WorldWideScience

Sample records for alignment

  1. Alignment validation

    Energy Technology Data Exchange (ETDEWEB)

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

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

  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. Vibrating wire alignment technique

    CERN Document Server

    Xiao-Long, Wang; lei, Wu; Chun-Hua, Li

    2013-01-01

    Vibrating wire alignment technique is a kind of method which through measuring the spatial distribution of magnetic field to do the alignment and it can achieve very high alignment accuracy. Vibrating wire alignment technique can be applied for magnet fiducialization and accelerator straight section components alignment, it is a necessary supplement for conventional alignment method. This article will systematically expound the international research achievements of vibrating wire alignment technique, including vibrating wire model analysis, system frequency calculation, wire sag calculation and the relation between wire amplitude and magnetic induction intensity. On the basis of model analysis this article will introduce the alignment method which based on magnetic field measurement and the alignment method which based on amplitude and phase measurement. Finally, some basic questions will be discussed and the solutions will be given.

  4. 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...

  5. 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 ...

  6. 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, ...

  7. 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.

  8. Ontology alignment with OLA

    OpenAIRE

    Euzenat, Jérôme; Loup, David; Touzani, Mohamed; Valtchev, Petko

    2004-01-01

    euzenat2004d; International audience; Using ontologies is the standard way to achieve interoperability of heterogeneous systems within the Semantic web. However, as the ontologies underlying two systems are not necessarily compatible, they may in turn need to be aligned. Similarity-based approaches to alignment seems to be both powerful and flexible enough to match the expressive power of languages like OWL. We present an alignment tool that follows the similarity-based paradigm, called OLA. ...

  9. 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...

  10. 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...

  11. 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...

  12. 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 ...

  13. SPEAR3 Construction Alignment

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-08-17

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

  14. 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...

  15. Physics of Grain Alignment

    CERN Document Server

    Lazarian, A

    2000-01-01

    Aligned grains provide one of the easiest ways to study magnetic fields in diffuse gas and molecular clouds. How reliable our conclusions about the inferred magnetic field depends critically on our understanding of the physics of grain alignment. Although grain alignment is a problem of half a century standing recent progress achieved in the field makes us believe that we are approaching the solution of this mystery. I review basic physical processes involved in grain alignment and show why mechanisms that were favored for decades do not look so promising right now. I also discuss why the radiative torque mechanism ignored for more than 20 years looks right now the most powerful means of grain alignment.

  16. 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.

  17. Discriminative Shape Alignment

    DEFF Research Database (Denmark)

    Loog, M.; de Bruijne, M.

    2009-01-01

    The alignment of shape data to a common mean before its subsequent processing is an ubiquitous step within the area shape analysis. Current approaches to shape analysis or, as more specifically considered in this work, shape classification perform the alignment in a fully unsupervised way......, not 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......-dimensional shapes from a two-class recognition problem....

  18. 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...

  19. 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...

  20. 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...

  1. Incremental Alignment Manifold Learning

    Institute of Scientific and Technical Information of China (English)

    Zhi Han; De-Yu Meng; Zong-Sen Xu; Nan-Nan Gu

    2011-01-01

    A new manifold learning method, called incremental alignment method (IAM), is proposed for nonlinear dimensionality reduction of high dimensional data with intrinsic low dimensionality. The main idea is to incrementally align low-dimensional coordinates of input data patch-by-patch to iteratively generate the representation of the entire dataset. The method consists of two major steps, the incremental step and the alignment step. The incremental step incrementally searches neighborhood patch to be aligned in the next step, and the alignment step iteratively aligns the low-dimensional coordinates of the neighborhood patch searched to generate the embeddings of the entire dataset. Compared with the existing manifold learning methods, the proposed method dominates in several aspects: high efficiency, easy out-of-sample extension, well metric-preserving, and averting of the local minima issue. All these properties are supported by a series of experiments performed on the synthetic and real-life datasets. In addition, the computational complexity of the proposed method is analyzed, and its efficiency is theoretically argued and experimentally demonstrated.

  2. 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…

  3. MaxAlign: maximizing usable data in an alignment

    DEFF Research Database (Denmark)

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

    2007-01-01

    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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. Orientation and Alignment Echoes

    CERN Document Server

    Karras, G; Billard, F; Lavorel, B; Hartmann, J -M; Faucher, O; Gershnabel, E; Prior, Y; Averbukh, I Sh

    2015-01-01

    We present what is probably the simplest classical system featuring the echo phenomenon - a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation/alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO_2 molecules excited by a pair of femtosecond laser pulses.

  10. Group Based Interference Alignment

    CERN Document Server

    Ma, Yanjun; Chen, Rui; Yao, Junliang

    2010-01-01

    in $K$-user single-input single-output (SISO) frequency selective fading interference channels, it is shown that the achievable multiplexing gain is almost surely $K/2$ by using interference alignment (IA). However when the signaling dimensions is limited, allocating all the resource to all the users simultaneously is not optimal. According to this problem, a group based interference alignment (GIA) scheme is proposed and a search algorithm is designed to get the group patterns and the resource allocation among them. Analysis results show that our proposed scheme achieves a higher multiplexing gain when the resource is limited.

  11. PILOT optical alignment

    Science.gov (United States)

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

    2016-07-01

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

  12. Aligning Theory with Practice

    Science.gov (United States)

    Kurz, Terri L.; Batarelo, Ivana

    2009-01-01

    This article describes a structure to help preservice teachers get invaluable field experience by aligning theory with practice supported by the integration of elementary school children into their university mathematics methodology course. This course structure allowed preservice teachers to learn about teaching mathematics in a nonthreatening…

  13. 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...

  14. Alignment of concerns

    DEFF Research Database (Denmark)

    Andersen, Tariq Osman; Bansler, Jørgen P.; Kensing, Finn;

    2014-01-01

    The emergence of patient-centered eHealth systems introduces new challenges, where patients come to play an increasingly important role. Realizing the promises requires an in-depth understanding of not only the technology, but also the needs of both clinicians and patients. However, insights from...... as a design rationale for successful eHealth, termed 'alignment of concerns'....

  15. 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...

  16. 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.

  17. 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.

  18. MUSE alignment onto VLT

    Science.gov (United States)

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

    2014-07-01

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

  19. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  20. Aligning component upgrades

    Directory of Open Access Journals (Sweden)

    Roberto Di Cosmo

    2011-08-01

    Full Text Available Modern software systems, like GNU/Linux distributions or Eclipse-based development environment, are often deployed by selecting components out of large component repositories. Maintaining such software systems by performing component upgrades is a complex task, and the users need to have an expressive preferences language at their disposal to specify the kind of upgrades they are interested in. Recent research has shown that it is possible to develop solvers that handle preferences expressed as a combination of a few basic criteria used in the MISC competition, ranging from the number of new components to the freshness of the final configuration. In this work we introduce a set of new criteria that allow the users to specify their preferences for solutions with components aligned to the same upstream sources, provide an efficient encoding and report on the experimental results that prove that optimising these alignment criteria is a tractable problem in practice.

  1. 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.

  2. Alignment of concerns

    DEFF Research Database (Denmark)

    Andersen, Tariq Osman; Bansler, Jørgen P.; Kensing, Finn;

    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 insight...... 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’....

  3. Nuclear reactor alignment plate configuration

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Orbit IMU alignment: Error analysis

    Science.gov (United States)

    Corson, R. W.

    1980-01-01

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

  5. 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...

  6. RECAT - Redundant Channel Alignment Technique

    Science.gov (United States)

    2016-06-07

    distribution unlimited 13. SUPPLEMENTARY NOTES NUWC2015 14. ABSTRACT A problem in the analog-to- digital , (A/D), conversion of broadband tape recorded...Alignment Technique, is used to align data taken on one pass with data from any other pass. The accuracy of this alignment is a function of the digital ...Redundant Channel Alignment Technique; analog-to- digital ; A/D; Broadband Bearing Time Processing 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF

  7. Method for alignment of microwires

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-01-24

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

  8. 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...... connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster...

  9. ATLAS Inner Detector Alignment

    CERN Document Server

    Bocci, A

    2008-01-01

    The ATLAS experiment is a multi-purpose particle detector that will study high-energy particle collisions produced by the Large Hadron Collider at CERN. In order to achieve its physics goals, the ATLAS tracking requires that the positions of the silicon detector elements have to be known to a precision better than 10 μm. Several track-based alignment algorithms have been developed for the Inner Detector. An extensive validation has been performed with simulated events and real data coming from the ATLAS. Results from such validation are reported in this paper.

  10. CELT optics Alignment Procedure

    Science.gov (United States)

    Mast, Terry S.; Nelson, Jerry E.; Chanan, Gary A.; Noethe, Lothar

    2003-01-01

    The California Extremely Large Telescope (CELT) is a project to build a 30-meter diameter telescope for research in astronomy at visible and infrared wavelengths. The current optical design calls for a primary, secondary, and tertiary mirror with Ritchey-Chretién foci at two Nasmyth platforms. The primary mirror is a mosaic of 1080 actively-stabilized hexagonal segments. This paper summarizes a CELT report that describes a step-by-step procedure for aligning the many degrees of freedom of the CELT optics.

  11. TSGC and JSC Alignment

    Science.gov (United States)

    Sanchez, Humberto

    2013-01-01

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

  12. 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...

  13. Testing the tidal alignment model of galaxy intrinsic alignment

    CERN Document Server

    Blazek, Jonathan; Seljak, Uros

    2011-01-01

    Weak gravitational lensing has become a powerful probe of large-scale structure and cosmological parameters. Precision weak lensing measurements require an understanding of the intrinsic alignment of galaxy ellipticities, which can in turn inform models of galaxy formation. It is hypothesized that elliptical galaxies align with the background tidal field and that this alignment mechanism dominates the correlation between ellipticities on cosmological scales (in the absence of lensing). We use recent large-scale structure measurements from the Sloan Digital Sky Survey to test this picture with several statistics: (1) the correlation between ellipticity and galaxy overdensity, w_{g+}; (2) the intrinsic alignment auto-correlation functions; (3) the correlation functions of curl-free, E, and divergence-free, B, modes (the latter of which is zero in the linear tidal alignment theory); (4) the alignment correlation function, w_g(r_p,theta), a recently developed statistic that generalizes the galaxy correlation func...

  14. Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

    Science.gov (United States)

    Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

    2016-03-01

    Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

  15. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  16. Onorbit IMU alignment error budget

    Science.gov (United States)

    Corson, R. W.

    1980-01-01

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

  17. Lunar Alignments - Identification and Analysis

    Science.gov (United States)

    González-García, A. César

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

  18. 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.

  19. 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.

  20. Mask alignment system for semiconductor processing

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-02-14

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

  1. CATO: The Clone Alignment Tool.

    Directory of Open Access Journals (Sweden)

    Peter V Henstock

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

  2. CATO: The Clone Alignment Tool.

    Science.gov (United States)

    Henstock, Peter V; LaPan, Peter

    2016-01-01

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

  3. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan

    2014-01-01

    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 alig...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter.......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...... two or more sequences. The advantage of this algorithm over those that separate the folding and alignment steps is that it makes better predictions. The disadvantage is that it is slower and requires more computer memory to run. The amount of computational resources needed to run the Sankoff algorithm...

  4. Lexical alignment in triadic communication.

    Science.gov (United States)

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

    2015-01-01

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

  5. Vacuum Alignment with more Flavors

    DEFF Research Database (Denmark)

    Ryttov, Thomas

    2014-01-01

    We study the alignment of the vacuum in gauge theories with $N_f$ Dirac fermions transforming according to a complex representation of the gauge group. The alignment of the vacuum is produced by adding a small mass perturbation to the theory. We study in detail the $N_f=2,3$ and $4$ case. For $N...

  6. 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.

  7. Alignment of flexible protein structures.

    Science.gov (United States)

    Shatsky, M; Fligelman, Z Y; Nussinov, R; Wolfson, H J

    2000-01-01

    We present two algorithms which align flexible protein structures. Both apply efficient structural pattern detection and graph theoretic techniques. The FlexProt algorithm simultaneously detects the hinge regions and aligns the rigid subparts of the molecules. It does it by efficiently detecting maximal congruent rigid fragments in both molecules and calculating their optimal arrangement which does not violate the protein sequence order. The FlexMol algorithm is sequence order independent, yet requires as input the hypothesized hinge positions. Due its sequence order independence it can also be applied to protein-protein interface matching and drug molecule alignment. It aligns the rigid parts of the molecule using the Geometric Hashing method and calculates optimal connectivity among these parts by graph-theoretic techniques. Both algorithms are highly efficient even compared with rigid structure alignment algorithms. Typical running times on a standard desktop PC (400 MHz) are about 7 seconds for FlexProt and about 1 minute for FlexMol.

  8. 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.

  9. Downlink Interference Alignment

    CERN Document Server

    Suh, Changho; Tse, David

    2010-01-01

    We develop an interference alignment (IA) technique for a downlink cellular system. In the uplink, IA schemes need channel-state-information exchange across base-stations of different cells, but our downlink IA technique requires feedback only within a cell. As a result, the proposed scheme can be implemented with a few changes to an existing cellular system where the feedback mechanism (within a cell) is already being considered for supporting multi-user MIMO. Not only is our proposed scheme implementable with little effort, it can in fact provide substantial gain especially when interference from a dominant interferer (base-station) is significantly stronger than the remaining interference: it is shown that in the two-isolated cell layout, our scheme provides four-fold gain in throughput performance over a standard multi-user MIMO technique. We show through simulations that our technique provides respectable gain under more realistic scenarios: it gives approximately 55% and 20% gain for a linear cell layou...

  10. Interference Alignment for Secrecy

    CERN Document Server

    Koyluoglu, Onur Ozan; Lai, Lifeng; Poor, H Vincent

    2008-01-01

    This paper studies the frequency/time selective $K$-user Gaussian interference channel with secrecy constraints. Two distinct models, namely the interference channel with confidential messages and the one with an external eavesdropper, are analyzed. The key difference between the two models is the lack of channel state information (CSI) about the external eavesdropper. Using interference alignment along with secrecy pre-coding, it is shown that each user can achieve non-zero secure Degrees of Freedom (DoF) for both cases. More precisely, the proposed coding scheme achieves $\\frac{K-2}{2K-2}$ secure DoF {\\em with probability one} per user in the confidential messages model. For the external eavesdropper scenario, on the other hand, it is shown that each user can achieve $\\frac{K-2}{2K}$ secure DoF {\\em in the ergodic setting}. Remarkably, these results establish the {\\em positive impact} of interference on the secrecy capacity region of wireless networks.

  11. Space Mirror Alignment System

    Science.gov (United States)

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

    2011-01-01

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

  12. Magnetic alignment and the Poisson alignment reference system

    Science.gov (United States)

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

    1990-08-01

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

  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. Magnetic axis alignment and the Poisson alignment reference system

    Science.gov (United States)

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

    1989-01-01

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

  15. RF Jitter Modulation Alignment Sensing

    Science.gov (United States)

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

    2017-01-01

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

  16. Sensing Characteristics of A Precision Aligner Using Moire Gratings for Precision Alignment System

    Institute of Scientific and Technical Information of China (English)

    ZHOU Lizhong; Hideo Furuhashi; Yoshiyuki Uchida

    2001-01-01

    Sensing characteristics of a precision aligner using moire gratings for precision alignment sysem has been investigated. A differential moire alignment system and a modified alignment system were used. The influence of the setting accuracy of the gap length and inclination of gratings on the alignment accuracy has been studied experimentally and theoretically. Setting accuracy of the gap length less than 2.5μm is required in modified moire alignment. There is no influence of the gap length on the alignment accuracy in the differential alignment system. The inclination affects alignment accuracies in both differential and modified moire alignment systems.

  17. DIDA: Distributed Indexing Dispatched Alignment.

    Directory of Open Access Journals (Sweden)

    Hamid Mohamadi

    Full Text Available One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through http://www.bcgsc.ca/platform/bioinfo/software/dida. The software is released under the British Columbia Cancer Agency License (BCCA, and is free for academic use.

  18. General Alignment Concept of the CMS experiment

    CERN Document Server

    Lampen, T

    2006-01-01

    Efficient and accurate track reconstruction requires proper alignment of the tracking devices used. Here we describe the general alignment strategy envisaged for the CMS experiment. The hardware alignment devices of CMS are presented as well as the different track based alignment approaches.

  19. Photosensitive Polymers for Liquid Crystal Alignment

    Science.gov (United States)

    Mahilny, U. V.; Stankevich, A. I.; Trofimova, A. V.; Muravsky, A. A.; Murauski, A. A.

    The peculiarities of alignment of liquid crystal (LC) materials by the layers of photocrosslinkable polymers with side benzaldehyde groups are considered. The investigation of mechanism of photostimulated alignment by rubbed benzaldehyde layer is performed. The methods of creation of multidomain aligning layers on the basis of photostimulated rubbing alignment are described.

  20. Alignment method for parabolic trough solar concentrators

    Science.gov (United States)

    Diver, Richard B.

    2010-02-23

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

  1. 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.

  2. Laser shaft alignment measurement model

    Science.gov (United States)

    Mo, Chang-tao; Chen, Changzheng; Hou, Xiang-lin; Zhang, Guoyu

    2007-12-01

    Laser beam's track which is on photosensitive surface of the a receiver will be closed curve, when driving shaft and the driven shaft rotate with same angular velocity and rotation direction. The coordinate of arbitrary point which is on the curve is decided by the relative position of two shafts. Basing on the viewpoint, a mathematic model of laser alignment is set up. By using a data acquisition system and a data processing model of laser alignment meter with single laser beam and a detector, and basing on the installation parameter of computer, the state parameter between two shafts can be obtained by more complicated calculation and correction. The correcting data of the four under chassis of the adjusted apparatus moving on the level and the vertical plane can be calculated. This will instruct us to move the apparatus to align the shafts.

  3. The alignment-distribution graph

    Science.gov (United States)

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

    1993-01-01

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

  4. 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.

  5. The Rigors of Aligning Performance

    Science.gov (United States)

    2015-06-01

    organization must consider and work closely with its many stakeholders so as to guarantee satisfaction ; this idea is especially important as there is no...define success. Methodology includes a literature review, employee and customer surveys and a Strength, Weaknesses, Opportunities, Threats...bearing in mind customer perceptions. Recommendations include employee training centered on goal alignment, which is vital to highlight the

  6. Aligning Assessments for COSMA Accreditation

    Science.gov (United States)

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

    2015-01-01

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

  7. 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.

  8. Progressive multiple sequence alignments from triplets

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2007-07-01

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

  9. Aligned Layers of Silver Nano-Fibers

    Directory of Open Access Journals (Sweden)

    Andrii B. Golovin

    2012-02-01

    Full Text Available 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 polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.

  10. Aligning seminars with Bologna requirements

    DEFF Research Database (Denmark)

    Lueg, Klarissa; Lueg, Rainer; Lauridsen, Ole

    2016-01-01

    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...

  11. 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.

  12. Shuttle onboard IMU alignment methods

    Science.gov (United States)

    Henderson, D. M.

    1976-01-01

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

  13. 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.

  14. The Cluster Substructure - Alignment Connection

    OpenAIRE

    Plionis, Manolis

    2001-01-01

    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 ...

  15. Grain alignment in starless cores

    Energy Technology Data Exchange (ETDEWEB)

    Jones, T. J.; Bagley, M. [Minnesota Institute for Astrophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Krejny, M. [Cree Inc., 4600 Silicon Dr., Durham, NC (United States); Andersson, B.-G. [SOFIA Science Center, USRA, Moffett Field, CA (United States); Bastien, P., E-mail: tjj@astro.umn.edu [Centre de recherche en astrophysique du Québec and Départment de Physique, Université de Montréal, Montréal (Canada)

    2015-01-01

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

  16. Cactus: Algorithms for genome multiple sequence alignment

    OpenAIRE

    Paten, Benedict; Earl, Dent; Nguyen, Ngan; Diekhans, Mark; Zerbino, Daniel; Haussler, David

    2011-01-01

    Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms...

  17. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    NARCIS (Netherlands)

    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 pr

  18. 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.

  19. An Overview of Multiple Sequence Alignment Systems

    CERN Document Server

    Saeed, Fahad

    2009-01-01

    An overview of current multiple alignment systems to date are described.The useful algorithms, the procedures adopted and their limitations are presented.We also present the quality of the alignments obtained and in which cases(kind of alignments, kind of sequences etc) the particular systems are useful.

  20. 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...

  1. Inferring comprehensible business/ICT alignment rules

    NARCIS (Netherlands)

    Cumps, B.; Martens, D.; De Backer, M.; Haesen, R.; Viaene, S.; Dedene, G.; Baesens, B.; Snoeck, M.

    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 reputati

  2. Shift dynamics of capillary self-alignment

    NARCIS (Netherlands)

    Arutinov, G.; Mastrangeli, M.; Smits, E.C.P.; Heck, G.V.; Schoo, H.F.M.; Toonder, J.J.M. den; Dietzel, A.H.

    2014-01-01

    This paper describes the dynamics of capillary self-alignment of components with initial shift offsets from matching receptor sites. The analysis of the full uniaxial self-alignment dynamics of foil-based mesoscopic dies from pre-alignment to final settling evidenced three distinct, sequential regim

  3. Alignment of lower-limb prostheses.

    Science.gov (United States)

    Zahedi, M S; Spence, W D; Solomonidis, S E; Paul, J P

    1986-04-01

    Alignment of a prosthesis is defined as the position of the socket relative to the other prosthetic components of the limb. During dynamic alignment the prosthetist, using subjective judgment and feedback from the patient, aims to achieve the most suitable limb geometry for best function and comfort. Until recently it was generally believed that a patient could only be satisfied with a unique "optimum alignment." The purpose of this systematic study of lower-limb alignment parameters was to gain an understanding of the factors that make a limb configuration or optimum alignment, acceptable to the patient, and to obtain a measure of the variation of this alignment that would be acceptable to the amputee. In this paper, the acceptable range of alignments for 10 below- and 10 above-knee amputees are established. Three prosthetists were involved in the majority of the 183 below-knee and 100 above-knee fittings, although several other prosthetists were also involved. The effects of each different prosthetist on the established range of alignment for each patient are reported to be significant. It is now established that an amputee can tolerate several alignments ranging in some parameters by as much as 148 mm in shifts and 17 degrees in tilts. This paper describes the method of defining and measuring the alignment of lower-limb prostheses. It presents quantitatively established values for bench alignment position and the range of adjustment required for incorporation into the design of new alignment units.

  4. Aligning Projection Images from Binary Volumes

    NARCIS (Netherlands)

    Bleichrodt, F.; Beenhouwer, J. de; Sijbers, J.; Batenburg, K.J.

    2014-01-01

    In tomography, slight differences between the geometry of the scanner hardware and the geometric model used in the reconstruction lead to alignment artifacts. To exploit high-resolution detectors used in many applications of tomography, alignment of the projection data is essential. Markerless align

  5. 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.

  6. 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 o...

  7. 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....

  8. Subsonic Mechanical Alignment of Irregular Grains

    CERN Document Server

    Lazarian, Alex

    2007-01-01

    We show that grains can be efficiently aligned by interacting with a subsonic gaseous flow. The alignment arises from grains having irregularities that scatter atoms with different efficiency in the right and left directions. The grains tend to align with long axes perpendicular to magnetic field, which corresponds to Davis-Greenstein predictions, but does not involve magnetic field. For rather conservative factors characterizing the grain helicity and scattering efficiency of impinging atoms, the alignment of helical grains is much more efficient than the Gold-type alignment processes.

  9. Galaxy alignments: Theory, modelling and simulations

    CERN Document Server

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

    2015-01-01

    The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in large-scale structure tend to align the shapes and angular momenta of nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both $N$-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the ...

  10. Alignment method for solar collector arrays

    Science.gov (United States)

    Driver, Jr., Richard B

    2012-10-23

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

  11. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

    Science.gov (United States)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra

    2013-04-01

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

  12. 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.

  13. 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.

  14. MEANS FOR DETERMINING CENTRIFUGE ALIGNMENT

    Science.gov (United States)

    Smith, W.Q.

    1958-08-26

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

  15. Velocity-aligned Doppler spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Z.; Koplitz, B.; Wittig, C.

    1989-03-01

    The technique of velocity-aligned Doppler spectrosocopy (VADS) is presented and discussed. For photolysis/probe experiments with pulsed initiation, VADS can yield Doppler profiles for nascent photofragments that allow detailed center-of-mass (c.m.) kinetic energy distributions to be extracted. When compared with traditional forms of Doppler spectroscopy, the improvement in kinetic energy resolution is dramatic. Changes in the measured profiles are a consequence of spatial discrimination (i.e., focused and overlapping photolysis and probe beams) and delayed observation. These factors result in the selective detection of species whose velocities are aligned with the wave vector of the probe radiation k/sub pr/, thus revealing the speed distribution along k/sub pr/ rather than the distribution of nascent velocity components projected upon this direction. Mathematical details of the procedure used to model VADS are given, and experimental illustrations for HI, H/sub 2/S, and NH/sub 3/ photodissociation are presented. In these examples, pulsed photodissociation produces H atoms that are detected by sequential two-photon, two-frequency ionization via Lyman-..cap alpha.. with a pulsed laser (121.6+364.7 nm), and measuring the Lyman-..cap alpha.. Doppler profile as a function of probe delay reveals both internal and c.m. kinetic energy distributions for the photofragments. Strengths and weaknesses of VADS as a tool for investigating photofragmentation phenomena are also discussed.

