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. Molecular orbital imaging for partially aligned molecules

    NASA Astrophysics Data System (ADS)

    Qin, Meiyan; Zhu, Xiaosong

    2017-01-01

    We investigate molecular orbital reconstruction using high-order harmonic emissions from partially aligned molecular ensembles. By carrying out the reconstruction procedure using the harmonic sampling with or without the spectral minimum, the roles of the harmonic phase and amplitude modulation due to the partial alignment can be separately studied. It is found that with the prior knowledge of the orbital symmetry, the reconstructed result is very sensitive to the modulation of the harmonic phase for the πg orbital, while in the case of σg orbital, the reconstructed result is mainly determined by the harmonic amplitude. These results can provide an important reference for the future experiment of molecular orbital imaging.

  3. A novel partial sequence alignment tool for finding large deletions.

    PubMed

    Aruk, Taner; Ustek, Duran; Kursun, Olcay

    2012-01-01

    Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method.

  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. 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.

  6. 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.

  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. 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.

  9. 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.

  10. 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° -55

  11. 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.

  12. MP-Align: alignment of metabolic pathways

    PubMed Central

    2014-01-01

    Background Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction. The approaches are based on some simplified representation of metabolic pathways and on a related definition of a similarity score (or distance measure) between two pathways. More recent comparative research focuses on alignment techniques that can identify similar parts between pathways. Results We propose a methodology for the pairwise comparison and alignment of metabolic pathways that aims at providing the largest conserved substructure of the pathways under consideration. The proposed methodology has been implemented in a tool called MP-Align, which has been used to perform several validation tests. The results showed that our similarity score makes it possible to discriminate between different domains and to reconstruct a meaningful phylogeny from metabolic data. The results further demonstrate that our alignment algorithm correctly identifies subpathways sharing a common biological function. Conclusion The results of the validation tests performed with MP-Align are encouraging. A comparison with another proposal in the literature showed that our alignment algorithm is particularly well-suited to finding the largest conserved subpathway of the pathways under examination. PMID:24886436

  13. 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.

  14. Tidal alignment of galaxies

    SciTech Connect

    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.

  15. Tidal alignment of galaxies

    SciTech Connect

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš E-mail: zvlah@stanford.edu

    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.

  16. High-performance partially aligned semiconductive single-walled carbon nanotube transistors achieved with a parallel technique.

    PubMed

    Wang, Yilei; Pillai, Suresh Kumar Raman; Chan-Park, Mary B

    2013-09-09

    Single-walled carbon nanotubes (SWNTs) are widely thought to be a strong contender for next-generation printed electronic transistor materials. However, large-scale solution-based parallel assembly of SWNTs to obtain high-performance transistor devices is challenging. SWNTs have anisotropic properties and, although partial alignment of the nanotubes has been theoretically predicted to achieve optimum transistor device performance, thus far no parallel solution-based technique can achieve this. Herein a novel solution-based technique, the immersion-cum-shake method, is reported to achieve partially aligned SWNT networks using semiconductive (99% enriched) SWNTs (s-SWNTs). By immersing an aminosilane-treated wafer into a solution of nanotubes placed on a rotary shaker, the repetitive flow of the nanotube solution over the wafer surface during the deposition process orients the nanotubes toward the fluid flow direction. By adjusting the nanotube concentration in the solution, the nanotube density of the partially aligned network can be controlled; linear densities ranging from 5 to 45 SWNTs/μm are observed. Through control of the linear SWNT density and channel length, the optimum SWNT-based field-effect transistor devices achieve outstanding performance metrics (with an on/off ratio of ~3.2 × 10(4) and mobility 46.5 cm(2) /Vs). Atomic force microscopy shows that the partial alignment is uniform over an area of 20 × 20 mm(2) and confirms that the orientation of the nanotubes is mostly along the fluid flow direction, with a narrow orientation scatter characterized by a full width at half maximum (FWHM) of <15° for all but the densest film, which is 35°. This parallel process is large-scale applicable and exploits the anisotropic properties of the SWNTs, presenting a viable path forward for industrial adoption of SWNTs in printed, flexible, and large-area electronics.

  17. 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.

  18. 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.

  19. 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.

  20. Progressive multiple sequence alignments from triplets

    PubMed Central

    Kruspe, Matthias; Stadler, Peter F

    2007-01-01

    Background The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors. Research Here we present a modified variant of progressive sequence alignments that addresses both issues. Instead of pairwise alignments we use exact dynamic programming to align sequence or profile triples. This avoids a large fractions of the ambiguities arising in pairwise alignments. In the subsequent aggregation steps we follow the logic of the Neighbor-Net algorithm, which constructs a phylogenetic network by step-wisely replacing triples by pairs instead of combining pairs to singletons. To this end the three-way alignments are subdivided into two partial alignments, at which stage all-gap columns are naturally removed. This alleviates the "once a gap, always a gap" problem of progressive alignment procedures. Conclusion The three-way Neighbor-Net based alignment program aln3nn is shown to compare favorably on both protein sequences and nucleic acids sequences to other progressive alignment tools. In the latter case one easily can include scoring terms that consider secondary structure features. Overall, the quality of resulting alignments in general exceeds that of clustalw or other multiple alignments tools even though our software does not included heuristics for context dependent (mis)match scores. PMID:17631683

  1. Alignment of CEBAF cryomodules

    SciTech Connect

    Schneider, W.J.; Bisognano, J.J.; Fischer, J.

    1993-06-01

    CEBAF, the Continuous Electron Beam Accelerator Facility, when completed, will house a 4 GeV recirculating accelerator. Each of the accelerator`s two linacs contains 160 superconducting radio frequency (SRF) 1497 MHz niobium cavities in 20 cryomodules. Alignments of the cavities within the cryomodule with respect to beam axis is critical to achieving the optimum accelerator performance. This paper discusses the rationale for the current specification on cavity mechanical alignment: 2 mrad (rms) applied to the 0.5 m active length cavities. We describe the tooling that was developed to achieve the tolerance at the time of cavity pair assembly, to preserve and integrate alignment during cryomodule assembly, and to translate alignment to appropriate installation in the beam line.

  2. 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.

  3. 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…

  4. Magnetically Aligned Supramolecular Hydrogels

    PubMed Central

    Wallace, Matthew; Cardoso, Andre Zamith; Frith, William J; Iggo, Jonathan A; Adams, Dave J

    2014-01-01

    The magnetic-field-induced alignment of the fibrillar structures present in an aqueous solution of a dipeptide gelator, and the subsequent retention of this alignment upon transformation to a hydrogel upon the addition of CaCl2 or upon a reduction in solution pH is reported. Utilising the switchable nature of the magnetic field coupled with the slow diffusion of CaCl2, it is possible to precisely control the extent of anisotropy across a hydrogel, something that is generally very difficult to do using alternative methods. The approach is readily extended to other compounds that form viscous solutions at high pH. It is expected that this work will greatly expand the utility of such low-molecular-weight gelators (LMWG) in areas where alignment is key. PMID:25345918

  5. 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.

  6. 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.

  7. PILOT optical alignment

    NASA Astrophysics Data System (ADS)

    Longval, Y.; Mot, B.; Ade, P.; André, Y.; Aumont, J.; Baustista, L.; Bernard, J.-Ph.; Bray, N.; de Bernardis, P.; Boulade, O.; Bousquet, F.; Bouzit, M.; Buttice, V.; Caillat, A.; Charra, M.; Chaigneau, M.; Crane, B.; Crussaire, J.-P.; Douchin, F.; Doumayrou, E.; Dubois, J.-P.; Engel, C.; Etcheto, P.; Gélot, P.; Griffin, M.; Foenard, G.; Grabarnik, S.; Hargrave, P..; Hughes, A.; Laureijs, R.; Lepennec, Y.; Leriche, B.; Maestre, S.; Maffei, B.; Martignac, J.; Marty, C.; Marty, W.; Masi, S.; Mirc, F.; Misawa, R.; Montel, J.; Montier, L.; Narbonne, J.; Nicot, J.-M.; Pajot, F.; Parot, G.; Pérot, E.; Pimentao, J.; Pisano, G.; Ponthieu, N.; Ristorcelli, I.; Rodriguez, L.; Roudil, G.; Salatino, M.; Savini, G.; Simonella, O.; Saccoccio, M.; Tapie, P.; Tauber, J.; Torre, J.-P.; Tucker, C.

    2016-07-01

    PILOT is a balloon-borne astronomy experiment designed to study the polarization of dust emission in the diffuse interstellar medium in our Galaxy at wavelengths 240 μm with an angular resolution about two arcminutes. Pilot optics is composed an off-axis Gregorian type telescope and a refractive re-imager system. All optical elements, except the primary mirror, are in a cryostat cooled to 3K. We combined the optical, 3D dimensional measurement methods and thermo-elastic modeling to perform the optical alignment. The talk describes the system analysis, the alignment procedure, and finally the performances obtained during the first flight in September 2015.

  8. CLIP-ASAP-HSQC for fast and accurate extraction of one-bond couplings from isotropic and partially aligned molecules.

    PubMed

    Becker, Johanna; Luy, Burkhard

    2015-11-01

    Fast measurement of heteronuclear one-bond couplings, a class of NMR parameters valuable for structure elucidation, is highly desirable, especially if samples undergo chemical reactions or dynamic processes are observed. Methods presented so far face severe limitations in terms of resolution, accessible bandwidth, and sensitivity. We present the CLean InPhase-Acceleration by Sharing Adjacent Polarization-HSQC (CLIP-ASAP-HSQC) pulse sequence that allows fast acquisition of spectra with clean inphase multiplets in about 25 s. The performance in terms of accurate extraction of one-bond couplings is demonstrated on three test samples including partially aligned molecules.

  9. 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…

  10. 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.

  11. 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…

  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. Automatic Word Alignment

    DTIC Science & Technology

    2014-02-18

    strategy was evalu­ ated in the context of English -to-Pashto (E2P) and Pashto-to- English (P2E), a low-resource language pair. For E2P, the training and...improves the quality of automatic word alignment, for example for resource poor language pairs, thus improving Statistical Machine Translation (SMT...example for resource poor language pairs, thus improving Statistical Machine Translation (SMT) performance. 15. SUBJECT TERMS 16. SECURITY

  15. Orbit IMU alignment: Error analysis

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

    A comprehensive accuracy analysis of orbit inertial measurement unit (IMU) alignments using the shuttle star trackers was completed and the results are presented. Monte Carlo techniques were used in a computer simulation of the IMU alignment hardware and software systems to: (1) determine the expected Space Transportation System 1 Flight (STS-1) manual mode IMU alignment accuracy; (2) investigate the accuracy of alignments in later shuttle flights when the automatic mode of star acquisition may be used; and (3) verify that an analytical model previously used for estimating the alignment error is a valid model. The analysis results do not differ significantly from expectations. The standard deviation in the IMU alignment error for STS-1 alignments was determined to the 68 arc seconds per axis. This corresponds to a 99.7% probability that the magnitude of the total alignment error is less than 258 arc seconds.

  16. Nuclear reactor alignment plate configuration

    SciTech Connect

    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.

  17. Multiple protein structure alignment.

    PubMed Central

    Taylor, W. R.; Flores, T. P.; Orengo, C. A.

    1994-01-01

    A method was developed to compare protein structures and to combine them into a multiple structure consensus. Previous methods of multiple structure comparison have only concatenated pairwise alignments or produced a consensus structure by averaging coordinate sets. The current method is a fusion of the fast structure comparison program SSAP and the multiple sequence alignment program MULTAL. As in MULTAL, structures are progressively combined, producing intermediate consensus structures that are compared directly to each other and all remaining single structures. This leads to a hierarchic "condensation," continually evaluated in the light of the emerging conserved core regions. Following the SSAP approach, all interatomic vectors were retained with well-conserved regions distinguished by coherent vector bundles (the structural equivalent of a conserved sequence position). Each bundle of vectors is summarized by a resultant, whereas vector coherence is captured in an error term, which is the only distinction between conserved and variable positions. Resultant vectors are used directly in the comparison, which is weighted by their error values, giving greater importance to the matching of conserved positions. The resultant vectors and their errors can also be used directly in molecular modeling. Applications of the method were assessed by the quality of the resulting sequence alignments, phylogenetic tree construction, and databank scanning with the consensus. Visual assessment of the structural superpositions and consensus structure for various well-characterized families confirmed that the consensus had identified a reasonable core. PMID:7849601

  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. Method for alignment of microwires

    DOEpatents

    Beardslee, Joseph A.; Lewis, Nathan S.; Sadtler, Bryce

    2017-01-24

    A method of aligning microwires includes modifying the microwires so they are more responsive to a magnetic field. The method also includes using a magnetic field so as to magnetically align the microwires. The method can further include capturing the microwires in a solid support structure that retains the longitudinal alignment of the microwires when the magnetic field is not applied to the microwires.

  20. 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…

  1. Precision alignment and mounting apparatus

    NASA Technical Reports Server (NTRS)

    Preston, Dennis R. (Inventor)

    1993-01-01

    An alignment and mounting apparatus for mounting two modules (10,12) includes a first portion having a cylindrical alignment pin (16) projecting normal to a module surface, a second portion having a three-stage alignment guide (18) including a shoehorn flange (34), a Y-slot (42) and a V-block (22) which sequentially guide the alignment pin (16) with successively finer precision and a third portion in the form of a spring-loaded captive fastener (20) for connecting the two modules after alignment is achieved.

  2. Engineering cell alignment in vitro.

    PubMed

    Li, Yuhui; Huang, Guoyou; Zhang, Xiaohui; Wang, Lin; Du, Yanan; Lu, Tian Jian; Xu, Feng

    2014-01-01

    Cell alignment plays a critical role in various cell behaviors including cytoskeleton reorganization, membrane protein relocation, nucleus gene expression, and ECM remodeling. Cell alignment is also known to exert significant effects on tissue regeneration (e.g., neuron) and modulate mechanical properties of tissues including skeleton, cardiac muscle and tendon. Therefore, it is essential to engineer cell alignment in vitro for biomechanics, cell biology, tissue engineering and regenerative medicine applications. With advances in nano- and micro-scale technologies, a variety of approaches have been developed to engineer cell alignment in vitro, including mechanical loading, topographical patterning, and surface chemical treatment. In this review, we first present alignments of various cell types and their functionality in different tissues in vivo including muscle and nerve tissues. Then, we provide an overview of recent approaches for engineering cell alignment in vitro. Finally, concluding remarks and perspectives are addressed for future improvement of engineering cell alignment.

  3. 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.

  4. Nova laser alignment control system

    SciTech Connect

    Van Arsdall, P.J.; Holloway, F.W.; McGuigan, D.L.; Shelton, R.T.

    1984-03-29

    Alignment of the Nova laser requires control of hundreds of optical components in the ten beam paths. Extensive application of computer technology makes daily alignment practical. The control system is designed in a manner which provides both centralized and local manual operator controls integrated with automatic closed loop alignment. Menudriven operator consoles using high resolution color graphics displays overlaid with transport touch panels allow laser personnel to interact efficiently with the computer system. Automatic alignment is accomplished by using image analysis techniques to determine beam references points from video images acquired along the laser chain. A major goal of the design is to contribute substantially to rapid experimental turnaround and consistent alignment results. This paper describes the computer-based control structure and the software methods developed for aligning this large laser system.

  5. 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.

  6. 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.

  7. 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.

  8. The alignment strategy of HADES

    NASA Astrophysics Data System (ADS)

    Pechenova, O.; Pechenov, V.; Galatyuk, T.; Hennino, T.; Holzmann, R.; Kornakov, G.; Markert, J.; Müntz, C.; Salabura, P.; Schmah, A.; Schwab, E.; Stroth, J.

    2015-06-01

    The global as well as intrinsic alignment of any spectrometer impacts directly on its performance and the quality of the achievable physics results. An overview of the current alignment procedure of the DiElectron Spectrometer HADES is presented with an emphasis on its main features and its accuracy. The sequence of all steps and procedures is given, including details on photogrammetric and track-based alignment.

  9. Alignment of Helical Membrane Protein Sequences Using AlignMe

    PubMed Central

    Khafizov, Kamil; Forrest, Lucy R.

    2013-01-01

    Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their alignments. Existing approaches typically consider membrane-related information either by using membrane-specific substitution matrices or by assigning distinct penalties for gap creation in transmembrane and non-transmembrane regions. Here, we ask whether favoring matching of predicted transmembrane segments within a standard dynamic programming algorithm can improve the accuracy of pairwise membrane protein sequence alignments. We tested various strategies using a specifically designed program called AlignMe. An updated set of homologous membrane protein structures, called HOMEP2, was used as a reference for optimizing the gap penalties. The best of the membrane-protein optimized approaches were then tested on an independent reference set of membrane protein sequence alignments from the BAliBASE collection. When secondary structure (S) matching was combined with evolutionary information (using a position-specific substitution matrix (P)), in an approach we called AlignMePS, the resultant pairwise alignments were typically among the most accurate over a broad range of sequence similarities when compared to available methods. Matching transmembrane predictions (T), in addition to evolutionary information, and secondary-structure predictions, in an approach called AlignMePST, generally reduces the accuracy of the alignments of closely-related proteins in the BAliBASE set relative to AlignMePS, but may be useful in cases of extremely distantly related proteins for which sequence information is less informative. The open source AlignMe code is available at https://sourceforge.net/projects/alignme/, and at http://www.forrestlab.org, along with an online server and the HOMEP2 data set. PMID:23469223

  10. GS-align for glycan structure alignment and similarity measurement

    PubMed Central

    Lee, Hui Sun; Jo, Sunhwan; Mukherjee, Srayanta; Park, Sang-Jun; Skolnick, Jeffrey; Lee, Jooyoung; Im, Wonpil

    2015-01-01

    Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N-linked glycan library and PDB homologous/non-homologous N-glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. Availability and implementation: http://www.glycanstructure.org/gsalign. Contact: wonpil@ku.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25857669

  11. Degradation in Mechanical and Thermal Properties of Partially Aligned CNT/Epoxy Composites due to Seawater Absorption

    NASA Astrophysics Data System (ADS)

    Saha, Sunirmal; Bal, Smrutisikha

    2017-02-01

    This literature gives an overview of the effect of water uptake on the mechanical and thermal performances of partially aligned carbon nanotube (CNT)/ epoxy (having CNTs wt.%: 0.5, 0.75 and 1) along with pure epoxy composites. Weight change behaviour of all the composites immersed in seawater for a period of six months has been recorded. The state of CNT/matrix interface is believed to be influenced due to water absorption. Reduction in flexural modulus, strength, hardness and glass transition temperature (Tg ) of the specimens have been evaluated as compared to their unexposed counterparts due to adverse effect of water absorption. Results demonstrated 35-46% reduction in flexural modulus, 43-56% decrement in flexural strength, 4-7 MPa reduction in hardness and minor deterioration in Tg values for all the composites. However, the specimen having 0.75 wt.% CNT loading, exhibited minimum reduction in properties in all aspects compared to others. Scanning electron microscopy (SEM) has been employed to study the failure mechanism of the specimens after performing the mechanical tests.

  12. Mask alignment system for semiconductor processing

    DOEpatents

    Webb, Aaron P.; Carlson, Charles T.; Weaver, William T.; Grant, Christopher N.

    2017-02-14

    A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered onto the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.

  13. 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

  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. 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.

  16. 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.

  17. Alignment of the MINOS FD

    SciTech Connect

    Becker, B.; Boehnlein, D.; /Fermilab

    2004-11-01

    The results and procedure of the alignment of the MINOS Far Detector are presented. The far detector has independent alignments of SM1 and SM2. The misalignments have an estimated uncertainty of {approx}850 {micro}m for SM1 and {approx}750 {micro}m for SM2. The alignment has as inputs the average rotations of U and V as determined by optical survey and strip positions within modules measured from the module mapper. The output of this is a module-module correction for transverse mis-alignments. These results were verified by examining an independent set of data. These alignment constants on average contribute much less then 1% to the total uncertainty in the transverse strip position.

  18. Magnetic alignment and the Poisson alignment reference system

    NASA Astrophysics Data System (ADS)

    Griffith, L. V.; Schenz, R. F.; Sommargren, G. E.

    1990-08-01

    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This article begins with a review of the motivation for developing an alignment system that will assure better than 100-μm accuracy in the alignment of the magnetic axis throughout an FEL. The 100-μm accuracy is an error circle about an ideal axis for 300 m or more. The article describes techniques for identifying the magnetic axes of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development of a straight-line reference based on the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. The Poisson alignment reference system should be accurate to 25 μm over 300 m, which is believed to be a factor-of-4 improvement over earlier techniques. An error budget shows that only 25% of the total budgeted tolerance is used for the alignment reference system, so the remaining tolerances should fall within the allowable range for FEL alignment.

  19. 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.

  20. BAYESIAN PROTEIN STRUCTURE ALIGNMENT1

    PubMed Central

    RODRIGUEZ, ABEL; SCHMIDLER, SCOTT C.

    2015-01-01

    The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key “gap” parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence–structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples. PMID:26925188

  1. 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.

  2. 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.

  3. Magnetic axis alignment and the Poisson alignment reference system

    NASA Astrophysics Data System (ADS)

    Griffith, Lee V.; Schenz, Richard F.; Sommargren, Gary E.

    1989-01-01

    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This paper begins with a review of the motivation for developing an alignment system that will assure better than 100 micrometer accuracy in the alignment of the magnetic axis throughout an FEL. The paper describes techniques for identifying the magnetic axis of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development and use of the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. An error budget shows that the Poisson alignment reference system will make it possible to meet the alignment tolerances for an FEL.

  4. 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.

  5. 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.

  6. 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.

  7. Fixture for aligning motor assembly

    SciTech Connect

    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.

  8. Stellar Alignments - Identification and Analysis

    NASA Astrophysics Data System (ADS)

    Ruggles, Clive L. N.

    Fortuitous stellar alignments can be fitted to structural orientations with relative ease by the unwary. Nonetheless, cautious approaches taking into account a broader range of cultural evidence, as well as paying due attention to potential methodological pitfalls, have been successful in identifying credible stellar alignments—and constructing plausible assessments of their cultural significance—in a variety of circumstances. These range from single instances of alignments upon particular asterisms where the corroborating historical or ethnographic evidence is strong to repeated instances of oriented structures with only limited independent cultural information but where systematic, data-driven approaches can be productive. In the majority of cases, the identification and interpretation of putative stellar alignments relates to groups of similar monuments or complex single sites and involves a balance between systematic studies of the alignments themselves, backed up by statistical analysis where appropriate, and the consideration of a range of contextual evidence, either derived from the archaeological record alone or from other relevant sources.

  9. RF Jitter Modulation Alignment Sensing

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  10. 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.

  11. The Rigors of Aligning Performance

    DTIC Science & Technology

    2015-06-01

    bearing in mind customer perceptions. Recommendations include employee training centered on goal alignment, which is vital to highlight the...appeared to be lacking in some areas when bearing in mind customer perceptions. Recommendations include employee training centered on goal alignment...through the strategic plan and CONOPS. However, the extent of goal accomplishment appears to be lacking in some areas when bearing in mind the

  12. National Ignition Facility system alignment.

    PubMed

    Burkhart, S C; Bliss, E; Di Nicola, P; Kalantar, D; Lowe-Webb, R; McCarville, T; Nelson, D; Salmon, T; Schindler, T; Villanueva, J; Wilhelmsen, K

    2011-03-10

    The National Ignition Facility (NIF) is the world's largest optical instrument, comprising 192 37 cm square beams, each generating up to 9.6 kJ of 351 nm laser light in a 20 ns beam precisely tailored in time and spectrum. The Facility houses a massive (10 m diameter) target chamber within which the beams converge onto an ∼1 cm size target for the purpose of creating the conditions needed for deuterium/tritium nuclear fusion in a laboratory setting. A formidable challenge was building NIF to the precise requirements for beam propagation, commissioning the beam lines, and engineering systems to reliably and safely align 192 beams within the confines of a multihour shot cycle. Designing the facility to minimize drift and vibration, placing the optical components in their design locations, commissioning beam alignment, and performing precise system alignment are the key alignment accomplishments over the decade of work described herein. The design and positioning phases placed more than 3000 large (2.5 m×2 m×1 m) line-replaceable optics assemblies to within ±1 mm of design requirement. The commissioning and alignment phases validated clear apertures (no clipping) for all beam lines, and demonstrated automated laser alignment within 10 min and alignment to target chamber center within 44 min. Pointing validation system shots to flat gold-plated x-ray emitting targets showed NIF met its design requirement of ±50 μm rms beam pointing to target chamber. Finally, this paper describes the major alignment challenges faced by the NIF Project from inception to present, and how these challenges were met and solved by the NIF design and commissioning teams.

  13. 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.

  14. 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

  15. Cavity alignment using fringe scanning

    NASA Astrophysics Data System (ADS)

    Sinkunaite, Laura Paulina; Kawabe, Keita; Landry, Michael

    2017-01-01

    LIGO employs two 4-km long Fabry-Pérot arm cavities, which need to be aligned in order for an interferometer to be locked on a TEM00 mode. Once the cavity is locked, alignment signals can be derived from wave-front sensors which measure the TEM01 mode content. However, the alignment state is not always good enough for locking on TEM00. Even when this is the case, the alignment can be evaluated using a free swinging cavity, that shows flashes when higher-order modes become resonant. By moving test masses, small changes are made to the mirror orientation, and hence the TEM00 mode can be optimized iteratively. Currently, this is a manual procedure, and thus it is very time-consuming. Therefore, this project is aimed to study another possible way to lock the cavity on the TEM00 mode. Misalignment information can also be extracted from the power of the higher-order modes transmitted through the cavity. This talk will present an algorithm for this alternative and faster way to derive the alignment state of the arm cavities. Supported by APS FIP, NSF, and Caltech SFP.

  16. 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.

  17. 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.

  18. An introduction to the Lagan alignment toolkit.

    PubMed

    Brudno, Michael

    2007-01-01

    The Lagan Toolkit is a software package for comparison of genomic sequences. It includes the CHAOS local alignment program, LAGAN global alignment program for two, or more sequences and Shuffle-LAGAN, a "glocal" alignment method that handles genomic rearrangements in a global alignment framework. The alignment programs included in the Lagan Toolkit have been widely used to compare genomes of many organisms, from bacteria to large mammalian genomes. This chapter provides an overview of the algorithms used by the LAGAN programs to construct genomic alignments, explains how to build alignments using either the standalone program or the web server, and discusses some of the common pitfalls users encounter when using the toolkit.

  19. 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.

  20. Multiple sequence alignment with hierarchical clustering.

    PubMed Central

    Corpet, F

    1988-01-01

    An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers. The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment scores. The closest sequences are aligned creating groups of aligned sequences. Then close groups are aligned until all sequences are aligned in one group. The pairwise alignments included in the multiple alignment form a new matrix that is used to produce a hierarchical clustering. If it is different from the first one, iteration of the process can be performed. The method is illustrated by an example: a global alignment of 39 sequences of cytochrome c. PMID:2849754

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. ALIGN_MTX--an optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment.

    PubMed

    Vishnepolsky, Boris; Pirtskhalava, Malak

    2009-06-01

    The presented program ALIGN_MTX makes alignment of two textual sequences with an opportunity to use any several characters for the designation of sequence elements and arbitrary user substitution matrices. It can be used not only for the alignment of amino acid and nucleotide sequences but also for sequence-structure alignment used in threading, amino acid sequence alignment, using preliminary known PSSM matrix, and in other cases when alignment of biological or non-biological textual sequences is required. This distinguishes it from the majority of similar alignment programs that make, as a rule, alignment only of amino acid or nucleotide sequences represented as a sequence of single alphabetic characters. ALIGN_MTX is presented as downloadable zip archive at http://www.imbbp.org/software/ALIGN_MTX/ and available for free use. As application of using the program, the results of comparison of different types of substitution matrix for alignment quality in distantly related protein pair sets were presented. Threading matrix SORDIS, based on side-chain orientation in relation to hydrophobic core centers with evolutionary change-based substitution matrix BLOSUM and using multiple sequence alignment information position-specific score matrices (PSSM) were taken for test alignment accuracy. The best performance shows PSSM matrix, but in the reduced set with lower sequence similarity threading matrix SORDIS shows the same performance and it was shown that combined potential with SORDIS and PSSM can improve alignment quality in evolutionary distantly related protein pairs.

