High Precision Survey and Alignment of Large Linear Accelerators

CERN Document Server

Prenting, J

2004-01-01

For the future linear accelerator TESLA the demanded accuracy for the alignment of the components is 0.5 mm horizontal and 0.2 mm vertical, both on each 600 m section. Other accelerators require similar accuracies. These demands can not be fulfilled with open-air geodetic methods, mainly because of refraction. Therefore the RTRS (Rapid Tunnel Reference Surveyor), a measurement train performing overlapping multipoint alignment on a reference network is being developed. Two refraction-free realizations of this concept are being developed at the moment: the first one (GeLiS) measures the horizontal co-ordinates using stretched wires, combined with photogrammetric split-image sensors in a distance measurement configuration. In areas of the tunnel where the accelerator is following the earth curvature GeLiS measures the height using a new hydrostatic leveling system. The second concept (LiCAS) is based on laser straightness monitors (LSM) combined with frequency scanning interferometry (FSI) in an evacuated system...

Cleaved-edge overgrowth of aligned quantum dots on strained layers of InGaAs

International Nuclear Information System (INIS)

Wasserman, D.; Lyon, S.A.

2004-01-01

Strain aligned InAs quantum dots were grown on the cleaved edges of first growth samples containing strained In x Ga (1-x) As layers of varying thickness and indium fraction. The formation of the cleaved-edge quantum dots was observed by means of atomic force microscopy. 100% linear alignment of InAs quantum dots over the InGaAs strain layers of the first growth sample is demonstrated. Linear density of the aligned dots was found to depend on the properties of the underlying InGaAs strain layers. Vertical alignment of an additional InAs quantum dot layer over the buried, linearly aligned, initial dot layer was observed for thin GaAs spacer layers

Linear to Circular Polarisation Conversion using Birefringent Properties of Aligned Crystals for Multi-GeV Photons

CERN Document Server

Apyan, A.; Badelek, B.; Ballestrero, S.; Biino, C.; Birol, I.; Cenci, P.; Connell, S.H.; Eichblatt, S.; Fonseca, T.; Freund, A.; Gorini, B.; Groess, R.; Ispirian, K.; Ketel, T.J.; Kononets, Yu.V.; Lopez, A.; Mangiarotti, A.; van Rens, B.; Sellschop, J.P.F.; Shieh, M.; Sona, P.; Strakhovenko, V.; Uggerhoj, E.; Uggerhj, Ulrik Ingerslev; Unel, G.; Velasco, M.; Vilakazi, Z.Z.; Wessely, O.; Kononets, Yu.V.

2003-01-01

We present the first experimental results on the use of a thick aligned Si crystal acting as a quarter wave plate to induce a degree of circular polarisation in a high energy linearly polarised photon beam. The linearly polarised photon beam is produced from coherent bremsstrahlung radiation by 178 GeV unpolarised electrons incident on an aligned Si crystal, acting as a radiator. The linear polarisation of the photon beam is characterised by measuring the asymmetry in electron-positron pair production in a Ge crystal, for different crystal orientations. The Ge crystal therefore acts as an analyser. The birefringence phenomenon, which converts the linear polarisation to circular polarisation, is observed by letting the linearly polarised photons beam pass through a thick Si quarter wave plate crystal, and then measuring the asymmetry in electron-positron pair production again for a selection of relative angles between the crystallographic planes of the radiator, analyser and quarter wave plate. The systematics...

An ice-templated, linearly aligned chitosan-alginate scaffold for neural tissue engineering.

Science.gov (United States)

Francis, Nicola L; Hunger, Philipp M; Donius, Amalie E; Riblett, Benjamin W; Zavaliangos, Antonios; Wegst, Ulrike G K; Wheatley, Margaret A

2013-12-01

Several strategies have been investigated to enhance axonal regeneration after spinal cord injury, however, the resulting growth can be random and disorganized. Bioengineered scaffolds provide a physical substrate for guidance of regenerating axons towards their targets, and can be produced by freeze casting. This technique involves the controlled directional solidification of an aqueous solution or suspension, resulting in a linearly aligned porous structure caused by ice templating. In this study, freeze casting was used to fabricate porous chitosan-alginate (C/A) scaffolds with longitudinally oriented channels. Chick dorsal root ganglia explants adhered to and extended neurites through the scaffold in parallel alignment with the channel direction. Surface adsorption of a polycation and laminin promoted significantly longer neurite growth than the uncoated scaffold (poly-L-ornithine + Laminin = 793.2 ± 187.2 μm; poly-L-lysine + Laminin = 768.7 ± 241.2 μm; uncoated scaffold = 22.52 ± 50.14 μm) (P < 0.001). The elastic modulus of the hydrated scaffold was determined to be 5.08 ± 0.61 kPa, comparable to reported spinal cord values. The present data suggested that this C/A scaffold is a promising candidate for use as a nerve guidance scaffold, because of its ability to support neuronal attachment and the linearly aligned growth of DRG neurites. Copyright © 2013 Wiley Periodicals, Inc., a Wiley Company.

Photodisintegration of aligned deuterons at astrophysical energies using linearly polarized photons

International Nuclear Information System (INIS)

Shilpashree, S.P.; Sirsi, Swarnamala; Ramachandran, G.

2013-01-01

Following the model independent approach to deuteron photodisintegration with linearly polarized γ-rays, we show that the measurements of the tensor analyzing powers on aligned deuterons along with the differential cross-section involve five different linear combinations of the isovector E1 ν j ; j = 0, 1, 2 amplitudes interfering with the isoscalar M1 s and E2 s amplitudes. This is of current interest in view of the recent experimental finding [M. A. Blackston et al., Phys. Rev. C78 (2008) 034003] that the three E1 ν j amplitudes are distinct and also the reported experimental observation [B. D. Sawatzky, Ph.D. thesis, University of Virginia (2005)] on the front–back (polar angle) asymmetry in the differential cross-section. (author)

Note: A simple image processing based fiducial auto-alignment method for sample registration.

Science.gov (United States)

Robertson, Wesley D; Porto, Lucas R; Ip, Candice J X; Nantel, Megan K T; Tellkamp, Friedjof; Lu, Yinfei; Miller, R J Dwayne

2015-08-01

A simple method for the location and auto-alignment of sample fiducials for sample registration using widely available MATLAB/LabVIEW software is demonstrated. The method is robust, easily implemented, and applicable to a wide variety of experiment types for improved reproducibility and increased setup speed. The software uses image processing to locate and measure the diameter and center point of circular fiducials for distance self-calibration and iterative alignment and can be used with most imaging systems. The method is demonstrated to be fast and reliable in locating and aligning sample fiducials, provided here by a nanofabricated array, with accuracy within the optical resolution of the imaging system. The software was further demonstrated to register, load, and sample the dynamically wetted array.

Inducing elliptically polarized high-order harmonics from aligned molecules with linearly polarized femtosecond pulses

DEFF Research Database (Denmark)

Etches, Adam; Madsen, Christian Bruun; Madsen, Lars Bojer

2010-01-01

A recent paper reported elliptically polarized high-order harmonics from aligned N2 using a linearly polarized driving field [X. Zhou et al., Phys. Rev. Lett. 102, 073902 (2009)]. This observation cannot be explained in the standard treatment of the Lewenstein model and has been ascribed to many...

A rheo-optical apparatus for real time kinetic studies on shear-induced alignment of self-assembled soft matter with small sample volumes

Science.gov (United States)

Laiho, Ari; Ikkala, Olli

2007-01-01

In soft materials, self-assembled nanoscale structures can allow new functionalities but a general problem is to align such local structures aiming at monodomain overall order. In order to achieve shear alignment in a controlled manner, a novel type of rheo-optical apparatus has here been developed that allows small sample volumes and in situ monitoring of the alignment process during the shear. Both the amplitude and orientation angles of low level linear birefringence and dichroism are measured while the sample is subjected to large amplitude oscillatory shear flow. The apparatus is based on a commercial rheometer where we have constructed a flow cell that consists of two quartz teeth. The lower tooth can be set in oscillatory motion whereas the upper one is connected to the force transducers of the rheometer. A custom made cylindrical oven allows the operation of the flow cell at elevated temperatures up to 200 °C. Only a small sample volume is needed (from 9 to 25 mm3), which makes the apparatus suitable especially for studying new materials which are usually obtainable only in small quantities. Using this apparatus the flow alignment kinetics of a lamellar polystyrene-b-polyisoprene diblock copolymer is studied during shear under two different conditions which lead to parallel and perpendicular alignment of the lamellae. The open device geometry allows even combined optical/x-ray in situ characterization of the alignment process by combining small-angle x-ray scattering using concepts shown by Polushkin et al. [Macromolecules 36, 1421 (2003)].

Theoretical and practical feasibility demonstration of a micrometric remotely controlled pre-alignment system for the CLIC linear collider

CERN Document Server

Mainaud Durand, H; Chritin, N; Griffet, S; Kemppinen, J; Sosin, M; Touze, T

2011-01-01

The active pre-alignment of the Compact Linear Collider (CLIC) is one of the key points of the project: the components must be pre-aligned w.r.t. a straight line within a few microns over a sliding window of 200 m, along the two linacs of 20 km each. The proposed solution consists of stretched wires of more than 200 m, overlapping over half of their length, which will be the reference of alignment. Wire Positioning Sensors (WPS), coupled to the supports to be pre-aligned, will perform precise and accurate measurements within a few microns w.r.t. these wires. A micrometric fiducialisation of the components and a micrometric alignment of the components on common supports will make the strategy of pre-alignment complete. In this paper, the global strategy of active pre-alignment is detailed and illustrated by the latest results demonstrating the feasibility of the proposed solution.

Polarization properties of below-threshold harmonics from aligned molecules H2+ in linearly polarized laser fields.

Science.gov (United States)

Dong, Fulong; Tian, Yiqun; Yu, Shujuan; Wang, Shang; Yang, Shiping; Chen, Yanjun

2015-07-13

We investigate the polarization properties of below-threshold harmonics from aligned molecules in linearly polarized laser fields numerically and analytically. We focus on lower-order harmonics (LOHs). Our simulations show that the ellipticity of below-threshold LOHs depends strongly on the orientation angle and differs significantly for different harmonic orders. Our analysis reveals that this LOH ellipticity is closely associated with resonance effects and the axis symmetry of the molecule. These results shed light on the complex generation mechanism of below-threshold harmonics from aligned molecules.

Transient reflectivity on vertically aligned single-wall carbon nanotubes

Energy Technology Data Exchange (ETDEWEB)

Galimberti, Gianluca; Ponzoni, Stefano; Ferrini, Gabriele [Interdisciplinary Laboratory for Advanced Materials Physics (i-LAMP) and Dipartimento di Matematica e Fisica, Università Cattolica del Sacro Cuore, I-25121 Brescia (Italy); Hofmann, Stephan [Department of Engineering, University of Cambridge, Cambridge CB3 0FA (United Kingdom); Arshad, Muhammad [Zernike Institute for Advanced Materials, University of Groningen (Netherlands); ICTP, Strada Costiera 11, I-34151 Trieste (Italy); National Centre for Physics Quaid-i-Azam University Islamabad (Pakistan); Cepek, Cinzia [Istituto Officina dei Materiali — CNR, Laboratorio TASC, Area Science Park, Basovizza, I-34149 Trieste (Italy); Pagliara, Stefania, E-mail: pagliara@dmf.unicatt.it [Interdisciplinary Laboratory for Advanced Materials Physics (i-LAMP) and Dipartimento di Matematica e Fisica, Università Cattolica del Sacro Cuore, I-25121 Brescia (Italy)

2013-09-30

One-color transient reflectivity measurements are carried out on two different samples of vertically aligned single-wall carbon nanotube bundles and compared with the response recently published on unaligned bundles. The negative sign of the optical response for both samples indicates that the free electron character revealed on unaligned bundles is only due to the intertube interactions favored by the tube bending. Neither the presence of bundles nor the existence of structural defects in aligned bundles is able to induce a free-electron like behavior of the photoexcited carriers. This result is also confirmed by the presence of non-linear excitonic effects in the transient response of the aligned bundles. - Highlights: • Transient reflectivity measurements on two aligned carbon nanotube samples • Relationship between unalignment and/or bundling and intertube interaction • The bundling is not able to modify the intertube interactions • The presence of structural defects does not affect the intertube interactions • A localized exciton-like behavior has been revealed in these samples.

Laboratory Guide for Residual Stress Sample Alignment and Experiment Planning-October 2011 Version

Energy Technology Data Exchange (ETDEWEB)

Cornwell, Paris A [ORNL; Bunn, Jeffrey R [ORNL; Schmidlin, Joshua E [ORNL; Hubbard, Camden R [ORNL

2012-04-01

The December 2010 version of the guide, ORNL/TM-2008/159, by Jeff Bunn, Josh Schmidlin, Camden Hubbard, and Paris Cornwell, has been further revised due to a major change in the GeoMagic Studio software for constructing a surface model. The Studio software update also includes a plug-in module to operate the FARO Scan Arm. Other revisions for clarity were also made. The purpose of this revision document is to guide the reader through the process of laser alignment used by NRSF2 at HFIR and VULCAN at SNS. This system was created to increase the spatial accuracy of the measurement points in a sample, reduce the use of neutron time used for alignment, improve experiment planning, and reduce operator error. The need for spatial resolution has been driven by the reduction in gauge volumes to the sub-millimeter level, steep strain gradients in some samples, and requests to mount multiple samples within a few days for relating data from each sample to a common sample coordinate system. The first step in this process involves mounting the sample on an indexer table in a laboratory set up for offline sample mounting and alignment in the same manner it would be mounted at either instrument. In the shared laboratory, a FARO ScanArm is used to measure the coordinates of points on the sample surface ('point cloud'), specific features and fiducial points. A Sample Coordinate System (SCS) needs to be established first. This is an advantage of the technique because the SCS can be defined in such a way to facilitate simple definition of measurement points within the sample. Next, samples are typically mounted to a frame of 80/20 and fiducial points are attached to the sample or frame then measured in the established sample coordinate system. The laser scan probe on the ScanArm can then be used to scan in an 'as-is' model of the sample as well as mounting hardware. GeoMagic Studio 12 is the software package used to construct the model from the point cloud the

Laboratory Guide for Residual Stress Sample Alignment and Experiment Planning-October 2011 Version

International Nuclear Information System (INIS)

Cornwell, Paris A.; Bunn, Jeffrey R.; Schmidlin, Joshua E.; Hubbard, Camden R.

2012-01-01

The December 2010 version of the guide, ORNL/TM-2008/159, by Jeff Bunn, Josh Schmidlin, Camden Hubbard, and Paris Cornwell, has been further revised due to a major change in the GeoMagic Studio software for constructing a surface model. The Studio software update also includes a plug-in module to operate the FARO Scan Arm. Other revisions for clarity were also made. The purpose of this revision document is to guide the reader through the process of laser alignment used by NRSF2 at HFIR and VULCAN at SNS. This system was created to increase the spatial accuracy of the measurement points in a sample, reduce the use of neutron time used for alignment, improve experiment planning, and reduce operator error. The need for spatial resolution has been driven by the reduction in gauge volumes to the sub-millimeter level, steep strain gradients in some samples, and requests to mount multiple samples within a few days for relating data from each sample to a common sample coordinate system. The first step in this process involves mounting the sample on an indexer table in a laboratory set up for offline sample mounting and alignment in the same manner it would be mounted at either instrument. In the shared laboratory, a FARO ScanArm is used to measure the coordinates of points on the sample surface ('point cloud'), specific features and fiducial points. A Sample Coordinate System (SCS) needs to be established first. This is an advantage of the technique because the SCS can be defined in such a way to facilitate simple definition of measurement points within the sample. Next, samples are typically mounted to a frame of 80/20 and fiducial points are attached to the sample or frame then measured in the established sample coordinate system. The laser scan probe on the ScanArm can then be used to scan in an 'as-is' model of the sample as well as mounting hardware. GeoMagic Studio 12 is the software package used to construct the model from the point cloud the scan arm creates. Once

Sample volume and alignment analysis for an optical particle counter sizer, and other applications

International Nuclear Information System (INIS)

Holve, D.J.; Davis, G.W.