  16. Multiple sequence alignment accuracy and phylogenetic inference.

    Science.gov (United States)

    Ogden, T Heath; Rosenberg, Michael S

    2006-04-01

    Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our results indicate that as alignment error increases, topological accuracy decreases. This trend was much more pronounced for data sets derived from more pectinate topologies. In contrast, for balanced, ultrametric, equal branch length tree shapes, alignment inaccuracy had little average effect on tree reconstruction. These conclusions are based on average trends of many analyses under different conditions, and any one specific analysis, independent of the alignment accuracy, may recover very accurate or inaccurate topologies. Maximum likelihood and Bayesian, in general, outperformed neighbor joining and maximum parsimony in terms of tree reconstruction accuracy. Results also indicated that as the length of the branch and of the neighboring branches increase, alignment accuracy decreases, and the length of the neighboring branches is the major factor in topological accuracy. Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction.

  17. Galaxy alignment on large and small scales

    Science.gov (United States)

    Kang, X.; Lin, W. P.; Dong, X.; Wang, Y. O.; Dutton, A.; Macciò, A.

    2016-10-01

    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 extent of mis-alignment. The massive haloes have stronger alignment than haloes in filament which connect massive haloes. This is contrary to the naive expectation that cosmic filament is the cause of halo alignment.

  18. 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...

  19. 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

  20. 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.

  1. Velocity-aligned Doppler spectroscopy

    Science.gov (United States)

    Xu, Z.; Koplitz, B.; Wittig, C.

    1989-03-01

    The use of velocity-aligned Doppler spectroscopy (VADS) to measure center-of-mass kinetic-energy distributions of nascent photofragments produced in pulsed-initiation photolysis/probe experiments is described and demonstrated. In VADS, pulsed photolysis and probe laser beams counterpropagate through the ionization region of a time-of-flight mass spectrometer. The theoretical principles of VADS and the mathematical interpretation of VADS data are explained and illustrated with diagrams; the experimental setup is described; and results for the photodissociation of HI, H2S, and NH3 are presented in graphs and characterized in detail. VADS is shown to give much higher kinetic-energy resolution than conventional Doppler spectroscopy.

  2. Aligned carbon nanotubes for nanoelectronics

    Science.gov (United States)

    Choi, Won Bong; Bae, Eunju; Kang, Donghun; Chae, Soodoo; Cheong, Byung-ho; Ko, Ju-hye; Lee, Eungmin; Park, Wanjun

    2004-10-01

    We discuss the central issues to be addressed for realizing carbon nanotube (CNT) nanoelectronics. We focus on selective growth, electron energy bandgap engineering and device integration. We have introduced a nanotemplate to control the selective growth, length and diameter of CNTs. Vertically aligned CNTs are synthesized for developing a vertical CNT-field effect transistor (FET). The ohmic contact of the CNT/metal interface is formed by rapid thermal annealing. Diameter control, synthesis of Y-shaped CNTs and surface modification of CNTs open up the possibility for energy bandgap modulation. The concepts of an ultra-high density transistor based on the vertical-CNT array and a nonvolatile memory based on the top gate structure with an oxide-nitride-oxide charge trap are also presented. We suggest that the deposited memory film can be used for the quantum dot storage due to the localized electric field created by a nano scale CNT-electron channel.

  3. Microwave Emission from Aligned Dust

    CERN Document Server

    Lazarian, A

    2003-01-01

    Polarized microwave emission from dust is an important foreground that may contaminate polarized CMB studies unless carefully accounted for. We discuss potential difficulties associated with this foreground, namely, the existence of different grain populations with very different emission/polarization properties and variations of the polarization yield with grain temperature. In particular, we discuss observational evidence in favor of rotational emission from tiny PAH particles with dipole moments, i.e. ``spinning dust'', and also consider magneto-dipole emission from strongly magnetized grains. We argue that in terms of polarization, the magneto-dipole emission may dominate even if its contribution to total emissivity is subdominant. Addressing polarized emission at frequencies larger than approsimately 100 GHz, we discuss the complications arising from the existence of dust components with different temperatures and possibly different alignment properties.

  4. Multilingual alignments by monolingual string differences

    OpenAIRE

    Lardilleux, Adrien; Lepage, Yves

    2008-01-01

    International audience; We propose a method to obtain subsentential alignments from several languages simultaneously. The method handles several languages at once, and avoids the complexity explosion due to the usual pair-by-pair processing. It can be used for different units (characters, morphemes, words, chunks). An evaluation of word alignments with a trilingual machine translation corpus has been conducted. A comparison of the results with those obtained by state of the art alignment soft...

  5. Distributed Interference Alignment with Low Overhead

    CERN Document Server

    Ma, Yanjun; Chen, Rui

    2011-01-01

    Based on closed-form interference alignment (IA) solutions, a low overhead distributed interference alignment (LOIA) scheme is proposed in this paper for the $K$-user SISO interference channel, and extension to multiple antenna scenario is also considered. Compared with the iterative interference alignment (IIA) algorithm proposed by Gomadam et al., the overhead is greatly reduced. Simulation results show that the IIA algorithm is strictly suboptimal compared with our LOIA algorithm in the overhead-limited scenario.

  6. COS to FGS Alignment {NUV}

    Science.gov (United States)

    Hartig, George

    2009-07-01

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

  7. Some aspects of SR beamline alignment

    Energy Technology Data Exchange (ETDEWEB)

    Gaponov, Yu.A., E-mail: Yury.Gaponov@maxlab.lu.se [MAX-lab, Lund University, P.O.B. 118, SE-221 00 Lund (Sweden); Cerenius, Y. [MAX-lab, Lund University, P.O.B. 118, SE-221 00 Lund (Sweden); Nygaard, J. [Faculty of Life Sciences, University of Copenhagen, DK-1871 Frederiksberg C (Denmark); Ursby, T.; Larsson, K. [MAX-lab, Lund University, P.O.B. 118, SE-221 00 Lund (Sweden)

    2011-09-01

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

  8. The twilight zone of cis element alignments.

    Science.gov (United States)

    Sebastian, Alvaro; Contreras-Moreira, Bruno

    2013-02-01

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

  9. The art of editing RNA structural alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth

    2014-01-01

    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 re......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...

  10. 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.

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

    Science.gov (United States)

    Jordan, Gregory; Goldman, Nick

    2012-04-01

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

  12. Bayesian coestimation of phylogeny and sequence alignment

    Directory of Open Access Journals (Sweden)

    Jensen Jens

    2005-04-01

    Full Text Available Abstract Background Two central problems in computational biology are the determination of the alignment and phylogeny of a set of biological sequences. The traditional approach to this problem is to first build a multiple alignment of these sequences, followed by a phylogenetic reconstruction step based on this multiple alignment. However, alignment and phylogenetic inference are fundamentally interdependent, and ignoring this fact leads to biased and overconfident estimations. Whether the main interest be in sequence alignment or phylogeny, a major goal of computational biology is the co-estimation of both. Results We developed a fully Bayesian Markov chain Monte Carlo method for coestimating phylogeny and sequence alignment, under the Thorne-Kishino-Felsenstein model of substitution and single nucleotide insertion-deletion (indel events. In our earlier work, we introduced a novel and efficient algorithm, termed the "indel peeling algorithm", which includes indels as phylogenetically informative evolutionary events, and resembles Felsenstein's peeling algorithm for substitutions on a phylogenetic tree. For a fixed alignment, our extension analytically integrates out both substitution and indel events within a proper statistical model, without the need for data augmentation at internal tree nodes, allowing for efficient sampling of tree topologies and edge lengths. To additionally sample multiple alignments, we here introduce an efficient partial Metropolized independence sampler for alignments, and combine these two algorithms into a fully Bayesian co-estimation procedure for the alignment and phylogeny problem. Our approach results in estimates for the posterior distribution of evolutionary rate parameters, for the maximum a-posteriori (MAP phylogenetic tree, and for the posterior decoding alignment. Estimates for the evolutionary tree and multiple alignment are augmented with confidence estimates for each node height and alignment column

  13. Alignments between galaxies, satellite systems and haloes

    Science.gov (United States)

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

    2016-08-01

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

  14. AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

    OpenAIRE

    Krishnadev Oruganty; Srinivasan Narayanaswamy

    2011-01-01

    Abstract Background Sensitive remote homology detection and accurate alignments especially in the midnight zone of sequence similarity are needed for better function annotation and structural modeling of proteins. An algorithm, AlignHUSH for HMM-HMM alignment has been developed which is capable of recognizing distantly related domain families The method uses structural information, in the form of predicted secondary structure probabilities, and hydrophobicity of amino acids to align HMMs of t...

  15. Protein sequence alignment analysis by local covariation: coevolution statistics detect benchmark alignment errors.

    Directory of Open Access Journals (Sweden)

    Russell J Dickson

    Full Text Available The use of sequence alignments to understand protein families is ubiquitous in molecular biology. High quality alignments are difficult to build and protein alignment remains one of the largest open problems in computational biology. Misalignments can lead to inferential errors about protein structure, folding, function, phylogeny, and residue importance. Identifying alignment errors is difficult because alignments are built and validated on the same primary criteria: sequence conservation. Local covariation identifies systematic misalignments and is independent of conservation. We demonstrate an alignment curation tool, LoCo, that integrates local covariation scores with the Jalview alignment editor. Using LoCo, we illustrate how local covariation is capable of identifying alignment errors due to the reduction of positional independence in the region of misalignment. We highlight three alignments from the benchmark database, BAliBASE 3, that contain regions of high local covariation, and investigate the causes to illustrate these types of scenarios. Two alignments contain sequential and structural shifts that cause elevated local covariation. Realignment of these misaligned segments reduces local covariation; these alternative alignments are supported with structural evidence. We also show that local covariation identifies active site residues in a validated alignment of paralogous structures. Loco is available at https://sourceforge.net/projects/locoprotein/files/.

  16. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

    The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...

  17. Business and IT alignment in context

    NARCIS (Netherlands)

    Silvius, A.J.G.

    2013-01-01

    Already for more than two decades, the necessity and desirability of aligning business needs and information technology (IT) capabilities is considered to be one of the key issues in IT management. However, several studies report quite low scores on business and IT alignment (BIA). The question “Why

  18. 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.

  19. 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...

  20. Compositions for directed alignment of conjugated polymers

    Science.gov (United States)

    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).

  1. 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…

  2. Probabilistic sequence alignment of stratigraphic records

    Science.gov (United States)

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

    2014-10-01

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

  3. 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

  4. Instructional Alignment under No Child Left Behind

    Science.gov (United States)

    Polikoff, Morgan S.

    2012-01-01

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

  5. Vacuum alignment with and without elementary scalars

    DEFF Research Database (Denmark)

    Alanne, Tommi; Gertov, Helene; Meroni, Aurora;

    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....

  6. Optical packet switching without packet alignment

    DEFF Research Database (Denmark)

    Hansen, Peter Bukhave; Danielsen, Søren Lykke; Stubkjær, Kristian

    1998-01-01

    Operation without packet alignment of an all-optical packet switch is proposed and predicted feasible through a detailed traffic analysis. Packet alignment units are eliminated resulting in a simple switch architecture while optimal traffic performance is maintained through the flexibility provided...

  7. Evaluating Alignment between Curriculum, Assessment, and Instruction

    Science.gov (United States)

    Martone, Andrea; Sireci, Stephen G.

    2009-01-01

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

  8. Partial Automated Alignment and Integration System

    Science.gov (United States)

    Kelley, Gary Wayne (Inventor)

    2014-01-01

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

  9. A precise CT phantom alignment procedure.

    Science.gov (United States)

    Schneiders, N J; Bushong, S C

    1980-01-01

    Two of the AAPM CT performance phantom inserts require precise alignment. We present a method for aligning an insert which makes use of the partial volume effect. We demonstrate that the procedure is sensitive to tilts of less than one degree and, using the slice thickness insert, allows reproducible positioning.

  10. 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

  11. Aligning application architecture to the business context

    NARCIS (Netherlands)

    Wieringa, R.J.; Blanken, H.M.; Fokkinga, M.M.; Grefen, P.W.P.J.; Eder, J.; Missikoff, M.

    2003-01-01

    Alignment of application architecture to business architecture is a central problem in the design, acquisition and implementation of information systems in current large-scale information-processing organizations. Current research in architecture alignment is either too strategic or too software imp

  12. What is the Constructivism in Constructive Alignment?

    Science.gov (United States)

    Jervis, Loretta M.; Jervis, Les

    2005-01-01

    This paper examines the concept of constructive alignment in respect of science education. The concept is placed in the context of its two contributory components--constructivism and instructional alignment. The former has a well-established body of critical literature that highlights the challenges of constructivism for both science and science…

  13. 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.

  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. Accelerated large-scale multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Lloyd Scott

    2011-12-01

    Full Text Available Abstract Background Multiple sequence alignment (MSA is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations according to Amdahl's Law. This work is the first known to accelerate the third stage of progressive alignment on reconfigurable hardware. Results We reduce subgroups of aligned sequences into discrete profiles before they are pairwise aligned on the accelerator. Using an FPGA accelerator, an overall speedup of up to 150 has been demonstrated on a large data set when compared to a 2.4 GHz Core2 processor. Conclusions Our parallel algorithm and architecture accelerates large-scale MSA with reconfigurable computing and allows researchers to solve the larger problems that confront biologists today. Program source is available from http://dna.cs.byu.edu/msa/.

  16. Alignment-free phylogenetics and population genetics.

    Science.gov (United States)

    Haubold, Bernhard

    2014-05-01

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

  17. 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 ...

  18. Grassmannian Differential Limited Feedback for Interference Alignment

    CERN Document Server

    Ayach, Omar El

    2011-01-01

    Channel state information (CSI) in the interference channel can be used to precode, align, and reduce the dimension of interference at the receivers, to achieve the channel's maximum multiplexing gain, through what is known as interference alignment. Most interference alignment algorithms require knowledge of all the interfering channels to compute the alignment precoders. CSI, considered available at the receivers, can be shared with the transmitters via limited feedback. When alignment is done by coding over frequency extensions in a single antenna system, the required CSI lies on the Grassmannian manifold and its structure can be exploited in feedback. Unfortunately, the number of channels to be shared grows with the square of the number of users creating too much overhead with conventional feedback methods. This paper proposes Grassmannian differential feedback to reduce feedback overhead by exploiting both the channel's temporal correlation and Grassmannian structure. The performance of the proposed algo...

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

    Science.gov (United States)

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

    2010-01-01

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

  20. Algorithms for Automatic Alignment of Arrays

    Science.gov (United States)

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

    1996-01-01

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

  1. 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.

  2. 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...

  3. Sparse alignment for robust tensor learning.

    Science.gov (United States)

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

    2014-10-01

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

  4. Coelostat and heliostat - Theory of alignment

    Science.gov (United States)

    Demianski, M.; Pasachoff, J. M.

    1984-06-01

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

  5. Rotational Alignment Altered by Source Position Correlations

    Science.gov (United States)

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

    2010-01-01

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

  6. Robust and resistant 2D shape alignment

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Eiriksson, Hrafnkell

    2001-01-01

    \\_\\$\\backslash\\$infty\\$ norm alignments are formulated as linear programming problems. The linear vector function formulation along with the different norms results in alignment methods that are both resistant from influence from outliers, robust wrt. errors in the annotation and capable of handling missing datapoints......We express the alignment of 2D shapes as the minimization of the norm of a linear vector function. The minimization is done in the \\$l\\_1\\$, \\$l\\_2\\$ and the \\$l\\_\\$\\backslash\\$infty\\$ norms using well known standard numerical methods. In particular, the \\$l\\_1\\$ and the \\$l...

  7. 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.

  8. Aligning parallel arrays to reduce communication

    Science.gov (United States)

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

    1994-01-01

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

  9. Alignment free characterization of 2D gratings

    CERN Document Server

    Madsen, Morten Hannibal; Hansen, Poul-Erik; Jørgensen, Jan Friis

    2015-01-01

    Fast characterization of 2-dimensional gratings is demonstrated using a Fourier lens optical system and a differential optimization algorithm. It is shown that both the grating specific parameters such as the basis vectors and the angle between them and the alignment of the sample, such as the rotation of the sample around the x-, y-, and z-axis, can be deduced from a single measurement. More specifically, the lattice vectors and the angle between them have been measured, while the corrections of the alignment parameters are used to improve the quality of the measurement, and hence reduce the measurement uncertainty. Alignment free characterization is demonstrated on both a 2D hexagonal grating with a period of 700 nm and a checkerboard grating with a pitch of 3000 nm. The method can also be used for both automatic alignment and in-line characterization of gratings.

  10. 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}.

  11. 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).

  12. Robust and Efficient Parametric Face Alignment

    NARCIS (Netherlands)

    Tzimiropoulos, Georgios; Zafeiriou, Stefanos; Pantic, Maja

    2011-01-01

    We propose a correlation-based approach to parametric object alignment particularly suitable for face analysis applications which require efficiency and robustness against occlusions and illumination changes. Our algorithm registers two images by iteratively maximizing their correlation coefficient

  13. Molecular focusing and alignment with plasmon fields.

    Science.gov (United States)

    Artamonov, Maxim; Seideman, Tamar

    2010-12-01

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

  14. 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.

  15. The Nonlinear Evolution of Galaxy Intrinsic Alignments

    OpenAIRE

    Lee, Jounghun; Pen, Ue-Li

    2007-01-01

    The non-Gaussian contribution to the intrinsic halo spin alignments is analytically modeled and numerically detected. Assuming that the growth of non-Gaussianity in the density fluctuations caused the tidal field to have nonlinear-order effect on the orientations of the halo angular momentum, we model the intrinsic halo spin alignments as a linear scaling of the density correlations on large scales, which is different from the previous quadratic-scaling model based on the linear tidal torque ...

  16. 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.

  17. Aligned natural inflation: Monodromies of two axions

    Directory of Open Access Journals (Sweden)

    Rolf Kappl

    2014-10-01

    Full Text Available Natural (axionic inflation [1] can accommodate sizeable primordial tensor modes but suffers from the necessity of trans-Planckian variations of the inflaton field. This problem can be solved via the mechanism of aligned axions [2], where the aligned axion spirals down in the potential of other axions. We elaborate on the mechanism in view of the recently reported observations of the BICEP2 collaboration [3].

  18. Aligned natural inflation: Monodromies of two axions

    Energy Technology Data Exchange (ETDEWEB)

    Kappl, Rolf, E-mail: kappl@th.physik.uni-bonn.de; Krippendorf, Sven, E-mail: krippendorf@th.physik.uni-bonn.de; Nilles, Hans Peter, E-mail: nilles@th.physik.uni-bonn.de

    2014-10-07

    Natural (axionic) inflation [1] can accommodate sizeable primordial tensor modes but suffers from the necessity of trans-Planckian variations of the inflaton field. This problem can be solved via the mechanism of aligned axions [2], where the aligned axion spirals down in the potential of other axions. We elaborate on the mechanism in view of the recently reported observations of the BICEP2 collaboration [3].

  19. 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).

  20. 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 ...

  1. Radiative torque alignment: Essential Physical Processes

    CERN Document Server

    Hoang, Thiem

    2007-01-01

    We study physical processes that affect the alignment of grains subject to radiative torques (RATs). To describe the action of the RATs we use the analytical model (AMO) of RATs introduced in Paper I, namely, in Lazarian & Hoang (2007). We focus our discussion on the RAT alignment by anisotropic radiation flux in respect to magnetic field. Such an alignment does not invoke paramagnetic, i.e. Davis-Greenstein, dissipation, but, nevertheless, grains tend to align with long axes perpendicular to magnetic field. We use phase space trajectory maps to describe the alignment. When we account for thermal fluctuations within grain material, we show that for grains, which are characterized by a triaxial ellipsoid of inertia, the zero-J attractor point obtained in our earlier study develops into a low-J attractor point. Value at the latter point is the order of thermal angular momentum corresponding to the grain temperature. We show that the alignment of grains with long axes parallel to magnetic field (``wrong alig...

  2. 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...

  3. The Galaxy Alignment Effect in Abell 1689

    Science.gov (United States)

    Hung, Li-wei; Banados, E.; De Propris, R.; West, M. J.

    2011-01-01

    We examined alignments for galaxies in the galaxy cluster Abell 1689 (z = 0.18) based on archival Hubble Space Telescope WFPC2 F606W and F814W images. The sources were extracted using SExtractor. We used distance from the color-magnitud relation (defined by the bright galaxies) as a proxy to select likely cluster members. We carried out a series of simulations with artificial galaxies in order to understand the limit of our position angle measurement. Based on the cluster member selection and the result of our simulations, we isolated a sample of galaxies lying on the red sequence with I 0.2 to study the alignment effect. By applying the Kuiper test, we find evidence of alignment among faint galaxies and galaxies in the inner 500 kpc of the cluster. The best mechanism to produce this alignment result is tidal torquing. Akin to the Earth-Moon system, tidal effects would (re)create alignments between galaxies. Under the presence of the tidal field, fainter galaxies, especially in the center, will align themselves more rapidly than brighter galaxies.

  4. Can technology improve alignment during knee arthroplasty.

    Science.gov (United States)

    Thienpont, Emmanuel; Fennema, Peter; Price, Andrew

    2013-09-01

    Component malalignment remains a concern in total knee arthroplasty (TKA); therefore, a series of technologies have been developed to improve alignment. The authors conducted a systematic review to compare computer-assisted navigation with conventional instrumentation, and assess the current evidence for patient-matched instrumentation and robot-assisted implantation. An extensive search of the PubMed database for relevant meta-analyses, systematic reviews and original articles was performed, with each study scrutinised by two reviewers. Data on study characteristics and outcomes were extracted from each study and compared. In total 30 studies were included: 10 meta-analyses comparing computer-assisted navigation and conventional instrumentation, 13 studies examining patient-matched instrumentation, and seven investigating robot-assisted implantation. Computer-assisted navigation showed significant and reproducible improvements in mechanical alignment over conventional instrumentation. Patient-matched instrumentation appeared to achieve a high degree of mechanical alignment, although the majority of studies were of poor quality. The data for robot-assisted surgery was less indicative. Computer-assisted navigation improves alignment during TKA over conventional instrumentation. For patient-matched instrumentation and robot-assisted implantation, alignment benefits have not been reliably demonstrated. For all three technologies, clinical benefits cannot currently be assumed, and further studies are required. Although current technologies to improve alignment during TKA appear to result in intra-operative benefits, their clinical impact remains unclear, and surgeons should take this into account when considering their adoption.

  5. Mango: multiple alignment with N gapped oligos.

    Science.gov (United States)

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2008-06-01

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

  6. 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.

  7. LCLS Undulator Commissioning, Alignment, and Performance

    Energy Technology Data Exchange (ETDEWEB)

    Nuhn, Heinz-Dieter

    2009-10-30

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

  8. 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.

  9. 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.

  10. 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.

  11. Nuclear Spin Alignment and Alignment Correlation Terms in Mass A = 8 System

    Energy Technology Data Exchange (ETDEWEB)

    Sumikama, T., E-mail: sumikama@riken.jp [RIKEN (Japan); Iwakoshi, T.; Nagatomo, T.; Ogura, M.; Nakashima, Y.; Fujiwara, H.; Matsuta, K.; Minamisono, T.; Mihara, M.; Fukuda, M. [Osaka University, Department of Physics (Japan); Minamisono, K. [TRIUMF (Canada); Yamaguchi, T. [Saitama University, Department of Physics (Japan)

    2004-12-15

    The pure nuclear spin alignments of {sup 8}Li and {sup 8}B were produced from the nuclear spin polarization applying the {beta}-NMR method. The alignment correlation terms in the {beta}-ray angular distribution were observed to test the G parity conservation in the nuclear {beta} decay.

  12. 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...

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

    Science.gov (United States)

    2010-07-01

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

  14. Measuring prosodic alignment in cooperative task-based conversations

    NARCIS (Netherlands)

    Truong, Khiet P.; Heylen, Dirk

    2012-01-01

    In this paper, we investigate prosodic alignment in task-based conversations. We use the HCRC Map Task Corpus and investigate how familiarity affects prosodic alignment and how task success is related to prosodic alignment. A variety of existing alignment measures is used and applied to our data. In

  15. Self-Aligned Interdigitated Transducers for Acoustofluidics

    Directory of Open Access Journals (Sweden)

    Zhichao Ma

    2016-11-01

    Full Text Available The surface acoustic wave (SAW is effective for the manipulation of fluids and particles at microscale. The current approach of integrating interdigitated transducers (IDTs for SAW generation into microfluidic channels involves complex and laborious microfabrication steps. These steps often require full access to clean room facilities and hours to align the transducers to the precise location. This work presents an affordable and innovative method for fabricating SAW-based microfluidic devices without the need for clean room facilities and alignment. The IDTs and microfluidic channels are fabricated using the same process and thus are precisely self-aligned in accordance with the device design. With the use of the developed fabrication approach, a few types of different SAW-based microfluidic devices have been fabricated and demonstrated for particle separation and active droplet generation.

  16. 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.

  17. High-harmonic spectroscopy of aligned molecules

    Science.gov (United States)

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

    2017-01-01

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

  18. 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.

  19. 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.

  20. 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.

  1. LumiCal alignment system - Status report

    CERN Document Server

    Daniluk, W.; Lesiak, T.; Moszczyński, A.; Pawlik, B.; Wojtoń, T.; Zawiejski, L.