  9. Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments

    PubMed Central

    2010-01-01

    Background While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor and a similar structure; pairwise sequence alignments often fail to represent accurately the structural alignments inferred from three-dimensional coordinates. Since sequence alignment algorithms produce optimal alignments, the best structural alignments must reflect suboptimal sequence alignment scores. Thus, we have examined a range of suboptimal sequence alignments and a range of scoring parameters to understand better which sequence alignments are likely to be more structurally accurate. Results We compared near-optimal protein sequence alignments produced by the Zuker algorithm and a set of probabilistic alignments produced by the probA program with structural alignments produced by four different structure alignment algorithms. There is significant overlap between the solution spaces of structural alignments and both the near-optimal sequence alignments produced by commonly used scoring parameters for sequences that share significant sequence similarity (E-values < 10-5) and the ensemble of probA alignments. We constructed a logistic regression model incorporating three input variables derived from sets of near-optimal alignments: robustness, edge frequency, and maximum bits-per-position. A ROC analysis shows that this model more accurately classifies amino acid pairs (edges in the alignment path graph) according to the likelihood of appearance in structural alignments than the robustness score alone. We investigated various trimming protocols for removing incorrect edges from the optimal sequence alignment; the most effective protocol is to remove matches from the semi-global optimal alignment that are outside the boundaries of the local alignment, although trimming according to the model-generated probabilities achieves a similar level of improvement. The model can also be used to

  10. Tonal Alignment in Irish Dialects

    ERIC Educational Resources Information Center

    Dalton, Martha; Ni Chasaide, Ailbhe

    2005-01-01

    A comparison of the contour alignment of nuclear and initial prenuclear accents was carried out for the Irish dialects of Gaoth Dobhair in Ulster (GD-U) and Cois Fharraige in Connaught (CF-C). This was done across conditions where the number of unstressed syllables following the nuclear and preceding the initial prenuclear accents was varied from…

  11. Alignment in Second Language Dialogue

    ERIC Educational Resources Information Center

    Costa, Albert; Pickering, Martin; Sorace, Antonella

    2008-01-01

    This paper considers the nature of second language dialogues, involving at least one non-native (L2) speaker. We assume that dialogue is characterised by a process in which interlocutors develop similar mental states to each other (Pickering & Garrod, 2004). We first consider various means in which interlocutors align their mental states, and…

  12. 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…

  13. Laser-optic instruments improve machinery alignment

    SciTech Connect

    Bloch, H.P.

    1987-10-12

    Laser-optic alignment systems are fast becoming cost-effective devices that improve the accuracy and speed of machinery shaft alignment. Because of the difficulty, if not impossibility, of aligning operating machinery, cold alignment specifications must be determined to compensate for thermal growth so that the shaft alignment remains within tolerances when the machine reaches normal operating temperature. Some methods for accomplishing this are reviewed here. Three years' field experience with laser-optic alignment systems shows that many of these limitations can be eliminated, resulting in a more accurate alignment in less time. Some actual field alignments are given as examples of the improvement achieved by the use of laser equipment, and a procedure is given that shows how the laser-optic system may be used to determine running alignment changes caused by thermal growth.

  14. An efficient method for multiple sequence alignment

    SciTech Connect

    Kim, J.; Pramanik, S.

    1994-12-31

    Multiple sequence alignment has been a useful method in the study of molecular evolution and sequence-structure relationships. This paper presents a new method for multiple sequence alignment based on simulated annealing technique. Dynamic programming has been widely used to find an optimal alignment. However, dynamic programming has several limitations to obtain optimal alignment. It requires long computation time and cannot apply certain types of cost functions. We describe detail mechanisms of simulated annealing for multiple sequence alignment problem. It is shown that simulated annealing can be an effective approach to overcome the limitations of dynamic programming in multiple sequence alignment problem.

  15. Bokeh mirror alignment for Cherenkov telescopes

    NASA Astrophysics Data System (ADS)

    Mueller, S. A.; Adam, J.; Ahnen, M. L.; Baack, D.; Balbo, M.; Bergmann, M.; Biland, A.; Blank, M.; Bretz, T.; Bruegge, K. A.; Buss, J.; Dmytriiev, A.; Dorner, D.; Einecke, S.; Hempfling, C.; Hildebrand, D.; Hughes, G.; Linhoff, L.; Mannheim, K.; Neise, D.; Neronov, A.; Noethe, M.; Paravac, A.; Pauss, F.; Rhode, W.; Shukla, A.; Temme, F.; Thaele, J.; Walter, R.

    2016-08-01

    Segmented imaging reflectors are a great choice for Imaging Atmospheric Cherenkov Telescopes (IACTs). However, the alignment of the individual mirror facets is challenging. We align a segmented reflector by observing and optimizing its Bokeh function. Bokeh alignment can already be done with very little resources and little preparation time. Further, Bokeh alignment can be done anytime, even during the day. We present a first usage of Bokeh alignment on FACT, a 4m IACT on Canary Island La Palma, Spain and further a first Bokeh alignment test on the CTA MST IACT prototype in Brelin Adlershof.

  16. Shuttle onboard IMU alignment methods

    NASA Technical Reports Server (NTRS)

    Henderson, D. M.

    1976-01-01

    The current approach to the shuttle IMU alignment is based solely on the Apollo Deterministic Method. This method is simple, fast, reliable and provides an accurate estimate for the present cluster to mean of 1,950 transformation matrix. If four or more star sightings are available, the application of least squares analysis can be utilized. The least squares method offers the next level of sophistication to the IMU alignment solution. The least squares method studied shows that a more accurate estimate for the misalignment angles is computed, and the IMU drift rates are a free by-product of the analysis. Core storage requirements are considerably more; estimated 20 to 30 times the core required for the Apollo Deterministic Method. The least squares method offers an intermediate solution utilizing as much data that is available without a complete statistical analysis as in Kalman filtering.

  17. 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.

  18. 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.

  19. Aligning incentives in supply chains.

    PubMed

    Narayanan, V G; Raman, Ananth

    2004-11-01

    Most companies don't worry about the behavior of their supply chain partners. Instead, they expect the supply chain to work efficiently without interference, as if guided by Adam Smith's famed invisible hand. In their study of more than 50 supply networks, V.G. Narayanan and Ananth Raman found that companies often looked out for their own interests and ignored those of their network partners. Consequently, supply chains performed poorly. Those results aren't shocking when you consider that supply chains extend across several functions and many companies, each with its own priorities and goals. Yet all those functions and firms must pull in the same direction for a chain to deliver goods and services to consumers quickly and cost-effectively. According to the authors, a supply chain works well only if the risks, costs, and rewards of doing business are distributed fairly across the network. In fact, misaligned incentives are often the cause of excess inventory, stock-outs, incorrect forecasts, inadequate sales efforts, and even poor customer service. The fates of all supply chain partners are interlinked: If the firms work together to serve consumers, they will all win. However, they can do that only if incentives are aligned. Companies must acknowledge that the problem of incentive misalignment exists and then determine its root cause and align or redesign incentives. They can improve alignment by, for instance, adopting revenue-sharing contracts, using technology to track previously hidden information, or working with intermediaries to build trust among network partners. It's also important to periodically reassess incentives, because even top-performing networks find that changes in technology or business conditions alter the alignment of incentives.

  20. 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.

  1. 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.

  2. 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.

  3. Aligning Plasma-Arc Welding Oscillations

    NASA Technical Reports Server (NTRS)

    Norris, Jeff; Fairley, Mike

    1989-01-01

    Tool aids in alignment of oscillator probe on variable-polarity plasma-arc welding torch. Probe magnetically pulls arc from side to side as it moves along joint. Tensile strength of joint depends on alignment of weld bead and on alignment of probe. Operator installs new tool on front of torch body, levels it with built-in bubble glass, inserts probe in slot on tool, and locks probe in place. Procedure faster and easier and resulting alignment more accurate and repeatable.

  4. Use laser-optics for machinery alignment

    SciTech Connect

    Bloch, H.P.

    1987-10-01

    Many sources attribute most bearing overload and destructive vibration in industrial machinery to shaft misalignment. There is considerable disagreement as to the alignment quality required. There is also little agreement on suitable calculation methods and achievable accuracy for anticipated thermal growth of machinery (necessary if running alignment is to remain acceptable). This article examines existing alignment quality guidelines for relevance and consistency, and reviews the application of laser-optic alignment systems based on three years of field experience.

  5. Vertically aligned nanostructure scanning probe microscope tips

    DOEpatents

    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.

  6. 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.

  7. Aligning Two Genomic Sequences That Contain Duplications

    NASA Astrophysics Data System (ADS)

    Hou, Minmei; Riemer, Cathy; Berman, Piotr; Hardison, Ross C.; Miller, Webb

    It is difficult to properly align genomic sequences that contain intra-species duplications. With this goal in mind, we have developed a tool, called TOAST (two-way orthologous alignment selection tool), for predicting whether two aligned regions from different species are orthologous, i.e., separated by a speciation event, as opposed to a duplication event. The advantage of restricting alignment to orthologous pairs is that they constitute the aligning regions that are most likely to share the same biological function, and most easily analyzed for evidence of selection. We evaluate TOAST on 12 human/mouse gene clusters.

  8. 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.

  9. 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.

  10. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

    NASA Astrophysics Data System (ADS)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra

    2013-04-01

    In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a time gain of (70-90)% for highly similar nucleotide sequences (> 80% similarity), and (54-70)% for sequences having (30-80)% similarity. For other sequences, it terminates with an approximate score. For protein sequences, the average time gain is between (25-40)%. Compared to three heuristic global alignment methods, the quality of alignment is improved by about 23%-53%. FOGSAA is, in general, suitable for aligning any two sequences defined over a finite alphabet set, where the quality of the global alignment is of supreme importance.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.

    PubMed

    Haas, Brian J; Delcher, Arthur L; Mount, Stephen M; Wortman, Jennifer R; Smith, Roger K; Hannick, Linda I; Maiti, Rama; Ronning, Catherine M; Rusch, Douglas B; Town, Christopher D; Salzberg, Steven L; White, Owen

    2003-10-01

    The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing variations. Complete and partial gene structures identified by this method were used to improve The Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0). The alignment assemblies permitted the automated modeling of several novel genes and >1000 alternative splicing variations as well as updates (including UTR annotations) to nearly half of the approximately 27 000 annotated protein coding genes. The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.

  19. 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.

  20. 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.

  1. 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.

  2. IAIMFAST: Alignment Implementation for Manufacturing

    SciTech Connect

    Andraka, Charles E.

    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. 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.

  3. Tonal alignment in Irish dialects.

    PubMed

    Dalton, Martha; Chasaide, Ailbhe Ní

    2005-01-01

    A comparison of the contour alignment of nuclear and initial prenuclear accents was carried out for the Irish dialects of Gaoth Dobhair in Ulster (GD-U) and Cois Fharraige in Connaught (CF-C). This was done across conditions where the number of unstressed syllables following the nuclear and preceding the initial prenuclear accents was varied from 2-0. This tests a variable peak hypothesis prompted by findings for other languages, that peak timing drifts as a function of the number of syllables preceding (the prenuclear) and following (the nuclear) accent. These data also test a second hypothesis that the L*+H dominant accent of GD-U might be viewed as being underlyingly the same as the dominant H* or H*+L accent of the CF-C dialect. According to this realignment hypothesis, the difference between these Ulster and Connaught dialects lies in the way that the melodic tier is aligned to the segmental tier: GD-U would be viewed as having a delayed realization of the peak relative to the Connaught dialect. Results do not support the variable peak hypothesis for Irish, as in either dialect, the peak appeared to be rather fixed across the three conditions examined (though not necessarily identical for prenuclear and nuclear positions). The results also militate against the realignment hypothesis, which rather than providing a more simple unifying account, would greatly complicate it. One reason is that there is a peak timing difference between the nuclear and prenuclear accents of CF-C, not mirrored in GD-U. Furthermore, even if one were to limit consideration to a single (e.g., prenuclear) context, a simple realignment of the accents in one dialect does not generate the appropriate contour in the other.

  4. 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

  5. Free-space optical communication alignment system

    NASA Astrophysics Data System (ADS)

    Mariola, M.; Petruccione, F.

    2016-10-01

    Optical communication systems in free space require a coarse and fine alignment system to align the receiver and transmitter. In general a coarse alignment is not entirely accurate to transmit the laser beacon in the exact direction of the visible field of the camera. During this process, some algorithms such as the raster, spiral and raster spiral scan algorithm can be used to find the spot of the laser beacon. Applications that require to transmit data in form of polarization signals, such as quantum cryptography, requires a polarisation bases alignment system to transmit and receive the photons. In this paper we present a fine alignment system using a polarised laser beacon. The system proposed was subdivided into a coarse and fine alignment system. The coarse alignment was implemented by using the GPS to acquire the geographical position of the transmitter, receiver and a reference point. The fine alignment was achieved by using a polarised laser beacon from the receiver to the transmitter and a camera located on the transmitter side. The algorithm presented was capable of excluding the background noise. Furthermore the polarisation of the laser beacon was used to align the polarisation bases of the transmitter and the receiver.

  6. Some aspects of SR beamline alignment

    NASA Astrophysics Data System (ADS)

    Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

    2011-09-01

    Based on the Synchrotron Radiation (SR) beamline optical element-by-element alignment with analysis of the alignment results an optimized beamline alignment algorithm has been designed and developed. The alignment procedures have been designed and developed for the MAX-lab I911-4 fixed energy beamline. It has been shown that the intermediate information received during the monochromator alignment stage can be used for the correction of both monochromator and mirror without the next stages of alignment of mirror, slits, sample holder, etc. Such an optimization of the beamline alignment procedures decreases the time necessary for the alignment and becomes useful and helpful in the case of any instability of the beamline optical elements, storage ring electron orbit or the wiggler insertion device, which could result in the instability of angular and positional parameters of the SR beam. A general purpose software package for manual, semi-automatic and automatic SR beamline alignment has been designed and developed using the developed algorithm. The TANGO control system is used as the middle-ware between the stand-alone beamline control applications BLTools, BPMonitor and the beamline equipment.

  7. VIRUS spectrograph assembly and alignment procedures

    NASA Astrophysics Data System (ADS)

    Prochaska, Travis; Allen, Richard D.; Boster, Emily; DePoy, D. L.; Herbig, Benjamin; Hill, Gary J.; Lee, Hanshin; Marshall, Jennifer L.; Martin, Emily C.; Meador, William; Rheault, Jean-Philippe; Tuttle, Sarah E.; Vattiat, Brian L.

    2012-09-01

    We describe the mechanical assembly and optical alignment processes used to construct the Visual Integral-Field Replicable Unit Spectrograph (VIRUS) instrument. VIRUS is a set of 150+ optical spectrographs designed to support observations for the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX). To meet the instrument's manufacturing constraints, a production line will be set up to build subassemblies in parallel. To aid in the instrument's assembly and alignment, specialized fixtures and adjustment apparatuses have been developed. We describe the design and operations of the various optics alignment apparatuses, as well as the mirrors' alignment and bonding fixtures.

  8. Optimizing femorotibial alignment in high tibial osteotomy

    PubMed Central

    Rudan, John; Harrison, Mark; Simurda, Michael A

    Objective To study factors that affect femorotibial (F-T) alignment after valgus closing wedge tibial osteotomy. Study design A review of standardized standing radiographs. Femorotibial alignment was measured 1 year postoperatively for over- and under-correction. Changes in F–T alignment and in tibial plateau angle were measured. Setting An urban hospital and orthopedic clinic. Patients Eighty-two patients with osteoarthritis and varus femorotibial alignment underwent valgus closing wedge tibial osteotomy. Patients having a diagnosis of inflammatory arthritis or a prior osteotomy about the knee were excluded. Results A 1° wedge removed from the tibia resulted in an average correction of F–T alignment of 1.2°. A knee that had increased valgus orientation of the distal femur had a greater degree of correction, averaging 1.46° in F–T alignment per degree of tibial wedge. This resulted in excessive postoperative valgus alignment for some patients who had increased valgus tilt of the distal femur. Optimal F–T alignment of 6° to 14° of valgus occurred when the postoperative tibial inclination was 4° to 8° of valgus. Conclusions There was a trend for knees with increased valgus orientation of the distal femur to have greater correction in F–T alignment after tibial osteotomy, likely because of a greater opening up of the medial joint space during stance. Surgeons need to account for this in their preoperative planning. PMID:10526522

  9. 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.

  10. The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

    PubMed

    Jordan, Gregory; Goldman, Nick

    2012-04-01

    When detecting positive selection in proteins, the prevalence of errors resulting from misalignment and the ability of alignment filters to mitigate such errors are not well understood, but filters are commonly applied to try to avoid false positive results. Focusing on the sitewise detection of positive selection across a wide range of divergence levels and indel rates, we performed simulation experiments to quantify the false positives and false negatives introduced by alignment error and the ability of alignment filters to improve performance. We found that some aligners led to many false positives, whereas others resulted in very few. False negatives were a problem for all aligners, increasing with sequence divergence. Of the aligners tested, PRANK's codon-based alignments consistently performed the best and ClustalW performed the worst. Of the filters tested, GUIDANCE performed the best and Gblocks performed the worst. Although some filters showed good ability to reduce the error rates from ClustalW and MAFFT alignments, none were found to substantially improve the performance of PRANK alignments under most conditions. Our results revealed distinct trends in error rates and power levels for aligners and filters within a biologically plausible parameter space. With the best aligner, a low false positive rate was maintained even with extremely divergent indel-prone sequences. Controls using the true alignment and an optimal filtering method suggested that performance improvements could be gained by improving aligners or filters to reduce the prevalence of false negatives, especially at higher divergence levels and indel rates.

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

    PubMed

    Li, Yan; Gu, Leon; Kanade, Takeo

    2011-09-01

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

  12. Shear alignment of a disordered lamellar mesophase.

    PubMed

    Kumaran, V; Raman, D S S

    2011-03-01

    The shear alignment of an initially disordered lamellar phase is examined using lattice Boltzmann simulations of a mesoscopic model based on a free-energy functional for the concentration modulation. For a small shear cell of width 8λ, the qualitative features of the alignment process are strongly dependent on the Schmidt number Sc=ν/D (ratio of kinematic viscosity and mass diffusion coefficient). Here, λ is the wavelength of the concentration modulation. At low Schmidt number, it is found that there is a significant initial increase in the viscosity, coinciding with the alignment of layers along the extensional axis, followed by a decrease at long times due to the alignment along the flow direction. At high Schmidt number, alignment takes place due to the breakage and reformation of layers because diffusion is slow compared to shear deformation; this results in faster alignment. The system size has a strong effect on the alignment process; perfect alignment takes place for a small systems of width 8λ and 16λ, while a larger system of width 32λ does not align completely even at long times. In the larger system, there appears to be a dynamical steady state in which the layers are not perfectly aligned--where there is a balance between the annealing of defects due to shear and the creation due to an instability of the aligned lamellar phase under shear. We observe two types of defect creation mechanisms: the buckling instability under dilation, which was reported earlier, as well as a second mechanism due to layer compression.

  13. 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.

  14. 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.

  15. 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.…

  16. 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…

  17. 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.

  18. 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.

  19. The GEM Detector projective alignment simulation system

    SciTech Connect

    Wuest, C.R.; Belser, F.C.; Holdener, F.R.; Roeben, M.D.; Paradiso, J.A.; Mitselmakher, G.; Ostapchuk, A.; Pier-Amory, J.

    1993-07-09

    Precision position knowledge (< 25 microns RMS) of the GEM Detector muon system at the Superconducting Super Collider Laboratory (SSCL) is an important physics requirement necessary to minimize sagitta error in detecting and tracking high energy muons that are deflected by the magnetic field within the GEM Detector. To validate the concept of the sagitta correction function determined by projective alignment of the muon detectors (Cathode Strip Chambers or CSCs), the basis of the proposed GEM alignment scheme, a facility, called the ``Alignment Test Stand`` (ATS), is being constructed. This system simulates the environment that the CSCs and chamber alignment systems are expected to experience in the GEM Detector, albeit without the 0.8 T magnetic field and radiation environment. The ATS experimental program will allow systematic study and characterization of the projective alignment approach, as well as general mechanical engineering of muon chamber mounting concepts, positioning systems and study of the mechanical behavior of the proposed 6 layer CSCs. The ATS will consist of a stable local coordinate system in which mock-ups of muon chambers (i.e., non-working mechanical analogs, representing the three superlayers of a selected barrel and endcap alignment tower) are implemented, together with a sufficient number of alignment monitors to overdetermine the sagitta correction function, providing a self-consistency check. This paper describes the approach to be used for the alignment of the GEM muon system, the design of the ATS, and the experiments to be conducted using the ATS.

  20. 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…

  1. Overlay improvement by zone alignment strategy

    NASA Astrophysics Data System (ADS)

    Huang, Chun-Yen; Lee, Ai-Yi; Shih, Chiang-Lin; Yang, Richer; Yuan, Michael; Chen, Henry; Chang, Ray

    2008-03-01

    It is evident that DRAM ground rule continues to shrink down to 90nm and beyond, overlay performance has become more and more critical and important. Wafer edge shows different behavior from center by processes, e.g. a tremendous misalignment at wafer edge makes yield loss . When a conventional linear model is used for alignment correction, higher uncorrectable overlay residuals mostly happen at wafer edge. Therefore, it's obviously necessary to introduce an innovational alignment correction methdology to reduce unwanted wafer edge effect. In this study, we demonstrate the achievement of moderating poor overlay in wafer edge area by a novel zone-dependent alignment strategy, the so-called "Zone Alignment (ZA)". The main difference between the conventional linear model and zone alignment strategy is that the latter compensates an improper averaging effect from first modeling through weighting all surrounding marks with a nonlinear model. In addition, the effects of mark quantity and sampling distribution from "Zone Alignment" are also introduced in this paper. The results of this study indicate that ZA can reduce uncorrectable overlay residual and improve wafer-to-wafer variation significantly. Furthermore, obvious yield improvement is verified by ZA strategy. In conclusion, Zone alignment is the noteworthy strategy for overlay improvement. Moreover, suitable alignment map and mark numbers should be taken into consideration carefully when ZA is applied for further technology node.

  2. Alignment of Developments in Higher Education

    ERIC Educational Resources Information Center

    Cowan, John; George, Judith W.; Pinheiro-Torres, Andreia

    2004-01-01

    This study builds upon the concept of alignment within the curriculum (due to Biggs) and suggests, in the context of two current examples, an integrated methodology for effectively aligned development activities within universities. Higher Education institutions face important challenges. Firstly, quality enhancement of the curriculum is now an…

  3. 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).

  4. Optical alignment of a pupil imaging spectrometer

    NASA Technical Reports Server (NTRS)

    Horchem, Stephen D.; Kohrman, Richard J.

    1989-01-01

    The GOES Sounder is a 19-channel discrete filter spectrometer with an additional channel for star sensing. This paper presents the GOES Sounder's instrument optics and compensations, alignment rationale, and alignment mechanism and sensitivities. The results of a line of sight tolerance analysis of the instrument are described, and the prealignment and instrument coregistration are addressed.

  5. 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.

  6. 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…

  7. Alignment-free phylogenetics and population genetics.

    PubMed

    Haubold, Bernhard

    2014-05-01

    Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on comparative data, today usually DNA sequences. These have become so plentiful that alignment-free sequence comparison is of growing importance in the race between scientists and sequencing machines. In phylogenetics, efficient distance computation is the major contribution of alignment-free methods. A distance measure should reflect the number of substitutions per site, which underlies classical alignment-based phylogeny reconstruction. Alignment-free distance measures are either based on word counts or on match lengths, and I apply examples of both approaches to simulated and real data to assess their accuracy and efficiency. While phylogeny reconstruction is based on the number of substitutions, in population genetics, the distribution of mutations along a sequence is also considered. This distribution can be explored by match lengths, thus opening the prospect of alignment-free population genomics.

  8. 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.

  9. Vane segment support and alignment device

    SciTech Connect

    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.

  10. 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.

  11. 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.

  12. 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.

  13. Recursions for statistical multiple alignment

    PubMed Central

    Hein, Jotun; Jensen, Jens Ledet; Pedersen, Christian N. S.

    2003-01-01

    Algorithms are presented that allow the calculation of the probability of a set of sequences related by a binary tree that have evolved according to the Thorne–Kishino–Felsenstein model for a fixed set of parameters. The algorithms are based on a Markov chain generating sequences and their alignment at nodes in a tree. Depending on whether the complete realization of this Markov chain is decomposed into the first transition and the rest of the realization or the last transition and the first part of the realization, two kinds of recursions are obtained that are computationally similar but probabilistically different. The running time of the algorithms is \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}O({\\Pi}_{i}^{d}=1~L_{i})\\end{equation*}\\end{document}, where Li is the length of the ith observed sequences and d is the number of sequences. An alternative recursion is also formulated that uses only a Markov chain involving the inner nodes of a tree. PMID:14657378

  14. 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.

  15. Dislocation mediated alignment during metal nanoparticle coalescence

    SciTech Connect

    Lange, A. P.; Samanta, A.; Majidi, H.; Mahajan, S.; Ging, J.; Olson, T. Y.; van Benthem, K.; Elhadj, S.

    2016-09-13

    Dislocation mediated alignment processes during gold nanoparticle coalescence were studied at low and high temperatures using molecular dynamics simulations and transmission electron microscopy. Particles underwent rigid body rotations immediately following attachment in both low temperature (500 K) simulated coalescence events and low temperature (~315 K) transmission electron microscopy beam heating experiments. In many low temperature simulations, some degree of misorientation between particles remained after rigid body rotations, which was accommodated by grain boundary dislocation nodes. These dislocations were either sessile and remained at the interface for the duration of the simulation or dissociated and cross-slipped through the adjacent particles, leading to improved co-alignment. Minimal rigid body rotations were observed during or immediately following attachment in high temperature (1100 K) simulations, which is attributed to enhanced diffusion at the particles' interface. However, rotation was eventually induced by {111} slip on planes parallel to the neck groove. These deformation modes led to the formation of single and multi-fold twins whose structures depended on the initial orientation of the particles. The driving force for {111} slip is attributed to high surface stresses near the intersection of low energy {111} facets in the neck region. The details of this twinning process were examined in detail using simulated trajectories, and the results reveal possible mechanisms for the nucleation and propagation of Shockley partials on consecutive planes. Deformation twinning was also observed in-situ using transmission electron microscopy, which resulted in the co-alignment of a set of the particles' {111} planes across their grain boundary and an increase in their dihedral angle. As a result, this constitutes the first detailed experimental observation of deformation twinning during nanoparticle coalescence, validating simulation results

  16. Dislocation mediated alignment during metal nanoparticle coalescence

    DOE PAGES

    Lange, A. P.; Samanta, A.; Majidi, H.; ...

    2016-09-13

    Dislocation mediated alignment processes during gold nanoparticle coalescence were studied at low and high temperatures using molecular dynamics simulations and transmission electron microscopy. Particles underwent rigid body rotations immediately following attachment in both low temperature (500 K) simulated coalescence events and low temperature (~315 K) transmission electron microscopy beam heating experiments. In many low temperature simulations, some degree of misorientation between particles remained after rigid body rotations, which was accommodated by grain boundary dislocation nodes. These dislocations were either sessile and remained at the interface for the duration of the simulation or dissociated and cross-slipped through the adjacent particles, leadingmore » to improved co-alignment. Minimal rigid body rotations were observed during or immediately following attachment in high temperature (1100 K) simulations, which is attributed to enhanced diffusion at the particles' interface. However, rotation was eventually induced by {111} slip on planes parallel to the neck groove. These deformation modes led to the formation of single and multi-fold twins whose structures depended on the initial orientation of the particles. The driving force for {111} slip is attributed to high surface stresses near the intersection of low energy {111} facets in the neck region. The details of this twinning process were examined in detail using simulated trajectories, and the results reveal possible mechanisms for the nucleation and propagation of Shockley partials on consecutive planes. Deformation twinning was also observed in-situ using transmission electron microscopy, which resulted in the co-alignment of a set of the particles' {111} planes across their grain boundary and an increase in their dihedral angle. As a result, this constitutes the first detailed experimental observation of deformation twinning during nanoparticle coalescence, validating simulation results

  17. 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.

  18. Beam and target alignment at the National Ignition Facility using the Target Alignment Sensor (TAS)

    NASA Astrophysics Data System (ADS)

    Di Nicola, P.; Kalantar, D.; McCarville, T.; Klingmann, J.; Alvarez, S.; Lowe-Webb, R.; Lawson, J.; Datte, P.; Danforth, P.; Schneider, M.; Di Nicola, J.-M.; Jackson, J.; Orth, C.; Azevedo, S.; Tommasini, R.; Manuel, A.; Wallace, R.

    2012-10-01

    The requirements for beam and target alignment for successful ignition experiments on the National Ignition Facility (NIF) are stringent: the average of beams to the target must be within 25 μm. Beam and target alignment are achieved with the Target Alignment Sensor (TAS). The TAS is a precision optical device that is inserted into target chamber center to facilitate both beam and target alignment. It incorporates two camera views (upper/lower and side) mounted on each of two stage assemblies (jaws) to view and align the target. It also incorporates a large mirror on each of the two assemblies to reflect the alignment beams onto the upper/lower cameras for beam alignment. The TAS is located in the chamber using reference features by viewing it with two external telescope views. The two jaws are adjusted in elevation to match the desired beam and target alignment locations. For some shot setups, a sequence of TAS positions is required to achieve the full setup and alignment. In this paper we describe the TAS, the characterization of the TAS coordinates for beam and target alignment, and summarize pointing shots that demonstrate the accuracy of beam-target alignment.

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

    PubMed

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

    2015-10-05

    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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Coelostat and heliostat - Theory of alignment

    NASA Astrophysics Data System (ADS)

    Demianski, M.; Pasachoff, J. M.

    1984-06-01

    For perfectly aligned heliostats and coelostats tracking at the solar rate and half the solar rate, respectively, the solar beam has no translational motion. But, particularly in the field at eclipses, it is not possible to align heliostats and coelostats with infinite precision. The authors derive the effect of small misalignments on the translational motion of the beam, and give tables to allow the calculation of the accuracy to which the instruments must be mounted and adjusted to attain a desired accuracy over a given duration. Further, it is shown how to derive the necessary adjustments to improve alignment, given measurements of the tracking error.

