WorldWideScience

Sample records for alignment

  1. Alignment validation

    CERN Document Server

    Golling, T

    2007-01-01

    The four experiments, ALICE, ATLAS, CMS and LHCb are currently under construction at 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 and the muon system requires an accurate alignment of all detector elements. Alignment information 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.

  2. Beyond Alignment

    DEFF Research Database (Denmark)

    Beyond Alignment: Applying Systems Thinking to Architecting Enterprises is a comprehensive reader about how enterprises can apply systems thinking in their enterprise architecture practice, for business transformation and for strategic execution. The book's contributors find that systems thinking...... is a valuable way of thinking about the viable enterprise and how to architect it....

  3. Image alignment

    Science.gov (United States)

    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.

  4. DNA Align Editor: DNA Alignment Editor Tool

    Science.gov (United States)

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

  5. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez.

    Since June of 2009, the muon alignment group has focused on providing new alignment constants and on finalizing the hardware alignment reconstruction. Alignment constants for DTs and CSCs were provided for CRAFT09 data reprocessing. For DT chambers, the track-based alignment was repeated using CRAFT09 cosmic ray muons and validated using segment extrapolation and split cosmic tools. One difference with respect to the previous alignment is that only five degrees of freedom were aligned, leaving the rotation around the local x-axis to be better determined by the hardware system. Similarly, DT chambers poorly aligned by tracks (due to limited statistics) were aligned by a combination of photogrammetry and hardware-based alignment. For the CSC chambers, the hardware system provided alignment in global z and rotations about local x. Entire muon endcap rings were further corrected in the transverse plane (global x and y) by the track-based alignment. Single chamber track-based alignment suffers from poor statistic...

  6. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and J. Pivarski

    2011-01-01

    Alignment efforts in the first few months of 2011 have shifted away from providing alignment constants (now a well established procedure) and focussed on some critical remaining issues. The single most important task left was to understand the systematic differences observed between the track-based (TB) and hardware-based (HW) barrel alignments: a systematic difference in r-φ and in z, which grew as a function of z, and which amounted to ~4-5 mm differences going from one end of the barrel to the other. This difference is now understood to be caused by the tracker alignment. The systematic differences disappear when the track-based barrel alignment is performed using the new “twist-free” tracker alignment. This removes the largest remaining source of systematic uncertainty. Since the barrel alignment is based on hardware, it does not suffer from the tracker twist. However, untwisting the tracker causes endcap disks (which are aligned ...

  7. Fast statistical alignment.

    Directory of Open Access Journals (Sweden)

    Robert K Bradley

    2009-05-01

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

  8. Fast statistical alignment.

    Science.gov (United States)

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

    2009-05-01

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

  9. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    The main developments in muon alignment since March 2010 have been the production, approval and deployment of alignment constants for the ICHEP data reprocessing. In the barrel, a new geometry, combining information from both hardware and track-based alignment systems, has been developed for the first time. The hardware alignment provides an initial DT geometry, which is then anchored as a rigid solid, using the link alignment system, to a reference frame common to the tracker. The “GlobalPositionRecords” for both the Tracker and Muon systems are being used for the first time, and the initial tracker-muon relative positioning, based on the link alignment, yields good results within the photogrammetry uncertainties of the Tracker and alignment ring positions. For the first time, the optical and track-based alignments show good agreement between them; the optical alignment being refined by the track-based alignment. The resulting geometry is the most complete to date, aligning all 250 DTs, ...

  10. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Z. Szillasi and G. Gomez.

    2013-01-01

    When CMS is opened up, major components of the Link and Barrel Alignment systems will be removed. This operation, besides allowing for maintenance of the detector underneath, is needed for making interventions that will reinforce the alignment measurements and make the operation of the alignment system more reliable. For that purpose and also for their general maintenance and recalibration, the alignment components will be transferred to the Alignment Lab situated in the ISR area. For the track-based alignment, attention is focused on the determination of systematic uncertainties, which have become dominant, since now there is a large statistics of muon tracks. This will allow for an improved Monte Carlo misalignment scenario and updated alignment position errors, crucial for high-momentum muon analysis such as Z′ searches.

  11. Fast Statistical Alignment

    OpenAIRE

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

    2009-01-01

    We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multi...

  12. Horizontal carbon nanotube alignment.

    Science.gov (United States)

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

    2016-09-21

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

  13. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    Most of the work in muon alignment since December 2009 has focused on the geometry reconstruction from the optical systems and improvements in the internal alignment of the DT chambers. The barrel optical alignment system has progressively evolved from reconstruction of single active planes to super-planes (December 09) to a new, full barrel reconstruction. Initial validation studies comparing this full barrel alignment at 0T with photogrammetry provide promising results. In addition, the method has been applied to CRAFT09 data, and the resulting alignment at 3.8T yields residuals from tracks (extrapolated from the tracker) which look smooth, suggesting a good internal barrel alignment with a small overall offset with respect to the tracker. This is a significant improvement, which should allow the optical system to provide a start-up alignment for 2010. The end-cap optical alignment has made considerable progress in the analysis of transfer line data. The next set of alignment constants for CSCs will there...

  14. Orthodontics and Aligners

    Science.gov (United States)

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

  15. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    The main progress of the muon alignment group since March has been in the refinement of both the track-based alignment for the DTs and the hardware-based alignment for the CSCs. For DT track-based alignment, there has been significant improvement in the internal alignment of the superlayers inside the DTs. In particular, the distance between superlayers is now corrected, eliminating the residual dependence on track impact angles, and good agreement is found between survey and track-based corrections. The new internal geometry has been approved to be included in the forthcoming reprocessing of CRAFT samples. The alignment of DTs with respect to the tracker using global tracks has also improved significantly, since the algorithms use the latest B-field mapping, better run selection criteria, optimized momentum cuts, and an alignment is now obtained for all six degrees of freedom (three spatial coordinates and three rotations) of the aligned DTs. This work is ongoing and at a stage where we are trying to unders...

  16. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2011-01-01

    The Muon Alignment work now focuses on producing a new track-based alignment with higher track statistics, making systematic studies between the results of the hardware and track-based alignment methods and aligning the barrel using standalone muon tracks. Currently, the muon track reconstruction software uses a hardware-based alignment in the barrel (DT) and a track-based alignment in the endcaps (CSC). An important task is to assess the muon momentum resolution that can be achieved using the current muon alignment, especially for highly energetic muons. For this purpose, cosmic ray muons are used, since the rate of high-energy muons from collisions is very low and the event statistics are still limited. Cosmics have the advantage of higher statistics in the pT region above 100 GeV/c, but they have the disadvantage of having a mostly vertical topology, resulting in a very few global endcap muons. Only the barrel alignment has therefore been tested so far. Cosmic muons traversing CMS from top to bottom are s...

  17. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    Since December, the muon alignment community has focused on analyzing the data recorded so far in order to produce new DT and CSC Alignment Records for the second reprocessing of CRAFT data. Two independent algorithms were developed which align the DT chambers using global tracks, thus providing, for the first time, a relative alignment of the barrel with respect to the tracker. These results are an important ingredient for the second CRAFT reprocessing and allow, for example, a more detailed study of any possible mis-modelling of the magnetic field in the muon spectrometer. Both algorithms are constructed in such a way that the resulting alignment constants are not affected, to first order, by any such mis-modelling. The CSC chambers have not yet been included in this global track-based alignment due to a lack of statistics, since only a few cosmics go through the tracker and the CSCs. A strategy exists to align the CSCs using the barrel as a reference until collision tracks become available. Aligning the ...

  18. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2011-01-01

    A new set of muon alignment constants was approved in August. The relative position between muon chambers is essentially unchanged, indicating good detector stability. The main changes concern the global positioning of the barrel and of the endcap rings to match the new Tracker geometry. Detailed studies of the differences between track-based and optical alignment of DTs have proven to be a valuable tool for constraining Tracker alignment weak modes, and this information is now being used as part of the alignment procedure. In addition to the “split-cosmic” analysis used to investigate the muon momentum resolution at high momentum, a new procedure based on reconstructing the invariant mass of di-muons from boosted Zs is under development. Both procedures show an improvement in the momentum precision of Global Muons with respect to Tracker-only Muons. Recent developments in track-based alignment include a better treatment of the tails of residual distributions and accounting for correla...

  19. Real Interference Alignment

    CERN Document Server

    Motahari, Abolfazl Seyed; Maddah-Ali, Mohammad-Ali; Khandani, Amir Keyvan

    2010-01-01

    In this paper, we show that the total Degrees-Of-Freedoms (DOF) of the $K$-user Gaussian Interference Channel (GIC) can be achieved by incorporating a new alignment technique known as \\emph{real interference alignment}. This technique compared to its ancestor \\emph{vector interference alignment} performs on a single real line and exploits the properties of real numbers to provide optimal signaling. The real interference alignment relies on a new coding scheme in which several data streams having fractional multiplexing gains are sent by transmitters and interfering streams are aligned at receivers. The coding scheme is backed up by a recent result in the field of Diophantine approximation, which states that the convergence part of the Khintchine-Groshev theorem holds for points on non-degenerate manifolds.

  20. Alignment for CSR

    International Nuclear Information System (INIS)

    Cooled Storage Ring of Heavy Ion Research Facility in Lanzhou (HIRFL-CSR) belongs to China great scientific project in China. The alignment for it is very difficult because of very large area and very high accuracy. For the special case in HIRFL-CSR, some new methods and new instruments are used, including the construction of survey control network, the usage of laser tracker, and CSR alignment database system with applications developed to store and analyze data. The author describes the whole procedure of CSR alignment

  1. Galaxy alignments: An overview

    CERN Document Server

    Joachimi, Benjamin; Kitching, Thomas D; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Hoekstra, Henk; Kiessling, Alina; Kirk, Donnacha; Rassat, Anais

    2015-01-01

    The alignments between galaxies, their underlying matter structures, and the cosmic web constitute vital ingredients for a comprehensive understanding of gravity, the nature of matter, and structure formation in the Universe. We provide an overview on the state of the art in the study of these alignment processes and their observational signatures, aimed at a non-specialist audience. The development of the field over the past one hundred years is briefly reviewed. We also discuss the impact of galaxy alignments on measurements of weak gravitational lensing, and discuss avenues for making theoretical and observational progress over the coming decade.

  2. Tidal alignment of galaxies

    CERN Document Server

    Blazek, Jonathan; Seljak, Uroš

    2015-01-01

    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 ...

  3. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    Since September, the muon alignment system shifted from a mode of hardware installation and commissioning to operation and data taking. All three optical subsystems (Barrel, Endcap and Link alignment) have recorded data before, during and after CRAFT, at different magnetic fields and during ramps of the magnet. This first data taking experience has several interesting goals: •    study detector deformations and movements under the influence of the huge magnetic forces; •    study the stability of detector structures and of the alignment system over long periods, •    study geometry reproducibility at equal fields (specially at 0T and 3.8T); •    reconstruct B=0T geometry and compare to nominal/survey geometries; •    reconstruct B=3.8T geometry and provide DT and CSC alignment records for CMSSW. However, the main goal is to recons...

  4. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    S. Szillasi

    2013-01-01

    The CMS detector has been gradually opened and whenever a wheel became exposed the first operation was the removal of the MABs, the sensor structures of the Hardware Barrel Alignment System. By the last days of June all 36 MABs have arrived at the Alignment Lab at the ISR where, as part of the Alignment Upgrade Project, they are refurbished with new Survey target holders. Their electronic checkout is on the way and finally they will be recalibrated. During LS1 the alignment system will be upgraded in order to allow more precise reconstruction of the MB4 chambers in Sector 10 and Sector 4. This requires new sensor components, so called MiniMABs (pictured below), that have already been assembled and calibrated. Image 6: Calibrated MiniMABs are ready for installation For the track-based alignment, the systematic uncertainties of the algorithm are under scrutiny: this study will enable the production of an improved Monte Carlo misalignment scenario and to update alignment position errors eventually, crucial...

  5. ATLAS Muon Endcap Alignment

    CERN Document Server

    Bensinger, J R

    2005-01-01

    To align the endcap muon chambers of the ATLAS experiment, an optical grid is set up between aluminum “alignment bars” nested in each layer of chambers. Optical lines are made of laser diodes and CCD cameras that form an alignment grid. The alignment bars are self-aligning. They are then carefully measured using a large coordinate measuring machine (CMM). The subsequent shape changes of the bar are determined by calculations that are corrected by the readings of the internal monitors. The relationship between the bars is then established by a network of sensors that measure the bearing angle of light sources on the other parts of the system. The system is over-determined and the location and orientation of each bar is determined using a fitting program. Chambers are then referenced to the alignment grid using proximity sensors. This information is used to provide corrections to the nominal chamber positions before calculating track momentum. The performance of the system has been validated in a test beam ...

  6. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2012-01-01

      A new muon alignment has been produced for 2012 A+B data reconstruction. It uses the latest Tracker alignment and single-muon data samples to align both DTs and CSCs. Physics validation has been performed and shows a modest improvement in stand-alone muon momentum resolution in the barrel, where the alignment is essentially unchanged from the previous version. The reference-target track-based algorithm using only collision muons is employed for the first time to align the CSCs, and a substantial improvement in resolution is observed in the endcap and overlap regions for stand-alone muons. This new alignment is undergoing the approval process and is expected to be deployed as part of a new global tag in the beginning of December. The pT dependence of the φ-bias in curvature observed in Monte Carlo was traced to a relative vertical misalignment between the Tracker and barrel muon systems. Moving the barrel as a whole to match the Tracker cures this pT dependence, leaving only the &phi...

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

    Science.gov (United States)

    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…

  8. MaxAlign: maximizing usable data in an alignment

    OpenAIRE

    Pedersen Anders G; Sackett Peter W; Gouveia-Oliveira Rodrigo

    2007-01-01

    Abstract Background The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. Results MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns – the alignment area – by selecting the ...

  9. Ergodic Secret Alignment

    CERN Document Server

    Bassily, Raef

    2010-01-01

    In this paper, we introduce two new achievable schemes for the fading multiple access wiretap channel (MAC-WT). In the model that we consider, we assume that perfect knowledge of the state of all channels is available at all the nodes in a causal fashion. Our schemes use this knowledge together with the time varying nature of the channel model to align the interference from different users at the eavesdropper perfectly in a one-dimensional space while creating a higher dimensionality space for the interfering signals at the legitimate receiver hence allowing for better chance of recovery. While we achieve this alignment through signal scaling at the transmitters in our first scheme (scaling based alignment (SBA)), we let nature provide this alignment through the ergodicity of the channel coefficients in the second scheme (ergodic secret alignment (ESA)). For each scheme, we obtain the resulting achievable secrecy rate region. We show that the secrecy rates achieved by both schemes scale with SNR as 1/2log(SNR...

  10. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2010-01-01

    For the last three months, the Muon Alignment group has focussed on providing a new, improved set of alignment constants for the end-of-year data reprocessing. These constants were delivered on time and approved by the CMS physics validation team on November 17. The new alignment incorporates several improvements over the previous one from March for nearly all sub-systems. Motivated by the loss of information from a hardware failure in May (an entire MAB was lost), the optical barrel alignment has moved from a modular, super-plane reconstruction, to a full, single loop calculation of the entire geometry for all DTs in stations 1, 2 and 3. This makes better use of the system redundancy, mitigating the effect of the information loss. Station 4 is factorised and added afterwards to make the system smaller (and therefore faster to run), and also because the MAB calibration at the MB4 zone is less precise. This new alignment procedure was tested at 0 T against photogrammetry resulting in precisions of the order...

  11. Alignment telescope for Antares

    International Nuclear Information System (INIS)

    The Antares Automatic Alignment System employs a specially designed telescope for alignment of its laser beamlines. There are two telescopes in the system, and since each telescope is a primary alignment reference, stringent boresight accuracy and stability over the focus range were required. Optical and mechanical designs, which meet this requirement as well as that of image quality over a wide wavelength band, are described. Special test techniques for initial assembly and alignment of the telescope are also presented. The telescope, which has a 180-mm aperture FK51-KZF2 type glass doublet objective, requires a boresight accuracy of 2.8 μrad at two focal lengths, and object distances between 11 meters and infinity. Travel of a smaller secondary doublet provides focus from 11 m to infinity with approximately 7.8 m effective focal length. By flipping in a third doublet, the effective focal length is reduced to 2.5 m. Telescope alignment was accomplished by using a rotary air bearing to establish an axis in front of the system and placing the focus of a Laser Unequal Path Interferometer (LUPI) at the image plane

  12. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    2012-01-01

      The new alignment for the DT chambers has been successfully used in physics analysis starting with the 52X Global Tag. The remaining main areas of development over the next few months will be preparing a new track-based CSC alignment and producing realistic APEs (alignment position errors) and MC misalignment scenarios to match the latest muon alignment constants. Work on these items has been delayed from the intended timeline, mostly due to a large involvement of the muon alignment man-power in physics analyses over the first half of this year. As CMS keeps probing higher and higher energies, special attention must be paid to the reconstruction of very-high-energy muons. Recent muon POG reports from mid-June show a φ-dependence in curvature bias in Monte Carlo samples. This bias is observed already at the tracker level, where it is constant with muon pT, while it grows with pT as muon chamber information is added to the tracks. Similar studies show a much smaller effect in data, at le...

  13. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    M. Dallavalle

    2013-01-01

    A new Muon misalignment scenario for 2011 (7 TeV) Monte Carlo re-processing was re-leased. The scenario is based on running of standard track-based reference-target algorithm (exactly as in data) using single-muon simulated sample (with the transverse-momentum spectrum matching data). It used statistics similar to what was used for alignment with 2011 data, starting from an initially misaligned Muon geometry from uncertainties of hardware measurements and using the latest Tracker misalignment geometry. Validation of the scenario (with muons from Z decay and high-pT simulated muons) shows that it describes data well. The study of systematic uncertainties (dominant by now due to huge amount of data collected by CMS and used for muon alignment) is finalised. Realistic alignment position errors are being obtained from the estimated uncertainties and are expected to improve the muon reconstruction performance. Concerning the Hardware Alignment System, the upgrade of the Barrel Alignment is in progress. By now, d...

  14. The CMS Tracker Alignment Strategy

    CERN Document Server

    Weber, Martin

    2006-01-01

    CMS silicon Tracker alignment consists of three key components: Survey during tracker construction, measurements with the Laser Alignment System during operation and track based alignment. Methods and results are explained in detail, with a special focus on track based alignment due to its enormous complexity and numerical challenges.

  15. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan

    Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...

  16. MUSE optical alignment procedure

    Science.gov (United States)

    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.

  17. Strategic Alignment of Business Intelligence

    OpenAIRE

    Cederberg, Niclas

    2010-01-01

    This thesis is about the concept of strategic alignment of business intelligence. It is based on a theoretical foundation that is used to define and explain business intelligence, data warehousing and strategic alignment. By combining a number of different methods for strategic alignment a framework for alignment of business intelligence is suggested. This framework addresses all different aspects of business intelligence identified as relevant for strategic alignment of business intelligence...

  18. RHIC survey and alignment

    International Nuclear Information System (INIS)

    The Relativistic Heavy Ion Collider consists of two interlaced plane rings, a pair of mirror-symmetric beam injection arcs, a spatially curved beam transfer line from the Alternating Gradient Synchrotron, and a collection of precisely positioned and aligned magnets, on appropriately positioned support stands, threaded on those arcs. RHIC geometry is defined by six beam crossing points exactly in a plane, lying precisely at the vertices of a regular hexagon of specified size position and orientation of this hexagon are defined geodetically. Survey control and alignment procedures, currently in use to construct RHIC, are described

  19. Discriminative Shape Alignment

    DEFF Research Database (Denmark)

    Loog, M.; de Bruijne, M.

    taking into account that eventually the shapes are to be assigned to two or more different classes. This work introduces a discriminative variation to well-known Procrustes alignment and demonstrates its benefit over this classical method in shape classification tasks. The focus is on two...

  20. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and Y. Pakhotin

    2012-01-01

      A new track-based alignment for the DT chambers is ready for deployment: an offline tag has already been produced which will become part of the 52X Global Tag. This alignment was validated within the muon alignment group both at low and high momentum using a W/Z skim sample. It shows an improved mass resolution for pairs of stand-alone muons, improved curvature resolution at high momentum, and improved DT segment extrapolation residuals. The validation workflow for high-momentum muons used to depend solely on the “split cosmics” method, looking at the curvature difference between muon tracks reconstructed in the upper or lower half of CMS. The validation has now been extended to include energetic muons decaying from heavily boosted Zs: the di-muon invariant mass for global and stand-alone muons is reconstructed, and the invariant mass resolution is compared for different alignments. The main areas of development over the next few months will be preparing a new track-based C...

  1. Aligning Mental Representations

    DEFF Research Database (Denmark)

    Kano Glückstad, Fumiko

    2013-01-01

    This work introduces a framework that implements asymmetric communication theory proposed by Sperber and Wilson [1]. The framework applies a generalization model known as the Bayesian model of generalization (BMG) [2] for aligning knowledge possessed by two communicating parties. The work focuses...

  2. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  3. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  4. MaxAlign: maximizing usable data in an alignment

    Directory of Open Access Journals (Sweden)

    Pedersen Anders G

    2007-08-01

    Full Text Available Abstract Background The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. Results MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid symbols that are present in gap-free columns – the alignment area – by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS that we consider useful for comparing tree topologies. Conclusion We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

  5. Jet activity versus alignment

    CERN Document Server

    Lokhtin, I P; Sarycheva, L I; Snigirev, A M

    2005-01-01

    The hypothesis about the relation between the observed alignment of spots in the x-ray film in cosmic ray emulsion experiments and the features of events in which jets prevail at super high energies is tested. Due to strong correlation between jet axis directions and that between momenta (almost collinearity) of jet particles, the evaluated degree of alignment is considerably larger than that at randomly selected chaoticly located spots in the x-ray film. It appears comparable with experimental data provided that the height of primary interaction, the collision energy and the total energy of selected clusters meet certain conditions. The Monte Carlo generator PYTHIA, which basically well describes jet events in hadron-hadron interactions, was used for the analysis.

  6. Inflation by alignment

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, C.P. [PH -TH Division, CERN,CH-1211, Genève 23 (Switzerland); Department of Physics & Astronomy, McMaster University,1280 Main Street West, Hamilton ON (Canada); Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo ON (Canada); Roest, Diederik [Van Swinderen Institute for Particle Physics and Gravity, University of Groningen,Nijenborgh 4, 9747 AG Groningen (Netherlands)

    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.

  7. Alignments of RNA structures.

    Science.gov (United States)

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

    2010-01-01

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

  8. Alignment of concerns

    DEFF Research Database (Denmark)

    Andersen, Tariq Osman; Bansler, Jørgen P.; Kensing, Finn; Moll, Jonas; Nielsen, Karen Dam

    E-health promises to enable and support active patient participation in chronic care. However, these fairly recent innovations are complicated matters and emphasize significant challenges, such as patients’ and clinicians’ different ways of conceptualizing disease and illness. Informed by insights...... from medical phenomenology and our own empirical work in telemonitoring and medical care of heart patients, we propose a design rationale for e-health systems conceptualized as the ‘alignment of concerns’....

  9. Nuclear reactor alignment plate configuration

    Science.gov (United States)

    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.

  10. Seeking the perfect alignment

    CERN Multimedia

    2002-01-01

    The first full-scale tests of the ATLAS Muon Spectrometer are about to begin in Prévessin. The set-up includes several layers of Monitored Drift Tubes Chambers (MDTs) and will allow tests of the performance of the detectors and of their highly accurate alignment system.   Monitored Drift Chambers in Building 887 in Prévessin, where they are just about to be tested. Muon chambers are keeping the ATLAS Muon Spectrometer team quite busy this summer. Now that most people go on holiday, the beam and alignment tests for these chambers are just starting. These chambers will measure with high accuracy the momentum of high-energy muons, and this implies very demanding requirements for their alignment. The MDT chambers consist of drift tubes, which are gas-filled metal tubes, 3 cm in diameter, with wires running down their axes. With high voltage between the wire and the tube wall, the ionisation due to traversing muons is detected as electrical pulses. With careful timing of the pulses, the position of the muon t...

  11. Alignment at the ESRF

    International Nuclear Information System (INIS)

    The ESRF Survey and Alignment group is responsible for the installation, control and periodic realignment of the accelerators and experiments which produce high quality x-rays used by scientists from Europe and around the world. Alignment tolerances are typically less than one millimetre and often in the order of several micrometers. The group is composed of one engineer, five highly trained survey technicians, one electronic and one computer technician. This team is fortified during peak periods by technicians from an external survey company. First an overview and comparative study of the main large-scale survey instrumentation and methods used by the group is made. Secondly a discussion of long term deformation on the ESRF site is presented. This is followed by presentation of the methods used in the realignment of the various machines. Two important aspects of our work, beamline and front-end alignment, and the so-called machine exotic devices are briefly discussed. Finally, the ESRF calibration bench is presented. (authors)

  12. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne;

    2007-01-01

    We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily...... the SARSE editor makes it a flexible tool to improve all RNA alignments with relatively little human intervention. Online documentation and software are available at (http://sarse.ku.dk)....

  13. Alignment as a Teacher Variable

    Science.gov (United States)

    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…

  14. GPCODON ALIGNMENT: A GLOBAL PAIRWISE CODON BASED SEQUENCE ALIGNMENT APPROACH

    Directory of Open Access Journals (Sweden)

    Zeinab A. Fareed

    2016-02-01

    Full Text Available The alignment of two DNA sequences is a basic step in the analysis of biological data. Sequencing a long DNA sequence is one of the most interesting problems in bioinformatics. Several techniques have been developed to solve this sequence alignment problem like dynamic programming and heuristic algorithms. In this paper, we introduce (GPCodon alignment a pairwise DNA-DNA method for global sequence alignment that improves the accuracy of pairwise sequence alignment. We use a new scoring matrix to produce the final alignment called the empirical codon substitution matrix. Using this matrix in our technique enabled the discovery of new relationships between sequences that could not be discovered using traditional matrices. In addition, we present experimental results that show the performance of the proposed technique over eleven datasets of average length of 2967 bps. We compared the efficiency and accuracy of our techniques against a comparable tool called “Pairwise Align Codons” [1].

  15. The CMS Muon System Alignment

    CERN Document Server

    Martinez Ruiz-Del-Arbol, P

    2009-01-01

    The alignment of the muon system of CMS is performed using different techniques: photogrammetry measurements, optical alignment and alignment with tracks. For track-based alignment, several methods are employed, ranging from a hit and impact point (HIP) algorithm and a procedure exploiting chamber overlaps to a global fit method based on the Millepede approach. For start-up alignment as long as available integrated luminosity is still significantly limiting the size of the muon sample from collisions, cosmic muon and beam halo signatures play a very strong role. During the last commissioning runs in 2008 the first aligned geometries have been produced and validated with data. The CMS offline computing infrastructure has been used in order to perform improved reconstructions. We present the computational aspects related to the calculation of alignment constants at the CERN Analysis Facility (CAF), the production and population of databases and the validation and performance in the official reconstruction. Also...

  16. Beam alignment system

    International Nuclear Information System (INIS)

    A patent is claimed for the invention of a beam alignment system. The aim of the invention is the obtention of an accurate monitoring of the beam position and direction. It is of great interest in the nuclear industry. The invention can be applied in an infrared laser beam for welding operations. An auxiliar radiation source is incorporated to the device. The system's configuration allows a simultaneous and separated utilisation of two beams. The description and the design of the proposed system are provided

  17. Alignment in hadronic interactions

    CERN Document Server

    Wibig, T

    2000-01-01

    The alignment of the products of very high energy interactions seen in mountain altitude experiments is one of the most puzzling phenomena in cosmic ray physics for quite a long time. The observations of the Pamir and Chacaltaya emulsion chamber groups and by the Tien-Shan extensive air shower experiment, together with a very clear event seen in the Concorde French-Japanese experiment in the stratosphere, makes the experimental basis very substantial. In the present paper a novel possible explanation is put forward.

  18. All about alignment

    CERN Multimedia

    2006-01-01

    The ALICE absorbers, iron wall and superstructure have been installed with great precision. The ALICE front absorber, positioned in the centre of the detector, has been installed and aligned. Weighing more than 400 tonnes, the ALICE absorbers and the surrounding support structures have been installed and aligned with a precision of 1-2 mm, hardly an easy task but a very important one. The ALICE absorbers are made of three parts: the front absorber, a 35-tonne cone-shaped structure, and two small-angle absorbers, long straight cylinder sections weighing 18 and 40 tonnes. The three pieces lined up have a total length of about 17 m. In addition to these, ALICE technicians have installed a 300-tonne iron filter wall made of blocks that fit together like large Lego pieces and a surrounding metal support structure to hold the tracking and trigger chambers. The absorbers house the vacuum chamber and are also the reference surface for the positioning of the tracking and trigger chambers. For this reason, the ab...

  19. Computing alignment plots efficiently

    CERN Document Server

    Krusche, Peter

    2009-01-01

    Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of fixed-size windows in the input strings. Commonly, the Hamming distance is used since it can be computed in linear time. However, the Hamming distance is a rather crude measure of string similarity, and using an alignment-based edit distance can greatly improve the sensitivity of the dot plot method. In this paper, we show how to compute alignment plots of the latter type efficiently. Given two strings of length m and n and a window size w, this problem consists in computing the edit distance between all pairs of substrings of length w, one from each input string. The problem can be solved by repeated application of the standard dynamic programming algorithm in time O(mnw^2). This paper gives an improved data-parallel algorithm, running in time $O(mnw/\\gamma/p)$ using vector operations that work on $\\gamma$ values in parallel and $p$ processors. We show ex...

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

    Science.gov (United States)

    Kim, Minyoung

    2013-11-01

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

  1. Dust alignment in astrophysical environments

    Science.gov (United States)

    Lazarian, Alex; Thiem Hoang, Chi

    Dust is known to be aligned in interstellar medium and the arising polarization is extensively used to trace magnetic fields. What process aligns dust grains was one of the most long-standing problems of astrophysics in spite of the persistent efforts to solve it. For years the Davis-Greenstein paramagnetic alignment was the primary candidate for explaining grain alignment. However, the situation is different now and the most promising mechanism is associated with radiative torques (RATs) acting on irregular grains. I shall present the analytical theory of RAT alignment, discuss the observational tests that support this theory. I shall also discuss in what situations we expect to see the dominance of paramagnetic alignment.

  2. Nova laser alignment control system

    International Nuclear Information System (INIS)

    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

  3. Nuclear reactor internals alignment configuration

    Science.gov (United States)

    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.

  4. Catalyzing alignment processes

    DEFF Research Database (Denmark)

    Lauridsen, Erik Hagelskjær; Jørgensen, Ulrik

    2004-01-01

    time and in combination with other social processes establish more aligned and standardized environmental performance between countries. However, examples of the introduction of environmental management suggests that EMS’ only plays a minor role in developing the actual environmental objectives......This paper describes how environmental management systems (EMS) spur the circulation of processes that support the constitution of environmental issues as specific environ¬mental objects and objectives. EMS catalyzes alignmentprocesses that produce coherence among the different elements involved...... they are implemented in and how the changing context is reflected in the environmental objectives that are established and prioritised. Our argument is, that the ability of the standard to achieve an impact is dependant on the constitution of ’coherent’ environmental issues in the context, where the management system...