    2015-01-01

    The paper describes the status of the laser-based alignment-system for the luminosity detector, LumiCal, taking into considerations the conditions of the International Large Detector in the International Linear Collider project. The design of the system comprises two parts: the first one containing semi-transparent silicon sensors used to deliver simultaneous position measurements in the X,Y directions of the monitored object, and the second one in which the interferometric technique, i.e. the Frequency Scanning Interferometry (FSI), is proposed. Two laboratory prototypes for both components of the system were built and the preliminary measurements of the DUT displacements demonstrated their utility in the design of the final alignment system. The alignment of the LumiCal detector will allow us to monitor the detector displacements and possible deformations in its internal structure. Lack of information of the displacements will introduce a systematic effect which will have an impact on the accuracy of the fi...

  2. Purification process for vertically aligned carbon nanofibers

    Science.gov (United States)

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

    2003-01-01

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

  3. Mechanical alignment of substrates to a mask

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-11-08

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

  4. 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.

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

    Science.gov (United States)

    Chavez, Melissa A.

    2011-01-01

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

  6. Spatial and kinematic alignments between central and satellite halos

    OpenAIRE

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

    2007-01-01

    Based on a cosmological N-body simulation we analyze spatial and kinematic alignments of satellite halos within six times the virial radius of group size host halos (Rvir). We measure three different types of spatial alignment: halo alignment between the orientation of the group central substructure (GCS) and the distribution of its satellites, radial alignment between the orientation of a satellite and the direction towards its GCS, and direct alignment between the orientation of the GCS and...

  7. Alignment of D-state Rydberg molecules

    CERN Document Server

    Krupp, Alexander T; Balewski, Jonathan B; Ilzhöfer, Philipp; Hofferberth, Sebastian; Löw, Robert; Pfau, Tilman; Kurz, Markus; Schmelcher, Peter

    2014-01-01

    We report on the formation of ultralong-range Rydberg D-state molecules via photoassociation in an ultracold cloud of rubidium atoms. By applying a magnetic offset field on the order of 10 G and high resolution spectroscopy, we are able to resolve individual rovibrational molecular states. A full theory, using the Born-Oppenheimer approximation including s- and p-wave scattering, reproduces the measured binding energies. The calculated molecular wavefunctions show that in the experiment we can selectively excite stationary molecular states with an extraordinary degree of alignment or anti-alignment with respect to the magnetic field axis.

  8. Alignment Pins for Assembling and Disassembling Structures

    Science.gov (United States)

    Campbell, Oliver C.

    2008-01-01

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

  9. Fine alignment of a large segmented mirror

    Science.gov (United States)

    Dey, Thomas William (Inventor)

    2010-01-01

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

  10. 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...... for interference alignment. We also show that the iterative leakage minimization algorithm by Gomadam et al. and the alternating minimization algorithm by Peters and Heath, Jr. are instances of our method. Finally, we assess the performance of the proposed algorithm through computer simulations....

  11. Aligning the demonstration model of CHEOPS

    Science.gov (United States)

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

    2016-07-01

    CHEOPS (CHaracterizing ExOPlanets Satellite) is an ESA Small Mission, planned to be launched in mid-2018 and whose main goal is the photometric precise characterization of radii of exoplanets orbiting bright stars (Vflight representative and whose mechanics provides the same interfaces of the flight model, but is not thermally representative. In this paper, we describe CHEOPS Demonstration Model handling, integration, tests, alignment and characterization, emphasizing the verification of the uncertainties in the optical quality measurements introduced by the starlight simulator and the way the alignment and optical surfaces are measured.

  12. 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.

  13. Drift Chamber Alignment using Cosmic Rays

    CERN Document Server

    Kotwal, Ashutosh V

    2014-01-01

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

  14. Evaluation of alignment marks using ASML ATHENA alignment system in 90nm BEOL process

    CERN Document Server

    Tan Chin Boon; Koh Hui Peng; Koo Chee, Kiong; Siew Yong Kong; Yeo Swee Hock

    2003-01-01

    As the critical dimension (CD) in integrated circuit (IC) device reduces, the total overlay budget needs to be more stringent. Typically, the allowable overlay error is 1/3 of the CD in the IC device. In this case, robustness of alignment mark is critical, as accurate signal is required by the scanner's alignment system to precisely align a layer of pattern to the previous layer. Alignment issue is more severe in back-end process partly due to the influenced of Chemical Mechanical Polishing (CMP), which contribute to the asymmetric or total destruction of the alignment marks. Alignment marks on the wafer can be placed along the scribe-line of the IC pattern. ASML scanner allows such type of wafer alignment using phase grating mark, known as Scribe-line Primary Mark (SPM) which can be fit into a standard 80um scribe-line. In this paper, we have studied the feasibility of introducing Narrow SPM (NSPM) to enable a smaller scribe-line. The width of NSPM has been shrunk down to 70% of the SPM and the length remain...

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

    Science.gov (United States)

    Lizotte, Todd E.

    2011-10-01

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

  16. A situational alignment framework for PACS.

    NARCIS (Netherlands)

    Wetering, R. van de; Batenburg, R.; Oudkerk, M.; Ooijen, P. van; Brinkkemper, S.; Scheper, W.

    2011-01-01

    This paper reports the outcomes of a study on an integrated situational alignment framework for picture archiving and communication systems (PACS) labeled as PISA. Following the design research cycle, complementary validation methods and pilot cases were used to assess the proposed framework and its

  17. A Situational Alignment Framework for PACS

    NARCIS (Netherlands)

    van de Wetering, Rogier; Batenburg, Ronald; Oudkerk, Matthijs; van Ooijen, Peter; Brinkkemper, Sjaak; Scheper, Wim

    2011-01-01

    This paper reports the outcomes of a study on an integrated situational alignment framework for picture archiving and communication systems (PACS) labeled as PISA. Following the design research cycle, complementary validation methods and pilot cases were used to assess the proposed framework and its

  18. Aligning English Language Testing with Curriculum

    Science.gov (United States)

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

    2016-01-01

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

  19. 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 show...

  20. Alignment modification for pencil eye shields

    Energy Technology Data Exchange (ETDEWEB)

    Evans, M.D.; Pla, M.; Podgorsak, E.B. (McGill Univ., Quebec (Canada))

    1989-01-01

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

  1. 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

  2. Stimulating Strategically Aligned Behaviour Among Employees

    NARCIS (Netherlands)

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

    2007-01-01

    textabstractIn recent years it has become increasingly important for companies to ensure strategically aligned behaviour, i.e., employee actions that are consistent with the company’s strategy. This study provides insights into the way companies can stimulate such behaviour through motivating and in

  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 ...

  4. Using local alignments for relation recognition

    NARCIS (Netherlands)

    S. Katrenko; P. Adriaans; M. van Someren

    2010-01-01

    This paper discusses the problem of marrying structural similarity with semantic relatedness for Information Extraction from text. Aiming at accurate recognition of relations, we introduce local alignment kernels and explore various possibilities of using them for this task. We give a definition of

  5. Bokeh mirror alignment for Cherenkov telescopes

    Science.gov (United States)

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

    2016-09-01

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

  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. Face Alignment Using Boosting and Evolutionary Search

    NARCIS (Netherlands)

    Zhang, Hua; Liu, Duanduan; Poel, Mannes; Nijholt, Anton; Zha, H.; Taniguchi, R.-I.; Maybank, S.

    2010-01-01

    In this paper, we present a face alignment approach using granular features, boosting, and an evolutionary search algorithm. Active Appearance Models (AAM) integrate a shape-texture-combined morphable face model into an efficient fitting strategy, then Boosting Appearance Models (BAM) consider the f

  8. 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.

  9. 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

  10. Image Alignment by Piecewise Planar Region Matching

    NARCIS (Netherlands)

    Lou, Z.; Gevers, T.

    2014-01-01

    Robust image registration is a challenging problem, especially when dealing with severe changes in illumination and viewpoint. Previous methods assume a global geometric model (e.g., homography) and, hence, are only able to align images under predefined constraints (e.g., planar scenes and parallax-

  11. Security Policy Alignment: A Formal Approach

    NARCIS (Netherlands)

    Pieters, W.; Dimkov, T.; Pavlovic, D.

    2012-01-01

    Security policy alignment concerns the matching of security policies specified at different levels in socio-technical systems, and delegated to different agents, technical and human. For example, the policy that sales data should not leave an organization is refined into policies on door locks, fire

  12. Microvariation in Accentual Alignment in Basque Spanish

    Science.gov (United States)

    Elordieta, Gorka; Calleja, Nagore

    2005-01-01

    This paper presents patterns of accentual alignment in two varieties of Spanish spoken in the Basque Country: Lekeitio Spanish (LS), with speakers whose other native language is Lekeitio Basque (LB); and Vitoria Spanish (VS), with monolingual speakers of Spanish from the city of Vitoria. These patterns are compared to those of Madrid Spanish (MS),…

  13. 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…

  14. Alignment correlation term in the {beta}-ray angular distribution from spin aligned {sup 20}Na

    Energy Technology Data Exchange (ETDEWEB)

    Minamisono, K. [TRIUMF, 4004 Wesbrook Mall, Vancouver, B. C., V6T 2A3 (Canada); Matsuta, K. [Department of Physics, Osaka University, Toyonaka 560-0043, Osaka (Japan); Minamisono, T. [Department of Physics, Osaka University, Toyonaka 560-0043, Osaka (Japan); Levy, C.D.P. [TRIUMF, 4004 Wesbrook Mall, Vancouver, B. C., V6T 2A3 (Canada); Nagatomo, T. [Department of Physics, Osaka University, Toyonaka 560-0043, Osaka (Japan); Ogura, M. [Department of Physics, Osaka University, Toyonaka 560-0043, Osaka (Japan); Sumikama, T. [Department of Physics, Osaka University, Toyonaka 560-0043, Osaka (Japan); Behr, J.A. [TRIUMF, 4004 Wesbrook Mall, Vancouver, B. C., V6T 2A3 (Canada); Jackson, K.P. [TRIUMF, 4004 Wesbrook Mall, Vancouver, B. C., V6T 2A3 (Canada); Fujiwara, H. [Department of Physics, Osaka University, Toyonaka 560-0043, Osaka (Japan); Mihara, M. [Department of Physics, Osaka University, Toyonaka 560-0043, Osaka (Japan); Fukuda, M. [Department of Physics, Osaka University, Toyonaka 560-0043, Osaka (Japan)

    2004-12-27

    The alignment correlation term in the {beta}-ray angular distribution from nuclear-spin aligned {sup 20}Na(I{sup {pi}} = 2{sup +}, T{sub 1/2} = 449.7 ms) has been measured for the first time. A large enhancement of the time component d in the main axial vector current was preliminarily obtained and the higher order matrices j{sub 2} and j{sub 3} were also evaluated. In order to extract very small G-parity violating induced tensor term, the alignment correlation term of the mirror partner {sup 20}F have to be measured.

  15. INFORMATION TECHNOLOGY STRATEGIC ALIGNMENT: ANALYSIS OF ALIGNMENT MODELS AND PROPOSALS FOR FUTURE RESEARCH

    Directory of Open Access Journals (Sweden)

    Fabrício Sobrosa Affeldt

    2009-10-01

    Full Text Available Information Technology (IT is a resource capable of supporting businesses, which provides agile operations and mobility and decision support tools. The link between IT and business strategy has been studied regarding the best fitted model to improve company performance. This paper analyzes, through bibliographic research, the strategic alignment concept and the evolution of the strategic alignment theoretical models that are considered references in this area. The paper presents a comparison between these referential models and some perspectives for future research related IT strategic alignment.

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

    CERN Document Server

    Chatrchyan, S; Sirunyan, A M; Adam, W; Arnold, B; Bergauer, H; Bergauer, T; Dragicevic, M; Eichberger, M; Erö, J; Friedl, M; Frühwirth, R; Ghete, V M; Hammer, J; Hänsel, S; Hoch, M; Hörmann, N; Hrubec, J; Jeitler, M; Kasieczka, G; Kastner, K; Krammer, M; Liko, D; Magrans de Abril, I; Mikulec, I; Mittermayr, F; Neuherz, B; Oberegger, M; Padrta, M; Pernicka, M; Rohringer, H; Schmid, S; Schöfbeck, R; Schreiner, T; Stark, R; Steininger, H; Strauss, J; Taurok, A; Teischinger, F; Themel, T; Uhl, D; Wagner, P; Waltenberger, W; Walzel, G; Widl, E; Wulz, C E; Chekhovsky, V; Dvornikov, O; Emeliantchik, I; Litomin, A; Makarenko, V; Marfin, I; Mossolov, V; Shumeiko, N; Solin, A; Stefanovitch, R; Suarez Gonzalez, J; Tikhonov, A; Fedorov, A; Karneyeu, A; Korzhik, M; Panov, V; Zuyeuski, R; Kuchinsky, P; Beaumont, W; Benucci, L; Cardaci, M; De Wolf, E A; Delmeire, E; Druzhkin, D; Hashemi, M; Janssen, X; Maes, T; Mucibello, L; Ochesanu, S; Rougny, R; Selvaggi, M; Van Haevermaet, H; Van Mechelen, P; Van Remortel, N; Adler, V; Beauceron, S; Blyweert, S; D'Hondt, J; De Weirdt, S; Devroede, O; Heyninck, J; Kalogeropoulos, A; Maes, J; Maes, M; Mozer, M U; Tavernier, S; Van Doninck, W; Van Mulders, P; Villella, I; Bouhali, O; Chabert, E C; Charaf, O; Clerbaux, B; De Lentdecker, G; Dero, V; Elgammal, S; Gay, A P R; Hammad, G H; Marage, P E; Rugovac, S; Vander Velde, C; Vanlaer, P; Wickens, J; Grunewald, M; Klein, B; Marinov, A; Ryckbosch, D; Thyssen, F; Tytgat, M; Vanelderen, L; Verwilligen, P; Basegmez, S; Bruno, G; Caudron, J; Delaere, C; Demin, P; Favart, D; Giammanco, A; Grégoire, G; Lemaitre, V; Militaru, O; Ovyn, S; Piotrzkowski, K; Quertenmont, L; Schul, N; Beliy, N; Daubie, E; Alves, G A; Pol, M E; Souza, M H G; Carvalho, W; De Jesus Damiao, D; De Oliveira Martins, C; Fonseca De Souza, S; Mundim, L; Oguri, V; Santoro, A; Silva Do Amaral, S M; Sznajder, A; Fernandez Perez Tomei, T R; Ferreira Dias, M A; Gregores, E M; Novaes, S F; Abadjiev, K; Anguelov, T; Damgov, J; Darmenov, N; Dimitrov, L; Genchev, V; Iaydjiev, P; Piperov, S; Stoykova, S; Sultanov, G; Trayanov, R; Vankov, I; Dimitrov, A; Dyulendarova, M; Kozhuharov, V; Litov, L; Marinova, E; Mateev, M; Pavlov, B; Petkov, P; Toteva, Z; Chen, G M; Chen, H S; Guan, W; Jiang, C H; Liang, D; Liu, B; Meng, X; Tao, J; Wang, J; Wang, Z; Xue, Z; Zhang, Z; Ban, Y; Cai, J; Ge, Y; Guo, S; Hu, Z; Mao, Y; Qian, S J; Teng, H; Zhu, B; Avila, C; Baquero Ruiz, M; Carrillo Montoya, C A; Gomez, A; Gomez Moreno, B; Ocampo Rios, A A; Osorio Oliveros, A F; Reyes Romero, D; Sanabria, J C; Godinovic, N; Lelas, K; Plestina, R; Polic, D; Puljak, I; Antunovic, Z; Dzelalija, M; Brigljevic, V; Duric, S; Kadija, K; Morovic, S; Fereos, R; Galanti, M; Mousa, J; Papadakis, A; Ptochos, F; Razis, P A; Tsiakkouri, D; Zinonos, Z; Hektor, A; Kadastik, M; Kannike, K; Müntel, M; Raidal, M; Rebane, L; Anttila, E; Czellar, S; Härkönen, J; Heikkinen, A; Karimäki, V; Kinnunen, R; Klem, J; Kortelainen, M J; Lampén, T; Lassila-Perini, K; Lehti, S; Lindén, T; Luukka, P; Mäenpää, T; Nysten, J; Tuominen, E; Tuominiemi, J; Ungaro, D; Wendland, L; Banzuzi, K; Korpela, A; Tuuva, T; Nedelec, P; Sillou, D; Besancon, M; Chipaux, R; Dejardin, M; Denegri, D; Descamps, J; Fabbro, B; Faure, J L; Ferri, F; Ganjour, S; Gentit, F X; Givernaud, A; Gras, P; Hamel de Monchenault, G; Jarry, P; Lemaire, M C; Locci, E; Malcles, J; Marionneau, M; Millischer, L; Rander, J; Rosowsky, A; Rousseau, D; Titov, M; Verrecchia, P; Baffioni, S; Bianchini, L; Bluj, M; Busson, P; Charlot, C; Dobrzynski, L; Granier de Cassagnac, R; Haguenauer, M; Miné, P; Paganini, P; Sirois, Y; Thiebaux, C; Zabi, A; Agram, J L; Besson, A; Bloch, D; Bodin, D; Brom, J M; Conte, E; Drouhin, F; Fontaine, J C; Gelé, D; Goerlach, U; Gross, L; Juillot, P; Le Bihan, A C; Patois, Y; Speck, J; Van Hove, P; Baty, C; Bedjidian, M; Blaha, J; Boudoul, G; Brun, H; Chanon, N; Chierici, R; Contardo, D; Depasse, P; Dupasquier, T; El Mamouni, H; Fassi, F; Fay, J; Gascon, S; Ille, B; Kurca, T; Le Grand, T; Lethuillier, M; Lumb, N; Mirabito, L; Perries, S; Vander Donckt, M; Verdier, P; Djaoshvili, N; Roinishvili, N; Roinishvili, V; Amaglobeli, N; Adolphi, R; Anagnostou, G; Brauer, R; Braunschweig, W; Edelhoff, M; Esser, H; Feld, L; Karpinski, W; Khomich, A; Klein, K; Mohr, N; Ostaptchouk, A; Pandoulas, D; Pierschel, G; Raupach, F; Schael, S; Schultz von Dratzig, A; Schwering, G; Sprenger, D; Thomas, M; Weber, M; Wittmer, B; Wlochal, M; Actis, O; Altenhöfer, G; Bender, W; Biallass, P; Erdmann, M; Fetchenhauer, G; Frangenheim, J; Hebbeker, T; Hilgers, G; Hinzmann, A; Hoepfner, K; Hof, C; Kirsch, M; Klimkovich, T; Kreuzer, P; Lanske, D; Merschmeyer, M; Meyer, A; Philipps, B; Pieta, H; Reithler, H; Schmitz, S A; Sonnenschein, L; Sowa, M; Steggemann, J; Szczesny, H; Teyssier, D; Zeidler, C; Bontenackels, M; Davids, M; Duda, M; Flügge, G; Geenen, H; Giffels, M; Haj Ahmad, W; Hermanns, T; Heydhausen, D; Kalinin, S; Kress, T; Linn, A; Nowack, A; Perchalla, L; Poettgens, M; Pooth, O; Sauerland, P; Stahl, A; Tornier, D; Zoeller, M H; Aldaya Martin, M; Behrens, U; Borras, K; Campbell, A; Castro, E; Dammann, D; Eckerlin, G; Flossdorf, A; Flucke, G; Geiser, A; Hatton, D; Hauk, J; Jung, H; Kasemann, M; Katkov, I; Kleinwort, C; Kluge, H; Knutsson, A; Kuznetsova, E; Lange, W; Lohmann, W; Mankel, R; Marienfeld, M; Meyer, A B; Miglioranzi, S; Mnich, J; Ohlerich, M; Olzem, J; Parenti, A; Rosemann, C; Schmidt, R; Schoerner-Sadenius, T; Volyanskyy, D; Wissing, C; Zeuner, W D; Autermann, C; Bechtel, F; Draeger, J; Eckstein, D; Gebbert, U; Kaschube, K; Kaussen, G; Klanner, R; Mura, B; Naumann-Emme, S; Nowak, F; Pein, U; Sander, C; Schleper, P; Schum, T; Stadie, H; Steinbrück, G; Thomsen, J; Wolf, R; Bauer, J; Blüm, P; Buege, V; Cakir, A; Chwalek, T; De Boer, W; Dierlamm, A; Dirkes, G; Feindt, M; Felzmann, U; Frey, M; Furgeri, A; Gruschke, J; Hackstein, C; Hartmann, F; Heier, S; Heinrich, M; Held, H; Hirschbuehl, D; Hoffmann, K H; Honc, S; Jung, C; Kuhr, T; Liamsuwan, T; Martschei, D; Mueller, S; Müller, Th; Neuland, M B; Niegel, M; Oberst, O; Oehler, A; Ott, J; Peiffer, T; Piparo, D; Quast, G; Rabbertz, K; Ratnikov, F; Ratnikova, N; Renz, M; Saout, C; Sartisohn, G; Scheurer, A; Schieferdecker, P; Schilling, F P; Schott, G; Simonis, H J; Stober, F M; Sturm, P; Troendle, D; Trunov, A; Wagner, W; Wagner-Kuhr, J; Zeise, M; Zhukov, V; Ziebarth, E B; Daskalakis, G; Geralis, T; Karafasoulis, K; Kyriakis, A; Loukas, D; Markou, A; Markou, C; Mavrommatis, C; Petrakou, E; Zachariadou, A; Gouskos, L; Katsas, P; Panagiotou, A; Evangelou, I; Kokkas, P; Manthos, N; Papadopoulos, I; Patras, V; Triantis, F A; Bencze, G; Boldizsar, L; Debreczeni, G; Hajdu, C; Hernath, S; Hidas, P; Horvath, D; Krajczar, K; Laszlo, A; Patay, G; Sikler, F; Toth, N; Vesztergombi, G; Beni, N; Christian, G; Imrek, J; Molnar, J; Novak, D; Palinkas, J; Szekely, G; Szillasi, Z; Tokesi, K; Veszpremi, V; Kapusi, A; Marian, G; Raics, P; Szabo, Z; Trocsanyi, Z L; Ujvari, B; Zilizi, G; Bansal, S; Bawa, H S; Beri, S B; Bhatnagar, V; Jindal, M; Kaur, M; 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Yarba, J; Yumiceva, F; Yun, J C; Acosta, D; Avery, P; Barashko, V; Bourilkov, D; Chen, M; Di Giovanni, G P; Dobur, D; Drozdetskiy, A; Field, R D; Fu, Y; Furic, I K; Gartner, J; Holmes, D; Kim, B; Klimenko, S; Konigsberg, J; Korytov, A; Kotov, K; Kropivnitskaya, A; Kypreos, T; Madorsky, A; Matchev, K; Mitselmakher, G; Pakhotin, Y; Piedra Gomez, J; Prescott, C; Rapsevicius, V; Remington, R; Schmitt, M; Scurlock, B; Wang, D; Yelton, J; Ceron, C; Gaultney, V; Kramer, L; Lebolo, L M; Linn, S; Markowitz, P; Martinez, G; Rodriguez, J L; Adams, T; Askew, A; Baer, H; Bertoldi, M; Chen, J; Dharmaratna, W G D; Gleyzer, S V; Haas, J; Hagopian, S; Hagopian, V; Jenkins, M; Johnson, K F; Prettner, E; Prosper, H; Sekmen, S; Baarmand, M M; Guragain, S; Hohlmann, M; Kalakhety, H; Mermerkaya, H; Ralich, R; Vodopiyanov, I; Abelev, B; Adams, M R; Anghel, I M; Apanasevich, L; Bazterra, V E; Betts, R R; Callner, J; Castro, M A; Cavanaugh, R; Dragoiu, C; Garcia-Solis, E J; Gerber, C E; Hofman, D J; Khalatian, S; Mironov, C; Shabalina, E; Smoron, A; Varelas, N; Akgun, U; Albayrak, E A; Ayan, A S; Bilki, B; Briggs, R; Cankocak, K; Chung, K; Clarida, W; Debbins, P; Duru, F; Ingram, F D; Lae, C K; McCliment, E; Merlo, J P; Mestvirishvili, A; Miller, M J; Moeller, A; Nachtman, J; Newsom, C R; Norbeck, E; Olson, J; Onel, Y; Ozok, F; Parsons, J; Schmidt, I; Sen, S; Wetzel, J; Yetkin, T; Yi, K; Barnett, B A; Blumenfeld, B; Bonato, A; Chien, C Y; Fehling, D; Giurgiu, G; Gritsan, A V; Guo, Z J; Maksimovic, P; Rappoccio, S; Swartz, M; Tran, N V; Zhang, Y; Baringer, P; Bean, A; Grachov, O; Murray, M; Radicci, V; Sanders, S; Wood, J S; Zhukova, V; Bandurin, D; Bolton, T; Kaadze, K; Liu, A; Maravin, Y; Onoprienko, D; Svintradze, I; Wan, Z; Gronberg, J; Hollar, J; Lange, D; Wright, D; Baden, D; Bard, R; Boutemeur, M; Eno, S C; Ferencek, D; Hadley, N J; Kellogg, R G; Kirn, M; Kunori, S; Rossato, K; Rumerio, P; Santanastasio, F; Skuja, A; Temple, J; Tonjes, M B; Tonwar, S C; Toole, T; Twedt, E; Alver, B; Bauer, G; Bendavid, J; Busza, W; Butz, E; Cali, I A; Chan, M; D'Enterria, D; Everaerts, P; Gomez Ceballos, G; Hahn, K A; Harris, P; Jaditz, S; Kim, Y; Klute, M; Lee, Y J; Li, W; Loizides, C; Ma, T; Miller, M; Nahn, S; Paus, C; Roland, C; Roland, G; Rudolph, M; Stephans, G; Sumorok, K; Sung, K; Vaurynovich, S; Wenger, E A; Wyslouch, B; Xie, S; Yilmaz, Y; Yoon, A S; Bailleux, D; Cooper, S I; Cushman, P; Dahmes, B; De Benedetti, A; Dolgopolov, A; Dudero, P R; Egeland, R; Franzoni, G; Haupt, J; Inyakin, A; Klapoetke, K; Kubota, Y; Mans, J; Mirman, N; Petyt, D; Rekovic, V; Rusack, R; Schroeder, M; Singovsky, A; Zhang, J; Cremaldi, L M; Godang, R; Kroeger, R; Perera, L; Rahmat, R; Sanders, D A; Sonnek, P; Summers, D; Bloom, K; Bockelman, B; Bose, S; Butt, J; Claes, D R; Dominguez, A; Eads, M; Keller, J; Kelly, T; Kravchenko, I; Lazo-Flores, J; Lundstedt, C; Malbouisson, H; Malik, S; Snow, G R; Baur, U; Iashvili, I; Kharchilava, A; Kumar, A; Smith, K; Strang, M; Alverson, G; Barberis, E; Boeriu, O; Eulisse, G; Govi, G; McCauley, T; Musienko, Y; Muzaffar, S; Osborne, I; Paul, T; Reucroft, S; Swain, J; Taylor, L; Tuura, L; Anastassov, A; Gobbi, B; Kubik, A; Ofierzynski, R A; Pozdnyakov, A; Schmitt, M; Stoynev, S; Velasco, M; Won, S; Antonelli, L; Berry, D; Hildreth, M; Jessop, C; Karmgard, D J; Kolberg, T; Lannon, K; Lynch, S; Marinelli, N; Morse, D M; Ruchti, R; Slaunwhite, J; Warchol, J; Wayne, M; Bylsma, B; Durkin, L S; Gilmore, J; Gu, J; Killewald, P; Ling, T Y; Williams, G; Adam, N; Berry, E; Elmer, P; Garmash, A; Gerbaudo, D; Halyo, V; Hunt, A; Jones, J; Laird, E; Marlow, D; Medvedeva, T; Mooney, M; Olsen, J; Piroué, P; Stickland, D; Tully, C; Werner, J S; Wildish, T; Xie, Z; Zuranski, A; Acosta, J G; Bonnett Del Alamo, M; Huang, X T; Lopez, A; Mendez, H; Oliveros, S; Ramirez Vargas, J E; Santacruz, N; Zatzerklyany, A; Alagoz, E; Antillon, E; Barnes, V E; Bolla, G; Bortoletto, D; Everett, A; Garfinkel, A F; Gecse, Z; Gutay, L; Ippolito, N; Jones, M; Koybasi, O; Laasanen, A T; Leonardo, N; Liu, C; Maroussov, V; Merkel, P; Miller, D H; Neumeister, N; Sedov, A; Shipsey, I; Yoo, H D; Zheng, Y; Jindal, P; Parashar, N; Cuplov, V; Ecklund, K M; Geurts, F J M; Liu, J H; Maronde, D; Matveev, M; Padley, B P; Redjimi, R; Roberts, J; Sabbatini, L; Tumanov, A; Betchart, B; Bodek, A; Budd, H; Chung, Y S; de Barbaro, P; Demina, R; Flacher, H; Gotra, Y; Harel, A; Korjenevski, S; Miner, D C; Orbaker, D; Petrillo, G; Vishnevskiy, D; Zielinski, M; Bhatti, A; Demortier, L; Goulianos, K; Hatakeyama, K; Lungu, G; Mesropian, C; Yan, M; Atramentov, O; Bartz, E; Gershtein, Y; Halkiadakis, E; Hits, D; Lath, A; Rose, K; Schnetzer, S; Somalwar, S; Stone, R; Thomas, S; Watts, T L; Cerizza, G; Hollingsworth, M; Spanier, S; Yang, Z C; York, A; Asaadi, J; Aurisano, A; Eusebi, R; Golyash, A; Gurrola, A; Kamon, T; Nguyen, C N; Pivarski, J; Safonov, A; Sengupta, S; Toback, D; Weinberger, M; Akchurin, N; Berntzon, L; Gumus, K; Jeong, C; Kim, H; Lee, S W; Popescu, S; Roh, Y; Sill, A; Volobouev, I; Washington, E; Wigmans, R; Yazgan, E; Engh, D; Florez, C; Johns, W; Pathak, S; Sheldon, P; Andelin, D; Arenton, M W; Balazs, M; Boutle, S; Buehler, M; Conetti, S; Cox, B; Hirosky, R; Ledovskoy, A; Neu, C; Phillips II, D; Ronquest, M; Yohay, R; Gollapinni, S; Gunthoti, K; Harr, R; Karchin, P E; Mattson, M; Sakharov, A; Anderson, M; Bachtis, M; Bellinger, J N; Carlsmith, D; Crotty, I; Dasu, S; Dutta, S; Efron, J; Feyzi, F; Flood, K; Gray, L; Grogg, K S; Grothe, M; Hall-Wilton, R; Jaworski, M; Klabbers, P; Klukas, J; Lanaro, A; Lazaridis, C; Leonard, J; Loveless, R; Magrans de Abril, M; Mohapatra, A; Ott, G; Polese, G; Reeder, D; Savin, A; Smith, W H; Sourkov, A; Swanson, J; Weinberg, M; Wenman, D; Wensveen, M; White, A

