farkas, Illés J.; Kun, Jeromos; Jin, Yi; He, Gaoqi; Xu, Mingliang

    2015-01-01

    The cohesive collective motion (flocking, swarming) of autonomous agents is ubiquitously observed and exploited in both natural and man-made settings, thus, minimal models for its description are essential. In a model with continuous space and time we find that if two particles arrive symmetrically in a plane at a large angle, then (i) radial repulsion and (ii) linear self-propelling toward a fixed preferred speed are sufficient for them to depart at a smaller angle. For this local gain of momentum explicit velocity alignment is not necessary, nor are adhesion or attraction, inelasticity or anisotropy of the particles, or nonlinear drag. With many particles obeying these microscopic rules of motion we find that their spatial confinement to a square with periodic boundaries (which is an indirect form of attraction) leads to stable macroscopic ordering. As a function of the strength of added noise we see—at finite system sizes—a critical slowing down close to the order-disorder boundary and a discontinuous transition. After varying the density of particles at constant system size and varying the size of the system with constant particle density we predict that in the infinite system size (or density) limit the hysteresis loop disappears and the transition becomes continuous. We note that animals, humans, drones, etc., tend to move asynchronously and are often more responsive to motion than positions. Thus, for them velocity-based continuous models can provide higher precision than coordinate-based models. An additional characteristic and realistic feature of the model is that convergence to the ordered state is fastest at a finite density, which is in contrast to models applying (discontinuous) explicit velocity alignments and discretized time. To summarize, we find that the investigated model can provide a minimal description of flocking.

  19. Keeping speed and distance for aligned motion.

    PubMed

    Farkas, Illés J; Kun, Jeromos; Jin, Yi; He, Gaoqi; Xu, Mingliang

    2015-01-01

    The cohesive collective motion (flocking, swarming) of autonomous agents is ubiquitously observed and exploited in both natural and man-made settings, thus, minimal models for its description are essential. In a model with continuous space and time we find that if two particles arrive symmetrically in a plane at a large angle, then (i) radial repulsion and (ii) linear self-propelling toward a fixed preferred speed are sufficient for them to depart at a smaller angle. For this local gain of momentum explicit velocity alignment is not necessary, nor are adhesion or attraction, inelasticity or anisotropy of the particles, or nonlinear drag. With many particles obeying these microscopic rules of motion we find that their spatial confinement to a square with periodic boundaries (which is an indirect form of attraction) leads to stable macroscopic ordering. As a function of the strength of added noise we see--at finite system sizes--a critical slowing down close to the order-disorder boundary and a discontinuous transition. After varying the density of particles at constant system size and varying the size of the system with constant particle density we predict that in the infinite system size (or density) limit the hysteresis loop disappears and the transition becomes continuous. We note that animals, humans, drones, etc., tend to move asynchronously and are often more responsive to motion than positions. Thus, for them velocity-based continuous models can provide higher precision than coordinate-based models. An additional characteristic and realistic feature of the model is that convergence to the ordered state is fastest at a finite density, which is in contrast to models applying (discontinuous) explicit velocity alignments and discretized time. To summarize, we find that the investigated model can provide a minimal description of flocking. PMID:25679657

  20. Multiscale field-aligned current analyzer

    NASA Astrophysics Data System (ADS)

    Bunescu, C.; Marghitu, O.; Constantinescu, D.; Narita, Y.; Vogt, J.; Blǎgǎu, A.

    2015-11-01

    The magnetosphere-ionosphere coupling is achieved, essentially, by a superposition of quasi-stationary and time-dependent field-aligned currents (FACs), over a broad range of spatial and temporal scales. The planarity of the FAC structures observed by satellite data and the orientation of the planar FAC sheets can be investigated by the well-established minimum variance analysis (MVA) of the magnetic perturbation. However, such investigations are often constrained to a predefined time window, i.e., to a specific scale of the FAC. The multiscale field-aligned current analyzer, introduced here, relies on performing MVA continuously and over a range of scales by varying the width of the analyzing window, appropriate for the complexity of the magnetic field signatures above the auroral oval. The proposed technique provides multiscale information on the planarity and orientation of the observed FACs. A new approach, based on the derivative of the largest eigenvalue of the magnetic variance matrix with respect to the length of the analysis window, makes possible the inference of the current structures' location (center) and scale (thickness). The capabilities of the FAC analyzer are explored analytically for the magnetic field profile of the Harris sheet and tested on synthetic FAC structures with uniform current density and infinite or finite geometry in the cross-section plane of the FAC. The method is illustrated with data observed by the Cluster spacecraft on crossing the nightside auroral region, and the results are cross checked with the optical observations from the Time History of Events and Macroscale Interactions during Substorms ground network.

  1. Cooperative Ordering and Kinetics of Cellulose Nanocrystal Alignment in a Magnetic Field.

    PubMed

    De France, Kevin J; Yager, Kevin G; Hoare, Todd; Cranston, Emily D

    2016-08-01

    Cellulose nanocrystals (CNCs) are emerging nanomaterials that form chiral nematic liquid crystals above a critical concentration (C*) and additionally orient within electromagnetic fields. The control over CNC alignment is significant for materials processing and end use; to date, magnetic alignment has been demonstrated using only strong fields over extended or arbitrary time scales. This work investigates the effects of comparatively weak magnetic fields (0-1.2 T) and CNC concentration (1.65-8.25 wt %) on the kinetics and degree of CNC ordering using small-angle X-ray scattering. Interparticle spacing, correlation length, and orientation order parameters (η and S) increased with time and field strength following a sigmoidal profile. In a 1.2 T magnetic field for CNC suspensions above C*, partial alignment occurred in under 2 min followed by slower cooperative ordering to achieve nearly perfect alignment in under 200 min (S = -0.499 where S = -0.5 indicates perfect antialignment). At 0.56 T, nearly perfect alignment was also achieved, yet the ordering was 36% slower. Outside of a magnetic field, the order parameter plateaued at 52% alignment (S = -0.26) after 5 h, showcasing the drastic effects of relatively weak magnetic fields on CNC alignment. For suspensions below C*, no magnetic alignment was detected. PMID:27407001

  2. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

    PubMed

    Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

    2015-01-01

    Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system. PMID:26710335

  3. Beam-based alignment of the final focus test beam

    SciTech Connect

    Tenenbaum, P.; Burke, D.; Helm, R.; Irwin, J.; Raimondi, P.; Oide, K.; Floettmann, K.