  5. On aligning trees

    CERN Document Server

    Calder, J

    1997-01-01

    The increasing availability of corpora annotated for linguistic structure prompts the question: if we have the same texts, annotated for phrase structure under two different schemes, to what extent do the annotations agree on structuring within the text? We suggest the term tree alignment to indicate the situation where two markup schemes choose to bracket off the same text elements. We propose a general method for determining agreement between two analyses. We then describe an efficient implementation, which is also modular in that the core of the implementation can be reused regardless of the format of markup used in the corpora. The output of the implementation on the Susanne and Penn treebank corpora is discussed.

  6. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal

    2012-11-01

    Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

  7. MaxAlign: maximizing usable data in an alignment

    DEFF Research Database (Denmark)

    Oliveira, Rodrigo Gouveia; Sackett, Peter Wad; Pedersen, Anders Gorm

    2007-01-01

    of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand...

  8. Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number

    CERN Document Server

    Saeed, Fahad

    2009-01-01

    Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment of pyrosequenceing reads is complex mainly because of 2 factors. One being the huge number of reads, making the use of traditional heuristics,that scale very poorly for large number, unsuitable. The second reason is that the alignment cannot be performed arbitrarily, because the position of the reads with respect to the original genome is important and has to be taken into account.In this report we present a short description of the multiple alignment system for pyrosequencing reads.

  9. Lexical alignment in triadic communication

    Directory of Open Access Journals (Sweden)

    Anouschka eFoltz

    2015-02-01

    Full Text Available 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.

  10. Alignments in the nobelium isotopes

    Institute of Scientific and Technical Information of China (English)

    ZHENG Shi-Zie; XU Fu-Rong; YUAN Cen-Xi; QI Chong

    2009-01-01

    Total-Routhian-Surface calculations have been performed to investigate the deformation and align-ment properties of the No isotopes. It is found that normal deformed and superdeformed states in these nuclei can coexist at low excitation energies. In neutron-deficient No isotopes, the superdeformed shapes can even become the ground states. Moreover, we plotted the kinematic moments of inertia of the No isotopes, which follow very nicely available experimental data. It is noted that, as the rotational frequency increases, align-ments develop at hω=0.2-0.3 MeV. Our calculations show that the occupation of the vj orbital plays an important role in the alignments of the No isotopes.

  11. The CMS Silicon Tracker Alignment

    CERN Document Server

    Castello, R

    2008-01-01

    The alignment of the Strip and Pixel Tracker of the Compact Muon Solenoid experiment, with its large number of independent silicon sensors and its excellent spatial resolution, is a complex and challenging task. Besides high precision mounting, survey measurements and the Laser Alignment System, track-based alignment is needed to reach the envisaged precision.\\\\ Three different algorithms for track-based alignment were successfully tested on a sample of cosmic-ray data collected at the Tracker Integration Facility, where 15\\% of the Tracker was tested. These results, together with those coming from the CMS global run, will provide the basis for the full-scale alignment of the Tracker, which will be carried out with the first \\emph{p-p} collisions.

  12. Testing the tidal alignment model of galaxy intrinsic alignment

    International Nuclear Information System (INIS)

    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, wg+; (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, wg(rp,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 wg(rp,θ) is simply wg+(rp)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

  13. Aligning for Innovation - Alignment Strategy to Drive Innovation

    Science.gov (United States)

    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.

  14. Muon System alignment with tracks

    CERN Document Server

    Calderón, Alicia; Virto, A L; Martínez, P; Martínez-Rivero, C; Matorras, Francisco; Rodrigo, Teresa; Sobron, M; Vila, Ivan

    2006-01-01

    We describe here some of the techniques foreseen to align the Muon System with muon tracks. Two methods are proposed, one based on the Tracker which measures the position of a Muon chamber with respect to the Tracker, and another one which aligns internally the Muon System. A mathematical model is described for the general case. It is simplified for several particular cases of the Muon System alignment and applied to realistic examples on full simulation. Some estimates of the expected precision and limitation of the method are presented.

  15. Tracking and Alignment in the CMS detector

    CERN Document Server

    Ronga, Frederic Jean

    2007-01-01

    This Report summarises the alignment strategy of the CMS detector. Track reconstruction in the silicon tracker and muon chambers is briefly described. We then present the different sources of alignment information, in particular alignment algorithms using reconstructed tracks.

  16. Harmonic Analysis of Linac Alignment

    CERN Document Server

    McCrady, Rodney C

    2005-01-01

    We have analyzed the requirements on alignment of the focusing elements (quadrupole doublets) in the Los Alamos Neutron Science Center (LANSCE) side coupled linac. The analysis is performed in terms of harmonics of the quardrupole spacing. This allows us to determine the effect of intentional deviations from a straight line, such as following the curvature of the Earth, and of unintentional deviations introduced by measurement and alignment errors. Results are compared to measured positions of the doublets.

  17. Expressive alignment language and implementation

    OpenAIRE

    Euzenat, Jérôme; Scharffe, François; Zimmermann, Antoine

    2007-01-01

    euzenat2007e This deliverable provides the description of an alignment language which is both expressive and independent from ontology languages. It defines the language through its abstract syntax and semantics depending on ontology language semantics. It then describes two concrete syntax: an exchange syntax in RDF/XML and a surface syntax for human consumption. Finally, it presents the current implementation of this expressive language within the Alignment API taking advantage of the OM...

  18. Geodetic alignment of laser power installations

    International Nuclear Information System (INIS)

    Main problems occuring in applied geodesy under initial alignment of laser power installation optical channel are considered. Attention is paid to alignment of lens beamguide telescopic pairs and alignment quality control. Methods and means of geodetic measurements under alignment are indicated. Conclusions are made about the degree of working through certain aspects of the problem

  19. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  20. Strategic Alignment and New Product Development

    DEFF Research Database (Denmark)

    Acur, Nuran; Kandemir, Destan; Boer, Harry

    2012-01-01

    Strategic alignment is widely accepted as a prerequisite for a firm’s success, but insight into the role of alignment in, and its impact on, the new product evelopment (NPD) process and its performance is less well developed. Most publications on this topic either focus on one form of alignment or...... of NPD performance indicators. Strategic planning and innovativeness appear to affect technological, market, and NPD-marketing alignment positively. Environmental munificence is negatively associated with NPD-marketing alignment, but has no effect on the two other forms of alignment. Technological...... change has a positive effect on technological alignment, a negative effect on NPD-marketing alignment, but no effect on market alignment. These findings suggest that internal capabilities are more likely to be associated with the development of strategic alignment than environmental factors are...

  1. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

    Directory of Open Access Journals (Sweden)

    Skolnick Jeffrey

    2008-12-01

    Full Text Available Abstract Background Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TM-align, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9% and coverage (~7% in comparison to those generated by TM-align. Fr-TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr-TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/.

  2. Topology independent protein structural alignment

    Directory of Open Access Journals (Sweden)

    DasGupta Bhaskar

    2007-10-01

    Full Text Available Abstract Background Identifying structurally similar proteins with different chain topologies can aid studies in homology modeling, protein folding, protein design, and protein evolution. These include circular permuted protein structures, and the more general cases of non-cyclic permutations between similar structures, which are related by non-topological rearrangement beyond circular permutation. We present a method based on an approximation algorithm that finds sequence-order independent structural alignments that are close to optimal. We formulate the structural alignment problem as a special case of the maximum-weight independent set problem, and solve this computationally intensive problem approximately by iteratively solving relaxations of a corresponding integer programming problem. The resulting structural alignment is sequence order independent. Our method is also insensitive to insertions, deletions, and gaps. Results Using a novel similarity score and a statistical model for significance p-value, we are able to discover previously unknown circular permuted proteins between nucleoplasmin-core protein and auxin binding protein, between aspartate rasemase and 3-dehydrogenate dehydralase, as well as between migration inhibition factor and arginine repressor which involves an additional strand-swapping. We also report the finding of non-cyclic permuted protein structures existing in nature between AML1/core binding factor and ribofalvin synthase. Our method can be used for large scale alignment of protein structures regardless of the topology. Conclusion The approximation algorithm introduced in this work can find good solutions for the problem of protein structure alignment. Furthermore, this algorithm can detect topological differences between two spatially similar protein structures. The alignment between MIF and the arginine repressor demonstrates our algorithm's ability to detect structural similarities even when spatial

  3. Aligned Layers of Silver Nano-Fibers

    OpenAIRE

    Golovin, Andrii B.; Liubov Kreminska; Jeremy Stromer

    2012-01-01

    We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polariz...

  4. Hardware Accelerated Sequence Alignment with Traceback

    OpenAIRE

    Scott Lloyd; Snell, Quinn O

    2009-01-01

    Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is pres...

  5. Measurements of magnetic field alignment

    International Nuclear Information System (INIS)

    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. XUV ionization of aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)

    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.

  7. Position list word aligned hybrid

    DEFF Research Database (Denmark)

    Deliege, Francois; Pedersen, Torben Bach

    2010-01-01

    Compressed bitmap indexes are increasingly used for efficiently querying very large and complex databases. The Word Aligned Hybrid (WAH) bitmap compression scheme is commonly recognized as the most efficient compression scheme in terms of CPU efficiency. However, WAH compressed bitmaps use a lot...... of storage space. This paper presents the Position List Word Aligned Hybrid (PLWAH) compression scheme that improves significantly over WAH compression by better utilizing the available bits and new CPU instructions. For typical bit distributions, PLWAH compressed bitmaps are often half the size of WAH...

  8. Aligned natural inflation with modulations

    Science.gov (United States)

    Choi, Kiwoon; Kim, Hyungjin

    2016-08-01

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

  9. Aligned natural inflation with modulations

    CERN Document Server

    Choi, Kiwoon

    2015-01-01

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

  10. Aligned natural inflation with modulations

    Directory of Open Access Journals (Sweden)

    Kiwoon Choi

    2016-08-01

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

  11. Aligned natural inflation with modulations

    OpenAIRE

    Kiwoon Choi; Hyungjin Kim

    2016-01-01

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

  12. Grain Alignment and CMB Polarization Studies

    CERN Document Server

    Lazarian, A

    2008-01-01

    Polarized microwave emission from dust is an important foreground that may contaminate polarized CMB studies unless carefully accounted for. Modeling of polarization from dust requires a quantitative understanding of grain alignment. I review the current status of grain alignment theory outlining recent advances in quantitative description of the alignment. In particular, I show that the grain-alignment theory is a predictive one, and its results nicely match observations. Those indicate that the most important process of alignment is related to radiative torques acting on irregular grains. The recently developed analytical model of radiative torque alignment has proven to be a very efficient tool for predicting the degree of grain alignment. We expect the alignment theory to further mature before CMBPol flight, which would ensure a better accounting for the dust-related polarization. At the same time, CMBPol should provide the additional testing of grain alignment, clarifying the reliability of polarimetry f...

  13. Pin-Align: A New Dynamic Programming Approach to Align Protein-Protein Interaction Networks

    OpenAIRE

    Farid Amir-Ghiasvand; Abbas Nowzari-Dalini; Vida Momenzadeh

    2014-01-01

    To date, few tools for aligning protein-protein interaction networks have been suggested. These tools typically find conserved interaction patterns using various local or global alignment algorithms. However, the improvement of the speed, scalability, simplification, and accuracy of network alignment tools is still the target of new researches. In this paper, we introduce Pin-Align, a new tool for local alignment of protein-protein interaction networks. Pin-Align accuracy is tested on protein...

  14. Prism Window for Optical Alignment

    Science.gov (United States)

    Tang, Hong

    2008-01-01

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

  15. Aligning seminars with Bologna requirements

    DEFF Research Database (Denmark)

    Lueg, Klarissa; Lueg, Rainer; Lauridsen, Ole

    2015-01-01

    Changes in public policy, such as the Bologna Process, require students to be equipped with multifunctional competencies to master relevant tasks in unfamiliar situations. Achieving this goal might imply a change in many curricula toward deeper learning. As a didactical means to achieve deep...... learning results, the authors suggest reciprocal peer tutoring (RPT); as a conceptual framework the authors suggest the SOLO (Structure of Observed Learning Outcomes) taxonomy and constructive alignment as suggested by Biggs and Tang. Our study presents results from the introduction of RPT in a large...... course. The authors find that RPT produces satisfying learning outcomes, active students, and ideal constructive alignments of the seminar content with the exam, the intended learning outcomes, and the requirements of the Bologna Process. Our data, which comprise surveys and evaluations from both faculty...

  16. Aligned mesoporous architectures and devices.

    Energy Technology Data Exchange (ETDEWEB)

    Brinker, C. Jeffrey; Lu, Yunfeng (University of California Los Angeles, Los Angeles, CA)

    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.

  17. RDF Graph Alignment with Bisimulation

    OpenAIRE

    Buneman, Peter; Staworko, Sławek

    2016-01-01

    We investigate the problem of aligning two RDF databases, an essential problem in understanding the evolution of ontologies. Our approaches address three fundamental challenges: 1) the use of "blank" (null) names, 2) ontology changes in which different names are used to identify the same entity, and 3) small changes in the data values as well as small changes in the graph structure of the RDF database. We propose approaches inspired by the classical notion of graph bisimulation and extend the...

  18. Interest alignment and competitive advantage

    OpenAIRE

    Gottschalg, Oliver; Zollo, Mauricio

    2006-01-01

    This paper articulates a theory of the conditions under which the alignment between individual and collective interests generates sustainable competitive advantage. The theory is based on the influence of tacitness, context-specificity and casual ambiguity in the determinants of different types of motivation (extrinsic, normative intrinsic and hedonic intrinsic), under varying conditions of environmental dynamism. The analysis indicates the need to consider mitivational processes as a complem...

  19. SIM Lite: ground alignment of the instrument

    Science.gov (United States)

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

    2010-07-01

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

  20. Intrinsic Galaxy Alignments and Weak Gravitational Lensing

    CERN Document Server

    Heavens, A F

    2001-01-01

    Gravitational lensing causes background galaxy images to become aligned, and the statistical characteristics of the image alignments can then be used to constrain the power spectrum of mass fluctuations. Analyses of gravitational lensing assume that intrinsic galaxy alignments are negligible, but if this assumption does not hold, then the interpretation of image alignments will be in error. As gravitational lensing experiments become more ambitious and seek very low-level alignments arising from lensing by large-scale structure, it becomes more important to estimate the level of intrinsic alignment in the galaxy population. In this article, I review the cluster of independent theoretical studies of this issue, as well as the current observational status. Theoretically, the calculation of intrinsic alignments is by no means straightforward, but some consensus has emerged from the existing works, despite each making very different assumptions. This consensus is that a) intrinsic alignments are a small but non-n...

  1. Structural analysis of aligned RNAs.

    Science.gov (United States)

    Voss, Björn

    2006-01-01

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

  2. Suspended photonic waveguide arrays for submicrometer alignment

    OpenAIRE

    Peters, T. J.; Tichem, M.; Staufer, U.

    2014-01-01

    This paper presents a new alignment concept for the alignment of multichannel photonic intergrated circuits (PICs) using flexible photonic waveguides on one of the PICs that are positionable by integrated micro electro mechanical system (MEMS) actuators. The concept aims for high precision and high degree of assembly process automation. The proposed concept includes pre-alignment of both PICs on a common substrate followed by fine-alignment using the on-chip flexible waveguides and MEMS funct...

  3. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    OpenAIRE

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of protein or DNA sequences. An accurate alignment can provide valuable information for experimentation on the newly found sequences. It is indispensable in basic research as well as in practical applic...

  4. Trust and Transparency from an Alignment Perspective

    OpenAIRE

    Gryning, Morten

    2015-01-01

    The academic literature suggests that firms cannot stay competitive if their business and IT departments are not aligned. Several theories have provided insights into how to achieve alignment, yet most IT and business departments still struggle to fulfill each other’s expectations, with dissatisfaction and low trust as a result. Some scholars argue that alignment is about finding the right mechanical configuration for a given organization. Others argue that alignment theory should...

  5. Inferring comprehensible business/ICT alignment rules.

    OpenAIRE

    Cumps, Bjorn; Martens, David; De Backer, Manu; Haesen, Raf; Viaene, Stijn; Dedene, Guido; Baesens, Bart; Snoeck, Monique

    2009-01-01

    We inferred business rules for business/ICT alignment by applying a novel rule induction algorithm on a data set containing rich alignment information polled from 641 organisations in 7 European countries. The alignment rule set was created using AntMiner+, a rule induction technique with a reputation of inducing accurate, comprehensible, and intuitive predictive models from data. Our data set consisted of 18 alignment practices distilled from an analysis of relevant publications and validate...

  6. Beam alignment system for laser welding system

    International Nuclear Information System (INIS)

    The patent describes a beam alignment system for laser welding work pieces, such as fuel rod grids for nuclear fuel assemblies. The apparatus for performing various laser-machining comprises a beam alignment system including alignment target means, as well as means for emitting, directing and focusing the laser beam. (U.K.)

  7. Physician-Hospital Alignment in Orthopedic Surgery.

    Science.gov (United States)

    Bushnell, Brandon D

    2015-09-01

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

  8. Vertically aligned nanostructure scanning probe microscope tips

    Science.gov (United States)

    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.

  9. Ultrafast electron diffraction from aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Centurion, Martin [Univ. of Nebraska, Lincoln, NE (United States)

    2015-08-17

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

  10. Aligning molecules with intense nonresonant laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Safvan, C.P.; Sakai, H.;

    1999-01-01

    Molecules in a seeded supersonic beam are aligned by the interaction between an intense nonresonant linearly polarized laser field and the molecular polarizability. We demonstrate the general applicability of the scheme by aligning I2, ICl, CS2, CH3I, and C6H5I molecules. The alignment is probed by...... mass selective two dimensional imaging of the photofragment ions produced by femtosecond laser pulses. Calculations on the degree of alignment of I2 are in good agreement with the experiments. We discuss some future applications of laser aligned molecules....

  11. How accurately is ncRNA aligned within whole-genome multiple alignments?

    Directory of Open Access Journals (Sweden)

    Ruzzo Walter L

    2007-10-01

    Full Text Available Abstract Background Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated. Results We evaluate the alignment accuracy of certain noncoding regions using noncoding RNA alignments from Rfam as a reference. We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for all the human sequences in the Rfam seed alignments. In particular, we find 638 instances of chimeric and partial alignments to human noncoding RNA elements, of which at least 225 can be improved by straightforward means. As a byproduct of our procedure, we predict many novel instances of known ncRNA families that are suggested by the alignment. Conclusion MULTIZ does a fairly accurate job of aligning these genomes in these difficult regions. However, our experiments indicate that better alignments exist in some regions.

  12. Multiscale peak alignment for chromatographic datasets.

    Science.gov (United States)

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

    2012-02-01

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

  13. Antares beam-alignment-system performance

    International Nuclear Information System (INIS)

    The beam alignment system for the 24-beam-sector Antares CO2 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 CO2 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

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

    Science.gov (United States)

    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.

  15. How accurately is ncRNA aligned within whole-genome multiple alignments?

    OpenAIRE

    Ruzzo Walter L; Wang Adrienne X; Tompa Martin

    2007-01-01

    Abstract Background Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated. Results We evaluate the alignment accuracy of certain noncoding regions using noncoding RNA alignments from Rfam as a reference. We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for...

  16. NON-ALIGNEMENT IN AFRICA

    Directory of Open Access Journals (Sweden)

    G. Jacobs

    2012-02-01

    Full Text Available The first indications to the Western world that African non-alignment had achieved conscious political form became apparent only in the late 1940's. This strand of thought within the tapestry of Africanism reached its zenith with the declarations of Kwame Nkrumah, Jomo Kenyatta and Julius Nyerere in the years after the Pan-African Congress in Manchester in 1945. The causes of the movement go back far beyond the first official expressions of an African solidarity in the 1940's. As a mature expression of group attitudes tqwards foreign pol icy, nonalignment can be traced back to the roots of African nationalism.

  17. The Cluster Substructure - Alignment Connection

    CERN Document Server

    Plionis, M

    2002-01-01

    Using the APM cluster data we investigate whether the dynamical status of clusters is related to the large-scale structure of the Universe. We find that cluster substructure is strongly correlated with the tendency of clusters to be aligned with their nearest neighbour and in general with the nearby clusters that belong to the same supercluster. Furthermore, dynamically young clusters are more clustered than the overall cluster population. These are strong indications that cluster develop in a hierarchical fashion by anisotropy merging along the large-scale filamentary superclusters within which they are embedded.

  18. The Substructure-Alignment Connection

    CERN Document Server

    Plionis, M; Plionis, Manolis; Basilakos, Spyros

    2001-01-01

    Using a sample of 903 APM clusters we investigate whether their dynamical status, as evidenced by the presence of significant substructures, is related to the large-scale structure of the Universe. We find that the cluster dynamical activity is strongly correlated with the tendency of clusters to be aligned with their nearest neighbour and in general with the nearby clusters that belong to the same supercluster. Furthermore, dynamically active clusters are more clustered than the overall cluster population. These are strong indications that clusters develop in a hierarchical fashion by anisotropic merging along the large-scale filaments within which they are embedded.

  19. Aligned interactions in cosmic rays

    Science.gov (United States)

    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.

  20. Aligned interactions in cosmic rays

    Energy Technology Data Exchange (ETDEWEB)

    Kempa, J., E-mail: kempa@pw.plock.pl [Warsaw University of Technology Branch Plock (Poland)

    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.

  1. Strategies for active alignment of lenses

    Science.gov (United States)

    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.

  2. Visa undulator fiducialization and alignment

    International Nuclear Information System (INIS)

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

  3. Galaxy alignments: Observations and impact on cosmology

    CERN Document Server

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

    2015-01-01

    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 astrophysics of galaxy formation and evolution as well as the growth of structure in the Universe. In this review paper we summarise key measurements of intrinsic 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 took 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 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 mitigat...

  4. Magnetic alignment and patterning of cellulose fibers

    International Nuclear Information System (INIS)

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

  5. Magnetic alignment and patterning of cellulose fibers

    Directory of Open Access Journals (Sweden)

    Fumiko Kimura and Tsunehisa Kimura

    2008-01-01

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

  6. Magnetic alignment and patterning of cellulose fibers

    Energy Technology Data Exchange (ETDEWEB)

    Kimura, Fumiko; Kimura, Tsunehisa [Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502 (Japan)], E-mail: tkimura@kais.kyoto-u.ac.jp

    2008-04-01

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

  7. Innovative optical alignment technique for CMP wafers

    Science.gov (United States)

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

    2002-07-01

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

  8. Recursions for Statistical Multiple Alignment

    DEFF Research Database (Denmark)

    Hein, Jotun; Pedersen, Christian Nørgaard Storm; Jensen, Jens Ledet

    2002-01-01

    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 , 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....

  9. Scintillation counter: photomultiplier tube alignment

    International Nuclear Information System (INIS)

    A scintillation counter, particularly for counting gamma ray photons, includes a massive lead radiation shield surrounding a sample-receiving zone. The shield is disassembleable into a plurality of segments to allow facile installation and removal of a photomultiplier tube assembly, the segments being so constructed as to prevent straight-line access of external radiation through the shield into the sample receiving zone. Provisions are made for accurately aligning the photomultiplier tube with respect to one or more sample-transmitting bores extending through the shield to the sample receiving zone. A sample elevator, used in transporting samples into the zone, is designed to provide a maximum gamma-receiving aspect to maximize the gamma detecting efficiency. (auth)

  10. Adjusting scoring matrices to correct overextended alignments

    OpenAIRE

    Mills, Lauren J.; Pearson, William R.

    2013-01-01

    Motivation: Sequence similarity searches performed with BLAST, SSEARCH and FASTA achieve high sensitivity by using scoring matrices (e.g. BLOSUM62) that target low identity (33% identity). Adjusting the scoring matrix to reflect the identity of the homologous sequence can correct higher identity overextended alignment boundaries. In addition, the scoring matrix that produced a correct alignment could be reliably predicted based on the sequence identity seen in the original BLOSUM62 alignment....

  11. FUSE: Multiple Network Alignment via Data Fusion

    OpenAIRE

    Gligorijević, Vladimir; Malod-Dognin, Noël; Pržulj, Nataša

    2014-01-01

    Discovering patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. The objective of a multiple network alignment is to create clusters of nodes that are evolutionarily conserved and functionally consistent across all networks. Unfortunately, the alignment methods ...

  12. Measurement of alignment between standards and assessment

    OpenAIRE

    Näsström, Gunilla

    2008-01-01

    Many educational systems of today are standards-based and aim at for alignment, i.e. consistency, among the components of the educational system: standards, teaching and assessment. To conclude whether the alignment is sufficiently high, analyses with a useful model are needed. This thesis investigates the usefulness of models for analyzing alignment between standards and assessments, with emphasis on one method: Bloom’s revised taxonomy. The thesis comprises an introduction and five articles...

  13. Lower extremity alignment normogram of Turkish population

    OpenAIRE

    Sezen, Sedat; Kuyurtar, Fehmi; ERDOGAN, Murat; Karaoglanoglu, Mustafa

    2004-01-01

    Extremity alignment normogram is useful in planning arthroplasty, osteotomy and treatment of fracture and malunion. The aim of this study is to get a lower extremity alignment normogram of Turkish population. Lower extremity plain radiographs of a hundred healthy volunteer are obtained and 21 parameters are measured in each of them. Results are statistically analyzed. Mechanical factors depending on aging, alters lower extremity alignment normogram parameters in Turkish population. When lower...

  14. Overlay Alignment Using Two Photonic Crystals

    CERN Document Server

    Peng, C; Morton, K; Yu, Z; Chou, Stephen Y.; Morton, Keith; Peng, Can; Yu, Zhaoning

    2005-01-01

    In this paper we proposed a novel overlay alignment method using two sets of identical photonic crystals (PhCs). In this method the reflection or transmission spectrum of the two overlaid photonic crystals is measured to help wafer tilt, yaw rotation, and translation aligning. The initial testing results with two 1D photonic crystals and analysis of the alignment accuracy are presented. This method is particularly useful in building photonic crystal stacks with nanoimprint lithography (NIL).

  15. Using Student Reflections to Explore Curriculum Alignment

    OpenAIRE

    Marina Harvey; Chris Baumann

    2012-01-01

    The concept of curriculum alignment is held as a guiding principle of good curriculum design in higher education. Curriculum alignment can be mapped using a variety of strategies and tools. This paper reports on a project that expands the horizons of curriculum review by applying a novel methodology, word clouds, to investigate the use of student reflections for exploring curriculum alignment.Students, from Australia and Denmark, engaged in written reflections about their learning in a Busine...

  16. Molecular alignment using circularly polarized laser pulses

    CERN Document Server

    Smeenk, C T L

    2013-01-01

    We show that circularly polarized femtosecond laser pulses produce field-free alignment in linear and planar molecules. We study the rotational wavepacket evolution of O$_2$ and benzene created by circularly polarized light. For benzene, we align the molecular plane to the plane of polarization. For O$_2$, we demonstrate that circular polarization yields a net alignment along the laser propagation axis at certain phases of the evolution. Circular polarization gives us the ability to control alignment of linear molecules outside the plane of polarization, providing new capabilities for molecular imaging.

  17. Track Based Alignment of Composite Detector Structures

    CERN Document Server

    Karimäki, V; Schilling, F P

    2006-01-01

    An iterative algorithm for track based alignment is presented. The algorithm can be applied to rigid composite detector structures or to individual modules. The iterative process involves track reconstruction and alignment, in which the chi-2 function of the hit residuals of each alignable object is minimized. Six alignment parameters per structure or per module, three for location and three for orientation, can be computed. The method is computationally light and easily parallelizable. The performance of the method is demonstrated with simulated tracks in the CMS pixel detector and tracks reconstructed from experimental data recorded with a test beam setup.

  18. A cross-species alignment tool (CAT)

    DEFF Research Database (Denmark)

    Li, Heng; Guan, Liang; Liu, Tao;

    2007-01-01

    sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web at...... http://xat.sourceforge.net/. CONCLUSIONS: Examined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT and...

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

    Energy Technology Data Exchange (ETDEWEB)

    Mohammadi, Shahin [Purdue Univ., West Lafayette, IN (United States); Gleich, David F. [Purdue Univ., West Lafayette, IN (United States); Kolda, Tamara G. [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Grama, Ananth [Purdue Univ., West Lafayette, IN (United States)

    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.

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

    Science.gov (United States)

    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.

  1. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.;

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  2. On comparing two structured RNA multiple alignments.

    Science.gov (United States)

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

    2010-12-01

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

  3. Sambamba: fast processing of NGS alignment formats

    NARCIS (Netherlands)

    Tarasov, A.; Vilella, A.J.; Cuppen, E.; Nijman, I.J.; Prins, J.C.P.

    2015-01-01

    Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces proc

  4. The GEM Detector projective alignment simulation system

    International Nuclear Information System (INIS)

    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

  5. STELLAR: fast and exact local alignments

    Directory of Open Access Journals (Sweden)

    Weese David

    2011-10-01

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

  6. SOA-Driven Business-Software Alignment

    NARCIS (Netherlands)

    Shishkov, Boris; Sinderen, van Marten; Quartel, Dick

    2006-01-01

    The alignment of business processes and their supporting application software is a major concern during the initial software design phases. This paper proposes a design approach addressing this problem of business-software alignment. The approach takes an initial business model as a basis in derivin

  7. Sambamba : Fast processing of NGS alignment formats

    NARCIS (Netherlands)

    Tarasov, Artem; Vilella, Albert J.; Cuppen, Edwin; Nijman, Isaac J.; Prins, Pjotr

    2015-01-01

    Summary: Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically red

  8. Aligning the μs-ALEX Setup.

    Science.gov (United States)

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

    2015-11-01

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

  9. Achieving Organisational Change through Values Alignment

    Science.gov (United States)

    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…

  10. Automatic alignment of hieroglyphs and transliteration

    OpenAIRE

    Nederhof, Mark Jan

    2009-01-01

    Automatic alignment has important applications in philology, facilitating study of texts on the basis of electronic resources produced by different scholars. A simple technique is presented to realise such alignment for Ancient Egyptian hieroglyphic texts and transliteration. Preliminary experiments with the technique are reported, and plans for future work are discussed. Postprint

  11. Compositions for directed alignment of conjugated polymers

    Energy Technology Data Exchange (ETDEWEB)

    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).

  12. Vacuum alignment with(out) elementary scalars

    CERN Document Server

    Alanne, Tommi; Meroni, Aurora; Sannino, Francesco

    2016-01-01

    We systematically elucidate differences and similarities of the vacuum alignment issue in composite and renormalizable elementary extensions of the Standard Model featuring a pseudo-Goldstone Higgs. We also provide general conditions for the stability of the vacuum in the elementary framework, thereby extending previous studies of the vacuum alignment.