1985-01-01

Optical methods for particle size distribution measurements in practical high temperature environments are approaching feasibility and offer significant advantages over conventional sampling methods. A key requirement of single particle counting techniques is the need to know features of the sample volume intensity distribution which in general are a function of the particle scattering properties and optical system geometry. In addition, the sample volume intensity distribution is sensitive to system alignment and thus calculations of alignment sensitivity are required for assessment of practical alignment tolerances. To this end, an analysis of sample volume characteristics for single particle counters in general has been developed. Results from the theory are compared with experimental measurements and shown to be in good agreement. A parametric sensitivity analysis is performed and a criterion for allowable optical misalignment is derived for conditions where beam steering caused by fluctuating refractive-index gradients is significant

Beam-based alignment technique for the SLC [Stanford Linear Collider] linac

International Nuclear Information System (INIS)

Adolphsen, C.E.; Lavine, T.L.; Atwood, W.B.

1989-03-01

Misalignment of quadrupole magnets and beam position monitors (BPMs) in the linac of the SLAC Linear Collider (SLC) cause the electron and positron beams to be steered off-center in the disk-loaded waveguide accelerator structures. Off-center beams produce wakefields which limit the SLC performance at high beam intensities by causing emittance growth. Here, we present a general method for simultaneously determining quadrupole magnet and BPM offsets using beam trajectory measurements. Results from the application of the method to the SLC linac are described. The alignment precision achieved is approximately 100 μm, which is significantly better than that obtained using optical surveying techniques. 2 refs., 4 figs

Linear accelerator section alignment in a vacuum chamber

International Nuclear Information System (INIS)

Vengrov, R.M.; Vinogradskij, N.N.; Danil'tsev, E.N.; Iosseliani, D.D.; Kosyak, V.S.; Porubaj, N.I.; Ugarov, S.B.

1989-01-01

Alignment technique for multisectional accelerating structures, that may be used in designing new accelerators for experimental and applied purposes, is described. The accuracy of the alignment of four-chamber resonator sections directly in an accelerator vacuum volume without its depressurization is not less than 100 μm. 8 refs.; 5 figs.; 5 tabs

Linear Fresnel zone plate based two-state alignment system for 0.25 micron x-ray lithography

International Nuclear Information System (INIS)

Chen, G.

1993-01-01

X-ray lithography has proven to be a cost effective and promising technique for fabricating Integrated Circuits (ICs) with minimum feature sizes of less than 0.25 μm. Since IC fabrication is a multilevel process, to preserve the functionality of devices, circuit patterns printed at each lithography level must match existing patterns on the wafer with an accuracy of less than 1/3 ∼ 1/5 of the minimum feature size. An alignment system is used to position the mask relative to the wafer so that mask circuit patterns can be printed on the wafer at the designed position. As the minimum printed feature size shrinks, the overlay requirements of a lithography tool become more stringent. A stepper for 0.25 μm feature device fabrication requires an overlay accuracy of 0.075 μm, of which only 0.05 μm (mean + 3σ) is allocated to its alignment system. This thesis presents the development of a linear Fresnel zone late based two-state alignment (TSA) method for a 0.25 μm x-ray lithography tool. The authors first analyze the overlay requirement in a lithography process and the error allocation to the alignment system for a 0.25 μ feature x-ray lithography tool. They then describe the principle of the two-state alignment, its computer simulation and the optimal alignment mark design. They carried out an optical bench test for the one-axes alignment setup and experimentally evaluated the performance of the system. They developed a three-axes TSA system and integrated the system with the ES-3 x-ray beamline to construct the CXrL aligner, an experimental x-ray exposure system in CXrL. They measured the alignment accuracy of the exposure system to be better than 0.035 μm (3σ) on both metal and dielectric alignment mark substrates. They also studied the effect of processing coatings on the alignment signal with different wafer mark substrates. They successfully printed the 0.5 μm gate level patterns for the first NMOS test chip at CXrL

Controlling the branching ratio of photodissociation using aligned molecules

DEFF Research Database (Denmark)

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

1999-01-01

Using a sample of iodine molecules, aligned by a strong, linearly polarized laser pulse, we control the branching ratio of the I+I and I+I* photodissociation channels by a factor of 26. The control relies on selective photoexcitation of two potential curves that each correlate adiabatically...

Study and development of a laser based alignment system for the compact linear collider

CERN Document Server

AUTHOR|(CDS)2083149

The first objective of the PhD thesis is to develop a new type of positioning sensor to align components at micrometre level over 200 m with respect to a laser beam as straight line reference. The second objective is to estimate the measurement accuracy of the total alignment system over 200 m. The context of the PhD thesis is the Compact Linear Collider project, which is a study for a future particle accelerator. The proposed positioning sensor is made of a camera and an open/close shutter. The sensor can measure the position of the laser beam with respect to its own coordinate system. To do a measurement, the shutter closes, a laser spot appears on it, the camera captures a picture of the laser spot and the coordinates of the laser spot centre are reconstructed in the sensor coordinate system with image processing. Such a measurement requires reference targets on the positioning sensor. To reach the rst objective of the PhD thesis, we used laser theory...

SYSTEMATIC SAMPLING FOR NON - LINEAR TREND IN MILK YIELD DATA

OpenAIRE

Tanuj Kumar Pandey; Vinod Kumar

2014-01-01

The present paper utilizes systematic sampling procedures for milk yield data exhibiting some non-linear trends. The best fitted mathematical forms of non-linear trend present in the milk yield data are obtained and the expressions of average variances of the estimators of population mean under simple random, usual systematic and modified systematic sampling procedures have been derived for populations showing non-linear trend. A comparative study is made among the three sampli...

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law

Science.gov (United States)

Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

2015-01-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

Science.gov (United States)

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. Copyright © 2015 Elsevier Inc. All rights reserved.

Propagation and stability characteristics of a 500-m-long laser-based fiducial line for high-precision alignment of long-distance linear accelerators.

Science.gov (United States)

Suwada, Tsuyoshi; Satoh, Masanori; Telada, Souichi; Minoshima, Kaoru

2013-09-01

A laser-based alignment system with a He-Ne laser has been newly developed in order to precisely align accelerator units at the KEKB injector linac. The laser beam was first implemented as a 500-m-long fiducial straight line for alignment measurements. We experimentally investigated the propagation and stability characteristics of the laser beam passing through laser pipes in vacuum. The pointing stability at the last fiducial point was successfully obtained with the transverse displacements of ±40 μm level in one standard deviation by applying a feedback control. This pointing stability corresponds to an angle of ±0.08 μrad. This report contains a detailed description of the experimental investigation for the propagation and stability characteristics of the laser beam in the laser-based alignment system for long-distance linear accelerators.

Aligning the unalignable: bacteriophage whole genome alignments.

Science.gov (United States)

Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

2016-01-13

In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

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.)

Software alignment of the LHCb inner tracker sensors

International Nuclear Information System (INIS)

Maciuc, Florin

2009-01-01

This work uses the Millepede linear alignment method, which is essentially a χ 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 χ 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 χ 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.)

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.)

Revival structures of linear molecules in a field-free alignment condition as probed by high-order harmonic generation

International Nuclear Information System (INIS)

Lee, G. H.; Kim, H. T.; Park, J. Y.; Nam, C. H.; Kim, T. K.; Lee, J. H.; Ihee, H.

2006-01-01

Revival structures (rotational coherence) of three linear molecules (N 2 , O 2 , and CO 2 ) in a field free alignment condition have been investigated using high-order harmonic generation. The harmonic yields of these molecules were measured in a pump-probe manner by using a weak femtosecond (fs) laser pulse for field-free alignment of molecules and another intense fs laser pulse for harmonic generation. The harmonic intensities from 23rd to 29th order with respect to the time delay between the pump and the probe pulses showed revival structures in the condition of a field-free alignment of molecules. While the revival structure of a N 2 molecule had one-fourth the period of the full revival time and different degrees of modulation among different fractional revival times, the revival structures of O 2 and CO 2 molecules showed one-eighth the periods of the full revival time and similar degrees of modulation among all fractional revival times. The revival structures could be interpreted in terms of the nature of the highest occupied molecular orbital and the total nuclear spin.

Alternate MIMO AF relaying networks with interference alignment: Spectral efficient protocol and linear filter design

KAUST Repository

Park, Kihong

2013-02-01

In this paper, we study a two-hop relaying network consisting of one source, one destination, and three amplify-and-forward (AF) relays with multiple antennas. To compensate for the capacity prelog factor loss of 1/2$ due to the half-duplex relaying, alternate transmission is performed among three relays, and the inter-relay interference due to the alternate relaying is aligned to make additional degrees of freedom. In addition, suboptimal linear filter designs at the nodes are proposed to maximize the achievable sum rate for different fading scenarios when the destination utilizes a minimum mean-square error filter. © 1967-2012 IEEE.

Automated, feature-based image alignment for high-resolution imaging mass spectrometry of large biological samples

NARCIS (Netherlands)

Broersen, A.; Liere, van R.; Altelaar, A.F.M.; Heeren, R.M.A.; McDonnell, L.A.

2008-01-01

High-resolution imaging mass spectrometry of large biological samples is the goal of several research groups. In mosaic imaging, the most common method, the large sample is divided into a mosaic of small areas that are then analyzed with high resolution. Here we present an automated alignment

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.

Measurement of Coherent Emission and Linear Polarization of Photons by Electrons in the Strong Fields of Aligned Crystals

CERN Document Server

Apyan, A.; Badelek, B.; Ballestrero, S.; Biino, C.; Birol, I.; Cenci, P.; Connell, S.H.; Eichblatt, S.; Fonseca, T.; Freund, A.; Gorini, B.; Groess, R.; Ispirian, K.; Ketel, T.J.; Kononets, Yu.V.; Lopez, A.; Mangiarotti, A.; van Rens, B.; Sellschop, J.P.F.; Shieh, M.; Sona, P.; Strakhovenko, V.; Uggerhoj, E.; Uggerhj, Ulrik Ingerslev; Unel, G.; Velasco, M.; Vilakazi, Z.Z.; Wessely, O.; Kononets, Yu.V.

2004-01-01

We present new results regarding the features of high energy photon emission by an electron beam of 178 GeV penetrating a 1.5 cm thick single Si crystal aligned at the Strings-Of-Strings (SOS) orientation. This concerns a special case of coherent bremsstrahlung where the electron interacts with the strong fields of successive atomic strings in a plane and for which the largest enhancement of the highest energy photons is expected. The polarization of the resulting photon beam was measured by the asymmetry of electron-positron pair production in an aligned diamond crystal analyzer. By the selection of a single pair the energy and the polarization of individual photons could be measured in an the environment of multiple photons produced in the radiator crystal. Photons in the high energy region show less than 20% linear polarization at the 90% confidence level.

Simple and multiple linear regression: sample size considerations.

Science.gov (United States)

Hanley, James A

2016-11-01

The suggested "two subjects per variable" (2SPV) rule of thumb in the Austin and Steyerberg article is a chance to bring out some long-established and quite intuitive sample size considerations for both simple and multiple linear regression. This article distinguishes two of the major uses of regression models that imply very different sample size considerations, neither served well by the 2SPV rule. The first is etiological research, which contrasts mean Y levels at differing "exposure" (X) values and thus tends to focus on a single regression coefficient, possibly adjusted for confounders. The second research genre guides clinical practice. It addresses Y levels for individuals with different covariate patterns or "profiles." It focuses on the profile-specific (mean) Y levels themselves, estimating them via linear compounds of regression coefficients and covariates. By drawing on long-established closed-form variance formulae that lie beneath the standard errors in multiple regression, and by rearranging them for heuristic purposes, one arrives at quite intuitive sample size considerations for both research genres. Copyright © 2016 Elsevier Inc. All rights reserved.

Vortex-Induced Alignment of a Water Soluble Supramolecular Nanofiber Composed of an Amphiphilic Dendrimer

Directory of Open Access Journals (Sweden)

Akihiko Tsuda

2013-06-01

Full Text Available We have synthesized a novel amphiphilic naphthalene imide bearing a cationic dendrimer wedge (NID. NID molecules in water self-assemble to form a two-dimensional ribbon, which further coils to give a linear supramolecular nanofiber. The sample solution showed linear dichroism (LD upon stirring of the solution, where NID nanofibers dominantly align at the center of vortex by hydrodynamic interaction with the downward torsional flows.

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.

Visuo-manual tracking: does intermittent control with aperiodic sampling explain linear power and non-linear remnant without sensorimotor noise?

Science.gov (United States)

Gollee, Henrik; Gawthrop, Peter J; Lakie, Martin; Loram, Ian D

2017-11-01

A human controlling an external system is described most easily and conventionally as linearly and continuously translating sensory input to motor output, with the inevitable output remnant, non-linearly related to the input, attributed to sensorimotor noise. Recent experiments show sustained manual tracking involves repeated refractoriness (insensitivity to sensory information for a certain duration), with the temporary 200-500 ms periods of irresponsiveness to sensory input making the control process intrinsically non-linear. This evidence calls for re-examination of the extent to which random sensorimotor noise is required to explain the non-linear remnant. This investigation of manual tracking shows how the full motor output (linear component and remnant) can be explained mechanistically by aperiodic sampling triggered by prediction error thresholds. Whereas broadband physiological noise is general to all processes, aperiodic sampling is associated with sensorimotor decision making within specific frontal, striatal and parietal networks; we conclude that manual tracking utilises such slow serial decision making pathways up to several times per second. The human operator is described adequately by linear translation of sensory input to motor output. Motor output also always includes a non-linear remnant resulting from random sensorimotor noise from multiple sources, and non-linear input transformations, for example thresholds or refractory periods. Recent evidence showed that manual tracking incurs substantial, serial, refractoriness (insensitivity to sensory information of 350 and 550 ms for 1st and 2nd order systems respectively). Our two questions are: (i) What are the comparative merits of explaining the non-linear remnant using noise or non-linear transformations? (ii) Can non-linear transformations represent serial motor decision making within the sensorimotor feedback loop intrinsic to tracking? Twelve participants (instructed to act in three prescribed

Magnetic field alignment for a 20 MeV linear induction accelerator

International Nuclear Information System (INIS)

Zhang Wenwei; Pan Haifeng; Li Hong; Liu Yunlong; Zhang Linwen

2002-01-01

'Dragon-1' accelerator now is being constructed in CAEP. It will produce high current pulse electron beams. The main components of the accelerator include 72 induction accelerating cells and 18 connection cells with ports for beam di gnostic hardware and vacuum pump. In order to acquire high quality beams, a lot of problems have to be addressed such as to reduce the emittance, to control the increase of corkscrew and so on. The alignment of the focus magnetic field is the most concerned. A laser track has been used for mechanical alignment, magnetic alignment is performed by using pulsed-wire technique, and the natural tilt errors is corrected by a pair of steering coil, which is located inside the cell

SWAMP+: multiple subsequence alignment using associative massive parallelism

Energy Technology Data Exchange (ETDEWEB)

Steinfadt, Shannon Irene [Los Alamos National Laboratory; Baker, Johnnie W [KENT STATE UNIV.