    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.

  17. Spatial and kinematic alignments between central and satellite halos

    CERN Document Server

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

    2007-01-01

    Based on a cosmological N-body simulation we analyze spatial and kinematic alignments of satellite halos within six times the virial radius of group size host halos (Rvir). We measure three different types of spatial alignment: halo alignment between the orientation of the group central substructure (GCS) and the distribution of its satellites, radial alignment between the orientation of a satellite and the direction towards its GCS, and direct alignment between the orientation of the GCS and that of its satellites. In analogy we use the directions of satellite velocities and probe three further types of alignment: the radial velocity alignment between the satellite velocity and connecting line between satellite and GCS, the halo velocity alignment between the orientation of the GCS and satellite velocities and the auto velocity alignment between the satellites orientations and their velocities. We find that satellites are preferentially located along the major axis of the GCS. Within at least 6 Rvir (the ran...

  18. Primordial alignment of elliptical galaxies in intermediate redshift clusters

    CERN Document Server

    Rong, Yu; Liao, Jin-Yuan

    2015-01-01

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

  19. Isolated digit recognition without time alignment

    Science.gov (United States)

    Gay, Jeffrey Mark

    1994-12-01

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

  20. Multiple Whole Genome Alignments Without a Reference Organism

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-16

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

  1. 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 ...

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

    Science.gov (United States)

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

    2017-04-01

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

  3. Quantum Phase Analysis of Field-Free Molecular Alignment

    CERN Document Server

    Yun, Sang Jae; Lee, Jongmin; Nam, Chang Hee

    2015-01-01

    We present quantum mechanical explanations for unresolved phenomena observed in field-free molecular alignment by a femtosecond laser pulse. Quantum phase analysis of molecular rotational states reveals the physical origin of the following phenomena: strong alignment peaks appear periodically, and the temporal shape of each alignment peak changes in an orderly fashion depending on molecular species; the strongest alignment is not achieved at the first peak; the transition between aligned and anti-aligned states is very fast compared to the time scale of rotational dynamics. These features are understood in a unified way analogous to that describing a carrier-envelope-phase-stabilized mode-locked laser.

  4. Assembly and alignment of infrared refractive system

    Science.gov (United States)

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

    2013-09-01

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

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

    Science.gov (United States)

    Louey, Melissa Gar Yee; Sangeux, Morgan

    2016-09-01

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

  6. Molecular orbital imaging for partially aligned molecules

    Science.gov (United States)

    Qin, Meiyan; Zhu, Xiaosong

    2017-01-01

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

  7. 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 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...... of the composite were measured. For composites with a fibre content of 37 % by volume, stiffness is about 20 GPa and failure stress is about 180 MPa. The tensile properties of the composites are analysed with a modified rule of mixtures model, which includes the effect of porosity. The experimental results...

  8. Index Coding - An Interference Alignment Perspective

    CERN Document Server

    Maleki, Hamed; Jafar, Syed A

    2012-01-01

    The index coding problem is studied from an interference alignment perspective, providing new results as well as new insights into, and generalizations of, previously known results. An equivalence is established between multiple unicast index coding where each message is desired by exactly one receiver, and multiple groupcast index coding where a message can be desired by multiple receivers, which settles the heretofore open question of insufficiency of linear codes for the multiple unicast index coding problem by equivalence with multiple groupcast settings where this question has previously been answered. Necessary and sufficient conditions for the achievability of rate half per message are shown to be a natural consequence of interference alignment constraints, and generalizations to feasibility of rate $\\frac{1}{L+1}$ per message when each destination desires at least $L$ messages, are similarly obtained. Finally, capacity optimal solutions are presented to a series of symmetric index coding problems insp...

  9. 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.

  10. Aligning Astronomical Telescopes via Identification of Stars

    Science.gov (United States)

    Whorton, Mark

    2010-01-01

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

  11. Evryscope Robotilter automated camera / ccd alignment system

    Science.gov (United States)

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

    2016-08-01

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

  12. 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...

  13. Laser alignment measurement model with double beam

    Science.gov (United States)

    Mo, Changtao; Zhang, Lili; Hou, Xianglin; Wang, Ming; Lv, Jia; Du, Xin; He, Ping

    2012-10-01

    Double LD-Double PSD schedule.employ a symmetric structure and there are a laser and a PSD receiver on each axis. The Double LD-Double PSD is used, and the rectangular coordinate system is set up by use of the relationship of arbitrary two points coordinates, and then the parameter formula is deduced by the knowledge of solid geometry. Using the data acquisition system and the data processing model of laser alignment meter with double laser beam and two detector , basing on the installation parameter of the computer, we can have the state parameter between the two shafts by more complicated calculation and correction. The correcting data of the four under chassis of the adjusted apparatus moving on the level and the vertical plane can be calculated using the computer. This will instruct us to move the apparatus to align the shafts.

  14. Alignment of cryo-electron tomography datasets.

    Science.gov (United States)

    Amat, Fernando; Castaño-Diez, Daniel; Lawrence, Albert; Moussavi, Farshid; Winkler, Hanspeter; Horowitz, Mark

    2010-01-01

    Data acquisition of cryo-electron tomography (CET) samples described in previous chapters involves relatively imprecise mechanical motions: the tilt series has shifts, rotations, and several other distortions between projections. Alignment is the procedure of correcting for these effects in each image and requires the estimation of a projection model that describes how points from the sample in three-dimensions are projected to generate two-dimensional images. This estimation is enabled by finding corresponding common features between images. This chapter reviews several software packages that perform alignment and reconstruction tasks completely automatically (or with minimal user intervention) in two main scenarios: using gold fiducial markers as high contrast features or using relevant biological structures present in the image (marker-free). In particular, we emphasize the key decision points in the process that users should focus on in order to obtain high-resolution reconstructions.

  15. Interference Alignment with Analog Channel State Feedback

    CERN Document Server

    Ayach, Omar El

    2010-01-01

    Interference alignment (IA) is a multiplexing gain optimal transmission strategy for the interference channel with an arbitrary number of users. While the achieved sum rate with IA is much higher than previously thought possible, the improvement comes at the cost of requiring network channel state information at the transmitters. This can be achieved by explicit feedback, a flexible yet costly approach that incurs large overhead and limits throughput. We propose using analog feedback as an alternative to limited feedback or reciprocity based alignment. We show that the full multiplexing gain observed with perfect channel knowledge is preserved by analog feedback and the mean loss in sum rate is bounded by a constant when signal-to-noise ratio is comparable in both forward and feedback channels. When such feedback quality is not quite possible, a fraction of the degrees of freedom is achieved. We consider the overhead of training and feedback and use this framework to optimize the system's effective throughput...

  16. 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...

  17. Opportunistic Interference Alignment for Random Access Networks

    OpenAIRE

    Jin, Hu; Jeon, Sang-Woon; Jung, Bang Chul

    2015-01-01

    An interference management problem among multiple overlapped random access networks (RANs) is investigated, each of which operates with slotted ALOHA protocol. Assuming that access points and users have multiple antennas, a novel opportunistic interference alignment~(OIA) is proposed to mitigate interference among overlapped RANs. The proposed technique intelligently combines the transmit beamforming technique at the physical layer and the opportunistic packet transmission at the medium acces...

  18. Vertical bounce of two vertically aligned balls

    Science.gov (United States)

    Cross, Rod

    2007-11-01

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

  19. 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.

  20. Superposition and alignment of labeled point clouds.

    Science.gov (United States)

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

    2011-01-01

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

  1. Secure Fingerprint Alignment and Matching Protocols

    OpenAIRE

    Bayatbabolghani, Fattaneh; Blanton, Marina; Aliasgari, Mehrdad; Goodrich, Michael

    2017-01-01

    We present three secure privacy-preserving protocols for fingerprint alignment and matching, based on what are considered to be the most precise and efficient fingerprint recognition algorithms-those based on the geometric matching of "landmarks" known as minutia points. Our protocols allow two or more honest-but-curious parties to compare their respective privately-held fingerprints in a secure way such that they each learn nothing more than a highly-accurate score of how well the fingerprin...

  2. Interference Alignment via Improved Subspace Conditioning

    CERN Document Server

    Kim, Douglas

    2010-01-01

    For the K user, single input single output (SISO), frequency selective interference channel, a new low complexity transmit beamforming design that improves the achievable sum rate is presented. Jointly employing the interference alignment (IA) scheme presented by Cadambe and Jafar in [1] and linear minimum mean square error (MMSE) decoding at the transmitters and receivers, respectively, the new IA precoding design improves the average sum rate while preserving the achievable degrees of freedom of the Cadambe and Jafar scheme, K/2.

  3. Regional Alignment: Phase Zero Logistics Implications

    Science.gov (United States)

    2014-05-01

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

  4. Mounting and Alignment of IXO Mirror Segments

    Science.gov (United States)

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

    2010-01-01

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

  5. Alignment Mirror Mechanisms for Space Use

    Science.gov (United States)

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

    2011-01-01

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

  6. Bell's theorem without inequalities and without alignments

    CERN Document Server

    Cabello, A

    2003-01-01

    A proof of Bell's theorem without inequalities is presented which exhibits three remarkable properties: (a) reduced local states are immune to collective decoherence, (b) local setups do not need to be aligned, since the required perfect correlations are achieved for any local rotation of the local setups, and (c) local measurements require only individual measurements on the qubits. Indeed, it is shown that this proof is essentially the only one which fulfils (a), (b), and (c).

  7. Alignment technology and applications of liquid crystal devices

    CERN Document Server

    Takatoh, Kohki; Hasegawa, Ray; Koden, Mitsushiro; Itoh, Nobuyuki; Hasegawa, Masaki

    2005-01-01

    Alignment phenomena are characteristic of liquid crystalline materials, and understanding them is critically important in understanding the essential features and behavior of liquid crystals and the performance of Liquid Crystal Devices (LCDs). Furthermore, in LCD production lines, the alignment process is of practical importance. Alignment Technologies and Applications of Liquid Crystal Devices demonstrates both the fundamental and practical aspects of alignment phenomena in liquid crystals. The physical basis of alignment phenomena is first introduced in order to aid the understanding of the various physical phenomena observed in the interface between liquid crystalline materials and alignment layer surfaces. Methods for the characterization of surfaces, which induce the alignment phenomena, and of the alignment layer itself are introduced. These methods are useful for the research of liquid crystalline materials and devices in academic research as well as in industry. In the practical sections, the alignme...

  8. 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.

  9. Collective alignment of polar filaments by molecular motors.

    Science.gov (United States)

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

    2009-04-01

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

  10. Towards optimal alignment of protein structure distance matrices

    NARCIS (Netherlands)

    Wohlers, I.; Domingues, F.S.; Klau, G.W.

    2010-01-01

    MOTIVATION: Structural alignments of proteins are important for identification of structural similarities, homology detection and functional annotation. The structural alignment problem is well studied and computationally difficult. Many different scoring schemes for structural similarity as well as

  11. 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......To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; instead, rather ad hoc models are generally favoured. Here...... 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...

  12. NANOIMPRINT LITHOGRAPHY TECHNOLOGY WITH AUTOMATIC ALIGNMENT

    Institute of Scientific and Technical Information of China (English)

    FAN Xiqiu; ZHANG Honghai; WANG Xuefang; HU Xiaofeng; JIA Ke; LIU Sheng

    2007-01-01

    Nanoimprint lithography (NIL) is recognized as one of the most promising candidates for the next generation lithography (NGL) to obtain sub-100 nm patterns because of its simplicity,high-throughput and low-cost. While substantial effort has been expending on NIL for producing smaller and smaller feature sizes, considerably less effort has been devoted to the equally important issue-alignment between template and substrate. A homemade prototype nanoimprint lithography enable the substrate to move towards the desired position automatically. Linear motors with 300 mm travel range and 1 μm step resolution are used as macro actuators, and piezoelectric translators with 50 μm travel range and 1 nm step resolution are used as micro actuators. In addition, the prototype provides one translation (z displacement) and two tilting motion(α and β) to automatically bring uniform intact contact between the template and substrate surfaces by using a flexure stage. As a result, 10 μm coarse alignment accuracy and 20 nm fine alignment accuracy can be achieved. Finally,some results of nanostructures and micro devices such as nanoscale trenches and holes, gratings and microlens array fabricated using the prototype tool are presented, and hot embossing lithography, one typical NIL technology, are depicted by taking nanoscale gratings fabrication as an example.

  13. 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.

  14. Optical alignment using the Point Source Microscope

    Science.gov (United States)

    Parks, Robert E.; Kuhn, William P.

    2005-08-01

    We give an example of a Point Source Microscope (PSM) and describe its uses as an aid in the alignment of optical systems including the referencing of optical to mechanical datums. The PSM is a small package (about 100x150x30 mm), including a point source of light, beam splitter, microscope objective and digital CCD camera to detect the reflected light spot. A software package in conjunction with a computer video display locates the return image in three degrees of freedom relative to an electronic spatial reference point. The PSM also includes a Koehler illumination source so it may be used as a portable microscope for ordinary imaging and the microscope can be zoomed under computer control. For added convenience, the laser diode point source can be made quite bright to facilitate initial alignment under typical laboratory lighting conditions. The PSM is particularly useful in aligning optical systems that do not have circular symmetry or are distributed in space such as off-axis systems. The PSM is also useful for referencing the centers of curvatures of optical surfaces to mechanical datums of the structure in which the optics are mounted. By removing the microscope objective the PSM can be used as an electronic autocollimator because of the infinite conjugate optical design.

  15. 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.

  16. Functionalization of vertically aligned carbon nanotubes

    Directory of Open Access Journals (Sweden)

    Eloise Van Hooijdonk

    2013-02-01

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

  17. 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.

  18. JWST science instrument pupil alignment measurements

    Science.gov (United States)

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

    2016-09-01

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

  19. IVUS coronary volume alignment for distinct phases

    Science.gov (United States)

    Matsumoto, Monica Mitiko Soares; Lemos, Pedro Alves; Furuie, Sergio Shiguemi

    2009-02-01

    Image-based intravascular ultrasound (IVUS) cardiac phase detection allows coronary volume reconstruction in different phases. Consecutive volumes are not necessarily spatially aligned due to longitudinal movement of the catheter. Besides ordinary pullback velocity, there is a relative longitudinal movement of the heart vessel walls and the transducer, due to myocardial contraction. In this manuscript, we aim to spatially align cardiac phase coronary IVUS volumes. In addition, we want to investigate this non-linear longitudinal catheter movement. With this purpose, we have analyzed 120 simulated IVUS images and 10 real IVUS pullbacks. We implemented the following methodology. Firstly, we built IVUS volume for each distinct phase. Secondly, each IVUS volume was transformed into a parametric signal of average frame intensity. We have used these signals to make correlation in space with a reference one. Then we estimated the spatial distance between the distinct IVUS volumes and the reference. We have tested in simulated images and real examinations. We have also observed similar pattern in real IVUS examinations. This spatial alignment method is feasible and useful as a step towards dynamic studies of IVUS examination.

  20. Camber Angle Inspection for Vehicle Wheel Alignments

    Science.gov (United States)

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

    2017-01-01

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

  1. Camber Angle Inspection for Vehicle Wheel Alignments

    Directory of Open Access Journals (Sweden)

    Jieh-Shian Young

    2017-02-01

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

  2. Stochastic sampling of the RNA structural alignment space

    OpenAIRE

    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...

  3. A new accelerator alignment concept using laser trackers

    Energy Technology Data Exchange (ETDEWEB)

    Friedsam, H.

    1994-07-01

    This paper outlines the basic principle of the laser tracker and the new and simplified alignment concept for the APS based on the use of these laser trackers. These instruments not only provide the necessary accuracy for positioning of beam components but are also reducing the time and manpower requirements for the alignment of beam elements. The presented alignment concept will be especially valuable when considering the alignment of small scale accelerators.

  4. 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.

  5. 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

  6. Convergent algorithms for protein structural alignment

    Directory of Open Access Journals (Sweden)

    Martínez José

    2007-08-01

    Full Text Available Abstract Background Many algorithms exist for protein structural alignment, based on internal protein coordinates or on explicit superposition of the structures. These methods are usually successful for detecting structural similarities. However, current practical methods are seldom supported by convergence theories. In particular, although the goal of each algorithm is to maximize some scoring function, there is no practical method that theoretically guarantees score maximization. A practical algorithm with solid convergence properties would be useful for the refinement of protein folding maps, and for the development of new scores designed to be correlated with functional similarity. Results In this work, the maximization of scoring functions in protein alignment is interpreted as a Low Order Value Optimization (LOVO problem. The new interpretation provides a framework for the development of algorithms based on well established methods of continuous optimization. The resulting algorithms are convergent and increase the scoring functions at every iteration. The solutions obtained are critical points of the scoring functions. Two algorithms are introduced: One is based on the maximization of the scoring function with Dynamic Programming followed by the continuous maximization of the same score, with respect to the protein position, using a smooth Newtonian method. The second algorithm replaces the Dynamic Programming step by a fast procedure for computing the correspondence between Cα atoms. The algorithms are shown to be very effective for the maximization of the STRUCTAL score. Conclusion The interpretation of protein alignment as a LOVO problem provides a new theoretical framework for the development of convergent protein alignment algorithms. These algorithms are shown to be very reliable for the maximization of the STRUCTAL score, and other distance-dependent scores may be optimized with same strategy. The improved score optimization

  7. Robust precision alignment algorithm for micro tube laser forming

    NARCIS (Netherlands)

    Folkersma, K.G.P.; Brouwer, D.M.; Römer, G.R.B.E.; Herder, J.L.

    2016-01-01

    Tube laser forming on a small diameter tube can be used as a high precision actuator to permanently align small (optical)components. Applications, such as the alignment of optical fibers to photonic integrated circuits, often require sub-micron alignment accuracy. Although the process causes signifi

  8. 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...... molecular surfaces. Furthermore, we consider the implications of a dynamic bias to structure determination using data from the weak alignment method....

  9. Qualitative Variation in Constructive Alignment in Curriculum Design

    Science.gov (United States)

    Trigwell, Keith; Prosser, Michael

    2014-01-01

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

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

    Science.gov (United States)

    Polikoff, Morgan S.; Fulmer, Gavin W.

    2013-01-01

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

  11. Algorithm Engineering for Optimal Alignment of Protein Structure Distance Matrices

    NARCIS (Netherlands)

    Wohlers, I.; Andonov, R.; Klau, G.W.

    2011-01-01

    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,

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

    DEFF Research Database (Denmark)

    Andersen, Jonas Lohmann Elkjær; Landex, Alex

    2010-01-01

    Planning of urban railways like Metro and especially Light Rail Transit often result in multiple alignment alternatives from where it can be difficult to select the best one. Travel demand is a good foundation for evaluating a railway alignment for its ability to attract passengers. Therefore...... and can be applied as decision support in different stages of the urban railway alignment planning....

  13. Maturing Business/IT Alignment Capability; the Practitioner's view.

    NARCIS (Netherlands)

    Silvius, Gilbert; Smit, Kobus

    2011-01-01

    Aligning IT and business needs is still one of the most important concerns for senior management. The message of Business and IT Alignment (BIA) is logical and undisputed, but implementation is apparently difficult. Luftman and Kempaiah [11] conclude that business and IT alignment needs a tool that

  14. Aligned, isotropic and patterned carbon nanotube substrates that control the growth and alignment of Chinese hamster ovary cells

    Energy Technology Data Exchange (ETDEWEB)

    Abdullah, Che Azurahanim Che; Asanithi, Piyapong; Brunner, Eric W; Jurewicz, Izabela; Bo, Chiara; Sear, Richard P; Dalton, Alan B [Department of Physics and Surrey Materials Institute, University of Surrey, Guildford, Surrey GU2 7XH (United Kingdom); Azad, Chihye Lewis; Ovalle-Robles, Raquel; Fang Shaoli; Lima, Marcio D; Lepro, Xavier; Collins, Steve; Baughman, Ray H, E-mail: r.sear@surrey.ac.uk [Alan G MacDiarmid NanoTech Institute, The University of Texas at Dallas, Richardson, TX 75080-3021 (United States)

    2011-05-20

    Here we culture Chinese hamster ovary cells on isotropic, aligned and patterned substrates based on multiwall carbon nanotubes. The nanotubes provide the substrate with nanoscale topography. The cells adhere to and grow on all substrates, and on the aligned substrate, the cells align strongly with the axis of the bundles of the multiwall nanotubes. This control over cell alignment is required for tissue engineering; almost all tissues consist of oriented cells. The aligned substrates are made using straightforward physical chemistry techniques from forests of multiwall nanotubes; no lithography is required to make inexpensive large-scale substrates with highly aligned nanoscale grooves. Interestingly, although the cells strongly align with the nanoscale grooves, only a few also elongate along this axis: alignment of the cells does not require a pronounced change in morphology of the cell. We also pattern the nanotube bundles over length scales comparable to the cell size and show that the cells follow this pattern.