  13. Using Student Reflections to Explore Curriculum Alignment

    Directory of Open Access Journals (Sweden)

    Marina Harvey

    2012-10-01

    Full Text Available The concept of curriculum alignment is held as a guiding principle of good curriculum design in higher education. Curriculum alignment can be mapped using a variety of strategies and tools. This paper reports on a project that expands the horizons of curriculum review by applying a novel methodology, word clouds, to investigate the use of student reflections for exploring curriculum alignment.Students, from Australia and Denmark, engaged in written reflections about their learning in a Business Brand Marketing subject. These reflections provide the data that is analysed for its alignment with the subject’s learning outcomes. The word cloud analysis is found to be useful in providing evidence of curriculum alignment and indicators for directing deeper textual analysis.

  14. Semiautomatic beam-based LHC collimator alignment

    CERN Document Server

    Valentino, Gianluca; Bruce, Roderik; Wollmann, Daniel; Sammut, Nicholas; Rossi, Adriana; Redaelli, Stefano

    2012-01-01

    Full beam-based alignment of the LHC collimation system was a time-consuming procedure (up to 28 hours) as the collimators were set up manually. A yearly alignment campaign has been sufficient for now, although in the future due to tighter tolerances this may lead to a decrease in the cleaning efficiency if machine parameters such as the beam orbit drift over time. Automating the collimator setup procedure can reduce the beam time for collimator setup and allow for more frequent alignments, therefore reducing the risk of performance degradation. This article describes the design and testing of a semiautomatic algorithm as a first step towards a fully automatic setup procedure. The parameters used to measure the accuracy and performance of the alignment are defined and determined from experimental data. A comparison of these measured parameters at 450 GeV and 3.5 TeV with manual and semiautomatic alignment is provided.

  15. Bokeh Mirror Alignment for Cherenkov Telescopes

    CERN Document Server

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

    2016-01-01

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

  16. Operational performance of the Antares alignment system

    International Nuclear Information System (INIS)

    A review of the operational performance of the alignment system for the large Antares optical system is presented. The alignment of twenty-four optical channels consisting of two hundred optical elements is verified and established as required prior to each target shot for this CO2 laser fusion test facility. The overall system design included features such as automatic operation, data base driven controls, self calibration, provisions for initial optical alignment set up, and system aided fault location. The system approach employed two alignment stations which sequentially viewed the 24 optical channels (sectors) and could be used for prealignments and calibrations. Closed-loop operations via the computer permit rapid mirror alignments. The performance of the applied techniques and devices is evaluated and compared to the required performance specifically from the standpoint of accuracy and shot rate. Overall system performance with verification by actual target shots is presented

  17. Array tomography: semiautomated image alignment.

    Science.gov (United States)

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

    2010-11-01

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

  18. Tracing magnetic fields with aligned grains

    Energy Technology Data Exchange (ETDEWEB)

    Lazarian, A. [Astronomy Department, University of Wisconsin-Madison, 475 N. Charter St., Madison, WI 53706 (United States)]. E-mail: lazarian@astro.wisc.edu

    2007-07-15

    Magnetic fields play a crucial role in various astrophysical processes, including star formation, accretion of matter, transport processes (e.g., transport of heat), and cosmic rays. One of the easiest ways to determine the magnetic field direction is via polarization of radiation resulting from extinction or/and emission by aligned dust grains. Reliability of interpretation of the polarization maps in terms of magnetic fields depends on how well we understand the grain-alignment theory. Explaining what makes grains aligned has been one of the big issues of the modern astronomy. Numerous exciting physical effects have been discovered in the course of research undertaken in this field. As both the theory and observations matured, it became clear that the grain-alignment phenomenon is inherent not only in diffuse interstellar medium or molecular clouds but also is a generic property of the dust in circumstellar regions, interplanetary space and cometary comae. Currently the grain-alignment theory is a predictive one, and its results nicely match observations. Among its predictions is a subtle phenomenon of radiative torques. This phenomenon, after having stayed in oblivion for many years after its discovery, is currently viewed as the most powerful means of alignment. In this article, I shall review the basic physical processes involved in grain alignment, and the currently known mechanisms of alignment. I shall also discuss possible niches for different alignment mechanisms. I shall dwell on the importance of the concept of grain helicity for understanding of many properties of grain alignment, and shall demonstrate that rather arbitrarily shaped grains exhibit helicity when they interact with gaseous and radiative flows.

  19. Polyimide photo-alignment layers for inclined homeotropic alignment of liquid crystal molecules

    International Nuclear Information System (INIS)

    We have succeeded in realizing an inclined homeotropic alignment of liquid crystal (LC) molecules by using photo-aligned films of a polyimide containing azobenzene in the backbone structure. To induce such an LC alignment, a side chain structure was introduced into the backbone structure. The LC pretilt angle, measured from the surface normal, could be controlled up to 1.75o by varying the light exposure in oblique angle irradiation with unpolarized light. Its thermal stability was examined by annealing the LC cell at 100 deg. C. No change was observed in the pretilt angle even after annealing for 36 h, indicative of its excellent thermal stability. Since photo-alignment has patterning capability, the photo-aligned polyimide film is expected as a promising alignment film for multi-domain vertical alignment mode LC displays

  20. Proper alignment of the microscope.

    Science.gov (United States)

    Rottenfusser, Rudi

    2013-01-01

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

  1. Galaxy alignment on large and small scales

    CERN Document Server

    Kang, X; Wang, Y O; Dutton, A; Macciò, A

    2014-01-01

    Galaxies are not randomly distributed across the universe but showing different kinds of alignment on different scales. On small scales satellite galaxies have a tendency to distribute along the major axis of the central galaxy, with dependence on galaxy properties that both red satellites and centrals have stronger alignment than their blue counterparts. On large scales, it is found that the major axes of Luminous Red Galaxies (LRGs) have correlation up to 30Mpc/h. Using hydro-dynamical simulation with star formation, we investigate the origin of galaxy alignment on different scales. It is found that most red satellite galaxies stay in the inner region of dark matter halo inside which the shape of central galaxy is well aligned with the dark matter distribution. Red centrals have stronger alignment than blue ones as they live in massive haloes and the central galaxy-halo alignment increases with halo mass. On large scales, the alignment of LRGs is also from the galaxy-halo shape correlation, but with some ex...

  2. Alignment of chirped-pulse compressor

    International Nuclear Information System (INIS)

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

  3. The art of editing RNA structural alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth

    2014-01-01

    rewarded by great insight into the evolution of structure and function of your favorite RNA molecule. In this chapter I will review the methods and considerations that go into constructing RNA structural alignments at the secondary and tertiary structure level; introduce software, databases, and algorithms......Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious, it is...

  4. Alignment of chirped-pulse compressor

    Energy Technology Data Exchange (ETDEWEB)

    Yakovlev, I V [Institute of Applied Physics, Russian Academy of Sciences, Nizhny Novgorod (Russian Federation)

    2012-11-30

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

  5. Aligned Fibrous Scaffold Induced Aligned Growth of Corneal Stroma Cells in vitro Culture

    Institute of Scientific and Technical Information of China (English)

    GAO Yan; YAN Jing; CUI Xue-jun; WANG Hong-yan; WANG Qing

    2012-01-01

    To investigate the contribution of fibre arrangement to guiding the aligned growth of corneal stroma cells,aligned and randomly oriented fibrous scaffolds of gelatin and poly-L-lactic acid(PLLA) were fabricated by electrospinning.A comparative study of two different systems with corneal stroma cells on randomly organized and aligned fibres were conducted.The efficiency of the scaffolds for inducing the aligned growth of cells was assessed by morphological observation and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide(MTT) assay.Results show that the cells cultured on both randomly oriented and aligned scaffolds maintained normal morphology and well spreading as well as long term proliferation.Importantly,corneal stroma cells grew high orderly on the aligned scaffold,while the cells grew disordered on the randomly oriented scaffold.Moreover,the cells exhibited higher viability in aligned scaffold than that in randomly oriented scaffold.These results indcate that electrospinng to prepare aligned fibrous scaffolds has provided an effective approach to the aligned growth of corneal stroma cells in vitro.Our findings that fiber arrangement plays a crucial role in guiding the aligned growth of cells may be helpful to the development of better biomaterials for tissue engineered cornea.

  6. EURRECA—Framework for Aligning Micronutrient Recommendations

    NARCIS (Netherlands)

    Veer, van 't P.; Grammatikaki, E.; Matthys, C.; Raats, M.M.; Contor, L.

    2013-01-01

    There is currently no standard approach for deriving micronutrient recommendations, and large variations exist across Europe, causing confusion among consumers, food producers, and policy makers. More aligned information could influence dietary behaviors and potentially lead to a healthier populatio

  7. Aligner for Elastic Collisions of Dropped Balls.

    Science.gov (United States)

    Mellen, Walter Roy

    1995-01-01

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

  8. Alignment studies for the CERN linear collider

    International Nuclear Information System (INIS)

    Transverse alignment tolerances of a few microns are required for the CERN Linear Collider (CLIC) in order to limit the emittance blow-up due to transversely deflecting wakefields to reasonable values. Such tight tolerances over long distances can only be obtained by beam-based active alignment systems using precision micromovers and beam position monitors. Development work being carried out at CERN on closed-loop controlled micron-displacement systems, micron-resolution beam position monitors, active optical pre-alignment schemes and beam blow-up computer simulations for given overall alignment tolerances using both one-to-one and dispersion-free correction algorithms is described. (Author) 11 figs., 8 refs

  9. Alignment of the NOMAD-STAR detector

    CERN Document Server

    Cervera-Villanueva, A

    2000-01-01

    This note describes the alignment of the NOMAD-STAR detector. This is the B/sub 4/C-silicon target installed in the NOMAD spectrometer in 1997. NOMAD-STAR is composed of modules of 12 silicon detectors each giving a total length of 72 cm. Ten of these modules (called ladders) are assembled to form a layer. There are five layers interleaved with passive boron carbide plates. The total surface of silicon is 1.14 m /sup 2/. Energetic muons from the flat-top of the CERN SPS cycle provide the necessary information to perform a very precise software alignment. This alignment is needed to ensure that the impact parameter measurement needed for the identification of taus in a detector like NOMAD-STAR will not be limited by the error in the alignment. (15 refs).

  10. Angular momentum alignment in molecular beam scattering

    International Nuclear Information System (INIS)

    It is shown how the angular momentum alignment in a molecular beam can be determined using laser-induced fluorescence in combination with precession of the angular momenta in a magnetic field. After a general analysis of the method, some results are presented to illustrate the possibilities of the method. Experimental data are presented on the alignment production for Na2 molecules that made a collision induced angular momentum transition. Magnitude as well as direction of the alignment have been determined for scattering with several scattering partners and for a large number of scattering angles and transitions. The last chapter deals with the total alignment production in a final J-state, i.e. without state selection of the initial rotational state. (orig.)

  11. Commissioning the CMS alignment and calibration framework

    International Nuclear Information System (INIS)

    The CMS experiment has developed a powerful framework to ensure the precise and prompt alignment and calibration of its components, which is a major prerequisite to achieve the optimal performance for physics analysis. The prompt alignment and calibration strategy harnesses computing resources both at the Tier-0 site and the CERN Analysis Facility (CAF) to ensure fast turnaround for updating the corresponding database payloads. An essential element is the creation of dedicated data streams concentrating the specific event information required by the various alignment and calibration workflows. The resulting low latency is required for feeding the resulting constants into the prompt reconstruction process, which is essential for achieving swift physics analysis of the LHC data. This report discusses the implementation and the computational aspects of the alignment and calibration framework. Recent commissioning campaigns with cosmic muons, beam halo and simulated data have been used to gain detailed experience with this framework, and results of this validation are reported.

  12. Faster exon assembly by sparse spliced alignment

    CERN Document Server

    Tiskin, Alexander

    2007-01-01

    Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \\emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon chains within a DNA sequence of length $m$ by comparing them to a known related gene sequence of length n, $m = \\Theta(n)$. Gelfand et al.\\ gave an algorithm for spliced alignment running in time O(n^3). Kent et al.\\ considered sparse spliced alignment, where the number of candidate exons is O(n), and proposed an algorithm for this problem running in time O(n^{2.5}). We improve on this result, by proposing an algorithm for sparse spliced alignment running in time O(n^{2.25}). Our approach is based on a new framework of \\emph{quasi-local string comparison}.

  13. Precision alignment of permanent magnet drift tubes

    International Nuclear Information System (INIS)

    The Lawrence Berkeley National Laboratory (LBNL) technique of drift-tube alignment has been resurrected at Los Alamos for the precision alignment of 1-cm-core drift tubes that carry high gradient rare-earth-cobalt quadrupoles. Because the quadrupoles cannot be switched off, this technique is not applicable to a drift-tube assembly, but tests indicate that individual magnetic centers can be detected with a precision of +/-0.003 mm. Methods of transferring this information to machined alignment flats on the sides of the drift-tube body are discussed. With measurements of drift tubes designed for a 100-mA, 425-MHz drift-tube linac, offsets between the geometric and magnetic axes of up to +/-0.05 mm were detected following final assembly and welding. This degree of offset is serious if not accommodated, because it represents the entire alignment tolerance for the 40-cell tank. The measurement equipment and technique are described

  14. Aligning sourcing activities with corporate strategy

    OpenAIRE

    Buczek, Kristopher

    2014-01-01

    In this paper I set out to discover how global firms ensure that sourcing activities are aligned with corporate strategy. In order to understand this, I broke the problem down into three specific questions, which were: 1) How does strategy flow through the sourcing departments of large firms? 2) What hurdles do sourcing departments face when trying to implement corporate strategy? 3) What tools are available in improving the alignment between corporate strategies and sourcing activi...

  15. Optimal Nonlinear Filter for INS Alignment

    Institute of Scientific and Technical Information of China (English)

    赵瑞; 顾启泰

    2002-01-01

    All the methods to handle the inertial navigation system (INS) alignment were sub-optimal in the past. In this paper, particle filtering (PF) as an optimal method is used for solving the problem of INS alignment. A sub-optimal two-step filtering algorithm is presented to improve the real-time performance of PF. The approach combines particle filtering with Kalman filtering (KF). Simulation results illustrate the superior performance of these approaches when compared with extended Kalman filtering (EKF).

  16. Strategic alignment: a performance tool for SMEs

    OpenAIRE

    Jouirou, Nihel; Kalika, Michel

    2004-01-01

    The purpose of this research is to investigate whether the alignment of IT with the strategy (particularly the partnership strategy or cooperation practice) and organizational structure of an SME could have a decisive influence on its performance. We constructed a model and tested it empirically using data from 381 SMEs operating in different sectors. A multivariate perspective, modelled with structural equations, was used to test the alignment between strategy, structure and IT. The alignmen...

  17. Technology Alignment and Portfolio Prioritization (TAPP)

    Science.gov (United States)

    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.

  18. Alignments between galaxies, satellite systems and haloes

    OpenAIRE

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

    2016-01-01

    The spatial distribution of the satellite populations of the Milky Way and Andromeda are puzzling in that they are nearly perpendicular to the disks of their central galaxies. To understand the origin of such configurations we study the alignment of the central galaxy, satellite system and dark matter halo in the largest of the "Evolution and Assembly of GaLaxies and their Environments" (EAGLE) simulation. We find that centrals and their satellite systems tend to be well aligned with their ha...

  19. Unscented Kalman filter for SINS alignment

    Institute of Scientific and Technical Information of China (English)

    Zhou Zhanxin; Gao Yanan; Chen Jiabin

    2007-01-01

    In order to improve the filter accuracy for the nonlinear error model of strapdown inertial navigation system (SINS) alignment, Unscented Kalman Filter (UKF) is presented for simulation with stationary base and moving base of SINS alignment.Simulation results show the superior performance of this approach when compared with classical suboptimal techniques such as extended Kalman filter in cases of large initial misalignment.The UKF has good performance in case of small initial misalignment.

  20. SOA-Driven Business-Software Alignment

    OpenAIRE

    Shishkov, Boris; Sinderen, van, Marten; Quartel, Dick

    2006-01-01

    The alignment of business processes and their supporting application software is a major concern during the initial software design phases. This paper proposes a design approach addressing this problem of business-software alignment. The approach takes an initial business model as a basis in deriving refined models that target a service-oriented software implementation. The approach explicitly identifies a software modeling level at which software modules are represented as services in a tech...

  1. Control rod housing alignment and repair method

    International Nuclear Information System (INIS)

    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

  2. A Markov Model for Ontology Alignment

    OpenAIRE

    Cotterell, Michael E.; Medina, Terrance

    2013-01-01

    The explosion of available data along with the need to integrate and utilize that data has led to a pressing interest in data integration techniques. In terms of Semantic Web technologies, Ontology Alignment is a key step in the process of integrating heterogeneous knowledge bases. In this paper, we present the Edge Confidence technique, a modification and improvement over the popular Similarity Flooding technique for Ontology Alignment.

  3. Genome Update: alignment of bacterial chromosomes

    DEFF Research Database (Denmark)

    Ussery, David; Jensen, Mette; Poulsen, Tine Rugh;

    2004-01-01

    There are four new microbial genomes listed in this month's Genome Update, three belonging to Gram-positive bacteria and one belonging to an archaeon that lives at pH 0; all of these genomes are listed in Table 1⇓. The method of genome comparison this month is that of genome alignment and......, as an example, an alignment of seven Staphylococcus aureus genomes and one Staphylococcus epidermidis genome is presented....

  4. Orthodontics Align Crooked Teeth and Boost Self-Esteem

    Science.gov (United States)

    ... 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 ...

  5. Alignments between galaxies, satellite systems and haloes

    CERN Document Server

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

    2016-01-01

    The spatial distribution of the satellite populations of the Milky Way and Andromeda are puzzling in that they are nearly perpendicular to the disks of their central galaxies. To understand the origin of such configurations we study the alignment of the central galaxy, satellite system and dark matter halo in the largest of the "Evolution and Assembly of GaLaxies and their Environments" (EAGLE) simulation. We find that centrals and their satellite systems tend to be well aligned with their haloes, with a median misalignment angle of $33^{\\circ}$ in both cases. While the centrals are better aligned with the inner $10$ kpc halo, the satellite systems are better aligned with the entire halo indicating that satellites preferentially trace the outer halo. The central - satellite alignment is weak (median misalignment angle of $52^{\\circ}$) and we find that around $20\\%$ of systems have a misalignment angle larger than $78^{\\circ}$, which is the value for the Milky Way. The central - satellite alignment is a conseq...

  6. An implicit spatial memory alignment effect.

    Science.gov (United States)

    Cerles, Mélanie; Gomez, Alice; Rousset, Stéphane

    2015-09-01

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

  7. Assessing strategic, tactical and operational alignment factors for SMEs: Alignment across the organisation's value chain

    OpenAIRE

    Gutierrez, A.; Serrano, A.

    2008-01-01

    The strategic use of Information Technology (IT), better known as strategic alignment, has significantly increased, as a result of the strong dependence of organisational activity on Information Systems (IS) and their related technologies. Strategic alignment is considered as a key element to improve performance on organisations, enhance efficiency and allow organisations to be more competitive in their respective industry. One of the first steps towards achieving strategic alignment is to ha...

  8. Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization

    Directory of Open Access Journals (Sweden)

    Paten Benedict

    2011-05-01

    Full Text Available Abstract Background Continuing research into the global multiple sequence alignment problem has resulted in more sophisticated and principled alignment methods. Unfortunately these new algorithms often require large amounts of time and memory to run, making it nearly impossible to run these algorithms on large datasets. As a solution, we present two general methods, Crumble and Prune, for breaking a phylogenetic alignment problem into smaller, more tractable sub-problems. We call Crumble and Prune meta-alignment methods because they use existing alignment algorithms and can be used with many current alignment programs. Crumble breaks long alignment problems into shorter sub-problems. Prune divides the phylogenetic tree into a collection of smaller trees to reduce the number of sequences in each alignment problem. These methods are orthogonal: they can be applied together to provide better scaling in terms of sequence length and in sequence depth. Both methods partition the problem such that many of the sub-problems can be solved independently. The results are then combined to form a solution to the full alignment problem. Results Crumble and Prune each provide a significant performance improvement with little loss of accuracy. In some cases, a gain in accuracy was observed. Crumble and Prune were tested on real and simulated data. Furthermore, we have implemented a system called Job-tree that allows hierarchical sub-problems to be solved in parallel on a compute cluster, significantly shortening the run-time. Conclusions These methods enabled us to solve gigabase alignment problems. These methods could enable a new generation of biologically realistic alignment algorithms to be applied to real world, large scale alignment problems.

  9. Laser alignment of rotating equipment at PNL

    International Nuclear Information System (INIS)

    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

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

    Science.gov (United States)

    Banihashemi, Mohamadreza

    2016-10-01

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

  11. Evolution of shiva laser alignment systems

    International Nuclear Information System (INIS)

    The Shiva oscillator pulse is preamplified and divided into twenty beams. Each beam is then amplified, spatially filtered, directed, and focused onto a target a few hundred micrometers in size producing optical intensities up to 1016W/cm2. The laser was designed and built with three automatic alignment systems: the oscillator alignment system, which aligns each of the laser's three oscillators to a reference beamline; the chain input pointing system, which points each beam into its respective chain; and the chain output pointing, focusing and centering system which points, centers and focuses the beam onto the target. Recently the alignment of the laser's one hundred twenty spatial filter pinholes was also automated. This system uses digitized video images of back-illuminated pinholes and computer analysis to determine current positions. The offset of each current position from a desired center point is then translated into stepper motor commands and the pinhole is moved the proper distance. While motors for one pinhole are moving, the system can digitize, analyze, and send commands to other motors, allowing the system to efficiently align several pinholes in parallel

  12. Large Telescope Segmented Primary Mirror Alignment

    Science.gov (United States)

    Rud, Mayer

    2010-01-01

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

  13. Alignment and Integration of Lightweight Mirror Segments

    Science.gov (United States)

    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.

  14. Enabling Process Alignment for IT Entrepreneurship

    Directory of Open Access Journals (Sweden)

    Sonia D. Bot

    2012-11-01

    Full Text Available All firms use information technology (IT. Larger firms have IT organizations whose business function is to supply and manage IT infrastructure and applications to support the firm's business objectives. Regardless of whether the IT function has been outsourced or is resident within a firm, the objectives of the IT organization must be aligned to the strategic needs of the business. It is often a challenge to balance the demand for IT against the available supply within the firm. Most IT organizations have little capacity to carry out activities that go beyond the incremental ones that are needed to run the immediate needs of the business. A process-ambidexterity framework for IT improves the IT organization's entrepreneurial ability, which in turn, better aligns the IT function with the business functions in the firm. Process ambidexterity utilizes both process alignment and process adaptability. This article presents a framework for process alignment in IT. This is useful for understanding how the processes in Business Demand Management, a core component of the process-ambidexterity framework for IT, relate to those in IT Governance and IT Supply Chain Management. The framework is presented through three lenses (governance, business, and technology along with real-world examples from major firms in the USA. Enabling process alignment in the IT function, and process ambidexterity overall, benefits those who govern IT, the executives who lead IT, as well as their peers in the business functions that depend on IT.

  15. DoSA: Database of Structural Alignments.

    Science.gov (United States)

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

    2013-01-01

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

  16. New alignment marks for improved measurement maturity

    Science.gov (United States)

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

    2008-04-01

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

  17. IT-Business Alignment Challenge: Enterprise Architecture as an Enabler for Strategic Alignment

    Directory of Open Access Journals (Sweden)

    Hanieh Sadat Beiryaei

    2011-03-01

    Full Text Available One of the most important organizational challenges is the strategic alignment between information technology (IT and business objectives. Organizations have deployed different approaches to achieve strategic alignment and competitive advantage. Enterprise architecture (EA has been viewed as an effective approach not only for optimum management of IT, but also for strategic alignment of IT applications and business needs. EA maturity indicates the degree of attaining EA project goals, out of which, is the IT-Business alignment. In this paper, the relationship between enterprise architecture maturity (EAM and strategic alignment maturity model (SAMM has been investigated to declare whether EAM can act as enabler for SAMM . Research population includes enterprises in which, the EA project is implemented. Pearson’s correlation and regression test have been used for analyzing the data gathered by questionnaire. The findings indicate that the success of EA significantly influences strategic alignment maturity.     Keywords : IT-business strategic alignment, Enterprise Architecture, Strategic Alignment Maturity Model, Enterprise Architecture Maturity

  18. A unified model of grain alignment: Radiative Alignment of Interstellar Grains with magnetic inclusions

    CERN Document Server

    Hoang, Thiem

    2016-01-01

    The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by a number of earlier studies. The alignment of such grains depends on the so-called RAT parameter $q^{\\max}$ that is determined by the grain shape. For interstellar grains with a broad range of $q^{\\max}$, a significant fraction of grains is expected to get aligned with low angular momentum at the so-called low-J attractor points, which entail degrees of alignment between 20 or 30 percent, irrespectively of the strength of RATs. The latter value may not be sufficient for explaining the observed interstellar alignment in the diffuse medium. In this paper, we elaborate our model of radiative alignment for grains with enhanced magnetic susceptibility due to magnetic inclusions, such that both Magnetic torque and RAdiative Torque (MRAT) play a role in grain alignment. Such grains can get aligned with high angular momentum at the so-called high-J attractor points, which achieve a high degree...

  19. Exploring the alignment space – lexical and gestural alignment with real and virtual humans

    Directory of Open Access Journals (Sweden)

    Kirsten eBergmann

    2015-05-01

    Full Text Available Communication is characterized by speakers' dynamic adaptations and coordination of both linguistic and nonverbal behaviors. Understanding this phenomenon of alignment and its underlying mechanisms and processes in both human-human and human-computer interaction is of particular importance when building artificial interlocutors. In this paper we contribute to the exploration of the still fragmentary alignment space with two controlled experiments on lexical and gestural alignment. Our results show, on the one hand, that human interlocutors align their lexical choice and gesture handedness in similar ways when interacting with real versus virtual humans. On the other hand we found, however, also subtle differences. We discuss our findings in terms of a dynamic interplay of multiple components (automatic and strategic and mechanisms (communicative and social of alignment.

  20. Contextual alignment of cognitive and neural dynamics.

    Science.gov (United States)

    Ames, Daniel L; Honey, Christopher J; Chow, Michael A; Todorov, Alexander; Hasson, Uri

    2015-04-01

    Effective real-world communication requires the alignment of multiple individuals to a common perspective or mental framework. To study how this alignment occurs at the level of the brain, we measured BOLD response during fMRI while participants (n = 24) listened to a series of vignettes either in the presence or absence of a valid contextual cue. The valid contextual cue was necessary to understand the information in each vignette. We then examined where and to what extent the shared valid context led to greater intersubject similarity of neural processing. Regions of the default mode network including posterior cingulate cortex and medial pFC became more aligned when participants shared a valid contextual framework, whereas other regions, including primary sensory cortices, responded to the stimuli reliably regardless of contextual factors. Taken in conjunction with previous research, the present results suggest that default mode regions help the brain to organize incoming verbal information in the context of previous knowledge. PMID:25244122

  1. Prosody and alignment: a sequential perspective

    Science.gov (United States)

    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.

  2. The relationship between pelvic alignment and dysmenorrhea

    Science.gov (United States)

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

    2016-01-01

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

  3. The alignment of bootstrap current in tokamak

    International Nuclear Information System (INIS)

    By calculating the trapped particle fraction, solving the Grand-Shafranov equation describing plasma equilibrium, and using Harris model, the magnitude and alignment of the bootstrap current in tokamak are calculated and analysed under the conventional shear regimes and also the negative central shear regimes. The conclusion authors obtained are: through adjusting the profile parameters of plasma density, temperature and current, and the elongation k and triangularity d which describe the plasma shape, the alignment of bootstrap current profile with the equilibrium current profile can be produced; the negative central shear regimes are advantage ous to produce bootstrap current, and the profile of bootstrap current is well-aligned with the equilibrium current profile. By comparing authors' calculated results, the optimized parameters are obtained under the conventional shear and the negative central shear regimes

  4. Plasmonic Properties of Vertically Aligned Nanowire Arrays

    Directory of Open Access Journals (Sweden)

    Hua Qi

    2012-01-01

    Full Text Available Nanowires (NWs/Ag sheath composites were produced to investigate plasmonic coupling between vertically aligned NWs for surface-enhanced Raman scattering (SERS applications. In this investigation, two types of vertical NW arrays were studied; those of ZnO NWs grown on nanosphere lithography patterned sapphire substrate via vapor-liquid-solid (VLS mechanism and Si NW arrays produced by wet chemical etching. Both types of vertical NW arrays were coated with a thin layer of silver by electroless silver plating for SERS enhancement studies. The experimental results show extremely strong SERS signals due to plasmonic coupling between the NWs, which was verified by COMSOL electric field simulations. We also compared the SERS enhancement intensity of aligned and random ZnO NWs, indicating that the aligned NWs show much stronger and repeatable SERS signal than those grown in nonaligned geometries.

  5. Opportunistic Interference Alignment in MIMO Interference Channels

    CERN Document Server

    Perlaza, Samir Medina; Lasaulce, Samson; Chaufray, Jean Marie

    2008-01-01

    We present two interference alignment techniques such that an opportunistic point-to-point multiple input multiple output (MIMO) link can reuse, without generating any additional interference, the same frequency band of a similar pre-existing primary link. In this scenario, we exploit the fact that under power constraints, although each radio maximizes independently its rate by water-filling on their channel transfer matrix singular values, frequently, not all of them are used. Therefore, by aligning the interference of the opportunistic radio it is possible to transmit at a significant rate while insuring zero-interference on the pre-existing link. We propose a linear pre-coder for a perfect interference alignment and a power allocation scheme which maximizes the individual data rate of the secondary link. Our numerical results show that significant data rates are achieved even for a reduced number of antennas.

  6. Micrometric alignment metrology means, developments and applications

    CERN Document Server

    Mainaud-Durand, H

    2004-01-01

    In order to meet the ever-increasing drastic alignment tolerances concerning the future particle accelerators, a new generation of sensors has been developed. Whether they are based on ultrasonic, optical or capacitive technology, these sensors, of micrometric resolution, allow continuous measurements in an often hostile environment (strong radiations, strong electro-magnetic fields) and thereby revolutionize alignment possibilities. After a brief presentation of the different sensors tested, used and indeed developed by our group, we present the past, present and future applications linked to the particle accelerators - in the short term concerning micrometric alignment of the low-beta quadrupoles of the LHC, and in the long term concerning the prealignment of the CLIC - or linked to other applications.

  7. HAMSA: Highly Accelerated Multiple Sequence Aligner

    Directory of Open Access Journals (Sweden)

    Naglaa M. Reda

    2016-06-01

    Full Text Available For biologists, the existence of an efficient tool for multiple sequence alignment is essential. This work presents a new parallel aligner called HAMSA. HAMSA is a bioinformatics application designed for highly accelerated alignment of multiple sequences of proteins and DNA/RNA on a multi-core cluster system. The design of HAMSA is based on a combination of our new optimized algorithms proposed recently of vectorization, partitioning, and scheduling. It mainly operates on a distance vector instead of a distance matrix. It accomplishes similarity computations and generates the guide tree in a highly accelerated and accurate manner. HAMSA outperforms MSAProbs with 21.9- fold speedup, and ClustalW-MPI of 11-fold speedup. It can be considered as an essential tool for structure prediction, protein classification, motive finding and drug design studies.