    1995-12-01

    Beam-based alignment of quadrupole and sextupole magnets is crucial for the overall performance of linear collider final focus systems, especially for elimination of backgrounds and higher-order aberrations. At the Final Focus Test Beam (FFTB), alignment tolerances required for achieving the desired spot size are 100 microns in the horizontal and 30 microns in the vertical. Using a combination of independent magnet power supplies, hi-h-resolution stripline beam position monitors and precision magnet movers, the FFTB can be aligned to these tolerances in about 8 hours. Description of the algorithm, presentation of alignment results, and possible improvements to the system are discussed.

  4. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics

    PubMed Central

    Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M.

    2015-01-01

    Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system. PMID:26710335

  5. Automatic generation of alignments for 3D QSAR analyses.

    PubMed

    Jewell, N E; Turner, D B; Willett, P; Sexton, G J

    2001-01-01

    Many 3D QSAR methods require the alignment of the molecules in a dataset, which can require a fair amount of manual effort in deciding upon a rational basis for the superposition. This paper describes the use of FBSS, a program for field-based similarity searching in chemical databases, for generating such alignments automatically. The CoMFA and CoMSIA experiments with several literature datasets show that the QSAR models resulting from the FBSS alignments are broadly comparable in predictive performance with the models resulting from manual alignments. PMID:11774998

  6. PATHWAY ALIGNED WITH PICNIC PAVILION LOOKING SOUTHWEST FROM THE EASTERN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    PATHWAY ALIGNED WITH PICNIC PAVILION LOOKING SOUTHWEST FROM THE EASTERN EDGE OF THE BOTANIC GARDEN - John Bartram House & Garden, 54th Street & Lindbergh Boulevard, Philadelphia, Philadelphia County, PA

  7. Liquid crystallinity driven highly aligned large graphene oxide composites

    SciTech Connect

    Lee, Kyung Eun; Oh, Jung Jae; Yun, Taeyeong; Kim, Sang Ouk

    2015-04-15

    Graphene is an emerging graphitic carbon materials, consisting of sp{sup 2} hybridized two dimensinal honeycomb structure. It has been widely studied to incorporate graphene with polymer to utilize unique property of graphene and reinforce electrical, mechanical and thermal property of polymer. In composite materials, orientation control of graphene significantly influences the property of composite. Until now, a few method has been developed for orientation control of graphene within polymer matrix. Here, we demonstrate facile fabrication of high aligned large graphene oxide (LGO) composites in polydimethylsiloxane (PDMS) matrix exploiting liquid crystallinity. Liquid crystalline aqueous dispersion of LGO is parallel oriented within flat confinement geometry. Freeze-drying of the aligned LGO dispersion and subsequent infiltration with PDMS produce highly aligned LGO/PDMS composites. Owing to the large shape anisotropy of LGO, liquid crystalline alignment occurred at low concentration of 2 mg/ml in aqueous dispersion, which leads to the 0.2 wt% LGO loaded composites. - Graphical abstract: Liquid crystalline LGO aqueous dispersions are spontaneous parallel aligned between geometric confinement for highly aligned LGO/polymer composite fabrication. - Highlights: • A simple fabrication method for highly aligned LGO/PDMS composites is proposed. • LGO aqueous dispersion shows nematic liquid crystalline phase at 0.8 mg/ml. • In nematic phase, LGO flakes are highly aligned by geometric confinement. • Infiltration of PDMS into freeze-dried LGO allows highly aligned LGO/PDMS composites.

  8. Matt: local flexibility aids protein multiple structure alignment.

    PubMed

    Menke, Matthew; Berger, Bonnie; Cowen, Lenore

    2008-01-01

    Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core and average root

  9. Ultra-large alignments using phylogeny-aware profiles.

    PubMed

    Nguyen, Nam-Phuong D; Mirarab, Siavash; Kumar, Keerthana; Warnow, Tandy

    2015-01-01

    Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments and phylogenetic trees of large datasets. However, accurate large-scale multiple sequence alignment is very difficult, especially when the dataset contains fragmentary sequences. We present UPP, a multiple sequence alignment method that uses a new machine learning technique, the ensemble of hidden Markov models, which we propose here. UPP produces highly accurate alignments for both nucleotide and amino acid sequences, even on ultra-large datasets or datasets containing fragmentary sequences. UPP is available at https://github.com/smirarab/sepp . PMID:26076734

  10. Photo-aligned ferroelectric liquid crystals in microchannels.

    PubMed

    Budaszewski, Daniel; Srivastava, Abhishek K; Tam, Alwin M W; Wolinski, Tomasz R; Chigrinov, Vladimir G; Kwok, Hoi-Sing

    2014-08-15

    In this Letter we disclose a method to realize a good alignment of ferroelectric liquid crystals (FLCs) in microchannels, based on photo-alignment. The sulfonic azo dye used in our research offers variable anchoring energy depending on the irradiation energy and thus provides good control on the FLC alignment in microchannels. The good FLC alignment has been observed only when anchoring energy normalized to the capillary diameter is less than the elastic energy of the FLC helix. The same approach can also be used for the different microstructures viz. photonic crystal fibers, microwaveguides, etc. which gives an opportunity for designing a photonic devices based on FLC. PMID:25121847

  11. Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

    PubMed Central

    Smith, Stephen A.; Brown, Joseph W.; Hinchliff, Cody E.