  15. Aligned, isotropic and patterned carbon nanotube substrates that control the growth and alignment of Chinese hamster ovary cells

    Science.gov (United States)

    Azurahanim Che Abdullah, Che; Asanithi, Piyapong; Brunner, Eric W.; Jurewicz, Izabela; Bo, Chiara; Azad, Chihye Lewis; Ovalle-Robles, Raquel; Fang, Shaoli; Lima, Marcio D.; Lepro, Xavier; Collins, Steve; Baughman, Ray H.; Sear, Richard P.; Dalton, Alan B.

    2011-05-01

    Here we culture Chinese hamster ovary cells on isotropic, aligned and patterned substrates based on multiwall carbon nanotubes. The nanotubes provide the substrate with nanoscale topography. The cells adhere to and grow on all substrates, and on the aligned substrate, the cells align strongly with the axis of the bundles of the multiwall nanotubes. This control over cell alignment is required for tissue engineering; almost all tissues consist of oriented cells. The aligned substrates are made using straightforward physical chemistry techniques from forests of multiwall nanotubes; no lithography is required to make inexpensive large-scale substrates with highly aligned nanoscale grooves. Interestingly, although the cells strongly align with the nanoscale grooves, only a few also elongate along this axis: alignment of the cells does not require a pronounced change in morphology of the cell. We also pattern the nanotube bundles over length scales comparable to the cell size and show that the cells follow this pattern.

  16. AlignNemo: a local network alignment method to integrate homology and topology.

    Science.gov (United States)

    Ciriello, Giovanni; Mina, Marco; Guzzi, Pietro H; Cannataro, Mario; Guerra, Concettina

    2012-01-01

    Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.

  17. Erasing errors due to alignment ambiguity when estimating positive selection.

    Science.gov (United States)

    Redelings, Benjamin

    2014-08-01

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

  18. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-01-01

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

  1. Alignment and focus of mirrored facets of a heliosat

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-11-12

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

  2. Ontology Alignment at the Instance and Schema Level

    CERN Document Server

    Suchanek, Fabian; Senellart, Pierre

    2011-01-01

    We present PARIS, an approach for the automatic alignment of ontologies. PARIS aligns not only instances, but also relations and classes. Alignments at the instance-level cross-fertilize with alignments at the schema-level. Thereby, our system provides a truly holistic solution to the problem of ontology alignment. The heart of the approach is probabilistic. This allows PARIS to run without any parameter tuning. We demonstrate the efficiency of the algorithm and its precision through extensive experiments. In particular, we obtain a precision of around 80% in experiments with two of the world's largest ontologies.

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

    Science.gov (United States)

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

    2017-02-21

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

  4. Scaling statistical multiple sequence alignment to large datasets

    Directory of Open Access Journals (Sweden)

    Michael Nute

    2016-11-01

    Full Text Available Abstract Background Multiple sequence alignment is an important task in bioinformatics, and alignments of large datasets containing hundreds or thousands of sequences are increasingly of interest. While many alignment methods exist, the most accurate alignments are likely to be based on stochastic models where sequences evolve down a tree with substitutions, insertions, and deletions. While some methods have been developed to estimate alignments under these stochastic models, only the Bayesian method BAli-Phy has been able to run on even moderately large datasets, containing 100 or so sequences. A technique to extend BAli-Phy to enable alignments of thousands of sequences could potentially improve alignment and phylogenetic tree accuracy on large-scale data beyond the best-known methods today. Results We use simulated data with up to 10,000 sequences representing a variety of model conditions, including some that are significantly divergent from the statistical models used in BAli-Phy and elsewhere. We give a method for incorporating BAli-Phy into PASTA and UPP, two strategies for enabling alignment methods to scale to large datasets, and give alignment and tree accuracy results measured against the ground truth from simulations. Comparable results are also given for other methods capable of aligning this many sequences. Conclusions Extensions of BAli-Phy using PASTA and UPP produce significantly more accurate alignments and phylogenetic trees than the current leading methods.

  5. 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.

  6. Efficient Word Alignment with Markov Chain Monte Carlo

    Directory of Open Access Journals (Sweden)

    Östling Robert

    2016-10-01

    Full Text Available We present EFMARAL, a new system for efficient and accurate word alignment using a Bayesian model with Markov Chain Monte Carlo (MCMC inference. Through careful selection of data structures and model architecture we are able to surpass the fast_align system, commonly used for performance-critical word alignment, both in computational efficiency and alignment accuracy. Our evaluation shows that a phrase-based statistical machine translation (SMT system produces translations of higher quality when using word alignments from EFMARAL than from fast_align, and that translation quality is on par with what is obtained using GIZA++, a tool requiring orders of magnitude more processing time. More generally we hope to convince the reader that Monte Carlo sampling, rather than being viewed as a slow method of last resort, should actually be the method of choice for the SMT practitioner and others interested in word alignment.

  7. Grain Alignment by Radiative Torques in Special Conditions and Implications

    CERN Document Server

    Hoang, Thiem

    2014-01-01

    Grain alignment by radiative torques (RATs) has been extensively studied for various environment conditions, including interstellar medium, dense molecular clouds, and accretion disks, thanks to significant progress in observational, theoretical and numerical studies. In this paper, we explore the alignment by RATs and provide quantitative predictions of dust polarization for a set of astrophysical environments that can be tested observationally. We first consider the alignment of grains in the local interstellar medium and compare predictions for linear polarization by aligned grains with recent observational data for nearby stars. We then revisit the problem of grain alignment in accretions disks by taking into account the dependence of RAT alignment efficiency on the anisotropic direction of radiation fields relative to magnetic fields. Moreover, we study the grain alignment in interplanetary medium, including diffuse Zodiacal cloud and cometary comae, and calculate the degree of circular polarization (CP)...

  8. 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...

  9. Aligned Natural Inflation in String Theory

    CERN Document Server

    Long, Cody; McGuirk, Paul

    2014-01-01

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

  10. Alignment of the LHCb tracking system

    CERN Document Server

    Märki, Raphael

    2011-01-01

    The LHCb experiment at the LHC is dedicated to precision measurements of $CP$-violation and rare decays in the $b$ and $c$ sectors. The experiment features a tracking system consisting of silicon strip detectors and straw tube drift chambers up- and downstream of the magnet to precisely measure the vertex position and the momentum resolution of the particles travelling through the detector. An important ingredient to the track parameter resolution is the spatial alignment of the tracking system on which we report here.

  11. CMS Tracker Alignment Performance Results Summer 2016

    CERN Document Server

    CMS Collaboration

    2016-01-01

    The tracking system of the CMS detector provides excellent resolution for charged particle tracks and an efficient way of tagging jets. In order to reconstruct good quality tracks, the position and orientation of each silicon pixel and strip modules need to be determined with a precision of several micrometers. The performance of the CMS tracker alignment in 2016 using cosmic-ray data recorded at 0 T magnetic field and proton-proton collision data recorded at 3.8 T magnetic field has been studied. The data-driven validation of the results are presented. The time-dependent movement of the pixel detector's large-scale structure is demonstrated.

  12. Study of wafer pre-aligning approaches

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Wafer pre-aligning system is an important component in IC manufacturing industry. A wafer prealigning platform with a CCD sensor is presented in this paper. The centering and notch detecting approaches are extended based on this platform. Least square circle fitting approach is adopted to calculate the center and radius of the wafer, and a formula for calculating the fitting error is derived. An approach called edge variation rate is also proposed to detect the range of wafer notch, and the fiducial is calculated by curve fitting approach. These approaches can improve the accuracy effectively as indicated by experiments.

  13. Interference Alignment in Dense Wireless Networks

    CERN Document Server

    Niesen, Urs

    2009-01-01

    We consider arbitrary dense wireless networks, in which $n$ nodes are placed in an arbitrary (deterministic) manner on a square region of unit area and communicate with each other over Gaussian fading channels. We provide inner and outer bounds for the $n\\times n$-dimensional unicast and the $n\\times 2^n$-dimensional multicast capacity regions of such a wireless network. These inner and outer bounds differ only by a factor $O(\\log(n))$, yielding a fairly tight scaling characterization of the entire regions. The communication schemes achieving the inner bounds use interference alignment as a central technique and are surprisingly simple.

  14. 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).

  15. Accuracy of structure-based sequence alignment of automatic methods

    Directory of Open Access Journals (Sweden)

    Lee Byungkook

    2007-09-01

    Full Text Available Abstract Background Accurate sequence alignments are essential for homology searches and for building three-dimensional structural models of proteins. Since structure is better conserved than sequence, structure alignments have been used to guide sequence alignments and are commonly used as the gold standard for sequence alignment evaluation. Nonetheless, as far as we know, there is no report of a systematic evaluation of pairwise structure alignment programs in terms of the sequence alignment accuracy. Results In this study, we evaluate CE, DaliLite, FAST, LOCK2, MATRAS, SHEBA and VAST in terms of the accuracy of the sequence alignments they produce, using sequence alignments from NCBI's human-curated Conserved Domain Database (CDD as the standard of truth. We find that 4 to 9% of the residues on average are either not aligned or aligned with more than 8 residues of shift error and that an additional 6 to 14% of residues on average are misaligned by 1–8 residues, depending on the program and the data set used. The fraction of correctly aligned residues generally decreases as the sequence similarity decreases or as the RMSD between the Cα positions of the two structures increases. It varies significantly across CDD superfamilies whether shift error is allowed or not. Also, alignments with different shift errors occur between proteins within the same CDD superfamily, leading to inconsistent alignments between superfamily members. In general, residue pairs that are more than 3.0 Å apart in the reference alignment are heavily (>= 25% on average misaligned in the test alignments. In addition, each method shows a different pattern of relative weaknesses for different SCOP classes. CE gives relatively poor results for β-sheet-containing structures (all-β, α/β, and α+β classes, DaliLite for "others" class where all but the major four classes are combined, and LOCK2 and VAST for all-β and "others" classes. Conclusion When the sequence

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

    Science.gov (United States)

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

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

  17. Effects of aligning pulse duration on the degree and the slope of nitrogen field-free alignment

    Institute of Scientific and Technical Information of China (English)

    Wang Fei; Jiang Hong-Bing; Gong Qi-Huang

    2012-01-01

    Through theoretical analysis,we show how aligning pulse durations affect the degree and the time-rate slope of nitrogen field-free alignment at a fixed pulse intensity.It is found that both the degree and the slope first increase,then saturate,and finally decrease with the increasing pump duration.The optimal durations for the maximum degree and the maximum slope of the alignment are found to be different.Additionally,they are found to mainly depend on the molecular rotational period,and are affected by the temperature and the aligning pump intensities.The mechanism of molecular alignment is also discussed.

  18. Alignment of the ATLAS Inner Detector

    CERN Document Server

    Marti-Garcia, Salvador; The ATLAS collaboration

    2016-01-01

    The Run-2 of the LHC has presented new challenges to track and vertex reconstruction with higher energies, denser jets and higher rates. In addition, the Insertable B-layer (IBL) is a fourth pixel layer, which has been deployed at the centre of ATLAS during the longshutdown-1 of the LHC. The physics performance of the experiment requires a high resolution and unbiased measurement of all charged particle kinematic parameters. In its turn, the performance of the tracking depends, among many other issues, on the accurate determination of the alignment parameters of the tracking sensors. The offline track based alignment of the ATLAS tracking system has to deal with more than 700,000 degrees of freedom (DoF). This represents a considerable numerical challenge in terms of both CPU time and precision. During Run-2, a mechanical distortion of the IBL staves up to 20um has been observed during data-taking, plus other short time scale movements. The talk will also describe the procedures implemented to detect and remo...

  19. Optical alignment of Centaur's inertial guidance system

    Science.gov (United States)

    Gordan, Andrew L.

    1987-01-01

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

  20. Vertically aligned biaxially textured molybdenum thin films

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, Rahul [Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 (United States); Riley, Michael [Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 (United States); Lee, Sabrina [US Army Armament Research, Development and Engineering Center, Benet Labs, Watervliet, New York 12189 (United States); Lu, Toh-Ming [Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York 12180 (United States)

    2011-09-15

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

  1. Steerable wavelet analysis of CMB structures alignment

    CERN Document Server

    Vielva, P; Martínez-González, E; Vandergheynst, P

    2006-01-01

    This paper reviews the application of a novel methodology for analysing the isotropy of the universe by probing the alignment of local structures in the CMB. The strength of the proposed methodology relies on the steerable wavelet filtering of the CMB signal. One the one hand, the filter steerability renders the computation of the local orientation of the CMB features affordable in terms of computation time. On the other hand, the scale-space nature of the wavelet filtering allows to explore the alignment of the local structures at different scales, probing possible different phenomena. We present the WMAP first-year data analysis recently performed by the same authors (Wiaux et al.), where an extremely significant anisotropy was found. In particular, a preferred plane was detected, having a normal direction with a northern end position close to the northern end of the CMB dipole axis. In addition, a most preferred direction was found in that plane, with a northern end direction very close to the north eclipt...

  2. DNA Sequence Alignment during Homologous Recombination.

    Science.gov (United States)

    Greene, Eric C

    2016-05-27

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

  3. Product Grammars for Alignment and Folding.

    Science.gov (United States)

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

    2015-01-01

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

  4. 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...

  5. 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.

  6. Multiple sequence alignment with user-defined anchor points

    Directory of Open Access Journals (Sweden)

    Pöhler Dirk

    2006-04-01

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

  7. 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.)

  8. 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.

  9. Alignment of magnetic uniaxial particles in a magnetic field: Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Golovnia, O.A., E-mail: golovnya@imp.uran.ru [Institute of Metal Physics, Str. S. Kovalevskoy, 18, 620990 Ekaterinburg (Russian Federation); Popov, A.G [Institute of Metal Physics, Str. S. Kovalevskoy, 18, 620990 Ekaterinburg (Russian Federation); Sobolev, A.N. [South Ural State University (National Research University), av. Lenina, 76, 454080 Chelyabinsk (Russian Federation); Hadjipanayis, G.C. [Department of Physics and Astronomy, University of Delaware, 217 Sharp Lab, Newark, DE 19716 (United States)

    2014-09-01

    The numerical investigations of the process of alignment of magnetically uniaxial Nd–Fe–B powders in an applied magnetic field were carried out using the discrete element method (DEM). It is shown that magnetic alignment of ensemble of spherical particles provides extremely high degree of alignment, which is achieved in low magnetic fields. A model of formation of anisotropic particles as a combination of spherical particles is suggested. The influence of the shape anisotropy and friction coefficient on the alignment degree was analyzed. The increase in the friction coefficient leads to a decrease in the alignment degree; the simulation results are in qualitative agreement with experimental dependences. It is shown that in magnetic fields higher than 5 T, the calculated field dependences of the alignment degree quantitatively render the experimental data. The increase of about 6% in the alignment degree in the experiments with addition of internal lubricant can be explained by the decrease of 14% in friction coefficient. - Highlights: • We simulate the magnetic alignment of ensemble of Nd–Fe–B spherical uniaxial particles. • Anisotropic particles as a combination of spherical particles are constructed. • Influence of the particle shape anisotropy and friction on the alignment is analyzed. • We compare calculated and experimental data on field dependence of magnetic alignment. • The results render the experimental dependence.

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

    Science.gov (United States)

    Knudsen, Bjarne; Miyamoto, Michael M

    2003-10-17

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

  11. 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].

  12. Grain Alignment: Role of Radiative Torques and Paramagnetic Relaxation

    CERN Document Server

    Lazarian, A; Hoang, Thiem

    2015-01-01

    Polarization arising from aligned dust grains presents a unique opportunity to study magnetic fields in the diffuse interstellar medium and molecular clouds. Polarization from circumstellar regions, accretion disks and comet atmospheres can also be related to aligned dust.To reliably trace magnetic fields quantitative theory of grain alignment is required. Formulating the theory that would correspond to observations was one of the longstanding problems in astrophysics. Lately this problem has been successfully addressed and in this review we summarize some of the most important theoretical advances in the theory of grain alignment by radiative torques (RATs) that act on realistic irregular dust grains. We discuss an analytical model of RATs and the ways to make RAT alignment more efficient, e.g. through paramagnetic relaxation when grains have inclusions with strong magnetic response. For very small grains for which RAT alignment is inefficient, we also discuss paramagnetic relaxation and a process termed res...

  13. 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...

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

    Science.gov (United States)

    Afridi, Muhammad Ishaq

    2013-01-01

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

  15. 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.

  16. 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...... combined with a Markov Random Field regularisation method. Conceptually, the method maintains an implicit ideal description of the sought surface. This implicit surface is iteratively updated by realigning the input point sets and Markov Random Field regularisation. The regularisation is based on a prior...... 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....

  17. 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.

  18. Portable weighing system with alignment features

    Science.gov (United States)

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

    2012-11-06

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

  19. 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.

  20. Galaxy pairs align with galactic filaments

    CERN Document Server

    Tempel, Elmo

    2015-01-01

    Context. Gravitational collapse theory and numerical simulations suggest that the velocity field within large-scale galaxy filaments is dominated by motions along the filaments. Aims. Our aim is to check whether observational data reveal any preferred orientation of galaxy pairs with respect to the underlying filaments as a result of the expectedly anisotropic velocity field. Methods. We use galaxy pairs and galaxy filaments identified from the Sloan Digital Sky Survey data. For filament extraction, we use the Bisous model that is based the marked point process technique. During the filament detection, we use the centre point of each pair instead of the positions of galaxies to avoid a built-in influence of pair orientation on the filament construction. For pairs lying within filaments (3012 cases), we calculate the angle between the line connecting galaxies of each pair and their host filament. To avoid redshift-space distortions, the angle is measured in the plain of the sky. Results. The alignment analysis...

  1. 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.

  2. Image denoising using local tangent space alignment

    Science.gov (United States)

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

    2010-07-01

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

  3. Interference Alignment for Clustered Multicell Joint Decoding

    CERN Document Server

    Chatzinotas, Symeon

    2010-01-01

    Multicell joint processing has been proven to be very efficient in overcoming the interference-limited nature of the cellular paradigm. However, for reasons of practical implementation global multicell joint decoding is not feasible and thus clusters of cooperating Base Stations have to be considered. In this context, intercluster interference has to be mitigated in order to harvest the full potential of multicell joint processing. In this paper, four scenarios of intercluster interference are investigated, namely a) global multicell joint processing, b) interference alignment, c) resource division multiple access and d) cochannel interference allowance. Each scenario is modelled and analyzed using the per-cell ergodic sum-rate capacity as a figure of merit. In this process, a number of theorems are derived for analytically expressing the asymptotic eigenvalue distributions of the channel covariance matrices. The analysis is based on principles from Free Probability theory and especially properties in the R a...

  4. Frequency Scanned Interferometry for ILC Tracker Alignment

    CERN Document Server

    Yang, Hai-Jun; Riles, Keith

    2011-01-01

    In this paper, we report high-precision absolute distance and vibration measurements performed with frequency scanned interferometry. Absolute distance was determined by counting the interference fringes produced while scanning the laser frequency. High-finesse Fabry-Perot interferometers were used to determine frequency changes during scanning. A dual-laser scanning technique was used to cancel drift errors to improve the absolute distance measurement precision. A new dual-channel FSI demonstration system is also presented which is an interim stage toward practical application of multi-channel distance measurement. Under realistic conditions, a precision of 0.3 microns was achieved for an absolute distance of 0.57 meters. A possible optical alignment system for a silicon tracker is also presented.

  5. Aligning English Language Testing With Curriculum

    Directory of Open Access Journals (Sweden)

    Marcela Palacio

    2016-07-01

    Full Text Available Frustrations with traditional testing led a group of teachers at the English for adults program at Universidad EAFIT (Colombia to design tests aligned with the institutional teaching philosophy and classroom practices. This article reports on a study of an item-by-item evaluation of a series of English exams for validity and reliability in an effort to guarantee the quality of the process of test design. The study included descriptive statistics, item analysis, correlational analyses, reliability estimates, and validity analyses. The results show that the new tests are an excellent addition to the program and an improvement over traditional tests. Implications are discussed and recommendations given for the development of any institutional testing program.

  6. Impact of Baryonic Physics on Intrinsic Alignments

    Science.gov (United States)

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

    2017-01-01

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

  7. Yukawa alignment from natural flavor conservation

    CERN Document Server

    Cree, Graham

    2011-01-01

    We study the charged Higgs couplings to fermions in the "democratic" three-Higgs-doublet model, in which one doublet couples to down-type quarks, one to up-type quarks, and one to charged leptons. Flavor-changing neutral Higgs couplings are absent because the Glashow-Weinberg-Paschos condition for natural flavor conservation is in effect. We show that this model reproduces the coupling structure of the charged Higgs boson in the recently-proposed Yukawa-aligned two-Higgs-doublet model, with two subtle constraints that arise from the unitarity of the charged Higgs mixing matrix. Adding a fourth Higgs doublet with no couplings to fermions eliminates these constraints.

  8. Impact of Baryonic Physics on Intrinsic Alignments

    Energy Technology Data Exchange (ETDEWEB)

    Tenneti, Ananth [Carnegie Mellon U.; Gnedin, Nickolay Y. [Fermilab; Feng, Yu [UC, Berkeley

    2016-07-24

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

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

    CERN Document Server

    Blazek, Jonathan; Mandelbaum, Rachel

    2015-01-01

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

  10. 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.

  11. Alignment-free three-dimensional optical metamaterials.

    Science.gov (United States)

    Zhao, Yang; Shi, Jinwei; Sun, Liuyang; Li, Xiaoqin; Alù, Andrea

    2014-03-01

    Three-dimensional optical metamaterials based on multilayers typically rely on critical vertical alignment to achieve the desired functionality. Here the conditions under which three-dimensional metamaterials with different functionalities may be realized without constraints on alignment are analyzed and demonstrated experimentally. This study demonstrates that the release of alignment constraints for multilayered metamaterials is allowed, while their anomalous interaction with light is preserved.

  12. LOOSE PHRASE EXTRACTION WITH n-BEST ALIGNMENTS

    Institute of Scientific and Technical Information of China (English)

    Xue Yongzeng; Li Sheng

    2007-01-01

    Loose phrase extraction method is proposed and applied for phrase-based statistical machine translation. The method extracts phrase pairs that are not strictly consistent with word alignments. Two types of constraints on word positions are investigated for this method. Furthermore,n-best alignments are introduced for phrase extraction instead of the one-best. Experimental results show that the proposed approach outperforms the baseline system, Pharaoh system, for both one-best and n-best alignments.

  13. Continuous Growth of Vertically Aligned Carbon Nanotubes Forests

    OpenAIRE

    Guzman de Villoria, Roberto; Wardle, Brian L.

    2011-01-01

    Vertically aligned carbon nanotubes are one of the most promising materials due their numerous applications in flexible electronic devices, biosensors and multifunctional aircraft materials, among others. However, the costly production of aligned carbon nanotubes, generally in a batch process, prevents their commercial use. For the first time, a controlled process to grow aligned carbon nanotubes in a continuous manner is presented. Uniform growth is achieved using 2D and 3D substrates. A sig...

  14. Perception of socket alignment perturbations in amputees with transtibial prostheses

    OpenAIRE

    David A. Boone, PhD; Toshiki Kobayashi, PhD; Teri G . Chou, PhD; Adam K. Arabian, PhD; Kim L. Coleman, MS; Michael S. Orendurff, PhD; Ming Zhang, Ph

    2012-01-01

    A person with amputation’s subjective perception is the only tool available to describe fit and comfort to a prosthetist. However, few studies have investigated the effect of alignment on this perception. The aim of this article is to determine whether people with amputation could perceive the alignment perturbations of their prostheses and effectively communicate them. A randomized controlled perturbation of angular (3 and 6 degrees) and translational (5 and 10 mm) alignments in the sagittal...

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

    2016-01-01

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

  18. Permanent bending and alignment of ZnO nanowires.

    Science.gov (United States)

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

    2011-05-06

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

  19. Permanent bending and alignment of ZnO nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Borschel, Christian; Spindler, Susann; Oertel, Michael; Ronning, Carsten [Institut fuer Festkoerperphysik, Friedrich-Schiller-Universitaet Jena, Max-Wien-Platz 1, 07743 Jena (Germany); Lerose, Damiana [MPI fuer Mikrostrukturphysik, Weinberg 2, 06120 Halle/Saale (Germany); Institut fuer Photonische Technologien, Albert-Einstein-Strasse 9, 07745 Jena (Germany); Bochmann, Arne [Institut fuer Photonische Technologien, Albert-Einstein-Strasse 9, 07745 Jena (Germany); Christiansen, Silke H. [Institut fuer Photonische Technologien, Albert-Einstein-Strasse 9, 07745 Jena (Germany); MPI fuer die Physik des Lichts, Guenther-Scharowsky-Str. 1, 91058 Erlangen (Germany); Nietzsche, Sandor [Zentrum fuer Elektronenmikroskopie, Friedrich-Schiller-Universitaet Jena, Ziegelmuehlenweg 1, 07743 Jena (Germany)

    2011-07-01

    Ion beams can be used to bend or re-align nanowires permanently, after they have been grown. We have irradiated ZnO nanowires with ions of different species and energy, achieving bending and alignment in various directions. We study the bending of single nanowires as well as the simultaneous alignment of large ensembles of ZnO nanowires in detail. Computer simulations show that the bending is initiated by ion beam induced damage. Dislocations are identified to relax stresses and make the bending and alignment permanent and resistant against annealing procedures.