  6. Switchable Fresnel lens based on micropatterned alignment.

    PubMed

    Wang, Xiao-Qian; Srivastava, Abhishek K; Chigrinov, Vladimir G; Kwok, Hoi-Sing

    2013-06-01

    In this Letter we disclose a method to fabricate a liquid crystal (LC) Fresnel zone lens (FZL) with higher efficiency. The LCFZL, based on alternate twisted nematic (TN) and planar aligned (PA) regions, has been prepared by means of a two-step photo-alignment process. The FZL profile for both optical regimes, i.e., in TN and PA alignment domains, generates the same focal length (f). Thus, the proposed LCFZL manifests double light intensity at the focal point and therefore offers double the efficiency of existing FZLs. Moreover, because of lower driving voltage and fast response, these elements could find application in many modern devices.

  7. 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.

  8. 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.

  9. Energy band alignment at the nanoscale

    NASA Astrophysics Data System (ADS)

    Deuermeier, Jonas; Fortunato, Elvira; Martins, Rodrigo; Klein, Andreas

    2017-01-01

    The energy band alignments at interfaces often determine the electrical functionality of a device. Along with the size reduction into the nanoscale, functional coatings become thinner than a nanometer. With the traditional analysis of the energy band alignment by in situ photoelectron spectroscopy, a critical film thickness is needed to determine the valence band offset. By making use of the Auger parameter, it becomes possible to determine the energy band alignment to coatings, which are only a few Ångström thin. This is demonstrated with experimental data of Cu2O on different kinds of substrate materials.

  10. 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

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

    PubMed

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

    2012-05-16

    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.

  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. 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.

  14. 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.

  15. Regionally Aligned Forces: Concept Viability and Implementation

    DTIC Science & Technology

    2015-03-01

    Carlisle Compendia of Collaborative Research United States Army War College Student Publications Regionally Aligned Forces: Concept Viability and...Concept Viability and Implementation 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER...Carlisle Compendia of Collaborative Research United States Army War College Student Publications Regionally Aligned Forces: Concept Viability and

  16. 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.

  17. Control rod housing alignment and repair method

    SciTech Connect

    Dixon, R.C.; Deaver, G.A.; Punches, J.R.; Singleton, G.E.; Erbes, J.G.; Offer, H.P.

    1992-04-07

    This patent describes a method for underwater welding of a control rod drive housing inserted through a stub tube to maintain requisite alignment and elevation of the top of the control rod drive housing to an overlying and corresponding aperture in a core plate as measured by an alignment device which determines the relative elevation and angularity with respect to the aperture. It comprises providing a welding cylinder dependent from the alignment device such that the elevation of the top of the welding cylinder is in a fixed relationship to the alignment device and is gas-proof; pressurizing the welding cylinder with inert welding gas sufficient to maintain the interior of the welding cylinder dry; lowering the welding cylinder through the aperture in the core plate by depending the cylinder with respect to the alignment device, the lowering including lowering through and adjusting the elevation relationship of the welding cylinder to the alignment device such that when the alignment device is in position to measure the elevation and angularity of the new control rod drive housing, the lower distal end of the welding cylinder extends below the upper periphery of the stub where welding is to occur; inserting a new control rod drive housing through the stub tube and positioning the control rod drive housing to a predetermined relationship to the anticipated final position of the control rod drive housing; providing welding implements transversely rotatably mounted interior of the welding cylinder relative to the alignment device such that the welding implements may be accurately positioned for dispensing weldment around the periphery of the top of the stub tube and at the side of the control rod drive housing; measuring the elevation and angularity of the control rod drive housing; and dispensing weldment along the top of the stub tube and at the side of the control rod drive housing.

  18. Molecular focusing and alignment with plasmon fields.

    PubMed

    Artamonov, Maxim; Seideman, Tamar

    2010-12-08

    We show the possibility of simultaneously aligning molecules and focusing their center-of-mass motion near a metal nanoparticle in the field intensity gradient created by the surface plasmon enhancement of incident light. The rotational motion is described quantum mechanically while the translation is treated classically. The effects of the nanoparticle shape on the alignment and focusing are explored. Our results carry interesting implications to the field of molecular nanoplasmonics and suggest several potential applications in nanochemistry.

  19. A Tracker Alignment Framework for Augmented Reality

    DTIC Science & Technology

    2003-01-01

    A Tracker Alignment Framework for Augmented Reality Yohan Baillot and Simon J. Julier ITT Advanced Engineering & Sciences 2560 Huntington Ave...with as few as three measurements. 1. Introduction Almost all Augmented Reality (AR) systems use a track- ing system to capture motion of objects in...DATES COVERED 00-00-2003 to 00-00-2003 4. TITLE AND SUBTITLE A Tracker Alignment Framework for Augmented Reality 5a. CONTRACT NUMBER 5b. GRANT

  20. Differential Heating of Magnetically Aligned Dust Grains

    NASA Astrophysics Data System (ADS)

    Vaillancourt, John E.; Andersson, B.

    2013-01-01

    We use far-infrared photometric maps from IRAS and Herschel to search for the differential heating of asymmetric dust grains aligned with respect to an interstellar magnetic field and heated by a localized radiation source. The grains are known to be asymmetric and have a net alignment of their axes from observations of background starlight polarization. Modern theories on grain alignment suggest that photons from stars embedded in the foreground cloud are a key ingredient of the physical mechanism responsible for alignment (i.e., radiative torques). This theory predicts a relation between the grain alignment efficiency and the angle between the magnetic field and the direction to the aligning radiation source. This effect has been tentatively observed in a source with a very simple geometry (Andersson et al. 2011): the aligning photons are primarily from a single localized source (i.e., a single star) and the local magnetic field direction is known to be fairly uniform. Such a region also has consequences for the distribution of grain heating. For example, asymmetric grains whose largest cross-sections are normal to the incident stellar radiation will reach warmer equilibrium temperatures compared to grains whose largest cross-section is parallel to that direction. This should be observed as an azimuthal dependence of the dust color temperature. We present evidence of such a dependence using IRAS data at 60 and 100 micron. We expect this effect to be stronger using longer wavelength (i.e., 160 micron) data better coupled to the "big-grain" dust population, grains which are also more efficiently aligned with the local magnetic field. Here we also present the results of our on-going work to search for this signal using Herschel maps towards three candidate stars.

  1. Unconventional High Density Vertically Aligned Conducting Polymer

    DTIC Science & Technology

    2014-08-21

    electrodes with unique and controlled nano-morphologies: highly aligned carbon nanotubes (A-CNT) and graphene. This program also developed the...highly aligned carbon nanotubes forests (A-CNTs) and graphene. As synthesized A- CNTs have low volume fraction of CNT (~ 1 %). Traditional method to... nanotubes (A-CNTs). In contract to the electric double layer capacitors (EDLC) which store charges on the surface of the electrodes, conducting

  2. Alignment of photoions far from threshold

    NASA Astrophysics Data System (ADS)

    Das, Romith; Wu, Chuanyong; Mihill, A. G.; Poliakoff, E. D.; Wang, Kwanghsi; McKoy, V.

    1994-09-01

    We present results of measurements and calculations of the alignment for CO+(B 2Σ+) photoions over an extended energy range (0≤Ek≤210 eV). The polarization of CO+(B 2Σ+→X 2Σ+) fluorescence indicates that the photoions retain significant alignment even at high energies. Agreement between the measured and calculated polarization of the fluorescence is excellent.

  3. Orthodontics Align Crooked Teeth and Boost Self-Esteem

    MedlinePlus

    ... desktop! more... Orthodontics Align Crooked Teeth and Boost Self- esteem Article Chapters Orthodontics Align Crooked Teeth and Boost Self- esteem Orthodontics print full article print this chapter email ...

  4. Uniaxially aligned nanofibrous cylinders by electrospinning.

    PubMed

    Jana, Soumen; Cooper, Ashleigh; Ohuchi, Fumio; Zhang, Miqin

    2012-09-26

    Aligned nanofibers have drawn increasing interest for applications in biomedical engineering, electronics, and energy storage systems owing to the unique physicochemical properties provided by their anisotropy and high surface-to-volume ratio. Nevertheless, direct fabrication or assembly of aligned nanofibers into a 3-dimensional standalone construct with practically applicable dimensions presents an enormous challenge. We report a facile method to fabricate aligned nanofibrous cylinders, a widely used geometric form, by electrospinning aligned nanofibers across the gap between a pair of pin electrodes placed apart uniaxially. With this approach, cylindrical nanofibrous constructs of several millimeters in diameter and several centimeters in length can be readily produced. The versatility of the approach was demonstrated with several commonly used polymeric and ceramic materials, including polycaprolactone (PCL), chitosan/PCL, polyvinylidene fluoride, and titania. For a model application in tissue engineering, skeletal muscle cells were cultured on nanofibrous cylinders, which effectively produced highly aligned and densely populated myotubes along the nanofiber orientation, favorable for muscle tissue regeneration. With high structural integrity and stability, these can be directly integrated into devices or implanted in vivo as a standalone construct without the support of a substrate, thus increasing the portability, efficiency, and applicability of aligned nanofibers.

  5. DALIX: optimal DALI protein structure alignment.

    PubMed

    Wohlers, Inken; Andonov, Rumen; Klau, Gunnar W

    2013-01-01

    We present a mathematical model and exact algorithm for optimally aligning protein structures using the DALI scoring model. This scoring model is based on comparing the interresidue distance matrices of proteins and is used in the popular DALI software tool, a heuristic method for protein structure alignment. Our model and algorithm extend an integer linear programming approach that has been previously applied for the related, but simpler, contact map overlap problem. To this end, we introduce a novel type of constraint that handles negative score values and relax it in a Lagrangian fashion. The new algorithm, which we call DALIX, is applicable to any distance matrix-based scoring scheme. We also review options that allow to consider fewer pairs of interresidue distances explicitly because their large number hinders the optimization process. Using four known data sets of varying structural similarity, we compute many provably score-optimal DALI alignments. This allowed, for the first time, to evaluate the DALI heuristic in sound mathematical terms. The results indicate that DALI usually computes optimal or close to optimal alignments. However, we detect a subset of small proteins for which DALI fails to generate any significant alignment, although such alignments do exist.

  6. Orthodontic Tooth Movement with Clear Aligners

    PubMed Central

    Drake, Carl T.; McGorray, Susan P.; Dolce, Calogero; Nair, Madhu; Wheeler, Timothy T.

    2012-01-01

    Clear aligners provide a convenient model to measure orthodontic tooth movement (OTM). We examined the role of in vivo aligner material fatigue and subject-specific factors in tooth movement. Fifteen subjects seeking orthodontic treatment at the University of Florida were enrolled. Results were compared with data previously collected from 37 subjects enrolled in a similar protocol. Subjects were followed prospectively for eight weeks. An upper central incisor was programmed to move 0.5 mm. every two weeks using clear aligners. A duplicate aligner was provided for the second week of each cycle. Weekly polyvinyl siloxane (PVS) impressions were taken, and digital models were fabricated to measure OTM. Initial and final cone beam computed tomography (CBCT) images were obtained to characterize OTM. Results were compared to data from a similar protocol, where subjects received a new aligner biweekly. No significant difference was found in the amount of OTM between the two groups, with mean total OTM of 1.11 mm. (standard deviation (SD) 0.30) and 1.07 mm. (SD 0.33) for the weekly aligner and biweekly control groups, respectively (P = 0.72). Over eight weeks, in two-week intervals, material fatigue does not play a significant role in the rate or amount of tooth movement. PMID:22928114

  7. Observational Evidence for Radiative Interstellar Grain Alignment

    NASA Astrophysics Data System (ADS)

    Andersson, B.; Potter, S. B.; Andersson, B.; Potter, S.

    2011-11-01

    The alignment mechanisms of interstellar dust grains is a long standing astrophysical problem. Interstellar polarization was first discovered in 1949 and soon thereafter attributed to dichroic extinction caused by asymmetric dust grains aligned with the magnetic field. For a long time the alignment mechanism was thought to involve paramagnetic relaxation in rapidly spinning dust grains. Modern theory indicates that the classical alignment mechanisms are likely not efficient, but rather favor alignment through direct radiative torques. We have used multi-band polarimetry towards stars probing six nearby clouds to show that the wavelength of maximum polarization is linearly correlated with the visual extinction (Andersson & Potter 2007; AP07; where further details can be found). We find a universal relation with a common positive slope between the clouds and a DC offset correlated with the average of the total-to-selective extinction < RV > . These results provide strong observational support for radiatively driven grain alignment. Recent observations of an additional set of ≍60 sightlines in the Taurus cloud confirm and strengthen these results.

  8. 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.

  9. Mango: multiple alignment with N gapped oligos.

    PubMed

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2008-06-01

    Multiple sequence alignment is a classical and challenging task. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state-of-the-art works suffer from the "once a gap, always a gap" phenomenon. Is there a radically new way to do multiple sequence alignment? In this paper, we introduce a novel and orthogonal multiple sequence alignment method, using both multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole and tries to build the alignment vertically, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds have proved significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks, showing that MANGO compares favorably, in both accuracy and speed, against state-of-the-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, ProbConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0, and Kalign 2.0. We have further demonstrated the scalability of MANGO on very large datasets of repeat elements. MANGO can be downloaded at http://www.bioinfo.org.cn/mango/ and is free for academic usage.

  10. Laser alignment of rotating equipment at PNL

    SciTech Connect

    Berndt, R.H.

    1994-05-01

    Lateral vibration in direct-drive equipment is usually caused by misalignment. Over the years, because of the need to improve on techniques and ways of working more efficiently, various types of alignment methods have evolved. In the beginning, craftsmen used a straight-edge scale across the coupling with a feeler gauge measuring the misalignment error. This is still preferred today for aligning small couplings. The industry has since decided that alignment of large direct-drive equipment needed a more accurate type of instrumentation. Rim and face is another of the first alignment methods and is used on all sizes of equipment. A disadvantage of the rim and face method is that in most cases the coupling has to be disassembled. This can cause alignment problems when the coupling is reassembled. Also, the rim and face method is not fast enough to work satisfactorily on alignment of thermally hot equipment. Another concern is that the coupling has to be manufactured accurately for correct rim and face readings. Reverse dial alignment is an improvement over the rim and face method, and depending on the operator`s experience, this method can be very accurate. A good training program along with field experience will bring the operator to a proper level of proficiency for a successful program. A hand-held computer with reverse dial calculations in memory is a must for job efficiency. An advantage over the rim and face method is that the coupling is not disassembled and remains locked together. Reverse dial instrumentation measures from both shaft center lines, rather than the coupling surface so the machining of the coupling during manufacture is not a major concern.

  11. 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.

  12. Alignment of voids in the cosmic web

    NASA Astrophysics Data System (ADS)

    Platen, Erwin; van de Weygaert, Rien; Jones, Bernard J. T.

    2008-06-01

    We investigate the shapes and mutual alignment of voids in the large-scale matter distribution of a Λ cold dark matter (ΛCDM) cosmology simulation. The voids are identified using the novel watershed void finder (WVF) technique. The identified voids are quite non-spherical and slightly prolate, with axis ratios in the order of c:b:a ~ 0.5:0.7:1. Their orientations are strongly correlated with significant alignments spanning scales >30h-1Mpc. We also find an intimate link between the cosmic tidal field and the void orientations. Over a very wide range of scales we find a coherent and strong alignment of the voids with the tidal field computed from the smoothed density distribution. This orientation-tide alignment remains significant on scales exceeding twice the typical void size, which shows that the long-range external field is responsible for the alignment of the voids. This confirms the view that the large-scale tidal force field is the main agent for the large-scale spatial organization of the cosmic web.

  13. 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.

  14. 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).

  15. FRESCO: flexible alignment with rectangle scoring schemes.

    PubMed

    Dalca, A V; Brudno, M

    2008-01-01

    While the popular DNA sequence alignment tools incorporate powerful heuristics to allow for fast and accurate alignment of DNA, most of them still optimize the classical Needleman Wunsch scoring scheme. The development of novel scoring schemes is often hampered by the difficulty of finding an optimizing algorithm for each non-trivial scheme. In this paper we define the broad class of rectangle scoring schemes, and describe an algorithm and tool that can align two sequences with an arbitrary rectangle scoring scheme in polynomial time. Rectangle scoring schemes encompass some of the popular alignment scoring metrics currently in use, as well as many other functions. We investigate a novel scoring function based on minimizing the expected number of random diagonals observed with the given scores and show that it rivals the LAGAN and Clustal-W aligners, without using any biological or evolutionary parameters. The FRESCO program, freely available at http://compbio.cs.toronto.edu/fresco, gives bioinformatics researchers the ability to quickly compare the performance of other complex scoring formulas without having to implement new algorithms to optimize them.

  16. Leveraging FPGAs for Accelerating Short Read Alignment.

    PubMed

    Arram, James; Kaplan, Thomas; Luk, Wayne; Jiang, Peiyong

    2016-02-29

    One of the key challenges facing genomics today is how to efficiently analyse the massive amounts of data produced by next-generation sequencing platforms. With general-purpose computing systems struggling to address this challenge, specialised processors such as the Field-Programmable Gate Array (FPGA) are receiving growing interest. The means by which to leverage this technology for accelerating genomic data analysis is however largely unexplored. In this paper we present a runtime reconfigurable architecture for accelerating short read alignment using FPGAs. This architecture exploits the reconfigurability of FPGAs to allow the development of fast yet flexible alignment designs. We apply this architecture to develop an alignment design which supports exact and approximate alignment with up to 2 mismatches. Our design is based on the FM-index, with optimisations to improve the alignment performance. In particular, the n-step FM-index, index oversampling, a seedand- compare stage, and bi-directional backtracking are included. Our design is implemented and evaluated on a 1U Maxeler MPC-X2000 dataflow node with 8 Altera Stratix-V FPGAs. Measurements show that our design is 28 times faster than Bowtie2 running with 16 threads on dual Intel Xeon E5-2640 CPUs, and 9 times faster than Soap3-dp running on an NVIDIA Tesla C2070 GPU.

  17. Multiple alignment tensors from a denatured protein.

    PubMed

    Gebel, Erika B; Ruan, Ke; Tolman, Joel R; Shortle, David

    2006-07-26

    The structural content of the denatured state has yet to be fully characterized. In recent years, large residual dipolar couplings (RDCs) from denatured proteins have been observed under alignment conditions produced by bicelles and strained polyacrylamide gels. In this report, we describe efforts to extend our picture of the residual structure in denatured nuclease by measuring RDCs with multiple alignment tensors. Backbone amide 15N-1H RDCs were collected from 4 M urea for a total of eight RDC data sets. The RDCs were analyzed by singular value decomposition (SVD) to determine the number of independent alignment tensors present in the data. On the basis of the resultant singular values and propagated error estimates, it is clear that there are at least three independent alignment tensors. These three independent RDC datasets can be reconstituted as orthogonal linear combinations, (OLC)-RDC datasets, of the eight actually recorded. The first, second, and third OLC-RDC datasets are highly robust to the removal of any single experimental RDC dataset, establishing the presence of three independent alignment tensors, sampled well above the level of experimental uncertainty. The observation that the RDC data span three or more dimensions of the five-dimensional parameter space demonstrates that the ensemble average structure of denatured nuclease must be asymmetric with respect to these three orthogonal principal axes, which is not inconsistent with earlier work demonstrating that it has a nativelike topology.

  18. 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.

  19. 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.

  20. 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…

  1. TM-align: a protein structure alignment algorithm based on the TM-score

    PubMed Central

    Zhang, Yang; Skolnick, Jeffrey

    2005-01-01

    We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is ∼4 times faster than CE and 20 times faster than DALI and SAL. On average, the resulting structure alignments have higher accuracy and coverage than those provided by these most often-used methods. TM-align is applied to an all-against-all structure comparison of 10 515 representative protein chains from the Protein Data Bank (PDB) with a sequence identity cutoff <95%: 1996 distinct folds are found when a TM-score threshold of 0.5 is used. We also use TM-align to match the models predicted by TASSER for solved non-homologous proteins in PDB. For both folded and misfolded models, TM-align can almost always find close structural analogs, with an average root mean square deviation, RMSD, of 3 Å and 87% alignment coverage. Nevertheless, there exists a significant correlation between the correctness of the predicted structure and the structural similarity of the model to the other proteins in the PDB. This correlation could be used to assist in model selection in blind protein structure predictions. The TM-align program is freely downloadable at . PMID:15849316

  2. 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…

  3. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

    PubMed Central

    Dowell, Robin D; Eddy, Sean R

    2006-01-01

    Background We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. Results We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. Conclusion Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses. PMID:16952317

  4. 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…

  5. Alignment of Standards and Assessments as an Accountability Criterion.

    ERIC Educational Resources Information Center

    La Marca, Paul M.

    2001-01-01

    Provides an overview of the concept of alignment and the role it plays in assessment and accountability systems. Discusses some methodological issues affecting the study of alignment and explores the relationship between alignment and test score interpretation. Alignment is not only a methodological requirement but also an ethical requirement.…

  6. Inexact Local Alignment Search over Suffix Arrays.

    PubMed

    Ghodsi, Mohammadreza; Pop, Mihai

    2009-11-01

    We describe an algorithm for finding approximate seeds for DNA homology searches. In contrast to previous algorithms that use exact or spaced seeds, our approximate seeds may contain insertions and deletions. We present a generalized heuristic for finding such seeds efficiently and prove that the heuristic does not affect sensitivity. We show how to adapt this algorithm to work over the memory efficient suffix array with provably minimal overhead in running time.We demonstrate the effectiveness of our algorithm on two tasks: whole genome alignment of bacteria and alignment of the DNA sequences of 177 genes that are orthologous in human and mouse. We show our algorithm achieves better sensitivity and uses less memory than other commonly used local alignment tools.

  7. MAPPER alignment sensor evaluation on process wafers

    NASA Astrophysics Data System (ADS)

    Vergeer, N.; Lattard, L.; de Boer, G.; Couweleers, F.; Dave, D.; Pradelles, J.; Bustos, J.

    2013-03-01

    MAPPER Lithography is developing a maskless lithography technology based on massively-parallel electron-beam writing. In order to reduce costs and to minimize the footprint of this tool a new alignment sensor has been developed; based on technologies used for DVD optical heads. A wafer with an alignment mark is scanned with the sensor, resulting in an intensity pattern versus position. From this pattern the mark position can be calculated. Evaluations have been made over the performance of this type of sensor using different mark designs at several lithography process steps for FEOL and BEOL manufacturing. It has been shown that sub-nanometer reproducibility (3σ std) of alignment mark readings can be achieved while being robust against various process steps.

  8. 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.

  9. Mechanical alignment of substrates to a mask

    SciTech Connect

    Webb, Aaron P.; Carlson, Charles T.; Honan, Michael; Amato, Luigi G.; Grant, Christopher Neil; Strassner, James D.

    2016-11-08

    A plurality of masks is attached to the underside of a mask frame. This attachment is made such that each mask can independently move relative to the mask frame in three directions. This relative movement allows each mask to adjust its position to align with respective alignment pins disposed on a working surface. In one embodiment, each mask is attached to the mask frame using fasteners, where the fasteners have a shaft with a diameter smaller than the diameter of the mounting hole disposed on the mask. A bias element may be used to allow relative movement between the mask and the mask frame in the vertical direction. Each mask may also have kinematic features to mate with the respective alignment pins on the working surface.

  10. Alignment method for spectrograms of DNA sequences.

    PubMed

    Bucur, Anca; van Leeuwen, Jasper; Dimitrova, Nevenka; Mittal, Chetan

    2010-01-01

    DNA spectrograms express the periodicities of each of the four nucleotides A, T, C, and G in one or several genomic sequences to be analyzed. DNA spectral analysis can be applied to systematically investigate DNA patterns, which may correspond to relevant biological features. As opposed to looking at nucleotide sequences, spectrogram analysis may detect structural characteristics in very long sequences that are not identifiable by sequence alignment. Alignment of DNA spectrograms can be used to facilitate analysis of very long sequences or entire genomes at different resolutions. Standard clustering algorithms have been used in spectral analysis to find strong patterns in spectra. However, as they use a global distance metric, these algorithms can only detect strong patterns coexisting in several frequencies. In this paper, we propose a new method and several algorithms for aligning spectra suitable for efficient spectral analysis and allowing for the easy detection of strong patterns in both single frequencies and multiple frequencies.

  11. 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

  12. High-harmonic spectroscopy of aligned molecules

    NASA Astrophysics Data System (ADS)

    Yun, Hyeok; Yun, Sang Jae; Lee, Gae Hwang; Nam, Chang Hee

    2017-01-01

    High harmonics emitted from aligned molecules driven by intense femtosecond laser pulses provide the opportunity to explore the structural information of molecules. The field-free molecular alignment technique is an expedient tool for investigating the structural characteristics of linear molecules. The underlying physics of field-free alignment, showing the characteristic revival structure specific to molecular species, is clearly explained from the quantum-phase analysis of molecular rotational states. The anisotropic nature of molecules is shown from the harmonic polarization measurement performed with spatial interferometry. The multi-orbital characteristics of molecules are investigated using high-harmonic spectroscopy, applied to molecules of N2 and CO2. In the latter case the two-dimensional high-harmonic spectroscopy, implemented using a two-color laser field, is applied to distinguish harmonics from different orbitals. Molecular high-harmonic spectroscopy will open a new route to investigate ultrafast dynamics of molecules.

  13. 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.

  14. Identifying subset errors in multiple sequence alignments.

    PubMed

    Roy, Aparna; Taddese, Bruck; Vohra, Shabana; Thimmaraju, Phani K; Illingworth, Christopher J R; Simpson, Lisa M; Mukherjee, Keya; Reynolds, Christopher A; Chintapalli, Sree V

    2014-01-01

    Multiple sequence alignment (MSA) accuracy is important, but there is no widely accepted method of judging the accuracy that different alignment algorithms give. We present a simple approach to detecting two types of error, namely block shifts and the misplacement of residues within a gap. Given a MSA, subsets of very similar sequences are generated through the use of a redundancy filter, typically using a 70-90% sequence identity cut-off. Subsets thus produced are typically small and degenerate, and errors can be easily detected even by manual examination. The errors, albeit minor, are inevitably associated with gaps in the alignment, and so the procedure is particularly relevant to homology modelling of protein loop regions. The usefulness of the approach is illustrated in the context of the universal but little known [K/R]KLH motif that occurs in intracellular loop 1 of G protein coupled receptors (GPCR); other issues relevant to GPCR modelling are also discussed.

  15. 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.

  16. On the alignment for precession electron diffraction

    PubMed Central

    Liao, Yifeng; Marks, Laurence D.

    2013-01-01

    Precession electron diffraction has seen a fast increase in its adoption as a technique for solving crystallographic structures as well as an alternative to conventional selected-area and converged-beam diffraction methods. One of the key issues of precession is the pivot point alignment, as a stationary apparent beam does not guarantee a fixed pivot point. A large precession tilt angle, along with pre-field and post-field misalignment, induces shift in the image plane. We point out here that the beam should be aligned to the pre-field optic axis to keep the electron illumination stationary during the rocking process. A practical alignment procedure is suggested with the focus placed on minimizing the beam wandering on the specimen, and is demonstrated for a (110)-oriented silicon single crystal and for a carbide phase (~20 nm in size) within a cast cobalt–chromium–molybdenum alloy. PMID:22634134

  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. System and method for 2D workpiece alignment

    DOEpatents

    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.

  19. A Unified Model of Grain Alignment: Radiative Alignment of Interstellar Grains with Magnetic Inclusions

    NASA Astrophysics Data System (ADS)

    Hoang, Thiem; Lazarian, A.

    2016-11-01

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

  20. 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.

  1. Two Hybrid Algorithms for Multiple Sequence Alignment

    NASA Astrophysics Data System (ADS)

    Naznin, Farhana; Sarker, Ruhul; Essam, Daryl

    2010-01-01

    In order to design life saving drugs, such as cancer drugs, the design of Protein or DNA structures has to be accurate. These structures depend on Multiple Sequence Alignment (MSA). MSA is used to find the accurate structure of Protein and DNA sequences from existing approximately correct sequences. To overcome the overly greedy nature of the well known global progressive alignment method for multiple sequence alignment, we have proposed two different algorithms in this paper; one is using an iterative approach with a progressive alignment method (PAMIM) and the second one is using a genetic algorithm with a progressive alignment method (PAMGA). Both of our methods started with a "kmer" distance table to generate single guide-tree. In the iterative approach, we have introduced two new techniques: the first technique is to generate Guide-trees with randomly selected sequences and the second is of shuffling the sequences inside that tree. The output of the tree is a multiple sequence alignment which has been evaluated by the Sum of Pairs Method (SPM) considering the real value data from PAM250. In our second GA approach, these two techniques are used to generate an initial population and also two different approaches of genetic operators are implemented in crossovers and mutation. To test the performance of our two algorithms, we have compared these with the existing well known methods: T-Coffee, MUSCEL, MAFFT and Probcon, using BAliBase benchmarks. The experimental results show that the first algorithm works well for some situations, where other existing methods face difficulties in obtaining better solutions. The proposed second method works well compared to the existing methods for all situations and it shows better performance over the first one.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Electrospinning of continuous aligned polymer fibers

    NASA Astrophysics Data System (ADS)

    Sundaray, Bibekananda; Subramanian, V.; Natarajan, T. S.; Xiang, Rong-Zheng; Chang, Chia-Cheng; Fann, Wun-Shain

    2004-02-01

    Electrospinning is a technique employed for preparing polymer fibers having diameters in the range of 10 μm-10 nm using high electrostatic field. In this letter, we report the formation of aligned polymer fibers, several centimeters in length, with separation between the fibers in the range of 5-100 μm. Achieving alignment is an important step toward the exploitation of these fibers in applications. We have employed about 4500 V and a separation distance of about 1-3 cm between the electrodes. Smaller distance between electrodes, we believe, provides better control on the formation of the fibers.