    2013-01-01

    Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe. PMID:24086118

  12. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

    PubMed

    Martin, Andrew C R

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

  13. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)

    PubMed Central

    Martin, Andrew C. R.

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

  14. Alignment, reverse alignment, and wrong sign Yukawa couplings in two Higgs doublet models

    NASA Astrophysics Data System (ADS)

    Biswas, Ambalika; Lahiri, Amitabha

    2016-06-01

    We consider two Higgs doublet models with a softly broken U(1) symmetry, for various limiting values of the scalar mixing angles α and β . These correspond to the Standard Model Higgs particle being the lighter C P -even scalar (alignment) or the heavier C P -even scalar (reverse alignment), and also the limit in which some of the Yukawa couplings of this particle are the opposite sign of the vector boson couplings (wrong sign). In these limits we impose a criterion for naturalness by demanding that quadratic divergences cancel at one loop. We plot the allowed masses of the remaining physical scalars based on naturalness, stability, perturbative unitarity, and constraints coming from the ρ parameter. We also calculate the h →γ γ decay width in the wrong sign limit.

  15. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

    PubMed Central

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-01-01

    Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

  16. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

    PubMed

    Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

    2013-07-01

    The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643

  17. Protein multiple sequence alignment by hybrid bio-inspired algorithms.

    PubMed

    Cutello, Vincenzo; Nicosia, Giuseppe; Pavone, Mario; Prizzi, Igor

    2011-03-01

    This article presents an immune inspired algorithm to tackle the Multiple Sequence Alignment (MSA) problem. MSA is one of the most important tasks in biological sequence analysis. Although this paper focuses on protein alignments, most of the discussion and methodology may also be applied to DNA alignments. The problem of finding the multiple alignment was investigated in the study by Bonizzoni and Vedova and Wang and Jiang, and proved to be a NP-hard (non-deterministic polynomial-time hard) problem. The presented algorithm, called Immunological Multiple Sequence Alignment Algorithm (IMSA), incorporates two new strategies to create the initial population and specific ad hoc mutation operators. It is based on the 'weighted sum of pairs' as objective function, to evaluate a given candidate alignment. IMSA was tested using both classical benchmarks of BAliBASE (versions 1.0, 2.0 and 3.0), and experimental results indicate that it is comparable with state-of-the-art multiple alignment algorithms, in terms of quality of alignments, weighted Sums-of-Pairs (SP) and Column Score (CS) values. The main novelty of IMSA is its ability to generate more than a single suboptimal alignment, for every MSA instance; this behaviour is due to the stochastic nature of the algorithm and of the populations evolved during the convergence process. This feature will help the decision maker to assess and select a biologically relevant multiple sequence alignment. Finally, the designed algorithm can be used as a local search procedure to properly explore promising alignments of the search space. PMID:21071394

  18. 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.

  19. FlexSnap: Flexible Non-sequential Protein Structure Alignment

    PubMed Central

    2010-01-01

    Background Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins that have gone through conformational changes can be captured effectively if flexibility is considered. Topologically unrelated proteins that preserve secondary structure packing interactions can be detected if both flexibility and Sequential permutations are considered. We propose the FlexSnap algorithm for flexible non-topological protein structural alignment. Results The effectiveness of FlexSnap is demonstrated by measuring the agreement of its alignments with manually curated non-sequential structural alignments. FlexSnap showed competitive results against state-of-the-art algorithms, like DALI, SARF2, MultiProt, FlexProt, and FATCAT. Moreover on the DynDom dataset, FlexSnap reported longer alignments with smaller rmsd. Conclusions We have introduced FlexSnap, a greedy chaining algorithm that reports both sequential and non-sequential alignments and allows twists (hinges). We assessed the quality of the FlexSnap alignments by measuring its agreements with manually curated non-sequential alignments. On the FlexProt dataset, FlexSnap was competitive to state-of-the-art flexible alignment methods. Moreover, we demonstrated the benefits of introducing hinges by showing significant improvements in the alignments reported by FlexSnap for the structure pairs for which rigid alignment methods reported alignments with either low coverage or large rmsd. Availability An implementation of the FlexSnap algorithm will be made available online at http://www.cs.rpi.edu/~zaki/software/flexsnap. PMID:20047669

  20. Radar Image and Rain-gauge Alignment using the Multi-resolution Viscous Alignment (MVA) Algorithm

    NASA Astrophysics Data System (ADS)

    Chatdarong, V.