  8. System and method for 2D workpiece alignment

    Energy Technology Data Exchange (ETDEWEB)

    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.

  9. Face Alignment using Boosted Appeareance Model (Discriminative Appearance Model)

    OpenAIRE

    Muddamsetty, Satya Mahesh

    2009-01-01

    This thesis explores decriminative face alignment using Boosted Appearance Model (BAM). In this method face alignment is done by maximizing the score of the trained two classifier which learns both correct and incorrect alignment and is able to distinguish correct and incorrect alignment so that the correct alignment gets maximum positve score. During the training stage we trained Point Distribution Model (PDM) which acts as shape model and a boosting based classifier based on Haar like Recta...

  10. Determination of Vertical Alignment of Track using Accelerometer Readings

    OpenAIRE

    O'Brien, Eugene J.; Bowe, Cathal; Quirke, Paraic

    2015-01-01

    Railway track vertical alignment is an important indicator of serviceability condition. Through comparisons with past history, track alignment also informs maintenance planning. The vertical alignment of a railway track excites a dynamic response in a train which can potentially be used to determine that alignment. A method is proposed in this paper for the detection of the alignment through an analysis of vehicle accelerations resulting from the train/track dynamic interaction. The Cross Ent...

  11. Algorithms for Large, Sparse Network Alignment Problems

    CERN Document Server

    Bayati, Mohsen; Gleich, David F; Saberi, Amin; Wang, Ying

    2009-01-01

    We propose a new distributed algorithm for sparse variants of the network alignment problem that occurs in a variety of data mining areas including systems biology, database matching, and computer vision. Our algorithm uses a belief propagation heuristic and provides near optimal solutions for an NP-hard combinatorial optimization problem. We show that our algorithm is faster and outperforms or nearly ties existing algorithms on synthetic problems, a problem in bioinformatics, and a problem in ontology matching. We also provide a unified framework for studying and comparing all network alignment solvers.

  12. Alignment and geodesy for the ESRF project

    International Nuclear Information System (INIS)

    New generation accelerators and storage rings for synchrotron radiation require ever increasing precision of alignment, precision which moreover must be preserved over a maximum length of time. The use of ever smaller beam dimensions, and ever narrower vacuum chambers leads the magnet positioning tolerances to be reduced to a minimum. Thus, unlike in the past, annual realignment due to progressive deterioration of the ground stability can no longer be envisaged. Permanent monitoring of the ground stability must be guaranteed and its effects compensated, as soon as significant deterioration is recorded. It is this viewpoint that has dictated the choices made by ESRF in the field of alignment and monitoring

  13. Tracing magnetic fields with ground state alignment

    International Nuclear Information System (INIS)

    Observational studies of magnetic fields are vital as magnetic fields play a crucial role in various astrophysical processes, including star formation, accretion of matter, transport processes (e.g. transport of heat), and cosmic rays. The existing ways of magnetic field studies have their limitations. Therefore, it is important to explore new effects that can bring information about magnetic field. We identified a process “ground state alignment” as a new way to determine the magnetic field direction in diffuse medium. The consequence of the process is the polarization of spectral lines resulting from scattering and absorption from aligned atomic/ionic species with fine or hyperfine structure. The alignment is due to anisotropic radiation impinging on the atom/ion, while the magnetic field induces precession and realign the atom/ion and therefore the polarization of the emitted or absorbed radiation reflects the direction of the magnetic field. The atoms get aligned at their low levels and, as the life-time of the atoms/ions we deal with is long, the alignment induced by anisotropic radiation is susceptible to extremely weak magnetic fields (1G≳B≳10-15G). Compared to the upper level Hanle effect, atomic realignment is most suitable for the studies of magnetic field in the diffuse medium, where magnetic field is relatively weak. The corresponding physics of alignment is based on solid foundations of quantum electrodynamics and in a different physical regime the alignment has become a part of solar spectroscopy. In fact, the effects of atomic/ionic alignment, including the realignment in magnetic field, were studied in the laboratory decades ago, mostly in relation to the maser research. Recently, the atomic effect has been already detected in observations from circumstellar medium and this is a harbinger of future extensive magnetic field studies. It is very encouraging that a variety of atoms with fine or hyperfine splitting of the ground or metastable

  14. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

    in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

  15. Wire alignment system for ATF LINAC

    International Nuclear Information System (INIS)

    A wire based alignment system is adopted to make less than 40μm precision alignment for injector linac of Accelerator Test Facility (ATF). The system consists of two stretched SUS wires, pickup coils and active mover stages. The position of pickup coils in a mount which will be installed into LINAC stages is set to the calculated wire position prior to installation. All of LINAC stages are then moved to keep the calculated position by the active mover. The test results of wire position detection in a long term are described. (author)

  16. Carbon nanotube alignment driven rapid actuations

    International Nuclear Information System (INIS)

    Suspended micro-beams made from aligned carbon nanotubes and parylene deflect reversibly in an ac field and the deflection rate is three orders of magnitude greater than those for existing devices. The direction of beam deflection is determined by the area moment of inertia and the actuation mechanism involves rapid accumulation of charges at tube surfaces, the creation of Coulomb repulsive forces between tubes, beam dilation and the formation of compressive stresses at beam ends. Tube alignment plays a crucial role in the first step as is verified by experimental data and calculation. (paper)

  17. EST Reading Curriculum & Instruction: An Alignment Analysis

    OpenAIRE

    Lubna Ali Mohammed; 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 theoretical grounding of the Yemeni EST senior secondary curriculum is in alignment with its communicative-based curriculum label. In line with its label, th...

  18. Dissecting multiple sequence alignment methods : the analysis, design and development of generic multiple sequence alignment components in SeqAn

    OpenAIRE

    Rausch, T.

    2010-01-01

    Multiple sequence alignments are an indispensable tool in bioinformatics. Many applications rely on accurate multiple alignments, including protein structure prediction, phylogeny and the modeling of binding sites. In this thesis we dissected and analyzed the crucial algorithms and data structures required to construct such a multiple alignment. Based upon that dissection, we present a novel graph-based multiple sequence alignment program and a new method for multi-read alignments occurring i...

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

    Science.gov (United States)

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

    2015-09-01

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

  20. SVM with discriminative dynamic time alignment

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In the past several years, support vector machines (SVM) have achieved a huge success in many field, especially in pattern recognition. But the standard SVM cannot deal with length-variable vectors, which is one severe obstacle for its applications to some important areas, such as speech recognition and part-of-speech tagging. The paper proposed a novel SVM with discriminative dynamic time alignment (DDTA-SVM) to solve this problem. When training DDTA-SVM classifier, according to the category information of the training Samples, different time alignment strategies were adopted to manipulate them in the kernel functions, which contributed to great improvement for training speed and generalization capability of the classifier. Since the alignment operator was embedded in kernel functions, the training algorithms of standard SVM were still compatible in DDTA-SVM. In order to increase the reliability of the classification, a new classification algorithm was suggested. The preliminary experimental results on Chinese confusable syllables speech classification task show that DDTA-SVM obtains faster convergence speed and better classification performance than dynamic time alignment kernel SVM (DTAK-SVM).Moreover, DDTA-SVM also gives higher classification precision compared to the conventional HMM. This proves that the proposed method is effective, especially for confusable lengthvariable pattern classification tasks.

  1. Status of the SLS alignment system

    International Nuclear Information System (INIS)

    The Swiss Light Source (SLS), a third generation light source, is a high brilliance machine designed for extremely low emittance, which is, therefore, highly sensitive to alignment errors. The SLS consists of linac, booster, storage ring, transfer line and beam lines. Its several hundreds of magnets and other components were aligned in 2000. A relative accuracy of one tenth of millimeter has been achieved for most magnets and other important components. At the first attempt the injected beam immediately passed through both, the booster in July and the storage ring in December 2000 with all correctors switched off. On the third day of storage ring commissioning, a 2 mA electron beam was stored with a lifetime of 8.5 minutes. All global machine parameters, as energy, current and emittance were achieved according to specifications in 2001. The first images from experiments of the four beam lines have been taken within a few days after installation and alignment. Several new beam lines will be installed in the near future. The SLS alignment system will be presented in this paper. (author)

  2. Strategic Data Warehousing Achieving Alignment with Business

    CERN Document Server

    Bhansali, Neera

    2009-01-01

    Organization of data warehouses are vital but often ignored aspects of growing enterprises. This work merges technological know-how with managerial practices to show both the business manager and the IT professional how better alignment between data warehouse plans and business strategies can lead to a successful data warehouse adoption

  3. Interference Alignment Using Variational Mean Field Annealing

    DEFF Research Database (Denmark)

    Badiu, Mihai Alin; Guillaud, Maxime; Fleury, Bernard Henri

    2014-01-01

    We study the problem of interference alignment in the multiple-input multiple- output interference channel. Aiming at minimizing the interference leakage power relative to the receiver noise level, we use the deterministic annealing approach to solve the optimization problem. In the corresponding...

  4. Bunch Compressor for Beam-Based Alignment

    CERN Document Server

    Latina, A; Schulte, D

    2007-01-01

    Misalignments in the main linac of future linear colliders can lead to significant emittance growth. Beam-based alignment algorithms, such as Dispersion Free Steering (DFS), are necessary to mitigate these effects. We study how to use the Bunch Compressor to create the off-energy beams necessary for DFS and discuss the effectiveness of this method.

  5. Alignment of the MSGC barrel support structure

    International Nuclear Information System (INIS)

    The MSGC barrel is a sub-part of the tracking system of the CMS experiment at the LHC. The mechanical support structure of the MSGC barrel consists of ladder-like support beams carrying the detector modules and of four disks supporting the ladders. The required alignment precision of the modules, a few tens of micrometers, is designed to be obtained by precise part manufacture and by careful measurement of the alignment during the assembly of the structure. In the paper the use of digital photogrammetry for the measurement of the alignment of the disks and for the structural verification is presented. Digital photogrammetry was chosen from a number of potential methods after a careful evaluation. The use of photogrammetry for the structural verification of a prototype is presented. The displacements were measured both of unloaded and loaded disk by using photogrammetry and linear displacement transducers for verification. The displacements obtained from the two measurement methods corresponded well, not only to each other, but also to the results given by finite element analysis. The structural verification will be done and the alignment procedure will be tested with a full-sized prototype of a half of the MSGC barrel. Preparations for the photogrammetry measurements are presented and the design of the required supplementary equipment is shown. (authors)

  6. Alignment of voids in the cosmic web

    NARCIS (Netherlands)

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

    2008-01-01

    We investigate the shapes and mutual alignment of voids in the large-scale matter distribution of a Lambda cold dark matter (Lambda CDM) cosmology simulation. The voids are identified using the novel watershed void finder (WVF) technique. The identified voids are quite non-spherical and slightly pro

  7. Constructing Aligned Assessments Using Automated Test Construction

    Science.gov (United States)

    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…

  8. A Clustal Alignment Improver Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene; Fogel, Gary B.; Krink, Thimo

    2002-01-01

    Multiple sequence alignment (MSA) is a crucial task in bioinformatics. In this paper we extended previous work with evolutionary algorithms (EA) by using MSA solutions obtained from the wellknown Clustal V algorithm as a candidate solution seed of the initial EA population. Our results clearly sh...

  9. Mechanical equipment for magnet measurement and alignment

    International Nuclear Information System (INIS)

    The mechanical equipment for measuring and aligning (or fiducializing) magnets is described by reference to devices designed and built by a number of laboratories. Some of these are now available commercially. The descriptions are supplemented by a list of representative sources of hardware

  10. Aligning Technology Education Teaching with Brain Development

    Science.gov (United States)

    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…

  11. The Ability to Align Vision and Kinaesthesia

    NARCIS (Netherlands)

    J.J. van den Dobbelsteen (John)

    2003-01-01

    textabstractWe investigated the human ability to align visually and kinaesthetically perceived end positions of arm movements. We specifically looked at the spatial characteristics of movement endpoints and the responses of the visuomotor system to altered relationships between visual and kinaesthet

  12. Stimulating Strategically Aligned Behaviour among Employees

    NARCIS (Netherlands)

    C.B.M. van Riel (Cees); G.A.J.M. Berens (Guido); M. Dijkstra (Majorie)

    2008-01-01

    textabstractStrategically aligned behaviour (SAB), i.e., employee action that is consistent with the company’s strategy, is of vital importance to companies. This study provides insights into the way managers can promote such behaviour among employees by stimulating employee motivation and by inform

  13. Linear collider accelerator physics issues regarding alignment

    International Nuclear Information System (INIS)

    The next generation of linear colliders will require more stringent alignment tolerances than those for the SLC with regard to the accelerating structures, quadrupoles, and beam position monitors. New techniques must be developed to achieve these tolerances. A combination of mechanical-electrical and beam-based methods will likely be needed

  14. Ditransitive Alignment and Referential Hierarchies in Araki

    Directory of Open Access Journals (Sweden)

    Alexandre François

    2012-01-01

    Full Text Available Since Bossong (1985, referential hierarchies have proven useful in accounting for patterns of differential object marking (DOM in mono‑transitive clauses. More recent studies (Siewierska 1998; Haspelmath 2005; Bickel 2008; papers in this volume have also shown the relevance of such hierarchies in explaining the alignment patterns of ditransitive verbs – that is, how languages treat formally the Theme and the recipient or Goal. Araki, a highly endangered Oceanic language of Vanuatu, not only shows DOM with its transitive verbs, but is also sensitive to referential properties of arguments in its handling of ditransitive alignment. On a hierarchy defined by the features [±local] (i.e. speech-act participant and [±human], the higher-ranking participant receives the status of object, while the other one is demoted to a peripheral role. The result is a pattern of regular alternation between indirective and secundative alignment, depending on the relative properties of the Theme and the Goal. The present article will describe these patterns, and discuss cases of variation. Ultimately, rules of ditransitive alignment in Araki can be explained functionally as a competition between non-agent participants on a scale of affectedness.

  15. Survey and alignment at the ALS

    International Nuclear Information System (INIS)

    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 ampersand A) at the ALS have been written that may further elucidate some details of the methods and systems described in this paper

  16. Multiple Sequence Alignment using GA and NN

    Directory of Open Access Journals (Sweden)

    Shuting Wu

    2008-12-01

    Full Text Available Multiple sequence alignment (MSA is an important tool in biological analysis. However, it is difficult to solve this class of problems, due to their exponential complexity. This paper presents an algorithm combining the genetic algorithm and a self-organizing neural network for solution to MSA. This approach demonstrates improved performance in long DNA and RNA data sets exhibiting small similarity.

  17. Aligning The Organization For Successful Relationships

    OpenAIRE

    Kothandaraman, P; Wilson, D. T.

    1999-01-01

    The domain of interest, while investigating inter-organizational relationships has been the boundary functions of marketing and purchasing. Understanding the impact of proper aligning of the critical value creating functions within the organization on the success of relationship marketing outcome requires attention. This paper explores the impact.

  18. Further solar alignments of Greek Byzantine churches

    Science.gov (United States)

    Liritzis, I.; Vasiliou, H.

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

  19. Aligning the CMS Muon Chambers with the Muon Alignment System during an Extended Cosmic Ray Run

    CERN Document Server

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    2010-01-01

    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 microns and 30-200 microradians. Systematic errors on displacements are estimated to be 340-590 microns based on comparisons with independent photogrammetry measurements.

  20. Test procedure for calibration, grooming and alignment of the LDUA Optical Alignment Scope

    International Nuclear Information System (INIS)

    The Light Duty Utility Arm (LDUA) is a remotely operated manipulator used to enter into underground waste tanks through one of the tank risers. The LDUA must be carefully aligned with the tank riser during the installation process. The Optical Alignment Scope (OAS) is used to determine when optimum alignment has been achieved between the LDUA and the riser. This procedure is used to assure that the instrumentation and equipment comprising the OAS is properly adjusted in order to achieve its intended functions successfully

  1. Image correlation method for DNA sequence alignment.

    Directory of Open Access Journals (Sweden)

    Millaray Curilem Saldías

    Full Text Available 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.

  2. Elements of Cellular Blind Interference Alignment --- Aligned Frequency Reuse, Wireless Index Coding and Interference Diversity

    CERN Document Server

    Jafar, Syed A

    2012-01-01

    We explore degrees of freedom (DoF) characterizations of partially connected wireless networks, especially cellular networks, with no channel state information at the transmitters. Specifically, we introduce three fundamental elements --- aligned frequency reuse, wireless index coding and interference diversity --- through a series of examples, focusing first on infinite regular arrays, then on finite clusters with arbitrary connectivity and message sets, and finally on heterogeneous settings with asymmetric multiple antenna configurations. Aligned frequency reuse refers to the optimality of orthogonal resource allocations in many cases, but according to unconventional reuse patterns that are guided by interference alignment principles. Wireless index coding highlights both the intimate connection between the index coding problem and cellular blind interference alignment, as well as the added complexity inherent to wireless settings. Interference diversity refers to the observation that in a wireless network ...

  3. A benchmark of multiple sequence alignment programs upon structural RNAs

    DEFF Research Database (Denmark)

    Gardner, P. P.; Wilm, A.; Washietl, S.

    2005-01-01

    , we systematically test the performance of existing alignment algorithms on structural RNAs. This work was aimed at achieving the following goals: (i) to determine conditions where it is appropriate to apply common sequence alignment methods to the structural RNA alignment problem. This indicates...... where and when researchers should consider augmenting the alignment process with auxiliary information, such as secondary structure and (ii) to determine which sequence alignment algorithms perform well under the broadest range of conditions. We find that sequence alignment alone, using the current...

  4. Self-Aligning Solar Panel : Construction of a self-aligning platform for solar panels

    OpenAIRE

    Dahlqvist, Mattias; Nilsson-Hedman, Tommy

    2015-01-01

    The purpose of this project is to create a self-aligning platform for solar panels for better utilization of the renewable solar energy source that is available. The difference between present self-aligning solutions and the proposed one is its two repositioning modes to find the optimal position which implies higher efficiency in terms of harnessing the solar energy. The movement is based on two axes rotation. The objective is to compare the final prototype with a stationary support structur...

  5. Two Influential Primate Classifications Logically Aligned

    Science.gov (United States)

    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

  6. Two Influential Primate Classifications Logically Aligned.

    Science.gov (United States)

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

    2016-07-01

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

  7. Alignment techniques for DRAGON-Ⅰ LIA

    Institute of Scientific and Technical Information of China (English)

    DAI Zhi-Yong; XIE Yu-Tong; LI Hong; ZHANG Wen-Wei; LIU Yun-Long; PAN Hai-Feng; ZHANG Lin-Wen; DENG Jian-Jun

    2009-01-01

    DRAGON-Ⅰ designed and manufactured by CAEP is a linear induction accelerator which can produce a 20 MeV-3 kA-60 us electron beam. The high performance required for the machine is determined by the beam quality and thus is greatly dependent on the accelerator alignment. In order to reduce the chromatic effect of the beam, the stretched wire technique has been developed to measure magnetic axes of the cells precisely, and the dipole steering magnets have been equipped into each cell to correct its magnetic axis misalignment. Finally, the laser tracker has been used to examine the installation error of the accelerator. In this paper, different alignment techniques and the primary results are presented and discussed.

  8. Nimble Protein Sequence Alignment in Grid (NPSAG

    Directory of Open Access Journals (Sweden)

    K. Somasundaram

    2008-01-01

    Full Text Available In Bio-Informatics application, the analysis of protein sequence is a kind of computation driven science which has rapidly and quickly growing biological data. Also databases used in these applications are heterogeneous in nature and alignment of protein sequence using physical techniques is expensive, slow and results are not always guaranteed/accurate. So this application requires cross-platform, cost-effective and more computing power algorithm for sequence matching and searching a sequence in database. Grid is one of the most emerging technologies of cost effective computing paradigm for large class of data and compute intensive application which enables large-scale aggregation and sharing of computational data and other resources across institutional boundaries. We proposed the Grid architecture for searching of distributed, heterogeneous genomic databases which contained protein sequences to speed up the analysis of large scale sequence data and performed sequence alignment for residues match.

  9. Alignment procedures for the CMS silicon tracker

    CERN Document Server

    Behr, Joerg

    2012-01-01

    The CMS all-silicon tracker consists of 16588 modules. Therefore its alignment procedures require sophisticated algorithms. Advanced tools of computing, tracking and data analysis have been deployed for reaching the targeted performance. Ultimate local precision is now achieved by the determination of sensor curvatures, challenging the algorithms to determine about 200k parameters simultaneously. Systematic biases in the geometry are controlled by adding further information into the alignment workflow, e.g. the mass of decaying resonances. The orientation of the tracker with respect to the magnetic field of CMS is determined with a stand-alone chi-square minimization procedure. The geometries are finally carefully validated. The monitored quantities include the basic track quantities for tracks from both collisions and cosmic muons and physics observables.

  10. Tevatron Alignment Issues 2003-2004

    CERN Document Server

    Volk, James T; Elementi, Luciano; Gelfand, Norman M; Gollwitzer, Keith; Greenwood, John A; Martens, Michael A; Moore, Craig D; Nobrega, Alfred; Russell, Allison D; Sager, Terry; Shiltsev, Vladimir; Stefanski, Raymond; Syphers, Michael J; Wojcik, George

    2005-01-01

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

  11. Alignment strategy for the CMS Tracker

    CERN Document Server

    Weber, M

    2008-01-01

    The CMS Tracker measures the momentum of charged particles created in proton-proton interactions with 14\\,TeV nominal center-of-mass energy close to the interaction region. Its excellent single-point position resolution of 9--60\\,$\\mu$m\\ is far below typical construction tolerances, and together with its high granularity renders the alignment a demanding task, which needs to aim at micro-meter level precision. A strategy to align the CMS tracker with its 15\\,148 silicon strip and 1\\,440 silicon pixel modules, starting from survey measurements during construction, incorporating information from the laser hardware monitoring system and finally using collision and non-collision tracks for highest precision has been developed and is detailed in this article.

  12. Strategies and tools for whole genome alignments

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. Intrinsic Alignments in the Illustris Simulation

    CERN Document Server

    Hilbert, Stefan; Schneider, Peter; Springel, Volker; Vogelsberger, Mark; Hernquist, Lars

    2016-01-01

    We study intrinsic alignments (IA) of galaxy image shapes within the Illustris cosmic structure formation simulations. We investigate how IA correlations depend on observable galaxy properties such as stellar mass, apparent magnitude, redshift, and photometric type, and on the employed shape measurement method. The correlations considered include the matter density-intrinsic ellipticity (mI), galaxy density-intrinsic ellipticity (dI), gravitational shear-intrinsic ellipticity (GI), and intrinsic ellipticity-intrinsic ellipticity (II) correlations. We find stronger correlations for more massive and more luminous galaxies, as well as for earlier photometric types, in agreement with observations. Moreover, shape measurement methods that down-weight the outer parts of galaxy images produce much weaker IA signals on intermediate and large scales than methods employing flat radial weights. Thus, the expected contribution of intrinsic alignments to the observed ellipticity correlation in tomographic cosmic shear sur...

  14. Only marginal alignment of disc galaxies

    CERN Document Server

    Andrae, Rene

    2011-01-01

    Testing theories of angular-momentum acquisition of rotationally supported disc galaxies is the key to understand the formation of this type of galaxies. The tidal-torque theory tries to explain this acquisition process in a cosmological framework and predicts positive autocorrelations of angular-momentum orientation and spiral-arm handedness on distances of 1Mpc/h. This disc alignment can also cause systematic effects in weak-lensing measurements. Previous observations claimed discovering such correlations but did not account for errors in redshift, ellipticity and morphological classifications. We explain how to rigorously propagate all important errors. Analysing disc galaxies in the SDSS database, we find that positive autocorrelations of spiral-arm handedness and angular-momentum orientations on distances of 1Mpc/h are plausible but not statistically significant. This result agrees with a simple hypothesis test in the Local Group, where we find no evidence for disc alignment. Moreover, we demonstrate tha...

  15. Alignment procedures for the CMS silicon tracker

    International Nuclear Information System (INIS)

    The CMS all-silicon tracker consists of 16588 modules. Therefore its alignment procedures require sophisticated algorithms. Advanced tools of computing, tracking and data analysis have been deployed for reaching the targeted performance. Ultimate local precision is now achieved by the determination of sensor curvatures, challenging the algorithms to determine about 200k parameters simultaneously. Systematic biases in the geometry are controlled by adding further information into the alignment workflow, e.g. the mass of decaying resonances. The orientation of the tracker with respect to the magnetic field of CMS is determined with a stand-alone chi-square minimization procedure. The geometries are finally carefully validated. The monitored quantities include the basic track quantities for tracks from both collisions and cosmic muons and physics observables.

  16. The surveyors' quest for perfect alignment

    CERN Multimedia

    2003-01-01

    Photogrammetry of a CMS endcap and part of the hadronic calorimeter.The structure was covered with targets photographed by digital cameras. Perfect alignment.... Although CERN's surveyors do not claim to achieve it, they are constantly striving for it and deploy all necessary means to come as close as they can. In their highly specialised field of large-scale metrology, the solution lies in geodesy and photogrammetry, both of which are based on increasingly sophisticated instruments and systems. In civil engineering, these techniques are used for non-destructive inspection of bridges, dams and other structures, while industrial applications include dimensional verification and deformation measurement in large mechanical assemblies. The same techniques also come into play for the metrology of research tools such as large telescopes and of course, particle accelerators. Particle physics laboratories are especially demanding customers, and CERN has often asked for the impossible. As a result, the alignment metro...

  17. Controlled Deposition and Alignment of Carbon Nanotubes

    Science.gov (United States)

    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.

  18. Interference Alignment with Analog Channel State Feedback

    OpenAIRE

    Ayach, Omar El; Heath Jr, Robert W.

    2010-01-01

    Interference alignment (IA) is a multiplexing gain optimal transmission strategy for the interference channel. While the achieved sum rate with IA is much higher than previously thought possible, the improvement often comes at the cost of requiring network channel state information at the transmitters. This can be achieved by explicit feedback, a flexible yet potentially costly approach that incurs large overhead. In this paper we propose analog feedback as an alternative to limited feedback ...

  19. Anatomically Plausible Surface Alignment and Reconstruction

    DEFF Research Database (Denmark)

    Paulsen, Rasmus R.; Larsen, Rasmus

    2010-01-01

    With the increasing clinical use of 3D surface scanners, there is a need for accurate and reliable algorithms that can produce anatomically plausible surfaces. In this paper, a combined method for surface alignment and reconstruction is proposed. It is based on an implicit surface representation...... energy that has earlier proved to be particularly well suited for human surface scans. The method has been tested on full cranial scans of ten test subjects and on several scans of the outer human ear....

  20. Capacitive Sensors And Targets Would Measure Alignments

    Science.gov (United States)

    Jenstrom, Del T.

    1994-01-01

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

  1. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    OpenAIRE

    Arabi E. keshk

    2014-01-01

    The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between se...

  2. Physical processes behind the alignment effect

    OpenAIRE

    Mendoza, S.; Hidalgo, JC

    2004-01-01

    The radio/optical alignment effect for small powerful radio galaxies has been shown to be produced by shock waves formed by the interaction of the head of the jet and/or cocoon with clouds embedded in the interstellar/intergalactic medium. We present here preliminary results of analytical and numerical solutions that have been made to account for the production of implosive shock waves induced by embedding cold clouds in the radio lobe of expanding powerful radio sources.

  3. Efficient alignment-free DNA barcode analytics

    OpenAIRE

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-01-01

    Background In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient ...

  4. Automatic face alignment by maximizing similarity score

    OpenAIRE

    Boom, Bas; Spreeuwers, Luuk; Veldhuis, Raymond; Fred, A.; Jain, A. K.

    2007-01-01

    Accurate face registration is of vital importance to the performance of a face recognition algorithm. We propose a face registration method which searches for the optimal alignment by maximizing the score of a face recognition algorithm. In this paper we investigate the practical usability of our face registration method. Experiments show that our registration method achieves better results in face verification than the landmark based registration method. We even obtain face verification resu...

  5. Alignment of high Rydberg states in hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Berry, H.G.; DeHaes, J.C.; Neek, D.K.; Somerville, L.P.

    1984-01-01

    We have measured the light yields and polarizations of the light emitted from several Balmer transitions in atomic hydrogen following beam foil excitation of protons at energies of 50 to 150 keV. The polarizations have been measured as a function of distance downbeam from the exciter foil for several transitions. The measurements indicate a very strong initial alignment which is then perturbed by surface fields out to several mm from the surface. 8 references, 7 figures.

  6. Strength of Coriolis alignment in actinide nuclei

    International Nuclear Information System (INIS)

    Analysis of aligned angular momenta i/sub α/(ω) in different rotational bands extracted from experimental data with a linear spin term approx.BI in the formulas for E/sub rot/(I) reveal that, in actinide nuclei in the levels with modest spin I< or =23, i/sub α/(ω) usually is very small (< or approx. =0.7), i.e., is much smaller than in rare earth nuclei

  7. Plasmonic Properties of Vertically Aligned Nanowire Arrays

    OpenAIRE

    Hua Qi; Glembocki, O. J.; Prokes, S. M.

    2012-01-01

    Nanowires (NWs)/Ag sheath composites were produced to investigate plasmonic coupling between vertically aligned NWs for surface-enhanced Raman scattering (SERS) applications. In this investigation, two types of vertical NW arrays were studied; those of ZnO NWs grown on nanosphere lithography patterned sapphire substrate via vapor-liquid-solid (VLS) mechanism and Si NW arrays produced by wet chemical etching. Both types of vertical NW arrays were coated with a thin layer of silver by electrole...

  8. Agent-based argumentation for ontology alignments

    OpenAIRE

    Laera, Loredana; Tamma, Valentina; Bench-Capon, Trevor; Euzenat, Jérôme

    2006-01-01

    laera2006a International audience When agents communicate they do not necessarily use the same vocabulary or ontology. For them to interact successfully they must find correspondences between the terms used in their ontologies. While many proposals for matching two agent ontologies have been presented in the literature, the resulting alignment may not be satisfactory to both agents and can become the object of further negotiation between them. This paper describes our work constructing ...

  9. Theory of the deformation of aligned polyethylene

    OpenAIRE

    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 w...

  10. SPA: a probabilistic algorithm for spliced alignment.

    OpenAIRE

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

    2006-01-01

    Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of the repertoire of splice variants, and to gain insight into the mechanisms of alternative splicing, it is essential that cDNAs are very accurately mapped to their respective genomes. Currently available algorithms for cDNA-to-genome alignment do not reach the necessary level of accuracy because the...