2010-10-18

A new parallel algorithm SWAMP+ incorporates the Smith-Waterman sequence alignment on an associative parallel model known as ASC. It is a highly sensitive parallel approach that expands traditional pairwise sequence alignment. This is the first parallel algorithm to provide multiple non-overlapping, non-intersecting subsequence alignments with the accuracy of Smith-Waterman. The efficient algorithm provides multiple alignments similar to BLAST while creating a better workflow for the end users. The parallel portions of the code run in O(m+n) time using m processors. When m = n, the algorithmic analysis becomes O(n) with a coefficient of two, yielding a linear speedup. Implementation of the algorithm on the SIMD ClearSpeed CSX620 confirms this theoretical linear speedup with real timings.

Tests of Alignment among Assessment, Standards, and Instruction Using Generalized Linear Model Regression

Science.gov (United States)

Fulmer, Gavin W.; Polikoff, Morgan S.

2014-01-01

An essential component in school accountability efforts is for assessments to be well-aligned with the standards or curriculum they are intended to measure. However, relatively little prior research has explored methods to determine statistical significance of alignment or misalignment. This study explores analyses of alignment as a special case…

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....

Polarization and ellipticity of high-order harmonics from aligned molecules generated by linearly polarized intense laser pulses

International Nuclear Information System (INIS)

Le, Anh-Thu; Lin, C. D.; Lucchese, R. R.

2010-01-01

We present theoretical calculations for polarization and ellipticity of high-order harmonics from aligned N 2 , CO 2 , and O 2 molecules generated by linearly polarized lasers. Within the rescattering model, the two polarization amplitudes of the harmonics are determined by the photo-recombination amplitudes for photons emitted with polarization parallel or perpendicular to the direction of the same returning electron wave packet. Our results show clear species-dependent polarization states, in excellent agreement with experiments. We further note that the measured polarization ellipse of the harmonic furnishes the needed parameters for a 'complete' experiment in molecules.

Parameter selection for peak alignment in chromatographic sample profiling: Objective quality indicators and use of control samples

NARCIS (Netherlands)

Peters, S.; van Velzen, E.; Janssen, H.-G.

2009-01-01

In chromatographic profiling applications, peak alignment is often essential as most chromatographic systems exhibit small peak shifts over time. When using currently available alignment algorithms, there are several parameters that determine the outcome of the alignment process. Selecting the

XRD alignment, calibration and performance

International Nuclear Information System (INIS)

Davy, L.

2002-01-01

Full text: The quality of any diffractometer system is very much dependent on the alignment, calibration and performance. The three subjects are very much related. Firstly, you must know how to carry out the full diffractometer alignment. XRD alignment is easy once you know how. The presentation will show you step by step to carry out the full alignment. Secondly, you need to know how to calibrate the diffractometer system. The presentation will show you how to calibrate the goniometer, detector etc. Thirdly, to prove the system is working within the manufacturer specification. The presentation will show you how to carry out the resolution, reproducibility and linearity test. Copyright (2002) Australian X-ray Analytical Association Inc

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...

A general assignment method for oriented sample (OS) solid-state NMR of proteins based on the correlation of resonances through heteronuclear dipolar couplings in samples aligned parallel and perpendicular to the magnetic field.

Science.gov (United States)

Lu, George J; Son, Woo Sung; Opella, Stanley J

2011-04-01

A general method for assigning oriented sample (OS) solid-state NMR spectra of proteins is demonstrated. In principle, this method requires only a single sample of a uniformly ¹⁵N-labeled membrane protein in magnetically aligned bilayers, and a previously assigned isotropic chemical shift spectrum obtained either from solution NMR on micelle or isotropic bicelle samples or from magic angle spinning (MAS) solid-state NMR on unoriented proteoliposomes. The sequential isotropic resonance assignments are transferred to the OS solid-state NMR spectra of aligned samples by correlating signals from the same residue observed in protein-containing bilayers aligned with their normals parallel and perpendicular to the magnetic field. The underlying principle is that the resonances from the same residue have heteronuclear dipolar couplings that differ by exactly a factor of two between parallel and perpendicular alignments. The method is demonstrated on the membrane-bound form of Pf1 coat protein in phospholipid bilayers, whose assignments have been previously made using an earlier generation of methods that relied on the preparation of many selectively labeled (by residue type) samples. The new method provides the correct resonance assignments using only a single uniformly ¹⁵N-labeled sample, two solid-state NMR spectra, and a previously assigned isotropic spectrum. Significantly, this approach is equally applicable to residues in alpha helices, beta sheets, loops, and any other elements of tertiary structure. Moreover, the strategy bridges between OS solid-state NMR of aligned samples and solution NMR or MAS solid-state NMR of unoriented samples. In combination with the development of complementary experimental methods, it provides a step towards unifying these apparently different NMR approaches. Copyright © 2011 Elsevier Inc. All rights reserved.

Sampled-data models for linear and nonlinear systems

CERN Document Server

Yuz, Juan I

2014-01-01

Sampled-data Models for Linear and Nonlinear Systems provides a fresh new look at a subject with which many researchers may think themselves familiar. Rather than emphasising the differences between sampled-data and continuous-time systems, the authors proceed from the premise that, with modern sampling rates being as high as they are, it is becoming more appropriate to emphasise connections and similarities. The text is driven by three motives: ·      the ubiquity of computers in modern control and signal-processing equipment means that sampling of systems that really evolve continuously is unavoidable; ·      although superficially straightforward, sampling can easily produce erroneous results when not treated properly; and ·      the need for a thorough understanding of many aspects of sampling among researchers and engineers dealing with applications to which they are central. The authors tackle many misconceptions which, although appearing reasonable at first sight, are in fact either p...

Effects of variable attachment shapes and aligner material on aligner retention.

Science.gov (United States)

Dasy, Hiltrud; Dasy, Andreas; Asatrian, Greg; Rózsa, Noémi; Lee, Hao-Fu; Kwak, Jin Hee

2015-11-01

To evaluate the retention of four types of aligners on a dental arch with various attachments. For this study, three casts were manufactured, two of which contained attachments (ellipsoid and beveled), and one without any attachments to serve as a control. Four types of aligners were thermoformed: Clear-Aligner (CA)-soft, CA-medium, and CA-hard, with various thicknesses, and Essix ACE. Measurements of vertical displacement force during aligner removal were performed with the Gabo Qualimeter Eplexor. Means and standard deviations were next compared between different aligner thicknesses and attachment shapes. CA-soft, CA-medium, and CA-hard did not present a significant increase in retention, except when used in the presence of attachments. Additionally, CA-medium and CA-hard required significantly more force for removal. Essix ACE demonstrated a significant decrease in retention when used with ellipsoid attachments. The force value for Essix ACE removal from the cast with beveled attachments was comparable to that of CA-medium. Forces for aligner removal from the model without attachments showed a linear trend. Essix ACE did not show a continuous increase in retention for each model. Overall, ellipsoid attachments did not present a significant change in retention. In contrast, beveled attachments improved retention. Ellipsoid attachments had no significant influence on the force required for aligner removal and hence on aligner retention. Essix ACE showed significantly less retention than CA-hard on the models with attachments. Furthermore, beveled attachments were observed to increase retention significantly, compared with ellipsoid attachments and when using no attachments.

Tidal alignment of galaxies

Energy Technology Data Exchange (ETDEWEB)

Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

2015-08-01

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

ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

Science.gov (United States)

Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

2006-12-15

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

Two media method for linear attenuation coefficient determination of irregular soil samples

International Nuclear Information System (INIS)

Vici, Carlos Henrique Georges

2004-01-01

In several situations of nuclear applications, the knowledge of gamma-ray linear attenuation coefficient for irregular samples is necessary, such as in soil physics and geology. This work presents the validation of a methodology for the determination of the linear attenuation coefficient (μ) of irregular shape samples, in such a way that it is not necessary to know the thickness of the considered sample. With this methodology irregular soil samples (undeformed field samples) from Londrina region, north of Parana were studied. It was employed the two media method for the μ determination. It consists of the μ determination through the measurement of a gamma-ray beam attenuation by the sample sequentially immersed in two different media, with known and appropriately chosen attenuation coefficients. For comparison, the theoretical value of μ was calculated by the product of the mass attenuation coefficient, obtained by the WinXcom code, and the measured value of the density sample. This software employs the chemical composition of the samples and supplies a table of the mass attenuation coefficients versus the photon energy. To verify the validity of the two media method, compared with the simple gamma ray transmission method, regular pome stone samples were used. With these results for the attenuation coefficients and their respective deviations, it was possible to compare the two methods. In this way we concluded that the two media method is a good tool for the determination of the linear attenuation coefficient of irregular materials, particularly in the study of soils samples. (author)

An Alignment of J-PARC Linac

CERN Document Server

Morishita, Takatoshi; Hasegawa, Kazuo; Ikegami, Masanori; Ito, Takashi; Kubota, Chikashi; Naito, Fujio; Takasaki, Eiichi; Tanaka, Hirokazu; Ueno, Akira; Yoshino, Kazuo

2005-01-01

J-PARC linear accelerator components are now being installed in the accelerator tunnel, whose total length is more than 400 m including the beam transport line to RCS (Rapid Cycling Synchrotron). A precise alignment of accelerator components is essential for a high quality beam acceleration. In this paper, planned alignment schemes for the installation of linac components, the fine alignment before beam acceleration, and watching the long term motion of the building are described. Guide points are placed on the floor, which acts as a reference for the initial alignment at the installation and also as a relay point for the long surveying network linking at the fine alignment. For a straight line alignment, the wire position sensor is placed on the offset position with respect to the beam center by a target holder, then a single wire can cover the accelerator cavities and the focusing magnets at the DTL-SDTL section (120m). The hydrostatic levering system (HLS) is used for watching the floor elevation (changes)...

A General Linear Method for Equating with Small Samples

Science.gov (United States)

Albano, Anthony D.

2015-01-01

Research on equating with small samples has shown that methods with stronger assumptions and fewer statistical estimates can lead to decreased error in the estimated equating function. This article introduces a new approach to linear observed-score equating, one which provides flexible control over how form difficulty is assumed versus estimated…

Multiciliated cell basal bodies align in stereotypical patterns coordinated by the apical cytoskeleton

Science.gov (United States)

Herawati, Elisa; Kanoh, Hatsuho

2016-01-01

Multiciliated cells (MCCs) promote fluid flow through coordinated ciliary beating, which requires properly organized basal bodies (BBs). Airway MCCs have large numbers of BBs, which are uniformly oriented and, as we show here, align linearly. The mechanism for BB alignment is unexplored. To study this mechanism, we developed a long-term and high-resolution live-imaging system and used it to observe green fluorescent protein–centrin2–labeled BBs in cultured mouse tracheal MCCs. During MCC differentiation, the BB array adopted four stereotypical patterns, from a clustering “floret” pattern to the linear “alignment.” This alignment process was correlated with BB orientations, revealed by double immunostaining for BBs and their asymmetrically associated basal feet (BF). The BB alignment was disrupted by disturbing apical microtubules with nocodazole and by a BF-depleting Odf2 mutation. We constructed a theoretical model, which indicated that the apical cytoskeleton, acting like a viscoelastic fluid, provides a self-organizing mechanism in tracheal MCCs to align BBs linearly for mucociliary transport. PMID:27573463

Estimation of Alignment and Transverse Load in Multi-Bearing Rotor System

OpenAIRE

Tom J. Chalko; Dong-Xu Li

1997-01-01

The paper presents a method for estimation of a multi-bearing machine alignment on the basis of measured eccentricities of the shaft in machine bearings. The method uses a linear FEM model of the rotor and the non-linear models of machine bearings. In the presented example, the non-linear models of hydrodynamic bearings are used, but it is shown, that the method could be easily applied to other types of bearings. In addition to the alignment estimation, the method allows to estimate the unkno...

Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples.

Directory of Open Access Journals (Sweden)

Andrew Cron

Full Text Available Flow cytometry is the prototypical assay for multi-parameter single cell analysis, and is essential in vaccine and biomarker research for the enumeration of antigen-specific lymphocytes that are often found in extremely low frequencies (0.1% or less. Standard analysis of flow cytometry data relies on visual identification of cell subsets by experts, a process that is subjective and often difficult to reproduce. An alternative and more objective approach is the use of statistical models to identify cell subsets of interest in an automated fashion. Two specific challenges for automated analysis are to detect extremely low frequency event subsets without biasing the estimate by pre-processing enrichment, and the ability to align cell subsets across multiple data samples for comparative analysis. In this manuscript, we develop hierarchical modeling extensions to the Dirichlet Process Gaussian Mixture Model (DPGMM approach we have previously described for cell subset identification, and show that the hierarchical DPGMM (HDPGMM naturally generates an aligned data model that captures both commonalities and variations across multiple samples. HDPGMM also increases the sensitivity to extremely low frequency events by sharing information across multiple samples analyzed simultaneously. We validate the accuracy and reproducibility of HDPGMM estimates of antigen-specific T cells on clinically relevant reference peripheral blood mononuclear cell (PBMC samples with known frequencies of antigen-specific T cells. These cell samples take advantage of retrovirally TCR-transduced T cells spiked into autologous PBMC samples to give a defined number of antigen-specific T cells detectable by HLA-peptide multimer binding. We provide open source software that can take advantage of both multiple processors and GPU-acceleration to perform the numerically-demanding computations. We show that hierarchical modeling is a useful probabilistic approach that can provide a

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

Science.gov (United States)

Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

2016-02-01

The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Alignment and stability of future machines

International Nuclear Information System (INIS)

Shiltsev, V.D.

1996-06-01

Leading accelerator laboratories mount serious efforts in alignment and vibration studies concerning stability of future accelerator facilities such as photon and meson factories, future linear colliders (LCs), and hadron supercolliders (HCs). Some 200 publications covered the topic since late 80s, following pioneering works of G.E. Fischer. Four International workshops on accelerator alignment were held since 1989 at SLAC, DESY, CERN and KEK. The SSCL hosted the workshop on vibration control and dynamic alignment (1992). This article briefly covers some present achievements and issues in the field. We discuss major effects and tolerances for the future accelerators, results of measurements up-to-date, correction techniques and make some conclusions

Selective Deposition and Alignment of Single-Walled Carbon Nanotubes Assisted by Dielectrophoresis: From Thin Films to Individual Nanotubes

Science.gov (United States)

Li, Pengfei; Xue, Wei

2010-06-01

Dielectrophoresis has been used in the controlled deposition of single-walled carbon nanotubes (SWNTs) with the focus on the alignment of nanotube thin films and their applications in the last decade. In this paper, we extend the research from the selective deposition of SWNT thin films to the alignment of small nanotube bundles and individual nanotubes. Electrodes with “teeth”-like patterns are fabricated to study the influence of the electrode width on the deposition and alignment of SWNTs. The entire fabrication process is compatible with optical lithography-based techniques. Therefore, the fabrication cost is low, and the resulting devices are inexpensive. A series of SWNT solutions is prepared with concentrations ranging from 0.0125 to 0.2 mg/ml. The alignment of SWNT thin films, small bundles, and individual nanotubes is achieved under the optimized experimental conditions. The electrical properties of these samples are characterized; the linear current-voltage plots prove that the aligned SWNTs are mainly metallic nanotubes. The microscopy inspection of the samples demonstrates that the alignment of small nanotube bundles and individual nanotubes can only be achieved using narrow electrodes and low-concentration solutions. Our investigation shows that it is possible to deposit a controlled amount of SWNTs in desirable locations using dielectrophoresis.