  7. 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.

  8. Image Alignment and Correlation System.

    DTIC Science & Technology

    1980-07-01

    THRESHOLD VS. THRESHOLD SET THRESHOLD TO GIVE NPT POINTS SEARCH FOR PROMINENT SPATIAL FREOENCIES ANDCOMPUTE S1U, SlV , SIUV VARIABLES FORENTER N LEAST...SIU, SlV , S1UV VARIABUS FOR LEAST SQUARES Y Figurell Flow Diagram for Subroutine MEASRE -54- CCIPUrE SlUP *SIVP VARIABLES FR LEASTr SJARES Lm . -55...table to the position of maximum correlation. Subroutine SUMPAR computes UU, UV, VV, UP and VP from the partial products SIU, SlV , SlUV, SlUP and S1VP

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

    PubMed Central

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

    2015-01-01

    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

  10. Reducing beam shaper alignment complexity: diagnostic techniques for alignment and tuning

    NASA Astrophysics Data System (ADS)

    Lizotte, Todd E.

    2011-10-01

    Safe and efficient optical alignment is a critical requirement for industrial laser systems used in a high volume manufacturing environment. Of specific interest is the development of techniques to align beam shaping optics within a beam line; having the ability to instantly verify by a qualitative means that each element is in its proper position as the beam shaper module is being aligned. There is a need to reduce these types of alignment techniques down to a level where even a newbie to optical alignment will be able to complete the task. Couple this alignment need with the fact that most laser system manufacturers ship their products worldwide and the introduction of a new set of variables including cultural and language barriers, makes this a top priority for manufacturers. Tools and methodologies for alignment of complex optical systems need to be able to cross these barriers to ensure the highest degree of up time and reduce the cost of maintenance on the production floor. Customers worldwide, who purchase production laser equipment, understand that the majority of costs to a manufacturing facility is spent on system maintenance and is typically the largest single controllable expenditure in a production plant. This desire to reduce costs is driving the trend these days towards predictive and proactive, not reactive maintenance of laser based optical beam delivery systems [10]. With proper diagnostic tools, laser system developers can develop proactive approaches to reduce system down time, safe guard operational performance and reduce premature or catastrophic optics failures. Obviously analytical data will provide quantifiable performance standards which are more precise than qualitative standards, but each have a role in determining overall optical system performance [10]. This paper will discuss the use of film and fluorescent mirror devices as diagnostic tools for beam shaper module alignment off line or in-situ. The paper will also provide an overview

  11. 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…

  12. 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.

  13. 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.)

  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. 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…

  16. EST Reading Curriculum & Instruction: An Alignment Analysis

    ERIC Educational Resources Information Center

    Mohammed, Lubna Ali; Sidek, H. M.

    2015-01-01

    In order for a curriculum to achieve its goals, it is imperative that the curriculum is coherent at all levels. In order to determine the coherency of a curriculum, the alignment of its theoretical underpinning and the label of a curriculum is one of the aspects that can be examined. The purpose of the current study was to examine if the…

  17. 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…

  18. Aligned genomic data compression via improved modeling.

    PubMed

    Ochoa, Idoia; Hernaez, Mikel; Weissman, Tsachy

    2014-12-01

    With the release of the latest Next-Generation Sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing the whole genome of a human is expected to drop to a mere $1000. This milestone in sequencing history marks the era of affordable sequencing of individuals and opens the doors to personalized medicine. In accord, unprecedented volumes of genomic data will require storage for processing. There will be dire need not only of compressing aligned data, but also of generating compressed files that can be fed directly to downstream applications to facilitate the analysis of and inference on the data. Several approaches to this challenge have been proposed in the literature; however, focus thus far has been on the low coverage regime and most of the suggested compressors are not based on effective modeling of the data. We demonstrate the benefit of data modeling for compressing aligned reads. Specifically, we show that, by working with data models designed for the aligned data, we can improve considerably over the best compression ratio achieved by previously proposed algorithms. Our results indicate that the pareto-optimal barrier for compression rate and speed claimed by Bonfield and Mahoney (2013) [Bonfield JK and Mahoneys MV, Compression of FASTQ and SAM format sequencing data, PLOS ONE, 8(3):e59190, 2013.] does not apply for high coverage aligned data. Furthermore, our improved compression ratio is achieved by splitting the data in a manner conducive to operations in the compressed domain by downstream applications.

  19. Photoionization of aligned molecular excited states

    NASA Astrophysics Data System (ADS)

    Appling, J. R.; White, M. G.; Kessler, W. J.; Fernandez, R.; Poliakoff, E. D.

    1988-02-01

    Photoelectron angular distributions of several excited states of NO have been measured in an effort to better elucidate the role of alignment in resonant multiphoton excitation processes of molecules. In contrast to previous molecular REMPI measurements on NO, (2+1) angular distributions taken for low rotational levels of the E 2Σ+ (4sσ) Rydberg state of NO exhibit complex angular behavior which is characteristic of strong spatial alignment of the optically prepared levels. Photoelectron angular distributions were also found to be strongly branch and J dependent with the lowest rotational levels of the R21+S11 branch exhibiting the full anisotropy expected for an overall three-photon process. Fluorescence anisotropies extracted from complementary two-photon fluorescence angular distribution measurements reveal small, but nonzero alignment in all rotational levels with J>1/2, in contrast to the photoelectron results. Additional photoelectron angular distributions taken for (1+1) REMPI via the A 2Σ+ (3sσ), v=0 state exhibit near ``cos2θ'' distributions characteristic of photoionization of unaligned target states. The observed photoelectron data are qualitatively interpreted on the basis of the angular momentum constraints of the excitation-induced alignment and photoionization dynamics which determine the observable moments in the angular distribution.

  20. P-16 Alignment of Educational Success

    ERIC Educational Resources Information Center

    Sanchez, Jafeth; Thornton, Bill; Usinger, Janet

    2009-01-01

    This paper focuses on the concept of P-16 alignment of educational systems. At a basic level, evidence of school efforts, improved student achievement, and stakeholder support are necessary for effective accountability. The needs and benefits for stakeholders' understanding of P-16 education are addressed, particularly for educational leaders at…

  1. ON ALIGNMENT OF SUN, EARTH, AND SATELLITE

    DTIC Science & Technology

    The results are reported of an investigation of the relations among the launch parameters of an earth satellite and the time and position of alignment of the sun , the earth, and the satellite. The effects of variations of the launch conditions upon the satellite’s time of transit across the solar disc are determined. (Author)

  2. Alignment for Learning: Reorganizing Classrooms and Campuses

    ERIC Educational Resources Information Center

    Tagg, John

    2004-01-01

    Students nowadays are getting mixed messages about the meaning of education. Evidence has emerged that what colleges have been saying to students were not aligned with what colleges have been doing for students. Students found that the values that seemed to drive policy shifted from department to department, course to course, term to term. As a…

  3. Dielectric Properties of Aligned Conducting Polymers

    DTIC Science & Technology

    1991-10-01

    It has been demonstrated that aligned polyacetylene and polyaniline possess remarkably enhanced conductivities. The increase in crystallinity and...and thermal stability compared to other CPs such as polyacetylenes, polythiophenes, and polyaniline . These favorable properties and the commercial...stretch-orientation of BF4- doped PPy films electrochemically deposited at -30,C, 7 pyrrole electropolymerization at a xylene/water interface, 8 and

  4. Scalable cell alignment on optical media substrates.

    PubMed

    Anene-Nzelu, Chukwuemeka G; Choudhury, Deepak; Li, Huipeng; Fraiszudeen, Azmall; Peh, Kah-Yim; Toh, Yi-Chin; Ng, Sum Huan; Leo, Hwa Liang; Yu, Hanry

    2013-07-01

    Cell alignment by underlying topographical cues has been shown to affect important biological processes such as differentiation and functional maturation in vitro. However, the routine use of cell culture substrates with micro- or nano-topographies, such as grooves, is currently hampered by the high cost and specialized facilities required to produce these substrates. Here we present cost-effective commercially available optical media as substrates for aligning cells in culture. These optical media, including CD-R, DVD-R and optical grating, allow different cell types to attach and grow well on them. The physical dimension of the grooves in these optical media allowed cells to be aligned in confluent cell culture with maximal cell-cell interaction and these cell alignment affect the morphology and differentiation of cardiac (H9C2), skeletal muscle (C2C12) and neuronal (PC12) cell lines. The optical media is amenable to various chemical modifications with fibronectin, laminin and gelatin for culturing different cell types. These low-cost commercially available optical media can serve as scalable substrates for research or drug safety screening applications in industry scales.

  5. 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…

  6. '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

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. Image Correlation Method for DNA Sequence Alignment

    PubMed Central

    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

  12. Robust Nonnegative Patch Alignment for Dimensionality Reduction.

    PubMed

    You, Xinge; Ou, Weihua; Chen, Chun Lung Philip; Li, Qiang; Zhu, Ziqi; Tang, Yuanyan

    2015-11-01

    Dimensionality reduction is an important method to analyze high-dimensional data and has many applications in pattern recognition and computer vision. In this paper, we propose a robust nonnegative patch alignment for dimensionality reduction, which includes a reconstruction error term and a whole alignment term. We use correntropy-induced metric to measure the reconstruction error, in which the weight is learned adaptively for each entry. For the whole alignment, we propose locality-preserving robust nonnegative patch alignment (LP-RNA) and sparsity-preserviing robust nonnegative patch alignment (SP-RNA), which are unsupervised and supervised, respectively. In the LP-RNA, we propose a locally sparse graph to encode the local geometric structure of the manifold embedded in high-dimensional space. In particular, we select large p -nearest neighbors for each sample, then obtain the sparse representation with respect to these neighbors. The sparse representation is used to build a graph, which simultaneously enjoys locality, sparseness, and robustness. In the SP-RNA, we simultaneously use local geometric structure and discriminative information, in which the sparse reconstruction coefficient is used to characterize the local geometric structure and weighted distance is used to measure the separability of different classes. For the induced nonconvex objective function, we formulate it into a weighted nonnegative matrix factorization based on half-quadratic optimization. We propose a multiplicative update rule to solve this function and show that the objective function converges to a local optimum. Several experimental results on synthetic and real data sets demonstrate that the learned representation is more discriminative and robust than most existing dimensionality reduction methods.

  13. 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.

  14. Isolated digit recognition without time alignment

    NASA Astrophysics Data System (ADS)

    Gay, Jeffrey Mark

    1994-12-01

    This thesis examines methods for isolated digit recognition without using time alignment. Resource requirements for isolated word recognizers that use time alignment can become prohibitively large as the vocabulary to be classified grows. Thus, methods capable of achieving recognition rates comparable to those obtained with current methods using these techniques are needed. The goals of this research are to find feature sets for speech recognition that perform well without using time alignment, and to identify classifiers that provide good performance with these features. Using the digits from the TI46 database, baseline speaker-independent recognition rates of 95.2% for the complete speaker set and 98.1% for the male speaker set are established using dynamic time warping (DTW). This work begins with features derived from spectrograms of each digit. Based on a critical band frequency scale covering the telephone bandwidth (300-3000 Hz), these critical band energy features are classified alone and in combination with several other feature sets, with several different classifiers. With this method, there is one 'short' feature vector per word. For speaker-independent recognition using the complete speaker set and a multi-layer perceptron (MLP) classifier, a recognition rate of 92.4% is achieved. For the same classifier with the male speaker set, a recognition rate of 97.1% is achieved. For the male speaker set, there is no statistical difference between results using DTW, and those using the MLP and no time alignment. This shows that there are feature sets that may provide high recognition rates for isolated word recognition without the need for time alignment.

  15. 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.

  16. Multiple whole-genome alignments without a reference organism.

    PubMed

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

    2009-04-01

    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 six Drosophila 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.

  17. The Effect of Alignment Changes on Unilateral Transtibial Amputee’s Gait: A Systematic Review

    PubMed Central

    Jonkergouw, Niels; Prins, Maarten R.; Buis, Arjan W. P.; van der Wurff, Peter

    2016-01-01

    Introduction Prosthetic alignment, positioning of a prosthetic foot relative to a socket, is an iterative process in which an amputee’s gait is optimized through repetitive optical gait observation and induction of alignment adjustments when deviations are detected in spatiotemporal and kinematic gait parameters. An important limitation of the current prosthetic alignment approach is the subjectivity and the lack of standardized quantifiable baseline values. The purpose of this systematic review is to investigate if an optimal alignment criterion can be derived from published articles. Moreover, we investigated the effect of alignment changes on spatiotemporal, kinematic and kinetic gait parameters. Results A total of 11 studies were included, two controlled before-and-after studies and nine-interrupted time series studies. Discussion The results demonstrate that alignment changes have a predictable influence on the included kinetic parameters. However, the effect of alignment changes on spatio-temporal and kinematic gait parameters are generally unpredictable. These findings suggest that it is imperative to include kinetics in the process of dynamic prosthetic alignment. Partially this can be established by communication with the prosthetic user in terms of perceived socket comfort, but the use of measurement tools should also be considered. While current literature is not conclusive about an optimal alignment, future alignment research should focus on alignment optimisation based on kinetic outcomes. PMID:27923050

  18. Retinal pigment epithelium cell alignment on nanostructured collagen matrices.

    PubMed

    Ulbrich, Stefan; Friedrichs, Jens; Valtink, Monika; Murovski, Simo; Franz, Clemens M; Müller, Daniel J; Funk, Richard H W; Engelmann, Katrin

    2011-01-01

    We investigated attachment and migration of human retinal pigment epithelial cells (primary, SV40-transfected and ARPE-19) on nanoscopically defined, two-dimensional matrices composed of parallel-aligned collagen type I fibrils. These matrices were used non-cross-linked (native) or after riboflavin/UV-A cross-linking to study cell attachment and migration by time-lapse video microscopy. Expression of collagen type I and IV, MMP-2 and of the collagen-binding integrin subunit α(2) were examined by immunofluorescence and Western blotting. SV40-RPE cells quickly attached to the nanostructured collagen matrices and aligned along the collagen fibrils. However, they disrupted both native and cross-linked collagen matrices within 5 h. Primary RPE cells aligned more slowly without destroying either native or cross-linked substrates. Compared to primary RPE cells, ARPE-19 cells showed reduced alignment but partially disrupted the matrices within 20 h after seeding. Expression of the collagen type I-binding integrin subunit α(2) was highest in SV40-RPE cells, lower in primary RPE cells and almost undetectable in ARPE-19 cells. Thus, integrin α(2) expression levels directly correlated with the degree of cell alignment in all examined RPE cell types. Specific integrin subunit α(2)-mediated matrix binding was verified by preincubation with an α(2)-function-blocking antibody, which impaired cell adhesion and alignment to varying degrees in primary and SV40-RPE cells. Since native matrices supported extended and directed primary RPE cell growth, optimizing the matrix production procedure may in the future yield nanostructured collagen matrices serving as transferable cell sheet carriers.

  19. Statistics of interpulse radio pulsars: the key to solving the alignment/counter-alignment problem

    NASA Astrophysics Data System (ADS)

    Arzamasskiy, L. I.; Beskin, V. S.; Pirov, K. K.

    2017-04-01

    At present, there are theoretical models of radio pulsar evolution that predict both the alignment, i.e. evolution of inclination angle χ between magnetic and rotational axes to 0°, and its counter-alignment, i.e. evolution to 90°. At the same time, both models describe well the pulsar distribution on the P-dot{P} diagram. For this reason, up to now it was impossible to determine the braking mechanisms since it was rather difficult to estimate the evolution of the inclination angle based on observations. In this paper, we demonstrate that the statistics of interpulse pulsars can give us the key to solve the alignment/counter-alignment problem as the number of interpulse pulsars (having both χ ∼ 0° and χ ∼ 90°) drastically depends on the evolution of the inclination angle.

  20. 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

  1. 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

  2. ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches.

    PubMed

    Rognes, T

    2001-04-01

    There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to perform many operations in parallel. The ParAlign algorithm has been specifically designed to take advantage of this technology. The new algorithm initially exploits parallelism to perform a very rapid computation of the exact optimal ungapped alignment score for all diagonals in the alignment matrix. Then, a novel heuristic is employed to compute an approximate score of a gapped alignment by combining the scores of several diagonals. This approximate score is used to select the most interesting database sequences for a subsequent Smith-Waterman alignment, which is also parallelised. The resulting method represents a substantial improvement compared to existing heuristics. The sensitivity and specificity of ParAlign was found to be as good as Smith-Waterman implementations when the same method for computing the statistical significance of the matches was used. In terms of speed, only the significantly less sensitive NCBI BLAST 2 program was found to outperform the new approach. Online searches are available at http://dna.uio.no/search/

  3. 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.

  4. 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

  5. DKIST visible broadband imager alignment in laboratory: first results

    NASA Astrophysics Data System (ADS)

    Sekulic, Predrag; Gregory, Scott B.; Hegwer, Steve L.; Ferayorni, Andrew; Woeger, Friedrich

    2016-08-01

    The Visible Broadband Imager (VBI) Blue and Red channels are the first Daniel K. Inouye Solar Telescope (DKIST) instruments that have been aligned and tested in a laboratory. This paper describes the optical alignment method of the VBI as performed in the laboratory. The objective of this preliminary alignment is to test and validate the optical alignment method that will be used during final alignment on the telescope, to measure the VBI performances and to verify that it meets specification. The optical alignment method is defined by three major steps. The first step is realized by combining the optical and mechanical models into the Spatial Analyzer (SA) software, and extracting the data serving as target values during alignment. The second step is the mechanical alignment and allows to accurately position the optics in the instrument coordinate system by using a Coordinate Measurement Machine (CMM) arm and a theodolite. This step has led to a great initial positioning and has allowed reaching an initial wavefront error before optical alignment close to the specification. The last step, performed by interferometry, allows fine alignment to compensate the residual aberrations created by misalignment and manufacturing tolerances. This paper presents also an alignment method to compute the shifts and tilts of compensating lenses to correct the residual aberrations. This paper describes first results of the VBI instruments performances measured in the laboratory and confirm the validity of the alignment process that will be reproduced during final alignment on the telescope.

  6. Shod wear and foot alignment in clinical gait analysis.

    PubMed

    Louey, Melissa Gar Yee; Sangeux, Morgan

    2016-09-01

    Sagittal plane alignment of the foot presents challenges when the subject wears shoes during gait analysis. Typically, visual alignment is performed by positioning two markers, the heel and toe markers, aligned with the foot within the shoe. Alternatively, software alignment is possible when the sole of the shoe lies parallel to the ground, and the change in the shoe's sole thickness is measured and entered as a parameter. The aim of this technical note was to evaluate the accuracy of visual and software foot alignment during shod gait analysis. We calculated the static standing ankle angles of 8 participants (mean age: 8.7 years, SD: 2.9 years) wearing bilateral solid ankle foot orthoses (BSAFOs) with and without shoes using the visual and software alignment methods. All participants were able to stand with flat feet in both static trials and the ankle angles obtained in BSAFOs without shoes was considered the reference. We showed that the current implementation of software alignment introduces a bias towards more ankle dorsiflexion, mean=3°, SD=3.4°, p=0.006, and proposed an adjusted software alignment method. We found no statistical differences using visual alignment and adjusted software alignment between the shoe and shoeless conditions, p=0.19 for both. Visual alignment or adjusted software alignment are advised to represent foot alignment accurately.

  7. Stakeholder Alignment and Changing Geospatial Information Capabilities

    NASA Astrophysics Data System (ADS)

    Winter, S.; Cutcher-Gershenfeld, J.; King, J. L.

    2015-12-01

    Changing geospatial information capabilities can have major economic and social effects on activities such as drought monitoring, weather forecasts, agricultural productivity projections, water and air quality assessments, the effects of forestry practices and so on. Whose interests are served by such changes? Two common mistakes are assuming stability in the community of stakeholders and consistency in stakeholder behavior. Stakeholder communities can reconfigure dramatically as some leave the discussion, others enter, and circumstances shift — all resulting in dynamic points of alignment and misalignment . New stakeholders can bring new interests, and existing stakeholders can change their positions. Stakeholders and their interests need to be be considered as geospatial information capabilities change, but this is easier said than done. New ways of thinking about stakeholder alignment in light of changes in capability are presented.

  8. Optical alignment of oval graphene flakes.

    PubMed

    Mobini, E; Rahimzadegan, A; Alaee, R; Rockstuhl, C

    2017-03-15

    Patterned graphene, as an atomically thin layer, supports localized surface plasmon polaritons at mid-infrared or far-infrared frequencies. This provides a pronounced optical force/torque in addition to large optical cross sections and will make it an ideal candidate for optical manipulation. Here, we study the optical force and torque exerted by a linearly polarized plane wave on circular and oval graphene flakes (single layers of graphene). While the torque vanishes for circular flakes, the finite torque allows rotating and orienting oval flakes relative to the electric field polarization. Depending on the wavelength, the alignment is either parallel or perpendicular to the electric field vector. In our contribution, we rely on a full-wave numerical simulation and also on an analytical model that treats the graphene flakes in a dipole approximation. The presented results reveal a good level of control on the spatial alignment of graphene flakes subjected to far-infrared illumination.

  9. 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.

  10. 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.

  11. Uniformly spaced field-aligned ionization ducts

    NASA Technical Reports Server (NTRS)

    Gross, S. H.; Muldrew, D. B.

    1984-01-01

    A number of interesting cases of combination mode ducted echoes for mid- and low-latitude regions are presented that show nearly uniformly spaced multiple combination mode traces on the ionograms in the frequency range above 1 MHz. These traces suggest that a parallel system of field-aligned ducts is present. Ray tracing studies are made to determine the structure that would explain the observations using the electron density profile derivable from the vertical trace and assuming field-aligned ducts. Spacing perpendicular to the ducts is found to be as much as 70 km. Some of these parallel duct structures are found to extend to the conjugate hemisphere, possibly to the F peak.

  12. Alignment of the Fermilab D0 Detector

    SciTech Connect

    Babatunde O'Sheg Oshinowo

    2001-07-20

    The Fermilab D0 detector was used for the discovery of the top quark during Run I in 1996. It is currently being upgraded to exploit the physics potential to be presented by the Main Injector and the Tevatron Collider during Run II in the Fall of 2000. Some of the essential elements of this upgrade is the upgrade of the Solenoid Magnet, the Central Fiber Tracker, the Preshower Detectors, the Calorimeter System, and the Muon System. This paper discusses the survey and alignment of the these detectors with emphasis on the Muon detector system. The alignment accuracy is specified as better than 0.5mm. A combination of the Laser Tracker, BETS, and V-STARS systems are used for the survey.

  13. Aligning the demonstration model of CHEOPS

    NASA Astrophysics Data System (ADS)

    Bergomi, M.; Biondi, F.; Marafatto, L.; Dima, M.; Greggio, D.; Farinato, J.; Magrin, D.; Ragazzoni, R.; Viotto, V.; Gullieuszik, M.; Farisato, G.; Lessio, L.; Portaluri, E.; Munari, M.; Pagano, I.; Marinai, M.; Novi, A.; Pompei, C.; Piazza, D.; Beck, T.; Cessa, V.; Benz, W.

    2016-07-01

    CHEOPS (CHaracterizing ExOPlanets Satellite) is an ESA Small Mission, planned to be launched in mid-2018 and whose main goal is the photometric precise characterization of radii of exoplanets orbiting bright stars (V<12) already known to host planets. Given the fast-track nature of this mission, we developed a non-flying Demonstration Model, whose optics are flight representative and whose mechanics provides the same interfaces of the flight model, but is not thermally representative. In this paper, we describe CHEOPS Demonstration Model handling, integration, tests, alignment and characterization, emphasizing the verification of the uncertainties in the optical quality measurements introduced by the starlight simulator and the way the alignment and optical surfaces are measured.

  14. Evryscope Robotilter automated camera / ccd alignment system

    NASA Astrophysics Data System (ADS)

    Ratzloff, Jeff K.; Law, Nicholas M.; Fors, Octavi; Ser, Daniel d.; Corbett, Henry T.

    2016-08-01

    We have deployed a new class of telescope, the Evryscope, which opens a new parameter space in optical astronomy - the ability to detect short time scale events across the entire sky simultaneously. The system is a gigapixel-scale array camera with an 8000 sq. deg. field of view, 13 arcsec per pixel sampling, and the ability to detect objects brighter than g = 16 in each 2-minute exposure. The Evryscope is designed to find transiting exoplanets around exotic stars, as well as detect nearby supernovae and provide continuous records of distant relativistic explosions like gamma-ray-bursts. The Evryscope uses commercially available CCDs and optics; the machine and assembly tolerances inherent in the mass production of these parts introduce problematic variations in the lens / CCD alignment which degrades image quality. We have built an automated alignment system (Robotilters) to solve this challenge. In this paper we describe the Robotilter system, mechanical and software design, image quality improvement, and current status.

  15. Regional Alignment: Phase Zero Logistics Implications

    DTIC Science & Technology

    2014-05-01

    operations in OIF affected doctrinal language and organizational change in the shift from a regional aligned structure. 17John Sloan Brown, Kevlar ...26John Sloan Brown, Kevlar Legions: The Transformations of the United States Army 1989-2005 (Washington, DC: Center of Military History, 2011), 139...it remains the preeminent information age Army. To do this Force XXI incorporates a holistic approach to change. The innovative approach that we

  16. Postgrowth Microwave Treatment to Align Carbon Nanotubes

    DTIC Science & Technology

    2013-03-01

    pp. 8671–8675. [47] Chen, C. M., Chen, M., Peng, Y. W., Yu, H. W., and Chen, C. F., 2006, “High Efficiency Microwave Digestion Purification of Multi...Y. W., Lin, C. H., Chang, L. W., and Chen, C. F., 2005, “ Microwave Digestion and Acidic Treatment Procedures for the Purification of Multi-Walled...Postgrowth Microwave Treatment to Align Carbon Nanotubes J. J. Nguyen T. L. Bougher P. Pour Shahid Saeed Abadi A. Sharma George W. Woodruff School of

  17. Superposition and alignment of labeled point clouds.

    PubMed

    Fober, Thomas; Glinca, Serghei; Klebe, Gerhard; Hüllermeier, Eyke

    2011-01-01

    Geometric objects are often represented approximately in terms of a finite set of points in three-dimensional euclidean space. In this paper, we extend this representation to what we call labeled point clouds. A labeled point cloud is a finite set of points, where each point is not only associated with a position in three-dimensional space, but also with a discrete class label that represents a specific property. This type of model is especially suitable for modeling biomolecules such as proteins and protein binding sites, where a label may represent an atom type or a physico-chemical property. Proceeding from this representation, we address the question of how to compare two labeled points clouds in terms of their similarity. Using fuzzy modeling techniques, we develop a suitable similarity measure as well as an efficient evolutionary algorithm to compute it. Moreover, we consider the problem of establishing an alignment of the structures in the sense of a one-to-one correspondence between their basic constituents. From a biological point of view, alignments of this kind are of great interest, since mutually corresponding molecular constituents offer important information about evolution and heredity, and can also serve as a means to explain a degree of similarity. In this paper, we therefore develop a method for computing pairwise or multiple alignments of labeled point clouds. To this end, we proceed from an optimal superposition of the corresponding point clouds and construct an alignment which is as much as possible in agreement with the neighborhood structure established by this superposition. We apply our methods to the structural analysis of protein binding sites.

  18. 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.

  19. 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.

  20. Alignment of Liquid Crystals by Surface Gratings

    DTIC Science & Technology

    1979-10-31

    UV / ozone cleaning 30 is effective in removing traces of most organic contaminants including evapo- rated carbon films. Substrates which were UV...the substrates to short wavelength UV. Even the UV / ozone cleaning may not guarantee that substrates will be free from organic contaminants, though it...homeotropic alignment of M1313A (and the heptyl/butyl mixture) is obtained. Exposure of the DMOAP-coated quartz to the UV / ozone cleaning process for

  1. 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.

  2. Self-Aligning, Spline-Locking Fastener

    NASA Technical Reports Server (NTRS)

    Vranish, John M.

    1992-01-01

    Self-aligning, spline-locking fastener is two-part mechanism operated by robot, using one tool and simple movements. Spline nut on springloaded screw passes through mating spline fitting. Operator turns screw until vertical driving surfaces on spline nut rest against corresponding surfaces of spline fitting. Nut rides upward, drawing pieces together. Used to join two parts of structure, to couple vehicles, or to mount payload in vehicle.

  3. 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.

  4. 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.

  5. 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.