  20. 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.

  1. IRT studies of many groups: The alignment method

    Directory of Open Access Journals (Sweden)

    Bengt eMuthen

    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.

  2. A nano-scale alignment method for imprint lithography

    Institute of Scientific and Technical Information of China (English)

    WANG Li; LU Bing-heng; DING Yu-cheng; QIU Zhi-hui; LIU Hong-zhong

    2006-01-01

    A novel nano-scale alignment technique based generated by two pairs of quadruple gratings on mold and wafer are optically projected onto two photo-detector arrays,alignment errors in the x and y directions.The experiment sensitive to relative displacement of the mold and wafer,and the alignment accuracy obtained in the x and y directions and in θare ±20 nm,±25 nm and ±1 μrad (3σ),respectively.They can meet the requirements of alignment accuracy for submicron imprint lithography.

  3. Alignment of the ATLAS Inner Detector Tracking System

    CERN Document Server

    Gorfine, Grant

    2009-01-01

    The ATLAS detector, built at one of the interaction points of the Large Hadron Collider, is operational and has been collecting data from cosmic rays. This paper describes the track based alignment of the ATLAS Inner Detector tracker which was performed using cosmic rays collected in 2008. The alignment algorithms are described and the performance of the alignment is demonstrated by showing the resulting hit residuals and comparing track parameters of upper and lower segments of tracks. The impact of the alignment on physics measurements is discussed.

  4. Metabolic network alignment in large scale by network compression

    Directory of Open Access Journals (Sweden)

    Ay Ferhat

    2012-03-01

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

  5. 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.

  6. Anchor-based English-Chinese Bilingual Chunk Alignment Model

    Institute of Scientific and Technical Information of China (English)

    WU We-lin; CHENG Chang-sheng; XU Liang-xian; LU Ru-zhan

    2005-01-01

    Chunk alignment for the bilingual corpus is the base of Example-based Machine Translation. An anchor-based English-Chinese bilingual chunk alignment model and the corresponding algorithm of alignment are presented in this paper. It can effectively overcome the sparse data problem due to the limited size of the bilingual corpus. In this model, the chunk segmentation disambiguation is delayed to the alignment process, and hence the accuracy of chunk segmentation is improved. The experimental results demonstrate the feasibility and viability of this model.

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

    Directory of Open Access Journals (Sweden)

    Emanuel Santos

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

  8. Robust local intervertebral disc alignment for spinal MRI

    Science.gov (United States)

    Reisman, James; Höppner, Jan; Huang, Szu-Hao; Zhang, Li; Lai, Shang-Hong; Odry, Benjamin; Novak, Carol L.

    2006-03-01

    Magnetic resonance (MR) imaging is frequently used to diagnose abnormalities in the spinal intervertebral discs. Owing to the non-isotropic resolution of typical MR spinal scans, physicians prefer to align the scanner plane with the disc in order to maximize the diagnostic value and to facilitate comparison with prior and follow-up studies. Commonly a planning scan is acquired of the whole spine, followed by a diagnostic scan aligned with selected discs of interest. Manual determination of the optimal disc plane is tedious and prone to operator variation. A fast and accurate method to automatically determine the disc alignment can decrease examination time and increase the reliability of diagnosis. We present a validation study of an automatic spine alignment system for determining the orientation of intervertebral discs in MR studies. In order to measure the effectiveness of the automatic alignment system, we compared its performance with human observers. 12 MR spinal scans of adult spines were tested. Two observers independently indicated the intervertebral plane for each disc, and then repeated the procedure on another day, in order to determine the inter- and intra-observer variability associated with manual alignment. Results were also collected for the observers utilizing the automatic spine alignment system, in order to determine the method's consistency and its accuracy with respect to human observers. We found that the results from the automatic alignment system are comparable with the alignment determined by human observers, with the computer showing greater speed and consistency.

  9. 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.

  10. Sample-Align-D: A High Performance Multiple Sequence Alignment System using Phylogenetic Sampling and Domain Decomposition

    CERN Document Server

    Saeed, Fahad

    2009-01-01

    Multiple Sequence Alignment (MSA) is one of the most computationally intensive tasks in Computational Biology. Existing best known solutions for multiple sequence alignment take several hours (in some cases days) of computation time to align, for example, 2000 homologous sequences of average length 300. Inspired by the Sample Sort approach in parallel processing, in this paper we propose a highly scalable multiprocessor solution for the MSA problem in phylogenetically diverse sequences. Our method employs an intelligent scheme to partition the set of sequences into smaller subsets using kmer count based similarity index, referred to as k-mer rank. Each subset is then independently aligned in parallel using any sequential approach. Further fine tuning of the local alignments is achieved using constraints derived from a global ancestor of the entire set. The proposed Sample-Align-D Algorithm has been implemented on a cluster of workstations using MPI message passing library. The accuracy of the proposed solutio...

  11. 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/.

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

    Science.gov (United States)

    Li, Yan; Gu, Leon; Kanade, Takeo

    2011-09-01

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

  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. Connectivity independent protein-structure alignment: a hierarchical approach

    Directory of Open Access Journals (Sweden)

    Schmidt-Goenner Tobias

    2006-11-01

    Full Text Available Abstract Background Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure elements (SSE but differ in the underlying polypeptide chain connectivity (non-sequential SSE connectivity. Results We perform protein-structure alignment using a two-level hierarchical approach implemented in the program GANGSTA. On the first level, pair contacts and relative orientations between SSEs (i.e. α-helices and β-strands are maximized with a genetic algorithm (GA. On the second level residue pair contacts from the best SSE alignments are optimized. We have tested the method on visually optimized structure alignments of protein pairs (pairwise mode and for database scans. For a given protein structure, our method is able to detect significant structural similarity of functionally important folds with non-sequential SSE connectivity. The performance for structure alignments with strictly sequential SSE connectivity is comparable to that of other structure alignment methods. Conclusion As demonstrated for several applications, GANGSTA finds meaningful protein-structure alignments independent of the SSE connectivity. GANGSTA is able to detect structural similarity of protein folds that are assigned to different superfamilies but nevertheless possess similar structures and perform related functions, even if these proteins differ in SSE connectivity.

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

    Directory of Open Access Journals (Sweden)

    Tatusova Tatiana

    2008-05-01

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

  16. Aligning Business Needs and Instructional Assets (Recycling Instructional Assets)

    Science.gov (United States)

    Gendelman, Joel

    2009-01-01

    High-performing organizations and performance improvement professionals frequently speak about the alignment of their instructional curricula with the needs of the business. However, they often lack a systematic methodology for performing that alignment. This article presents such a method. The process provides the ability to better support…

  17. Nonlinear Alignment and Its Local Linear Iterative Solution

    Directory of Open Access Journals (Sweden)

    Sumin Zhang

    2016-01-01

    Full Text Available In manifold learning, the aim of alignment is to derive the global coordinate of manifold from the local coordinates of manifold’s patches. At present, most of manifold learning algorithms assume that the relation between the global and local coordinates is locally linear and based on this linear relation align the local coordinates of manifold’s patches into the global coordinate of manifold. There are two contributions in this paper. First, the nonlinear relation between the manifold’s global and local coordinates is deduced by making use of the differentiation of local pullback functions defined on the differential manifold. Second, the method of local linear iterative alignment is used to align the manifold’s local coordinates into the manifold’s global coordinate. The experimental results presented in this paper show that the errors of noniterative alignment are considerably large and can be reduced to almost zero within the first two iterations. The large errors of noniterative/linear alignment verify the nonlinear nature of alignment and justify the necessity of iterative alignment.

  18. Alignment between business process governance and IT governance

    DEFF Research Database (Denmark)

    Rahimi, Fatemeh; Møller, Charles; Hvam, Lars

    2014-01-01

    frameworks to enable business-IT strategic alignment, efficient process and IT requirements specification, and IT-enabled business value realization. We examine the actuality of this alignment in practice through a case study conducted in a relatively mature multinational corporation. The findings indicate...

  19. 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.

  20. Chunk Alignment for Corpus-Based Machine Translation

    Science.gov (United States)

    Kim, Jae Dong

    2011-01-01

    Since sub-sentential alignment is critically important to the translation quality of an Example-Based Machine Translation (EBMT) system, which operates by finding and combining phrase-level matches against the training examples, we developed a new alignment algorithm for the purpose of improving the EBMT system's performance. This new…

  1. Design, development and verification of the HIFI Alignment Camera System

    NARCIS (Netherlands)

    Boslooper, E.C.; Zwan, B.A. van der; Kruizinga, B.; Lansbergen, R.

    2005-01-01

    This paper presents the TNO share of the development of the HIFI Alignment Camera System (HACS), covering the opto-mechanical and thermal design. The HACS is an Optical Ground Support Equipment (OGSE) that is specifically developed to verify proper alignment of different modules of the HIFI instrume

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

    Science.gov (United States)

    Demkin, V V

    2010-01-01

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

  3. Clustering vessel trajectories with alignment kernels under trajectory compression

    NARCIS (Netherlands)

    de Vries, G.; van Someren, M.

    2010-01-01

    In this paper we apply a selection of alignment measures, such as dynamic time warping and edit distance, to the problem of clustering vessel trajectories. Vessel trajectories are an example of moving object trajectories, which have recently become an important research topic. The alignment measures

  4. Alignments of galaxies and halos in hydrodynamical simulations

    Science.gov (United States)

    Pahwa, Isha; Libeskind, Noam I.

    2016-10-01

    We use a 200 h -1Mpc cosmological hydrodynamical simulation to examine the alignments of galaxies with respect to the host halo. We do separate study for the different components of the halo, such as stars, gas and dark matter. We show that angular momentum of gas is more aligned with the angular momentum of host halo compared with the stellar component.

  5. 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

  6. Comparative Analysis of the Measurement of Total Instructional Alignment

    Science.gov (United States)

    Kick, Laura C.

    2013-01-01

    In 2007, Lisa Carter created the Total Instructional Alignment system--a process that aligns standards, curriculum, assessment, and instruction. Employed in several hundred school systems, the TIA process is a successful professional development program. The researcher developed an instrument to measure the success of the TIA process with the…

  7. 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.

  8. 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…

  9. 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 the…

  10. 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…

  11. Study on compound ultra-precision alignment technique

    Institute of Scientific and Technical Information of China (English)

    Zhang Jinlong; Yang Ankang; Liu Jingnan; Yoshiyuki Uchida

    2007-01-01

    A nano-displacement measurement system with duo-gratings is analyzed by using optics theory, a mathematic model for the system is established, and the characteristic of laser Moiré signals is studied through CAD simulation. To improve signal sensitivity and positioning accuracy, two methods of precision positioning are brought forward: differential Moiré positioning method and modified Moiré positioning method. A compound control system for precision positioning is set up by combining these 2 Moiré alignment methods, in which the modified Moiré alignment technique is used for coarse alignment and the differential Moiré alignment technique is used for fine alignment, and the system obtains positioning accuracy of ±10 nm in ±500 μm positioning range with shot response time.

  12. 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.

  13. General space-efficient sampling algorithm for suboptimal alignment

    Institute of Scientific and Technical Information of China (English)

    CHEN; Yi; BAI; Yan-qin

    2009-01-01

    Suboptimal alignments always reveal additional interesting biological features and have been successfully used to informally estimate the significance of an optimal alignment. Besides, traditional dynamic programming algorithms for sequence comparison require quadratic space, and hence are infeasible for long protein or DNA sequences. In this paper, a space-efficient sampling algorithm for computing suboptimal alignments is described. The algorithm uses a general gap model, where the cost associated with gaps is given by an affine score, and randomly selects an alignment according to the distribution of weights of all potential alignments. If x and y are two sequences with lengths n and m, respectively, then the space requirement of this algorithm is linear to the sum of n and m. Finally, an example illustrates the utility of the algorithm.

  14. 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.

  15. PARIS: Probabilistic Alignment of Relations, Instances, and Schema

    CERN Document Server

    Suchanek, Fabian M; Senellart, Pierre

    2011-01-01

    One of the main challenges that the Semantic Web faces is the integration of a growing number of independently designed ontologies. In this work, we present PARIS, an approach for the automatic alignment of ontologies. PARIS aligns not only instances, but also relations and classes. Alignments at the instance level cross-fertilize with alignments at the schema level. Thereby, our system provides a truly holistic solution to the problem of ontology alignment. The heart of the approach is probabilistic, i.e., we measure degrees of matchings based on probability estimates. This allows PARIS to run without any parameter tuning. We demonstrate the efficiency of the algorithm and its precision through extensive experiments. In particular, we obtain a precision of around 90% in experiments with some of the world's largest ontologies.

  16. A context dependent pair hidden Markov model for statistical alignment

    CERN Document Server

    Arribas-Gil, Ana

    2011-01-01

    This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and context dependent mutation rates relying on the observation of two homologous sequences. The procedure is based on a generalized pair-hidden Markov structure, where conditional on the alignment path, the nucleotide sequences follow a Markov distribution. We use a stochastic approximation expectation maximization (saem) algorithm to give accurate estimators of parameters and alignments. We provide results both on simulated data and vertebrate genomes, which are known to have a high mutation rate from CG dinucleotide. In particular, we establish that the method improves the accuracy of the alignment of a human pseudogene and its functional gene.

  17. 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...

  18. The Laser Shaft Alignment System with Dual PSDs

    Institute of Scientific and Technical Information of China (English)

    JIAO Guohua; LI Yulin; ZHANG Dongbo; LI Tonghai; HU Baowen

    2006-01-01

    Shaft alignment is an important technique during installation and maintenance of a rotating machine. A high-precision laser alignment system has been designed with dual PSDs (Position Sensing Detector) to change traditional manual way of shaft alignment and to make the measurement easier and more accurate. The system is comprised of two small measuring units (laser transmitter and detector) and a PDA (Personal Digital Assistant) with the measurement software. The laser alignment system with dual PSDs was improved on a single PSD system, and it gets higher measurement accuracy than the previous design, and it has been succeeded in designing and implement for actual shaft alignment. In the system, the range of offset measurement is ±4 mm, and the resolution is 1.5 μm, and the accuracy is less than 2 μm.

  19. A laser shaft alignment system with dual PSDs

    Institute of Scientific and Technical Information of China (English)

    JIAO Guo-hua; LI Yu-lin; ZHANG Dong-bo; LI Tong-hai; HU Bao-wen

    2006-01-01

    Shaft alignment is an important technique during installation and maintenance of a rotating machine. A high-precision laser alignment system has been designed with dual PSDs (Position Sensing Detector) to change traditional manual way of shaft alignment and to make the measurement easier and more accurate. The system is comprised of two small measuring units (laser transmitter and detector) and a PDA (Personal Digital Assistant) with measurement software. The laser alignment system with dual PSDs was improved on a single PSD system, and yields higher measurement accuracy than the previous design, and has been successful for designing and implements actual shaft alignment. In the system, the range of offset measurement is ±4 mm, and the resolution is 1.5 μm, with accuracy being less than 2 μm.

  20. Research on SINS Alignment Algorithm Based on FIR Filters

    Institute of Scientific and Technical Information of China (English)

    LIAN Jun-xiang; HU De-wen; WU Yuan-xin; HU Xiao-ping

    2007-01-01

    An inertial frame based alignment (IFBA) method is presented, especially for the applications on a rocking platform, e.g., marine applications. Defining the initial body frame as the inertial frame, the IFBA method achieves the alignment by virtue of a cascade of low-pass FIR filters, which attenuate the disturbing acceleration and maintain the gravity vector. The aligning time rests with the orders of the FIR filter group, and the method is suitable for large initial misali gnment case. An alignment scheme comprising a coarse phase by the IFBA method an d a fine phase by a Kalman filter is presented. Both vehicle-based and ship-based alignment experiments were carried out. The results show that the proposed scheme converges much faster than the traditional method at no cost of precision and also works well under any large initial misalignment.

  1. 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.

  2. 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.

  3. 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.

  4. Interference Alignment: A one-sided approach

    CERN Document Server

    Ghauch, Hadi G

    2011-01-01

    Interference Alignment (IA) is the process of designing signals in such a way that they cast overlapping shadows at their unintended receivers, while remaining distinguishable at the intended ones. Our goal in this paper is to come up with an algorithm for IA that runs at the transmitters only (and is transparent to the receivers), that doesn't require channel reciprocity, and that alleviates the need to alternate between the forward and reverse network as is the case in Distributed IA (Gomadam, Cadambe, Jafar 08'), thereby inducing significant overhead in certain environments where the channel changes frequently. Most importantly, our effort is focused on ensuring that this one-sided approach does not degrade the performance of the system w.r.t. Distributed IA (since it cannot improve it). As a first step, we model the interference in each receiver's desired signal as a function of the transmitters' beamforming vectors. We then propose a simple steepest descent (SD) algorithm and use it to minimize the inter...

  5. Interference Alignment with Partially Coordinated Transmit Precoding

    CERN Document Server

    Yousafzai, Aimal Khan

    2011-01-01

    In this paper, we introduce an efficient interference alignment (IA) algorithm exploiting partially coordinated transmit precoding to improve the number of concurrent interference-free transmissions, i.e., the multiplexing gain, in multicell downlink. The proposed coordination model is such that each base-station simultaneously transmits to two users and each user is served by two base-stations. First, we show in a K-user system operating at the information theoretic upper bound of degrees of freedom (DOF), the generic IA is proper when $K \\leq 3$, whereas the proposed partially coordinated IA is proper when $K \\leq 5$. Then, we derive a non-iterative, i.e., one shot, IA algorithm for the proposed scheme when $K \\leq 5$. We show that for a given latency, the backhaul data rate requirement of the proposed method grows linearly with K. Monte-Carlo simulation results show that the proposed one-shot algorithm offers higher system throughput than the iterative IA at practical SNR levels.

  6. CYLINDER LENS ALIGNMENT IN THE LTP

    Energy Technology Data Exchange (ETDEWEB)

    TAKACS, P.Z.

    2005-07-26

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

  7. Differential Phase Detector for Precise Phase Alignment

    CERN Document Server

    Olexa, Jakub

    2016-01-01

    This paper presents a differential phase detector circuit, whose phase-to-voltage characteristic has an extremum when its two input signals are exactly in phase. In this condition all its digital signals are of 50 % duty cycle so that the circuit characteristic does not have a dead zone. This feature allows a precise indication of the zero-phase condition, which is independent of the detector power supply and the offset of its ADC readout. Such a detector is used for a phase alignment of two reference clock signals with frequency about 11 kHz in front-ends processing signals from beam position monitors of the Large Hadron Collider (LHC) at CERN. The detector output voltage is digitized with a 24-bit ADC at the rate of the reference signals. The resulting samples are processed in the front-end FPGA and transmitted to the control system using an Ethernet data stream. After a detailed description of the differential phase detector its performance is demonstrated with laboratory measurements. The results show tha...

  8. Aligned-Braided Nanofibrillar Scaffold with Endothelial Cells Enhances Arteriogenesis.

    Science.gov (United States)

    Nakayama, Karina H; Hong, Guosong; Lee, Jerry C; Patel, Jay; Edwards, Bryan; Zaitseva, Tatiana S; Paukshto, Michael V; Dai, Hongjie; Cooke, John P; Woo, Y Joseph; Huang, Ngan F

    2015-07-28

    The objective of this study was to enhance the angiogenic capacity of endothelial cells (ECs) using nanoscale signaling cues from aligned nanofibrillar scaffolds in the setting of tissue ischemia. Thread-like nanofibrillar scaffolds with porous structure were fabricated from aligned-braided membranes generated under shear from liquid crystal collagen solution. Human ECs showed greater outgrowth from aligned scaffolds than from nonpatterned scaffolds. Integrin α1 was in part responsible for the enhanced cellular outgrowth on aligned nanofibrillar scaffolds, as the effect was abrogated by integrin α1 inhibition. To test the efficacy of EC-seeded aligned nanofibrillar scaffolds in improving neovascularization in vivo, the ischemic limbs of mice were treated with EC-seeded aligned nanofibrillar scaffold; EC-seeded nonpatterned scaffold; ECs in saline; aligned nanofibrillar scaffold alone; or no treatment. After 14 days, laser Doppler blood spectroscopy demonstrated significant improvement in blood perfusion recovery when treated with EC-seeded aligned nanofibrillar scaffolds, in comparison to ECs in saline or no treatment. In ischemic hindlimbs treated with scaffolds seeded with human ECs derived from induced pluripotent stem cells (iPSC-ECs), single-walled carbon nanotube (SWNT) fluorophores were systemically delivered to quantify microvascular density after 28 days. Near infrared-II (NIR-II, 1000-1700 nm) imaging of SWNT fluorophores demonstrated that iPSC-EC-seeded aligned scaffolds group showed significantly higher microvascular density than the saline or cells groups. These data suggest that treatment with EC-seeded aligned nanofibrillar scaffolds improved blood perfusion and arteriogenesis, when compared to treatment with cells alone or scaffold alone, and have important implications in the design of therapeutic cell delivery strategies.

  9. Computational design and engineering of polymeric orthodontic aligners.

    Science.gov (United States)

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

    2016-10-05

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

  10. Cervical spine alignment, sagittal deformity, and clinical implications: a review.

    Science.gov (United States)

    Scheer, Justin K; Tang, Jessica A; Smith, Justin S; Acosta, Frank L; Protopsaltis, Themistocles S; Blondel, Benjamin; Bess, Shay; Shaffrey, Christopher I; Deviren, Vedat; Lafage, Virginie; Schwab, Frank; Ames, Christopher P

    2013-08-01

    This paper is a narrative review of normal cervical alignment, methods for quantifying alignment, and how alignment is associated with cervical deformity, myelopathy, and adjacent-segment disease (ASD), with discussions of health-related quality of life (HRQOL). Popular methods currently used to quantify cervical alignment are discussed including cervical lordosis, sagittal vertical axis, and horizontal gaze with the chin-brow to vertical angle. Cervical deformity is examined in detail as deformities localized to the cervical spine affect, and are affected by, other parameters of the spine in preserving global sagittal alignment. An evolving trend is defining cervical sagittal alignment. Evidence from a few recent studies suggests correlations between radiographic parameters in the cervical spine and HRQOL. Analysis of the cervical regional alignment with respect to overall spinal pelvic alignment is critical. The article details mechanisms by which cervical kyphotic deformity potentially leads to ASD and discusses previous studies that suggest how postoperative sagittal malalignment may promote ASD. Further clinical studies are needed to explore the relationship of cervical malalignment and the development of ASD. Sagittal alignment of the cervical spine may play a substantial role in the development of cervical myelopathy as cervical deformity can lead to spinal cord compression and cord tension. Surgical correction of cervical myelopathy should always take into consideration cervical sagittal alignment, as decompression alone may not decrease cord tension induced by kyphosis. Awareness of the development of postlaminectomy kyphosis is critical as it relates to cervical myelopathy. The future direction of cervical deformity correction should include a comprehensive approach in assessing global cervicalpelvic relationships. Just as understanding pelvic incidence as it relates to lumbar lordosis was crucial in building our knowledge of thoracolumbar deformities, T

  11. 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…

  12. 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...

  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

    the 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 method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles. RESULTS: The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation...... by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic...

  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. Evaluation measures of multiple sequence alignments.

    Science.gov (United States)

    Gonnet, G H; Korostensky, C; Benner, S

    2000-01-01

    Multiple sequence alignments (MSAs) are frequently used in the study of families of protein sequences or DNA/RNA sequences. They are a fundamental tool for the understanding of the structure, functionality and, ultimately, the evolution of proteins. A new algorithm, the Circular Sum (CS) method, is presented for formally evaluating the quality of an MSA. It is based on the use of a solution to the Traveling Salesman Problem, which identifies a circular tour through an evolutionary tree connecting the sequences in a protein family. With this approach, the calculation of an evolutionary tree and the errors that it would introduce can be avoided altogether. The algorithm gives an upper bound, the best score that can possibly be achieved by any MSA for a given set of protein sequences. Alternatively, if presented with a specific MSA, the algorithm provides a formal score for the MSA, which serves as an absolute measure of the quality of the MSA. The CS measure yields a direct connection between an MSA and the associated evolutionary tree. The measure can be used as a tool for evaluating different methods for producing MSAs. A brief example of the last application is provided. Because it weights all evolutionary events on a tree identically, but does not require the reconstruction of a tree, the CS algorithm has advantages over the frequently used sum-of-pairs measures for scoring MSAs, which weight some evolutionary events more strongly than others. Compared to other weighted sum-of-pairs measures, it has the advantage that no evolutionary tree must be constructed, because we can find a circular tour without knowing the tree.

  16. AGORA: Assembly Guided by Optical Restriction Alignment

    Directory of Open Access Journals (Sweden)

    Lin Henry C

    2012-08-01

    Full Text Available Abstract Background Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs. Long range linking information, such as mate-pairs or mapping data, is necessary to help assembly software resolve repeats, thereby leading to a more complete reconstruction of genomes. Prior work has used optical maps for validating assemblies and scaffolding contigs, after an initial assembly has been produced. However, optical maps have not previously been used within the genome assembly process. Here, we use optical map information within the popular de Bruijn graph assembly paradigm to eliminate paths in the de Bruijn graph which are not consistent with the optical map and help determine the correct reconstruction of the genome. Results We developed a new algorithm called AGORA: Assembly Guided by Optical Restriction Alignment. AGORA is the first algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. Our simulations on bacterial genomes show that AGORA is effective at producing assemblies closely matching the reference sequences. Additionally, we show that noise in the optical map can have a strong impact on the final assembly quality for some complex genomes, and we also measure how various characteristics of the starting de Bruijn graph may impact the quality of the final assembly. Lastly, we show that a proper choice of restriction enzyme for the optical map may substantially improve the quality of the final assembly. Conclusions Our work shows that optical maps can be used effectively to assemble genomes within the de Bruijn graph assembly framework. Our experiments also provide insights into the characteristics of the mapping data that most affect the performance of our algorithm, indicating the

  17. 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...