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

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

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

  13. Automatic alignment of multiple magnets into Halbach cylinders

    International Nuclear Information System (INIS)

    Halbach cylinders have found various applications for their ability to produce strong and homogenous magnetostatic fields. Contrary to their conventional manual fabrication, we introduce a novel approach to automatically align multiple permanent magnets into a Halbach cylinder. The approach uses the magnetic field distribution from a diametrically magnetized cylindrical magnet to simultaneously align multiple magnets. The extent to which the automatic assembly can approximate a Halbach cylinder was analyzed using 3D Finite Element Modeling. Prototypes were built that demonstrated automatic alignment of eight magnets into Halbach cylinders. Automatic alignment eliminates the complexity of manually aligning Halbach cylinders. - Highlights: • A new method for fabricating cylindrical Halbach array. • Simultaneously alignment of multiple magnets into Halbach cylinders. • Automatic alignment eliminates the complexity of manually aligning Halbach cylinders

  14. Alignement automatise de fibres optiques amorces monomodes

    Science.gov (United States)

    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. The alignment of the CMS Silicon Tracker

    International Nuclear Information System (INIS)

    The complex system of the CMS all-silicon Tracker, with 15 148 silicon strip and 1440 silicon pixel modules, requires sophisticated alignment procedures. In order to achieve an optimal track-parameter resolution, the position and orientation of its modules need to be determined with a precision of few micrometers. We present results of the alignment of the full Tracker, in its final position, used for the reconstruction of the first collisions recorded by the CMS experiment. The aligned geometry is based on the analysis of several million reconstructed tracks recorded during the commissioning of the CMS experiment, both with cosmic rays and with the first proton-proton collisions. The geometry has been systematically monitored in the different periods of operation of the CMS detector. The results have been validated by several data-driven studies (laser beam cross-checks, track fit self-consistency, track residuals in overlapping module regions, and track parameter resolution) and compared with predictions obtained from a detailed detector simulation. (author)

  16. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    Directory of Open Access Journals (Sweden)

    Arabi E. keshk

    2014-05-01

    Full Text Available The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between sequences. This paper introduces an enhancement of dynamic algorithm of genome sequence alignment, which called EDAGSA. It is filling the three main diagonals without filling the entire matrix by the unused data. It gets the optimal solution with decreasing the execution time and therefore the performance is increased. To illustrate the effectiveness of optimizing the performance of the proposed algorithm, it is compared with the traditional methods such as Needleman-Wunsch, Smith-Waterman and longest common subsequence algorithms. Also, database is implemented for using the algorithm in multi-sequence alignments for searching the optimal sequence that matches the given sequence.

  17. Surface Dipole Control of Liquid Crystal Alignment.

    Science.gov (United States)

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

    2016-05-11

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

  18. Aligned flax fibre/polylactate composites

    DEFF Research Database (Denmark)

    Madsen, Bo; Lilholt, Hans; Thygesen, Anders;

    2008-01-01

    The potential of biocomposites in engineering applications is demonstrated by using aligned flax fibre/polylactate composites as a materials model system. The failure stress of flax fibres is measured by tensile testing of single fibres and fibre bundles. For both fibre configurations, it is foun...... flax fibre composites and traditional fibre composites (exemplified by glass fibre composites) are presented. The stiffness per volume, per weight and per cost is compared for these two types of composites.......The potential of biocomposites in engineering applications is demonstrated by using aligned flax fibre/polylactate composites as a materials model system. The failure stress of flax fibres is measured by tensile testing of single fibres and fibre bundles. For both fibre configurations, it is found...... that failure stress is decreased by increasing the tested fibre volume. Based on two types of flax fibre preforms: carded sliver and unidirectional non-crimp fabric, aligned flax fibre/polylactate composites were fabricated with variable fibre content. The volumetric composition and tensile properties...

  19. The Alignment of the CMS Silicon Tracker

    International Nuclear Information System (INIS)

    The complex system of the CMS all-silicon Tracker, with 15148 silicon strips and 1440 silicon pixel modules, requires sophisticated alignment procedures. In order to achieve an optimal track-parameter resolution, the position and orientation of its modules need to be determined with a precision of few micrometers. We present results of the alignment of the full Tracker, in its final position, used for the reconstruction of the first collisions recorded by the CMS experiment. The aligned geometry is based on the analysis of several million reconstructed tracks recorded during the commissioning of the CMS experiment, both with cosmic rays and with the first proton-proton collisions. The geometry has been systematically monitored in the different periods of operation of the CMS detector. The results have been validated by several data-driven studies (laser beam cross-checks, track fit self-consistency, track residuals in overlapping module regions, and track parameter resolution) and compared with predictions obtained from a detailed detector simulation.

  20. The CMS tracker alignment in pp collisions

    International Nuclear Information System (INIS)

    The CMS all-silicon tracker consists of 16,588 modules. Aligning these with the desired precision of a few micrometers is only feasible using track based alignment procedures. Ultimate local precision is now achieved by the determination of sensor curvatures. This faces the algorithms with about 200,000 parameters to be calculated simultaneously. The Millipede II program interfaced with CMS software is optimized to provide solution in one step. The main remaining challenges are systematic distortions in the achieved geometry that are systematically biasing the track parameters like the track momenta. These distortions are controlled by adding further information into the alignment workflow, e.g. the mass of decaying resonances. In addition, the orientation of the tracker with respect to the magnetic field of CMS is determined with a stand-alone chi-square minimization procedure. The geometries are finally carefully validated. The monitored quantities include the basic track quantities for tracks from both collisions and cosmic muons and physics observables like resonance masses

  1. Alignment limit of the NMSSM Higgs sector

    Science.gov (United States)

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

    2016-02-01

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

  2. Evaluation of microRNA alignment techniques.

    Science.gov (United States)

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

    2016-08-01

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

  3. Stochastic sampling of the RNA structural alignment space

    OpenAIRE

    Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H.

    2009-01-01

    A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the ‘structural alignment’ space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtu...

  4. A comparison of four pair-wise sequence alignment methods

    OpenAIRE

    Essoussi, Nadia; Fayech, Sondes

    2007-01-01

    Protein sequence alignment has become an essential task in modern molecular biology research. A number of alignment techniques have been documented in literature and their corresponding tools are made available as freeware and commercial software. The choice and use of these tools for sequence alignment through the complete interpretation of alignment results is often considered non-trivial by end-users with limited skill in Bioinformatics algorithm development. Here, we discuss the compariso...

  5. Multiple sequence alignment accuracy and evolutionary distance estimation

    OpenAIRE

    Rosenberg Michael S

    2005-01-01

    Abstract Background Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation analysis. This study used sequence simulation to examine the gain in accuracy of adding a third sequence to a pair wise alignment, particularly concentrating on how the phylogenetic positio...

  6. Alignment-free sequence comparison with spaced k-mers

    OpenAIRE

    Boden, Marcus; Schöneich, Martin; Horwege, Sebastian; Lindner, Sebastian; Leimeister, Chris; Morgenstern, Burkhard

    2013-01-01

    Alignment-free methods are increasingly used for genome analysis and phylogeny reconstruction since they circumvent various difficulties of traditional approaches that rely on multiple sequence alignments. In particular, they are much faster than alignment-based methods. Most alignment-free approaches work by analyzing the k-mer composition of sequences. In this paper, we propose to use 'spaced k-mers', i.e. patterns of deterministic and 'don't care' positions instead of contiguous k-me...

  7. LHCb: Experience with LHCb alignment software on first data

    CERN Multimedia

    Deissenroth, M

    2009-01-01

    We report results obtained with different track-based algorithms for the alignment of the LHCb detector with first data. The large-area Muon Detector and Outer Tracker have been aligned with a large sample of tracks from cosmic rays. The three silicon detectors --- VELO, TT-station and Inner Tracker --- have been aligned with beam-induced events from the LHC injection line. We compare the results from the track-based alignment with expectations from detector survey.

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

    International Nuclear Information System (INIS)

    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(regsign) 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.

  9. SPA: a probabilistic algorithm for spliced alignment.

    Directory of Open Access Journals (Sweden)

    Erik van Nimwegen

    2006-04-01

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

  10. SPA: A Probabilistic Algorithm for Spliced Alignment

    Science.gov (United States)

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

    2006-01-01

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

  11. The meaning of alignment: lessons from structural diversity

    OpenAIRE

    Heringa Jaap; Feenstra K Anton; Pirovano Walter

    2008-01-01

    Abstract 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 alterna...

  12. The meaning of alignment: lessons from structural diversity

    Directory of Open Access Journals (Sweden)

    Heringa Jaap

    2008-12-01

    Full Text Available Abstract 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 http://www.ibi.vu.nl/databases/stralivari.

  13. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2007-01-01

    correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the...

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

    Science.gov (United States)

    Iriyama, Satoshi; Ohya, Masanori

    2009-02-01

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

  15. Genomic multiple sequence alignments: refinement using a genetic algorithm

    Directory of Open Access Journals (Sweden)

    Lefkowitz Elliot J

    2005-08-01

    Full Text Available Abstract Background Genomic sequence data cannot be fully appreciated in isolation. Comparative genomics – the practice of comparing genomic sequences from different species – plays an increasingly important role in understanding the genotypic differences between species that result in phenotypic differences as well as in revealing patterns of evolutionary relationships. One of the major challenges in comparative genomics is producing a high-quality alignment between two or more related genomic sequences. In recent years, a number of tools have been developed for aligning large genomic sequences. Most utilize heuristic strategies to identify a series of strong sequence similarities, which are then used as anchors to align the regions between the anchor points. The resulting alignment is globally correct, but in many cases is suboptimal locally. We describe a new program, GenAlignRefine, which improves the overall quality of global multiple alignments by using a genetic algorithm to improve local regions of alignment. Regions of low quality are identified, realigned using the program T-Coffee, and then refined using a genetic algorithm. Because a better COFFEE (Consistency based Objective Function For alignmEnt Evaluation score generally reflects greater alignment quality, the algorithm searches for an alignment that yields a better COFFEE score. To improve the intrinsic slowness of the genetic algorithm, GenAlignRefine was implemented as a parallel, cluster-based program. Results We tested the GenAlignRefine algorithm by running it on a Linux cluster to refine sequences from a simulation, as well as refine a multiple alignment of 15 Orthopoxvirus genomic sequences approximately 260,000 nucleotides in length that initially had been aligned by Multi-LAGAN. It took approximately 150 minutes for a 40-processor Linux cluster to optimize some 200 fuzzy (poorly aligned regions of the orthopoxvirus alignment. Overall sequence identity increased only

  16. Structure alignment based on coding of local geometric measures

    Directory of Open Access Journals (Sweden)

    Rinne Andrew W

    2006-07-01

    Full Text Available Abstract Background A structure alignment method based on a local geometric property is presented and its performance is tested in pairwise and multiple structure alignments. In this approach, the writhing number, a quantity originating from integral formulas of Vassiliev knot invariants, is used as a local geometric measure. This measure is used in a sliding window to calculate the local writhe down the length of the protein chain. By encoding the distribution of writhing numbers across all the structures in the protein databank (PDB, protein geometries are represented in a 20-letter alphabet. This encoding transforms the structure alignment problem into a sequence alignment problem and allows the well-established algorithms of sequence alignment to be employed. Such geometric alignments offer distinct advantages over structural alignments in Cartesian coordinates as it better handles structural subtleties associated with slight twists and bends that distort one structure relative to another. Results The performance of programs for pairwise local alignment (TLOCAL and multiple alignment (TCLUSTALW are readily adapted from existing code for Smith-Waterman pairwise alignment and for multiple sequence alignment using CLUSTALW. The alignment algorithms employed a blocked scoring matrix (TBLOSUM generated using the frequency of changes in the geometric alphabet of a block of protein structures. TLOCAL was tested on a set of 10 difficult proteins and found to give high quality alignments that compare favorably to those generated by existing pairwise alignment programs. A set of protein comparison involving hinged structures was also analyzed and TLOCAL was seen to compare favorably to other alignment methods. TCLUSTALW was tested on a family of protein kinases and reveal conserved regions similar to those previously identified by a hand alignment. Conclusion These results show that the encoding of the writhing number as a geometric measure allow high

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

    Science.gov (United States)

    Sampler, Henry P.

    1990-01-01

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

  18. Dye alignment in luminescent solar concentrators: I. Vertical alignment for improved waveguide coupling

    Energy Technology Data Exchange (ETDEWEB)

    Mulder, Carlijn L.; Reusswig, Phil D.; Velazquez, Amador M.; Kim, Heekyung; Rotschild, Carmel; Baldo, Marc

    2010-04-26

    Luminescent solar concentrators (LSCs) use dye molecules embedded in a flat-plate waveguide to absorb solar radiation. Ideally, the dyes re-emit the absorbed light into waveguide modes that are coupled to solar cells. But some photons are always lost, re-emitted through the face of the LSC and coupled out of the waveguide. In this work, we improve the fundamental efficiency limit of an LSC by controlling the orientation of dye molecules using a liquid crystalline host. First, we present a theoretical model for the waveguide trapping efficiency as a function of dipole orientation. Next, we demonstrate an increase in the trapping efficiency from 66% for LSCs with no dye alignment to 81% for a LSC with vertical dye alignment. Finally, we show that the enhanced trapping efficiency is preserved for geometric gains up to 30, and demonstrate that an external diffuser can alleviate weak absorption in LSCs with vertically-aligned dyes.

  19. Fine-tuning structural RNA alignments in the twilight zone

    Directory of Open Access Journals (Sweden)

    Schirmer Stefanie

    2010-04-01

    Full Text Available Abstract Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

  20. INTRINSIC ALIGNMENT OF CLUSTER GALAXIES: THE REDSHIFT EVOLUTION

    International Nuclear Information System (INIS)

    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 (≥3σ) 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.

  1. Desktop aligner for fabrication of multilayer microfluidic devices

    Science.gov (United States)

    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.

  2. STAR/SVT alignment within a finite magnetic field

    International Nuclear Information System (INIS)

    We report on the development of SVT (Silicon Vertex Tracker) software for the purpose of the SVT and TPC (Time Projection Chamber) relative alignment as well as the internal alignment of the SVT components. The alignment procedure described complements the internal SVT alignment procedure discussed in Star Note 356. It involves track reconstruction in both the Star TPC and SVT for the calibration of the SVT geometry in the presence of a finite magnetic field. This new software has been integrated under the package SAL already running under STAR. Both the implementation and the performance of the alignment algorithm are described. We find that the current software implementation in SAL should enable a very satisfactory internal SVT alignment as well as an excellent SVT to TPC relative alignment

  3. Alignment of Dust by Radiative Torque: Recent Developments

    CERN Document Server

    Lazarian, A

    2009-01-01

    Alignment of dust by radiative torques (RATs) has proven to be the most promising mechanism to explain alignment in various astrophysical environments, from comet atmospheres to accretion disks, molecular clouds, and diffuse interstellar gas. We discuss some of the major advances, which include, first of all, formulating of the analytical model of RATs. This model was shown to reproduce well the torques acting on actual irregular dust grains and allowed studies of the parameter space for which the alignment happens with long axes perpendicular and parallel to the magnetic field. Such a study resulted in an important conclusion that, without any paramagnetic relaxation, the RAT alignment always happens for interstellar grains with long axes perpendicular to the magnetic field. We show that the gaseous bombardment in some cases increases the degree of alignment by knocking out grains from the positions of imperfect alignment when the grains rotate slowly to more stable positions of perfect alignment where grain...

  4. EST Reading Curriculum & Instruction: An Alignment Analysis

    Directory of Open Access Journals (Sweden)

    Lubna Ali Mohammed

    2015-02-01

    Full Text Available 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 theoretical grounding of the Yemeni EST senior secondary curriculum is in alignment with its communicative-based curriculum label. In line with its label, the reading curriculum embedded in the EST curriculum should be developed and designed based on the Communicative Language Teaching (CLT, which should be reflected in the EST reading instructional practice. In analysing the alignment of the communicative language teaching approach in the EST senior secondary school reading curriculum, the primary focus of the analysis was on the major SLA theories and L2 reading theories and the related instructional approaches. The data for this study were collected via an ESP textbook review as well as from the observation of the EST reading classroom instruction. The findings show that the EST senior secondary reading curriculum was not developed based on the socio-cognitive and socio-cultural theories which are the grounding principles of the communicative approach. Instead, the findings show that the EST senior secondary reading curriculum was primarily developed based on the cognitive information processing theory, in which teaching instruction reflects the student as an individual information processor and the focus on teaching vocabulary and grammatical rules using reading texts in non-communicative manner.Keywords: Communicative Approach, SLA Theories, L2 Reading Theories

  5. Shear adhesion strength of aligned electrospun nanofibers.

    Science.gov (United States)

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

    2014-09-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

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

    OpenAIRE

    Martin, A. 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 li...

  8. Interference Alignment with Incomplete CSIT Sharing

    OpenAIRE

    De Kerret, Paul; Gesbert, David

    2012-01-01

    In this work, we study the impact of having only incomplete channel state information at the transmitters (CSIT) over the feasibility of interference alignment (IA) in a K-user MIMO interference channel (IC). Incompleteness of CSIT refers to the perfect knowledge at each transmitter (TX) of only a sub-matrix of the global channel matrix, where the sub-matrix is specific to each TX. This paper investigates the notion of IA feasibility for CSIT configurations being as incomplete as possible, as...

  9. Advanced Alignment of the ATLAS Tracking System

    CERN Document Server

    Butti, P; The ATLAS collaboration

    2014-01-01

    In order to reconstruct the trajectories of charged particles, the ATLAS experiment exploits a tracking system built using different technologies, planar silicon modules or microstrips (PIX and SCT detectors) and gaseous drift tubes (TRT), all embedded in a 2T solenoidal magnetic field. Misalignments and deformations of the active detector elements deteriorate the track reconstruction resolution and lead to systematic biases on the measured track parameters. The alignment procedures exploits various advanced tools and techniques in order to determine for module positions and correct for deformations. For the LHC Run II, the system is being upgraded with the installation of a new pixel layer, the Insertable B-layer (IBL).

  10. Multiple Sequence Alignment Based on Chaotic PSO

    Science.gov (United States)

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

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

  11. Silicon on insulator self-aligned transistors

    Science.gov (United States)

    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.

  12. Alignment and nonlinear elasticity in biopolymer gels

    Science.gov (United States)

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

    2015-04-01

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

  13. HARPY: Hypernyms and Alignment of Relational Paraphrases

    OpenAIRE

    Grycner, A.; Weikum, G.

    2014-01-01

    Collections of relational paraphrases have been automatically constructed from \\u000Alarge text corpora, as a WordNet counterpart for the realm of binary predicates \\u000Aand their surface forms.\\u000AHowever, these resources fall short in their coverage of hypernymy links \\u000A(subsumptions) among the synsets of phrases. \\u000AThis paper closes this gap by computing a high‐quality alignment between the \\u000Arelational phrases of the Patty taxonomy, one of the largest collections of \\u000At...

  14. Datum definition problems in accelerator alignment

    International Nuclear Information System (INIS)

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

  15. Dipole Alignment in Rotating MHD Turbulence

    Science.gov (United States)

    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.

  16. Tracking and Alignment of the LHCb detector

    CERN Document Server

    Martinelli, Maurizio

    2014-01-01

    The LHCb experiment is designed to study $B$-decays at the LHC. This purpose is achieved by means of an outstanding track momentum resolution and excellent particle identification. The performance of the detector exceeds expectations, and the physics program of the collaboration is extended to the study of charm decays, QCD and electroweak physics. Both tracking and alignment play a key role for obtaining these results. The tracking efficiency in this high-occupancy environment has been measured during LHC Run I (2010-2012) to be larger than 95% over a wide range of momentum and pseudo-rapidity. The alignment of the detector is based on a Kalman filter fit of the tracks and provides an uncertainty on the momentum scale below 1 x 10$^{-4}$ and a momentum resolution of about 0.4%. These results allowed one to achieve high-precision mass measurements of many charm and $B$ hadrons so far. Starting from Run II of the LHC, the running conditions will continue to push the performance of the detector to its limits. A...

  17. Software alignment of the LHCb inner tracker sensors

    International Nuclear Information System (INIS)

    This work uses the Millepede linear alignment method, which is essentially a χ2 minimization algorithm, to determine simultaneously between 76 and 476 alignment parameters and several million track parameters. For the case of non-linear alignment models, Millepede is embedded in a Newton-Raphson iterative procedure. If needed a more robust approach is provided by adding quasi-Newton steps which minimize the approximate χ2 model function. The alignment apparatus is applied to locally align the LHCb's Inner Tracker sensors in an a priori fixed system of coordinate. An analytic measurement model was derived as function of track parameters and alignment parameters, for the two cases: null and nonnull magnetic field. The alignment problem is equivalent to solving a linear system of equations, and usually a matrix inversion is required. In general, as consequence of global degrees of freedom or poorly constrained modes, the alignment matrix is singular or near-singular. The global degrees of freedom are obtained: directly from χ2 function invariant transformations, and in parallel by an alignment matrix diagonalization followed by an extraction of the least constrained modes. The procedure allows to properly de ne the local alignment of the Inner Tracker. Using Monte Carlo data, the outlined procedure reconstructs the position of the IT sensors within micrometer precision or better. For rotations equivalent precision was obtained. (orig.)

  18. BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

    Directory of Open Access Journals (Sweden)

    Miklós István

    2009-08-01

    Full Text Available Abstract 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 http://www.stats.ox.ac.uk/~satija/BigFoot/

  19. Software alignment of the LHCb inner tracker sensors

    Energy Technology Data Exchange (ETDEWEB)

    Maciuc, Florin

    2009-04-20

    This work uses the Millepede linear alignment method, which is essentially a {chi}{sup 2} minimization algorithm, to determine simultaneously between 76 and 476 alignment parameters and several million track parameters. For the case of non-linear alignment models, Millepede is embedded in a Newton-Raphson iterative procedure. If needed a more robust approach is provided by adding quasi-Newton steps which minimize the approximate {chi}{sup 2} model function. The alignment apparatus is applied to locally align the LHCb's Inner Tracker sensors in an a priori fixed system of coordinate. An analytic measurement model was derived as function of track parameters and alignment parameters, for the two cases: null and nonnull magnetic field. The alignment problem is equivalent to solving a linear system of equations, and usually a matrix inversion is required. In general, as consequence of global degrees of freedom or poorly constrained modes, the alignment matrix is singular or near-singular. The global degrees of freedom are obtained: directly from {chi}{sup 2} function invariant transformations, and in parallel by an alignment matrix diagonalization followed by an extraction of the least constrained modes. The procedure allows to properly de ne the local alignment of the Inner Tracker. Using Monte Carlo data, the outlined procedure reconstructs the position of the IT sensors within micrometer precision or better. For rotations equivalent precision was obtained. (orig.)

  20. Parameter Identification Method for SINS Initial Alignment under Inertial Frame

    Directory of Open Access Journals (Sweden)

    Haijian Xue

    2016-01-01

    Full Text Available The performance of a strapdown inertial navigation system (SINS largely depends on the accuracy and rapidness of the initial alignment. The conventional alignment method with parameter identification has been already applied widely, but it needs to calculate the gyroscope drifts through two-position method; then the time of initial alignment is greatly prolonged. For this issue, a novel self-alignment algorithm by parameter identification method under inertial frame for SINS is proposed in this paper. Firstly, this coarse alignment method using the gravity in the inertial frame as a reference is discussed to overcome the limit of dynamic disturbance on a rocking base and fulfill the requirement for the fine alignment. Secondly, the fine alignment method by parameter identification under inertial frame is formulated. The theoretical analysis results show that the fine alignment model is fully self-aligned with no external reference information and the gyrodrifts can be estimated in real time. The simulation results demonstrate that the proposed method can achieve rapid and highly accurate initial alignment for SINS.

  1. Alignment and commissioning of the APS beamline front ends

    International Nuclear Information System (INIS)

    Fifteen out of forty initial beamline front ends have been installed in the storage-ring tunnel at the 7-GeV Advanced Photon Source (APS). For the front-end installation, a four-step alignment process was designed and consists of (1) prealigning the front-end components with support tables in the preassembly area, (2) installing the components with tables in the storage-ring tunnel and aligning relative to the APS global telescope survey network, (3) confirming the alignment using a tooling laser alignment system, and (4) performing adjustments with the synchrotron-radiation beam during commissioning. The laser alignment system and the prealignment database have been of great importance for the expedient maintenance of front-end components. These tools are very important to a large synchrotron radiation facility, such as the APS, since they make a quick alignment setup possible and minimize alignment time inside the tunnel. This paper will present the four-step alignment process, the laser alignment system, and discuss the alignment confirmation results. copyright 1996 American Institute of Physics

  2. A New Analytic Alignment Method for a SINS

    Directory of Open Access Journals (Sweden)

    Caiming Tan

    2015-11-01

    Full Text Available 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.

  3. Accelerator Technology: Geodesy and Alignment for Particle Accelerators

    CERN Document Server

    Missiaen, D

    2013-01-01

    This document is part of Subvolume C 'Accelerators and Colliders' of Volume 21 'Elementary Particles' of Landolt-Börnstein - Group I 'Elementary Particles, Nuclei and Atoms'. It contains the the Section '8.9 Geodesy and Alignment for Particle Accelerators' of the Chapter '8 Accelerator Technology' with the content: 8.9 Geodesy and Alignment for Particle Accelerators 8.9.1 Introduction 8.9.2 Reference and Co-ordinate Systems 8.9.3 Definition of the Beam Line on the Accelerator Site 8.9.4 Geodetic Network 8.9.5 Tunnel Preliminary Works 8.9.6 The Alignment References 8.9.7 Alignment of Accelerator Components 8.9.8 Permanent Monitoring and Remote Alignment of Low Beta Quadrupoles 8.9.9 Alignment of Detector Components

  4. Alignment of the magnet and a positioning method

    Science.gov (United States)

    Kim, Dae-Il

    2015-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    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].

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

    CERN Document Server

    Dong, Jianjin; Abukhdeir, Nasser Mohieddin

    2016-01-01

    A method for automated quantification of the alignment of one-dimensional nanostructures from microscopy imaging is presented. Nanostructure alignment metrics are formulated and shown to 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 rigorously compared using a similarity metric. The results of this work provide researchers in nanoscience and nanotechnology with a rigorous metho...

  7. Local Structural Alignment of RNA with Affine Gap Model

    Science.gov (United States)

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

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

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

    Science.gov (United States)

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

    2014-03-18

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

  9. First-order aggregation models with alignment

    Science.gov (United States)

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

    2016-06-01

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

  10. Dimensionality reduction via locally reconstructive patch alignment

    Science.gov (United States)

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

    2012-07-01

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

  11. Cover song identification by sequence alignment algorithms

    Science.gov (United States)

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

    2011-10-01

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

  12. A robust, automated alignment concept for robotics

    Energy Technology Data Exchange (ETDEWEB)

    Everett, L.J.; Redfield, R.C. (Texas A and M Univ., College Station, TX (United States). 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.

  13. Advanced alignment of the ATLAS tracking system

    CERN Document Server

    Butti, Pierfrancesco; The ATLAS collaboration

    2014-01-01

    In order to reconstruct the trajectories of charged particles, the ATLAS experiment exploits a tracking system built using different technologies, silicon planar modules or microstrips (PIX and SCT detectors) and gaseous drift tubes (TRT), all embedded in a 2T solenoidal magnetic field. Misalignments of the active detector elements and deformations of the structures (which can lead to \\textit{Weak Modes}) deteriorate resolution of the track reconstruction and lead to systematic biases on the measured track parameters. The applied alignment procedures exploit various advanced techniques in order to minimise track-hit residuals and remove detector deformations. For the LHC Run II, the Pixel Detector has been refurbished and upgraded with the installation of a new pixel layer, the Insertable B-layer (IBL).

  14. RAPID TRANSFER ALIGNMENT USING FEDERATED KALMAN FILTER

    Institute of Scientific and Technical Information of China (English)

    GUDong-qing; QINYong-yuan; PENGRong; LIXin

    2005-01-01

    The dimension number of the centralized Kalman filter (CKF) for the rapid transfer alignment (TA) is as high as 21 if the aircraft wing flexure motion is considered in the rapid TA. The 21-dimensional CKF brings the calculation burden on the computer and the difficulty to meet a high filtering updating rate desired by rapid TA. The federated Kalman filter (FKF) for the rapid TA is proposed to solve the dilemma. The structure and the algorithm of the FKF, which can perform parallel computation and has less calculation burden, are designed.The wing flexure motion is modeled, and then the 12-order velocity matching local filter and the 15-order attitud ematching local filter are devised. Simulation results show that the proposed EKE for the rapid TA almost has the same performance as the CKF. Thus the calculation burden of the proposed FKF for the rapid TA is markedly decreased.

  15. Impact of Baryonic Physics on Intrinsic Alignments

    CERN Document Server

    Tenneti, Ananth; Feng, Yu

    2016-01-01

    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. Effective Electrocardiogram Steganography Based on Coefficient Alignment.

    Science.gov (United States)

    Yang, Ching-Yu; Wang, Wen-Fong

    2016-03-01

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

  17. From Babylon to Bergen: On the usefulness of aligned texts

    OpenAIRE

    Signe Oksefjell Ebeling; Jarle Ebeling

    2013-01-01

    After outlining a short and select history of (the usefulness of) parallel texts and alignment, this paper presents a case study where the point of departure is a Norwegian text extract aligned against its translations into seven different target languages, using the Translation Corpus Aligner, originally developed by Knut Hofland. Our main concern is cases where there is not a one-to-one correspondence at sentence level between original (source) and translation ...

  18. IRT studies of many groups: The alignment method

    OpenAIRE

    BengtMuthen

    2014-01-01

    Asparouhov and Muthen (forthcoming) presented a new method for multiple-group confirmatory factor analysis (CFA), referred to as the alignment method. The alignment method can be used to estimate group-specific factor means and variances without requiring exact measurement invariance. A strength of the method is the ability to conveniently estimate models for many groups, such as with comparisons of countries. This paper focuses on IRT applications of the alignment method. An empirical i...

  19. IRT studies of many groups: the alignment method

    OpenAIRE

    Muthén, Bengt; Asparouhov, Tihomir

    2014-01-01

    Asparouhov and Muthén (2014) presented a new method for multiple-group confirmatory factor analysis (CFA), referred to as the alignment method. The alignment method can be used to estimate group-specific factor means and variances without requiring exact measurement invariance. A strength of the method is the ability to conveniently estimate models for many groups, such as with comparisons of countries. This paper focuses on IRT applications of the alignment method. An empirical investigation...

  20. PineSAP—sequence alignment and SNP identification pipeline

    OpenAIRE

    Jill L Wegrzyn; Lee, Jennifer M.; Liechty, John; Neale, David B.

    2009-01-01

    Summary: The Pine Alignment and SNP Identification Pipeline (PineSAP) provides a high-throughput solution to single nucleotide polymorphism (SNP) prediction using multiple sequence alignments from re-sequencing data. This pipeline integrates a hybrid of customized scripting, existing utilities and machine learning in order to increase the speed and accuracy of SNP calls. The implementation of this pipeline results in significantly improved multiple sequence alignments and SNP identifications ...

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

    Science.gov (United States)

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

    2016-05-25

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

  2. Three wavelength optical alignment of the Nova laser

    Energy Technology Data Exchange (ETDEWEB)

    Swift, C.D.; Bliss, E.S.; Jones, W.A.; Seppala, L.G.