    2007-12-01

    Rainfall is a complex environmental variable that is difficult to describe either deterministically or statistically. To understand rainfall behaviors, many types of instruments are employed to detect and collect rainfall information. Among them, radar seems to provide the most comprehensive rainfall measurement at fine spatial and temporal resolution and over a relatively wide area. Nevertheless, it does not detects surface rainfall directly like what rain-gauge does. The accuracy radar rainfall, therefore, depends greatly on the Z-R relationship which convert radar reflectivity (Z) to surface rainrate (R). This calibration is usually done by fitting the rain-gauge data with the corresponding radar reflectivity using the regression analysis. To best fit the data, the radar reflectivity at neighbor pixels are usually used to best match the rain-gauge data. However, when applying the Z-R relationship to the radar image, there is no position adjustment despite the calibration technique. Hence, it is desirable to adjust the position of the radar reflectivity images prior to applying the Z-R relationship to improve the accuracy of the rainfall estimation. In this research, the Multi-resolution Viscous Alignment (MVA) algorithm is applied to best align radar reflectivity images to rain-gauge data in order to improve rainfall estimation from the Z-R relationship. The MVA algorithm solves the motion estimation problems using a Bayesian formulation to minimize misfits between two data sets. In general, the problem are ill-posed; therefore, some regularizations and constraints based on smoothness and non-divergence assumptions are employed. This algorithm is superior to the conventional techniques and correlation based techniques. It is fast, robust, easy to implement, and does not require data training. In addition, it can handle higher-order, missing data, and small-scale deformations. The algorithm provides spatially dense, consistency, and smooth transition vector. The

  1. 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

  2. Solar Alignments of Greek Temples Revisited

    NASA Astrophysics Data System (ADS)

    Mickelson, M. E.; Higbie, C.

    2005-08-01

    The canonical opinion about the placement of Greek temples is that they are oriented east-west (Dinsmoor 1975). Major exceptions, such as the temple of Apollo at Bassae which faces approximately north-south, are noted in the literature, but many other temples are scattered across the Greek landscape in a variety of orientations but predominately (about 80 Although no surviving ancient author ever discusses the criteria for placing or orienting temples, we may assume from scattered remarks that Greeks had reasons for choosing the sites and orientations. In the last century, archaeologists and architects such as Nissen (1896), Penrose (1893) and Dinsmoor (1939), have measured the alignments of Greek temples on the Greek mainland, the west coast of Turkey, and the Aegean islands. Their data have varying degrees of precision and accuracy, as a recent paper by Papathanassiou (1994) makes clear. Parallel work done in Italy on Etruscan, Roman and Greek temples by Aveni and Romano (1994) provides further stimulus to re-investigate Greek temples. We have undertaken three field seasons in Greece in order to check previously reported alignments. Where possible, in addition to determining the orientation of foundations, we have attempted to determine the, location of doorways and other openings, placement of cult statues, horizon altitudes etc. In this preliminary study we hope to be able to discover patterns in the orientation of these temples which relate solar observations to temple ritual and thus extend Dinmoor's hypothesis. For some of these questions, we are dependent on literary and inscriptional evidence. This paper describes the preliminary measurements made over our three field seasons in Greece. Field methods and analysis of the data will be presented along with possible application. 1. Dinsmoor, W.B., The Architecture of Ancient Greece, 3rd ed. Rev. New York, 1975. 2. Nissen, H.,Das Templum,Antiquarische Untesuchungon (Berlin, 1896). 3. Penrose, F.C., Trans. Roy

  3. Interhemispheric Field-Aligned Currents: Simulation Results

    NASA Astrophysics Data System (ADS)

    Lyatsky, Sonya

    2016-04-01

    We present simulation results of the 3-D magnetosphere-ionosphere current system including the Region 1, Region 2, and interhemispheric (IHC) field-aligned currents flowing between the Northern and Southern conjugate ionospheres in the case of asymmetry in ionospheric conductivities in two hemispheres (observed, for instance, during the summer-winter seasons). We also computed the maps of ionospheric and equivalent ionospheric currents in two hemispheres. The IHCs are an important part of the global 3-D current system in high-latitude ionospheres. These currents are especially significant during summer and winter months. In the winter ionosphere, they may be comparable and even exceed both Region 1 and Region 2 field-aligned currents. An important feature of these interhemispheric currents is that they link together processes in two hemispheres, so that the currents observed in one hemisphere can provide us with information about the currents in the opposite hemisphere. Despite the significant role of these IHCs in the global 3-D current system, they have not been sufficiently studied yet. The main results of our research may be summarized as follows: 1) In winter hemisphere, the IHCs may significantly exceed and be a substitute for the local Region 1 and Region 2 currents; 2) The IHCs may strongly affect the magnitude, location, and direction of the ionospheric and equivalent ionospheric currents (especially in the nightside winter auroral ionosphere). 3) The IHCs in winter hemisphere may be, in fact, an important (and sometimes even major) source of the Westward Auroral Electrojet, observed in both hemispheres during substorm activity. The study of the contribution from the IHCs into the total global 3-D current system allows us to improve the understanding and forecasting of geomagnetic, auroral, and ionospheric disturbances in two hemispheres. The results of our studies of the Interhemispheric currents are presented in papers: (note: for publications my last

  4. Alignment of Human Resource Practices and Teacher Performance Competency

    ERIC Educational Resources Information Center

    Heneman III, Herbert G.; Milanowski, Anthony T.

    2004-01-01

    In this article, we argue that human resource (HR) management practices are important components of strategies for improving student achievement in an accountability environment. We present a framework illustrating the alignment of educational HR management practices to a teacher performance competency model, which in turn is aligned with student…

  5. Synthesis and orientation of barium hexaferrite ceramics by magnetic alignment

    NASA Astrophysics Data System (ADS)

    Autissier, Denis

    1990-01-01

    Particles of Ba 2Mn xZn 2- xFe 12O 22 with planar structure were prepared by chemical precipitation. They were processed by sleep casting in presence of a magnetic field. The degree of alignment was improved by a special sintering treatment. By this procedure an alignment as high as 99.9% is obtained.

  6. Teacher Education, Experience, and the Practice of Aligned Instruction

    ERIC Educational Resources Information Center

    Polikoff, Morgan S.