  6. Collective alignment of polar filaments by molecular motors.

    PubMed

    Ziebert, F; Vershinin, M; Gross, S P; Aranson, I S

    2009-04-01

    We study the alignment of polar biofilaments, such as microtubules and actin, subject to the action of multiple molecular motors attached simultaneously to more than one filament. Focusing on a paradigm model of only two filaments interacting with multiple motors, we were able to investigate in detail the alignment dynamics. While almost no alignment occurs in the case of a single motor, the filaments become rapidly aligned due to the collective action of the motors. Our analysis shows that the alignment time is governed by the number of bound motors and the magnitude of the motors' stepping fluctuations. We predict that the time scale of alignment is in the order of seconds, much faster than that reported for passive crosslink-induced bundling. In vitro experiments on the alignment of microtubules by multiple-motor covered beads are in qualitative agreement. We also discuss another mode of fast alignment of filaments, namely the cooperation between motors and passive crosslinks.

  7. SQUARE--determining reliable regions in sequence alignments.

    PubMed

    Tress, Michael L; Graña, Osvaldo; Valencia, Alfonso

    2004-04-12

    The Server for Quick Alignment Reliability Evaluation (SQUARE) is a Web-based version of the method we developed to predict regions of reliably aligned residues in sequence alignments. Given an alignment between a query sequence and a sequence of known structure, SQUARE is able to predict which residues are reliably aligned. The server accesses a database of profiles of sequences of known three-dimensional structures in order to calculate the scores for each residue in the alignment. SQUARE produces a graphical output of the residue profile-derived alignment scores along with an indication of the reliability of the alignment. In addition, the scores can be compared against template secondary structure, conserved residues and important sites.

  8. 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.

  9. Camber Angle Inspection for Vehicle Wheel Alignments

    PubMed Central

    Young, Jieh-Shian; Hsu, Hong-Yi; Chuang, Chih-Yuan

    2017-01-01

    This paper introduces an alternative approach to the camber angle measurement for vehicle wheel alignment. Instead of current commercial approaches that apply computation vision techniques, this study aims at realizing a micro-control-unit (MCU)-based camber inspection system with a 3-axis accelerometer. We analyze the precision of the inspection system for the axis misalignments of the accelerometer. The results show that the axes of the accelerometer can be aligned to the axes of the camber inspection system imperfectly. The calibrations that can amend these axis misalignments between the camber inspection system and the accelerometer are also originally proposed since misalignments will usually happen in fabrications of the inspection systems. During camber angle measurements, the x-axis or z-axis of the camber inspection system and the wheel need not be perfectly aligned in the proposed approach. We accomplished two typical authentic camber angle measurements. The results show that the proposed approach is applicable with a precision of ±0.015∘ and therefore facilitates the camber measurement process without downgrading the precision by employing an appropriate 3-axis accelerometer. In addition, the measured results of camber angles can be transmitted via the medium such as RS232, Bluetooth, and Wi-Fi. PMID:28165365

  10. Regular Language Constrained Sequence Alignment Revisited

    NASA Astrophysics Data System (ADS)

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

    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, Arslan [1] introduced the Regular Language Constrained Sequence Alignment Problem and proposed an O(n 2 t 4) time and O(n 2 t 2) space algorithm for solving it, where n is the length of the input strings and t is the number of states in the non-deterministic automaton, which is given as input. Chung et al. [2] proposed a faster O(n 2 t 3) time algorithm for the same problem. In this paper, we further speed up the algorithms for Regular Language Constrained Sequence Alignment by reducing their worst case time complexity bound to O(n 2 t 3/logt). 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 run time complexity in the worst case, our simulations show that both approaches are efficient in practice, especially when the input automata are dense.

  11. 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

  12. Alignment limit of the NMSSM Higgs sector

    DOE PAGES

    Carena, Marcela; Haber, Howard E.; Low, Ian; ...

    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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. Alignment limit of the NMSSM Higgs sector

    SciTech Connect

    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 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. 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.

  19. BARCHAN: Blob Alignment for Robust CHromatographic ANalysis.

    PubMed

    Couprie, Camille; Duval, Laurent; Moreaud, Maxime; Hénon, Sophie; Tebib, Mélinda; Souchon, Vincent

    2017-02-10

    Two-dimensional gas chromatography (GC×GC) plays a central role into the elucidation of complex samples. The automation of the identification of peak areas is of prime interest to obtain a fast and repeatable analysis of chromatograms. To determine the concentration of compounds or pseudo-compounds, templates of blobs are defined and superimposed on a reference chromatogram. The templates then need to be modified when different chromatograms are recorded. In this study, we present a chromatogram and template alignment method based on peak registration called BARCHAN. Peaks are identified using a robust mathematical morphology tool. The alignment is performed by a probabilistic estimation of a rigid transformation along the first dimension, and a non-rigid transformation in the second dimension, taking into account noise, outliers and missing peaks in a fully automated way. Resulting aligned chromatograms and masks are presented on two datasets. The proposed algorithm proves to be fast and reliable. It significantly reduces the time to results for GC×GC analysis.

  20. Camber Angle Inspection for Vehicle Wheel Alignments.

    PubMed

    Young, Jieh-Shian; Hsu, Hong-Yi; Chuang, Chih-Yuan

    2017-02-03

    This paper introduces an alternative approach to the camber angle measurement for vehicle wheel alignment. Instead of current commercial approaches that apply computation vision techniques, this study aims at realizing a micro-control-unit (MCU)-based camber inspection system with a 3-axis accelerometer. We analyze the precision of the inspection system for the axis misalignments of the accelerometer. The results show that the axes of the accelerometer can be aligned to the axes of the camber inspection system imperfectly. The calibrations that can amend these axis misalignments between the camber inspection system and the accelerometer are also originally proposed since misalignments will usually happen in fabrications of the inspection systems. During camber angle measurements, the x-axis or z-axis of the camber inspection system and the wheel need not be perfectly aligned in the proposed approach. We accomplished two typical authentic camber angle measurements. The results show that the proposed approach is applicable with a precision of ± 0.015 ∘ and therefore facilitates the camber measurement process without downgrading the precision by employing an appropriate 3-axis accelerometer. In addition, the measured results of camber angles can be transmitted via the medium such as RS232, Bluetooth, and Wi-Fi.

  1. 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.

  2. JWST science instrument pupil alignment measurements

    NASA Astrophysics Data System (ADS)

    Kubalak, Dave; Sullivan, Joe; Ohl, Ray; Antonille, Scott; Beaton, Alexander; Coulter, Phillip; Hartig, George; Kelly, Doug; Lee, David; Maszkiewicz, Michael; Schweiger, Paul; Telfer, Randal; Te Plate, Maurice; Wells, Martyn

    2016-09-01

    NASA's James Webb Space Telescope (JWST) is a 6.5m diameter, segmented, deployable telescope for cryogenic IR space astronomy ( 40K). The JWST Observatory architecture includes the Optical Telescope Element (OTE) and the Integrated Science Instrument Module (ISIM) element that contains four science instruments (SI), including a guider. OSIM is a full field, cryogenic, optical simulator of the JWST OTE. It is the "Master Tool" for verifying the cryogenic alignment and optical performance of ISIM by providing simulated point source/star images to each of the four Science Instruments in ISIM. Included in OSIM is a Pupil Imaging Module (PIM) - a large format CCD used for measuring pupil alignment. Located at a virtual stop location within OSIM, the PIM records superimposed shadow images of pupil alignment reference (PAR) targets located in the OSIM and SI pupils. The OSIM Pupil Imaging Module was described by Brent Bos, et al, at SPIE in 2011 prior to ISIM testing. We have recently completed the third and final ISIM cryogenic performance verification test before ISIM was integrated with the OTE. In this paper, we describe PIM implementation, performance, and measurement results.

  3. Fostering Understanding by Structural Alignment as a Route to Analogical Learning

    ERIC Educational Resources Information Center

    Mason, Lucia

    2004-01-01

    The purpose of this study was to extend previous research on the conditions that may promote understanding and abstraction via structural alignment, that is, through a comparison between two partially understood situations. Structural alignment is a route to analogical reasoning which differs from the typical route where an analogy is made by…

  4. 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…

  5. DatAlign - implementation of the new APS survey and alignment database.

    SciTech Connect

    Penicka, J. M.; Friedsam, H. W.; Accelerator Systems Division

    2004-01-01

    The Advanced Photon Source (APS) at Argonne National Laboratory is a national 3rd-generation synchrotron-radiation light source research facility located about twenty-five miles southwest of Chicago. The APS accelerator systems and X-ray beamlines are approximately six kilometers in length with more than four thousand precisely aligned components. The APS Survey and Alignment Group (SAG) is responsible for the correct positioning of beamline components for the APS accelerator systems. SAG fiducializes beamline components, aligns components in the accelerator tunnel and in the experiment hall, and maintains all necessary geodetic control networks to achieve required placement tolerances. All these tasks generate large amounts of data that have to be stored and readily accessible to the SAG members. As a result, the utilization of a database system is inevitable. During the 1990s, the SAG depended on Geonet software [1] for its data storage and management needs. Geonet was originally developed under the DOS environment at SLAC in the 1980s as an all-inclusive software package for the accelerator alignment community. After a decade of a reliable service, Geonet unavoidably became obsolete. First, some Geonet utilities, like data collection and data reduction programs, were phased out or replaced by new tools to keep up with advancements in survey and alignment technology. By the year 2002, a decision was made to also replace the database portion of Geonet with a new relational database. The conceptual design of the new APS Survey and Alignment Database [2] was completed in 2002. After a review of commercially available database management systems (DBMSs), Microsoft{reg_sign} Access 2000 was chosen for the implementation of our database design. The implementation of the new database (DB), under the name 'DatAlign,' commenced the following year.

  6. Aligned SWNT films from low-yield stress gels and their transparent electrode performance.

    PubMed

    Allen, Ranulfo; Fuller, Gerald G; Bao, Zhenan

    2013-08-14

    Carbon nanotube films are promising for transparent electrodes for solar cells and displays. Large-area alignment of the nanotubes in these films is needed to minimize the sheet resistance. We present a novel coating method to coat high-density, aligned nanotubes over large areas. Carbon nanotube gel dispersions used in this study have aligned domains and a low yield stress. A simple shearing force allows these domains to uniformly align. We use this to correlate the transparent electrode performance of single-walled carbon nanotube films with the level of partial alignment. We have found that the transparent electrode performance improves with increasing levels of alignment and in a manner slightly better than what has been previously predicted.

  7. 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.

  8. The meaning of alignment: lessons from structural diversity

    PubMed Central

    Pirovano, Walter; Feenstra, K Anton; Heringa, Jaap

    2008-01-01

    Background Protein structural alignment provides a fundamental basis for deriving principles of functional and evolutionary relationships. It is routinely used for structural classification and functional characterization of proteins and for the construction of sequence alignment benchmarks. However, the available techniques do not fully consider the implications of protein structural diversity and typically generate a single alignment between sequences. Results We have taken alternative protein crystal structures and generated simulation snapshots to explicitly investigate the impact of structural changes on the alignments. We show that structural diversity has a significant effect on structural alignment. Moreover, we observe alignment inconsistencies even for modest spatial divergence, implying that the biological interpretation of alignments is less straightforward than commonly assumed. A salient example is the GroES 'mobile loop' where sub-Ångstrom variations give rise to contradictory sequence alignments. Conclusion A comprehensive treatment of ambiguous alignment regions is crucial for further development of structural alignment applications and for the representation of alignments in general. For this purpose we have developed an on-line database containing our data and new ways of visualizing alignment inconsistencies, which can be found at . PMID:19105835

  9. 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…

  10. 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.

  11. Spatial and Kinematic Alignments between Central and Satellite Halos

    NASA Astrophysics Data System (ADS)

    Faltenbacher, A.; Jing, Y. P.; Li, Cheng; Mao, Shude; Mo, H. J.; Pasquali, Anna; van den Bosch, Frank C.

    2008-03-01

    Based on a cosmological N-body simulation, we analyze spatial and kinematic alignments of satellite halos within 6 times the virial radius of group-sized host halos (rvir). We measure three different types of spatial alignment: halo alignment between the orientation of the group central substructure (GCS) and the distribution of its satellites, radial alignment between the orientation of a satellite and the direction toward its GCS, and direct alignment between the orientation of the GCS and that of its satellites. Analogously, we use the directions of satellite velocities and probe three further types of alignment: the radial velocity alignment between the satellite velocity and the connecting line between the satellite and GCS, the halo velocity alignment between the orientation of the GCS and satellite velocities, and the autovelocity alignment between the satellite orientations and their velocities. We find that satellites are preferentially located along the major axis of the GCS within at least 6rvir (the range probed here). Furthermore, satellites preferentially point toward the GCS. The most pronounced signal is detected on small scales, but a detectable signal extends out to ~6rvir. The direct alignment signal is weaker; however, a systematic trend is visible at distances lesssim2rvir. All velocity alignments are highly significant on small scales. The halo velocity alignment is constant within 2rvir and declines rapidly beyond. The halo and the autovelocity alignments are maximal at small scales and disappear beyond 1rvir and 1.5rvir, respectively. Our results suggest that the halo alignment reflects the filamentary large-scale structure that extends far beyond the virial radii of the groups. In contrast, the main contribution to the radial alignment arises from the adjustment of the satellite orientations in the group tidal field. The projected data reveal good agreement with recent results derived from large galaxy surveys.

  12. Erasing Errors due to Alignment Ambiguity When Estimating Positive Selection

    PubMed Central

    Redelings, Benjamin

    2014-01-01

    Current estimates of diversifying positive selection rely on first having an accurate multiple sequence alignment. Simulation studies have shown that under biologically plausible conditions, relying on a single estimate of the alignment from commonly used alignment software can lead to unacceptably high false-positive rates in detecting diversifying positive selection. We present a novel statistical method that eliminates excess false positives resulting from alignment error by jointly estimating the degree of positive selection and the alignment under an evolutionary model. Our model treats both substitutions and insertions/deletions as sequence changes on a tree and allows site heterogeneity in the substitution process. We conduct inference starting from unaligned sequence data by integrating over all alignments. This approach naturally accounts for ambiguous alignments without requiring ambiguously aligned sites to be identified and removed prior to analysis. We take a Bayesian approach and conduct inference using Markov chain Monte Carlo to integrate over all alignments on a fixed evolutionary tree topology. We introduce a Bayesian version of the branch-site test and assess the evidence for positive selection using Bayes factors. We compare two models of differing dimensionality using a simple alternative to reversible-jump methods. We also describe a more accurate method of estimating the Bayes factor using Rao-Blackwellization. We then show using simulated data that jointly estimating the alignment and the presence of positive selection solves the problem with excessive false positives from erroneous alignments and has nearly the same power to detect positive selection as when the true alignment is known. We also show that samples taken from the posterior alignment distribution using the software BAli-Phy have substantially lower alignment error compared with MUSCLE, MAFFT, PRANK, and FSA alignments. PMID:24866534

  13. CSA: comprehensive comparison of pairwise protein structure alignments

    PubMed Central

    Wohlers, Inken; Malod-Dognin, Noël; Andonov, Rumen; Klau, Gunnar W.

    2012-01-01

    CSA is a web server for the computation, evaluation and comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance-based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared using a number of quality measures and intuitive visualizations. CSA brings new insight into the structural relationship of the protein pairs under investigation and is a valuable tool for studying structural similarities. It is available at http://csa.project.cwi.nl. PMID:22553365

  14. Protein Sequence Alignment Taking the Structure of Peptide Bond

    NASA Astrophysics Data System (ADS)

    Hara, Toshihide; Sato, Keiko; Ohya, Masanori

    2013-01-01

    In a previous paper1 we proposed a new method for performing pairwise alignment of protein sequences. The method, called MTRAP, achieves the highest performance compared with other alignment methods such as ClustalW22,3 on two benchmarks for alignment accuracy. In this paper, we introduce a new measure between two amino acids based on the formation of peptide bonds. The measure is implemented into MTRAP software to further improve alignment accuracy. Our alignment software is available at

  15. 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.

  16. CSA: comprehensive comparison of pairwise protein structure alignments.

    PubMed

    Wohlers, Inken; Malod-Dognin, Noël; Andonov, Rumen; Klau, Gunnar W

    2012-07-01

    CSA is a web server for the computation, evaluation and comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance-based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared using a number of quality measures and intuitive visualizations. CSA brings new insight into the structural relationship of the protein pairs under investigation and is a valuable tool for studying structural similarities. It is available at http://csa.project.cwi.nl.

  17. The influence of nanofiller alignment on transverse percolation and conductivity.

    PubMed

    Tallman, T N; Wang, K W

    2015-01-16

    Nanocomposites have unprecedented potential for conductivity-based damage identification when used as matrices in structural composites. Recent research has investigated nanofiller alignment in structural composites, but because damage identification often requires in-plane measurements, percolation and conductivity transverse to the alignment direction become crucial considerations. We herein contribute indispensable guidance to the development of nanocomposites with aligned nanofiller networks and insights into percolation trends transverse to the alignment direction by studying the influence of alignment on transverse critical volume fraction, conductivity, and rate of transition from non-percolating to percolating in three-dimensional carbon nanotube composite systems.

  18. Alignment and focus of mirrored facets of a heliosat

    DOEpatents

    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.

  19. Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism.

    PubMed

    Yu, Jia; Blom, Jochen; Sczyrba, Alexander; Goesmann, Alexander

    2017-02-21

    The introduction of next generation sequencing has caused a steady increase in the amounts of data that have to be processed in modern life science. Sequence alignment plays a key role in the analysis of sequencing data e.g. within whole genome sequencing or metagenome projects. BLAST is a commonly used alignment tool that was the standard approach for more than two decades, but in the last years faster alternatives have been proposed including RapSearch, GHOSTX, and DIAMOND. Here we introduce HAMOND, an application that uses Apache Hadoop to parallelize DIAMOND computation in order to scale-out the calculation of alignments. HAMOND is fault tolerant and scalable by utilizing large cloud computing infrastructures like Amazon Web Services. HAMOND has been tested in comparative genomics analyses and showed promising results both in efficiency and accuracy.

  20. Aligning the CMS muon chambers with the muon alignment system during an extended cosmic ray run

    NASA Astrophysics Data System (ADS)

    CMS Collaboration

    2010-03-01

    The alignment system for the muon spectrometer of the CMS detector comprises three independent subsystems of optical and analog position sensors. It aligns muon chambers with respect to each other and to the central silicon tracker. System commissioning at full magnetic field began in 2008 during an extended cosmic ray run. The system succeeded in tracking muon detector movements of up to 18 mm and rotations of several milliradians under magnetic forces. Depending on coordinate and subsystem, the system achieved chamber alignment precisions of 140-350 μm and 30-200 μrad, close to the precision requirements of the experiment. Systematic errors on absolute positions are estimated to be 340-590 μm based on comparisons with independent photogrammetry measurements.

  1. Silicon Alignment Pins: An Easy Way to Realize a Wafer-To-Wafer Alignment

    NASA Technical Reports Server (NTRS)

    Jung-Kubiak, Cecile (Inventor); Reck, Theodore (Inventor); Thomas, Bertrand (Inventor); Lin, Robert H. (Inventor); Peralta, Alejandro (Inventor); Gill, John J. (Inventor); Lee, Choonsup (Inventor); Siles, Jose V. (Inventor); Toda, Risaku (Inventor); Chattopadhyay, Goutam (Inventor)

    2016-01-01

    A silicon alignment pin is used to align successive layers of components made in semiconductor chips and/or metallic components to make easier the assembly of devices having a layered structure. The pin is made as a compressible structure which can be squeezed to reduce its outer diameter, have one end fit into a corresponding alignment pocket or cavity defined in a layer of material to be assembled into a layered structure, and then allowed to expand to produce an interference fit with the cavity. The other end can then be inserted into a corresponding cavity defined in a surface of a second layer of material that mates with the first layer. The two layers are in registry when the pin is mated to both. Multiple layers can be assembled to create a multilayer structure. Examples of such devices are presented.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Design of practical alignment device in KSTAR Thomson diagnostic

    NASA Astrophysics Data System (ADS)

    Lee, J. H.; Lee, S. H.; Yamada, I.

    2016-11-01

    The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak's Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broad wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR's Thomson scattering diagnostics.

  7. 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

  8. 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.

  9. HH jets aligned perpendicular to elephant trunks

    NASA Astrophysics Data System (ADS)

    Raga, A. C.; Lora, V.; Smith, N.

    2010-04-01

    We consider a system of outflows ejected from low mass young stars embedded in the tips of elephant trunks. We assume that these outflows have axes which are intrinsically perpendicular to the axes of the host elephant trunks. We then derive the distribution function expected for the angle between the projections of the outflow and elephant trunk axes on the plane of the sky. These distribution functions are useful for interpreting the alignments (or lack thereof) observed between HH outflow and elephant trunk axes in photoionized regions.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area

    PubMed Central

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

    Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue–residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue–residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

  15. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    PubMed

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

    Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

  16. 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.

  17. Normalized entropy measure for multimodality image alignment

    NASA Astrophysics Data System (ADS)

    Studholme, Colin; Hawkes, David J.; Hill, Derek L.

    1998-06-01

    Automated multi-modality 3D medical image alignment has been an active area of research for many years. There have been a number of recent papers proposing and investigating the use of entropy derived measures of brain image alignment. Any registration measure must allow us to choose between transformation estimates based on the similarity of images within their volume of overlap. Since 3D medical images often have a limited extent and overlap, the similarity measure for the two transformation estimates may be derived from two very different regions within the images. Direct measures of information such as the joint entropy and mutual information will therefore be a function of, not only image similarity in the region of overlap, but also of the local image content within the overlap. In this paper we present a new measure, normalized mutual information, which is simply the ratio of the sum of the marginal entropies and the joint entropy. The effect of changing overlap on current entropy measures and this normalized measure are compared using a simple image model and experiments on clinical MR-PET and MR-CT image data. Results indicate that the normalized entropy measure provides significantly improved behavior over a range of imaged fields of view.

  18. Controlled production of aligned-nanotube bundles

    NASA Astrophysics Data System (ADS)

    Terrones, M.; Grobert, N.; Olivares, J.; Zhang, J. P.; Terrones, H.; Kordatos, K.; Hsu, W. K.; Hare, J. P.; Townsend, P. D.; Prassides, K.; Cheetham, A. K.; Kroto, H. W.; Walton, D. R. M.

    1997-07-01

    Carbon nanotubes might be usefully employed in nanometre-scale engineering and electronics. Electrical conductivity measurements on the bulk material, on individual multi-walled and single-walled nanotubes and on bundles of single-walled nanotubes have revealed that they may behave as metallic, insulating or semiconducting nanowires, depending on the method of production-which controls the degree of graphitization, the helicity and the diameter. Measurements of Young's modulus show that single nanotubes are stiffer than commercial carbon fibres. Methods commonly used to generate nanotubes-carbon-arc discharge techniques, catalytic pyrolysis of hydrocarbons and condensed-phase electrolysis-generally suffer from the drawbacks that polyhedral particles are also formed and that the dimensions of the nanotubes are highly variable. Here we describe a method for generating aligned carbon nanotubes by pyrolysis of 2-amino-4,6-dichloro-s-triazine over thin films of a cobalt catalyst patterned on a silica substrate by laser etching. The use of a patterned catalyst apparently encourages the formation of aligned nanotubes. The method offers control over length (up to about 50μm) and fairly uniform diameters (30-50nm), as well as producing nanotubes in high yield, uncontaminated by polyhedral particles.

  19. 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.

  20. 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.

  1. Alignment of Tractograms As Graph Matching.

    PubMed

    Olivetti, Emanuele; Sharmin, Nusrat; Avesani, Paolo

    2016-01-01

    The white matter pathways of the brain can be reconstructed as 3D polylines, called streamlines, through the analysis of diffusion magnetic resonance imaging (dMRI) data. The whole set of streamlines is called tractogram and represents the structural connectome of the brain. In multiple applications, like group-analysis, segmentation, or atlasing, tractograms of different subjects need to be aligned. Typically, this is done with registration methods, that transform the tractograms in order to increase their similarity. In contrast with transformation-based registration methods, in this work we propose the concept of tractogram correspondence, whose aim is to find which streamline of one tractogram corresponds to which streamline in another tractogram, i.e., a map from one tractogram to another. As a further contribution, we propose to use the relational information of each streamline, i.e., its distances from the other streamlines in its own tractogram, as the building block to define the optimal correspondence. We provide an operational procedure to find the optimal correspondence through a combinatorial optimization problem and we discuss its similarity to the graph matching problem. In this work, we propose to represent tractograms as graphs and we adopt a recent inexact sub-graph matching algorithm to approximate the solution of the tractogram correspondence problem. On tractograms generated from the Human Connectome Project dataset, we report experimental evidence that tractogram correspondence, implemented as graph matching, provides much better alignment than affine registration and comparable if not better results than non-linear registration of volumes.

  2. 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.

  3. 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/.

  4. 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.

  5. Parallel sequence alignment in limited space.

    PubMed

    Grice, J A; Hughey, R; Speck, D

    1995-01-01

    Sequence comparison with affine gap costs is a problem that is readily parallelizable on simple single-instruction, multiple-data stream (SIMD) parallel processors using only constant space per processing element. Unfortunately, the twin problem of sequence alignment, finding the optimal character-by-character correspondence between two sequences, is more complicated. While the innovative O(n2)-time and O(n)-space serial algorithm has been parallelized for multiple-instruction, multiple-data stream (MIMD) computers with only a communication-time slowdown, typically O(log n), it is not suitable for hardware-efficient SIMD parallel processors with only local communication. This paper proposes several methods of computing sequence alignments with limited memory per processing element. The algorithms are also well-suited to serial implementation. The simpler algorithms feature, for an arbitrary integer L, a factor of L slowdown in exchange for reducing space requirements from O(n) to O(L square root of n) per processing element. Using this result, we describe an O(n log n) parallel time algorithm that requires O(log n) space per processing element on O(n) SIMD processing elements with only a mesh or linear interconnection network.

  6. 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

  7. Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

    PubMed Central

    Wadhwab, Gulshan; Upadhyayaa, K. C.

    2016-01-01

    The amount of data on molecular interactions is growing at an enormous pace, whereas the progress of methods for analysing this data is still lacking behind. Particularly, in the area of comparative analysis of biological networks, where one wishes to explore the similarity between two biological networks, this holds a potential problem. In consideration that the functionality primarily runs at the network level, it advocates the need for robust comparison methods. In this paper, we describe Net2Align, an algorithm for pairwise global alignment that can perform node-to-node correspondences as well as edge-to-edge correspondences into consideration. The uniqueness of our algorithm is in the fact that it is also able to detect the type of interaction, which is essential in case of directed graphs. The existing algorithm is only able to identify the common nodes but not the common edges. Another striking feature of the algorithm is that it is able to remove duplicate entries in case of variable datasets being aligned. This is achieved through creation of a local database which helps exclude duplicate links. In a pervasive computational study on gene regulatory network, we establish that our algorithm surpasses its counterparts in its results. Net2Align has been implemented in Java 7 and the source code is available as supplementary files. PMID:28356678

  8. Multiple sequence alignment with user-defined anchor points

    PubMed Central

    Morgenstern, Burkhard; Prohaska, Sonja J; Pöhler, Dirk; Stadler, Peter F

    2006-01-01

    Background Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments. Results Herein, we describe a semi-automatic version of the alignment program DIALIGN that can take pre-defined constraints into account. It is possible for the user to specify parts of the sequences that are assumed to be homologous and should therefore be aligned to each other. Our software program can use these sites as anchor points by creating a multiple alignment respecting these constraints. This way, our alignment method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. As a demonstration of how our method works, we apply our approach to genomic sequences around the Hox gene cluster and to a set of DNA-binding proteins. As a by-product, we obtain insights about the performance of the greedy algorithm that our program uses for multiple alignment and about the underlying objective function. This information will be useful for the further development of DIALIGN. The described alignment approach has been integrated into the TRACKER software system. PMID:16722533

  9. 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

  10. A New Analytic Alignment Method for a SINS.

    PubMed

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

    2015-11-04

    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.

  11. Frameshift alignment: statistics and post-genomic applications

    PubMed Central

    Frith, Martin C.; Spouge, John L.

    2014-01-01

    Motivation: The alignment of DNA sequences to proteins, allowing for frameshifts, is a classic method in sequence analysis. It can help identify pseudogenes (which accumulate mutations), analyze raw DNA and RNA sequence data (which may have frameshift sequencing errors), investigate ribosomal frameshifts, etc. Often, however, only ad hoc approximations or simulations are available to provide the statistical significance of a frameshift alignment score. Results: We describe a method to estimate statistical significance of frameshift alignments, similar to classic BLAST statistics. (BLAST presently does not permit its alignments to include frameshifts.) We also illustrate the continuing usefulness of frameshift alignment with two ‘post-genomic’ applications: (i) when finding pseudogenes within the human genome, frameshift alignments show that most anciently conserved non-coding human elements are recent pseudogenes with conserved ancestral genes; and (ii) when analyzing metagenomic DNA reads from polluted soil, frameshift alignments show that most alignable metagenomic reads contain frameshifts, suggesting that metagenomic analysis needs to use frameshift alignment to derive accurate results. Availability and implementation: The statistical calculation is available in FALP (http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/index/software.html), and giga-scale frameshift alignment is available in LAST (http://last.cbrc.jp/falp). Contact: spouge@ncbi.nlm.nih.gov or martin@cbrc.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25172925

  12. Intrinsic galaxy shapes and alignments - II. Modelling the intrinsic alignment contamination of weak lensing surveys

    NASA Astrophysics Data System (ADS)

    Joachimi, B.; Semboloni, E.; Hilbert, S.; Bett, P. E.; Hartlap, J.; Hoekstra, H.; Schneider, P.