Selective Deposition and Alignment of Single-Walled Carbon Nanotubes Assisted by Dielectrophoresis: From Thin Films to Individual Nanotubes

Directory of Open Access Journals (Sweden)

Li Pengfei

2010-01-01

Full Text Available Abstract Dielectrophoresis has been used in the controlled deposition of single-walled carbon nanotubes (SWNTs with the focus on the alignment of nanotube thin films and their applications in the last decade. In this paper, we extend the research from the selective deposition of SWNT thin films to the alignment of small nanotube bundles and individual nanotubes. Electrodes with “teeth”-like patterns are fabricated to study the influence of the electrode width on the deposition and alignment of SWNTs. The entire fabrication process is compatible with optical lithography-based techniques. Therefore, the fabrication cost is low, and the resulting devices are inexpensive. A series of SWNT solutions is prepared with concentrations ranging from 0.0125 to 0.2 mg/ml. The alignment of SWNT thin films, small bundles, and individual nanotubes is achieved under the optimized experimental conditions. The electrical properties of these samples are characterized; the linear current–voltage plots prove that the aligned SWNTs are mainly metallic nanotubes. The microscopy inspection of the samples demonstrates that the alignment of small nanotube bundles and individual nanotubes can only be achieved using narrow electrodes and low-concentration solutions. Our investigation shows that it is possible to deposit a controlled amount of SWNTs in desirable locations using dielectrophoresis.

Automated sample mounting and technical advance alignment system for biological crystallography at a synchrotron source

International Nuclear Information System (INIS)

Snell, Gyorgy; Cork, Carl; Nordmeyer, Robert; Cornell, Earl; Meigs, George; Yegian, Derek; Jaklevic, Joseph; Jin, Jian; Stevens, Raymond C.; Earnest, Thomas

2004-01-01

High-throughput data collection for macromolecular crystallography requires an automated sample mounting system for cryo-protected crystals that functions reliably when integrated into protein-crystallography beamlines at synchrotrons. Rapid mounting and dismounting of the samples increases the efficiency of the crystal screening and data collection processes, where many crystals can be tested for the quality of diffraction. The sample-mounting subsystem has random access to 112 samples, stored under liquid nitrogen. Results of extensive tests regarding the performance and reliability of the system are presented. To further increase throughput, we have also developed a sample transport/storage system based on 'puck-shaped' cassettes, which can hold sixteen samples each. Seven cassettes fit into a standard dry shipping Dewar. The capabilities of a robotic crystal mounting and alignment system with instrumentation control software and a relational database allows for automated screening and data collection to be developed

Photoresist thin-film effects on alignment process capability

Science.gov (United States)

Flores, Gary E.; Flack, Warren W.

1993-08-01

Two photoresists were selected for alignment characterization based on their dissimilar coating properties and observed differences on alignment capability. The materials are Dynachem OFPR-800 and Shipley System 8. Both photoresists were examined on two challenging alignment levels in a submicron CMOS process, a nitride level and a planarized second level metal. An Ultratech Stepper model 1500 which features a darkfield alignment system with a broadband green light for alignment signal detection was used for this project. Initially, statistically designed linear screening experiments were performed to examine six process factors for each photoresist: viscosity, spin acceleration, spin speed, spin time, softbake time, and softbake temperature. Using the results derived from the screening experiments, a more thorough examination of the statistically significant process factors was performed. A full quadratic experimental design was conducted to examine viscosity, spin speed, and spin time coating properties on alignment. This included a characterization of both intra and inter wafer alignment control and alignment process capability. Insight to the different alignment behavior is analyzed in terms of photoresist material properties and the physical nature of the alignment detection system.

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...

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...

Study on sampling of continuous linear system based on generalized Fourier transform

Science.gov (United States)

Li, Huiguang

2003-09-01

In the research of signal and system, the signal's spectrum and the system's frequency characteristic can be discussed through Fourier Transform (FT) and Laplace Transform (LT). However, some singular signals such as impulse function and signum signal don't satisfy Riemann integration and Lebesgue integration. They are called generalized functions in Maths. This paper will introduce a new definition -- Generalized Fourier Transform (GFT) and will discuss generalized function, Fourier Transform and Laplace Transform under a unified frame. When the continuous linear system is sampled, this paper will propose a new method to judge whether the spectrum will overlap after generalized Fourier transform (GFT). Causal and non-causal systems are studied, and sampling method to maintain system's dynamic performance is presented. The results can be used on ordinary sampling and non-Nyquist sampling. The results also have practical meaning on research of "discretization of continuous linear system" and "non-Nyquist sampling of signal and system." Particularly, condition for ensuring controllability and observability of MIMO continuous systems in references 13 and 14 is just an applicable example of this paper.

CSA: An efficient algorithm to improve circular DNA multiple alignment

Directory of Open Access Journals (Sweden)

Pereira Luísa

2009-07-01

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

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.

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...

Molecular and vibrational structure of diphenylether and its 4,4' -dibromo derivative. Infrared linear dichroism spectroscopy and density functional theory calculations

DEFF Research Database (Denmark)

Eriksen, Troels K; Karlsen, Eva; Spanget-Larsen, Jens

2015-01-01

The title compounds were investigated by means of Linear Dichroism (LD) IR spectroscopy on samples partially aligned in uniaxially stretched low-density polyethylene and by density functional theory calculations. Satisfactory overall agreement between observed and calculated vibrational wavenumbers...

Uni- and tridimensional alignment of molecules by femto-second laser pulse

International Nuclear Information System (INIS)

Rouzee, Arnaud

2007-01-01

This thesis is devoted to the study of the alignment of linear and asymmetric top molecules generated by an intense laser pulse. In the case of short pulses with respect to molecular rotation, periodic alignment appears in field-free conditions after the extinction of the field. We study theoretically and experimentally the effects of intensity, temperature and polarization of the electric field on produced alignment. If the field is linearly polarized, the interaction leads to the alignment of the most polarizable axis of the molecule. If the field is elliptically polarized, the pulse can generate a simultaneous alignment of the three principal axes of inertia of an asymmetric top molecule (3-D alignment). This alignment can be characterized experimentally using pump-probe techniques which exploit the optical properties of the medium. They require the use of a second pulse of low intensity temporally delayed. Three techniques were exploited during this thesis. The first technique measures a depolarization due to the birefringence of the medium when the molecules are aligned. The second is based on the defocusing of the pulse on a gradient of index created following the space variation of alignment with respect to the spatial profile of the field. The last involves the creation of a grading of index to the intersection of two intense pulses, which causes the diffraction of the probe. Finally, we show experimentally that the birefringence technique can be used to quantify the 3-D alignment of an asymmetric top molecule like ethylene. (author) [fr

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.

The CMS Muon System Alignment

CERN Document Server

Martinez Ruiz-Del-Arbol, P

2009-01-01

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

Sequential Optimization of Global Sequence Alignments Relative to Different Cost Functions

KAUST Repository

Odat, Enas M.

2011-01-01

The algorithm has been simulated using C#.Net programming language and a number of experiments have been done to verify the proved statements. The results of these experiments show that the number of optimal alignments is reduced after each step of optimization. Furthermore, it has been verified that as the sequence length increased linearly then the number of optimal alignments increased exponentially which also depends on the cost function that is used. Finally, the number of executed operations increases polynomially as the sequence length increase linearly.

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...

Orbital alignment effects in near-resonant Rydberg atoms-rare gas collisions

International Nuclear Information System (INIS)

Isaacs, W.A.; Morrison, M.A.

1993-01-01

Recent experimental and theoretical studies of near-resonant energy transfer collisions involving rare-gas atoms and alkali or alkaline earth atoms which have been initially excited to an aligned state via one or more linearly polarized rasters have yielded a wealth of insight into orbital alignment and related effects. We have extended this inquiry to initially aligned Rydberg states, examining state-to-state and alignment-selected cross sections using quantum collision theory augmented by approximations appropriate to the special characteristics of the Rydberg state (e.g., the quasi-free-electron model and the impulse approximation)

Understating Polarization in the Interstellar Medium Through the Theory of Radiative Torque Alignment

Science.gov (United States)

Caputo, Miranda; Andersson, B.-G.; Kulas, Kristin Rose

2018-06-01

Although it is known that the dust grains in the ISM align with magnetic fields, the alignment physics of these particles is still somewhat unclear. Utilizing direct observational data and Radiative Alignment Torque (RAT) theory, further constraints can be put onto this alignment. Due to the physics of this alignment, there is a linear relationship between the extinction of the light seen through a dust cloud (AV) and the wavelength of maximum polarization. A previous study, focusing on the Taurus cloud, found that there is a second, steeper relationship seen beyond an extinction of about four magnitudes, likely due to grain growth, in addition to the original linear relationship. We present early results from observations of low-to-medium extinction lines of sight in the starless cloud L183 (aka L134N), aimed at testing the Taurus results. We are currently extending the survey of stars behind L183 to higher extinctions to better probe the origins of the bifurcation seen in the Taurus results.

Iterative local Chi2 alignment algorithm for the ATLAS Pixel detector

CERN Document Server

Göttfert, Tobias

The existing local chi2 alignment approach for the ATLAS SCT detector was extended to the alignment of the ATLAS Pixel detector. This approach is linear, aligns modules separately, and uses distance of closest approach residuals and iterations. The derivation and underlying concepts of the approach are presented. To show the feasibility of the approach for Pixel modules, a simplified, stand-alone track simulation, together with the alignment algorithm, was developed with the ROOT analysis software package. The Pixel alignment software was integrated into Athena, the ATLAS software framework. First results and the achievable accuracy for this approach with a simulated dataset are presented.

Strategy and validation of fiducialisation for the pre-alignment of CLIC components

CERN Document Server

Griffet, S; Kemppinen, J; Mainaud Durand, H; Rude, V; Sterbini, G

2012-01-01

The feasibility of the high energy e+ e- linear collider CLIC (Compact Linear Collider) is very dependent on the ability to accurately pre-align its components. There are two 20 km long Main Linacs which meet in an interaction point (IP). The Main Linacs are composed of thousands of 2 m long modules. One of the challenges is to meet very tight alignment tolerances at the level of CLIC module: for example, the magnetic centre of a Drive Beam Quad needs to be aligned within 20 µm rms with respect to a straight line. Such accuracies cannot be achieved using usual measurement devices. Thus it is necessary to work in close collaboration with the metrology lab. To test and improve many critical points, including alignment, a CLIC mock-up is being assembled at CERN. This paper describes the application of the strategy of fiducialisation for the pre-alignment of CLIC mock-up components. It also deals with the first results obtained by performing measurements using a CMM (Coordinate Measuring Machine) to ensure the f...

Effect of alignment of easy axes on dynamic magnetization of immobilized magnetic nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Yoshida, Takashi, E-mail: t_yoshi@ees.kyushu-u.ac.jp [Department of Electrical and Electronic Engineering, Kyushu University, Fukuoka 819-0395 (Japan); Matsugi, Yuki; Tsujimura, Naotaka; Sasayama, Teruyoshi; Enpuku, Keiji [Department of Electrical and Electronic Engineering, Kyushu University, Fukuoka 819-0395 (Japan); Viereck, Thilo; Schilling, Meinhard; Ludwig, Frank [Institut für Elektrische Messtechnik und Grundlagen der Elektrotechnik, TU Braunschweig, Braunschweig 38106 (Germany)

2017-04-01

In some biomedical applications of magnetic nanoparticles (MNPs), the particles are physically immobilized. In this study, we explore the effect of the alignment of the magnetic easy axes on the dynamic magnetization of immobilized MNPs under an AC excitation field. We prepared three immobilized MNP samples: (1) a sample in which easy axes are randomly oriented, (2) a parallel-aligned sample in which easy axes are parallel to the AC field, and (3) an orthogonally aligned sample in which easy axes are perpendicular to the AC field. First, we show that the parallel-aligned sample has the largest hysteresis in the magnetization curve and the largest harmonic magnetization spectra, followed by the randomly oriented and orthogonally aligned samples. For example, 1.6-fold increase was observed in the area of the hysteresis loop of the parallel-aligned sample compared to that of the randomly oriented sample. To quantitatively discuss the experimental results, we perform a numerical simulation based on a Fokker-Planck equation, in which probability distributions for the directions of the easy axes are taken into account in simulating the prepared MNP samples. We obtained quantitative agreement between experiment and simulation. These results indicate that the dynamic magnetization of immobilized MNPs is significantly affected by the alignment of the easy axes. - Highlights: • We clarify how the alignment of easy axis of MNP affects the AC magnetization. • Parallel-aligned immobilized MNPs exhibit the largest AC hysteresis loop. • Parallel-aligned immobilized MNPs exhibit the largest harmonic magnetization spectra. • The AC magnetization is strongly affected by the alignment of the easy axes.

Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool

Directory of Open Access Journals (Sweden)

Ulrike H. Taron

2018-03-01

Full Text Available High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present ‘TAPAS’, (Testing of Alignment Parameters for Ancient Samples, a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang, for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.

Feature-based Alignment of Volumetric Multi-modal Images

Science.gov (United States)

Toews, Matthew; Zöllei, Lilla; Wells, William M.

2014-01-01

This paper proposes a method for aligning image volumes acquired from different imaging modalities (e.g. MR, CT) based on 3D scale-invariant image features. A novel method for encoding invariant feature geometry and appearance is developed, based on the assumption of locally linear intensity relationships, providing a solution to poor repeatability of feature detection in different image modalities. The encoding method is incorporated into a probabilistic feature-based model for multi-modal image alignment. The model parameters are estimated via a group-wise alignment algorithm, that iteratively alternates between estimating a feature-based model from feature data, then realigning feature data to the model, converging to a stable alignment solution with few pre-processing or pre-alignment requirements. The resulting model can be used to align multi-modal image data with the benefits of invariant feature correspondence: globally optimal solutions, high efficiency and low memory usage. The method is tested on the difficult RIRE data set of CT, T1, T2, PD and MP-RAGE brain images of subjects exhibiting significant inter-subject variability due to pathology. PMID:24683955

A Dynamic Alignment System for the Final Focus Test Beam

International Nuclear Information System (INIS)

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

2005-01-01

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

Method to evaluate steering and alignment algorithms for controlling emittance growth

International Nuclear Information System (INIS)

Adolphsen, C.; Raubenheimer, T.

1993-04-01

Future linear colliders will likely use sophisticated beam-based alignment and/or steering algorithms to control the growth of the beam emittance in the linac. In this paper, a mathematical framework is presented which simplifies the evaluation of the effectiveness of these algorithms. As an application, a quad alignment that uses beam data taken with the nominal linac optics, and with a scaled optics, is evaluated in terms of the dispersive emittance growth remaining after alignment

Alignment of Ion Accelerator for Surface Analysis using Theodolite and Laser Tracker

Energy Technology Data Exchange (ETDEWEB)

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

2016-05-15

The method of ion accelerator alignment is used two ways which are a theodolite and laser tracker. For the alignment and maintenance of the proton linear accelerator, the laser tracker is typically used at KOMAC. While the device for alignment by using laser tracker is not installed in all ion accelerator components, it was used in parallel in two methods. In this paper, alignment methods are introduced and the result and comparison of each alignment method are presented. The ion accelerator for surface analysis has aligned using theodolite and laser tracker. The two ways for alignment have advantage as well as weakness. But alignment using laser tracker is stronger than using theodolite. Because it is based on alignment and position data and it is more detailed. Also since the beam distribution is smaller than accelerator component that is direction of beam progress, main component (ex. Magnet, Chamber, Pelletron tank, etc.) alignment using laser tracker is enough to align the ion accelerator.

Face Alignment via Regressing Local Binary Features.