    1983-11-16

    The Nova laser, presently under construction at Lawrence Livermore National Laboratory, will be capable of delivering more than 100 kJ of focused energy to an Inertial Confinement Fusion (ICF) target. Operation at the fundamental wavelength of the laser (1.05 ..mu..m) and at the second and third harmonic will be possible. This paper will discuss the optical alignment systems and techniques being implemented to align the laser output to the target at these wavelengths prior to each target irradiation. When experiments require conversion of the laser light to wavelengths of 0.53 ..mu..m and 0.35 ..mu..m prior to target irradiation, this will be accomplished in harmonic conversion crystals located at the beam entrances to the target chamber. The harmonic alignment system will be capable of introducing colinear alignment beams of all three wavelengths into the laser chains at the final spatial filter. The alignment beam at 1.05 ..mu..m will be about three cm in diameter and intense enough to align the conversion crystals. Beams at 0.53 ..mu..m and 0.35 ..mu..m will be expanded by the spatial filter to full aperture (74 cm) and used to illuminate the target and other alignment aids at the target chamber focus. This harmonic illumination system will include viewing capability as well. A final alignment sensor will be located at the target chamber. It will view images of the chamber focal plane at all three wavelengths. In this way, each beam can be aligned at the desired wavelength to produce the focal pattern required for each target irradiation. The design of the major components in the harmonic alignment system will be described, and a typical alignment sequence for alignment to a target will be presented.

  3. Three wavelength optical alignment of the Nova laser

    International Nuclear Information System (INIS)

    The Nova laser, presently under construction at Lawrence Livermore National Laboratory, will be capable of delivering more than 100 kJ of focused energy to an Inertial Confinement Fusion (ICF) target. Operation at the fundamental wavelength of the laser (1.05 μm) and at the second and third harmonic will be possible. This paper will discuss the optical alignment systems and techniques being implemented to align the laser output to the target at these wavelengths prior to each target irradiation. When experiments require conversion of the laser light to wavelengths of 0.53 μm and 0.35 μm prior to target irradiation, this will be accomplished in harmonic conversion crystals located at the beam entrances to the target chamber. The harmonic alignment system will be capable of introducing colinear alignment beams of all three wavelengths into the laser chains at the final spatial filter. The alignment beam at 1.05 μm will be about three cm in diameter and intense enough to align the conversion crystals. Beams at 0.53 μm and 0.35 μm will be expanded by the spatial filter to full aperture (74 cm) and used to illuminate the target and other alignment aids at the target chamber focus. This harmonic illumination system will include viewing capability as well. A final alignment sensor will be located at the target chamber. It will view images of the chamber focal plane at all three wavelengths. In this way, each beam can be aligned at the desired wavelength to produce the focal pattern required for each target irradiation. The design of the major components in the harmonic alignment system will be described, and a typical alignment sequence for alignment to a target will be presented

  4. Retinal input instructs alignment of visual topographic maps

    OpenAIRE

    Triplett, Jason W.; Owens, Melinda T.; Yamada, Jena; Lemke, Greg; Cang, Jianhua; Stryker, Michael P.; Feldheim, David A.

    2009-01-01

    Sensory information is represented in the brain in the form of topographic maps, in which neighboring neurons respond to adjacent external stimuli. In the visual system, the superior colliculus receives topographic projections from the retina and primary visual cortex (V1) that are aligned. Alignment may be achieved through the use of a gradient of shared axon guidance molecules, or through a retinal-matching mechanism in which axons that monitor identical regions of visual space align. To di...

  5. Alignment of HR strategy to the business strategy

    OpenAIRE

    Lauko, Ondřej

    2011-01-01

    This diploma thesis draws its attention to the importance of aligning HR strategy to the business strategy. Both of these strategies are in detail described in the theoretical part o the thesis. The practical part is then devoted to a practical case of aligning the strategies. The case is HR transformation in one of the global leading companies where the process of the alignment is depicted and the impact of the HR transformation on the regional business and HR organization is observed.

  6. Transferring Landmark Annotations for Cross-Dataset Face Alignment

    OpenAIRE

    Zhu, Shizhan; Li, Cheng; Loy, Chen Change; Tang, Xiaoou

    2014-01-01

    Dataset bias is a well known problem in object recognition domain. This issue, nonetheless, is rarely explored in face alignment research. In this study, we show that dataset plays an integral part of face alignment performance. Specifically, owing to face alignment dataset bias, training on one database and testing on another or unseen domain would lead to poor performance. Creating an unbiased dataset through combining various existing databases, however, is non-trivial as one has to exhaus...

  7. Achieving business and IT alignment from organisational learning perspectives

    OpenAIRE

    Balhareth, Hamad B.; Liu, Kecheng; Manwani, Sharm

    2012-01-01

    Business and IT alignment has continued as a top concern for business and IT executives for almost three decades. Many researchers have conducted empirical studies on the relationship between business-IT alignment and performance. Yet, these approaches, lacking a social perspective, have had little impact on sustaining performance and competitive advantage. In addition to the limited alignment literature that explores organisational learning that is represented in shared understanding, commun...

  8. The SLS storage ring support and alignment systems

    CERN Document Server

    Zelenika, S; Rivkin, L; Rohrer, M; Rossetti, D; Ruland, R; Schlott, V; Streun, A; Wiegand, Peter

    2001-01-01

    Storage rings of third generation synchrotron radiation facilities pose severe challenges for lowering the beam emittances and increasing the lifetimes, requiring thus increasing positioning and alignment precisions that must be preserved over long time spans. This work describes the SLS storage ring mechanical support, alignment and disturbances compensation systems that allow to meet these requirements. In particular, their design, the tests done on the respective prototypes and the applicability of the developed arrangement to beam-based alignment are addressed.

  9. Algorithm engineering for optimal alignment of protein structure distance matrices

    OpenAIRE

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

    2011-01-01

    International audience Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring function. We introduce the structural alignment problem formally, which enables us to express a variety of scoring functions used in previous work as special cases in a unified framework. Further, we propose the first mathematical model...

  10. Controlling the branching ratio of photodissociation using aligned molecules

    DEFF Research Database (Denmark)

    Larsen, J.J.; Wendt-Larsen, I.; Stapelfeldt, H.

    1999-01-01

    Using a sample of iodine molecules, aligned by a strong, linearly polarized laser pulse, we control the branching ratio of the I+I and I+I* photodissociation channels by a factor of 26. The control relies on selective photoexcitation of two potential curves that each correlate adiabatically with...... one of the product channels. The selectivity is achieved by irradiating the aligned molecules with light polarized parallel or perpendicular to the polarization axis of the alignment laser....

  11. Towards robust context-sensitive sentence alignment for monolingual corpora

    OpenAIRE

    Shieber, Stuart; Nelken, Rani

    2006-01-01

    Aligning sentences belonging to comparable monolingual corpora has been suggested as a first step towards training text rewriting algorithms, for tasks such as summarization or paraphrasing. We present here a new monolingual sentence alignment algorithm, combining a sentence-based TF*IDF score, turned into a probability distribution using logistic regression, with a global alignment dynamic programming algorithm. Our approach provides a simpler and more robust solution achieving a substantial...

  12. Statistical analysis of Sequence-Structure Alignment Scores

    OpenAIRE

    Brunnert, Marcus; Thiele, Ralf; Mevissen, Heinz-Theodor; Urfer, Wolfgang

    2002-01-01

    The structural analysis of proteins is fundamental to the analysis of protein functions. In this context, sequence-structure alignment methods are important among the different empirical methods. In order to assess the quality of sequence-structure alignments, a statistical method using a Bayesian approach proposed by Lathrop et al. (1998) will be presented. Finally, the results of a developed statistical analysis of scores of RDP(recursive dynamic programming)-sequence-structure alignments (...

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

    Directory of Open Access Journals (Sweden)

    Pereira Luísa

    2009-07-01

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

  14. The alignment of the ATLAS Inner Detector in Run 2

    CERN Document Server

    Ripellino, Giulia; The ATLAS collaboration

    2016-01-01

    The ATLAS reconstruction of charged particle trajectories relies on the Inner Detector tracking system. The accuracy of the reconstruction is limited by the finite resolution of the detector elements and the imperfect knowledge about their positions. A precise alignment of the detector is therefore essential. Here, the strategy and the status of the Inner Detector alignment in ATLAS during the LHC Run 2 are presented and the alignment challenges related to the distortion of the new innermost Pixel layer, the IBL, are discussed.

  15. Keeping speed and distance for aligned motion

    Science.gov (United States)

    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.

  16. Aligning Structured and Unstructured Medical Problems Using UMLS

    OpenAIRE

    Carlo, Lorena; Chase, Herbert S.; Weng, Chunhua

    2010-01-01

    This paper reports a pilot study to align medical problems in structured and unstructured EHR data using UMLS. A total of 120 medical problems in discharge summaries were extracted using NLP software (MedLEE) and aligned with 87 ICD-9 diagnoses for 19 non-overlapping hospital visits of 4 patients. The alignment accuracy was evaluated by a medical doctor. The average overlap of medical problems between the two data sources obtained by our automatic alignment method was 23.8%, which was about h...

  17. Liquid crystallinity driven highly aligned large graphene oxide composites

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kyung Eun; Oh, Jung Jae; Yun, Taeyeong [Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701 (Korea, Republic of); Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701 (Korea, Republic of); Kim, Sang Ouk, E-mail: sangouk.kim@kaist.ac.kr [Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701 (Korea, Republic of); Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701 (Korea, Republic of)

    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.

  18. Transfer alignment of shipborne inertial-guided weapon systems

    Institute of Scientific and Technical Information of China (English)

    Sun Changyue; Deng Zhenglong

    2009-01-01

    The transfer alignment problem of the shipborne weapon inertial navigation system (INS) is addressed. Specifically, two transfer alignment algorithms subjected to the ship motions induced by the waves are discussed. To consider the limited maneuver level performed by the ship, a new filter algorithm for transfer alignment methods using velocity and angular rate matching is first derived. And then an improved method using integrated velocity and integrated angular rate matching is introduced to reduce the effect of the ship body flexure. The simulation results show the feasibility and validity of the proposed transfer alignment algorithms.

  19. IRT studies of many groups: The alignment method

    Directory of Open Access Journals (Sweden)

    BengtMuthen

    2014-09-01

    Full Text Available Asparouhov and Muthen (forthcoming presented a new method for multiple-group confirmatory factor analysis (CFA, referred to as the alignment method. The alignment method can be used to estimate group-specific factor means and variances without requiring exact measurement invariance. A strength of the method is the ability to conveniently estimate models for many groups, such as with comparisons of countries. This paper focuses on IRT applications of the alignment method. An empirical investigation is made of binary knowledge items administered in two separate surveys of a set of countries. A Monte Carlo study is presented that shows how the quality of the alignment can be assessed.

  20. Multiple sequence alignment accuracy and evolutionary distance estimation

    Directory of Open Access Journals (Sweden)

    Rosenberg Michael S

    2005-11-01

    Full Text Available Abstract Background Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation analysis. This study used sequence simulation to examine the gain in accuracy of adding a third sequence to a pair wise alignment, particularly concentrating on how the phylogenetic position of the additional sequence relative to the first pair changes the accuracy of the initial pair's alignment as well as their estimated evolutionary distance. Results The maximal gain in alignment accuracy was found not when the third sequence is directly intermediate between the initial two sequences, but rather when it perfectly subdivides the branch leading from the root of the tree to one of the original sequences (making it half as close to one sequence as the other. Evolutionary distance estimation in the multiple alignment framework, however, is largely unrelated to alignment accuracy and rather is dependent on the position of the third sequence; the closer the branch leading to the third sequence is to the root of the tree, the larger the estimated distance between the first two sequences. Conclusion The bias in distance estimation appears to be a direct result of the standard greedy progressive algorithm used by many multiple alignment methods. These results have implications for choosing new taxa and genomes to sequence when resources are limited.

  1. CMS Alignement and Calibration workflows lesson learned and future plans

    CERN Document Server

    De Guio, Federico

    2014-01-01

    We review the online and offline workflows designed to align and calibrate the CMS detector. Starting from the gained experience during the first LHC run, we discuss the expected developments for Run II. In particular, we describe the envisioned different stages, from the alignment using cosmic rays data to the detector alignment and calibration using the first proton-proton collisions data ( O(100 pb-1) ) and a larger dataset ( O(1 fb-1) ) to reach the target precision. The automatisation of the workflow and the integration in the online and offline activity (dedicated triggers and datasets, data skims, workflows to compute the calibration and alignment constants) are discussed.

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

    Science.gov (United States)

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

    2001-01-01

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

  3. Partial Alignment for Improvement of Beam Transmission at KOMAC

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Dong-Hyuk; Kim, Dae-Il; Ahn, Tae-Sung; Kim, Han-Sung; Kwon, Hyeok-Jung; Cho, Yong-Sub [KOMAC, Gyeongju (Korea, Republic of)

    2015-05-15

    The ion source and steering magnets were aligned for improving the beam transmission. It is expected that the re-alignment of accelerator components can reduce the beam loss which can occur for the dislocation among them. The center displacements of RFQ and 20MeV DTL are different to 100MeV DTL, so it is necessary to re-align in next maintenance period. 100MeV proton linac placed in KOMAC (Korea Multi-purpose Accelerator Complex) has been operated and provided to beam users. There are two maintenance periods every year, winter (Jan-Feb) and summer (Jul-Aug). In maintenance period, proton linac is re-aligned for the improvement of beam transmission. 4 newly steering magnet are installed in beam line. To align the steering magnet, network align in tunnel is measured using by laser tracker. In addition, the position of ion source is away from the position of RFQ in the result of the survey of network align. The alignment of steering magnet after installation is performed. At the same time, the position of accelerator component is checked and aligned partially.

  4. Predicting business/ICT alignment with AntMiner+.

    OpenAIRE

    Cumps, Bjorn; Martens, David; De Backer, Manu; Haesen, Raf; Viaene, Stijn; Dedene, Guido; Baesens, Bart; Snoeck, Monique

    2007-01-01

    In this paper we report on the results of a European survey on business/ICT alignment practices. The goal of this study is to come up with some practical guidelines for managers on how to strive for better alignment of ICT investments with business requirements. Based on Luftman's alignment framework we examine 18 ICT management practices belonging to 6 different competency clusters. We use AntMiner+, a rule induction technique, to create an alignment rule set. The results indicate that B/ICT...

  5. An Ant-Based Model for Multiple Sequence Alignment

    CERN Document Server

    Guinand, Frédéric

    2008-01-01

    Multiple sequence alignment is a key process in today's biology, and finding a relevant alignment of several sequences is much more challenging than just optimizing some improbable evaluation functions. Our approach for addressing multiple sequence alignment focuses on the building of structures in a new graph model: the factor graph model. This model relies on block-based formulation of the original problem, formulation that seems to be one of the most suitable ways for capturing evolutionary aspects of alignment. The structures are implicitly built by a colony of ants laying down pheromones in the factor graphs, according to relations between blocks belonging to the different sequences.

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

    Science.gov (United States)

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

    2015-01-01

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

  7. Liquid crystallinity driven highly aligned large graphene oxide composites

    International Nuclear Information System (INIS)

    Graphene is an emerging graphitic carbon materials, consisting of sp2 hybridized two dimensinal honeycomb structure. It has been widely studied to incorporate graphene with polymer to utilize unique property of graphene and reinforce electrical, mechanical and thermal property of polymer. In composite materials, orientation control of graphene significantly influences the property of composite. Until now, a few method has been developed for orientation control of graphene within polymer matrix. Here, we demonstrate facile fabrication of high aligned large graphene oxide (LGO) composites in polydimethylsiloxane (PDMS) matrix exploiting liquid crystallinity. Liquid crystalline aqueous dispersion of LGO is parallel oriented within flat confinement geometry. Freeze-drying of the aligned LGO dispersion and subsequent infiltration with PDMS produce highly aligned LGO/PDMS composites. Owing to the large shape anisotropy of LGO, liquid crystalline alignment occurred at low concentration of 2 mg/ml in aqueous dispersion, which leads to the 0.2 wt% LGO loaded composites. - Graphical abstract: Liquid crystalline LGO aqueous dispersions are spontaneous parallel aligned between geometric confinement for highly aligned LGO/polymer composite fabrication. - Highlights: • A simple fabrication method for highly aligned LGO/PDMS composites is proposed. • LGO aqueous dispersion shows nematic liquid crystalline phase at 0.8 mg/ml. • In nematic phase, LGO flakes are highly aligned by geometric confinement. • Infiltration of PDMS into freeze-dried LGO allows highly aligned LGO/PDMS composites

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

    Science.gov (United States)

    Martin, Andrew C R

    2014-01-01

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

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

    Science.gov (United States)

    Biswas, Ambalika; Lahiri, Amitabha

    2016-06-01

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

  10. Elements of Cellular Blind Interference Alignment --- Aligned Frequency Reuse, Wireless Index Coding and Interference Diversity

    OpenAIRE

    Jafar, Syed A.

    2012-01-01

    We explore degrees of freedom (DoF) characterizations of partially connected wireless networks, especially cellular networks, with no channel state information at the transmitters. Specifically, we introduce three fundamental elements --- aligned frequency reuse, wireless index coding and interference diversity --- through a series of examples, focusing first on infinite regular arrays, then on finite clusters with arbitrary connectivity and message sets, and finally on heterogeneous settings...

  11. Improving Multiple Sequence Alignments by Revising Sequence Families with Alignment Scoring Approaches

    OpenAIRE

    Levchuk, Aleksandr O.

    2011-01-01

    Characterizing the functional, structural, and evolutionary relationships of biological sequences is an important task in modern genomics and computational biology. Most of these applications involve the assembly of sequence families by similarity searching, subsequent formation of multiple sequence alignments (MSAs) and downstream phylogenetic analyses. Especially, MSAs play a central role in this modeling workflow. Thus, the quality of the MSAs is of critical importance for its success. In ...

  12. Intrinsic alignments in redMaPPer clusters - I. Central galaxy alignments and angular segregation of satellites

    Science.gov (United States)

    Huang, Hung-Jin; Mandelbaum, Rachel; Freeman, Peter E.; Chen, Yen-Chi; Rozo, Eduardo; Rykoff, Eli; Baxter, Eric J.

    2016-08-01

    The shapes of cluster central galaxies are not randomly oriented, but rather exhibit coherent alignments with the shapes of their parent clusters as well as with the surrounding large-scale structures. In this work, we aim to identify the galaxy and cluster quantities that most strongly predict the central galaxy alignment phenomenon among a large parameter space with a sample of 8237 clusters and 94817 members within 0.1 theories of central galaxy alignments, the impact of primordial alignments with tidal fields, and the importance of anisotropic accretion.

  13. Automatic alignment of double optical paths in excimer laser amplifier

    Science.gov (United States)

    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.

  14. Interhemispheric Field-Aligned Currents: Simulation Results

    Science.gov (United States)

    Lyatsky, Sonya

    2016-04-01

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

  15. R-Coffee: a method for multiple alignment of non-coding RNA

    OpenAIRE

    Wilm, Andreas; Desmond G Higgins; Notredame, Cédric

    2008-01-01

    R-Coffee is a multiple RNA alignment package, derived from T-Coffee, designed to align RNA sequences while exploiting secondary structure information. R-Coffee uses an alignment-scoring scheme that incorporates secondary structure information within the alignment. It works particularly well as an alignment improver and can be combined with any existing sequence alignment method. In this work, we used R-Coffee to compute multiple sequence alignments combining the pairwise output of sequence al...

  16. The Alignment effect of brightest cluster galaxies in the SDSS

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Rita S.J.; Annis, Jim; Strauss, Michael A.; Lupton, Robert H.; Bahcall, Neta A.; Gunn, James E.; Kepner, Jeremy V.; Postman, Marc

    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.

  17. Alignment of Human Resource Practices and Teacher Performance Competency

    Science.gov (United States)

    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…

  18. 33 CFR 101.205 - Department of Homeland Security alignment.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Department of Homeland Security... Department of Homeland Security alignment. The MARSEC Levels are aligned with the Department of Homeland Security's Homeland Security Advisory System (HSAS), established by Homeland Security...

  19. Beginning Learners' Development of Interactional Competence: Alignment Activity

    Science.gov (United States)

    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…

  20. Improving Business-IT Alignment through Business Architecture

    Science.gov (United States)

    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…

  1. Aligning IT and Business Strategy: An Australian University Case Study

    Science.gov (United States)

    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…

  2. Isotope-selective ionization using four-pulse alignment

    International Nuclear Information System (INIS)

    We have proposed a laser isotope separation method utilizing molecular alignment and non-resonant multiphoton ionization, and demonstrated isotope-selective ionization of 14N2 and 15N2 isotopomers, using one-pulse alignment. In the present work, we used a train of four identical pulses, instead of one pulse, to obtain the higher selectivity. (author)

  3. The Impact of National Cultures on Business & IT Alignment

    NARCIS (Netherlands)

    Silvius, A.J.G.

    2008-01-01

    Aligning IT to business needs is still one of the most important concerns for senior management. The message of Business & IT Alignment (BIA) is logical and undisputed, but implementation apparently difficult. As part of a research program on the differences between the theory and practice of BIA th

  4. Strategic Alignment in Business Education: The Second Magic Bullet

    Science.gov (United States)

    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…

  5. SOAP2: an improved ultrafast tool for short read alignment

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Yu, Chang; Li, Yingrui;

    2009-01-01

    SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for in...

  6. Conformational fluctuations affect protein alignment in dilute liquid crystal media

    DEFF Research Database (Denmark)

    Louhivuori, M.; Otten, R.; Lindorff-Larsen, Kresten;

    2006-01-01

    The discovery of dilute liquid crystalline media to align biological macromolecules has opened many new possibilities to study protein and nucleic acid structures by NMR spectroscopy. We inspect the basic alignment phenomenon for an ensemble of protein conformations to deduce relative contributions...

  7. Curriculum Alignment: Exploring Student Perception of Learning Achievement Measures

    Science.gov (United States)

    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…

  8. Kernel Contraction and Consolidation of Alignment under Ontology Change

    Directory of Open Access Journals (Sweden)

    Ahmed ZAHAF

    2016-08-01

    Full Text Available Alignment overcomes divergence in the specification of the semantics of vocabularies by different but overlapping ontologies. Therefore, it enhances semantic interoperability for many web based applications. However, ontology change following applications new requirements or new perception of domain knowledges can leads to undesirable knowledge such as inconsistent and therefore to a useless alignment. Ontologies and alignments are encoded in knowledge bases allowing applications to store only some explicit knowledge while they derive implicit ones by applying reasoning services on these knowledge bases. This underlying representation of ontologies and alignments leads us to follow base revision theory to deal with alignment revision under ontology change. For that purpose, we adapt kernel contraction framework to design rational operators and to formulate the set of postulates that characterize each class of these operators. We demonstrate the connection between each class of operators and the set of postulates that characterize them. Finally, we present algorithms to compute alignment kernels and incision functions. Kernels are sets of correspondences responsible of undesirable knowledge following alignment semantics. Incision functions determine the sets of correspondences to eliminate in order to restore alignment consistency or to realize a successful contraction.

  9. Method and apparatus for improving the alignment of radiographic images

    International Nuclear Information System (INIS)

    This invention relates generally to the field of radiology, and has to do particularly with a method and apparatus for improving the alignment of radiographic images taken at different times of the same tissue structure, so that the images can be sequentially shown in aligned condition, whereby changes in the structure can be noted. (author). 10 figs

  10. Symmetries for SM Alignment in multi-Higgs Doublet Models

    CERN Document Server

    Pilaftsis, Apostolos

    2016-01-01

    We derive the complete set of maximal symmetries for Standard Model (SM) alignment that may occur in the tree-level scalar potential of multi-Higgs Doublet Models, with $n > 2$ Higgs doublets. Our results generalize the symmetries of SM alignment, without decoupling of large mass scales or fine-tuning, previously obtained in the context of two-Higgs Doublet Models.

  11. LHCb's Time-Real Alignment in RunII

    CERN Multimedia

    Batozskaya, Varvara

    2015-01-01

    LHCb has introduced a novel real-time detector alignment and calibration strategy for LHC Run 2. Data collected at the start of the fill will be processed in a few minutes and used to update the alignment, while the calibration constants will be evaluated for each run. This procedure will improve the quality of the online alignment. Critically, this new real-time alignment and calibration procedure allows identical constants to be used in the online and offline reconstruction, thus improving the correlation between triggered and offline selected events. This offers the opportunity to optimise the event selection in the trigger by applying stronger constraints. The required computing time constraints are met thanks to a new dedicated framework using the multi-core farm infrastructure for the trigger. The motivation for a real-time alignment and calibration of the LHCb detector is discussed from both the operational and physics performance points of view. Specific challenges of this novel configur...

  12. Observability of Strapdown INS Alignment: A Global Perspective

    CERN Document Server

    Wu, Yuanxin; Wu, Meiping; Hu, Xiaoping; Hu, Dewen

    2011-01-01

    Alignment of the strapdown inertial navigation system (INS) has strong nonlinearity, even worse when maneuvers, e.g., tumbling techniques, are employed to improve the alignment. There is no general rule to attack the observability of a nonlinear system, so most previous works addressed the observability of the corresponding linearized system by implicitly assuming that the original nonlinear system and the linearized one have identical observability characteristics. Strapdown INS alignment is a nonlinear system that has its own characteristics. Using the inherent properties of strapdown INS, e.g., the attitude evolution on the SO(3) manifold, we start from the basic definition and develop a global and constructive approach to investigate the observability of strapdown INS static and tumbling alignment, highlighting the effects of the attitude maneuver on observability. We prove that strapdown INS alignment, considering the unknown constant sensor biases, will be completely observable if the strapdown INS is r...

  13. Alignment of atmospheric mineral dust due to electric field

    Science.gov (United States)

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

    2007-12-01

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

  14. Alignment of atmospheric mineral dust due to electric field

    Directory of Open Access Journals (Sweden)

    Z. Ulanowski

    2007-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. Liquid Crystal Microlens Using Nanoparticle-Induced Vertical Alignment

    Directory of Open Access Journals (Sweden)

    Shug-June Hwang

    2015-01-01

    Full Text Available The nanoparticle-induced vertical alignment (NIVA of the nematic liquid crystals (LC is applied to achieve an adaptive flat LC microlens with hybrid-aligned nematic (HAN mode by dropping polyhedral oligomeric silsesquioxane (POSS nanoparticle solution on a homogeneous alignment layer. The vertical alignment induced by the POSS nanoparticles resulted in the formation of a hybrid-aligned LC layer with concentric nonuniform distribution of the refractive index in the planar LC cell, which subsequently played the role of the lens, even in the absence of any applied voltages. The dimensions of the concentric HAN structure significantly depend on the volume of the microdroplet and the POSS concentration. The focus effect of this flat microlens was observed while electrically controlling its focal length using the applied voltages from −50 mm to −90 mm.

  17. Alignment methods for the OPERA drift tube detector

    Science.gov (United States)

    Büttner, B.; Ebert, J.; Ferber, T.; Göllnitz, C.; Goloubkov, D.; Hagner, C.; Hierholzer, M.; Hollnagel, A.; Lenkeit, J.; Rostovtseva, I.; Schmidt-Parzefall, W.; Wonsak, B.; Zaitsev, Y.

    2014-05-01

    The goal of the OPERA experiment is to give the first direct evidence for neutrino oscillations in the channel νμ→ντ. The OPERA detector is designed to observe the appearance of tau neutrinos in the originally pure muon neutrino CNGS beam. An important part of the magnetic spectrometer is the Precision Tracker (PT), a drift tube detector consisting of 9504 drift tubes. Its main task is the determination of the muon charge and momentum. The alignment strategy for the PT consists of two parts: the hardware measurement by theodolite and the software alignment using long muon tracks. In this paper, the hardware and the software alignment are described, and the track-based alignment methods are explained in detail. Results of the software alignment are presented with a focus on the analysis of cosmic particles.

  18. Alignment methods for the OPERA drift tube detector

    International Nuclear Information System (INIS)

    The goal of the OPERA experiment is to give the first direct evidence for neutrino oscillations in the channel νμ→ντ. The OPERA detector is designed to observe the appearance of tau neutrinos in the originally pure muon neutrino CNGS beam. An important part of the magnetic spectrometer is the Precision Tracker (PT), a drift tube detector consisting of 9504 drift tubes. Its main task is the determination of the muon charge and momentum. The alignment strategy for the PT consists of two parts: the hardware measurement by theodolite and the software alignment using long muon tracks. In this paper, the hardware and the software alignment are described, and the track-based alignment methods are explained in detail. Results of the software alignment are presented with a focus on the analysis of cosmic particles

  19. Improving your target-template alignment with MODalign.

    KAUST Repository

    Barbato, Alessandro

    2012-02-04

    SUMMARY: MODalign is an interactive web-based tool aimed at helping protein structure modelers to inspect and manually modify the alignment between the sequences of a target protein and of its template(s). It interactively computes, displays and, upon modification of the target-template alignment, updates the multiple sequence alignments of the two protein families, their conservation score, secondary structure and solvent accessibility values, and local quality scores of the implied three-dimensional model(s). Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modalign. Website implemented in HTML and JavaScript with all major browsers supported. CONTACT: jan.kosinski@uniroma1.it.

  20. Dynamic alignment models for neural coding.

    Directory of Open Access Journals (Sweden)

    Sepp Kollmorgen

    2014-03-01

    Full Text Available 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.

  1. Dynamic alignment models for neural coding.

    Science.gov (United States)

    Kollmorgen, Sepp; Hahnloser, Richard H R

    2014-03-01

    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

  2. Aligned carbon nanotube sheet piezoresistive strain sensors

    Science.gov (United States)

    Li, Ang; Bogdanovich, Alexander E.; Bradford, Philip D.

    2015-09-01

    Carbon nanotubes (CNTs) have a unique set of properties that may be useful in the production of next generation structural health monitoring composites. This research introduces a novel CNT based material system for strain and damage sensing applications. An aligned sheet of interconnected CNTs was drawn from a chemical vapor deposition grown CNT array and then bonded to the surface of glass fiber/epoxy composite coupons. Various types of mechanical tests were conducted, accompanied by real-time electrical data acquisition, in order to evaluate the electro-mechanical behavior of the developed sensing material. Specimens were loaded in the longitudinal and transverse CNT sheet orientations to investigate the anisotropy of the piezoresistive effect. The CNT sheets exhibited good sensing stability, linearity, sensitivity and repeatability within a practical strain range; which are crucial sensor features for health monitoring. It was also demonstrated that the CNT orientation in the sheet had a dramatic effect on the sensitivity, thus validating the usefulness of this sensing material for directional strain/damage monitoring. Finally, pre-straining of the CNT sheet sensors was conducted to further enhance the linearity of electro-mechanical response and long-term stability of the sensors during cyclic loading.

  3. Services supporting collaborative alignment of engineering networks

    Science.gov (United States)

    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.

  4. Shear alignment of lamellar mesophase systems

    Science.gov (United States)

    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.