  18. Iridium catalyzed growth of vertically aligned CNTs by APCVD

    Energy Technology Data Exchange (ETDEWEB)

    Sahoo, R.K.; Jacob, C., E-mail: cxj14_holiday@yahoo.com

    2014-07-01

    Highlights: • Growth of uniform-diameter vertically-aligned multi-walled CNTs by APCVD. • Use of high melting point low carbon solubility iridium nanoparticles as catalyst. • Optimization of growth time for uniform sized, uniformly aligned CNTs. • Growth model for the various features in the vertically aligned CNTs is proposed. - Abstract: Vertically aligned carbon nanotubes (VA-CNTs) have been synthesized using high temperature catalyst nanoparticles of iridium. The catalyst layer was prepared by DC sputtering. Particle density, circularity and average particle size of the catalyst were analyzed using field emission scanning electron microscopy. The alignment, morphology and the length of the as-grown CNTs were analyzed using field-emission scanning electron microscopy. High resolution transmission electron microscopy was carried out to observe the layers of graphitic stacking which form the carbon nanotubes. Micro Raman measurement was used for the analysis of the graphitic crystallinity of the as-grown carbon nano structures. Effects of growth time variation on growth morphology and alignment have been studied. The alignment has been explained on the basis of the crowding effect of the neighboring nanoparticles.

  19. Automatic array alignment in data-parallel programs

    Science.gov (United States)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert; Teng, Shang-Hua

    1993-01-01

    FORTRAN 90 and other data-parallel languages express parallelism in the form of operations on data aggregates such as arrays. Misalignment of the operands of an array operation can reduce program performance on a distributed-memory parallel machine by requiring nonlocal data accesses. Determining array alignments that reduce communication is therefore a key issue in compiling such languages. We present a framework for the automatic determination of array alignments in array-based, data-parallel languages. Our language model handles array sectioning, reductions, spreads, transpositions, and masked operations. We decompose alignment functions into three constituents: axis, stride, and offset. For each of these subproblems, we show how to solve the alignment problem for a basic block of code, possibly containing common subexpressions. Alignments are generated for all array objects in the code, both named program variables and intermediate results. We assign computation to processors by virtue of explicit alignment of all temporaries; the resulting work assignment is in general better than that provided by the 'owner-computes' rule. Finally, we present some ideas for dealing with control flow, replication, and dynamic alignments that depend on loop induction variables.

  20. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

    Chisari, Nora Elisa [Department of Astrophysical Sciences, Princeton University, 4 Ivy Lane, Princeton, NJ 08544 (United States); Dvorkin, Cora, E-mail: nchisari@astro.princeton.edu, E-mail: cdvorkin@ias.edu [Institute for Advanced Study, School of Natural Sciences, Einstein Drive, Princeton, NJ 08540 (United States)

    2013-12-01

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

  2. Magnetically aligned polymer-nanowire composites for solar energy harvesting

    Science.gov (United States)

    Majewski, Pawel; Pelligra, Candice; Osuji, Chinedum

    2013-03-01

    We present a solution-based approach of producing aligned arrays of ZnO nanowire-polythiophene composites for photovoltaic applications. We employ a two-step hierarchical self-assembly to maximize the efficiency of electron and hole transport in the system. First, we coat the wires with the polymer utilizing nanowire surface-directed crystallization and alignment of the polymer backbones along the long axes of the wires, then we employ magnetic fields to direct the assembly of the composites into the ordered arrays. We present quantitative SAXS data taken in-situ during the alignment process addressing the influence of paramagnetic doping level of ZnO and the magnetic field strength on the quality of the alignment. We compare the electrical conductivity of the aligned arrays of the composites to non-aligned ones and discuss the possible degree of conductivity enhancement upon the alignment in this and in analogous systems. This work is funded by the NSF under DMR-0847534 and DMR-0934520

  3. 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.

  4. 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. 

  5. How do we Take Care of Strategic Alignment?

    DEFF Research Database (Denmark)

    Simonsen, Jesper

    1999-01-01

    The article reviews the concept of ‘strategic alignment’ and presents the critique by Ciborra in SJIS (Vol. 9, No. 1) entitled “De profundis? Deconstructing the concept of strategic alignment”. We present a design approach that suggests how designers, conducting design projects in a specific orga...... environmental conditions, business strategies, and plans for IT are changing and hence challenge traditional approaches to strategic alignment. The results from the design project are described and related to IS literature and to Ciborra’s article.......The article reviews the concept of ‘strategic alignment’ and presents the critique by Ciborra in SJIS (Vol. 9, No. 1) entitled “De profundis? Deconstructing the concept of strategic alignment”. We present a design approach that suggests how designers, conducting design projects in a specific...... organization, can take care of and ensure that the design of IT is appropriately aligned with the organization’s overall business strategy. We describe a design project using this approach. The project presented took place in a small public organization. Focusing on alignment as part of the design process had...

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

    Science.gov (United States)

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2007-01-01

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

  7. 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.

  8. Spontaneous magnetic alignment behaviour in free-living lizards

    Science.gov (United States)

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

    2017-04-01

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

  9. 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.

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

    Science.gov (United States)

    Khan, Wajeeh

    2014-09-01

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

  11. Full Alignment of Molecules Using Elliptically Polarized Light

    DEFF Research Database (Denmark)

    Larsen, Jakob Juul; Hald, Kasper; Seideman, Tamar

    When a molecule with an anisotropic polarizability is placed in a strong nonresonant laser field the interaction occurs through the induced dipole moment. The outcome is that the molecule experiences an angular dependent potential energy. It is now well established that a linearly polarized laser...... of the molecule the third axis is also aligned. Experimentally, we investigate the effect by aligning 3,4-dibromothiophene molecules with a strong, nonresonant, nanosecond laser pulse. The alignment is probed by Coulomb exploding the molecules with an intense 20 femtosecond laser pulse. Detection of the emerging...

  12. Shear Flow Induced Alignment of Carbon Nanotubes in Natural Rubber

    Directory of Open Access Journals (Sweden)

    Yan He

    2015-01-01

    Full Text Available A new procedure for the fabrication of natural rubber composite with aligned carbon nanotubes is provided in this study. The two-step approach is based on (i the preparation of mixture latex of natural rubber, multiwalled carbon nanotubes, and other components and (ii the orientation of carbon nanotubes by a flow field. Rubber composite sheets filled with variable volume fraction of aligned carbon nanotubes were fabricated and then confirmed by transmission electron microscopy and Raman spectroscopy studies. An obvious increase in thermal conductivity has been obtained after the alignment of carbon nanotubes. The dynamic mechanical analysis was carried out in a tear mode for the composite.

  13. Fourier-transform and global contrast interferometer alignment methods

    Science.gov (United States)

    Goldberg, Kenneth A.

    2001-01-01

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

  14. An Improved Model Facet Method to Support EA Alignment

    Directory of Open Access Journals (Sweden)

    Jonathan Pepin

    2016-12-01

    Full Text Available Information System evolution requires a well-structured Enterprise Architecture and its rigorous management. The alignment of the elements in the architecture according to various abstraction layers may contribute to the management but appropriate tools are needed. We propose improvements to the Facet technique and we develop accompanying tools to master the difficulties of the alignment of the models used to structure an Enterprise Architecture. This technique has been experimented on many real life cases to demonstrate the effectiveness of our EA alignment method. The tools are already integrated in the Eclipse EMF Facet project.

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

    Science.gov (United States)

    Mcclain, C. R.

    1980-01-01

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

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

    Science.gov (United States)

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

    2007-01-01

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

  17. Alignment control of carbon nanotube forest from random to nearly perfectly aligned by utilizing the crowding effect.

    Science.gov (United States)

    Xu, Ming; Futaba, Don N; Yumura, Motoo; Hata, Kenji

    2012-07-24

    Alignment represents an important structural parameter of carbon nanotubes (CNTs) owing to their exceptionally high aspect ratio, one-dimensional property. In this paper, we demonstrate a general approach to control the alignment of few-walled CNT forests from nearly random to nearly ideally aligned by tailoring the density of active catalysts at the catalyst formation stage, which can be experimentally achieved by controlling the CNT forest mass density. Experimentally, we found that the catalyst density and the degree of alignment were inseparably linked because of a crowding effect from neighboring CNTs, that is, the increasing confinement of CNTs with increased density. Therefore, the CNT density governed the degree of alignment, which increased monotonically with the density. This relationship, in turn, allowed the precise control of the alignment through control of the mass density. To understand this behavior further, we developed a simple, first-order model based on the flexural modulus of the CNTs that could quantitatively describe the relationship between the degree of alignment (HOF) and carbon nanotube spacing (crowding effect) of any type of CNTs.

  18. Assessing lexical, syntactic, and conceptual turn-by-turn alignment in conversations involving conflict and deception

    DEFF Research Database (Denmark)

    Duran, Nicholas; Fusaroli, Riccardo; Paxton, Alexandra

    2015-01-01

    can modulate alignment processes consistently across multiple levels of linguistic abstraction. Contrary to previous findings on non-verbal coordination (Duran and Fusaroli, under review), deception disrupts verbal alignment, and alignment generally decreases over time. Moreover, for a subset...

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

    Science.gov (United States)

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

    2017-02-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Komatsoulis, G.A.; Waterman, M.S. [Univ. of Southern California, Los Angeles, CA (United States)

    1997-12-01

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

  1. 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.

  2. Non-stationary condition monitoring through event alignment

    DEFF Research Database (Denmark)

    Pontoppidan, Niels Henrik; Larsen, Jan

    2004-01-01

    We present an event alignment framework which enables change detection in non-stationary signals. change detection. Classical condition monitoring frameworks have been restrained to laboratory settings with stationary operating conditions, which are not resembling real world operation....... In this paper we apply the technique for non-stationary condition monitoring of large diesel engines based on acoustical emission sensor signals. The performance of the event alignment is analyzed in an unsupervised probabilistic detection framework based on outlier detection with either Principal Component...... Analysis or Gaussian Processes modeling. We are especially interested in the true performance of the condition monitoring performance with mixed aligned and unaligned data, e.g. detection of fault condition of unaligned examples versus false alarms of aligned normal condition data. Further, we expect...

  3. 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.

  4. 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.

  5. 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.

  6. CLIC BDS Tuning, Alignment and Feedbacks Integrated Simulations

    CERN Document Server

    Dalena, B; Schulte, D; Snuverink, J; Tomas, R; Jones, J; Latina, A; Resta, J

    2010-01-01

    The CLIC BDS tuning, alignment and feedbacks studies have been typically performed independently and only over particular sections of the BDS. An effort is being put to integrate all these procedures to realistically evaluate the luminosity performance.

  7. 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...

  8. 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.

  9. 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 indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports...... multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. AVAILABILITY: http://soap.genomics.org.cn....

  10. 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.

  11. 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...

  12. Polarizing effect of aligned nanoparticles in terahertz frequency region.

    Science.gov (United States)

    Polley, Debanjan; Ganguly, Arnab; Barman, Anjan; Mitra, Rajib Kumar

    2013-08-01

    We report the polarizing behavior of aligned Ni nanoparticles (NPs) having average diameter of 165±15 nm in ~210 μm thick polyvinyl alcohol (PVA) matrix in the frequency range of 0.2-1.6 THz. The NPs have been prepared via a wet chemical route and then aligned in PVA film by using an external magnetic field. When the polarization of THz electric field is parallel to the NPs alignment direction, a strong THz absorption is observed whereas a minimum THz absorption is noticed for the corresponding perpendicular configuration. Degree of polarization is calculated to be 0.9±0.08. Considering the good polarizing performance, ease of preparation, durability, and low maintenance, this aligned NP system is a perfect candidate to emerge as a potential THz polarizer.

  13. 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...

  14. Electrospun nanofiber reinforcement of dental composites with electromagnetic alignment approach

    Energy Technology Data Exchange (ETDEWEB)

    Uyar, Tansel [Department of Biomedical Engineering, Başkent University Bağlıca Campus, 06530 Ankara (Turkey); Çökeliler, Dilek, E-mail: cokeliler@baskent.edu.tr [Department of Biomedical Engineering, Başkent University Bağlıca Campus, 06530 Ankara (Turkey); Doğan, Mustafa [Department of Electrical and Electronics Engineering, Başkent University, Ankara 06180 (Turkey); Koçum, Ismail Cengiz [Department of Biomedical Engineering, Başkent University Bağlıca Campus, 06530 Ankara (Turkey); Karatay, Okan [Department of Electrical and Electronics Engineering, Başkent University, Ankara 06180 (Turkey); Denkbaş, Emir Baki [Department of Chemistry, Biochemistry Division, Hacettepe University, Ankara (Turkey)

    2016-05-01

    Polymethylmethacrylate (PMMA) is commonly used as a base acrylic denture material with benefits of rapid and easy handling, however, when it is used in prosthetic dentistry, fracturing or cracking problems can be seen due to the relatively low strength issues. Besides, acrylic resin is the still prominent material for denture fabrication due to its handy and low cost features. Numerous proposed fillers that are used to produce PMMA composites, however electrospun polyvinylalcohol (PVA) nanofiber fillers for production of PMMA composite resins are not studied as much as the others. The other focus of the practice is to compare both mechanical properties and efficiency of aligned fibers versus non-aligned PVA nanofibers in PMMA based dental composites. Field-controlled electrospinning system is manufactured and provided good alignment in lab scale as one of contributions. Some novel auxiliary electrodes in controlled structure are augmented to obtain different patterns of alignment with a certain range of fiber diameters. Scanning electron microscopy is used for physical characterization to determine the range of fiber diameters. Non-woven fiber has no unique pattern due to chaotic nature of electrospinning process, but aligned fibers have round pattern or crossed lines. These produced fibers are structured as layer-by-layer form with different features, and these features are used in producing PMMA dental composites with different volume ratios. The maximum flexural strength figure shows that fiber load by weight of 0.25% w/w and above improves in the maximum level. As a result, mechanical properties of PMMA dental composites are improved by using PVA nanofibers as a filler, however the improvement was higher when aligned PVA nanofibers are used. The maximum values were 5.1 MPa (flexural strength), 0.8 GPa (elastic modulus), and 170 kJ/m{sup 3} (toughness) in three-point bending test. In addition to the positive results of aligned and non-aligned nanofibers it was

  15. Supplemental vibrational force during orthodontic alignment: a randomized trial.

    Science.gov (United States)

    Woodhouse, N R; DiBiase, A T; Johnson, N; Slipper, C; Grant, J; Alsaleh, M; Donaldson, A N A; Cobourne, M T

    2015-05-01

    This prospective 3-arm parallel-group randomized clinical trial investigated the effect of supplemental vibrational force on rate of orthodontic tooth alignment with fixed appliances. Eighty-one subjects (40 males, 41 females; mean age, 14.1 y) undergoing first premolar extraction-based fixed appliance treatment were randomly allocated to treatment supplemented with daily use (20 min) of a removable intraoral vibrational device (AcceleDent; OrthoAccel Technologies Inc.; n = 29), an identical nonfunctional (sham) device (n = 25), or fixed appliances only (n = 27). Mandibular study casts were taken at baseline (treatment start: placement of 0.014-in. nickel-titanium arch wire), initial alignment (0.018-in. nickel-titanium arch wire), and final alignment (0.019 x 0.025-in. stainless steel arch wire). Overall mean irregularity index in the mandibular arch at baseline was 8.5 ± 3.8 mm (95% CI, 7.6 to 9.3) with no significant difference between groups (P = 0.73). For the total sample, mean irregularity index at initial alignment was 2.7 ± 2.8 mm (95% CI, 2.2 to 3.4) with no significant difference between groups (P = 0.40). Mean time from baseline to initial alignment was 59 ± 25 d (95% CI, 54.5 to 65.6); from initial to final alignment, 150 ± 62.5 d (95% CI, 136 to 165); and baseline to final alignment, 209 ± 65 d (95% CI, 195 to 224). Kaplan-Meier analysis demonstrated that patterns of alignment were not significantly different among the 3 groups (P = 0.66). Multivariate linear regression for initial and overall alignment rates using initial irregularity index as the covariate showed no significant differences among groups. The most important influence on both initial and overall rates of alignment was initial irregularity (P = 0.1 × 10(-4)). This prospective randomized clinical trial found no evidence that supplemental vibrational force can significantly increase the rate of initial tooth movement or reduce the amount of time required to achieve final alignment

  16. An Automatic High Efficient Method for Dish Concentrator Alignment

    OpenAIRE

    Yong Wang; Song Li; Jinshan Xu; Yijiang Wang; Xu Cheng; Changgui Gu; Shengyong Chen; Bin Wan

    2014-01-01

    Alignment of dish concentrator is a key factor to the performance of solar energy system. We propose a new method for the alignment of faceted solar dish concentrator. The isosceles triangle configuration of facet’s footholds determines a fixed relation between light spot displacements and foothold movements, which allows an automatic determination of the amount of adjustments. Tests on a 25 kW Stirling Energy System dish concentrator verify the feasibility, accuracy, and efficiency of our...

  17. 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.

  18. Word-level Alignment for Multilingual Resource Acquisition

    Science.gov (United States)

    2002-04-01

    SUBTITLE Word-level Alignment for Multilingual Resource Acquisition 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 Word-level Alignment for Multilingual Resource Acquisition Adam Lopez...parses to adhere to the constraints of a given monolingual parsing model. If we assume context-free grammars, then each parse must be context-free

  19. Optical Alignment System for the PHENIX Muon Tracking Chambers

    CERN Document Server

    Murata, J; Armendariz, R L; Brooks, M L; Horaguchi, T; Kamihara, N; Kobayashi, H; Lee, D M; Shibata, T A; Sondheim, W E

    2003-01-01

    A micron-precision optical alignment system (OASys) for the PHENIX muon tracking chambers is developed. To ensure the required mass resolution of vector meson detection, the relative alignment between three tracking station chambers must be monitored with a precision of 25$\\mu$m. The OASys is a straightness monitoring system comprised of a light source, lens and CCD camera, used for determining the initial placement as well as for monitoring the time dependent movement of the chambers on a micron scale.

  20. Epitaxial growth of aligned GaN nanowires and nanobridges

    OpenAIRE

    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...

  1. 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.

  2. 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.

  3. Improving polyphonic and poly-instrumental music to score alignment

    OpenAIRE

    Soulez, Ferréol; Rodet, Xavier; Schwarz, Diemo

    2003-01-01

    6pp; International audience; Music alignment links events in a score and points on the audio performance time axis. All the parts of a recording can be thus indexed according to score information. The automatic alignment presented in this paper is based on a dynamic time warping method. Local distances are computed using the signal's spectral features through an attack plus sustain note modeling. The method is applied to mixtures of harmonic sustained instruments, excluding percussion for the...

  4. Resource alignment in the category management of builders’ merchants

    OpenAIRE

    Ellström, Daniel; Rehme, Jakob

    2016-01-01

    Previous retailer-supplier research reports both positive and negative collaboration outcomes. Resource alignment, or how collaborating actors’ resources affect each other, is a concept that has been brought forward to explain when collaboration increases performance. As the category management of builders’ merchants involves actors with different sets of resources, the resource alignment framework can be used to better understand the outcomes of collaboration in category management. The aim ...

  5. 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.

  6. Optical alignment of high resolution Fourier transform spectrometers

    Science.gov (United States)

    Breckinridge, J. B.; Ocallaghan, F. G.; Cassie, A. G.

    1980-01-01

    Remote sensing, high resolution FTS instruments often contain three primary optical subsystems: Fore-Optics, Interferometer Optics, and Post, or Detector Optics. We discuss the alignment of a double-pass FTS containing a cat's-eye retro-reflector. Also, the alignment of fore-optics containing confocal paraboloids with a reflecting field stop which relays a field image onto a camera is discussed.

  7. 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.

  8. MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

    Science.gov (United States)

    Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E; Rost, Burkhard; Goldberg, Tatyana

    2016-11-15

    The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components.

  9. 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.

  10. Clinical implications of alignment of upper and lower cervical spine

    OpenAIRE

    Sherekar S; Yadav Y; Basoor A; Baghel Arvind; Adam Nelson

    2006-01-01

    Aims and Objectives: The alignment of upper and lower cervical spine is presumed to be closely interrelated and the knowledge of this is mandatory when performing occipito-cervical and upper cervical fusions. The aim of this study was to establish standard values for upper and lower cervical spine alignment in the Indian population. Materials and Methods: Five hundred eighteen asymptomatic volunteers (261 males and 257 females) between 12 and 80 years of age underwent lateral radiography w...

  11. 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.

  12. PipeAlign: A new toolkit for protein family analysis.

    Science.gov (United States)

    Plewniak, Frédéric; Bianchetti, Laurent; Brelivet, Yann; Carles, Annaick; Chalmel, Frédéric; Lecompte, Odile; Mochel, Thiebaut; Moulinier, Luc; Muller, Arnaud; Muller, Jean; Prigent, Veronique; Ripp, Raymond; Thierry, Jean-Claude; Thompson, Julie D; Wicker, Nicolas; Poch, Olivier

    2003-07-01

    PipeAlign is a protein family analysis tool integrating a five step process ranging from the search for sequence homologues in protein and 3D structure databases to the definition of the hierarchical relationships within and between subfamilies. The complete, automatic pipeline takes a single sequence or a set of sequences as input and constructs a high-quality, validated MACS (multiple alignment of complete sequences) in which sequences are clustered into potential functional subgroups. For the more experienced user, the PipeAlign server also provides numerous options to run only a part of the analysis, with the possibility to modify the default parameters of each software module. For example, the user can choose to enter an existing multiple sequence alignment for refinement, validation and subsequent clustering of the sequences. The aim is to provide an interactive workbench for the validation, integration and presentation of a protein family, not only at the sequence level, but also at the structural and functional levels. PipeAlign is available at http://igbmc.u-strasbg.fr/PipeAlign/.

  13. 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.

  14. Static rearfoot alignment: a comparison of clinical and radiographic measures.

    Science.gov (United States)

    Lamm, Bradley M; Mendicino, Robert W; Catanzariti, Alan R; Hillstrom, Howard J

    2005-01-01

    Foot structure is typically evaluated using static clinical and radiographic measures. To date, the literature is devoid of a correlation between rearfoot frontal plane radiographic parameters and clinical measures of alignment. In a repeated-measures study comparing radiographic and clinical rearfoot alignment in 24 healthy subjects, radiographic angular measurements were made from standard weightbearing anteroposterior, lateral, long leg calcaneal axial, and rearfoot alignment views. Clinical measurements were made using a jig and scanner to assess the malleolar valgus index and a goniometer to evaluate the resting and neutral calcaneal stance positions. There was a significant correlation between frontal plane radiographic angles (long leg calcaneal axial and rearfoot alignment views) (r = 0.814). Similarly, there was a significant correlation between clinical measures (resting calcaneal stance position and malleolar valgus index) (r = 0.714). A multivariate stepwise regression showed that resting calcaneal stance position can be accurately predicted from 3 of the 15 clinical and radiographic measurements collected: malleolar valgus index, rearfoot alignment view, and long leg calcaneal axial view (r = 0.829). In summary, a commonly used clinical measure of static rearfoot alignment, resting calcaneal stance position, was correlated closely with the malleolar valgus index and both frontal plane radiographic parameters.

  15. Validation of the CLIC alignment strategy on short range

    CERN Document Server

    Mainaud Durand, H; Griffet, S; Kemppinen, J; Rude, V; Sosin, M

    2012-01-01

    The pre-alignment of CLIC consists of aligning the components of linacs and beam delivery systems (BDS) in the most accurate possible way, so that a first pilot beam can circulate and allow the implementation of the beam based alignment. Taking into account the precision and accuracy needed: 10 µm rms over sliding windows of 200m, this pre-alignment must be active and it can be divided into two parts: the determination of a straight reference over 20 km, thanks to a metrological network and the determination of the component positions with respect to this reference, and their adjustment. The second part is the object of the paper, describing the steps of the proposed strategy: firstly the fiducialisation of the different components of CLIC; secondly, the alignment of these components on common supports and thirdly the active alignment of these supports using sensors and actuators. These steps have been validated on a test setup over a length of 4m, and the obtained results are analysed.

  16. Thermal characterization of magnetically aligned carbonyl iron/agar composites.

    Science.gov (United States)

    Diaz-Bleis, D; Vales-Pinzón, C; Freile-Pelegrín, Y; Alvarado-Gil, J J

    2014-01-01

    Composites of magnetic particles into polymeric matrices have received increasing research interest due to their capacity to respond to external magnetic or electromagnetic fields. In this study, agar from Gelidium robustum has been chosen as natural biocompatible polymer to build the matrix of the magnetic carbonyl iron particles (CIP) for their uses in biomedical fields. Heat transfer behavior of the CIP-agar composites containing different concentrations (5, 10, 15, 20, 25 and 30% w/w) of magnetically aligned and non-aligned CIP in the agar matrix was studied using photothermal radiometry (PTR) in the back-propagation emission configuration. The morphology of the CIP-agar composites with aligned and non-aligned CIP under magnetic field was also evaluated by scanning electron microscopy (SEM). The results revealed a dominant effect of CIP concentration over the alignment patterns induced by the magnetic field, which agrees with the behavior of the thermal diffusivity and thermal conductivity. Agar served as a perfect matrix to be used with CIP, and CIP-agar composites magnetically aligned at 20% CIP concentration can be considered as promising 'smart' material for hyperthermia treatments in the biomedical field.