Science.gov (United States)

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

2016-03-01

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

Relevance of sampling schemes in light of Ruelle's linear response theory

International Nuclear Information System (INIS)

Lucarini, Valerio; Wouters, Jeroen; Faranda, Davide; Kuna, Tobias

2012-01-01

We reconsider the theory of the linear response of non-equilibrium steady states to perturbations. We first show that using a general functional decomposition for space–time dependent forcings, we can define elementary susceptibilities that allow us to construct the linear response of the system to general perturbations. Starting from the definition of SRB measure, we then study the consequence of taking different sampling schemes for analysing the response of the system. We show that only a specific choice of the time horizon for evaluating the response of the system to a general time-dependent perturbation allows us to obtain the formula first presented by Ruelle. We also discuss the special case of periodic perturbations, showing that when they are taken into consideration the sampling can be fine-tuned to make the definition of the correct time horizon immaterial. Finally, we discuss the implications of our results in terms of strategies for analysing the outputs of numerical experiments by providing a critical review of a formula proposed by Reick

Effect of alignment of easy axes on dynamic magnetization of immobilized magnetic nanoparticles

Science.gov (United States)

Yoshida, Takashi; Matsugi, Yuki; Tsujimura, Naotaka; Sasayama, Teruyoshi; Enpuku, Keiji; Viereck, Thilo; Schilling, Meinhard; Ludwig, Frank

2017-04-01

In some biomedical applications of magnetic nanoparticles (MNPs), the particles are physically immobilized. In this study, we explore the effect of the alignment of the magnetic easy axes on the dynamic magnetization of immobilized MNPs under an AC excitation field. We prepared three immobilized MNP samples: (1) a sample in which easy axes are randomly oriented, (2) a parallel-aligned sample in which easy axes are parallel to the AC field, and (3) an orthogonally aligned sample in which easy axes are perpendicular to the AC field. First, we show that the parallel-aligned sample has the largest hysteresis in the magnetization curve and the largest harmonic magnetization spectra, followed by the randomly oriented and orthogonally aligned samples. For example, 1.6-fold increase was observed in the area of the hysteresis loop of the parallel-aligned sample compared to that of the randomly oriented sample. To quantitatively discuss the experimental results, we perform a numerical simulation based on a Fokker-Planck equation, in which probability distributions for the directions of the easy axes are taken into account in simulating the prepared MNP samples. We obtained quantitative agreement between experiment and simulation. These results indicate that the dynamic magnetization of immobilized MNPs is significantly affected by the alignment of the easy axes.

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.

Assessment of ethylene vinyl-acetate copolymer samples exposed to γ-rays via linearity analyses

Energy Technology Data Exchange (ETDEWEB)

Oliveira, Lucas N. de; Nascimento, Eriberto O. do; Schimidt, Fernando [Instituto Federal de Educação, Ciência e Tecnologia de Goiás (IFG), Goiânia, GO (Brazil); Antonio, Patrícia L.; Caldas, Linda V.E., E-mail: lcaldas@ipen.br [Instituto de Pesquisas Energéticas e Nucleares (IPEN/CNEN-SP), São Paulo, SP (Brazil)

2017-07-01

Materials with the potential to become dosimeters are of interest in radiation physics. In this research, the materials were analyzed and compared in relation to their linearity ranges. Samples of ethylene vinyl-acetate copolymer (EVA) were irradiated with doses from 10 Gy to 10 kGy using a {sup 60}Co Gamma-Cell system 220 and evaluated with the FTIR technique. The linearity analyses were applied through two methodologies, searching for linear regions in their response. The results show that both applied analyses indicate linear regions in defined dose interval. The radiation detectors EVA can be useful for radiation dosimetry in intermediate and high doses. (author)

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.

Science.gov (United States)

Nagar, Anurag; Hahsler, Michael

2013-01-01

Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to

Neutron sample cell suitable for the diffraction of aligned biomaterials and capable of exerting up to 370 MPa of hydrostatic pressure

International Nuclear Information System (INIS)

Watson, M.J.; Nieh, M.-P.; Harroun, T.A.; Katsaras, J.

2003-01-01

We describe a temperature controlled sample cell suitable for the study of biomimetic materials (e.g., lipid bilayers) using neutron diffraction, and capable of exerting hydrostatic pressures of up to 370 MPa. The advantage of this sample cell, compared to previous high-pressure cells of its type, is that it allows for the use of samples aligned on a solid support which, compared to 'powder' or so-called liposomal preparations, requires only small amounts of sample and allows for the clear differentiation between in-plane and out-of-plane structure

The ties that bind: interorganizational linkages and physician-system alignment.

Science.gov (United States)

Alexander, J A; Waters, T M; Burns, L R; Shortell, S M; Gillies, R R; Budetti, P P; Zuckerman, H S

2001-07-01

To examine the association between the degree of alignment between physicians and health care systems, and interorganizational linkages between physician groups and health care systems. The study used a cross sectional, comparative analysis using a sample of 1,279 physicians practicing in loosely affiliated arrangements and 1,781 physicians in 61 groups closely affiliated with 14 vertically integrated health systems. Measures of physician alignment were based on multiitem scales validated in previous studies and derived from surveys sent to individual physicians. Measures of interorganizational linkages were specified at the institutional, administrative, and technical core levels of the physician group and were developed from surveys sent to the administrator of each of the 61 physician groups in the sample. Two stage Heckman models with fixed effects adjustments in the second stage were used to correct for sample selection and clustering respectively. After accounting for sample selection, fixed effects, and group and individual controls, physicians in groups with more valued practice service linkages display consistently higher alignment with systems than physicians in groups that have fewer such linkages. Results also suggest that centralized administrative control lowers physician-system alignment for selected measures of alignment. Governance interlocks exhibited only weak associations with alignment. Our findings suggest that alignment generally follows resource exchanges that promote value-added contributions to physicians and physician groups while preserving control and authority within the group.

Biaxial magnetic grain alignment

International Nuclear Information System (INIS)

Staines, M.; Genoud, J.-Y.; Mawdsley, A.; Manojlovic, V.

2000-01-01

Full text: We describe a dynamic magnetic grain alignment technique which can be used to produce YBCO thick films with a high degree of biaxial texture. The technique is, however, generally applicable to preparing ceramics or composite materials from granular materials with orthorhombic or lower crystal symmetry and is therefore not restricted to superconducting applications. Because magnetic alignment is a bulk effect, textured substrates are not required, unlike epitaxial coated tape processes such as RABiTS. We have used the technique to produce thick films of Y-247 on untextured silver substrates. After processing to Y-123 the films show a clear enhancement of critical current density relative to identically prepared untextured or uniaxially textured samples. We describe procedures for preparing materials using magnetic biaxial grain alignment with the emphasis on alignment in epoxy, which can give extremely high texture. X-ray rocking curves with FWHM of as little as 1-2 degrees have been measured

Iterative local Chi2 alignment approach for the ATLAS SCT detector

CERN Document Server

Härtel, Roland

An approach for the alignment of SCT modules in the ATLAS Inner Detector with particle tracks was developed and implemented in the ATLAS software framework Athena. The approach uses distance of closest approach residuals and a linear least squares minimization to derive the most probable set of alignment parameters for each module. The procedure is iterative, i.e. with the first set of alignment constants a track refit is done and the alignment algorithm is repeated. Correlations between modules are only implicitly taken into account due to the improvement of track parameters through the iterations. A derivation of the underlying concepts is presented. The achievable accuracy and limits of the alignment approach were studied with Monte Carlo simulated tracks in the Athena framework. The results and limitations obtained with the present versions of Athena and the proposed alignment software are presented.

Miniaturized Stretchable and High-Rate Linear Supercapacitors

OpenAIRE

Zhu, Wenjun; Zhang, Yang; Zhou, Xiaoshuang; Xu, Jiang; Liu, Zunfeng; Yuan, Ningyi; Ding, Jianning

2017-01-01

Linear stretchable supercapacitors have attracted much attention because they are well suited to applications in the rapidly expanding field of wearable electronics. However, poor conductivity of the electrode material, which limits the transfer of electrons in the axial direction of the linear supercapacitors, leads to a serious loss of capacity at high rates. To solve this problem, we use gold nanoparticles to decorate aligned multiwall carbon nanotube to fabricate stretchable linear electr...

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...

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...... field can be used to align molecules along their axis of highest polarizability. Here we demonstrate, theoretically and experimentally, that an elliptically polarized laser field can be used to simultaneously force two axes of a molecule into alignment through the same mechanism. Due to the rigidity...

Survey and alignment for the Swiss Light Source

International Nuclear Information System (INIS)

Wei, F.Q.; Dreyer, K.; Fehlmann, U.; Pochon, J.L.; Wrulich, A.

1999-01-01

The Swiss Light Source (SLS) is a dedicated high brightness synchrotron light source currently under construction at the Paul Scherrer Institute (PSI) in Villigen. It will be commissioned in 2001. The accelerator complex includes a 2.4 GeV electron storage ring (SR) with 288 in circumference, a full energy injection booster synchrotron (Booster) and a 100 MeV linear pre-accelerator. The general alignment method and first results of the network measurements are presented. A laser tracker LTD500 is mainly adopted for network measurements and the alignment of storage ring components. (authors)

Spatio-temporal alignment of pedobarographic image sequences.

Science.gov (United States)

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

2011-07-01

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

Healthcare restructuring and hierarchical alignment: why do staff and managers perceive change outcomes differently?

Science.gov (United States)

Walston, Stephen L; Chou, Ann F

2006-09-01

Healthcare organizations have undergone major change efforts in the past decade. Sustained change is related to continued alignment among organizational participants and may fail with incongruent perceptions of change. This study identifies factors contributing to the alignment in perceptions of organizational change outcomes between executives and all other employees. The sample included 10 hospitals with survey responses from 421 executives and other employees. Using hierarchical linear modeling (HLM), perceptual alignment was modeled at the first level as a function of goal commitment, goal clarity, goal acceptance, goal specificity, staff participation, available skill set, and knowledge and at the second level as organizational size. Descriptive statistics showed employee perception of outcomes differed among personnel levels. HLM results showed that goal specificity, appropriate staff training, reward incentives, effective communication, information sharing, and organization's ability to sustain changes induced perceptual alignment in change outcomes. Staff involvement in designing change efforts increased perceptual misalignment, whereas involvement during implementation and maintenance phases increased alignment. This research uses cross-sectional data from 10 hospitals. Data were gathered from surveys that may have recall bias as hospitals were surveyed at different times after the implementation of their restructuring. Our findings enhance the understanding of processes and mechanisms that enable healthcare organizations to align organizational participants' efforts during change. Results suggest that decision-makers should create incentives to encourage innovative practices, institute effective communication mechanisms, selectively disseminate information, and involve participants in implementing and maintaining changes to achieve intended outcomes. ORIGINALITY/VALUE OF ARTICLE: This article provides unique insight into the importance and causes of

Alignment of symmetric top molecules by short laser pulses

DEFF Research Database (Denmark)

Hamilton, Edward; Seideman, Tamar; Ejdrup, Tine

2005-01-01

-resolved photofragment imaging. Using methyliodide and tert-butyliodide as examples, we calculate and measure the alignment dynamics, focusing on the temporal structure and intensity of the revival patterns, including their dependence on the pulse duration, and their behavior at long times, where centrifugal distortion......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...

Beam based alignment at the KEK accelerator test facility

International Nuclear Information System (INIS)

Ross, M.; Nelson, J.; Woodley, M.; Wolski, A.

2002-01-01

The KEK Accelerator Test Facility (ATF) damping ring is a prototype low emittance source for the NLC/JLC linear collider. To achieve the goal normalized vertical emittance gey = 20 nm-rad, magnet placement accuracy better than 30 mm must be achieved. Accurate beam-based alignment (BBA) is required. The ATF arc optics uses a FOBO cell with two horizontally focusing quadrupoles, two sextupoles and a horizontally defocusing gradient dipole, all of which must be aligned with BBA. BBA at ATF uses the quadrupole and sextupole trim windings to find the trajectory through the center of each magnet. The results can be interpreted to assess the accuracy of the mechanical alignment and the beam position monitor offsets

Halo Intrinsic Alignment: Dependence on Mass, Formation Time, and Environment

Energy Technology Data Exchange (ETDEWEB)

Xia, Qianli; Kang, Xi; Wang, Peng; Luo, Yu [Purple Mountain Observatory, the Partner Group of MPI für Astronomie, 2 West Beijing Road, Nanjing 210008 (China); Yang, Xiaohu; Jing, Yipeng [Center for Astronomy and Astrophysics, Shanghai Jiao Tong University, Shanghai 200240 (China); Wang, Huiyuan [Key Laboratory for Research in Galaxies and Cosmology, Department of Astronomy, University of Science and Technology of China, Hefei, Anhui 230026 (China); Mo, Houjun, E-mail: kangxi@pmo.ac.cn [Astronomy Department and Center for Astrophysics, Tsinghua University, Beijing 10084 (China)

2017-10-10

In this paper we use high-resolution cosmological simulations to study halo intrinsic alignment and its dependence on mass, formation time, and large-scale environment. In agreement with previous studies using N -body simulations, it is found that massive halos have stronger alignment. For the first time, we find that for a given halo mass older halos have stronger alignment and halos in cluster regions also have stronger alignment than those in filaments. To model these dependencies, we extend the linear alignment model with inclusion of halo bias and find that the halo alignment with its mass and formation time dependence can be explained by halo bias. However, the model cannot account for the environment dependence, as it is found that halo bias is lower in clusters and higher in filaments. Our results suggest that halo bias and environment are independent factors in determining halo alignment. We also study the halo alignment correlation function and find that halos are strongly clustered along their major axes and less clustered along the minor axes. The correlated halo alignment can extend to scales as large as 100 h {sup −1} Mpc, where its feature is mainly driven by the baryon acoustic oscillation effect.

Liquid Phase Micro-Extraction of Linear Alkylbenzene Sulfonate Anionic Surfactants in Aqueous Samples

Directory of Open Access Journals (Sweden)

Jan Åke Jönsson

2011-10-01

Full Text Available Hollow fiber liquid phase micro-extraction (LPME of linear alkylbenzene sulfonates (LAS from aqueous samples was studied. Ion pair extraction of C10, C11, C12 and C13 homologues was facilitated with trihexylamine as ion-pairing agent, using di-n-hexylether as solvent for the supported liquid membrane (SLM. Effects of extraction time, acceptor buffer concentration, stirring speed, sample volume, NaCl and humic acids were studied. At 10–50 µg L−1 linear R2-coefficients were 0.99 for C10 and C11 and 0.96 for C12. RSD was typically ~15%. Three observations were especially made. Firstly, LPME for these analytes was unusually slow with maximum enrichment observed after 15–24 h (depending on sample volume. Secondly, the enrichment depended on LAS sample concentration with 35–150 times enrichment below ~150 µg L−1 and 1850–4400 times enrichment at 1 mg L−1. Thirdly, lower homologues were enriched more than higher homologues at low sample concentrations, with reversed conditions at higher concentrations. These observations may be due to the fact that LAS and the amine counter ion themselves influence the mass transfer at the water-SLM interface. The observations on LPME of LAS may aid in LPME application to other compounds with surfactant properties or in surfactant enhanced membrane extraction of other compounds.