  5. CBESW: Sequence Alignment on the Playstation 3

    Directory of Open Access Journals (Sweden)

    Hieu Nim

    2008-09-01

    Full Text Available Abstract Background The exponential growth of available biological data has caused bioinformatics to be rapidly moving towards a data-intensive, computational science. As a result, the computational power needed by bioinformatics applications is growing exponentially as well. The recent emergence of accelerator technologies has made it possible to achieve an excellent improvement in execution time for many bioinformatics applications, compared to current general-purpose platforms. In this paper, we demonstrate how the PlayStation® 3, powered by the Cell Broadband Engine, can be used as a computational platform to accelerate the Smith-Waterman algorithm. Results For large datasets, our implementation on the PlayStation® 3 provides a significant improvement in running time compared to other implementations such as SSEARCH, Striped Smith-Waterman and CUDA. Our implementation achieves a peak performance of up to 3,646 MCUPS. Conclusion The results from our experiments demonstrate that the PlayStation® 3 console can be used as an efficient low cost computational platform for high performance sequence alignment applications.

  6. The non-aligned nuclear posture

    International Nuclear Information System (INIS)

    Though the cold war ended over a decade ago, it appears the nuclear-weapon States are not ready to give up their weapons. Despite quantitative reductions, those weapons remain at the heart of their military planning. Over a half of the world's population live in countries with nuclear weapons or are allied to such countries. The decision of India and Pakistan to explode nuclear devices in May 1998, as regrettable as they were, nevertheless shook the five nuclear-weapon States out of their complacency concerning their exclusive possession of nuclear weapons. Those actions also complicated the position of the countries of the Non-Aligned Movement on nuclear disarmament and non-proliferation, and led to highly diplomatic language to accommodate that fact in the latest summit meeting of the Movement in August-September 1998. Voting patterns in the General Assembly on nuclear disarmament show that the debate on who is a 'legitimate' nuclear-weapon State is in full swing. (author)

  7. Multiview alignment hashing for efficient image search.

    Science.gov (United States)

    Liu, Li; Yu, Mengyang; Shao, Ling

    2015-03-01

    Hashing is a popular and efficient method for nearest neighbor search in large-scale data spaces by embedding high-dimensional feature descriptors into a similarity preserving Hamming space with a low dimension. For most hashing methods, the performance of retrieval heavily depends on the choice of the high-dimensional feature descriptor. Furthermore, a single type of feature cannot be descriptive enough for different images when it is used for hashing. Thus, how to combine multiple representations for learning effective hashing functions is an imminent task. In this paper, we present a novel unsupervised multiview alignment hashing approach based on regularized kernel nonnegative matrix factorization, which can find a compact representation uncovering the hidden semantics and simultaneously respecting the joint probability distribution of data. In particular, we aim to seek a matrix factorization to effectively fuse the multiple information sources meanwhile discarding the feature redundancy. Since the raised problem is regarded as nonconvex and discrete, our objective function is then optimized via an alternate way with relaxation and converges to a locally optimal solution. After finding the low-dimensional representation, the hashing functions are finally obtained through multivariable logistic regression. The proposed method is systematically evaluated on three data sets: 1) Caltech-256; 2) CIFAR-10; and 3) CIFAR-20, and the results show that our method significantly outperforms the state-of-the-art multiview hashing techniques. PMID:25594968

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

    International Nuclear Information System (INIS)

    Aligned and random fibres of strontium hexa ferrite (SrM, SrFe12O19) and barium hexaferrite (BaM, BaFe12O19) 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 deg. C, at which point they still had submicron grains. In BaM random fibres M s=63.8 emu g-1 and H c=428.1 kA m-1, and in SrM random fibres M s=63.3 emu g-1 and H c=452.8 kA m-1, high values for polycrystalline materials. Fibres aligned parallel to the applied field had saturation magnetisation (M s) values equal to those of the random fibres, whilst fibres aligned perpendicular to the field had M s values 62% and 75% lower, for BaM and SrM, respectively. There was no change in coercivity (H c) between random or aligned fibres of any orientation, and fibres aligned 45 deg. 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

  9. The accuracy of several multiple sequence alignment programs for proteins

    Directory of Open Access Journals (Sweden)

    Tillier Elisabeth RM

    2006-10-01

    Full Text Available Abstract Background There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences. The "true" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs. Results We tested nine of the most often used protein alignment programs and compared their results using sequences generated with the simulation software Simprot which creates known alignments under realistic and controlled evolutionary scenarios. We have simulated more than 30000 alignment sets using various evolutionary histories in order to define strengths and weaknesses of each program tested. We found that alignment accuracy is extremely dependent on the number of insertions and deletions in the sequences, and that indel size has a weaker effect. We also considered benchmark alignments from the latest version of BAliBASE and the results relative to BAliBASE- and Simprot-generated data sets were consistent in most cases. Conclusion Our results indicate that employing Simprot's simulated sequences allows the creation of a more flexible and broader range of alignment classes than the usual methods for alignment accuracy assessment. Simprot also allows for a quick and efficient analysis of a wider range of possible evolutionary histories that might not be present in currently available alignment sets. Among the nine programs tested, the iterative approach available in Mafft (L-INS-i and ProbCons were consistently the most accurate, with Mafft being the faster of the two.

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

    Science.gov (United States)

    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…

  11. Intrinsic alignments in redMaPPer clusters -- I. Central galaxy alignments and angular segregation of satellites

    CERN Document Server

    Huang, Hung-Jin; Freeman, Peter E; Chen, Yen-Chi; Rozo, Eduardo; Rykoff, Eli; Baxter, Eric J

    2016-01-01

    The shapes of cluster central galaxies are not randomly oriented, but rather exhibit coherent alignments with the shapes of their parent clusters as well as with large-scale structure. In this work, we undertake a comprehensive study of the alignments of central galaxies at low redshift. Based on a sample of 8237 clusters and 94817 members in the redMaPPer cluster catalog with 0.1 < z < 0.35, we first quantify the alignment between the projected central galaxy shapes and the distribution of member satellites, to understand what central galaxy and cluster properties most strongly correlate with these alignments. Next, we investigate the angular segregation of satellites with respect to their central galaxy major axis directions, to identify the satellite properties that most strongly predict their angular segregation. We find that central galaxies are more aligned with their member galaxy distributions in clusters that are more elongated and have higher richness, and for central galaxies with larger phys...

  12. Alignment of the ATLAS Inner Detector tracking system

    International Nuclear Information System (INIS)

    ATLAS is a multipurpose experiment that records the products of the LHC collisions. To reconstruct trajectories of charged particles produced in these collisions, ATLAS is equipped with a tracking system built of silicon planar sensors and drift-tube based detectors. They constitute the ATLAS Inner Detector. In order to achieve its scientific goals, the alignment of the ATLAS tracking system requires the determination of its almost 36000 degrees of freedom (DoF) with high accuracy. Thus the demanded precision for the alignment of the silicon sensors is below 10 micrometers. This implies to use a large sample of high momentum and isolated charge particle tracks. The high level trigger selects those tracks online. Then the raw data with the hits information of the triggered tracks is stored in a calibration stream. Tracks from cosmic trigger during empty LHC bunches are also used as input for the alignment. The implementation of the track based alignment within the ATLAS software framework unifies different alignment approaches and allows the alignment of all tracking subsystems together. Primary vertexing and beam spot constraints have also been implemented, as well as constraints on survey measurements. As alignment algorithms are based on minimization of the track-hit residuals, one needs to solve a linear system with large number of DoF. The solving involves the inversion or diagonalization of a large matrix that may be dense. The alignment jobs are executed at the CERN Analysis Facility. The event processing is run in parallel in many jobs. The output matrices from all jobs are added before solving. We will present the results of the alignment of the ATLAS detector using real data recorded during the LHC start up run in 2009 plus the recent 7 TeV data collected during 2010 run. Validation of the alignment was performed by measuring the alignment observables as well as many other physics observables, notably resonance invariant masses. The results of the

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

    Energy Technology Data Exchange (ETDEWEB)

    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. The aligned K-center problem

    KAUST Repository

    Braß, Peter

    2011-04-01

    In this paper we study several instances of the aligned k-center problem where the goal is, given a set of points S in the plane and a parameter k ≥ 1, to find k disks with centers on a line ℓ such that their union covers S and the maximum radius of the disks is minimized. This problem is a constrained version of the well-known k-center problem in which the centers are constrained to lie in a particular region such as a segment, a line, or a polygon. We first consider the simplest version of the problem where the line ℓ is given in advance; we can solve this problem in time O(n log2 n). In the case where only the direction of ℓ is fixed, we give an O(n2 log 2 n)-time algorithm. When ℓ is an arbitrary line, we give a randomized algorithm with expected running time O(n4 log2 n). Then we present (1+ε)-approximation algorithms for these three problems. When we denote T(k, ε) = (k/ε2+(k/ε) log k) log(1/ε), these algorithms run in O(n log k + T(k, ε)) time, O(n log k + T(k, ε)/ε) time, and O(n log k + T(k, ε)/ε2) time, respectively. For k = O(n1/3/log n), we also give randomized algorithms with expected running times O(n + (k/ε2) log(1/ε)), O(n+(k/ε3) log(1/ε)), and O(n + (k/ε4) log(1/ε)), respectively. © 2011 World Scientific Publishing Company.

  15. Alignment of gold nanorods by angular photothermal depletion

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Adam B.; Chow, Timothy T. Y.; Chon, James W. M., E-mail: jchon@swin.edu.au [Centre for Micro-Photonics, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, P.O. Box 218, Hawthorn, 3122 VIC (Australia)

    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.

  16. Faster and More Accurate Sequence Alignment with SNAP

    CERN Document Server

    Zaharia, Matei; Curtis, Kristal; Fox, Armando; Patterson, David; Shenker, Scott; Stoica, Ion; Karp, Richard M; Sittler, Taylor

    2011-01-01

    We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent aligners based on the Burrows-Wheeler transform, SNAP uses a simple hash index of short seed sequences from the genome, similar to BLAST's. However, SNAP greatly reduces the number and cost of local alignment checks performed through several measures: it uses longer seeds to reduce the false positive locations considered, leverages larger memory capacities to speed index lookup, and excludes most candidate locations without fully computing their edit distance to the read. The result is an algorithm that scales well for reads from one hundred to thousands of bases long and provides a rich error model that can match classes of mutations (e.g., longer indels) that today's fast aligners ignore. We calculate that SNAP can align a dataset with 30x coverage of a human genome in le...

  17. The Alignment Effect of Brightest Cluster Galaxies in the SDSS

    CERN Document Server

    Kim, R S J; Strauss, M A; Lupton, R H; Bahcall, Neta A; Gunn, J E; Kepner, J V; Postman, M; Kim, Rita S. J.; Annis, Jim; Strauss, Michael A.; Lupton, Robert H.; Bahcall, Neta A.; Gunn, James E.; Kepner, Jeremy V.; Postman, Marc

    2002-01-01

    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...

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

    Science.gov (United States)

    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.

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

    International Nuclear Information System (INIS)

    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 fNL = 10, is only marginally significant in the intrinsic alignments signal with signal-to-noise ratios < 2 for the three surveys considered

  20. Towards a neural basis of interactive alignment in conversation

    Directory of Open Access Journals (Sweden)

    Laura eMenenti

    2012-06-01

    Full Text Available The interactive-alignment account of dialogue proposes that interlocutors achieve conversational success by aligning their understanding of the situation under discussion. Such alignment occurs because they prime each other at different levels of representation (e.g., phonology, syntax, semantics, and this is possible because these representations are shared across production and comprehension. In this paper, we briefly review the behavioural evidence, and then consider how findings from cognitive neuroscience might lend support to this account, on the assumption that alignment of neural activity corresponds to alignment of mental states. We first review work supporting representational parity between production and comprehension, and suggest that neural activity associated with phonological, lexical, and syntactic aspects of production and comprehension are closely related. We next consider evidence for the neural bases of the activation and use of situation models during production and comprehension, and how these demonstrate the activation of non-linguistic conceptual representations associated with language use. We then review evidence for alignment of neural mechanisms that are specific to the act of communication. Finally, we suggest some avenues of further research that need to be explored to test crucial predictions of the interactive alignment account.

  1. Radio-Optical Alignments in a Low Radio Luminosity Sample

    Science.gov (United States)

    Lacy, Mark; Ridgway, Susan E.; Wold, Margrethe; Lilje, Per B.; Rawlings, Steve

    1999-01-01

    We present an optically-based study of the alignment between the radio axes and the optical major axes of eight z approximately 0.7 radio galaxies in a 7C sample. The radio galaxies in this sample are approximately 20-times less radio luminous than 3C galaxies at the same redshift, and are significantly less radio-luminous than any other well-defined samples studied to date. Using Nordic Optical Telescope images taken in good seeing conditions at rest-frame wavelengths just longward of the 4000A break, we find a statistically significant alignment effect in the 7C sample. Furthermore, in two cases where the aligned components are well separated from the host we have been able to confirm spectroscopically that they are indeed at the same redshift as the radio galaxy. However, a quantitative analysis of the alignment in this sample and in a corresponding 3C sample from HST (Hubble Space Telescope) archival data indicates that the percentage of aligned flux may be lower and of smaller spatial scale in the 7C sample. Our study suggests that alignments on the 50-kpc scale are probably closely related to the radio luminosity, whereas those on the 15 kpc scale are not. We discuss these results in the context of popular models for the alignment effect.

  2. THE APPARATUS FOR ALIGNMENT OF THE PHOTOMETRIC LAMP FILAMENT

    Directory of Open Access Journals (Sweden)

    V. A. Dlugunovich

    2015-01-01

    Full Text Available During photometric measurements involving the use of photometric lamps it is necessary that the filament of lamp takes a strictly predetermined position with respect to the photodetector and the optical axis of the photometric setup. The errors in positioning of alignment filament with respect to the optical axis of the measuring system lead to increase the uncertainty of measurement of the photometric characteristics of the light sources. A typical method for alignment of filament of photometric lamps is based on the use a diopter tubes (telescopes. Using this method, the mounting of filament to the required position is carried out by successive approximations, which requires special concentration and a lot of time. The aim of this work is to develop an apparatus for alignment which allows simultaneous alignment of the filament of lamps in two mutually perpendicular planes. The method and apparatus for alignment of the photometric lamp filament during measurements of the photometric characteristics of light sources based on two digital video cameras is described in this paper. The apparatus allows to simultaneously displaying the image of lamps filament on the computer screen in two mutually perpendicular planes. The apparatus eliminates a large number of functional units requiring elementwise alignment and reduces the time required to carry out the alignment. The apparatus also provides the imaging of lamps filament with opaque coated on the bulb. The apparatus is used at the National standard of light intensity and illuminance units of the Republic of Belarus. 

  3. Aligned Immobilization of Proteins Using AC Electric Fields.

    Science.gov (United States)

    Laux, Eva-Maria; Knigge, Xenia; Bier, Frank F; Wenger, Christian; Hölzel, Ralph

    2016-03-01

    Protein molecules are aligned and immobilized from solution by AC electric fields. In a single-step experiment, the enhanced green fluorescent proteins are immobilized on the surface as well as at the edges of planar nanoelectrodes. Alignment is found to follow the molecules' geometrical shape with their longitudinal axes parallel to the electric field. Simultaneous dielectrophoretic attraction and AC electroosmotic flow are identified as the dominant forces causing protein movement and alignment. Molecular orientation is determined by fluorescence microscopy based on polarized excitation of the proteins' chromophores. The chromophores' orientation with respect to the whole molecule supports X-ray crystal data. PMID:26779699

  4. Aligning graphs and finding substructures by a cavity approach

    Science.gov (United States)

    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.

  5. REALITY OF ALIGNING IT WITH BUSINESS IN CZECH ORGANIZATIONS

    Directory of Open Access Journals (Sweden)

    Renata Kunstova

    2012-01-01

    Full Text Available Information technologies (IT supporting business strategies and business processes are often the most important factor for successful organizations. Aligning IT with the business depends on many factors, including communication and cooperation between the top management of organizations and the top management of IT departments in strategic decision making and planning. This paper discusses the outcomes of a survey conducted in six hundred organizations operating on the Czech market. The aim of the survey was to verify whether organizations operating on the Czech market meet basic assumptions for business/IT alignment or, in other words, to find out the reality of business/IT alignment in practice.

  6. Alignment analysis of urban railways based on passenger travel demand

    DEFF Research Database (Denmark)

    Andersen, Jonas Lohmann Elkjær; Landex, Alex

    2010-01-01

    , this article presents a computerised GIS based methodology that can be used as decision support for selecting the best alignment. The methodology calculates travel potential within defined buffers surrounding the alignment. The methodology has three different approaches depending on the desired level of detail......: the simple but straight-forward to implement line potential approach that perform corridor analysis, the detailed catchment area analysis based on stops on the alignment and the refined service area analysis that uses search distances in street networks. All three approaches produce trustworthy results...

  7. Automatic generation of alignments for 3D QSAR analyses

    OpenAIRE

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

    2001-01-01

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

  8. Optimal molecular alignment and orientation through rotational ladder climbing

    CERN Document Server

    Salomon, J; Turinici, G; Salomon, Julien; Dion, Claude M.; Turinici, Gabriel

    2005-01-01

    We study the control by electromagnetic fields of molecular alignment and orientation, in a linear, rigid rotor model. With the help of a monotonically convergent algorithm, we find that the optimal field is in the microwave part of the spectrum and acts by resonantly exciting the rotation of the molecule progressively from the ground state, i.e., by rotational ladder climbing. This mechanism is present not only when maximizing orientation or alignment, but also when using prescribed target states that simultaneously optimize the efficiency of orientation/alignment and its duration.

  9. Three dimensional alignment of molecules using elliptically polarized laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Bjerre, N.; Hald, K.;

    2000-01-01

    We demonstrate, theoretically and experimentally, that an intense, elliptically polarized, nonresonant laser field can simultaneously force all three axes of a molecule to align along given axes fixed in space, thus inhibiting the free rotation in all three Euler angles. Theoretically, the effect...... is illustrated through time dependent quantum mechanical calculations. Experimentally, 3, 4-dibromothiophene molecules are aligned with a nanosecond laser pulse. The alignment is probed by 2D ion imaging of the fragments from a 20 fs laser pulse induced Coulomb explosion....

  10. Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods

    OpenAIRE

    Muhammad Tariq Pervez; Masroor Ellahi Babar; Asif Nadeem; Muhammad Aslam; Ali Raza Awan; Naeem Aslam; Tanveer Hussain; Nasir Naveed; Salman Qadri; Usman Waheed; Muhammad Shoaib

    2014-01-01

    A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignments and sequence files were constructed using indel-Seq-Gen. A total of 4000 test alignments were gen...

  11. Accurate laboratory boresight alignment of transmitter/receiver optical axes

    Science.gov (United States)

    Martinek, Stephen J.

    1986-01-01

    An apparatus and procedure for the boresight alignment of the transmitter and receiver optical axes of a laser radar system are described. This accurate technique is applicable to both shared and dual aperture systems. A laser autostigmatic cube interferometer (LACI) is utilized to align a paraboloid in autocollimation. The LACI pinhole located at the paraboloid center of curvature becomes the far field receiver track and transmit reference point when illuminated by the transmit beam via a fiber optic pick-off/delay line. Boresight alignment accuracy better than 20 microrad is achievable.

  12. Helical coil alignment in the advanced toroidal facility

    International Nuclear Information System (INIS)

    This paper presents a brief overview of the helical coil design concept, detailed descriptions of the method for installation and alignment, and discussions of segment installation and alignment equipment. Alignment is accomplished by optical methods using electronic theodolites connected to a microcomputer to form a coordinate measurement system. The coordinate measurement system is described in detail, along with target selection and fixturing for manipulation of the helical coil segments during installation. In addition, software is described including vendor-supplied software used in the coordinate measurement system and in-house-developed software used to calibrate segment and positioning fixture motion. 2 refs., 8 figs

  13. Study and Development of a Laser Based Alignment System

    CERN Multimedia

    Stern, G

    2014-01-01

    CLIC (Compact Linear Collider) has tight requirements regarding pre-alignment of beam related components: 10 µm accuracy over a sliding window of 200 m along the 20 km of linac. To perform such an alignment, a new system is proposed combining laser beam as straight line reference and camera/shutter assemblies as sensors. The poster describes the alignment system and shows results regarding laser pointing stability with respect to time, shutter type, distance and environment. These results give a frame for future building and calibrating of sensors.

  14. Software for the alignment of the CMS experiment at CERN

    International Nuclear Information System (INIS)

    In the CMS experiment the position of the muon chambers has to be known with precision of the order of 100 μm. With this aim a complex optical alignment system has been designed, which is composed of three parts that correspond to the main parts of the detector: the alignment of the barre l muon chambers, the alignment of the end cap muon chambers, and the link between both chambers and the inner tracker sub-detector. The total number of elements in the three systems is around seven thousand. The purpose of the CMS optical alignment software is to analyze the data taken by all these elements and reconstruct the position of the muon chambers with respect to each other and with respect to the inner tracker reference system and to propagate the errors of the measurements to the errors in the positions of the chambers. (author)

  15. From Babylon to Bergen: On the usefulness of aligned texts

    Directory of Open Access Journals (Sweden)

    Signe Oksefjell Ebeling

    2013-04-01

    Full Text Available After outlining a short and select history of (the usefulness of parallel texts and alignment, this paper presents a case study where the point of departure is a Norwegian text extract aligned against its translations into seven different target languages, using the Translation Corpus Aligner, originally developed by Knut Hofland. Our main concern is cases where there is not a one-to-one correspondence at sentence level between original (source and translation (target text. We seek to answer questions such as why a translator, translating into a specific language has chosen to split, or merge, a sentence in the source texts, while translators, translating into other languages have chosen not to do so. The study shows that a multitude of contributing factors seem to be involved , including author and translator style, target language constraints and preferences and perhaps even country- or language-specific translation guidelines. Keywords: alignment; parallel texts; contrastive analysis; corpora; translation strategies

  16. Experiments in Aligning Threaded Parts Using a Robot Hand

    Science.gov (United States)

    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.

  17. Radiative Torques on Interstellar Grains; 2, Grain Alignment

    CERN Document Server

    Draine, B T; Weingartner, Joseph C.

    1996-01-01

    Radiative torques on irregular dust grains, in addition to producing superthermal rotation, play a direct dynamical role in the alignment of interstellar dust with the local magnetic field. The equations governing the orientation of spinning, precessing grains are derived; H_2 formation torques and paramagnetic dissipation are included in the dynamics. Stationary solutions (constant alignment angle and spin rate) are found; these solutions may be stable ("attractors") or unstable ("repellors"). The equations of motion are numerically integrated for three exemplary irregular grain geometries, exposed to anisotropic radiation with the spectrum of interstellar starlight. The resulting "trajectory maps" are classified as "noncyclic", "semicyclic", or "cyclic", with examples of each given. We find that radiative torques result in rapid grain alignment, even in the absence of paramagnetic dissipation. It appears that radiative torques due to starlight can account for the observed alignment of interstellar grains wi...

  18. Mechanism for collective cell alignment in Myxococcus xanthus bacteria

    CERN Document Server

    Balagam, Rajesh

    2015-01-01

    M. xanthus cells self-organize into clusters, aligned cell groups, at various stages of its lifecycle. Formation of these clusters is crucial for complex dynamic multi-cellular behavior of these bacteria. However the mechanism underlying the cell alignment and clustering is not fully understood. Motivated by studies of clustering in self-propelled rods, we hypothesized that M. xanthus cells can align and form clusters through pure mechanical interactions among cells and between cells and substrate. We test this hypothesis using an agent-based simulation framework where each agent is based on biophysical model of individual M. xanthus cell. We show that model agents, under realistic cell flexibility values, can align and form cell clusters but only when periodic reversals of cell directions are suppressed. However, by extending our model to introduce observed ability of cells to lay and follow slime trails, we show that effective trail following leads to clusters in reversing cells. Furthermore, we conclude th...

  19. Magnetic Alignment of Pulsed Solenoids Using the Pulsed Wire Method

    Energy Technology Data Exchange (ETDEWEB)

    Arbelaez, D.; Madur, A.; Lipton, T.M.; Waldron, W.L.; Kwan, J.W.

    2011-04-01

    A unique application of the pulsed-wire measurement method has been implemented for alignment of 2.5 T pulsed solenoid magnets. The magnetic axis measurement has been shown to have a resolution of better than 25 {micro}m. The accuracy of the technique allows for the identification of inherent field errors due to, for example, the winding layer transitions and the current leads. The alignment system is developed for the induction accelerator NDCX-II under construction at LBNL, an upgraded Neutralized Drift Compression experiment for research on warm dense matter and heavy ion fusion. Precise alignment is essential for NDCX-II, since the ion beam has a large energy spread associated with the rapid pulse compression such that misalignments lead to corkscrew deformation of the beam and reduced intensity at focus. The ability to align the magnetic axis of the pulsed solenoids to within 100 pm of the induction cell axis has been demonstrated.

  20. Inkjet printing of magnetic materials with aligned anisotropy

    Science.gov (United States)

    Song, Han; Spencer, Jeremy; Jander, Albrecht; Nielsen, Jeffrey; Stasiak, James; Kasperchik, Vladek; Dhagat, Pallavi

    2014-05-01

    3-D printing processes, which use drop-on-demand inkjet printheads, have great potential in designing and prototyping magnetic materials. Unlike conventional deposition and lithography, magnetic particles in the printing ink can be aligned by an external magnetic field to achieve both high permeability and low hysteresis losses, enabling prototyping and development of novel magnetic composite materials and components, e.g., for inductor and antennae applications. In this work, we report an inkjet printing technique with magnetic alignment capability. Magnetic films with and without particle alignment are printed, and their magnetic properties are compared. In the alignment-induced hard axis direction, an increase in high frequency permeability and a decrease in hysteresis losses are observed. Our results suggest that unique magnetic structures with arbitrary controllable anisotropy, not feasible otherwise, may be fabricated via inkjet printing.

  1. Magnetic Alignment of Pulsed Solenoids Using the Pulsed Wire Method

    International Nuclear Information System (INIS)

    A unique application of the pulsed-wire measurement method has been implemented for alignment of 2.5 T pulsed solenoid magnets. The magnetic axis measurement has been shown to have a resolution of better than 25 (micro)m. The accuracy of the technique allows for the identification of inherent field errors due to, for example, the winding layer transitions and the current leads. The alignment system is developed for the induction accelerator NDCX-II under construction at LBNL, an upgraded Neutralized Drift Compression experiment for research on warm dense matter and heavy ion fusion. Precise alignment is essential for NDCX-II, since the ion beam has a large energy spread associated with the rapid pulse compression such that misalignments lead to corkscrew deformation of the beam and reduced intensity at focus. The ability to align the magnetic axis of the pulsed solenoids to within 100 pm of the induction cell axis has been demonstrated.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. Software for the alignment of the CMS experiment at CERN

    Energy Technology Data Exchange (ETDEWEB)

    Arce, P. [Instituto de Fisica de Cantabria (Spain)

    1999-07-01

    In the CMS experiment the position of the muon chambers has to be known with precision of the order of 100 {mu}m. With this aim a complex optical alignment system has been designed, which is composed of three parts that correspond to the main parts of the detector: the alignment of the barre l muon chambers, the alignment of the end cap muon chambers, and the link between both chambers and the inner tracker sub-detector. The total number of elements in the three systems is around seven thousand. The purpose of the CMS optical alignment software is to analyze the data taken by all these elements and reconstruct the position of the muon chambers with respect to each other and with respect to the inner tracker reference system and to propagate the errors of the measurements to the errors in the positions of the chambers. (author)

  4. Software Alignment of the CMS Tracker using MILLEPEDE II

    CERN Document Server

    Schleper, Peter; Stoye, Markus

    2006-01-01

    The Alignment of the CMS tracker will require to determine about 10^5 alignment parameters. The Millepede program, a linear least-squares algorithm, is a promising candidate for this task, having been used successfully for alignment in several experiments. However, due to the inversion of a large matrix of linear equations, Millepede in its original form was limited to problems with about 10000 parameters. A new version of the program, Millepede II, provides an iterative method to determine the solution of the matrix, which should work for systems with 100000 parameters, if the matrix is sparse. This method is tested within the CMS object oriented reconstruction framework (ORCA). Its precision and CPU needs are studied and compared to the inversion method, using alignment scenarios of the CMS tracker with currently up to 12000 parameters.

  5. Practical procedure for coma-free alignment using caustic figure

    International Nuclear Information System (INIS)

    The practical procedure for coma-free alignment using a single defocused transmission electron microscopy (TEM) image is presented. Caustic figures observed in the defocused TEM image of a focused probe are utilized. Coma-free alignment can be carried out by coinciding a bright-field spot with the center of a caustic curve as observed in an underfocus TEM image. With this method, beam tilt misalignment is reduced to the sub-mrad order (e.g. 0.3 mrad for 300 kV FEG-TEM). This can be done without intentional beam tilting, an amorphous specimen, high-resolution TEM images, or fast Fourier transform for diffractogram or cross-correlation, which are used in previous methods. Residual coma aberration is detected using the multiple Bragg images of a known crystal. Similarity between the present coma-free alignment and well-known STEM alignment using shadow image is discussed

  6. Detection of Off-normal Images for NIF Automatic Alignment

    Energy Technology Data Exchange (ETDEWEB)

    Candy, J V; Awwal, A S; McClay, W A; Ferguson, S W; Burkhart, S C

    2005-07-11

    One of the major purposes of National Ignition Facility at Lawrence Livermore National Laboratory is to accurately focus 192 high energy laser beams on a nanoscale (mm) fusion target at the precise location and time. The automatic alignment system developed for NIF is used to align the beams in order to achieve the required focusing effect. However, if a distorted image is inadvertently created by a faulty camera shutter or some other opto-mechanical malfunction, the resulting image termed ''off-normal'' must be detected and rejected before further alignment processing occurs. Thus the off-normal processor acts as a preprocessor to automatic alignment image processing. In this work, we discuss the development of an ''off-normal'' pre-processor capable of rapidly detecting the off-normal images and performing the rejection. Wide variety of off-normal images for each loop is used to develop the criterion for rejections accurately.

  7. Plasma Enhanced Chemical Vapour Deposition of Horizontally Aligned Carbon Nanotubes

    Directory of Open Access Journals (Sweden)

    Matthew T. Cole

    2013-05-01

    Full Text Available A plasma-enhanced chemical vapour deposition reactor has been developed to synthesis horizontally aligned carbon nanotubes. The width of the aligning sheath was modelled based on a collisionless, quasi-neutral, Child’s law ion sheath where these estimates were empirically validated by direct Langmuir probe measurements, thereby confirming the proposed reactors ability to extend the existing sheath fields by up to 7 mm. A 7 mbar growth atmosphere combined with a 25 W plasma permitted the concurrent growth and alignment of carbon nanotubes with electric fields of the order of 0.04 V μm−1 with linear packing densities of up to ~5 × 104 cm−1. These results open up the potential for multi-directional in situ alignment of carbon nanotubes providing one viable route to the fabrication of many novel optoelectronic devices.

  8. Enhanced alignment of Mn 12-acetate micro-crystals

    Science.gov (United States)

    Seo, D.; Teizer, W.; Zhao, H.; Dunbar, K. R.