  17. Identifying and aligning expectations in a mentoring relationship.

    Science.gov (United States)

    Huskins, W Charles; Silet, Karin; Weber-Main, Anne Marie; Begg, Melissa D; Fowler, Vance G; Hamilton, John; Fleming, Michael

    2011-12-01

    The mentoring relationship between a scholar and their primary mentor is a core feature of research training. Anecdotal evidence suggests this relationship is adversely affected when scholar and mentor expectations are not aligned. We examined three questions: (1) What is the value in assuring that the expectations of scholars and mentors are mutually identified and aligned? (2) What types of programmatic interventions facilitate this process? (3) What types of expectations are important to identify and align? We addressed these questions through a systematic literature review, focus group interviews of mentors and scholars, a survey of Clinical and Translational Science Award (CTSA) KL2 program directors, and review of formal programmatic mechanisms used by KL2 programs. We found broad support for the importance of identifying and aligning the expectations of scholars and mentors and evidence that mentoring contracts, agreements, and training programs facilitate this process. These tools focus on aligning expectations with respect to the scholar's research, education, professional development and career advancement as well as support, communication, and personal conduct and interpersonal relations. Research is needed to assess test the efficacy of formal alignment activities.

  18. Influence of alignment of the pyramid on its beneficial effects.

    Science.gov (United States)

    Bhat, Surekha; Rao, Guruprasad; Murthy, K Dilip; Bhat, P Gopalakrishna

    2007-05-01

    The present study was aimed to find out whether a change in the alignment of the pyramid from the north-south axis causes any variation in the effects produced by it on plasma cortisol levels and markers of oxidative stress in erythrocytes of adult-female Wistar rats. Plasma cortisol and erythrocyte TBARS levels were significantly lower whereas erythrocyte GSH was significantly higher in rats kept in pyramid that was aligned on the four cardinal points--north, east, south and west, as compared to normal control rats. Although there was a significant difference in the plasma cortisol level between normal control group and the group of rats kept in randomly aligned pyramid, there was no significant difference between these two groups for the other parameters. Erythrocyte TBARS levels in the group of rats kept in the randomly aligned pyramid was significantly higher than that in the group kept in the magnetically aligned pyramid. The results suggest that the north-south alignment of the pyramid is crucial for its expected effects.

  19. 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.)

  20. Capillary Self-Alignment of Microchips on Soft Substrates

    Directory of Open Access Journals (Sweden)

    Bo Chang

    2016-03-01

    Full Text Available Soft micro devices and stretchable electronics have attracted great interest for their potential applications in sensory skins and wearable bio-integrated devices. One of the most important steps in building printed circuits is the alignment of assembled micro objects. Previously, the capillary self-alignment of microchips driven by surface tension effects has been shown to be able to achieve high-throughput and high-precision in the integration of micro parts on rigid hydrophilic/superhydrophobic patterned surfaces. In this paper, the self-alignment of microchips on a patterned soft and stretchable substrate, which consists of hydrophilic pads surrounded by a superhydrophobic polydimethylsiloxane (PDMS background, is demonstrated for the first time. A simple process has been developed for making superhydrophobic soft surface by replicating nanostructures of black silicon onto a PDMS surface. Different kinds of PDMS have been investigated, and the parameters for fabricating superhydrophobic PDMS have been optimized. A self-alignment strategy has been proposed that can result in reliable self-alignment on a soft PDMS substrate. Our results show that capillary self-alignment has great potential for building soft printed circuits.

  1. A Network Model of Interpersonal Alignment in Dialog

    Directory of Open Access Journals (Sweden)

    Alexander Mehler

    2010-06-01

    Full Text Available In dyadic communication, both interlocutors adapt to each other linguistically, that is, they align interpersonally. In this article, we develop a framework for modeling interpersonal alignment in terms of the structural similarity of the interlocutors’ dialog lexica. This is done by means of so-called two-layer time-aligned network series, that is, a time-adjusted graph model. The graph model is partitioned into two layers, so that the interlocutors’ lexica are captured as subgraphs of an encompassing dialog graph. Each constituent network of the series is updated utterance-wise. Thus, both the inherent bipartition of dyadic conversations and their gradual development are modeled. The notion of alignment is then operationalized within a quantitative model of structure formation based on the mutual information of the subgraphs that represent the interlocutor’s dialog lexica. By adapting and further developing several models of complex network theory, we show that dialog lexica evolve as a novel class of graphs that have not been considered before in the area of complex (linguistic networks. Additionally, we show that our framework allows for classifying dialogs according to their alignment status. To the best of our knowledge, this is the first approach to measuring alignment in communication that explores the similarities of graph-like cognitive representations.

  2. 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.

  3. Navigation improves accuracy of rotational alignment in total knee arthroplasty.

    Science.gov (United States)

    Stöckl, Bernd; Nogler, Michael; Rosiek, Rafal; Fischer, Martin; Krismer, Martin; Kessler, Oliver

    2004-09-01

    Successful total knee arthroplasty is dependent on the correct alignment of implanted prostheses. Major clinical problems can be related to poor femoral component positioning, including sagittal plane and rotational malalignment. A prospective randomized study was designed to test whether an optical navigation system for total knee arthroplasty achieved greater implantation precision than a nonnavigated technique. The primary variable was rotation of the femoral component in the transverse plane, measured from postoperative radiographs and computed tomography images. Sixty-four patients were included in the study. All patients received the Duracon total knee prosthesis. The patients were randomly divided into two groups: Group C patients had conventional total knee arthroplasty without navigation; Group N patients had total knee arthroplasty using a computer-assisted knee navigation system. Analysis showed that patients in Group N had significantly better rotational alignment and flexion angle of the femoral component than patients in Group C. In addition, superior postoperative alignment of the mechanical axis, posterior tibial slope, and rotational alignment was achieved for patients in Group N. The use of a navigation system provides improved alignment accuracy, and can help to avoid femoral malrotation and errors in axial alignment.

  4. Cryogenic Pupil Alignment Test Architecture for Aberrated Pupil Images

    Science.gov (United States)

    Bos, Brent; Kubalak, David A.; Antonille, Scott; Ohl, Raymond; Hagopian, John G.

    2009-01-01

    A document describes cryogenic test architecture for the James Webb Space Telescope (JWST) integrated science instrument module (ISIM). The ISIM element primarily consists of a mechanical metering structure, three science instruments, and a fine guidance sensor. One of the critical optomechanical alignments is the co-registration of the optical telescope element (OTE) exit pupil with the entrance pupils of the ISIM instruments. The test architecture has been developed to verify that the ISIM element will be properly aligned with the nominal OTE exit pupil when the two elements come together. The architecture measures three of the most critical pupil degrees-of-freedom during optical testing of the ISIM element. The pupil measurement scheme makes use of specularly reflective pupil alignment references located inside the JWST instruments, ground support equipment that contains a pupil imaging module, an OTE simulator, and pupil viewing channels in two of the JWST flight instruments. Pupil alignment references (PARs) are introduced into the instrument, and their reflections are checked using the instrument's mirrors. After the pupil imaging module (PIM) captures a reflected PAR image, the image will be analyzed to determine the relative alignment offset. The instrument pupil alignment preferences are specularly reflective mirrors with non-reflective fiducials, which makes the test architecture feasible. The instrument channels have fairly large fields of view, allowing PAR tip/tilt tolerances on the order of 0.5deg.

  5. Business Alignment: Measurement-Based Alignment of Software Strategies and Business Goals

    Science.gov (United States)

    Münch, Jürgen; Heidrich, Jens; Mandić, Vladimir

    Most of today’s products and services are software-based. Organizations that develop software want to maintain and improve their competitiveness by controlling software-related risks. To do this, they need to align their business goals with software development strategies and translate them into quantitative project management. There is also an increasing need to justify cost and resources for software and system development and other IT services by demonstrating their impact on an organization’s higher-level goals. For both, linking business goals and software-related efforts in an organization is necessary. However, this is a challenging task, and there is a lack of methods addressing this gap.

  6. Aligning carbon fibers in micro-extruded composite ink

    Science.gov (United States)

    Mahajan, Chaitanya G.

    Direct write processes include a wide range of additive manufacturing techniques with the ability to fabricate structures directly onto planar and non-planar surfaces. Most additive manufacturing techniques use unreinforced polymers to produce parts. By adding carbon fiber as a reinforcing material, properties such as mechanical strength, electrical conductivity, and thermal conductivity can be enhanced. Carbon fibers can be long and continuous, or short and discontinuous. The strength of carbon fiber composite parts is greatly increased when the fibers are preferentially aligned. This research focuses on increasing the strength of additively manufactured parts reinforced using discontinuous carbon fibers that have been aligned during the micro extrusion process. A design of experiments (DOE) approach was used to identify significant process parameters affecting fiber alignment. Factors such as the length of carbon fibers, nozzle diameter, fiber loading fraction, air pressure, translational speed and standoff distance were considered. A two dimensional Fast Fourier Transform (2D FFT) was used to quantify the degree of fiber alignment in the extruded composite inks. ImageJ software supported by an oval profile plugin was used with micrographs of printed samples to obtain the carbon fiber alignment values. The optimal value for the factors was derived by identifying the significant main and interaction effects. Based on the results of the DOE, tensile test samples were printed with fibers aligned parallel and perpendicular to the tensile axis. A standard test method for tensile properties of plastic revealed that the extruded parts with fibers aligned along the tensile axis were better in tensile strength and modulus.

  7. Local coordinates alignment with global preservation for dimensionality reduction.

    Science.gov (United States)

    Chen, Jing; Ma, Zhengming; Liu, Yang

    2013-01-01

    Dimensionality reduction is vital in many fields, and alignment-based methods for nonlinear dimensionality reduction have become popular recently because they can map the high-dimensional data into a low-dimensional subspace with the property of local isometry. However, the relationships between patches in original high-dimensional space cannot be ensured to be fully preserved during the alignment process. In this paper, we propose a novel method for nonlinear dimensionality reduction called local coordinates alignment with global preservation. We first introduce a reasonable definition of topology-preserving landmarks (TPLs), which not only contribute to preserving the global structure of datasets and constructing a collection of overlapping linear patches, but they also ensure that the right landmark is allocated to the new test point. Then, an existing method for dimensionality reduction that has good performance in preserving the global structure is used to derive the low-dimensional coordinates of TPLs. Local coordinates of each patch are derived using tangent space of the manifold at the corresponding landmark, and then these local coordinates are aligned into a global coordinate space with the set of landmarks in low-dimensional space as reference points. The proposed alignment method, called landmarks-based alignment, can produce a closed-form solution without any constraints, while most previous alignment-based methods impose the unit covariance constraint, which will result in the deficiency of global metrics and undesired rescaling of the manifold. Experiments on both synthetic and real-world datasets demonstrate the effectiveness of the proposed algorithm.

  8. Precise synaptic efficacy alignment suggests potentiation dominated learning

    Directory of Open Access Journals (Sweden)

    Christoph eHartmann

    2016-01-01

    Full Text Available Recent evidence suggests that parallel synapses from the same axonal branch onto the same dendritic branch have almost identical strength. It has been proposed that this alignment is only possible through learning rules that integrate activity over long time spans. However, learning mechanisms such as spike-timing-dependent plasticity (STDP are commonly assumed to be temporally local. Here, we propose that the combination of temporally local STDP and a multiplicative synaptic normalization mechanism is sufficient to explain the alignment of parallel synapses.To address this issue, we introduce three increasingly complex models: First, we model the idealized interaction of STDP and synaptic normalization in a single neuron as a simple stochastic process and derive analytically that the alignment effect can be described by a so-called Kesten process. From this we can derive that synaptic efficacy alignment requires potentiation-dominated learning regimes. We verify these conditions in a single-neuron model with independent spiking activities but more realistic synapses. As expected, we only observe synaptic efficacy alignment for long-term potentiation-biased STDP. Finally, we explore how well the findings transfer to recurrent neural networks where the learning mechanisms interact with the correlated activity of the network. We find that due to the self-reinforcing correlations in recurrent circuits under STDP, alignment occurs for both long-term potentiation- and depression-biased STDP, because the learning will be potentiation dominated in both cases due to the potentiating events induced by correlated activity. This is in line with recent results demonstrating a dominance of potentiation over depression during waking and normalization during sleep. This leads us to predict that individual spine pairs will be more similar in the morning than they are after sleep depriviation.In conclusion, we show that synaptic normalization in conjunction with

  9. The shapes and alignments of dark matter halos

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Michael D. [Lawrence Livermore National Laboratory, P.O. Box 808 L-210, Livermore, CA 94551-0808 (United States); Frenk, Carlos S.; Cole, Shaun, E-mail: schneider42@llnl.gov, E-mail: c.s.frenk@durham.ac.uk, E-mail: shaun.cole@durham.ac.uk [Institute for Computational Cosmology, Department of Physics, Durham University, South Road, Durham, DH1 3LE (United Kingdom)

    2012-05-01

    We present measurements of the triaxial dark matter halo shapes and alignment correlation functions in the Millennium and Millennium-2 dark matter N-body simulations. These two simulations allow us to measure the distributions of halo shapes down to 10% of the virial radius over a halo mass range of 6 × 10{sup 9}–2 × 10{sup 14} h{sup −1}M{sub s}un. We largely confirm previous results on the distributions of halo axis ratios as a function of halo mass, but we find that the median angle between halo major axes at different halo radii can vary by a factor of 2 between the Millennium-1 and 2 simulations because of the different mass resolution. Thus, error in the shape determinations from limited resolution is potentially degenerate with the misalignment of halo inner and outer shapes used to constrain Brightest Cluster Galaxy alignments in previous works. We also present simplifying parameterizations for the 3-D halo-mass alignment correlation functions that are necessary ingredients for triaxial halo models of large-scale structure and models of galaxy intrinsic alignments as contaminants for cosmic shear surveys. We measure strong alignments between halos of all masses and the surrounding dark matter overdensities out to several tens of h{sup −1} Mpc, in agreement with observed shear-galaxy and cluster shape correlations. We use these measurements to forecast the contribution to the weak lensing signal around galaxy clusters from correlated mass along the line-of-sight. For prolate clusters with major axes aligned with the line-of-sight the fraction of the weak lensing signal from mass external to the cluster can be twice that predicted if the excess halo alignment correlation is assumed to be zero.

  10. SU-E-J-33: Comparison Between Soft Tissue Alignment and Bony Alignment for Pancreatic Cancer Radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Y; Crane, C; Krishnan, S; Das, P; Koay, E; Beddar, S [UT MD Anderson Cancer Center, Houston, TX (United States)

    2015-06-15

    Purpose An IGRT modality for pancreatic cancer treatment with dose escalation at our institution is in-room daily CT imaging. The purpose of this study is to assess the difference between soft tissue alignment and bony alignment for pancreatic tumor localization. Methods Eighteen patients with pancreatic tumors who underwent IMRT treatment with an inspiration breath-hold technique between July 2012 and February 2015 are included in this study. Prior to each treatment, a CT scan was acquired. The CT image guidance started with auto-alignment to either the bony anatomy (vertebral bodies) or fiducials (for the six patients with the stent in/near the tumor) and then, when necessary, manual adjustments were made based on soft tissue alignment using clinical software (CT-Assisted Targeting system). The difference between soft tissue alignment and bony/fiducial alignment was evaluated. Results Of all 380 treatments, manual adjustment was made in 225 treatments, ranging from 11% (3 treatments out of 28) to 96% (27 treatments out of 28) per patient. The mean of the difference between soft tissue alignment and bony/fiducial alignment per patient ranged from −3.6 to 0.3 mm, −1.5 to 2.8 mm, and −3.3 to 3.4 mm in the AP, SI, and RL directions, respectively. The maximum difference over all treatments was −9.5, −14.6, and −14.6 mm in the AP, SI, and RL directions, respectively. Conclusion About 60% of the time, manual adjustment based on soft tissue alignment was required. The extent of manual adjustment was usually small but varied significantly from patient to patient. The ultimate goal of the IGRT modality using daily CT imaging is not to fully cover the target but to spare organs-at-risk as much as possible to avoid them moving into higher dose gradients than accepted in the treatment plan. To this end, manual adjustment based on soft tissue alignment is critically important.

  11. Incorporating evolution of transcription factor binding sites into annotated alignments

    Indian Academy of Sciences (India)

    Abha S Bais; Steffen Grossmann; Martin Vingron

    2007-08-01

    Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield ``conserved TFBSs”. Most current methods in this field adopt a multi-step approach that segregates the two aspects. Again, it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account. Although a plethora of approaches have been proposed for the prediction of conserved TFBSs, very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences. Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments. That is, alignments with parts annotated as gaplessly aligned TFBSs (pair-profile hits) are generated. Moreover, the pair-profile related parameters are derived in a sound statistical framework. In this article, we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework. We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models, previously used for modelling TFBS evolution. In a simulated setting, we provide a proof of concept that the approach works given the underlying assumptions, as compared to the original work. Finally, using a real dataset of experimentally verified binding sites in human-mouse sequence pairs, we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences, most comparative TFBS identification

  12. Peak alignment using wavelet pattern matching and differential evolution.

    Science.gov (United States)

    Zhang, Zhi-Min; Chen, Shan; Liang, Yi-Zeng

    2011-01-30

    Retention time shifts badly impair qualitative or quantitative results of chemometric analyses when entire chromatographic data are used. Hence, chromatograms should be aligned to perform further analysis. Being inspired and motivated by this purpose, a practical and handy peak alignment method (alignDE) is proposed, implemented in this research for one-way chromatograms, which basically consists of five steps: (1) chromatogram lengths equalization using linear interpolation; (2) accurate peak pattern matching by continuous wavelet transform (CWT) with the Mexican Hat and Haar wavelets as its mother wavelets; (3) flexible baseline fitting utilizing penalized least squares; (4) peak clustering when gap of two peaks is smaller than a certain threshold; (5) peak alignment using differential evolution (DE) to maximize linear correlation coefficient between reference signal and signal to be aligned. This method is demonstrated with both simulated chromatograms and real chromatograms, for example, chromatograms of fungal extracts and Red Peony Root obtained by HPLC-DAD. It is implemented in R language and available as open source software to a broad range of chromatograph users (http://code.google.com/p/alignde).

  13. Polarized light emission by deposition of aligned semiconductor nanorods

    Science.gov (United States)

    Mohammadimasoudi, Mohammad; Penninck, Lieven; Aubert, Tangi; Gomes, Raquel; Hens, Zeger; Strubbe, Filip; Neyts, Kristiaan

    2014-08-01

    The ability to control the position and orientation of nanorods in a device is interesting both from a scientific and a technological point of view. Because semiconductor nanorods exhibit anisotropic absorption, and spontaneous and stimulated emission, aligning individual NRs to a preferred axis is attractive for many applications in photonics such as solar cells, light-emitting devices, optical sensors, switches, etc. Electric-field-driven deposition from colloidal suspensions has proven to be an efficient method for the controlled positioning and alignment of anisotropic particles. In this work, we present a novel technique for the homogeneous deposition and alignment of CdSe/CdS NRs on a glass substrate patterned with transparent indium tin oxide interdigitated electrodes, with a spacing of a few micrometers. This method is based on applying a strong AC electric field over the electrodes during a dip-coating procedure and subsequent evaporation of the solvent. The reproducible and homogeneous deposition on large substrates is required for large size applications such as solar cells or OLEDs. The accumulation, alignment, and polarized fluorescence of the nanorods as a function of the electrical field during deposition are investigated. A preferential alignment with an order parameter of 0.92 has been achieved.

  14. LHCb’s Real-Time Alignment in Run II

    CERN Document Server

    Batozskaya, Varvara

    2015-01-01

    The LHCb collaboration has introduced a novel real-time detector alignment and calibration strategy for LHC Run II. The 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 oine reconstruction, thus improving the correlation between triggered and oine selected events. This oers 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 configu...

  15. ARE TIDAL EFFECTS RESPONSIBLE FOR EXOPLANETARY SPIN–ORBIT ALIGNMENT?

    Energy Technology Data Exchange (ETDEWEB)

    Li, Gongjie [Harvard-Smithsonian Center for Astrophysics, The Institute for Theory and Computation, 60 Garden Street, Cambridge, MA 02138 (United States); Winn, Joshua N., E-mail: gli@cfa.harvard.edu [Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States)

    2016-02-10

    The obliquities of planet-hosting stars are clues about the formation of planetary systems. Previous observations led to the hypothesis that for close-in giant planets, spin–orbit alignment is enforced by tidal interactions. Here, we examine two problems with this hypothesis. First, Mazeh and coworkers recently used a new technique—based on the amplitude of starspot-induced photometric variability—to conclude that spin–orbit alignment is common even for relatively long-period planets, which would not be expected if tides were responsible. We re-examine the data and find a statistically significant correlation between photometric variability and planetary orbital period that is qualitatively consistent with tidal interactions. However it is still difficult to explain quantitatively, as it would require tides to be effective for periods as long as tens of days. Second, Rogers and Lin argued against a particular theory for tidal re-alignment by showing that initially retrograde systems would fail to be re-aligned, in contradiction with the observed prevalence of prograde systems. We investigate a simple model that overcomes this problem by taking into account the dissipation of inertial waves and the equilibrium tide, as well as magnetic braking. We identify a region of parameter space where re-alignment can be achieved, but it only works for close-in giant planets, and requires some fine tuning. Thus, while we find both problems to be more nuanced than they first appeared, the tidal model still has serious shortcomings.

  16. Long Read Alignment with Parallel MapReduce Cloud Platform

    Directory of Open Access Journals (Sweden)

    Ahmed Abdulhakim Al-Absi

    2015-01-01

    Full Text Available 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.

  17. Alignment of continuous video onto 3D point clouds.

    Science.gov (United States)

    Zhao, Wenyi; Nister, David; Hsu, Steve

    2005-08-01

    We propose a general framework for aligning continuous (oblique) video onto 3D sensor data. We align a point cloud computed from the video onto the point cloud directly obtained from a 3D sensor. This is in contrast to existing techniques where the 2D images are aligned to a 3D model derived from the 3D sensor data. Using point clouds enables the alignment for scenes full of objects that are difficult to model; for example, trees. To compute 3D point clouds from video, motion stereo is used along with a state-of-the-art algorithm for camera pose estimation. Our experiments with real data demonstrate the advantages of the proposed registration algorithm for texturing models in large-scale semiurban environments. The capability to align video before a 3D model is built from the 3D sensor data offers new practical opportunities for 3D modeling. We introduce a novel modeling-through-registration approach that fuses 3D information from both the 3D sensor and the video. Initial experiments with real data illustrate the potential of the proposed approach.

  18. Multispectral optical telescope alignment testing for a cryogenic space environment

    Science.gov (United States)

    Newswander, Trent; Hooser, Preston; Champagne, James

    2016-09-01

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

  19. Alignment of the Muon System at the CMS Experiment

    Science.gov (United States)

    Mueller, Ryan; Perniè, Luca; Pakhotin, Yuriy; Kamon, Teruki; Safonov, Alexei; Brown, Malachi

    2017-01-01

    The muon detectors of the CMS experiment provide fast trigger decisions, muon identifications and muon track measurements. Alignment of the muon detectors is crucial for accurate reconstruction of events with high pT muons that are present in signatures for many new physics scenarios. The muon detector's relative positions and orientations with respect to the inner silicon tracker may be precisely measured using reconstructed tracks propagating from the interaction point. This track-based alignment procedure is capable of aligning individual muon detectors to within 100 microns along sensitive modes. However, weak (insensitive) modes may not be well measured due to the system's design and cause systematic miss-measurements. In this report, we present a new track-based procedure which enables all 6 alignment parameters - 3 positions and 3 rotations for each individual muon detector. The improved algorithm allows for measurement of weak modes and considerably reduced related systematic uncertainties. We describe results of the alignment procedure obtained with 2016 data.

  20. Magnetic alignment study of rare-earth-containing liquid crystals.

    Science.gov (United States)

    Galyametdinov, Yury G; Haase, Wolfgang; Goderis, Bart; Moors, Dries; Driesen, Kris; Van Deun, Rik; Binnemans, Koen

    2007-12-20

    The liquid-crystalline rare-earth complexes of the type [Ln(LH)3(DOS)3]-where Ln is Tb, Dy, Ho, Er, Tm, or Yb; LH is the Schiff base N-octadecyl-4-tetradecyloxysalicylaldimine; and DOS is dodecylsulfate-exhibit a smectic A phase. Because of the presence of rare-earth ions with a large magnetic anisotropy, the smectic A phase of these liquid crystals can be easier aligned in an external magnetic field than smectic A phases of conventional liquid crystals. The magnetic anisotropy of the [Ln(LH)3(DOS)3] complexes was determined by measurement of the temperature-dependence of the magnetic susceptibility using a Faraday balance. The highest value for the magnetic anisotropy was found for the dysprosium(III) complex. The magnetic alignment of these liquid crystals was studied by time-resolved synchrotron small-angle X-ray scattering experiments. Depending on the sign of the magnetic anisotropy, the director of the liquid-crystalline molecules was aligned parallel or perpendicular to the magnetic field lines. A positive value of the magnetic anisotropy (and parallel alignment) was found for the thulium(III) and the ytterbium(III) complexes, whereas a negative value of the magnetic anisotropy (and perpendicular alignment) was observed for the terbium(III) and dysprosium(III) complexes.