    2013-11-01

    Intrinsic galaxy alignments constitute the major astrophysical systematic of forthcoming weak gravitational lensing surveys but also yield unique insights into galaxy formation and evolution. We build analytic models for the distribution of galaxy shapes based on halo properties extracted from the Millennium Simulation, differentiating between early- and late-type galaxies as well as central galaxies and satellites. The resulting ellipticity correlations are investigated for their physical properties and compared to a suite of current observations. The best-faring model is then used to predict the intrinsic alignment contamination of planned weak lensing surveys. We find that late-type galaxy models generally have weak intrinsic ellipticity correlations, marginally increasing towards smaller galaxy separation and higher redshift. The signal for early-type models at fixed halo mass strongly increases by three orders of magnitude over two decades in galaxy separation, and by one order of magnitude from z = 0 to z = 2. The intrinsic alignment strength also depends strongly on halo mass, but not on galaxy luminosity at fixed mass, or galaxy number density in the environment. We identify models that are in good agreement with all observational data, except that all models overpredict alignments of faint early-type galaxies. The best model yields an intrinsic alignment contamination of a Euclid-like survey between 0.5 and 10 per cent at z > 0.6 and on angular scales larger than a few arcminutes. Cutting 20 per cent of red foreground galaxies using observer-frame colours can suppress this contamination by up to a factor of 2.

  13. Alignment enhanced photoconductivity in single wall carbon nanotube films.

    PubMed

    Liu, Ye; Lu, Shaoxin; Panchapakesan, Balaji

    2009-01-21

    In this paper we report, for the first time, the alignment enhanced photoconductivity of single wall carbon nanotube films upon laser illumination. The photoconductivity exhibited an increase, decrease or even 'negative' values when the laser spot was on different positions between contact electrodes, showing a 'position' dependent photoconductivity of partially aligned films of carbon nanotubes. Photon induced charge carrier generation in single wall carbon nanotubes and subsequent charge separation across the metal-carbon nanotube contacts is believed to cause the photoconductivity changes. A net photovoltage of approximately 4 mV and a photocurrent of approximately 10 microA were produced under the laser intensity of approximately 273 mW with a quantum efficiency of approximately 7.8% in vacuum. The photocurrent was observed to be in the direction of nanotube alignment. Finally, there was a strong dependence of the polarization of the incident light on the photocurrent and the orientation of the films influenced the dynamics of the rise and fall of the photocurrent. All of these phenomena clearly have significance in the area of design and fabrication of solar cells, micro-opto-mechanical systems and photodetectors based on carbon nanotubes.

  14. Learning Deep Sharable and Structural Detectors for Face Alignment.

    PubMed

    Liu, Hao; Lu, Jiwen; Feng, Jianjiang; Zhou, Jie

    2017-04-01

    Face alignment aims at localizing multiple facial landmarks for a given facial image, which usually suffers from large variances of diverse facial expressions, aspect ratios and partial occlusions, especially when face images were captured in wild conditions. Conventional face alignment methods extract local features and then directly concatenate these features for global shape regression. Unlike these methods which cannot explicitly model the correlation of neighbouring landmarks and motivated by the fact that individual landmarks are usually correlated, we propose a deep sharable and structural detectors (DSSD) method for face alignment. To achieve this, we firstly develop a structural feature learning method to explicitly exploit the correlation of neighbouring landmarks, which learns to cover semantic information to disambiguate the neighbouring landmarks. Moreover, our model selectively learns a subset of sharable latent tasks across neighbouring landmarks under the paradigm of the multi-task learning framework, so that the redundancy information of the overlapped patches can be efficiently removed. To better improve the performance, we extend our DSSD to a recurrent DSSD (R-DSSD) architecture by integrating with the complementary information from multi-scale perspectives. Experimental results on the widely used benchmark datasets show that our methods achieve very competitive performance compared to the state-of-the-arts.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Automatic alignment technology in high power laser system

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Dai, Wan-jun; Wang, Yuan-cheng; Lian, Bo; Yang, Ying; Yuan, Qiang; Deng, Xue-wei; Zhao, Jun-pu; Zhou, Wei

    2015-02-01

    The high power solid laser system is becoming larger and higher energy that requires the beam automatic alignment faster and higher precision to ensure safety running of laser system and increase the shooting success rate. This paper take SGIII laser facility for instance, introduce the basic principle of automatic alignment of large laser system. The automatic alignment based on digital image processing technology which use the imaging of seven-classes spatial filter pinholes for feedback to working. Practical application indicates that automatic alignment system of cavity mirror in SGIII facility can finish the work in 210 seconds of four bundles and will not exceed 270 seconds of all six bundles. The alignment precision promoted to 2.5% aperture from 8% aperture. The automatic alignment makes it possible for fast and safety running of lager laser system.

  1. Novel hybrid genetic algorithm for progressive multiple sequence alignment.

    PubMed

    Afridi, Muhammad Ishaq

    2013-01-01

    The family of evolutionary or genetic algorithms is used in various fields of bioinformatics. Genetic algorithms (GAs) can be used for simultaneous comparison of a large pool of DNA or protein sequences. This article explains how the GA is used in combination with other methods like the progressive multiple sequence alignment strategy to get an optimal multiple sequence alignment (MSA). Optimal MSA get much importance in the field of bioinformatics and some other related disciplines. Evolutionary algorithms evolve and improve their performance. In this optimisation, the initial pair-wise alignment is achieved through a progressive method and then a good objective function is used to select and align more alignments and profiles. Child and subpopulation initialisation is based upon changes in the probability of similarity or the distance matrix of the alignment population. In this genetic algorithm, optimisation of mutation, crossover and migration in the population of candidate solution reflect events of natural organic evolution.

  2. Sequence alignments and pair hidden Markov models using evolutionary history.

    PubMed

    Knudsen, Bjarne; Miyamoto, Michael M

    2003-10-17

    This work presents a novel pairwise statistical alignment method based on an explicit evolutionary model of insertions and deletions (indels). Indel events of any length are possible according to a geometric distribution. The geometric distribution parameter, the indel rate, and the evolutionary time are all maximum likelihood estimated from the sequences being aligned. Probability calculations are done using a pair hidden Markov model (HMM) with transition probabilities calculated from the indel parameters. Equations for the transition probabilities make the pair HMM closely approximate the specified indel model. The method provides an optimal alignment, its likelihood, the likelihood of all possible alignments, and the reliability of individual alignment regions. Human alpha and beta-hemoglobin sequences are aligned, as an illustration of the potential utility of this pair HMM approach.

  3. 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].

  4. Alignment Layers for Ferro and Antiferroelectric Liquid Crystal Cells

    NASA Astrophysics Data System (ADS)

    Negi, Yuvraj Singh; Yamamoto, Norio; Suzuki, Yoshiichi; Kawamura, Ichiro; Yamada, Yuichiro; Kakimoto, Masa-aki; Imai, Yoshio

    1992-12-01

    Aromatic fluorine and nonfluorine containing polyimides, polyamide-imides and polyamides were developed and utilized as alignment layers in ferroelectric (FLC) and antiferroelectric liquid crystal (AFLC) cells. The FLC and AFLC blend (AFLCB-1) of liquid crystals used in the experiment were CS-1011 and [S(-)4-(1-methylheptyloxycarbonyl) phenyl-4-octyloxybiphenyl-4-carboxylate (MHPOBC), R(+)4-(1-trifluoromethylheptyloxy carbonyl)phenyl-4-octyloxybiphenyl-4-carboxylate (TFMHPOBC), and other homologues, [AFLCB-1], respectively. The alignment layer deposited over an ITO-coated glass electrode plate with 2 μm cell gap showed good or random alignment of liquid crystal in FLC and AFLC cells. The AFLC cells exhibited contrast ratio values greater than 10:1 depending on the molecular structure of the alignment layer. The alignment quality of FLC and AFLC cells was also compared by using different molecular structure of polymer alignment layers.

  5. Real-time Optical Alignment and Diagnostic System (ROADS)

    NASA Technical Reports Server (NTRS)

    1972-01-01

    The ultimate and most frequent usage of ROADS will be the alignment of subassemblies (collector and collimator) prior to their installation in a chamber. The system as designed has inherent associated capabilities well applied to acceptance testing of the No. 4 mirror, prediction of in-chamber performance, generation of a catalog of test results and other data, providing data for the plotting of isointensity lines, and other applications which are discussed. The ROADS system will collect, process, display, analyze, and retain data as required for components, partial subassemblies, complete subassemblies, complete modules, and multimodular arrays.

  6. Active alignment scheme for the MPTS array

    SciTech Connect

    Iwasaki, R.

    1980-01-01

    In order to maximize the efficiency of the microwave power transmission system (MPTS), the surface of the array antenna must be extremely flat, which is difficult to achieve using passive techniques over the 1 km dimensions of the array. In order to achieve and maintain this required flatness, a rotating laser beam used for leveling applications on earth has been utilized as a reference system. A photoconductive sensor with a reflective collecting surface is used to determine the displacement and polarity of any misalignment and automatically engage a stepping motor to drive a variable-length mechanism to make the necessary corrections. A three-point subarray alignment arrangement is described which independently adjusts, in the three orthogonal directions, the height and tilt of subarrays within the MPTS array and readily adapts to any physical distortions of the secondary structure (such as that resulting from severe temperature extremes caused by an eclipse of the sun.

  7. 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.

  8. Impact of Baryonic Physics on Intrinsic Alignments

    NASA Astrophysics Data System (ADS)

    Tenneti, Ananth; Gnedin, Nickolay Y.; Feng, Yu

    2017-01-01

    We explore the effects of specific assumptions in the subgrid models of star formation and stellar and active galactic nucleus feedback on intrinsic alignments of galaxies in cosmological simulations of the “MassiveBlack-II” family. Using smaller-volume simulations, we explore the parameter space of the subgrid star formation and feedback model and find remarkable robustness of the observable statistical measures to the details of subgrid physics. The one observational probe most sensitive to modeling details is the distribution of misalignment angles. We hypothesize that the amount of angular momentum carried away by the galactic wind is the primary physical quantity that controls the orientation of the stellar distribution. Our results are also consistent with a similar study by the EAGLE simulation team.

  9. Micromagnet structures for magnetic positioning and alignment

    NASA Astrophysics Data System (ADS)

    Zanini, L. F.; Osman, O.; Frenea-Robin, M.; Haddour, N.; Dempsey, N. M.; Reyne, G.; Dumas-Bouchiat, F.

    2012-04-01

    High performance hard magnetic films (NdFeB, SmCo) have been patterned at the micron scale using thermo-magnetic patterning. Both out-of-plane and in-plane magnetized structures have been prepared. These micromagnet arrays have been used for the precise positioning and alignment of superparamagnetic nano- and microparticles. The specific spatial arrangement achieved is shown to depend on both the particle size and the size and orientation of the micromagnets. These micromagnet arrays were used to trap cells magnetically functionalized by endocytosis of 100 nm superparamagnetic particles. These simple, compact, and autonomous structures, which need neither an external magnetic field source nor a power supply, have much potential for use in a wide range of biological applications.

  10. 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.

  11. 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.

  12. Image denoising using local tangent space alignment

    NASA Astrophysics Data System (ADS)

    Feng, JianZhou; Song, Li; Huo, Xiaoming; Yang, XiaoKang; Zhang, Wenjun

    2010-07-01

    We propose a novel image denoising approach, which is based on exploring an underlying (nonlinear) lowdimensional manifold. Using local tangent space alignment (LTSA), we 'learn' such a manifold, which approximates the image content effectively. The denoising is performed by minimizing a newly defined objective function, which is a sum of two terms: (a) the difference between the noisy image and the denoised image, (b) the distance from the image patch to the manifold. We extend the LTSA method from manifold learning to denoising. We introduce the local dimension concept that leads to adaptivity to different kind of image patches, e.g. flat patches having lower dimension. We also plug in a basic denoising stage to estimate the local coordinate more accurately. It is found that the proposed method is competitive: its performance surpasses the K-SVD denoising method.

  13. 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.

  14. 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.

  15. Impact of Baryonic Physics on Intrinsic Alignments

    SciTech Connect

    Tenneti, Ananth; Gnedin, Nickolay Y.; Feng, Yu

    2016-07-24

    We explore the effects of specific assumptions in the subgrid models of star formation and stellar and AGN feedback on intrinsic alignments of galaxies in cosmological simulations of "MassiveBlack-II" family. Using smaller volume simulations, we explored the parameter space of the subgrid star formation and feedback model and found remarkable robustness of the observable statistical measures to the details of subgrid physics. The one observational probe most sensitive to modeling details is the distribution of misalignment angles. We hypothesize that the amount of angular momentum carried away by the galactic wind is the primary physical quantity that controls the orientation of the stellar distribution. Our results are also consistent with a similar study by the EAGLE simulation team.

  16. Extracting the polarizability anisotropy from the transient alignment of HBr.

    PubMed

    Pinkham, D; Vogt, T; Jones, R R

    2008-08-14

    We use 40 fs, 780 nm laser pulses to transiently align HBr molecules. We study the temporal dynamics of the resultant rotational wavepacket to gain insight into the electronic properties of the molecule. We show that the HBr polarization anisotropy can be extracted by comparing the time dependence of the HBr alignment with both the analogous alignment behavior of N(2) and the predictions of a rigid-rotor model.

  17. Large-scale structure and the intrinsic alignment of galaxies

    NASA Astrophysics Data System (ADS)

    Blazek, Jonathan; Seljak, Uroš; Mandelbaum, Rachel

    2016-10-01

    Coherent alignments of galaxy shapes, often called``intrinsic alignments'' (IA), are the most significant source of astrophysical uncertainty in weak lensing measurements. We develop the tidal alignment model of IA and demonstrate its success in describing observational data. We also describe a technique to separate IA from galaxy-galaxy lensing measurements. Applying this technique to luminous red galaxy lenses in the Sloan Digital Sky Survey, we constrain potential IA contamination from associated sources to be below a few percent.

  18. 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.

  19. 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.

  20. Alignment of Tractograms As Graph Matching

    PubMed Central

    Olivetti, Emanuele; Sharmin, Nusrat; Avesani, Paolo

    2016-01-01

    The white matter pathways of the brain can be reconstructed as 3D polylines, called streamlines, through the analysis of diffusion magnetic resonance imaging (dMRI) data. The whole set of streamlines is called tractogram and represents the structural connectome of the brain. In multiple applications, like group-analysis, segmentation, or atlasing, tractograms of different subjects need to be aligned. Typically, this is done with registration methods, that transform the tractograms in order to increase their similarity. In contrast with transformation-based registration methods, in this work we propose the concept of tractogram correspondence, whose aim is to find which streamline of one tractogram corresponds to which streamline in another tractogram, i.e., a map from one tractogram to another. As a further contribution, we propose to use the relational information of each streamline, i.e., its distances from the other streamlines in its own tractogram, as the building block to define the optimal correspondence. We provide an operational procedure to find the optimal correspondence through a combinatorial optimization problem and we discuss its similarity to the graph matching problem. In this work, we propose to represent tractograms as graphs and we adopt a recent inexact sub-graph matching algorithm to approximate the solution of the tractogram correspondence problem. On tractograms generated from the Human Connectome Project dataset, we report experimental evidence that tractogram correspondence, implemented as graph matching, provides much better alignment than affine registration and comparable if not better results than non-linear registration of volumes. PMID:27994537

  1. 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.

  2. 60. Adney Gap. View of curvilinear alignment of parkway passing ...

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

    60. Adney Gap. View of curvilinear alignment of parkway passing through agricultural lease lands. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

  3. Metabolic network alignment in large scale by network compression.

    PubMed

    Ay, Ferhat; Dang, Michael; Kahveci, Tamer

    2012-03-21

    Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic networks has been considered in the past, the computational complexity of the existing solutions has so far limited their use to moderately sized networks. In this paper, we address the problem of aligning two metabolic networks, particularly when both of them are too large to be dealt with using existing methods. We develop a generic framework that can significantly improve the scale of the networks that can be aligned in practical time. Our framework has three major phases, namely the compression phase, the alignment phase and the refinement phase. For the first phase, we develop an algorithm which transforms the given networks to a compressed domain where they are summarized using fewer nodes, termed supernodes, and interactions. In the second phase, we carry out the alignment in the compressed domain using an existing network alignment method as our base algorithm. This alignment results in supernode mappings in the compressed domain, each of which are smaller instances of network alignment problem. In the third phase, we solve each of the instances using the base alignment algorithm to refine the alignment results. We provide a user defined parameter to control the number of compression levels which generally determines the tradeoff between the quality of the alignment versus how fast the algorithm runs. Our experiments on the networks from KEGG pathway database demonstrate that the compression method we propose reduces the sizes of metabolic networks by almost half at each compression level which provides an expected speedup of more than an order of magnitude. We also observe that the alignments obtained by only one level of compression capture the original alignment results with high accuracy. Together, these suggest that our framework results in

  4. 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.

  5. 246. View showing the curvilinear alignment of the parkway on ...

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

    246. View showing the curvilinear alignment of the parkway on a ridge. Looking northeast. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

  6. 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.

  7. Machinery alignment tables: Face-OD and reverse indicator methods

    SciTech Connect

    Buck, G.S.

    1984-01-01

    Many alignment techniques are too complex for practical use, and guessing never provides the needed precision. The face-OD (face-rim) and reverse indicator methods are the two most popular techniques experienced millwrights use, but both methods require time-consuming calculations. These tables replace the graphs, formulas, and calculations used to determine shim requirements. Contents: Face-OD method and reverse indicator method: Setting up Data forms. Equations and calculations. Examples. Alignment Tolerances. Errors in taking data. Typical alignment tolerances. Indicator sag. Cause of indicator sag. Correction of indicator sag. Typical values of indicator sag. Hot alignment. References.

  8. Alignment of the Fibrin Network Within an Autologous Plasma Clot.

    PubMed

    Gessmann, Jan; Seybold, Dominik; Peter, Elvira; Schildhauer, Thomas Armin; Köller, Manfred

    2016-01-01

    Autologous plasma clots with longitudinally aligned fibrin fibers could serve as a scaffold for longitudinal axonal regrowth in cases of traumatic peripheral nerve injuries. Three different techniques for assembling longitudinally oriented fibrin fibers during the fibrin polymerization process were investigated as follows: fiber alignment was induced by the application of either a magnetic field or-as a novel approach-electric field or by the induction of orientated flow. Fiber alignment was characterized by scanning electron microscopy analysis followed by image processing using fast Fourier transformation (FFT). Besides FFT output images, area xmin to xmax, as well as full width at half maximum (FWHM) of the FFT graph plot peaks, was calculated to determine the relative degree of fiber alignment. In addition, fluorescently labeled human fibrinogen and mesenchymal stem cells (MSCs) were used to visualize fibrin and cell orientation in aligned and nonaligned plasma clots. Varying degrees of fiber alignment were achieved by the three different methods, with the electric field application producing the highest degree of fiber alignment. The embedded MSCs showed a longitudinal orientation in the electric field-aligned plasma clots. The key feature of this study is the ability to produce autologous plasma clots with aligned fibrin fibers using physical techniques. This orientated internal structure of an autologous biomaterial is promising for distinct therapeutic applications, such as a guiding structure for cell migration and growth dynamics.

  9. Permanent bending and alignment of ZnO nanowires.

    PubMed

    Borschel, Christian; Spindler, Susann; Lerose, Damiana; Bochmann, Arne; Christiansen, Silke H; Nietzsche, Sandor; Oertel, Michael; Ronning, Carsten

    2011-05-06

    Ion beams can be used to permanently bend and re-align nanowires after growth. We have irradiated ZnO nanowires with energetic ions, achieving bending and alignment in different directions. Not only the bending of single nanowires is studied in detail, but also the simultaneous alignment of large ensembles of ZnO nanowires. Computer simulations reveal how the bending is initiated by ion beam induced damage. Detailed structural characterization identifies dislocations to relax stresses and make the bending and alignment permanent, even surviving annealing procedures.

  10. 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

  11. Cooperative ordering and kinetics of cellulose nanocrystal alignment in a magnetic field

    DOE PAGES

    De France, Kevin J.; Yager, Kevin G.; Hoare, Todd; ...

    2016-07-13

    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 strengthmore » 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.« less

  12. Cooperative ordering and kinetics of cellulose nanocrystal alignment in a magnetic field

    SciTech Connect

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

    2016-07-13

    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.

  13. 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/.

  14. 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

  15. Polarization Raman Microscopic Study of Molecular Alignment Behavior in Liquid Crystal/Polymer Composite Films

    NASA Astrophysics Data System (ADS)

    Murashige, Takeshi; Fujikake, Hideo; Sato, Hiroto; Kikuchi, Hiroshi; Kurita, Taiichiro; Sato, Fumio

    2005-12-01

    We clarified that the molecular alignment of aggregated polymers is partially synchronized with liquid crystal (LC) director reorientation in an LC/polymer composite film. The molecular alignment behavior in composite films with LC- and polymer-rich regions formed by photopolymerization-induced phase separation was investigated using polarization Raman spectral microscopy. Raman scattering intensity induced by aligned side chains of polymers in the LC-rich region changed with LC director reorientation when voltage was applied to the composite film. It was confirmed for the first time that polymers capable of movement are formed in the LC-rich region.

  16. 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.

  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.

  18. Apse Alignment of the Uranian Rings

    NASA Astrophysics Data System (ADS)

    Mosqueira, Ignacio; Estrada, Paul R.

    2002-08-01

    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 (P. Goldreich and S. Tremaine 1979, Astron J.84, 1638-1641) 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 we 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 α 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 50 times the 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. We find that such a velocity dispersion profile would require a different mechanism than is currently envisioned for establishing a heating/cooling balance in a finite-sized, inelastic particle ring. Finally, we introduce an important

  19. 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

  20. 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

  1. 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…

  2. 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,…

  3. 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…

  4. 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…

  5. 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…

  6. 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…

  7. 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…

  8. 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…

  9. Low-level laser therapy and invisible removal aligners.

    PubMed

    Caccianiga, G; Crestale, C; Cozzani, M; Piras, A; Mutinelli, S; Lo Giudice, A; Cordasco, G

    2016-01-01

    It seems that Low Level Laser Therapy (LLLT) stimulates orthodontic tooth movements, increasing the alveolar bone turnover. The aim of this study is to evaluate how LLLT can influence the orthodontic treatment with invisible removal aligner. A sample of 21 subjects was divided into two groups, a laser group (10 patients) and a control group (11 patients). All subjects were instructed to wear each aligner 12 hours a day for 2 weeks. Laser external bio-stimulation was given in the laser group every second week. The laser group successfully finished the treatment, while at 3rd – 5th aligner the control group did not finish the treatment. Laser treatment seemed to be better than treatment without laser. LLLT combined with aligners is able to favour, in 12 hours, the same tooth movement obtained by wearing the aligner 22 hours a day, according to the traditional protocol. This aspect could be useful for those patients who prefer not to use the aligners during the day. LLLT makes invisible removal aligner treatment more comfortable also because during the day the patients have to wear the aligners less hours than the treatment without laser.

  10. 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…

  11. Photosensors used to maintain welding electrode-to-joint alignment

    NASA Technical Reports Server (NTRS)

    Bowen, J. B.

    1965-01-01

    Photosensors maintain electrode-to-joint alignment in automatic precision arc welding. They detect the presence and relative position of a joint to be welded and actuate a servomechanism to guide the welding head accordingly thus permitting alignment for more than straight line or true circle joints.

  12. 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…

  13. 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…

  14. 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

  15. 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.

  16. 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…

  17. 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 the…

  18. Splign: algorithms for computing spliced alignments with identification of paralogs

    PubMed Central

    Kapustin, Yuri; Souvorov, Alexander; Tatusova, Tatiana; Lipman, David

    2008-01-01

    Background The computation of accurate alignments of cDNA sequences against a genome is at the foundation of modern genome annotation pipelines. Several factors such as presence of paralogs, small exons, non-consensus splice signals, sequencing errors and polymorphic sites pose recognized difficulties to existing spliced alignment algorithms. Results We describe a set of algorithms behind a tool called Splign for computing cDNA-to-Genome alignments. The algorithms include a high-performance preliminary alignment, a compartment identification based on a formally defined model of adjacent duplicated regions, and a refined sequence alignment. In a series of tests, Splign has produced more accurate results than other tools commonly used to compute spliced alignments, in a reasonable amount of time. Conclusion Splign's ability to deal with various issues complicating the spliced alignment problem makes it a helpful tool in eukaryotic genome annotation processes and alternative splicing studies. Its performance is enough to align the largest currently available pools of cDNA data such as the human EST set on a moderate-sized computing cluster in a matter of hours. The duplications identification (compartmentization) algorithm can be used independently in other areas such as the study of pseudogenes. Reviewers This article was reviewed by: Steven Salzberg, Arcady Mushegian and Andrey Mironov (nominated by Mikhail Gelfand). PMID:18495041

  19. Alignment control study for the solar optical telescope

    NASA Technical Reports Server (NTRS)

    1976-01-01

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

  20. 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.

  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. 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.

  3. 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…

  4. [Tabular excel editor for analysis of aligned nucleotide sequences].

    PubMed

    Demkin, V V

    2010-01-01

    Excel platform was used for transition of results of multiple aligned nucleotide sequences obtained using the BLAST network service to the form appropriate for visual analysis and editing. Two macros operators for MS Excel 2007 were constructed. The array of aligned sequences transformed into Excel table and processed using macros operators is more appropriate for analysis than initial html data.

  5. 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.

  6. OBSERVATIONS OF ENHANCED RADIATIVE GRAIN ALIGNMENT NEAR HD 97300

    SciTech Connect

    Andersson, B-G; Potter, S. B. E-mail: sbp@saao.ac.z

    2010-09-10

    We have obtained optical multi-band polarimetry toward sightlines through the Chamaeleon I cloud, particularly in the vicinity of the young B9/A0 star HD 97300. We show, in agreement with earlier studies, that the radiation field impinging on the cloud in the projected vicinity of the star is dominated by the flux from the star, as evidenced by a local enhancement in the grain heating. By comparing the differential grain heating with the differential change in the location of the peak of the polarization curve, we show that the grain alignment is enhanced by the increase in the radiation field. We also find a weak, but measurable, variation in the grain alignment with the relative angle between the radiation field anisotropy and the magnetic field direction. Such an anisotropy in the grain alignment is consistent with a unique prediction of modern radiative alignment torque theory and provides direct support for radiatively driven grain alignment.

  7. Field-free alignment in repetitively kicked nitrogen gas

    SciTech Connect

    Cryan, James P.; Bucksbaum, Philip H.; Coffee, Ryan N.

    2009-12-15

    We demonstrate a high level of laser-induced transient alignment in room temperature and density N{sub 2} with a technique that avoids laser field ionization. Our measured alignment shows an improvement over previous one-pulse or two-pulse experimental alignment results and approaches the theoretical maximum value. We employ eight equally spaced ultrafast laser pulses with a separation that takes advantage of the periodic revivals for the ensemble of quantum rotors. Each successive pulse increases the transient alignment [(t)] and also moves the rotational population away from thermal equilibrium. These measurements are combined with simulations to determine the value of , the J-state distributions, and the functional dependencies of the alignment features.

  8. Sources of field-aligned currents in the auroral plasma

    SciTech Connect

    Marshall, J.A.; Burch, J.L. ); Kan, J.R. ); Reiff, P.H. ); Slavin, J.A. )

    1991-01-01

    Data from the Dynamics Explorer 1 High Altitude Plasma Instrument (HAPI) and magnetometer are used to investigate the sources of field-aligned currents in the nightside auroral zone. It is found that the formula developed by S. Knight predicts the field-aligned current density fairly accurately in regions where a significant potential drop can be inferred from the HAPI data; there are, however, regions in which the proportionality between potential drop and field-aligned current does not hold. In particular, the authors note occurrences of strong upward field-aligned current associated not with inverted-V events but instead with suprathermal bursts. In addition, upward field-aligned currents are often observed to peak near the edges of inverted-V events, rather than in the center as would be predicted by Knight.

  9. Sources of field-aligned currents in the auroral plasma

    NASA Astrophysics Data System (ADS)

    Marshall, J. A.; Burch, J. L.; Kan, J. R.; Reiff, P. H.; Slavin, J. A.

    1991-01-01

    Data from the Dynamics Explorer 1 High Altitude Plasma Instrument (HAPI) and magnetometer are used to investigate the sources of field-aligned currents in the nightside auroral zone. It is found that the formula developed by S. Knight predicts the field-aligned current density fairly accurately in regions where a significant potential drop can be inferred from the HAPI data; there are, however, regions in which the proportionality between potential drop and field-aligned current does not hold. In particular, occurrences of strong upward field-aligned current associated not with inverted-V events but instead with suprathermal bursts are noted. In addition, upward field-aligned currents are often observed to peak near the edges of inverted-V events, rather than in the center as would be predicted by Knight.

  10. SPAM: A precision alignment device for spectrometer sightlines

    NASA Astrophysics Data System (ADS)

    Ramsey, A. T.; Bartolick, J. M.