    2007-05-01

    A dilute Mn 12-acetate suspension composed of microscopic single crystals and single molecules in isopropanol was used for magnetic studies of Mn 12-acetate single molecule magnets. We observed magnetic properties of the frozen Mn 12-acetate suspension similar to large single crystals, specifically several sharp steps in the low-temperature hysteresis loop, indicating significantly enhanced alignment as compared to prior studies of micro-crystals. The greater the external magnetic field during alignment, the sharper the steps were in the low-temperature hysteresis loops, indicating that this method can be used for continuous control of alignment. A magnetic field of ˜0.5 T was sufficient to align the micro-crystals in the organic solvent to a degree previously observed only in much larger single crystals.

  9. Constructive Alignment for Teaching Model-Based Design for Concurrency

    DEFF Research Database (Denmark)

    Brabrand, Claus

    2007-01-01

    "How can we make sure our students learn what we want them to?" is the number one question in teaching. This paper is intended to provide the reader with: i) a general answer to this question based on the theory of constructive alignment by John Biggs; ii) relevant insights for bringing this answ...... from theory to practice; and iii) specific insights and experiences from using constructive alignment in teaching model-based design for concurrency (as a case study in implementing alignment)......."How can we make sure our students learn what we want them to?" is the number one question in teaching. This paper is intended to provide the reader with: i) a general answer to this question based on the theory of constructive alignment by John Biggs; ii) relevant insights for bringing this answer...

  10. Alignment of atmospheric mineral dust due to electric field

    Directory of Open Access Journals (Sweden)

    Z. Ulanowski

    2007-09-01

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

  11. Alignment of symmetric top molecules by short laser pulses

    DEFF Research Database (Denmark)

    Hamilton, Edward; Seideman, Tamar; Ejdrup, Tine;

    2005-01-01

    Nonadiabatic alignment of symmetric top molecules induced by a linearly polarized, moderately intense picosecond laser pulse is studied theoretically and experimentally. Our studies are based on the combination of a nonperturbative solution of the Schrodinger equation with femtosecond time...

  12. Proceedings of the first international workshop on accelerator alignment

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. Helical coil alignment in the Advanced Toroidal Facility

    International Nuclear Information System (INIS)

    The Advanced Toroidal Facility (ATF) is comprised of several major structural and magnetic coil systems tightly fitted around a thin helically contoured vacuum vessel. A critical parameter for successful operation of this device is the precise alignment of the various coil systems, with particular emphasis on the exact positioning of the helical field (HF) coils. This paper presents a brief overview of the helical coil design concept, detailed descriptions of the method for installation and alignment, and discussions of segment installation and alignment equipment. Alignment is accomplished by optical methods using electronic theodolites connected to a microcomputer to form a coordinate measurement system. The coordinate measurement system is described in detail, along with target selection and fixturing for manipulation of the helical coil segments during installation. In addition, software is described including vendor-supplied software used in the coordinate measurement system and in-house-developed software used to calibrate segment and positioning fixture motion

  14. Lagrangian analysis of alignment dynamics for isentropic compressible magnetohydrodynamics

    OpenAIRE

    Gibbon, J. D.; Holm, D. D.

    2006-01-01

    After a review of the isentropic compressible magnetohydrodynamics (ICMHD) equations, a quaternionic framework for studying the alignment dynamics of a general fluid flow is explained and applied to the ICMHD equations.

  15. Analytical alignment tolerances for off-plane reflection grating spectroscopy

    Science.gov (United States)

    Allured, Ryan; McEntaffer, Randall T.

    2013-12-01

    Future NASA X-ray Observatories will shed light on a variety of high-energy astrophysical phenomena. Off-plane reflection gratings can be used to provide high throughput and spectral resolution in the 0.3-1.5 keV band, allowing for unprecedented diagnostics of energetic astrophysical processes. A grating spectrometer consists of multiple aligned gratings intersecting the converging beam of a Wolter-I telescope. Each grating will be aligned such that the diffracted spectra overlap at the focal plane. Misalignments will degrade both spectral resolution and effective area. In this paper we present an analytical formulation of alignment tolerances that define grating orientations in all six degrees of freedom. We verify our analytical results with raytrace simulations to fully explore the alignment parameter space. We also investigate the effect of misalignments on diffraction efficiency.

  16. Analytical Alignment Tolerances for Off-Plane Reflection Grating Spectroscopy

    CERN Document Server

    Allured, Ryan

    2013-01-01

    Future NASA X-ray Observatories will shed light on a variety of high-energy astrophysical phenomena. Off-plane reflection gratings can be used to provide high throughput and spectral resolution in the 0.3--1.5 keV band, allowing for unprecedented diagnostics of energetic astrophysical processes. A grating spectrometer consists of multiple aligned gratings intersecting the converging beam of a Wolter-I telescope. Each grating will be aligned such that the diffracted spectra overlap at the focal plane. Misalignments will degrade both spectral resolution and effective area. In this paper we present an analytical formulation of alignment tolerances that define grating orientations in all six degrees of freedom. We verify our analytical results with raytrace simulations to fully explore the alignment parameter space. We also investigate the effect of misalignments on diffraction efficiency.

  17. Monitoring, alignment and control of the RICH detectors

    CERN Document Server

    D'Ambrosio, C; Gaspar, C; Laub, M; Lindner, R; Muheim, F; Papanestis, A; Soler, FJP

    2001-01-01

    The physical quantities of the RICH detectors need to be monitored throughout the duration of the experiment to ensure that their performance remains within the design specifications. The present note describes all the physical quantities that need to be monitored and a description of possible devices that could be implemented to achieve the specified level of control. In addition, the angular resolution of the RICH detectors depends on an accurate alignment of the system. Proposals for this alignment procedure are described.

  18. The alignment of the ATLAS Inner Detector in Run 2

    CERN Document Server

    Ripellino, Giulia; The ATLAS collaboration

    2016-01-01

    The ATLAS reconstruction of charged particle trajectories relies on the Inner Detector tracking system. The accuracy of the reconstruction is limited by the finite resolution of the detector elements and the knowledge about their positions. A precise alignment of the detector is therefore essential. In this poster we present the strategy and the status of the Inner Detector alignment in ATLAS during the LHC Run 2.

  19. Aligning ERP and Business Strategy after going live

    DEFF Research Database (Denmark)

    Koch, Christian

    2004-01-01

    Steering enterprises with Enterprise Resource Planning systems (ERP) is not only an issue of implementation and of “once and for all” aligning the ERP system with the strategy of the company, it is a long term exercise. This paper is about managing ERP systems after going live. It is argued that...... companies has to align the ERP systems with the strategy of the company and guidelines as to how this can be achieved is given....

  20. Mutual Community Detection across Multiple Partially Aligned Social Networks

    OpenAIRE

    Zhang, Jiawei; Yu, Philip S.

    2015-01-01

    Community detection in online social networks has been a hot research topic in recent years. Meanwhile, to enjoy more social network services, users nowadays are usually involved in multiple online social networks simultaneously, some of which can share common information and structures. Networks that involve some common users are named as multiple "partially aligned networks". In this paper, we want to detect communities of multiple partially aligned networks simultaneously, which is formall...

  1. L-GRAAL: Lagrangian graphlet-based network aligner

    OpenAIRE

    Malod-Dognin, Noël; Pržulj, Nataša

    2015-01-01

    Motivation: Discovering and understanding patterns in networks of protein–protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically...

  2. LASAGNA: A novel algorithm for transcription factor binding site alignment

    OpenAIRE

    Lee, Chih; Huang, Chun-Hsi

    2013-01-01

    Background Scientists routinely scan DNA sequences for transcription factor (TF) binding sites (TFBSs). Most of the available tools rely on position-specific scoring matrices (PSSMs) constructed from aligned binding sites. Because of the resolutions of assays used to obtain TFBSs, databases such as TRANSFAC, ORegAnno and PAZAR store unaligned variable-length DNA segments containing binding sites of a TF. These DNA segments need to be aligned to build a PSSM. While the TRANSFAC database provid...

  3. High-throughput sequence alignment using Graphics Processing Units

    Directory of Open Access Journals (Sweden)

    Trapnell Cole

    2007-12-01

    Full Text Available Abstract Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

  4. RNA-RNA interaction prediction based on multiple sequence alignments

    CERN Document Server

    Li, Andrew X; Qin, Jing; Reidys, Christian M

    2010-01-01

    Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes for pairs of RNA sequences. These algorithms and the biological requirement of more reliable interactions motivate to utilize the additional information contained in multiple sequence alignments and to generalize the above framework to the partition function and base pairing probabilities for multiple sequence alignments.

  5. Face Alignment Using Active Shape Model And Support Vector Machine

    OpenAIRE

    Le, Thai Hoang; Vo, Truong Nhat

    2012-01-01

    The Active Shape Model (ASM) is one of the most popular local texture models for face alignment. It applies in many fields such as locating facial features in the image, face synthesis, etc. However, the experimental results show that the accuracy of the classical ASM for some applications is not high. This paper suggests some improvements on the classical ASM to increase the performance of the model in the application: face alignment. Four of our major improvements include: i) building a mod...

  6. Face Alignment Using Active Shape Model And Support Vector Machine

    OpenAIRE

    Le Hoang Thai; Vo Nhat Truong

    2011-01-01

    The Active Shape Model (ASM) is one of the most popular local texture modelsfor face alignment. It applies in many fields such as locating facial features in theimage, face synthesis, etc. However, the experimental results show that theaccuracy of the classical ASM for some applications is not high. This papersuggests some improvements on the classical ASM to increase the performanceof the model in the application: face alignment. Four of our major improvementsinclude: i) building a model com...

  7. Survey, alignment, and beam stability at the Advanced Light Source

    International Nuclear Information System (INIS)

    This paper describes survey and alignment at the Lawrence Berkeley Laboratories Advanced Light Source (ALS) accelerators from 1993 to 1997. The ALS is a third generation light source requiring magnet alignment to within 150 microns. To accomplish this, a network of monuments was established and maintained. Monthly elevation surveys show the movement of the floor over time. Inclinometers have recently been employed to give real time information about magnet, vacuum tank and magnet girder motion in the ALS storage ring

  8. Rotating maps and readers: praxiological aspects of alignment and orientation

    OpenAIRE

    Laurier, Eric; Brown, Barry

    2008-01-01

    A longstanding topic in our notions of what geographic knowledge could be is the mental map, or, in its most recent form, mental spatial representations. In this paper we draw upon ethnomethodological critiques of cognition, and mind more generally, to re-specify navigation, orientation and alignment in terms of human practices of navigating, orienting and aligning in particular settings. Our ambition in the paper is less to dismantle notions of cognition still present in studies ...

  9. Rotating maps and users: praxiological aspects of alignment and orientation

    OpenAIRE

    Laurier, Eric; Brown, Barry

    2006-01-01

    A longstanding topic in our notions of what geographic knowledge could be is the mental map, or, in its most recent form, mental spatial representations. In this paper we draw upon ethnomethodological critiques of cognition, and mind more generally, to re-specify navigation, orientation and alignment in terms of human practices of navigating, orienting and aligning in particular settings. Our ambition in the paper is less to dismantle notions of cognition still present in studies ...

  10. Alignment and resolution studies of the MARS CT scanner

    International Nuclear Information System (INIS)

    This paper describes a procedure of alignment of the MARS CT scanner with cone-beam geometry. The position of the x-ray source relative to the detector, the tilt of the detector are measured during alignment. The mechanical precision of gantry movement is determined. Significant improvement in the quality of image reconstruction has been achieved as a result of the calibration. Spatial resolution (PTF) of the scanner is confirmed to be about 30 μm

  11. An Improved Method for Completely Uncertain Biological Network Alignment

    OpenAIRE

    2015-01-01

    With the continuous development of biological experiment technology, more and more data related to uncertain biological networks needs to be analyzed. However, most of current alignment methods are designed for the deterministic biological network. Only a few can solve the probabilistic network alignment problem. However, these approaches only use the part of probabilistic data in the original networks allowing only one of the two networks to be probabilistic. To overcome the weakness of curr...

  12. Strategic alignment: a performance tool (an empirical study of SMEs)

    OpenAIRE

    Jouirou, Nihel; Kalika, Michel

    2004-01-01

    The purpose of this research is to investigate whether the alignment of IT with the strategy (particularly the partnership strategy or cooperation practice) and organizational structure of an SME could have a decisive influence on its performance. We constructed a model and tested it empirically using data from 381 SMEs operating in different sectors. A multivariate perspective, modelled with structural equations, was used to test the alignment between strategy, structure and IT. The alignmen...

  13. A Framework for Developing and Aligning a Knowledge Management Strategy

    OpenAIRE

    Deborah E. Swain; Jean-Pierre Booto Ekionea

    2008-01-01

    Businesses today, including non-profits, recognise the need for knowledge management (KM). KM may require new strategies and goals before it can be implemented, or it can be aligned with current business strategies for quicker implementation. The framework presented here is for managers in companies and organisations to use to align their KM strategies with business strategies to improve performance involving financial growth, cost reduction and customer satisfaction. A study of three strateg...

  14. Modeling Competition-Driven Business Strategy for Business IT Alignment

    OpenAIRE

    Giannoulis, Constantinos; Petit, Michaël; Zdravkovic, Jelena

    2011-01-01

    Business strategy aims at supporting the vision of an enterprise, by paving the way to achieve it through goals that direct the strategy’s execution. Aligning business strategy to system requirements requires explicit models from both business strategy and requirements engineering. However, existing business strategy definition approaches are informal and their syntax is based on natural language, therefore, they cannot be used in model-driven alignment. An objective of our research is to def...

  15. Woven Glass Fiber Composites with Aligned Carbon Nanotube Sheet Interlayers

    OpenAIRE

    Hardik Bhanushali; Philip D. Bradford

    2016-01-01

    This investigation describes the design, fabrication, and testing of woven glass fiber reinforced epoxy matrix laminates with aligned CNT sheets integrated between plies in order to improve the matrix dominated through thickness properties such as the interlaminar fracture toughness at ply interfaces. Using aligned CNT sheets allows for a concentration of millimeter long CNTs at the most likely point of laminate failure. Mode I and Mode II interlaminar fracture toughness of various CNT modifi...

  16. FERMI@Elettra beam-based alignment simulations

    CERN Document Server

    Janeiro Costa, Raul Antonio; CERN. Geneva. BE Department

    2015-01-01

    In this report we present various simulations of the FERMI@Elettra linear accelerator performance with ideal and non-ideal element alignment, showing that a non-ideal machine’s emittance may be over 15 times its ideal counterpart. We then apply beam-based alignment techniques in order to correct this emittance growth, concluding that, under these conditions, dispersion-free steering is enough to reduce the emittance to within 30% of the beam’s original emittance.

  17. FootPrinter3: phylogenetic footprinting in partially alignable sequences

    OpenAIRE

    Fang, Fei; Blanchette, Mathieu

    2006-01-01

    FootPrinter3 is a web server for predicting transcription factor binding sites by using phylogenetic footprinting. Until now, phylogenetic footprinting approaches have been based either on multiple alignment analysis (e.g. PhyloVista, PhastCons), or on motif-discovery algorithms (e.g. FootPrinter2). FootPrinter3 integrates these two approaches, making use of local multiple sequence alignment blocks when those are available and reliable, but also allowing finding motifs in unalignable regions....

  18. The connections between values alignment and teamwork : A case study

    OpenAIRE

    Nyberg, Sandra; Nilsson, Anette; Skinstad, Erik

    2009-01-01

    Background: Research today highlights the importance of values alignment, but all of the research has been conducted on manufacturing companies. We found it interesting to investigate if the same theories are applicable to the knowledge-intense service sector, such as consultancy firms. Furthermore, research has identified a set of key attributes of successful teamwork, which we find closely related to values alignment. Despite this, we found no previous research within this area. Purpose: Th...

  19. Alignment of atmospheric mineral dust due to electric field

    OpenAIRE

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

    2007-01-01

    International audience Optical polarimetry observations on La Palma, Canary Islands, during a Saharan dust episode show dichroic extinction indicating the presence of vertically aligned particles in the atmosphere. Modelling of the extinction together with particle orientation indicates that the alignment could have been due to an electric field of the order of 2 kV/m. Two alternative mechanisms for the origin of the field are examined: the effect of reduced atmospheric conductivity and ch...

  20. Purchasing alignment under multiple contingencies: a configuration theory approach.

    OpenAIRE

    Mikalef, P; Pateli, A.; Batenburg, R.S.; Wetering, R. van de

    2015-01-01

    Purpose: Strategic alignment is a theory-based state that is considered as crucial for organizations in order to realize performance gains from information technology (IT) investments and deployments. Within the domain of purchasing and supply chain management there has been a growing interest on how purchasing strategy can be effectively aligned with IT and what conditions facilitate this state. The purpose of this paper is to investigate complex causal relationships of contingency elements ...

  1. Specification of a benchmarking methodology for alignment techniques

    OpenAIRE

    Euzenat, Jérôme; García Castro, Raúl; Ehrig, Marc

    2004-01-01

    This document considers potential strategies for evaluating ontology alignment algorithms. It identifies various goals for such an evaluation. In the context of the Knowledge web network of excellence, the most important objective is the improvement of existing methods. We examine general evaluation strategies as well as efforts that have already been undergone in the specific field of ontology alignment. We then put forward some methodological and practical guidelines for running such an eva...

  2. Alignment and operability analysis of a vertical sodium pump

    International Nuclear Information System (INIS)

    With the objective of identifying important alignment features of pumps such as FFTF, HALLAM, EBR II, PNC, PHENIX, and CRBR, alignment of the vertical sodium pump for the Clinch River Breeder Reactor Plant (CRBRP) is investigated. The CRBRP pump includes a flexibly coupled pump shaft and motor shaft, two oil-film tilting-pad hydrodynamic radial bearings in the motor plus a vertical thrust bearing, and two sodium hydrostatic bearings straddling the double-suction centrifugal impeller in the pump

  3. High resolution Fresnel zone plate laser alignment system

    International Nuclear Information System (INIS)

    The existing Fresnel zone plate laser alignment system is currently being extended and upgraded for the Final Focus Test Beam (FFTB), a 300 m final focus beam line extending from the end of the SLAC central beam. The existing laser alignment system, and recent work on the image detection system are described. Previously, the resolution of this system has been several tens of micrometers; after the upgrade, the resolution will be a few micrometers. (R.P.) 3 refs.; 11 figs

  4. BFAST: an alignment tool for large scale genome resequencing.

    Directory of Open Access Journals (Sweden)

    Nils Homer

    Full Text Available BACKGROUND: The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation. METHODOLOGY: We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels. CONCLUSIONS: We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net.

  5. Finding optimal interaction interface alignments between biological complexes

    KAUST Repository

    Cui, Xuefeng

    2015-06-13

    Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \\'blackbox preprocessing\\' to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein-DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \\'blackbox preprocessing\\'). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein-DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein-protein complex and a protein-RNA complex, which is biologically known as a protein-RNA mimicry case. © The Author 2015. Published by Oxford University Press.

  6. Epitaxial growth of aligned GaN nanowires and nanobridges

    OpenAIRE

    Kim, Kyungkon; Henry, Tania; Cui, George; Han, Jung; Song, Yoon-Kyu; Nurmikko, Arto V.; Tang, Hong

    2007-01-01

    Homo-epitaxialy grown aligned GaN nanowires were prepared on crystalline GaN mesas. The GaN nanowires showed preferential growth along the 〈100〉 direction (m-axis direction). By using selectively positioned and crystallographically well defined GaN epitaxial lateral overgrowth (ELO) mesas as substrate, we obtained horizontally aligned GaN nanowires, in comb-like arrays and hexagonal network interconnecting the ELO mesas. Preliminary testing of the nanomechanical behavior of horizontal nanowir...

  7. Business-IT Alignment with SEAM for Enterprise Architecture

    OpenAIRE

    Wegmann, Alain; Regev, Gil; Rychkova, Irina; Lê, Lam-Son; De La Cruz, José Diego; Julia, Philippe

    2007-01-01

    To align an IT system with an organization’s needs, it is necessary to understand the organization’s position within its environment a well as its internals. In SEAM for Enterprise Architecture the organization is considered as a hierarchy of systems that span from business down to IT. The alignment process addresses the complete hierarchy. We illustrate the use of SEAM for Enterprise Architecture with a real project in which a new hiring process and an IT system are developed.

  8. Aligning Business Process Quality and Information System Quality

    OpenAIRE

    Heinrich, Robert

    2013-01-01

    Business processes and information systems mutually affect each other in non-trivial ways. Frequently, the business process design and the information system design are not well aligned. This means that business processes are designed without taking the information system impact into account, and vice versa. Missing alignment at design time often results in quality problems at runtime, such as large response times of information systems, large process execution times, overloaded information s...

  9. Alignment and operability analysis of a vertical sodium pump

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, V.K.; Fair, C.E.

    1981-01-01

    With the objective of identifying important alignment features of pumps such as FFTF, HALLAM, EBR II, PNC, PHENIX, and CRBR, alignment of the vertical sodium pump for the Clinch River Breeder Reactor Plant (CRBRP) is investigated. The CRBRP pump includes a flexibly coupled pump shaft and motor shaft, two oil-film tilting-pad hydrodynamic radial bearings in the motor plus a vertical thrust bearing, and two sodium hydrostatic bearings straddling the double-suction centrifugal impeller in the pump.

  10. Parallel progressive multiple sequence alignment on reconfigurable meshes

    Directory of Open Access Journals (Sweden)

    Nguyen Ken D

    2011-12-01

    Full Text Available Abstract Background One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing extensive task. In addition, the advancement in DNA/RNA and Protein sequencing techniques has created a vast amount of sequences to be analyzed that exceeding the capability of traditional computing models. Therefore, an effective parallel multiple sequence alignment model capable of resolving these issues is in a great demand. Results We design O(1 run-time solutions for both local and global dynamic programming pair-wise alignment algorithms on reconfigurable mesh computing model. To align m sequences with max length n, we combining the parallel pair-wise dynamic programming solutions with newly designed parallel components. We successfully reduce the progressive multiple sequence alignment algorithm's run-time complexity from O(m × n4 to O(m using O(m × n3 processing units for scoring schemes that use three distinct values for match/mismatch/gap-extension. The general solution to multiple sequence alignment algorithm takes O(m × n4 processing units and completes in O(m time. Conclusions To our knowledge, this is the first time the progressive multiple sequence alignment algorithm is completely parallelized with O(m run-time. We also provide a new parallel algorithm for the Longest Common Subsequence (LCS with O(1 run-time using O(n3 processing units. This is a big improvement over the current best constant-time algorithm that uses O(n4 processing units.

  11. The Process of Alignment Between Strategy and Six Sigma Projects

    OpenAIRE

    Gonçalves, Bianca Soares De Oliveira; Musetti, Marcel Andreotti

    2010-01-01

    Regarding the systematization proposal presented, one should emphasize the importance of having in the literature a systematic alignment of the strategy with Six Sigma projects, given that this alignment is essential to the success of the program. In addition, the proposal assists companies that are implementing the Six Sigma program to be successful in selecting improvement projects. It was not within the overall objective to present a comprehensive proposal for all the improvement actions, ...

  12. Error estimation for accelerator alignment using surveying network

    International Nuclear Information System (INIS)

    Surveying networks are widely used for evaluating alignment of large particle accelerators. We analytically estimated error propagated to the results obtained by the surveying networks by using our stitching model. Here, we estimated effects of the measurement parameters, that is the total measurement length l, the partial measurement length lu, the measurement interval s, and overlapping ratio k for evaluating alignment of the components for approximately 100 m of circumference part of the cERL, which has been constructed in KEK. (author)

  13. A novel approach to multiple sequence alignment using hadoop data grids.

    Science.gov (United States)

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

    Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences. PMID:21224205

  14. Calibration and alignment of the CMS silicon tracking detector

    Energy Technology Data Exchange (ETDEWEB)

    Stoye, M.

    2007-07-15

    The Large Hadron Collider (LHC) will dominate the high energy physics program in the coming decade. The discovery of the standard model Higgs boson and the discovery of super-symmetric particles are within the reach at the energy scale explored by the LHC. However, the high luminosity and the high energy of the colliding protons lead to challenging demands on the detectors. The hostile radiation environment requires irradiation hard detectors, where the innermost subdetectors, consisting of silicon modules, are most affected. This thesis is devoted to the calibration and alignment of the silicon tracking detector. Electron test beam data, taken at DESY, have been used to investigate the performance of detector modules which previously were irradiated with protons up to a dose expected after 10 years of operation. The irradiated sensors turned out to be still better than required. The performance of the inner tracking systems will be dominated by the degree to which the positions of the sensors can be determined. Only a track based alignment procedure can reach the required precision. Such an alignment procedure is a major challenge given that about 50000 geometry constants need to be measured. Making use of the novel {chi}{sup 2} minimization program Millepede II an alignment strategy has been developed in which all detector components are aligned simultaneously, as many sources of information as possible are used, and all correlations between the position parameters of the detectors are taken into account. Utilizing simulated data, a proof of concept of the alignment strategy is shown. (orig.)

  15. Long Read Alignment with Parallel MapReduce Cloud Platform.

    Science.gov (United States)

    Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

    2015-01-01

    Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms. PMID:26839887

  16. Calibration/Survey/Alignment studies of STAR HFT Pixel Detector

    Science.gov (United States)

    Ma, Long

    2013-10-01

    As a critical component of the STAR inner tracking detector - Heavy Flavor Tracker (HFT), the pixel detector consists of 10 sectors with 400 million 20x20-micrometer pixels forming the two innermost layers of the HFT at radii of 2.5 and 8 cm, respectively. In Run-13, a three-sector prototype was installed and successfully integrated into STAR. To achieve physics goals of HFT, the alignment calibration of pixel detector to a high precision of ~10 microns is essential. The precision alignment to map out each pixel position within the sector is carried out via a survey measurement utilizing a Coordinate Measurement Machine with a repeatability of a few micrometers. The global position parameters of the pixel sectors with respect to the STAR TPC will be obtained via a track-based alignment method with beam collisions. Particularly, the sensitive area of the pixel detector is designed to have some overlaps in order to complete the relative alignment between sectors using tracks passing through the overlap region. In this presentation, we will present the alignment calibration procedure for the HFT pixel detector. Status of the alignment calibration for the pixel detector prototype in Run-13 will be discussed. for the STAR Collaboration

  17. Aligned and random nanofibrous nanocomposite scaffolds for bone tissue engineering

    Directory of Open Access Journals (Sweden)

    Amir Doustgani

    2013-01-01

    Full Text Available Abstract  Aligned and random nanocomposite nanofibrous scaffolds were electrospun from polycaprolactone (PCL, poly (vinyl alcohol (PVA and hydroxyapatite nanoparticles (nHA. The morphology and mechanical characteristics of the nanofibers were evaluated using scanning electron microscopy and tensile testing, respectively. Scanning electron microscopy revealed fibers with an average diameter of 123 ± 32 nm and 339 ± 107 nm for aligned and random nanofibers, respectively. The mechanical data indicated the higher tensile strength and elastic modulus of aligned nanofibers. The in vitro biocompatibility of aligned and random nanofibrous scaffolds was also assessed by growing mesenchymal stem cells (MSCs, and investigating the proliferation and alkaline phosphatase activity (ALP on different nanofibrous scaffolds. Our  findings  showed  that  the  alignment  orientation  of  nanofibers  enhanced  the osteogenic differentiation of stem cells. The in vitro results showed that the aligned biocomposite nanofibrous scaffolds of PCL/nHA/PVA could be a potential substrate for tissue engineering applications, especially in the field of artificial bone implant.

  18. Calibration and alignment of the CMS silicon tracking detector

    International Nuclear Information System (INIS)

    The Large Hadron Collider (LHC) will dominate the high energy physics program in the coming decade. The discovery of the standard model Higgs boson and the discovery of super-symmetric particles are within the reach at the energy scale explored by the LHC. However, the high luminosity and the high energy of the colliding protons lead to challenging demands on the detectors. The hostile radiation environment requires irradiation hard detectors, where the innermost subdetectors, consisting of silicon modules, are most affected. This thesis is devoted to the calibration and alignment of the silicon tracking detector. Electron test beam data, taken at DESY, have been used to investigate the performance of detector modules which previously were irradiated with protons up to a dose expected after 10 years of operation. The irradiated sensors turned out to be still better than required. The performance of the inner tracking systems will be dominated by the degree to which the positions of the sensors can be determined. Only a track based alignment procedure can reach the required precision. Such an alignment procedure is a major challenge given that about 50000 geometry constants need to be measured. Making use of the novel χ2 minimization program Millepede II an alignment strategy has been developed in which all detector components are aligned simultaneously, as many sources of information as possible are used, and all correlations between the position parameters of the detectors are taken into account. Utilizing simulated data, a proof of concept of the alignment strategy is shown. (orig.)

  19. Nanofibril Alignment in Flow Focusing: Measurements and Calculations.

    Science.gov (United States)

    Håkansson, Karl M O; Lundell, Fredrik; Prahl-Wittberg, Lisa; Söderberg, L Daniel

    2016-07-14

    Alignment of anisotropic supermolecular building blocks is crucial to control the properties of many novel materials. In this study, the alignment process of cellulose nanofibrils (CNFs) in a flow-focusing channel has been investigated using small-angle X-ray scattering (SAXS) and modeled using the Smoluchowski equation, which requires a known flow field as input. This flow field was investigated experimentally using microparticle-tracking velocimetry and by numerically applying the two-fluid level set method. A semidilute dispersion of CNFs was modeled as a continuous phase, with a higher viscosity as compared to that of water. Furthermore, implementation of the Smoluchowski equation also needed the rotational Brownian diffusion coefficient, which was experimentally determined in a shear viscosity measurement. The order of the nanofibrils was found to increase during extension in the flow-focusing channel, after which rotational diffusion acted on the orientation distribution, driving the orientation of the fibrils toward isotropy. The main features of the alignment and dealignment processes were well predicted by the numerical model, but the model overpredicted the alignment at higher rates of extension. The apparent rotational diffusion coefficient was seen to increase steeply as the degree of alignment increased. Thus, the combination of SAXS measurements and modeling provides the necessary framework for quantified studies of hydrodynamic alignment, followed by relaxation toward isotropy. PMID:27294285

  20. Vacuum mechatronic laser alignment system on the Nova laser

    International Nuclear Information System (INIS)

    The experiments conducted on NOVA are done to investigate inertially confined laser fusion reactions. To this end, the ten beams of the laser are aligned to within 30mm. The target chamber employs a vacuum mechatronic based reticle/target positioning system to accomplish this. It is a five degree-of-freedom chamber resident system, known as the Alignment Aids Positioner or AAP. The AAP aids in beam and diagnostic alignment by accurately positioning a reticle at target chamber center to with 7mm. The AAP system increases target positioning and alignment flexibility and accuracy through the use of a computer controlled multi degree-of-freedom stage assembly. This device uses microstepping DC stepper motors with encoders to achieve closed loop control in a 10-6 torr vacuum. The AAP has two positioning regimes to move the alignment reticle and do beam alignment. One is course positioning in the Y-Z plane that moves a high resolution stage assembly to target chamber center. The other regime is high resolution movement in the X,Y,Z and q directions. 5 refs., 9 figs