A Method for SINS Alignment with Large Initial Misalignment Angles Based on Kalman Filter with Parameters Resetting

Directory of Open Access Journals (Sweden)

Xixiang Liu

2014-01-01

Full Text Available In the initial alignment process of strapdown inertial navigation system (SINS, large initial misalignment angles always bring nonlinear problem, which causes alignment failure when the classical linear error model and standard Kalman filter are used. In this paper, the problem of large misalignment angles in SINS initial alignment is investigated, and the key reason for alignment failure is given as the state covariance from Kalman filter cannot represent the true one during the steady filtering process. According to the analysis, an alignment method for SINS based on multiresetting the state covariance matrix of Kalman filter is designed to deal with large initial misalignment angles, in which classical linear error model and standard Kalman filter are used, but the state covariance matrix should be multireset before the steady process until large misalignment angles are decreased to small ones. The performance of the proposed method is evaluated by simulation and car test, and the results indicate that the proposed method can fulfill initial alignment with large misalignment angles effectively and the alignment accuracy of the proposed method is as precise as that of alignment with small misalignment angles.

Adiabatic Field-Free Alignment of Asymmetric Top Molecules with an Optical Centrifuge.

Science.gov (United States)

Korobenko, A; Milner, V

2016-05-06

We use an optical centrifuge to align asymmetric top SO_{2} molecules by adiabatically spinning their most polarizable O-O axis. The effective centrifugal potential in the rotating frame confines the sulfur atoms to the plane of the laser-induced rotation, leading to the planar molecular alignment that persists after the molecules are released from the centrifuge. The periodic appearance of the full three-dimensional alignment, typically observed only with linear and symmetric top molecules, is also detected. Together with strong in-plane centrifugal forces, which bend the molecules by up to 10 deg, permanent field-free alignment offers new ways of controlling molecules with laser light.

Method for validating radiobiological samples using a linear accelerator.

Science.gov (United States)

Brengues, Muriel; Liu, David; Korn, Ronald; Zenhausern, Frederic

2014-04-29

There is an immediate need for rapid triage of the population in case of a large scale exposure to ionizing radiation. Knowing the dose absorbed by the body will allow clinicians to administer medical treatment for the best chance of recovery for the victim. In addition, today's radiotherapy treatment could benefit from additional information regarding the patient's sensitivity to radiation before starting the treatment. As of today, there is no system in place to respond to this demand. This paper will describe specific procedures to mimic the effects of human exposure to ionizing radiation creating the tools for optimization of administered radiation dosimetry for radiotherapy and/or to estimate the doses of radiation received accidentally during a radiation event that could pose a danger to the public. In order to obtain irradiated biological samples to study ionizing radiation absorbed by the body, we performed ex-vivo irradiation of human blood samples using the linear accelerator (LINAC). The LINAC was implemented and calibrated for irradiating human whole blood samples. To test the calibration, a 2 Gy test run was successfully performed on a tube filled with water with an accuracy of 3% in dose distribution. To validate our technique the blood samples were ex-vivo irradiated and the results were analyzed using a gene expression assay to follow the effect of the ionizing irradiation by characterizing dose responsive biomarkers from radiobiological assays. The response of 5 genes was monitored resulting in expression increase with the dose of radiation received. The blood samples treated with the LINAC can provide effective irradiated blood samples suitable for molecular profiling to validate radiobiological measurements via the gene-expression based biodosimetry tools.

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.

Sequential Optimization of Global Sequence Alignments Relative to Different Cost Functions

KAUST Repository

Odat, Enas M.

2011-05-01

The purpose of this dissertation is to present a methodology to model global sequence alignment problem as directed acyclic graph which helps to extract all possible optimal alignments. Moreover, a mechanism to sequentially optimize sequence alignment problem relative to different cost functions is suggested. Sequence alignment is mostly important in computational biology. It is used to find evolutionary relationships between biological sequences. There are many algo- rithms that have been developed to solve this problem. The most famous algorithms are Needleman-Wunsch and Smith-Waterman that are based on dynamic program- ming. In dynamic programming, problem is divided into a set of overlapping sub- problems and then the solution of each subproblem is found. Finally, the solutions to these subproblems are combined into a final solution. In this thesis it has been proved that for two sequences of length m and n over a fixed alphabet, the suggested optimization procedure requires O(mn) arithmetic operations per cost function on a single processor machine. The algorithm has been simulated using C#.Net programming language and a number of experiments have been done to verify the proved statements. The results of these experiments show that the number of optimal alignments is reduced after each step of optimization. Furthermore, it has been verified that as the sequence length increased linearly then the number of optimal alignments increased exponentially which also depends on the cost function that is used. Finally, the number of executed operations increases polynomially as the sequence length increase linearly.

Linear model correction: A method for transferring a near-infrared multivariate calibration model without standard samples

Science.gov (United States)

Liu, Yan; Cai, Wensheng; Shao, Xueguang

2016-12-01

Calibration transfer is essential for practical applications of near infrared (NIR) spectroscopy because the measurements of the spectra may be performed on different instruments and the difference between the instruments must be corrected. For most of calibration transfer methods, standard samples are necessary to construct the transfer model using the spectra of the samples measured on two instruments, named as master and slave instrument, respectively. In this work, a method named as linear model correction (LMC) is proposed for calibration transfer without standard samples. The method is based on the fact that, for the samples with similar physical and chemical properties, the spectra measured on different instruments are linearly correlated. The fact makes the coefficients of the linear models constructed by the spectra measured on different instruments are similar in profile. Therefore, by using the constrained optimization method, the coefficients of the master model can be transferred into that of the slave model with a few spectra measured on slave instrument. Two NIR datasets of corn and plant leaf samples measured with different instruments are used to test the performance of the method. The results show that, for both the datasets, the spectra can be correctly predicted using the transferred partial least squares (PLS) models. Because standard samples are not necessary in the method, it may be more useful in practical uses.

Method for validating radiobiological samples using a linear accelerator

International Nuclear Information System (INIS)

Brengues, Muriel; Liu, David; Korn, Ronald; Zenhausern, Frederic

2014-01-01

There is an immediate need for rapid triage of the population in case of a large scale exposure to ionizing radiation. Knowing the dose absorbed by the body will allow clinicians to administer medical treatment for the best chance of recovery for the victim. In addition, today's radiotherapy treatment could benefit from additional information regarding the patient's sensitivity to radiation before starting the treatment. As of today, there is no system in place to respond to this demand. This paper will describe specific procedures to mimic the effects of human exposure to ionizing radiation creating the tools for optimization of administered radiation dosimetry for radiotherapy and/or to estimate the doses of radiation received accidentally during a radiation event that could pose a danger to the public. In order to obtain irradiated biological samples to study ionizing radiation absorbed by the body, we performed ex-vivo irradiation of human blood samples using the linear accelerator (LINAC). The LINAC was implemented and calibrated for irradiating human whole blood samples. To test the calibration, a 2 Gy test run was successfully performed on a tube filled with water with an accuracy of 3% in dose distribution. To validate our technique the blood samples were ex-vivo irradiated and the results were analyzed using a gene expression assay to follow the effect of the ionizing irradiation by characterizing dose responsive biomarkers from radiobiological assays. The response of 5 genes was monitored resulting in expression increase with the dose of radiation received. The blood samples treated with the LINAC can provide effective irradiated blood samples suitable for molecular profiling to validate radiobiological measurements via the gene-expression based biodosimetry tools. (orig.)

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.

Decomposition and (importance) sampling techniques for multi-stage stochastic linear programs

Energy Technology Data Exchange (ETDEWEB)

Infanger, G.

1993-11-01

The difficulty of solving large-scale multi-stage stochastic linear programs arises from the sheer number of scenarios associated with numerous stochastic parameters. The number of scenarios grows exponentially with the number of stages and problems get easily out of hand even for very moderate numbers of stochastic parameters per stage. Our method combines dual (Benders) decomposition with Monte Carlo sampling techniques. We employ importance sampling to efficiently obtain accurate estimates of both expected future costs and gradients and right-hand sides of cuts. The method enables us to solve practical large-scale problems with many stages and numerous stochastic parameters per stage. We discuss the theory of sharing and adjusting cuts between different scenarios in a stage. We derive probabilistic lower and upper bounds, where we use importance path sampling for the upper bound estimation. Initial numerical results turned out to be promising.

Linear and Non-Linear Piezoresistance Coefficients in Cubic Semiconductors. I. Theoretical Formulations

Science.gov (United States)

Durand, S.; Tellier, C. R.

1996-02-01

This paper constitutes the first part of a work devoted to applications of piezoresistance effects in germanium and silicon semiconductors. In this part, emphasis is placed on a formal explanation of non-linear effects. We propose a brief phenomenological description based on the multi-valleys model of semiconductors before to adopt a macroscopic tensorial model from which general analytical expressions for primed non-linear piezoresistance coefficients are derived. Graphical representations of linear and non-linear piezoresistance coefficients allows us to characterize the influence of the two angles of cut and of directions of alignment. The second part will primarily deal with specific applications for piezoresistive sensors. Cette publication constitue la première partie d'un travail consacré aux applications des effets piézorésistifs dans les semiconducteurs germanium et silicium. Cette partie traite essentiellement de la modélisation des effets non-linéaires. Après une description phénoménologique à partir du modèle de bande des semiconducteurs nous développons un modèle tensoriel macroscopique et nous proposons des équations générales analytiques exprimant les coefficients piézorésistifs non-linéaires dans des repères tournés. Des représentations graphiques des variations des coefficients piézorésistifs linéaires et non-linéaires permettent une pré-caractérisation de l'influence des angles de coupes et des directions d'alignement avant l'étude d'applications spécifiques qui feront l'objet de la deuxième partie.

Alignment performance monitoring for ASML systems

Science.gov (United States)

Chung, Woong-Jae; Temchenko, Vlad; Hauck, Tarja; Schmidt, Sebastian

2006-03-01

In today's semiconductor industry downscaling of the IC design puts a stringent requirement on pattern overlay control. Tighter overlay requirements lead to exceedingly higher rework rates, meaning additional costs to manufacturing. Better alignment control became a target of engineering efforts to decrease rework rate for high-end technologies. Overlay performance is influenced by known parameters such as "Shift, Scaling, Rotation, etc", and unknown parameters defined as "Process Induced Variation", which are difficult to control by means of a process automation system. In reality, this process-induced variation leads to a strong wafer to wafer, or lot to lot variation, which are not easy to detect in the mass-production environment which uses sampling overlay measurements for only several wafers in a lot. An engineering task of finding and correcting a root cause for Process Induced Variations of overlay performance will be greatly simplified if the unknown parameters could be tracked for each wafer. This paper introduces an alignment performance monitoring method based on analysis of automatically generated "AWE" files for ASML scanner systems. Because "AWE" files include alignment results for each aligned wafer, it is possible to use them for monitoring, controlling and correcting the causes of "process induced" overlay performance without requiring extra measurement time. Since "AWE" files include alignment information for different alignment marks, it is also possible to select and optimize the best alignment recipe for each alignment strategy. Several case studies provided in our paper will demonstrate how AWE file analysis can be used to assist engineer in interpreting pattern alignment data. Since implementing our alignment data monitoring method, we were able to achieve significant improvement of alignment and overlay performance without additional overlay measurement time. We also noticed that the rework rate coming from alignment went down and

Alignment control of columnar liquid crystals with wavelength tunable CO2 laser irradiation

International Nuclear Information System (INIS)

Monobe, Hirosato; Awazu, Kunio; Shimizu, Yo

2008-01-01

Infrared-induced alignment change with wavelength tunable CO 2 laser irradiation for columnar liquid crystal domains was investigated for a liquid crystalline triphenylene derivative. A uniformly aligned alignment change of domains was observed when a chopped linearly polarized infrared laser light corresponding to the wavelength of the aromatic C-O-C stretching vibration band (9.65 μm) was irradiated. The results strongly imply that the infrared irradiation is a possible technique for device fabrication by use of columnar mesophase as a liquid crystalline semiconductor

CLIC main beam quadrupole active pre-alignment based on cam movers

CERN Document Server

Kemppinen, J; Leuxe, R; Mainaud Durand, H; Sandomierski, J; Sosin, M

2012-01-01

Compact Linear Collider (CLIC) is a study for a future 48 km long linear electron-positron collider in the multi TeV range. Its target luminosity can only be reached if the main beam quadrupoles (MB quads) are actively pre-aligned within 17 µm in sliding windows of 200 m with respect to a straight reference line. In addition to the positioning requirement, the pre-alignment system has to provide a rigid support for the nano-stabilization system to ensure that the first eigenfrequency is above 100 Hz. Re-adjustment based on cam movers was chosen for detailed studies to meet the stringent pre-alignment requirements. There are four different types of MB quads in CLIC. Their lengths and masses vary so that at least two types of cam movers have to be developed. The validation of the cams with less stringent space restrictions has proceeded to a test setup in 5 degrees of freedom (DOF). Prototypes of the more demanding, smaller cams have been manufactured and they are under tests in 1 DOF. This paper describes the...

Effect of the fluorinated groups on nematic liquid crystal alignment on monomer crosslinked film

International Nuclear Information System (INIS)

Yu Tao; Peng Zenghui; Ruan Shengping; Xuan Li

2004-01-01

It was found in this work that photosensitive monomers, bisphenol A dicinnamate ester and hexafluorobiphenol a dicinnamate ester were crosslinked under irradiation of linearly polarized ultraviolet light. The exposed films induced homogeneous and homeotropic alignment of liquid crystals (LC), respectively. We verified through experiments that it was fluorinated groups that caused the generation of LC homeotropic alignment on the crosslinked film. Photoreaction process was revealed by Fourier transform infrared spectra. There was no clear morphological anisotropy on these aligned films observed through atomic force microscope analysis. The surface energies were measured and homeotropic alignment reason was discussed in this work

Emittance control in linear colliders

International Nuclear Information System (INIS)

Ruth, R.D.

1991-01-01

Before completing a realistic design of a next-generation linear collider, the authors must first learn the lessons taught by the first generation, the SLC. Given that, they must make designs fault tolerant by including correction and compensation in the basic design. They must also try to eliminate these faults by improved alignment and stability of components. When these two efforts cross, they have a realistic design. The techniques of generation and control of emittance reviewed here provide a foundation for a design which can obtain the necessary luminosity in a next-generation linear collider

How genome complexity can explain the difficulty of aligning reads to genomes.

Science.gov (United States)

Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

2015-01-01

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

Cluster analysis of commercial samples of Bauhinia spp. using HPLC-UV/PDA and MCR-ALS/PCA without peak alignment procedure.

Science.gov (United States)

Ardila, Jorge Armando; Funari, Cristiano Soleo; Andrade, André Marques; Cavalheiro, Alberto José; Carneiro, Renato Lajarim

2015-01-01

Bauhinia forficata Link. is recognised by the Brazilian Health Ministry as a treatment of hypoglycemia and diabetes. Analytical methods are useful to assess the plant identity due the similarities found in plants from Bauhinia spp. HPLC-UV/PDA in combination with chemometric tools is an alternative widely used and suitable for authentication of plant material, however, the shifts of retention times for similar compounds in different samples is a problem. To perform comparisons between the authentic medicinal plant (Bauhinia forficata Link.) and samples commercially available in drugstores claiming to be "Bauhinia spp. to treat diabetes" and to evaluate the performance of multivariate curve resolution - alternating least squares (MCR-ALS) associated to principal component analysis (PCA) when compared to pure PCA. HPLC-UV/PDA data obtained from extracts of leaves were evaluated employing a combination of MCR-ALS and PCA, which allowed the use of the full chromatographic and spectrometric information without the need of peak alignment procedures. The use of MCR-ALS/PCA showed better results than the conventional PCA using only one wavelength. Only two of nine commercial samples presented characteristics similar to the authentic Bauhinia forficata spp., considering the full HPLC-UV/PDA data. The combination of MCR-ALS and PCA is very useful when applied to a group of samples where a general alignment procedure could not be applied due to the different chromatographic profiles. This work also demonstrates the need of more strict control from the health authorities regarding herbal products available on the market. Copyright © 2015 John Wiley & Sons, Ltd.