    1990-10-01

    As fusion devices become larger and their environments become harsher for instruments, diagnostics find themselves farther and farther away from the plasma. On TFTR, the UV survey spectrometer SPRED is over 9 m from the plasma. In these conditions, the alignment of the optical axis of the spectrometer to the desired portion of the plasma becomes both more critical and more difficult. We have developed a device which allows visual alignment along an optical axis both back into the spectrometer and toward the plasma. This SPRED alignment mechanism (SPAM) generates forward and backward laser alignment beams which are exactly coaxial, and gives coincident visual sightlines, also coaxial, in both directions. It is compact, hardy, precise, and cheap. SPAM also has been used to align visible and UV spectrometers with equal success.

  11. 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.

  12. 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.

  13. The electric field alignment of ice particles in thunderstorms

    NASA Technical Reports Server (NTRS)

    Weinheimer, Andrew J.; Few, Arthur A.

    1987-01-01

    Electrical and aerodynamic torques on atmospheric ice particles are calculaed in order to assess the degree of alignment of these particles with the electric fields in thunderstorms. In such clouds fields of many tens of kilovolts per meter are commonly measured, and values of 100 to 200 kV/m are not rare. For E = 100 kV/m the calculations indicate that electric field alignment occurs for crystals with major dimensions up to maximum values in the range from 200 microns to 1 mm, depending upon crystal type. Columns are aligned more easily than platelike crystals, except for dendrites which, by virtue of their smaller assumed density, have smaller fall velocities thereby experiencing weaker aerodynamic torques. Thus a substantial degree of alignment is expected for E = 100 kV/m. For E = 10 kV/m only much smaller crystals will be aligned, probably only ones with major dimensions of less than 50 microns or so.

  14. Absorber Alignment Measurement Tool for Solar Parabolic Trough Collectors: Preprint

    SciTech Connect

    Stynes, J. K.; Ihas, B.

    2012-04-01

    As we pursue efforts to lower the capital and installation costs of parabolic trough solar collectors, it is essential to maintain high optical performance. While there are many optical tools available to measure the reflector slope errors of parabolic trough solar collectors, there are few tools to measure the absorber alignment. A new method is presented here to measure the absorber alignment in two dimensions to within 0.5 cm. The absorber alignment is measured using a digital camera and four photogrammetric targets. Physical contact with the receiver absorber or glass is not necessary. The alignment of the absorber is measured along its full length so that sagging of the absorber can be quantified with this technique. The resulting absorber alignment measurement provides critical information required to accurately determine the intercept factor of a collector.

  15. Apparatus for connecting aligned abutted tubes

    DOEpatents

    Williams, R.E.

    1984-11-29

    An apparatus for connecting abutted tubes and for maintaining their rotary alignment during connection. The apparatus comprises first and second tubes, a rotation prevention element, a collar and a retainer. Each tube has inside and outside walls, and first and second ends, each end having an inside and outside edge. The first tube has portions defining a first plurality of cavities located at the outside edge of its first end. An external threaded portion is on the outside wall of the first tube and next to the first plurality of cavities. The second tube has portions defining a second plurality of cavities located at the outside edge of its first end. The first plurality has a different number than the second plurality. The first ends of the first and second tubes have substantially the same outside diameter and are abutted during connection so that an orifice is formed whenever first and second tube cavities substantially overlap. A rotation prevension element is placed in the orifice to prevent rotation of the first and second tubes. A collar with an internal threaded portion is slidably disposed about the second tube. The internal threaded portion engages the external threaded portion of the first tube to connect the tubes. A lip connected to the collar prevents separation of the collar from the second tube.

  16. Shear alignment of lamellar mesophase systems

    NASA Astrophysics Data System (ADS)

    Jaju, S. J.; Kumaran, V.

    2015-11-01

    Mixtures of oil, water and surfactants form different microphases. Some of these phases, e.g. lamellar, hexagonal phases, lead to complex rheological behaviour at macroscale due to inherent anisotropy and irregularities in the microstructures. We present a comprehensive simulation study to examine the structure-rheology relationship in lamellar phase flow. At mesoscale, Reynolds number (Re), Schmidt number (Sc), Ericksen number (Er), extent of segregation between hydrophilic and hydrophobic components (r), ratio of viscosity of the two components (Δμ /μ0), and system size to layer width ratio (L / λ) complete the lamellar phase description. We have used lattice Boltzmann simulations to study a two dimensional lamellar phase system of moderate size. The domains and grain boundaries seen at low Sc are replaced by isolated edge dislocations at high Sc. The alignment mechanism does not change with changes in layer bending moduli (Er), viscosity contrast or r. Increasing segregation, increases disorder; this however does not lead to higher resistance to flow. At high Er, the shear tries homogenise the concentration field and disrupt layer formation. We see significantly higher peak viscosity at low Er at high viscosity contrast and due to defect pinning. The authors would like to thank the Department of Science and Technology, Government of India for financial support, and Supercomputer Education and Research Centre at Indian Institute of Science for the computational resources.

  17. Haplotype assembly from aligned weighted SNP fragments.

    PubMed

    Zhao, Yu-Ying; Wu, Ling-Yun; Zhang, Ji-Hong; Wang, Rui-Sheng; Zhang, Xiang-Sun

    2005-08-01

    Given an assembled genome of a diploid organism the haplotype assembly problem can be formulated as retrieval of a pair of haplotypes from a set of aligned weighted SNP fragments. Known computational formulations (models) of this problem are minimum letter flips (MLF) and the weighted minimum letter flips (WMLF; Greenberg et al. (INFORMS J. Comput. 2004, 14, 211-213)). In this paper we show that the general WMLF model is NP-hard even for the gapless case. However the algorithmic solutions for selected variants of WMFL can exist and we propose a heuristic algorithm based on a dynamic clustering technique. We also introduce a new formulation of the haplotype assembly problem that we call COMPLETE WMLF (CWMLF). This model and algorithms for its implementation take into account a simultaneous presence of multiple kinds of data errors. Extensive computational experiments indicate that the algorithmic implementations of the CWMLF model achieve higher accuracy of haplotype reconstruction than the WMLF-based algorithms, which in turn appear to be more accurate than those based on MLF.

  18. Measurement of dichroism in aligned molecules

    NASA Astrophysics Data System (ADS)

    Lavorel, B.; Babilotte, Ph.; Karras, G.; Billard, F.; Hertz, E.; Faucher, O.

    2016-10-01

    We present dichroism measurements in molecules prealigned with a short and intense laser pulse, using a balanced detection and a pump-probe scheme. The birefringence signal is recorded under the same irradiation conditions along with the dichroism one. Our results show that the dichroism signal is of comparable order of magnitude as the one originating from birefringence and reflects the degree of alignment. The balanced detection scheme directly provides an heterodyne signal for both birefringence and dichroism. Experiments are first conducted in air and then in pure nitrogen and carbon dioxide gases. A general approach allows us to explain the temporal shape of the dichroic response and to extract the imaginary part of the polarizability anisotropy. Furthermore, a simple model invoking the finite response time of the molecule to the probe excitation provides a complementary perspective. Using this model, the phase shift between the oscillations of the probe electric field and the induced polarization can be estimated. We find that the phase shift corresponds to a time delay of about 130 as (10-18s) in both molecules. Calculation of the energy flow between the probe field and the molecules taking into account the phase shift is compared to the experimental data.

  19. CYLINDER LENS ALIGNMENT IN THE LTP

    SciTech Connect

    TAKACS, P.Z.

    2005-07-26

    The Long Trace Profiler (LTP), is well-suited for the measurement of the axial figure of cylindrical mirrors that usually have a long radius of curvature in the axial direction but have a short radius of curvature in the sagittal direction. The sagittal curvature causes the probe beam to diverge in the transverse direction without coming to a focus on the detector, resulting in a very weak signal. It is useful to place a cylinder lens into the optical system above the mirror under test to refocus the sagittal divergence and increase the signal level. A positive cylinder lens can be placed at two positions above the surface: the Cat's Eye reflection position and the Wavefront-Matching position. The Cat's Eye position, is very tolerant to mirror misalignment, which is not good if absolute axial radius of curvature is to be measured. Lateral positioning and rotational misalignments of lens and the mirror combine to produce unusual profile results. This paper looks at various alignment issues with measurements and by raytrace simulations to determine the best strategy to minimize radius of curvature errors in the measurement of cylindrical aspheres.

  20. Microtubule alignment and manipulation using AC electrokinetics.

    PubMed

    Uppalapati, Maruti; Huang, Ying-Ming; Jackson, Thomas N; Hancock, William O

    2008-09-01

    The kinesin-microtubule system plays an important role in intracellular transport and is a model system for integrating biomotor-driven transport into microengineered devices. AC electrokinetics provides a novel tool for manipulating and organizing microtubules in solution, enabling new experimental geometries for investigating and controlling the interactions of microtubules and microtubule motors in vitro. By fabricating microelectrodes on glass substrates and generating AC electric fields across solutions of microtubules in low-ionic-strength buffers, bundles of microtubules are collected and aligned and the electrical properties of microtubules in solution are measured. The AC electric fields result in electro-osmotic flow, electrothermal flow, and dielectrophoresis of microtubules, which can be controlled by varying the solution conductivity, AC frequency, and electrode geometry. By mapping the solution conductivity and AC frequency over which positive dielectrophoresis occurs, the apparent conductivity of taxol-stabilized bovine-brain microtubules in PIPES buffer is measured to be 250 mS m(-1). By maximizing dielectrophoretic forces and minimizing electro-osmotic and electrothermal flow, microtubules are assembled into opposed asters. These experiments demonstrate that AC electrokinetics provides a powerful new tool for kinesin-driven transport applications and for investigating the role of microtubule motors in development and maintenance of the mitotic spindle.

  1. Determining knee joint alignment using digital photographs.

    PubMed

    Schmitt, Holger; Kappel, Hannes; Moser, Michael T; Cardenas-Montemayor, Eloy; Engelleiter, Karoly; Kuni, Benita; Clarius, Michael

    2008-08-01

    The objective of this work is to find out how reliably knee joint alignment can be measured from a standardized photograph and what influence changes in the standing position have on the angles measured. The interrater, intrarater, and test-retest reliability were evaluated. The influence of image-object distance, the distance between the legs and leg rotation on the measured angles was evaluated. In addition to the digital photographs, 10 full-length radiographs were obtained in an upright position to determine whether the measured angles represent the anatomic axis or mechanical axis. There was high correlation between the interrater (ICC 0.997), intrarater (ICC 0.989) and test-retest reliability (ICC 0.904). Only slight deviation was found with the changes in radiograph-object distance (0 degrees -1.8 degrees ). With feet together varus malalignment was greater. Leg rotation showed a strong influence on the measured results (ICC 0.658). The angle measured in the digital photographs reflects the mechanical axis with only slight deviation (0.12 degrees -1.9 degrees ). The measurement of the clinical axis using standardized radiography is highly reliable and can be used for individual follow-up of varus and valgus malalignments.

  2. Sequence Alignment to Predict Across Species Susceptibility ...

    EPA Pesticide Factsheets

    Conservation of a molecular target across species can be used as a line-of-evidence to predict the likelihood of chemical susceptibility. The web-based Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to simplify, streamline, and quantitatively assess protein sequence/structural similarity across taxonomic groups as a means to predict relative intrinsic susceptibility. The intent of the tool is to allow for evaluation of any potential protein target, so it is amenable to variable degrees of protein characterization, depending on available information about the chemical/protein interaction and the molecular target itself. To allow for flexibility in the analysis, a layered strategy was adopted for the tool. The first level of the SeqAPASS analysis compares primary amino acid sequences to a query sequence, calculating a metric for sequence similarity (including detection of candidate orthologs), the second level evaluates sequence similarity within selected domains (e.g., ligand-binding domain, DNA binding domain), and the third level of analysis compares individual amino acid residue positions identified as being of importance for protein conformation and/or ligand binding upon chemical perturbation. Each level of the SeqAPASS analysis provides increasing evidence to apply toward rapid, screening-level assessments of probable cross species susceptibility. Such analyses can support prioritization of chemicals for further ev

  3. Orienting members in a preselected rotary alignment

    DOEpatents

    Williams, Ray E.

    1987-01-01

    An apparatus for orienting members and for maintaining their rotary alignment during orienting members. The apparatus comprises first and second cylindrical elements, a rotation prevention element, a collar and a retainer. Each element has an outside wall, and first and second ends, each end having an outside edge. The first element has portions defining a first plurality of notches located at the outside edge of its first end. An external threaded portion is on the outside wall of the first element and next to the first plurality of notches. The second element has portions defining a second plurality of notches located at the outside edge of its first end. The first plurality has a different number than the second plurality. The first ends of the first and second tubes have substantially the same outside diameter and are abutted during connection so that a cavity is formed whenever first and second tube notches substantially overlap. A rotation prevention element is placed in the cavity to prevent rotation of the first and second elements. A collar with an internal threaded portion is slidably disposed about the second element. The internal threaded portion engages the external threaded portion of the first element to connect the elements. A lip connected to the collar prevents separation of the collar from the second element.

  4. Astronomical Alignments in a Neolithic Chinese Site?

    NASA Astrophysics Data System (ADS)

    Nelson, S.; Stencel, R. E.

    1997-12-01

    In the Manchurian province of Liaoning, near 41N19' and 119E30', exist ruins of a middle Neolithic society (2500 to 4000 BC) known as the Hongshan culture. This location, called Niuheliang, is comprised of 16 locations with monumental structures scattered over 80 square kilometers of hills. Most are stone burial structures that contain jade artifacts implying wealth and power. One structure is unique in being unusually shaped and containing oversized effigies of goddess figures. This structure also has a commanding view of the surrounding landscape. The presence of decorated pottery, jade and worked copper suggests the Hongshan people were sophisticated artisans and engaged in long-distance trading. During 1997, we've conducted a course at Denver as part of our Core Curriculum program for upper division students, that has examined the astronomical and cultural aspects of the Niuheliang site, to attempt to determine whether these contemporaries of the builders of Stonehenge may have included astronomical alignments into their constructions. The preliminary result of our studies suggests that certain monuments have potential for lunar standstill observation from the "goddess temple". For updates on these results, please see our website: www.du.edu/ rstencel/core2103.html.

  5. Dynamic Alignment Models for Neural Coding

    PubMed Central

    Kollmorgen, Sepp; Hahnloser, Richard H. R.

    2014-01-01

    Recently, there have been remarkable advances in modeling the relationships between the sensory environment, neuronal responses, and behavior. However, most models cannot encompass variable stimulus-response relationships such as varying response latencies and state or context dependence of the neural code. Here, we consider response modeling as a dynamic alignment problem and model stimulus and response jointly by a mixed pair hidden Markov model (MPH). In MPHs, multiple stimulus-response relationships (e.g., receptive fields) are represented by different states or groups of states in a Markov chain. Each stimulus-response relationship features temporal flexibility, allowing modeling of variable response latencies, including noisy ones. We derive algorithms for learning of MPH parameters and for inference of spike response probabilities. We show that some linear-nonlinear Poisson cascade (LNP) models are a special case of MPHs. We demonstrate the efficiency and usefulness of MPHs in simulations of both jittered and switching spike responses to white noise and natural stimuli. Furthermore, we apply MPHs to extracellular single and multi-unit data recorded in cortical brain areas of singing birds to showcase a novel method for estimating response lag distributions. MPHs allow simultaneous estimation of receptive fields, latency statistics, and hidden state dynamics and so can help to uncover complex stimulus response relationships that are subject to variable timing and involve diverse neural codes. PMID:24625448

  6. Services supporting collaborative alignment of engineering networks

    NASA Astrophysics Data System (ADS)

    Jansson, Kim; Uoti, Mikko; Karvonen, Iris

    2015-08-01

    Large-scale facilities such as power plants, process factories, ships and communication infrastructures are often engineered and delivered through geographically distributed operations. The competencies required are usually distributed across several contributing organisations. In these complicated projects, it is of key importance that all partners work coherently towards a common goal. VTT and a number of industrial organisations in the marine sector have participated in a national collaborative research programme addressing these needs. The main output of this programme was development of the Innovation and Engineering Maturity Model for Marine-Industry Networks. The recently completed European Union Framework Programme 7 project COIN developed innovative solutions and software services for enterprise collaboration and enterprise interoperability. One area of focus in that work was services for collaborative project management. This article first addresses a number of central underlying research themes and previous research results that have influenced the development work mentioned above. This article presents two approaches for the development of services that support distributed engineering work. Experience from use of the services is analysed, and potential for development is identified. This article concludes with a proposal for consolidation of the two above-mentioned methodologies. This article outlines the characteristics and requirements of future services supporting collaborative alignment of engineering networks.

  7. On the Efficiency of Grain Alignment in Dark Clouds

    NASA Astrophysics Data System (ADS)

    Lazarian, A.; Goodman, Alyssa A.; Myers, Philip C.

    1997-11-01

    A quantitative analysis of grain alignment in the filamentary dark cloud L1755 in Ophiuchus is presented. We show that the observed decrease of the polarization-to-extinction ratio for the inner parts of this quiescent dark cloud can be explained as a result of the decrease of the efficiency of grain alignment. We make quantitative estimates of grain alignment efficiency for six mechanisms involving grains with either thermal or suprathermal rotation, interacting with either magnetic field or gaseous flow. We also make semiquantitative estimates of grain alignment by radiative torques. We show that in conditions typical of dark cloud interiors, all known major mechanisms of grain alignment fail. All the studied mechanisms predict polarization at least an order of magnitude below the currently detectable levels of ~1%. On the contrary, in the dark cloud environments where Av < 1, the grain alignment can be much more efficient. There the alignment of suprathermally rotating grains with superparamagnetic inclusions, and possibly also radiative torques, account for observed polarization. These results apply to L1755, which we model in detail, and probably also to B216 and other similar dark clouds. Our study suggests an explanation for the difference in results obtained through polarimetry of background starlight and polarized thermal emission from the dust itself. We conjecture that the emission polarimetry selectively reveals aligned grains in the environment far from thermodynamic equilibrium, as opposed to starlight polarization studies that probe the alignment of grains all the way along the line of sight, including the interiors of dark quiescent clouds, where no alignment is possible. We dedicate this paper to the memory of Edward M. Purcell and Lyman Spitzer, Jr., two pioneers in the quantitative study of the interstellar medium.

  8. Computational design and engineering of polymeric orthodontic aligners.

    PubMed

    Barone, S; Paoli, A; Razionale, A V; Savignano, R

    2016-10-05

    Transparent and removable aligners represent an effective solution to correct various orthodontic malocclusions through minimally invasive procedures. An aligner-based treatment requires patients to sequentially wear dentition-mating shells obtained by thermoforming polymeric disks on reference dental models. An aligner is shaped introducing a geometrical mismatch with respect to the actual tooth positions to induce a loading system, which moves the target teeth toward the correct positions. The common practice is based on selecting the aligner features (material, thickness, and auxiliary elements) by only considering clinician's subjective assessments. In this article, a computational design and engineering methodology has been developed to reconstruct anatomical tissues, to model parametric aligner shapes, to simulate orthodontic movements, and to enhance the aligner design. The proposed approach integrates computer-aided technologies, from tomographic imaging to optical scanning, from parametric modeling to finite element analyses, within a 3-dimensional digital framework. The anatomical modeling provides anatomies, including teeth (roots and crowns), jaw bones, and periodontal ligaments, which are the references for the down streaming parametric aligner shaping. The biomechanical interactions between anatomical models and aligner geometries are virtually reproduced using a finite element analysis software. The methodology allows numerical simulations of patient-specific conditions and the comparative analyses of different aligner configurations. In this article, the digital framework has been used to study the influence of various auxiliary elements on the loading system delivered to a maxillary and a mandibular central incisor during an orthodontic tipping movement. Numerical simulations have shown a high dependency of the orthodontic tooth movement on the auxiliary element configuration, which should then be accurately selected to maximize the aligner

  9. The magnetic properties of aligned M hexa-ferrite fibres

    NASA Astrophysics Data System (ADS)

    Pullar, R. C.; Bhattacharya, A. K.

    2006-05-01

    Aligned and random fibres of strontium hexaferrite (SrM, SrFe 12O 19) and barium hexaferrite (BaM, BaFe 12O 19) were manufactured by blow spinning from an aqueous inorganic sol-gel precursor, which was then fired to give the hexagonal ferrite fibre. Their magnetic properties were studied by VSM, investigating the evolution of these properties with firing and measurement temperature, and in particular the effects of fibre alignment. It has been predicted that aligned ferrite fibres will demonstrate an enhanced magnetisation along the axis of alignment with respect to perpendicular to the axis, and this has been demonstrated here for the first time. The optimum firing temperature was 1000 °C, at which point they still had submicron grains. In BaM random fibres Ms=63.8 emu g -1 and Hc=428.1 kA m -1, and in SrM random fibres Ms=63.3 emu g -1 and Hc=452.8 kA m -1, high values for polycrystalline materials. Fibres aligned parallel to the applied field had saturation magnetisation ( Ms) values equal to those of the random fibres, whilst fibres aligned perpendicular to the field had Ms values 62% and 75% lower, for BaM and SrM, respectively. There was no change in coercivity ( Hc) between random or aligned fibres of any orientation, and fibres aligned 45° and parallel to H appeared identical. Therefore, properties along the axis of alignment were superior when compared to measurements perpendicular to the axis of alignment, giving a directionality to the magnetisation in an otherwise randomly oriented ferrite material.

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

    PubMed Central

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

    2013-01-01

    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

  11. Business-IT Alignment Maturity: The Correlation of Performance Indicators and Alignment Maturity within the Commercial Airline Industry

    ERIC Educational Resources Information Center

    Ryan, Timothy K.

    2010-01-01

    During the period from 1978 to 2009, more than 200 commercial airlines were forced to merge, cease operations, or file for bankruptcy protection. The purpose of this quantitative study is to evaluate the global commercial airline industry from an IT-business alignment perspective and correlate the alignment maturity level of each airline with…

  12. Information Technology (IT) Strategic Alignment: A Correlational Study between the Impact of IT Governance Structures and IT Strategic Alignment

    ERIC Educational Resources Information Center

    Asante, Keith K.

    2010-01-01

    This dissertation explored the extent to which Information Technology (IT) strategic alignment are impacted by IT governance structures. The study discusses several strategic alignment and IT governance literature that presents a gap in the literature domain. Subsequent studies researched issues surrounding why organizations are not able to align…

  13. Dye alignment in luminescent solar concentrators: II. Horizontal alignment for energy harvesting in linear polarizers

    SciTech Connect

    Mulder, Carlijn L.; Reusswig, Phil D.; Beyler, A. P.; Kim, Heekyung; Rotschild, Carmel; Baldo, Marc

    2010-04-26

    We describe Linearly Polarized Luminescent Solar Concentrators (LP-LSCs) to replace conventional, purely absorptive, linear polarizers in energy harvesting applications. As a proof of concept, we align 3-(2-Benzothiazolyl)-N,N-diethylumbelliferylamine (Coumarin 6) and 4-dicyanomethyl-6-dimethylaminostiryl-4H-pyran (DCM) dye molecules linearly in the plane of the substrate using a polymerizable liquid crystal host. We show that up to 38% of the photons polarized on the long axis of the dye molecules can be coupled to the edge of the device for an LP-LSC based on Coumarin 6 with an order parameter of 0.52.

  14. MANGO: a new approach to multiple sequence alignment.

    PubMed

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2007-01-01

    Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment? This paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds are provably significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks showing that MANGO compares favorably, in both accuracy and speed, against state-of-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, Prob-ConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0 and Kalign 2.0.

  15. Alignment of gold nanorods by angular photothermal depletion

    NASA Astrophysics Data System (ADS)

    Taylor, Adam B.; Chow, Timothy T. Y.; Chon, James W. M.

    2014-02-01

    In this paper, we demonstrate that a high degree of alignment can be imposed upon randomly oriented gold nanorod films by angular photothermal depletion with linearly polarized laser irradiation. The photothermal reshaping of gold nanorods is observed to follow quadratic melting model rather than the threshold melting model, which distorts the angular and spectral hole created on 2D distribution map of nanorods to be an open crater shape. We have accounted these observations to the alignment procedures and demonstrated good agreement between experiment and simulations. The use of multiple laser depletion wavelengths allowed alignment criteria over a large range of aspect ratios, achieving 80% of the rods in the target angular range. We extend the technique to demonstrate post-alignment in a multilayer of randomly oriented gold nanorod films, with arbitrary control of alignment shown across the layers. Photothermal angular depletion alignment of gold nanorods is a simple, promising post-alignment method for creating future 3D or multilayer plasmonic nanorod based devices and structures.

  16. Accurate multiple network alignment through context-sensitive random walk

    PubMed Central

    2015-01-01

    Background Comparative network analysis can provide an effective means of analyzing large-scale biological networks and gaining novel insights into their structure and organization. Global network alignment aims to predict the best overall mapping between a given set of biological networks, thereby identifying important similarities as well as differences among the networks. It has been shown that network alignment methods can be used to detect pathways or network modules that are conserved across different networks. Until now, a number of network alignment algorithms have been proposed based on different formulations and approaches, many of them focusing on pairwise alignment. Results In this work, we propose a novel multiple network alignment algorithm based on a context-sensitive random walk model. The random walker employed in the proposed algorithm switches between two different modes, namely, an individual walk on a single network and a simultaneous walk on two networks. The switching decision is made in a context-sensitive manner by examining the current neighborhood, which is effective for quantitatively estimating the degree of correspondence between nodes that belong to different networks, in a manner that sensibly integrates node similarity and topological similarity. The resulting node correspondence scores are then used to predict the maximum expected accuracy (MEA) alignment of the given networks. Conclusions Performance evaluation based on synthetic networks as well as real protein-protein interaction networks shows that the proposed algorithm can construct more accurate multiple network alignments compared to other leading methods. PMID:25707987

  17. Modeling of Field-Aligned Guided Echoes in the Plasmasphere

    NASA Technical Reports Server (NTRS)

    Fung, Shing F.; Green, James L.

    2004-01-01

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

  18. Cosmological information in the intrinsic alignments of luminous red galaxies

    SciTech Connect

    Chisari, Nora Elisa; Dvorkin, Cora E-mail: cdvorkin@ias.edu

    2013-12-01

    The intrinsic alignments of galaxies are usually regarded as a contaminant to weak gravitational lensing observables. The alignment of Luminous Red Galaxies, detected unambiguously in observations from the Sloan Digital Sky Survey, can be reproduced by the linear tidal alignment model of Catelan, Kamionkowski and Blandford (2001) on large scales. In this work, we explore the cosmological information encoded in the intrinsic alignments of red galaxies. We make forecasts for the ability of current and future spectroscopic surveys to constrain local primordial non-Gaussianity and Baryon Acoustic Oscillations (BAO) in the cross-correlation function of intrinsic alignments and the galaxy density field. For the Baryon Oscillation Spectroscopic Survey, we find that the BAO signal in the intrinsic alignments is marginally significant with a signal-to-noise ratio of 1.8 and 2.2 with the current LOWZ and CMASS samples of galaxies, respectively, and increasing to 2.3 and 2.7 once the survey is completed. For the Dark Energy Spectroscopic Instrument and for a spectroscopic survey following the EUCLID redshift selection function, we find signal-to-noise ratios of 12 and 15, respectively. Local type primordial non-Gaussianity, parametrized by f{sub NL} = 10, is only marginally significant in the intrinsic alignments signal with signal-to-noise ratios < 2 for the three surveys considered.

  19. Automated quantification of one-dimensional nanostructure alignment on surfaces

    NASA Astrophysics Data System (ADS)

    Dong, Jianjin; Goldthorpe, Irene A.; Mohieddin Abukhdeir, Nasser

    2016-06-01

    A method for automated quantification of the alignment of one-dimensional (1D) nanostructures from microscopy imaging is presented. Nanostructure alignment metrics are formulated and shown to be able to rigorously quantify the orientational order of nanostructures within a two-dimensional domain (surface). A complementary image processing method is also presented which enables robust processing of microscopy images where overlapping nanostructures might be present. Scanning electron microscopy (SEM) images of nanowire-covered surfaces are analyzed using the presented methods and it is shown that past single parameter alignment metrics are insufficient for highly aligned domains. Through the use of multiple parameter alignment metrics, automated quantitative analysis of SEM images is shown to be possible and the alignment characteristics of different samples are able to be quantitatively compared using a similarity metric. The results of this work provide researchers in nanoscience and nanotechnology with a rigorous method for the determination of structure/property relationships, where alignment of 1D nanostructures is significant.

  20. Patterned silk film scaffolds for aligned lamellar bone tissue engineering

    PubMed Central

    Tien, Lee W.; Gil, Eun Seok; Park, Sang-Hyug; Mandal, Biman B.; Kaplan, David L.

    2013-01-01

    Various porous biomaterial scaffolds have been utilized for bone tissue engineering; however, they are often limited in their ability to replicate the structural hierarchy and mechanics of native cortical bone. In this study, the alignment and osteogenic differentiation of human mesenchymal stem cells (MSCs) on patterned silk films (PF) was investigated as a bottom-up, biomimetic approach toward engineering cortical bone lamellae. Screening films cast with nine different micro and nano scale groove patterns showed that cellular alignment was mediated by an interplay between the width and depth of the patterns. MSCs were differentiated in osteogenic medium for four weeks on the PF that induced the highest degree of alignment, while flat films (FF) served as controls. Gene expression analysis and calcium quantification indicated that the PF supported osteogenic differentiation while also inducing robust lamellar alignment of cells and matrix deposition. A secondary alignment effect was noted on the PF where a new layer of aligned cells grew over the first layer, but rotated obliquely to the underlying pattern direction and first layer orientation. This layering and rotation of the aligned MSCs resembled the characteristic structural organization observed in native lamellar bone. The ability to control multilayered lamellar structural hierarchy from the interplay between a patterned 2D surface and cells suggests intriguing options for future biomaterial scaffolds designed to mimic native tissue structures. PMID:23070941

  1. Alignment of gold nanorods by angular photothermal depletion

    SciTech Connect

    Taylor, Adam B.; Chow, Timothy T. Y.; Chon, James W. M.