    2013-01-01

    Research over the past two decades has shown the alignment of teachers’ instruction with state standards is generally weak. Proposing that alignment is a useful measure of teachers' curricular knowledge (Shulman, 1986), this study uses a large database of teacher reports of their content coverage to understand the relationship of teacher…

  7. Improving Business-IT Alignment through Business Architecture

    ERIC Educational Resources Information Center

    Li, Chingmei

    2010-01-01

    The business and Information Technology (IT) alignment issue has become one of the Top-10 IT management issues since 1980. IT has continually strived to achieve alignment with business goals and objectives. These IT efforts include ERP implementation to benefit from the best practices; data center consolidation and server virtualization to keep…

  8. Directed 3D cell alignment and elongation in microengineered hydrogels.

    PubMed

    Aubin, Hug; Nichol, Jason W; Hutson, Ché B; Bae, Hojae; Sieminski, Alisha L; Cropek, Donald M; Akhyari, Payam; Khademhosseini, Ali

    2010-09-01

    Organized cellular alignment is critical to controlling tissue microarchitecture and biological function. Although a multitude of techniques have been described to control cellular alignment in 2D, recapitulating the cellular alignment of highly organized native tissues in 3D engineered tissues remains a challenge. While cellular alignment in engineered tissues can be induced through the use of external physical stimuli, there are few simple techniques for microscale control of cell behavior that are largely cell-driven. In this study we present a simple and direct method to control the alignment and elongation of fibroblasts, myoblasts, endothelial cells and cardiac stem cells encapsulated in microengineered 3D gelatin methacrylate (GelMA) hydrogels, demonstrating that cells with the intrinsic potential to form aligned tissues in vivo will self-organize into functional tissues in vitro if confined in the appropriate 3D microarchitecture. The presented system may be used as an in vitro model for investigating cell and tissue morphogenesis in 3D, as well as for creating tissue constructs with microscale control of 3D cellular alignment and elongation, that could have great potential for the engineering of functional tissues with aligned cells and anisotropic function. PMID:20638973

  9. What Did We Learn Today? The Importance of Instructional Alignment

    ERIC Educational Resources Information Center

    Petersen, Susan; Cruz, Luz

    2004-01-01

    One of the essential factors that accounts for learning (rather than mere participation) is instructional alignment, a factor often overlooked in the richly complex arena of the gymnasium. "Instructional alignment exists when there is a match in the stimulus conditions of intended outcomes, instructional processes, and instructional assessment"…

  10. Simple, generalizable route to highly aligned block copolymer thin films

    NASA Astrophysics Data System (ADS)

    Qiang, Zhe; Cavicchi, Kevin; Vogt, Bryan; University of Akron Team

    Macroscopic alignment of block copolymer domains in thin films is desired for many applications, such as cell responsive surfaces or optical polarizers. Alignment generally requires specialized tools that apply external fields, shear force gradient, or produce topological patterned substrates. This requirement limits the broad academic application of aligned BCPs. Here, we describe a simple modification of commonly utilized solvent vapor annealing (SVA) process for macroscopic alignment of BCPs. Adhering a flat, crosslinked elastomer pad to the BCP film leads to differential swelling between the elastomer pad and BCP to produce a shear force that aligns the ordered BCP domains. The role of elastomer properties, solvent quality, drying rate and degree of segregation of the block copolymer will be discussed to provide generalized rules for alignment with this technique. Cylindrical nanostructures formed in polystyrene-block-polydimethylsiloxane can be transformed into arrays of silica lines and increasing the thickness from a monolayer to bilayer can effectively halve the spacing of the lines. These results illustrate a generalized method for BCP alignment and a potential route for the generation of complex hierarchical assembled structures. A generalized method for block copolymer thin film alignment: solvent vapor annealing with shear.

  11. Strategic Alignment in Business Education: The Second Magic Bullet

    ERIC Educational Resources Information Center

    Alcoba, Jesu

    2014-01-01

    There is a need for strategic thinking in higher education. Loyalty to a business school's values and need to differentiate lead one to reflect on the actions undertaken within the institution and how they align with the business school's aims. This article contributes to this issue through what is called strategic alignment, which is…

  12. Heterogeneous Data Fusion via Space Alignment Using Nonmetric Multidimensional Scaling

    SciTech Connect

    Choo, Jaegul; Bohn, Shawn J.; Nakamura, Grant C.; White, Amanda M.; Park, Haesun

    2012-04-26

    Heterogeneous data sets are typically represented in different feature spaces, making it difficult to analyze relationships spanning different data sets even when they are semantically related. Data fusion via space alignment can remedy this task by integrating multiple data sets lying in different spaces into one common space. Given a set of reference correspondence data that share the same semantic meaning across different spaces, space alignment attempts to place the corresponding reference data as close together as possible, and accordingly, the entire data are aligned in a common space. Space alignment involves optimizing two potentially conflicting criteria: minimum deformation of the original relationships and maximum alignment between the different spaces. To solve this problem, we provide a novel graph embedding framework for space alignment, which converts each data set into a graph and assigns zero distance between reference correspondence pairs resulting in a single graph. We propose a graph embedding method for fusion based on nonmetric multidimensional scaling (MDS). Its criteria using the rank order rather than the distance allows nonmetric MDS to effectively handle both deformation and alignment. Experiments using parallel data sets demonstrate that our approach works well in comparison to existing methods such as constrained Laplacian eigenmaps, Procrustes analysis, and tensor decomposition. We also present standard cross-domain information retrieval tests as well as interesting visualization examples using space alignment.