Classification of Surface and Deep Soil Samples Using Linear Discriminant Analysis

International Nuclear Information System (INIS)

Wasim, M.; Ali, M.; Daud, M.

2015-01-01

A statistical analysis was made of the activity concentrations measured in surface and deep soil samples for natural and anthropogenic gamma-emitting radionuclides. Soil samples were obtained from 48 different locations in Gilgit, Pakistan covering about 50 km/sup 2/ areas at an average altitude of 1550 m above sea level. From each location two samples were collected: one from the top soil (2-6 cm) and another from a depth of 6-10 cm. Four radionuclides including /sup 226/Ra, /sup 232/Th, /sup 40/K and /sup 137/Cs were quantified. The data was analyzed using t-test to find out activity concentration difference between the surface and depth samples. At the surface, the median activity concentrations were 23.7, 29.1, 4.6 and 115 Bq kg/sup -1/ for 226Ra, 232Th, 137Cs and 40K respectively. For the same radionuclides, the activity concentrations were respectively 25.5, 26.2, 2.9 and 191 Bq kg/sup -1/ for the depth samples. Principal component analysis (PCA) was applied to explore patterns within the data. A positive significant correlation was observed between the radionuclides /sup 226/Ra and /sup 232/Th. The data from PCA was further utilized in linear discriminant analysis (LDA) for the classification of surface and depth samples. LDA classified surface and depth samples with good predictability. (author)

A unified model for transfer alignment at random misalignment angles based on second-order EKF

International Nuclear Information System (INIS)

Cui, Xiao; Qin, Yongyuan; Yan, Gongmin; Liu, Zhenbo; Mei, Chunbo

2017-01-01

In the transfer alignment process of inertial navigation systems (INSs), the conventional linear error model based on the small misalignment angle assumption cannot be applied to large misalignment situations. Furthermore, the nonlinear model based on the large misalignment angle suffers from redundant computation with nonlinear filters. This paper presents a unified model for transfer alignment suitable for arbitrary misalignment angles. The alignment problem is transformed into an estimation of the relative attitude between the master INS (MINS) and the slave INS (SINS), by decomposing the attitude matrix of the latter. Based on the Rodriguez parameters, a unified alignment model in the inertial frame with the linear state-space equation and a second order nonlinear measurement equation are established, without making any assumptions about the misalignment angles. Furthermore, we employ the Taylor series expansions on the second-order nonlinear measurement equation to implement the second-order extended Kalman filter (EKF2). Monte-Carlo simulations demonstrate that the initial alignment can be fulfilled within 10 s, with higher accuracy and much smaller computational cost compared with the traditional unscented Kalman filter (UKF) at large misalignment angles. (paper)

A unified model for transfer alignment at random misalignment angles based on second-order EKF

Science.gov (United States)

Cui, Xiao; Mei, Chunbo; Qin, Yongyuan; Yan, Gongmin; Liu, Zhenbo

2017-04-01

In the transfer alignment process of inertial navigation systems (INSs), the conventional linear error model based on the small misalignment angle assumption cannot be applied to large misalignment situations. Furthermore, the nonlinear model based on the large misalignment angle suffers from redundant computation with nonlinear filters. This paper presents a unified model for transfer alignment suitable for arbitrary misalignment angles. The alignment problem is transformed into an estimation of the relative attitude between the master INS (MINS) and the slave INS (SINS), by decomposing the attitude matrix of the latter. Based on the Rodriguez parameters, a unified alignment model in the inertial frame with the linear state-space equation and a second order nonlinear measurement equation are established, without making any assumptions about the misalignment angles. Furthermore, we employ the Taylor series expansions on the second-order nonlinear measurement equation to implement the second-order extended Kalman filter (EKF2). Monte-Carlo simulations demonstrate that the initial alignment can be fulfilled within 10 s, with higher accuracy and much smaller computational cost compared with the traditional unscented Kalman filter (UKF) at large misalignment angles.

Miniaturized Stretchable and High-Rate Linear Supercapacitors

Science.gov (United States)

Zhu, Wenjun; Zhang, Yang; Zhou, Xiaoshuang; Xu, Jiang; Liu, Zunfeng; Yuan, Ningyi; Ding, Jianning

2017-07-01

Linear stretchable supercapacitors have attracted much attention because they are well suited to applications in the rapidly expanding field of wearable electronics. However, poor conductivity of the electrode material, which limits the transfer of electrons in the axial direction of the linear supercapacitors, leads to a serious loss of capacity at high rates. To solve this problem, we use gold nanoparticles to decorate aligned multiwall carbon nanotube to fabricate stretchable linear electrodes. Furthermore, we have developed fine stretchable linear supercapacitors, which exhibited an extremely high elasticity up to 400% strain with a high capacitance of about 8.7 F g-1 at the discharge current of 1 A g-1.

Nanofabricated racks of aligned and anchored DNA substrates for single-molecule imaging.

Science.gov (United States)

Gorman, Jason; Fazio, Teresa; Wang, Feng; Wind, Shalom; Greene, Eric C

2010-01-19

Single-molecule studies of biological macromolecules can benefit from new experimental platforms that facilitate experimental design and data acquisition. Here we develop new strategies to construct curtains of DNA in which the molecules are aligned with respect to one another and maintained in an extended configuration by anchoring both ends of the DNA to the surface of a microfluidic sample chamber that is otherwise coated with an inert lipid bilayer. This "double-tethered" DNA substrate configuration is established through the use of nanofabricated rack patterns comprised of two distinct functional elements: linear barriers to lipid diffusion that align DNA molecules anchored by one end to the bilayer and antibody-coated pentagons that provide immobile anchor points for the opposite ends of the DNA. These devices enable the alignment and anchoring of thousands of individual DNA molecules, which can then be visualized using total internal reflection fluorescence microscopy under conditions that do not require continuous application of buffer flow to stretch the DNA. This unique strategy offers the potential for studying protein-DNA interactions on large DNA substrates without compromising measurements through application of hydrodynamic force. We provide a proof-of-principle demonstration that double-tethered DNA curtains made with nanofabricated rack patterns can be used in a one-dimensional diffusion assay that monitors the motion of quantum dot-tagged proteins along DNA.

AlignMe—a membrane protein sequence alignment web server

Science.gov (United States)

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

Optical properties of orthodontic aligners?spectrophotometry analysis of three types before and after aging

OpenAIRE

Lombardo, Luca; Arreghini, Angela; Maccarrone, Roberta; Bianchi, Anna; Scalia, Santo; Siciliani, Giuseppe

2015-01-01

Background The aim was to assess and compare absorbance and transmittance values of three types of clear orthodontic aligners before and after two cycles of in vitro aging. Methods Nine samples of orthodontic aligners from three different manufacturers (Invisalign, Align Technology, Santa Clara, CA, USA; All-In, Micerium, Avegno, GE, Italy; F22 Aligner, Sweden & Martina, Due Carrare, PD, Italy) were selected, and each sample was subjected to spectrophotometry analysis of both its transmittanc...

Sampled-Data Consensus of Linear Multi-agent Systems With Packet Losses.

Science.gov (United States)

Zhang, Wenbing; Tang, Yang; Huang, Tingwen; Kurths, Jurgen

In this paper, the consensus problem is studied for a class of multi-agent systems with sampled data and packet losses, where random and deterministic packet losses are considered, respectively. For random packet losses, a Bernoulli-distributed white sequence is used to describe packet dropouts among agents in a stochastic way. For deterministic packet losses, a switched system with stable and unstable subsystems is employed to model packet dropouts in a deterministic way. The purpose of this paper is to derive consensus criteria, such that linear multi-agent systems with sampled-data and packet losses can reach consensus. By means of the Lyapunov function approach and the decomposition method, the design problem of a distributed controller is solved in terms of convex optimization. The interplay among the allowable bound of the sampling interval, the probability of random packet losses, and the rate of deterministic packet losses are explicitly derived to characterize consensus conditions. The obtained criteria are closely related to the maximum eigenvalue of the Laplacian matrix versus the second minimum eigenvalue of the Laplacian matrix, which reveals the intrinsic effect of communication topologies on consensus performance. Finally, simulations are given to show the effectiveness of the proposed results.In this paper, the consensus problem is studied for a class of multi-agent systems with sampled data and packet losses, where random and deterministic packet losses are considered, respectively. For random packet losses, a Bernoulli-distributed white sequence is used to describe packet dropouts among agents in a stochastic way. For deterministic packet losses, a switched system with stable and unstable subsystems is employed to model packet dropouts in a deterministic way. The purpose of this paper is to derive consensus criteria, such that linear multi-agent systems with sampled-data and packet losses can reach consensus. By means of the Lyapunov function

Coordinate measurement machines as an alignment tool

International Nuclear Information System (INIS)

Wand, B.T.

1991-03-01

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

Alignment of the MSGC barrel support structure

International Nuclear Information System (INIS)

Kari, Tammi; Miikka, Kotamaki; Tommi, Vanhala; Antti, Onnela

1999-01-01

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

Alignment of the MSGC barrel support structure

Energy Technology Data Exchange (ETDEWEB)

Kari, Tammi; Miikka, Kotamaki; Tommi, Vanhala [HIP, Helsinki Institute of Physics, CERN/EP, Geneva (Switzerland); Antti, Onnela [CERN, Conseil Europeen pour la recherche nucleaire, Laboratoire europeen pour la physique des particules, Geneve (Switzerland)

1999-07-01

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

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.

A proof of the Woodward-Lawson sampling method for a finite linear array

Science.gov (United States)

Somers, Gary A.

1993-01-01

An extension of the continuous aperture Woodward-Lawson sampling theorem has been developed for a finite linear array of equidistant identical elements with arbitrary excitations. It is shown that by sampling the array factor at a finite number of specified points in the far field, the exact array factor over all space can be efficiently reconstructed in closed form. The specified sample points lie in real space and hence are measurable provided that the interelement spacing is greater than approximately one half of a wavelength. This paper provides insight as to why the length parameter used in the sampling formulas for discrete arrays is larger than the physical span of the lattice points in contrast with the continuous aperture case where the length parameter is precisely the physical aperture length.

Snow and Water Imaging Spectrometer (SWIS): first alignment and characterization results

Science.gov (United States)

Bender, Holly A.; Mouroulis, Pantazis; Haag, Justin; Smith, Christopher D.; Van Gorp, Byron E.

2017-09-01

The Snow and Water Imaging Spectrometer (SWIS) is a fast, high-uniformity, low-polarization sensitivity imaging spectrometer and telescope system designed for integration on a 6U CubeSat platform. Operating in the 350-1700 nm spectral region with 5.7 nm sampling, SWIS is capable of simultaneously addressing the demanding needs of coastal ocean science and snow and ice monitoring. New key technologies that facilitate the development of this instrument include a linear variable anti-reflection (LVAR) detector coating for stray light management, and a single drive on-board calibration mechanism utilizing a transmissive diffuser for solar calibration. We provide an overview of the SWIS instrument design and potential science applications and describe the instrument assembly and alignment, supported by laboratory measurements.

Alignment of the ATLAS Inner Detector Tracking System

CERN Document Server

Lacuesta, V; The ATLAS collaboration

2010-01-01

ATLAS is a multipurpose experiment that records the LHC collisions. To reconstruct trajectories of charged particles produced in these collisions, ATLAS tracking system is equipped with silicon planar sensors and drift‐tube based detectors. They constitute the ATLAS Inner Detector. In order to achieve its scientific goals, the alignment of the ATLAS tracking system requires the determine accurately its almost 36000 degrees of freedom. Thus the demanded precision for the alignment of the silicon sensors is below 10 micrometers. This implies to use a large sample of high momentum and isolated charge particle tracks. The high level trigger selects those tracks online. Then the raw data with the hits information of the triggered tracks is stored in a calibration stream. Tracks from cosmic trigger during empty LHC bunches are also used as input for the alignment. The implementation of the track based alignment within the ATLAS software framework unifies different alignment approaches and allows the alignment of ...

Linearly polarized photons at ELSA

Energy Technology Data Exchange (ETDEWEB)

Eberhardt, Holger [Physikalisches Institut, Universitaet Bonn (Germany)

2009-07-01

To investigate the nucleon resonance regime in meson photoproduction, double polarization experiments are currently performed at the electron accelerator ELSA in Bonn. The experiments make use of a polarized target and circularly or linearly polarized photon beams. Linearly polarized photons are produced by coherent bremsstrahlung from an accurately aligned diamond crystal. The orientation of the crystal with respect to the electron beam is measured using the Stonehenge-Technique. Both, the energy of maximum polarization and the plane of polarization, can be deliberately chosen for the experiment. The linearly polarized beam provides the basis for the measurement of azimuthal beam asymmetries, such as {sigma} (unpolarized target) and G (polarized target). These observables are extracted in various single and multiple meson photoproduction channels.

Magnetically aligned H I fibers and the rolling hough transform

Energy Technology Data Exchange (ETDEWEB)

Clark, S. E.; Putman, M. E.; Peek, J. E. G. [Department of Astronomy, Columbia University, New York, NY (United States)

2014-07-01

We present observations of a new group of structures in the diffuse Galactic interstellar medium (ISM): slender, linear H I features we dub 'fibers' that extend for many degrees at high Galactic latitude. To characterize and measure the extent and strength of these fibers, we present the Rolling Hough Transform, a new machine vision method for parameterizing the coherent linearity of structures in the image plane. With this powerful new tool we show that the fibers are oriented along the interstellar magnetic field as probed by starlight polarization. We find that these low column density (N{sub H} {sub I}≃5×10{sup 18} cm{sup –2}) fiber features are most likely a component of the local cavity wall, about 100 pc away. The H I data we use to demonstrate this alignment at high latitude are from the Galactic Arecibo L-Band Feed Array H I (GALFA-H I) Survey and the Parkes Galactic All Sky Survey. We find better alignment in the higher resolution GALFA-H I data, where the fibers are more visually evident. This trend continues in our investigation of magnetically aligned linear features in the Riegel-Crutcher H I cold cloud, detected in the Southern Galactic Plane Survey. We propose an application of the RHT for estimating the field strength in such a cloud, based on the Chandrasekhar-Fermi method. We conclude that data-driven, quantitative studies of ISM morphology can be very powerful predictors of underlying physical quantities.

Chicane and wiggler based bunch compressors for future linear colliders

International Nuclear Information System (INIS)

Raubenheimer, T.O.; Emma, P.; Kheifets, S.

1993-05-01

In this paper, we discuss bunch compressors for future linear colliders. In the past, the bunch compression optics has been based upon achromatic cells using strong sextupoles to correct the dispersive and betatron chromaticity. To preserve the very small emittances required in most future collider designs, these schemes tend to have very tight alignment tolerances. Here, we describe bunch compressors based upon magnetic chicanes or wigglers which do need sextupoles to correct the chromatic emittance dilution. The dispersive chromaticity cancels naturally and the betatron chromaticity is not a significant source of emittance dilution. Thus, these schemes allow for substantially reduced alignment tolerances. Finally, we present a detailed design for the NLC linear collider

Alignment of large image series using cubic B-splines tessellation: application to transmission electron microscopy data.