    2014-02-24

    In this paper, we demonstrate that a high degree of alignment can be imposed upon randomly oriented gold nanorod films by angular photothermal depletion with linearly polarized laser irradiation. The photothermal reshaping of gold nanorods is observed to follow quadratic melting model rather than the threshold melting model, which distorts the angular and spectral hole created on 2D distribution map of nanorods to be an open crater shape. We have accounted these observations to the alignment procedures and demonstrated good agreement between experiment and simulations. The use of multiple laser depletion wavelengths allowed alignment criteria over a large range of aspect ratios, achieving 80% of the rods in the target angular range. We extend the technique to demonstrate post-alignment in a multilayer of randomly oriented gold nanorod films, with arbitrary control of alignment shown across the layers. Photothermal angular depletion alignment of gold nanorods is a simple, promising post-alignment method for creating future 3D or multilayer plasmonic nanorod based devices and structures.

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

    NASA Astrophysics Data System (ADS)

    Qiang, Zhe; Cavicchi, Kevin; Vogt, Bryan

    2015-03-01

    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.

  3. Partial Geometric Frustration in Inorganic Supramolecular Spin Systems with One-Dimensional Trigonally Aligned Magnetic Chains ∞1(MCl4)2− (M = Fe2+, Co2+)

    PubMed Central

    Jiang, Xiao-Ming; Li, Xiao-Guo; Zhang, Ming-Jian; Liu, Zhi-Fa; Liu, Yong; Liu, Jun-Ming; Guo, Guo-Cong

    2015-01-01

    Exploration of new spin systems with low-dimensional subunits have been of great interest in the past decades due to their interesting physical properties and potential applications in molecular spintronics. Two inorganic supramolecular complexes, (Hg3S2)(FeCl4) and (Hg3S2)(CoCl4), with trigonally aligned 1-D infinite magnetic ∞1(FeCl4)2− or ∞1(CoCl4)2− chains have been prepared by solid-state reactions. They exhibit 3-D long-range spin order with strong field dependence and field induced metamagnetic behavior. The intrachain and interchain magnetic coupling constants were estimated by DFT+U and DFT+U+SOC calculations and the both complexes can be regarded as partially frustrated spin systems. The spin Hamiltonian was constructed, the ground state is proposed to be incommensurate spiral spin order, which differs from the commensurate 120° spin structure ground state of fully frustrated trigonal case by a little canted angle. This study shows that cooperative magnetic ordering induced by geometric frustration can be realized in inorganic supramolecular systems assembled by weak van der Waals’ interactions. PMID:26648133

  4. Spontaneous magnetic alignment behaviour in free-living lizards

    NASA Astrophysics Data System (ADS)

    Diego-Rasilla, Francisco J.; Pérez-Mellado, Valentín; Pérez-Cembranos, Ana

    2017-04-01

    Several species of vertebrates exhibit spontaneous longitudinal body axis alignment relative to the Earth's magnetic field (i.e., magnetic alignment) while they are performing different behavioural tasks. Since magnetoreception is still not fully understood, studying magnetic alignment provides evidence for magnetoreception and broadens current knowledge of magnetic sense in animals. Furthermore, magnetic alignment widens the roles of magnetic sensitivity in animals and may contribute to shed new light on magnetoreception. In this context, spontaneous alignment in two species of lacertid lizards ( Podarcis muralis and Podarcis lilfordi) during basking periods was monitored. Alignments in 255 P. muralis and 456 P. lilfordi were measured over a 5-year period. The possible influence of the sun's position (i.e., altitude and azimuth) and geomagnetic field values corresponding to the moment in which a particular lizard was observed on lizards' body axis orientation was evaluated. Both species exhibited a highly significant bimodal orientation along the north-northeast and south-southwest magnetic axis. The evidence from this study suggests that free-living lacertid lizards exhibit magnetic alignment behaviour, since their body alignments cannot be explained by an effect of the sun's position. On the contrary, lizard orientations were significantly correlated with geomagnetic field values at the time of each observation. We suggest that this behaviour might provide lizards with a constant directional reference while they are sun basking. This directional reference might improve their mental map of space to accomplish efficient escape behaviour. This study is the first to provide spontaneous magnetic alignment behaviour in free-living reptiles.

  5. A Dynamic Alignment System for the Final Focus Test Beam

    SciTech Connect

    Ruland, R.E.; Bressler, V.E.; Fischer, G.; Plouffe, D.; /SLAC

    2005-08-16

    The Final Focus Test Beam (FFTB) was conceived as a technological stepping stone on the way to the next linear collider. Nowhere is this more evident than with the alignment subsystems. Alignment tolerances for components prior to beam turn are almost an order of magnitude smaller than for previous projects at SLAC. Position monitoring systems which operate independent of the beam are employed to monitor motions of the components locally and globally with unprecedented precision. An overview of the FFTB alignment system is presented herein.

  6. Design of flood protection for transportation alignments on alluvial fans

    SciTech Connect

    French, R.H.

    1991-01-01

    The method of floodplain delineation on alluvial fans developed for the national flood insurance program is modified to provide estimates of peak flood flows at transportation alignments crossing an alluvial fan. The modified methodology divides the total alignment length into drainage design segments and estimates the peak flows that drainage structures would be required to convey as a function of the length of the drainage design segment, the return period of the event, and the location of the alignment on the alluvial fan. An example of the application of the methodology is provided. 16 refs., 5 figs.

  7. Shuttle orbit IMU alignment. Single-precision computation error

    NASA Technical Reports Server (NTRS)

    Mcclain, C. R.

    1980-01-01

    The source of computational error in the inertial measurement unit (IMU) onorbit alignment software was investigated. Simulation runs were made on the IBM 360/70 computer with the IMU orbit alignment software coded in hal/s. The results indicate that for small IMU misalignment angles (less than 600 arc seconds), single precision computations in combination with the arc cosine method of eigen rotation angle extraction introduces an additional misalignment error of up to 230 arc seconds per axis. Use of the arc sine method, however, produced negligible misalignment error. As a result of this study, the arc sine method was recommended for use in the IMU onorbit alignment software.

  8. Semicrystalline woodpile photonic crystals without complicated alignment via soft lithography

    SciTech Connect

    Lee, Jae-Hwang; Kuang, Ping; Leung, Wai; Kim, Yong-Sung; Park, Joong-Mok; Kang, Henry; Constant, Kristen; Ho, Kai-Ming

    2010-05-13

    We report the fabrication and characterization of woodpile photonic crystals with up to 12 layers through titania nanoparticle infiltration of a polymer template made by soft lithography. Because the complicated alignment in the conventional layer-by-layer fabrication associated with diamondlike symmetry is replaced by a simple 90{sup o} alignment, the fabricated photonic crystal has semicrystalline phase. However, the crystal performs similarly to a perfectly aligned crystal for the light propagation integrated from the surface normal to 30{sup o} at the main photonic band gap.

  9. FlexSnap: Flexible Non-sequential Protein Structure Alignment

    NASA Astrophysics Data System (ADS)

    Salem, Saeed; Zaki, Mohammed J.; Bystroff, Chris

    Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins which 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 sequence permutations are considered. We propose the FlexSnap algorithm for flexible non-topological protein structural alignment. 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.

  10. Fast Fiber-Laser Alignment: Beam Spot-Size Method

    NASA Astrophysics Data System (ADS)

    Zhang, Rong; Guo, Jingyan; Shi, Frank G.

    2005-03-01

    A novel fast and cost-effective method is introduced for the active alignment of a fiber to a laser diode: only four easy laser beam spot-size measurements are required for moving the fiber tip from the far field to the proximity of the optimal alignment position, thus dramatically reducing the total alignment time (at least five times faster than a conventional method),as experimentally confirmed. Moreover, in contrast to the existing methods,the new method is failure-proof. The principle of the proposed method can be applied generally to any type of packages and is illustrated by an example of a butterfly package.

  11. Block Copolymer Nanocomposites in Electric Fields: Kinetics of Alignment

    SciTech Connect

    Liedel, Clemens; Pester, Christian; Ruppel, Markus A; Lewin, Christian; Pavan, Mariela J.; Urban, Volker S; Shenhar, Roy; Bosecke, Peter; Boker, Alexander

    2013-01-01

    We investigate the kinetics of block copolymer/nanoparticle composite alignment in an electric field using in situ transmission small-angle X-ray scattering. As a model system, we employ a lamellae forming polystyrene-block-poly(2-vinyl pyridine) block copolymer with different contents of gold nanoparticles in thick films under solvent vapor annealing. While the alignment improves with increasing nanoparticle fraction, the kinetics slows down. This is explained by changes in the degree of phase separation and viscosity. Our findings provide extended insights into the basics of nanocomposite alignment.

  12. Aligning graphs and finding substructures by a cavity approach

    NASA Astrophysics Data System (ADS)

    Bradde, S.; Braunstein, A.; Mahmoudi, H.; Tria, F.; Weigt, M.; Zecchina, R.

    2010-02-01

    We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The algorithm allows to analyze large graphs and may find applications in fields such as computational biology. As a proof of concept we use our algorithm to align the similarity graphs of two interacting protein families involved in bacterial signal transduction, and to predict actually interacting protein partners between these families.

  13. Effects of diatomic reagent alignment on the A + BC reaction

    NASA Technical Reports Server (NTRS)

    Pattengill, M. D.; Zare, R. N.; Jaffe, R. L.

    1987-01-01

    A computational study is reported on the A + BC - AB + C bimolecular exchange reaction in which BC is aligned with respect to the approach direction of atom A so that the initial rotational angular momentum vector of BC is either parallel (or equivalently antiparallel) or perpendicular to the initial velocity vector of A. The calculations employ a modification of the extended LEPS potential, which permits straightforward generation of noncollinear minimum energy reaction paths. The calculations clearly demonstrate that diatomic reagent alignment can markedly affect the nature of reaction product early partitioning; they also demonstrate that diatomic reagent alignment affects reactive cross sections.

  14. Fourier-transform and global contrast interferometer alignment methods

    DOEpatents

    Goldberg, Kenneth A.

    2001-01-01

    Interferometric methods are presented to facilitate alignment of image-plane components within an interferometer and for the magnified viewing of interferometer masks in situ. Fourier-transforms are performed on intensity patterns that are detected with the interferometer and are used to calculate pseudo-images of the electric field in the image plane of the test optic where the critical alignment of various components is being performed. Fine alignment is aided by the introduction and optimization of a global contrast parameter that is easily calculated from the Fourier-transform.

  15. Polymer Alignment Behavior with Molecular Switching of Ferroelectric Liquid Crystal

    NASA Astrophysics Data System (ADS)

    Murashige, Takeshi; Fujikake, Hideo; Sato, Hiroto; Kikuchi, Hiroshi; Kurita, Taiichiro; Sato, Fumio

    2007-01-01

    This paper describes the molecular alignment behavior of polymer networks with switching of a ferroelectric liquid crystal (FLC) in a molecularly aligned FLC/polymer composite film. The polymer alignment in the composite film, which was slowly formed by photopolymerization-induced phase separation of a heated nematic-phase solution of FLC and monomers, was observed by polarization Raman spectral microscopy. Raman peak intensities originating from the polymers were changed with those from the FLC, when the applied voltage polarity was changed. The trace patterns of the Raman peak intensity with in-plane rotation of the composite film indicated that the formed flexible polymers can follow FLC molecular switching.

  16. [New concepts in aligner therapy with the orthocaps system].

    PubMed

    Khan, Wajeeh

    2014-09-01

    Orthodontic tooth movement with aligners poses challenges peculiar to removable appliances. The mechanical limitations of aligners can be overcome, to some extent, by increasing the aligner grip on teeth as well as by choosing elastic materials in their fabrication. Sound planning together with the use of auxiliaries can result in obtaining satisfactory results for the patients who seek an aesthetically pleasing and comfortable alternative to fixed appliance systems. The salient features of the Orthocaps System are the use of elastic thermoplastics, precision scanning, high pressure thermoforming, 3D interactive set-ups for treatment planning and approval, treatment evaluation at regular intervals during treatment and a unique attachment design (friction pads).

  17. Enamel stripping and the spring aligner appliance--an update.

    PubMed

    Lew, K K

    1993-12-01

    Irregularity of the mandibular incisors in an otherwise good occlusion is quite common in young adult patients. Through use of enamel stripping in the incisor region, it is possible to create sufficient space to align the teeth with a mandibular sectional removable appliance, commonly known as the spring aligner. This article reviews the methods of enamel stripping and describes the author's preferred technique of enamel stripping and the various modifications of the spring aligner appliances that can be prescribed by the general practitioner to correct mandibular anterior crowding.

  18. Light trapping in horizontally aligned silicon microwire solar cells.

    PubMed

    Martinsen, Fredrik A; Smeltzer, Benjamin K; Ballato, John; Hawkins, Thomas; Jones, Max; Gibson, Ursula J

    2015-11-30

    In this study, we demonstrate a solar cell design based on horizontally aligned microwires fabricated from 99.98% pure silicon via the molten core fiber drawing method. A similar structure consisting of 50 μm diameter close packed wires (≈ 0.97 packing density) on a Lambertian white back-reflector showed 86 % absorption for incident light of wavelengths up to 850 nm. An array with a packing fraction of 0.35 showed an absorption of 58 % over the same range, demonstrating the potential for effective light trapping. Prototype solar cells were fabricated to demonstrate the concept. Horizontal wire cells offer several advantages as they can be flexible, and partially transparent, and absorb light efficiently over a wide range of incident angles.

  19. Arrangement for facilitating correct coupling between distributor and driving shaft using alignment marks

    SciTech Connect

    Sasaki, Y.; Nishikawa, M.

    1986-12-30

    An arrangement is described for facilitating correct coupling between a distributor and a driving shaft using alignment marks located either on the distributor or on a cylinder head, the alignment marks consisting of: a first alignment mark provided on a coupling claw arranged at the end of a distributor shaft for coupling with a coupling groove at the end of a driving camshaft; a second alignment mark provided on a housing boss of the distributor; a third alignment mark provided on a housing body of the distributor; and a fourth alignment mark provided on the end of the cylinder head accommodating the driving camshaft; the second and third alignment marks arranged in a manner the the third and fourth alignment marks align when the first alignment mark on the coupling claw is aligned with the second alignment mark on the housing boss of the distributor and the coupling claw of the distributor is correctly coupled with the coupling groove of the driving camshaft.

  20. Effect of aligning pulse train on the orientation and alignment of a molecule in presence of orienting pulse

    NASA Astrophysics Data System (ADS)

    Tyagi, Ashish; Maan, Anjali; Ahlawat, Dharamvir Singh; Prasad, Vinod

    2017-02-01

    Field-free molecular alignment is studied theoretically in presence of orienting laser pulse and a delayed Infrared laser (IRL) pulse train. The pulse shapes taken are sine square (sin2) and square. The degree of alignment can be significantly enhanced by the combination of orienting pulse and IRL pulse train compared with only IRL pulse train. Special emphasis is laid on time delay between orienting and aligning pulse, the width and shape of the pulse train. By adjusting the time delay, width and intensity of coupling laser one can suppress a population of particular state while simultaneously enhancing the population of desired states.

  1. Effect of aligning pulse train on the orientation and alignment of a molecule in presence of orienting pulse.

    PubMed

    Tyagi, Ashish; Maan, Anjali; Ahlawat, Dharamvir Singh; Prasad, Vinod

    2017-02-15

    Field-free molecular alignment is studied theoretically in presence of orienting laser pulse and a delayed Infrared laser (IRL) pulse train. The pulse shapes taken are sine square (sin(2)) and square. The degree of alignment can be significantly enhanced by the combination of orienting pulse and IRL pulse train compared with only IRL pulse train. Special emphasis is laid on time delay between orienting and aligning pulse, the width and shape of the pulse train. By adjusting the time delay, width and intensity of coupling laser one can suppress a population of particular state while simultaneously enhancing the population of desired states.

  2. 58. Adney Gap. View of curvilinear. Alignment of parkway passing ...

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

    58. Adney Gap. View of curvilinear. Alignment of parkway passing through agricultural lease lands. Looking south-southwest. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

  3. Ocular alignment under general anesthesia in congenital esotropia.

    PubMed

    Castanera de Molina, A; Giner Muñoz, M L

    1991-01-01

    Ocular alignment is usually more divergent in strabismus patients under general anesthesia than in the awake state. Although clinical and anesthetized alignments have been reported to be correlated through the equation A = 0.8P + 30, significant differences in the amount of divergence under anesthesia have been reported between esotropes and exotropes. We found differences in response to general anesthesia in a group of 83 congenital esotropes. The averaged anesthetized alignment pertained to the whole group of 6.2 prism diopters of esotropia, which correlated poorly with the preoperative deviation. Mean anesthetized alignments were similar for any amount of preoperative deviation. Recommendations of intraoperative adjustment of surgery based on the anesthetized position should, in our opinion, be reconsidered and recalculated when treating congenital esotropes. A prediction of surgical results following these recommendations suggested an increase of the undercorrection rate, probably linked to an incorrect identification of normal and anomalous cases to the Apt-Romano test.

  4. Magnetic alignment of block copolymer microdomains by intrinsic chain anisotropy

    DOE PAGES

    Rokhlenko, Yekaterina; Yager, Kevin G.; Gopinadhan, Manesh; ...

    2015-12-18

    We examine the role of intrinsic chain susceptibility anisotropy in magnetic field directed self-assembly of a block copolymer using in situ x-ray scattering. Alignment of a lamellar mesophase is observed on cooling across the disorder-order transition with the resulting orientational order inversely proportional to the cooling rate. We discuss the origin of the susceptibility anisotropy, Δχ, that drives alignment and calculate its magnitude using coarse-grained molecular dynamics to sample conformations of surface-tethered chains, finding Δχ ≈ 2×10–8. From field-dependent scattering data, we estimate that grains of ≈ 1.2 μm are present during alignment. Furthermore, these results demonstrate that intrinsic anisotropymore » is sufficient to support strong field-induced mesophase alignment and suggest a versatile strategy for field control of orientational order in block copolymers.« less

  5. Proceedings of the first international workshop on accelerator alignment

    SciTech Connect

    Not Available

    1990-10-01

    This report contains papers on the following accelerator topics: current alignment topics; toolboxes: instrumentation, software, and methods; fiducialization of conventional magnets; fiducialization of superconducting magnets; and next generation linear colliders.

  6. Magnetic alignment of block copolymer microdomains by intrinsic chain anisotropy

    SciTech Connect

    Rokhlenko, Yekaterina; Yager, Kevin G.; Gopinadhan, Manesh; Osuji, Chinedum O.; Zhang, Kai; O'Hern, Corey S.; Larson, Steven R.; Gopalan, Padma; Majewski, Pawel W.

    2015-12-18

    We examine the role of intrinsic chain susceptibility anisotropy in magnetic field directed self-assembly of a block copolymer using in situ x-ray scattering. Alignment of a lamellar mesophase is observed on cooling across the disorder-order transition with the resulting orientational order inversely proportional to the cooling rate. We discuss the origin of the susceptibility anisotropy, Δχ, that drives alignment and calculate its magnitude using coarse-grained molecular dynamics to sample conformations of surface-tethered chains, finding Δχ ≈ 2×10–8. From field-dependent scattering data, we estimate that grains of ≈ 1.2 μm are present during alignment. Furthermore, these results demonstrate that intrinsic anisotropy is sufficient to support strong field-induced mesophase alignment and suggest a versatile strategy for field control of orientational order in block copolymers.

  7. Progressive alignment of genomic signals by multiple dynamic time warping.

    PubMed

    Skutkova, Helena; Vitek, Martin; Sedlar, Karel; Provaznik, Ivo

    2015-11-21

    This paper presents the utilization of progressive alignment principle for positional adjustment of a set of genomic signals with different lengths. The new method of multiple alignment of signals based on dynamic time warping is tested for the purpose of evaluating the similarity of different length genes in phylogenetic studies. Two sets of phylogenetic markers were used to demonstrate the effectiveness of the evaluation of intraspecies and interspecies genetic variability. The part of the proposed method is modification of pairwise alignment of two signals by dynamic time warping with using correlation in a sliding window. The correlation based dynamic time warping allows more accurate alignment dependent on local homologies in sequences without the need of scoring matrix or evolutionary models, because mutual similarities of residues are included in the numerical code of signals.

  8. Experiments in Aligning Threaded Parts Using a Robot Hand

    NASA Technical Reports Server (NTRS)

    Diftler, M. A.; Walker, I. D.

    1999-01-01

    Techniques for determining and correcting threaded part alignment using force and angular position data are developed to augment currently limited techniques for align- ing threaded parts. These new techniques are based on backspinning a nut with respect to a bolt and measuring the force change that occurs when the bolt "falls" into the nut. Kinematic models that describe the relationship between threaded parts during backspinning are introduced and are used to show how angular alignment may be determined. The models indicate how to distinguish between the aligned and misaligned cases of a bolt and a nut connection by using axial force data only. In addition, by tracking the in-plane relative attitude of the bolt during spinning, data can be obtained on the direction of the angular misalignment which, in turn, is used to correct the misalignment. Results from experiments using a bolt held in a specialized fixture and a three fingers Stanford/JPL hand are presented.

  9. Attitude sensor alignment calibration for the solar maximum mission

    NASA Technical Reports Server (NTRS)

    Pitone, Daniel S.; Shuster, Malcolm D.

    1990-01-01

    An earlier heuristic study of the fine attitude sensors for the Solar Maximum Mission (SMM) revealed a temperature dependence of the alignment about the yaw axis of the pair of fixed-head star trackers relative to the fine pointing Sun sensor. Here, new sensor alignment algorithms which better quantify the dependence of the alignments on the temperature are developed and applied to the SMM data. Comparison with the results from the previous study reveals the limitations of the heuristic approach. In addition, some of the basic assumptions made in the prelaunch analysis of the alignments of the SMM are examined. The results of this work have important consequences for future missions with stringent attitude requirements and where misalignment variations due to variations in the temperature will be significant.

  10. 21. VIEW OF GRAND CANAL, SHOWING OLD ALIGNMENT, LOOKING WEST ...

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

    21. VIEW OF GRAND CANAL, SHOWING OLD ALIGNMENT, LOOKING WEST LOCATION UNKNOWN. THE WIDE DRY BED OF THE SALT RIVER SPANS THE BACKGROUND. Photographer: Mark Durben, April 1989 - Grand Canal, North side of Salt River, Tempe, Maricopa County, AZ

  11. Enviroment, from southwest, showing Castle Garden Bridge and alignment of ...

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

    Enviroment, from southwest, showing Castle Garden Bridge and alignment of Township Road 343 over Bennetts Branch of Sinnemahoning Creek - Castle Garden Bridge, Township Route 343 over Bennetts Branch of Sinnemahoning Creek, Driftwood, Cameron County, PA

  12. Chemical strategies for die/wafer submicron alignment and bonding.

    SciTech Connect

    Martin, James Ellis; Baca, Alicia I.; Chu, Dahwey; Rohwer, Lauren Elizabeth Shea

    2010-09-01

    This late-start LDRD explores chemical strategies that will enable sub-micron alignment accuracy of dies and wafers by exploiting the interfacial energies of chemical ligands. We have micropatterned commensurate features, such as 2-d arrays of micron-sized gold lines on the die to be bonded. Each gold line is functionalized with alkanethiol ligands before the die are brought into contact. The ligand interfacial energy is minimized when the lines on the die are brought into registration, due to favorable interactions between the complementary ligand tails. After registration is achieved, standard bonding techniques are used to create precision permanent bonds. We have computed the alignment forces and torque between two surfaces patterned with arrays of lines or square pads to illustrate how best to maximize the tendency to align. We also discuss complex, aperiodic patterns such as rectilinear pad assemblies, concentric circles, and spirals that point the way towards extremely precise alignment.

  13. Automatic alignment of a displacement-measuring heterodyne interferometer

    NASA Astrophysics Data System (ADS)

    Logan, Jennifer E.; Halverson, Peter G.; Regehr, Martin W.; Spero, Robert E.

    2002-07-01

    A technique to align automatically the beams of displacement-measuring interferometric gauges is described. The pointing of the launched beam is modulated in a circular pattern, and the resulting displacement signal is demodulated synchronously to determine the alignment error. This error signal is used in a control system that maintains the alignment for maximum path between a pair of fiducial hollow-cube corner retroreflectors, which minimizes sensitivity to alignment drift. The technique is tested on a developmental gauge of the type intended for the Space Interferometry Mission. The displacement signal for the gauge is generated in digital form; and the lock-in amplifier functions of modulation, demodulation, and filtering are all implemented digitally.

  14. 115. Doughton Park Recreation Area. View of roadway alignment around ...

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

    115. Doughton Park Recreation Area. View of roadway alignment around alligator back and parking overlook in foreground. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

  15. Incorporating Linguistic Information to Statistical Word-Level Alignment

    NASA Astrophysics Data System (ADS)

    Cendejas, Eduardo; Barceló, Grettel; Gelbukh, Alexander; Sidorov, Grigori

    Parallel texts are enriched by alignment algorithms, thus establishing a relationship between the structures of the implied languages. Depending on the alignment level, the enrichment can be performed on paragraphs, sentences or words, of the expressed content in the source language and its translation. There are two main approaches to perform word-level alignment: statistical or linguistic. Due to the dissimilar grammar rules the languages have, the statistical algorithms usually give lower precision. That is why the development of this type of algorithms is generally aimed at a specific language pair using linguistic techniques. A hybrid alignment system based on the combination of the two traditional approaches is presented in this paper. It provides user-friendly configuration and is adaptable to the computational environment. The system uses linguistic resources and procedures such as identification of cognates, morphological information, syntactic trees, dictionaries, and semantic domains. We show that the system outperforms existing algorithms.

  16. Chimeric alignment by dynamic programming: Algorithm and biological uses

    SciTech Connect

    Komatsoulis, G.A.; Waterman, M.S.

    1997-12-01

    A new nearest-neighbor method for detecting chimeric 16S rRNA artifacts generated during PCR amplification from mixed populations has been developed. The method uses dynamic programming to generate an optimal chimeric alignment, defined as the highest scoring alignment between a query and a concatenation of a 5{prime} and a 3{prime} segment from two separate entries from a database of related sequences. Chimeras are detected by studying the scores and form of the chimeric and global sequence alignments. The chimeric alignment method was found to be marginally more effective than k-tuple based nearest-neighbor methods in simulation studies, but its most effective use is in concert with k-tuple methods. 15 refs., 3 figs., 1 tab.

  17. Attitude sensor alignment calibration for the solar maximum mission

    NASA Astrophysics Data System (ADS)

    Pitone, Daniel S.; Shuster, Malcolm D.

    1990-12-01

    An earlier heuristic study of the fine attitude sensors for the Solar Maximum Mission (SMM) revealed a temperature dependence of the alignment about the yaw axis of the pair of fixed-head star trackers relative to the fine pointing Sun sensor. Here, new sensor alignment algorithms which better quantify the dependence of the alignments on the temperature are developed and applied to the SMM data. Comparison with the results from the previous study reveals the limitations of the heuristic approach. In addition, some of the basic assumptions made in the prelaunch analysis of the alignments of the SMM are examined. The results of this work have important consequences for future missions with stringent attitude requirements and where misalignment variations due to variations in the temperature will be significant.

  18. 1. Old road alignment, now entrance to government parking area, ...

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

    1. Old road alignment, now entrance to government parking area, facing 24 degrees north northeast - Oak Creek Administrative Center, One half mile east of Zion-Mount Carmel Highway at Oak Creek, Springdale, Washington County, UT

  19. Flood damaged foot bridge at Tamarack Creek on alignment of ...

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

    Flood damaged foot bridge at Tamarack Creek on alignment of Old Big Oak Flat Road. Looking northeast - Big Oak Flat Road, Between Big Oak Flat Entrance & Merced River, Yosemite Village, Mariposa County, CA

  20. A self-assembly pathway to aligned monodomain gels

    SciTech Connect

    Zhang, Shuming; Greenfield, Megan A.; Mata, Alvaro; Palmer, Liam C.; Bitton, Ronit; Mantei, Jason R.; Aparicio, Conrado; Olvera de la Cruz, Monica; Stupp, Samuel I.

    2010-09-27

    Aggregates of charged amphiphilic molecules have been found to access a structure at elevated temperature that templates alignment of supramolecular fibrils over macroscopic scales. The thermal pathway leads to a lamellar plaque structure with fibrous texture that breaks on cooling into large arrays of aligned nanoscale fibres and forms a strongly birefringent liquid. By manually dragging this liquid crystal from a pipette onto salty media, it is possible to extend this alignment over centimetres in noodle-shaped viscoelastic strings. Using this approach, the solution of supramolecular filaments can be mixed with cells at physiological temperatures to form monodomain gels of aligned cells and filaments. The nature of the self-assembly process and its biocompatibility would allow formation of cellular wires in situ that have any length and customized peptide compositions for use in biological applications.