  13. Aligning Educational Outcomes and Practices. Occasional Paper #26

    ERIC Educational Resources Information Center

    Hutchings, Pat

    2016-01-01

    The notion of alignment has become increasingly prominent in efforts to improve student learning today. The term, as used in this paper, refers to the linking of intended student learning outcomes with the processes and practices needed to foster those outcomes. Alignment is not a new idea, but it has become more salient as increasing numbers of…

  14. Interactional Competence and the Development of Alignment Activity

    ERIC Educational Resources Information Center

    Dings, Abby

    2014-01-01

    Based on qualitative analysis of conversational interactions collected over the course of a Spanish language learner's academic year abroad, this article explores the development of interactional resources related to alignment activity in the learner's conversational participation. Alignment activity refers to the means interlocutors use…

  15. Integrated, Comprehensive Alignment as a Foundation for Measuring Student Progress

    ERIC Educational Resources Information Center

    Martineau, Joseph; Paek, Pamela; Keene, John; Hirsch, Thomas

    2007-01-01

    This paper describes a comprehensive model of alignment that provides a foundation for meaningful reporting of students' academic progress over time. The model includes both horizontal and vertical alignment as integral parts of the development of content standards, test blueprints, items, item pools, instruments, performance level descriptors,…

  16. Beginning Learners' Development of Interactional Competence: Alignment Activity

    ERIC Educational Resources Information Center

    Tecedor, Marta

    2016-01-01

    This study examined the development of interactional competence (Hall, 1993; He & Young, 1998) by beginning learners of Spanish as indexed by their use of alignment moves. Discourse analysis techniques and quantitative data analysis were used to explore how 52 learners expressed alignment and changes in participation patterns in two sets of…

  17. Aligning IT and Business Strategy: An Australian University Case Study

    ERIC Educational Resources Information Center

    Dent, Alan

    2015-01-01

    Alignment with business objectives is considered to be an essential outcome of information technology (IT) strategic planning. This case study examines the process of creating an IT strategy for an Australian university using an industry standard methodology. The degree of alignment is determined by comparing the strategic priorities supported by…

  18. Alignments of galaxies within cosmic filaments from SDSS DR7

    SciTech Connect

    Zhang, Youcai; Yang, Xiaohu; Wang, Huiyuan; Wang, Lei; Mo, H. J.; Van den Bosch, Frank C. E-mail: xyang@sjtu.edu.cn

    2013-12-20

    Using a sample of galaxy groups selected from the Sloan Digital Sky Survey Data Release 7, we examine the alignment between the orientation of galaxies and their surrounding large-scale structure in the context of the cosmic web. The latter is quantified using the large-scale tidal field, reconstructed from the data using galaxy groups above a certain mass threshold. We find that the major axes of galaxies in filaments tend to be preferentially aligned with the directions of the filaments, while galaxies in sheets have their major axes preferentially aligned parallel to the plane of the sheets. The strength of this alignment signal is strongest for red, central galaxies, and in good agreement with that of dark matter halos in N-body simulations. This suggests that red, central galaxies are well aligned with their host halos, in quantitative agreement with previous studies based on the spatial distribution of satellite galaxies. There is a luminosity and mass dependence that brighter and more massive galaxies in filaments and sheets have stronger alignment signals. We also find that the orientation of galaxies is aligned with the eigenvector associated with the smallest eigenvalue of the tidal tensor. These observational results indicate that galaxy formation is affected by large-scale environments and strongly suggest that galaxies are aligned with each other over scales comparable to those of sheets and filaments in the cosmic web.

  19. Alignment tool facilitates pin placement on irregular horizontal surfaces

    NASA Technical Reports Server (NTRS)

    Boyle, J. V.

    1966-01-01

    Alignment tool facilitates spotting and cementing plastic pins on the true vertical to irregular concave and convex surfaces. The tool consists of a wood tripod with individually adjustable legs, a wood block with a hole for placing the pins and two spirit levels at a 90 degree angle for easy alignment.

  20. Comparative Analysis of the Measurement of Total Instructional Alignment

    ERIC Educational Resources Information Center

    Kick, Laura C.

    2013-01-01

    In 2007, Lisa Carter created the Total Instructional Alignment system--a process that aligns standards, curriculum, assessment, and instruction. Employed in several hundred school systems, the TIA process is a successful professional development program. The researcher developed an instrument to measure the success of the TIA process with the…

  1. The Alignment effect of brightest cluster galaxies in the SDSS

    SciTech Connect

    Kim, R. S. J.; Annis, J.; Strauss, M. A.; Lupton, R. H.; Bahcall, N. A.; Gunn, J. E.; Kepner, J. V.; Postman, M.

    2001-10-01

    One of the most vital observational clues for unraveling the origin of Brightest Cluster Galaxies (BCG) is the observed alignment of the BCGs with their host cluster and its surroundings. We have examined the BCG-cluster alignment effect, using clusters of galaxies detected from the Sloan Digital Sky Survey (SDSS). We find that the BCGs are preferentially aligned with the principal axis of their hosts, to a much higher redshift (z >~ 0.3) than probed by previous studies (z <~ 0.1). The alignment effect strongly depends on the magnitude difference of the BCG and the second and third brightest cluster members: we find a strong alignment effect for the dominant BCGs, while less dominant BCGs do not show any departure from random alignment with respect to the cluster. We therefore claim that the alignment process originates from the same process that makes the BCG grow dominant, be it direct mergers in the early stage of cluster formation, or a later process that resembles the galactic cannibalism scenario. We do not find strong evidence for (or against) redshift evolution between 0alignment with redshift, richness and morphology of both the cluster and the BCG.

  2. Aligning Business Needs and Instructional Assets (Recycling Instructional Assets)

    ERIC Educational Resources Information Center

    Gendelman, Joel

    2009-01-01

    High-performing organizations and performance improvement professionals frequently speak about the alignment of their instructional curricula with the needs of the business. However, they often lack a systematic methodology for performing that alignment. This article presents such a method. The process provides the ability to better support…

  3. Alignment of Content and Effectiveness of Mathematics Assessment Items

    ERIC Educational Resources Information Center

    Kulm, Gerald; Dager Wilson, Linda; Kitchen, Richard

    2005-01-01

    Alignment has taken on increased importance given the current high-stakes nature of assessment. To make well-informed decisions about student learning on the basis of test results, assessment items need to be well aligned with standards. Project 2061 of the American Association for the Advancement of Science (AAAS) has developed a procedure for…

  4. Hydrostatic self-aligning axial/torsional mechanism

    DOEpatents

    O'Connor, Daniel G.; Gerth, Howard L.

    1990-01-01

    The present invention is directed to a self-aligning axial/torsional loading mechanism for testing the strength of brittle materials which are sensitive to bending moments. Disposed inside said self-aligning loading mechanism is a frictionless hydrostatic ball joint with a flexure ring to accommodate torsional loads through said ball joint.

  5. Visual Influences on Alignment to Voice Onset Time

    ERIC Educational Resources Information Center

    Sanchez, Kauyumari; Miller, Rachel M.; Rosenblum, Lawrence D.

    2010-01-01

    Purpose: Speech shadowing experiments were conducted to test whether alignment (inadvertent imitation) to voice onset time (VOT) can be influenced by visual speech information. Method: Experiment 1 examined whether alignment would occur to auditory /pa/ syllables manipulated to have 3 different VOTs. Nineteen female participants were asked to…

  6. The Impact of Alignment Coaching on Christian Teachers' Worthy Performance

    ERIC Educational Resources Information Center

    Hines, Linda M.

    2010-01-01

    "The Impact of Alignment Coaching on Christian Teachers' Worthy Performance" uses Human Performance Technology and "teleonomics" (Gilbert 2007) to document several intersecting vantage points as one performance improvement system of alignment coaching (AC). Coaching relationships and accomplishments of consistently (daily) reading the Bible,…

  7. Aligning Transition and Standards-Based Education: Issues and Strategies.

    ERIC Educational Resources Information Center

    Kochhar-Bryant, Carol, Ed.; Bassett, Diane S., Ed.

    Eleven papers address issues in the alignment of standards-based education and individualized transition planning and service development for students with disabilities including differences in assumptions and principles, the transition planning model as a framework for achieving this alignment, and educational practices resulting from this…

  8. Curriculum Alignment: Exploring Student Perception of Learning Achievement Measures

    ERIC Educational Resources Information Center

    Kuhn, Kerri-Ann L.; Rundle-Thiele, Sharyn R.

    2009-01-01

    The importance of constructively aligned curriculum is well understood in higher education. Based on the principles of constructive alignment, this research considers whether student perception of learning achievement measures can be used to gain insights into how course activities and pedagogy are assisting or hindering students in accomplishing…

  9. Chunk Alignment for Corpus-Based Machine Translation

    ERIC Educational Resources Information Center

    Kim, Jae Dong

    2011-01-01

    Since sub-sentential alignment is critically important to the translation quality of an Example-Based Machine Translation (EBMT) system, which operates by finding and combining phrase-level matches against the training examples, we developed a new alignment algorithm for the purpose of improving the EBMT system's performance. This new…

  10. MODELING THE ALIGNMENT PROFILE OF SATELLITE GALAXIES IN CLUSTERS

    SciTech Connect

    Song, Hyunmi; Lee, Jounghun E-mail: jounghun@astro.snu.ac.kr

    2012-04-01

    Analyzing the halo and galaxy catalogs from the Millennium Simulations at redshifts z = 0, 0.5, 1, we determine the alignment profiles of cluster galaxies by measuring the average alignments between the major axes of the pseudo inertia tensors from all satellites within a cluster's virial radius and from only those satellites within some smaller radius as a function of the top-hat scale difference. The alignment profiles quantify how well the satellite galaxies retain the memory of the external tidal fields after merging into their host clusters and how fast they lose the initial alignment tendency as the cluster's relaxation proceeds. It is found that the alignment profile drops faster at higher redshifts and on smaller mass scales. This result is consistent with the picture that the faster merging of the satellites and earlier onset of the nonlinear effect inside clusters tend to break the preferential alignments of the satellites with the external tidal fields. Modeling the alignment profile of cluster galaxies as a power law of the density correlation coefficient that is independent of the power spectrum normalization ({sigma}{sub 8}) and demonstrating that the density correlation coefficient varies sensitively with the density parameter ({Omega}{sub m}) and neutrino mass fraction (f{sub {nu}}), we suggest that the alignment profile of cluster galaxies might be useful for breaking the {Omega}{sub m}-{sigma}{sub 8} and f{sub {nu}}-{sigma}{sub 8} degeneracies.

  11. 33 CFR 101.205 - Department of Homeland Security alignment.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Department of Homeland Security... Department of Homeland Security alignment. The MARSEC Levels are aligned with the Department of Homeland Security's Homeland Security Advisory System (HSAS), established by Homeland Security...

  12. Auto-aligning stimulated emission depletion microscope using adaptive optics

    PubMed Central

    Gould, Travis J.; Kromann, Emil B.; Burke, Daniel; Booth, Martin J.; Bewersdorf, Joerg

    2013-01-01

    Stimulated emission depletion (STED) microscopy provides diffraction-unlimited resolution in fluorescence microscopy. Imaging at the nanoscale, however, requires precise alignment of the depletion and excitation laser foci of the STED microscope. We demonstrate here that adaptive optics can be implemented to automatically align STED and confocal images with a precision of 4.3 ± 2.3 nm. PMID:23722769

  13. Connectivity independent protein-structure alignment: a hierarchical approach

    PubMed Central

    Kolbeck, Bjoern; May, Patrick; Schmidt-Goenner, Tobias; Steinke, Thomas; Knapp, Ernst-Walter

    2006-01-01

    Background Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure elements (SSE) but differ in the underlying polypeptide chain connectivity (non-sequential SSE connectivity). Results We perform protein-structure alignment using a two-level hierarchical approach implemented in the program GANGSTA. On the first level, pair contacts and relative orientations between SSEs (i.e. α-helices and β-strands) are maximized with a genetic algorithm (GA). On the second level residue pair contacts from the best SSE alignments are optimized. We have tested the method on visually optimized structure alignments of protein pairs (pairwise mode) and for database scans. For a given protein structure, our method is able to detect significant structural similarity of functionally important folds with non-sequential SSE connectivity. The performance for structure alignments with strictly sequential SSE connectivity is comparable to that of other structure alignment methods. Conclusion As demonstrated for several applications, GANGSTA finds meaningful protein-structure alignments independent of the SSE connectivity. GANGSTA is able to detect structural similarity of protein folds that are assigned to different superfamilies but nevertheless possess similar structures and perform related functions, even if these proteins differ in SSE connectivity. PMID:17118190

  14. Corrected High-Frame Rate Anchored Ultrasound with Software Alignment

    ERIC Educational Resources Information Center

    Miller, Amanda L.; Finch, Kenneth B.

    2011-01-01

    Purpose: To improve lingual ultrasound imaging with the Corrected High Frame Rate Anchored Ultrasound with Software Alignment (CHAUSA; Miller, 2008) method. Method: A production study of the IsiXhosa alveolar click is presented. Articulatory-to-acoustic alignment is demonstrated using a Tri-Modal 3-ms pulse generator. Images from 2 simultaneous…

  15. 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. PMID:25820888

  16. Alignment sensing and control for squeezed vacuum states of light.

    PubMed

    Schreiber, E; Dooley, K L; Vahlbruch, H; Affeldt, C; Bisht, A; Leong, J R; Lough, J; Prijatelj, M; Slutsky, J; Was, M; Wittel, H; Danzmann, K; Grote, H

    2016-01-11

    Beam alignment is an important practical aspect of the application of squeezed states of light. Misalignments in the detection of squeezed light result in a reduction of the observable squeezing level. In the case of squeezed vacuum fields that contain only very few photons, special measures must be taken in order to sense and control the alignment of the essentially dark beam. The GEO 600 gravitational wave detector employs a squeezed vacuum source to improve its detection sensitivity beyond the limits set by classical quantum shot noise. Here, we present our design and implementation of an alignment sensing and control scheme that ensures continuous optimal alignment of the squeezed vacuum field at GEO 600 on long time scales in the presence of free-swinging optics. This first demonstration of a squeezed light automatic alignment system will be of particular interest for future long-term applications of squeezed vacuum states of light. PMID:26832246

  17. Understanding and overcoming shear alignment of fibers during extrusion.

    PubMed

    Martin, Joshua J; Riederer, Michael S; Krebs, Melissa D; Erb, Randall M

    2015-01-14

    Fiber alignment is the defining architectural characteristic of discontinuous fiber composites and is dictated by shear-dominated processing techniques including flow-injection molding, tape-casting, and mold-casting. However, recent colloidal assembly techniques have started to employ additional forces in fiber suspensions that have the potential to change the energy landscape of the shear-dominated alignment in conditions of flow. In this paper, we develop an energetics model to characterize the shear-alignment of rigid fibers under different flow conditions in the presence of magnetic colloidal alignment forces. We find that these colloidal forces can be sufficient to manipulate the energetic landscape and obtain tunable fiber alignment during flow within even small geometries, such as capillary flow. In most conditions, these colloidal forces work to freeze the fiber orientation during flow and prevent the structure disrupting phenomenon of Jeffrey's orbits that has been accepted to rule fiber suspensions under simple shear flow. PMID:25408494

  18. 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.

  19. ASM stepper alignment through thick epitaxial silicon films

    NASA Astrophysics Data System (ADS)

    Black, Iain

    1999-04-01

    High voltage bipolar and BiCMOS processes often use thick epitaxially grown layers of silicon. These films 12-24 micrometers thick offer a considerable challenge to the alignment of subsequent process layers due to the 'wash out' and image distortion, caused to any underlying pattern, which render automatic alignment mark recognition difficult it not impossible. Historically using projection aligner technology these immediately post Epi layers have been manually aligned with future automatic alignment target defined at the first opportunity post Epi. This is not possible using ASM steppers, as these depend upon marks etched into the silicon, before first processing, to create marks, to which all subsequent layers are registered. To allow the stepper to run wafers with these Epi films a new approach was required.

  20. Improving multiple sequence alignment by using better guide trees

    PubMed Central

    2015-01-01

    Progressive sequence alignment is one of the most commonly used method for multiple sequence alignment. Roughly speaking, the method first builds a guide tree, and then aligns the sequences progressively according to the topology of the tree. It is believed that guide trees are very important to progressive alignment; a better guide tree will give an alignment with higher accuracy. Recently, we have proposed an adaptive method for constructing guide trees. This paper studies the quality of the guide trees constructed by such method. Our study showed that our adaptive method can be used to improve the accuracy of many different progressive MSA tools. In fact, we give evidences showing that the guide trees constructed by the adaptive method are among the best. PMID:25859903