Science.gov (United States)

Dauguet, Julien; Bock, Davi; Reid, R Clay; Warfield, Simon K

2007-01-01

3D reconstruction from serial 2D microscopy images depends on non-linear alignment of serial sections. For some structures, such as the neuronal circuitry of the brain, very large images at very high resolution are necessary to permit reconstruction. These very large images prevent the direct use of classical registration methods. We propose in this work a method to deal with the non-linear alignment of arbitrarily large 2D images using the finite support properties of cubic B-splines. After initial affine alignment, each large image is split into a grid of smaller overlapping sub-images, which are individually registered using cubic B-splines transformations. Inside the overlapping regions between neighboring sub-images, the coefficients of the knots controlling the B-splines deformations are blended, to create a virtual large grid of knots for the whole image. The sub-images are resampled individually, using the new coefficients, and assembled together into a final large aligned image. We evaluated the method on a series of large transmission electron microscopy images and our results indicate significant improvements compared to both manual and affine alignment.

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...

Application of vertex and mass constraints in track-based alignment

International Nuclear Information System (INIS)

Amoraal, J.; Blouw, J.; Blusk, S.; Borghi, S.; Cattaneo, M.; Chiapolini, N.; Conti, G.; Deissenroth, M.; Dupertuis, F.; Eijk, R. van der; Fave, V.; Gersabeck, M.; Hicheur, A.; Hulsbergen, W.; Hutchcroft, D.; Kozlinskiy, A.; Lambert, R.W.

2013-01-01

The software alignment of planar tracking detectors using samples of charged particle trajectories may lead to global detector distortions that affect vertex and momentum resolution. We present an alignment procedure that constrains such distortions by making use of samples of decay vertices reconstructed from two or more trajectories and putting constraints on their invariant mass. We illustrate the method by using a sample of invariant-mass constrained vertices from D 0 →K − π + decays to remove a curvature bias in the LHCb spectrometer

Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map.

Science.gov (United States)

Rudd, K E; Miller, W; Ostell, J; Benson, D A

1990-01-25

We use the extensive published information describing the genome of Escherichia coli and new restriction map alignment software to align DNA sequence, genetic, and physical maps. Restriction map alignment software is used which considers restriction maps as strings analogous to DNA or protein sequences except that two values, enzyme name and DNA base address, are associated with each position on the string. The resulting alignments reveal a nearly linear relationship between the physical and genetic maps of the E. coli chromosome. Physical map comparisons with the 1976, 1980, and 1983 genetic maps demonstrate a better fit with the more recent maps. The results of these alignments are genomic kilobase coordinates, orientation and rank of the alignment that best fits the genetic data. A statistical measure based on extreme value distribution is applied to the alignments. Additional computer analyses allow us to estimate the accuracy of the published E. coli genomic restriction map, simulate rearrangements of the bacterial chromosome, and search for repetitive DNA. The procedures we used are general enough to be applicable to other genome mapping projects.

Miniaturized Stretchable and High-Rate Linear Supercapacitors.

Science.gov (United States)

Zhu, Wenjun; Zhang, Yang; Zhou, Xiaoshuang; Xu, Jiang; Liu, Zunfeng; Yuan, Ningyi; Ding, Jianning

2017-12-01

Linear stretchable supercapacitors have attracted much attention because they are well suited to applications in the rapidly expanding field of wearable electronics. However, poor conductivity of the electrode material, which limits the transfer of electrons in the axial direction of the linear supercapacitors, leads to a serious loss of capacity at high rates. To solve this problem, we use gold nanoparticles to decorate aligned multiwall carbon nanotube to fabricate stretchable linear electrodes. Furthermore, we have developed fine stretchable linear supercapacitors, which exhibited an extremely high elasticity up to 400% strain with a high capacitance of about 8.7 F g -1 at the discharge current of 1 A g -1 .

Impulsive Laser Induced Alignment of Molecules Dissolved in Helium Nanodroplets

DEFF Research Database (Denmark)

Pentlehner, Dominik; H. Nielsen, Jens; Slenczka, Alkwin

2013-01-01

We show that a 450 fs nonresonant, moderately intense, linearly polarized laser pulse can induce field-free molecular axis alignment of methyliodide (CH3I) molecules dissolved in a helium nanodroplet. Time-resolved measurements reveal rotational dynamics much slower than that of isolated molecules...

A Kalman Filter for SINS Self-Alignment Based on Vector Observation.

Science.gov (United States)

Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Tong, Jinwu

2017-01-29

In this paper, a self-alignment method for strapdown inertial navigation systems based on the q -method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate.

INTRINSIC ALIGNMENT OF CLUSTER GALAXIES: THE REDSHIFT EVOLUTION

International Nuclear Information System (INIS)

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

2011-01-01

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

A Python Script for Aligning the STIS Echelle Blaze Function

Science.gov (United States)

Baer, Malinda; Proffitt, Charles R.; Lockwood, Sean A.

2018-01-01

Accurate flux calibration for the STIS echelle modes is heavily dependent on the proper alignment of the blaze function for each spectral order. However, due to changes in the instrument alignment over time and between exposures, the blaze function can shift in wavelength. This may result in flux calibration inconsistencies of up to 10%. We present the stisblazefix Python module as a tool for STIS users to correct their echelle spectra. The stisblazefix module assumes that the error in the blaze alignment is a linear function of spectral order, and finds the set of shifts that minimizes the flux inconsistencies in the overlap between spectral orders. We discuss the uses and limitations of this tool, and show that its use can provide significant improvements to the default pipeline flux calibration for many observations.

Two media method for linear attenuation coefficient determination of irregular soil samples; Metodo dos dois meios para a determinacao do coeficiente de atenuacao linear de amostras irregulares de solos

Energy Technology Data Exchange (ETDEWEB)

Vici, Carlos Henrique Georges

2004-07-01

In several situations of nuclear applications, the knowledge of gamma-ray linear attenuation coefficient for irregular samples is necessary, such as in soil physics and geology. This work presents the validation of a methodology for the determination of the linear attenuation coefficient ({mu}) of irregular shape samples, in such a way that it is not necessary to know the thickness of the considered sample. With this methodology irregular soil samples (undeformed field samples) from Londrina region, north of Parana were studied. It was employed the two media method for the {mu} determination. It consists of the {mu} determination through the measurement of a gamma-ray beam attenuation by the sample sequentially immersed in two different media, with known and appropriately chosen attenuation coefficients. For comparison, the theoretical value of {mu} was calculated by the product of the mass attenuation coefficient, obtained by the WinXcom code, and the measured value of the density sample. This software employs the chemical composition of the samples and supplies a table of the mass attenuation coefficients versus the photon energy. To verify the validity of the two media method, compared with the simple gamma ray transmission method, regular pome stone samples were used. With these results for the attenuation coefficients and their respective deviations, it was possible to compare the two methods. In this way we concluded that the two media method is a good tool for the determination of the linear attenuation coefficient of irregular materials, particularly in the study of soils samples. (author)

Efficient and robust model-to-image alignment using 3D scale-invariant features.

Science.gov (United States)

Toews, Matthew; Wells, William M

2013-04-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. Copyright © 2012 Elsevier B.V. All rights reserved.

Differential pulse adsorptive stripping voltammetric determination of nanomolar levels of atorvastatin calcium in pharmaceutical and biological samples using a vertically aligned carbon nanotube/graphene oxide electrode.

Science.gov (United States)

Silva, Tiago Almeida; Zanin, Hudson; Vicentini, Fernando Campanhã; Corat, Evaldo José; Fatibello-Filho, Orlando

2014-06-07

A novel vertically aligned carbon nanotube/graphene oxide (VACNT-GO) electrode is proposed, and its ability to determine atorvastatin calcium (ATOR) in pharmaceutical and biological samples by differential pulse adsorptive stripping voltammetry (DPAdSV) is evaluated. VACNT films were prepared on a Ti substrate by a microwave plasma chemical vapour deposition method and then treated with oxygen plasma to produce the VACNT-GO electrode. The oxygen plasma treatment exfoliates the carbon nanotube tips exposing graphene foils and inserting oxygen functional groups, these effects improved the VACNT wettability (super-hydrophobic) which is crucial for its electrochemical application. The electrochemical behaviour of ATOR on the VACNT-GO electrode was studied by cyclic voltammetry, which showed that it underwent an irreversible oxidation process at a potential of +1.08 V in pHcond 2.0 (0.2 mol L(-1) buffer phosphate solution). By applying DPAdSV under optimized experimental conditions the analytical curve was found to be linear in the ATOR concentration range of 90 to 3.81 × 10(3) nmol L(-1) with a limit of detection of 9.4 nmol L(-1). The proposed DPAdSV method was successfully applied in the determination of ATOR in pharmaceutical and biological samples, and the results were in close agreement with those obtained by a comparative spectrophotometric method at a confidence level of 95%.

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.

Optimal image alignment with random projections of manifolds: algorithm and geometric analysis.

Science.gov (United States)

Kokiopoulou, Effrosyni; Kressner, Daniel; Frossard, Pascal

2011-06-01

This paper addresses the problem of image alignment based on random measurements. Image alignment consists of estimating the relative transformation between a query image and a reference image. We consider the specific problem where the query image is provided in compressed form in terms of linear measurements captured by a vision sensor. We cast the alignment problem as a manifold distance minimization problem in the linear subspace defined by the measurements. The transformation manifold that represents synthesis of shift, rotation, and isotropic scaling of the reference image can be given in closed form when the reference pattern is sparsely represented over a parametric dictionary. We show that the objective function can then be decomposed as the difference of two convex functions (DC) in the particular case where the dictionary is built on Gaussian functions. Thus, the optimization problem becomes a DC program, which in turn can be solved globally by a cutting plane method. The quality of the solution is typically affected by the number of random measurements and the condition number of the manifold that describes the transformations of the reference image. We show that the curvature, which is closely related to the condition number, remains bounded in our image alignment problem, which means that the relative transformation between two images can be determined optimally in a reduced subspace.

Simple methods of aligning four-circle diffractometers with crystal reflections

Energy Technology Data Exchange (ETDEWEB)

Mitsui, Y [Tokyo Univ. (Japan). Faculty of Pharmaceutical Sciences

1979-08-01

Simple methods of aligning four-circle diffractometers with crystal reflections are devised. They provide the methods to check (1) perpendicularity of chi plane to the incident beam, (2) zero point of 2theta and linearity of focus-chi center-receiving aperture and (3) zero point of chi.

The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

International Nuclear Information System (INIS)

Livingston, Ken

2009-01-01

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

The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

Energy Technology Data Exchange (ETDEWEB)

Livingston, Ken [Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom)], E-mail: k.livingston@physics.gla.ac.uk

2009-05-21

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

The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

Science.gov (United States)

Livingston, Ken

2009-05-01

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

Efficient alignment-free DNA barcode analytics.

Science.gov (United States)

Kuksa, Pavel; Pavlovic, Vladimir

2009-11-10

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

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, ...

Optical properties of orthodontic aligners--spectrophotometry analysis of three types before and after aging.

Science.gov (United States)

Lombardo, Luca; Arreghini, Angela; Maccarrone, Roberta; Bianchi, Anna; Scalia, Santo; Siciliani, Giuseppe

2015-01-01

The aim was to assess and compare absorbance and transmittance values of three types of clear orthodontic aligners before and after two cycles of in vitro aging. Nine samples of orthodontic aligners from three different manufacturers (Invisalign, Align Technology, Santa Clara, CA, USA; All-In, Micerium, Avegno, GE, Italy; F22 Aligner, Sweden & Martina, Due Carrare, PD, Italy) were selected, and each sample was subjected to spectrophotometry analysis of both its transmittance and absorbance a total of 27 times. Samples were subsequently aged in vitro at a constant temperature in artificial saliva supplemented with food colouring for two cycles of 14 days each. The spectrophotometry protocol was then repeated, and the resulting data were analysed and compared by means of ANOVA (p < 0.05). All types of aligners tested yielded lower transmittance and higher absorbance values after aging, but the difference was not significant in any case. That being said, the F22 aligners were found to be most transparent, both before and after aging, followed by Invisalign and All-In, and these differences were statistically significant. Commercial aligners possess significantly different optical, and therefore aesthetic, properties, both as delivered and following aging.

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

International Nuclear Information System (INIS)

Huang, Hung-Jin; Mandelbaum, Rachel; Freeman, Peter E.; Chen, Yen-Chi

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 the surrounding large-scale structures. In this work, we aim to identify the galaxy and cluster quantities that most strongly predict the central galaxy alignment phenomenon among a large parameter space with a sample of 8237 clusters and 94 817 members within 0.1 < z < 0.35, based on the red-sequence Matched-filter Probabilistic Percolation cluster catalogue constructed from the Sloan Digital Sky Survey. 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 physical size, higher luminosity and centring probability, and redder colour. Satellites with redder colour, higher luminosity, located closer to the central galaxy, and with smaller ellipticity show a stronger angular segregation towards their central galaxy major axes. Lastly, we provide physical explanations for some of the identified correlations, and discuss the connection to theories of central galaxy alignments, the impact of primordial alignments with tidal fields, and the importance of anisotropic accretion.

Transmission electron microscope sample holder with optical features

Science.gov (United States)

Milas, Mirko [Port Jefferson, NY; Zhu, Yimei [Stony Brook, NY; Rameau, Jonathan David [Coram, NY

2012-03-27

A sample holder for holding a sample to be observed for research purposes, particularly in a transmission electron microscope (TEM), generally includes an external alignment part for directing a light beam in a predetermined beam direction, a sample holder body in optical communication with the external alignment part and a sample support member disposed at a distal end of the sample holder body opposite the external alignment part for holding a sample to be analyzed. The sample holder body defines an internal conduit for the light beam and the sample support member includes a light beam positioner for directing the light beam between the sample holder body and the sample held by the sample support member.

PACMAN Project: A New Solution for the High-accuracy Alignment of Accelerator Components

CERN Document Server

Mainaud Durand, Helene; Buzio, Marco; Caiazza, Domenico; Catalán Lasheras, Nuria; Cherif, Ahmed; Doytchinov, Iordan; Fuchs, Jean-Frederic; Gaddi, Andrea; Galindo Munoz, Natalia; Gayde, Jean-Christophe; Kamugasa, Solomon; Modena, Michele; Novotny, Peter; Russenschuck, Stephan; Sanz, Claude; Severino, Giordana; Tshilumba, David; Vlachakis, Vasileios; Wendt, Manfred; Zorzetti, Silvia

2016-01-01

The beam alignment requirements for the next generation of lepton colliders have become increasingly challenging. As an example, the alignment requirements for the three major collider components of the CLIC linear collider are as follows. Before the first beam circulates, the Beam Position Monitors (BPM), Accelerating Structures (AS)and quadrupoles will have to be aligned up to 10 μm w.r.t. a straight line over 200 m long segments, along the 20 km of linacs. PACMAN is a study on Particle Accelerator Components' Metrology and Alignment to the Nanometre scale. It is an Innovative Doctoral Program, funded by the EU and hosted by CERN, providing high quality training to 10 Early Stage Researchers working towards a PhD thesis. The technical aim of the project is to improve the alignment accuracy of the CLIC components by developing new methods and tools addressing several steps of alignment simultaneously, to gain time and accuracy. The tools and methods developed will be validated on a test bench. This paper pr...

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.

Beam-based alignment at the KEK-ATF damping ring

International Nuclear Information System (INIS)

Woodley, Mark D.; Nelson, Janice; Ross, Marc; Turner, James; Wolski, A.; Kubo, Kiyoshi

2004-01-01

The damping rings of a future linear collider will have demanding alignment and stability requirements in order to achieve the low vertical emittance necessary for high luminosity. The Accelerator Test Facility (ATF) at KEK has successfully demonstrated the vertical emittance below 5 pm that is specified for the GLC/NLC Main Damping Rings. One contribution to this accomplishment has been the use of Beam Based Alignment (BBA) techniques. The mode of operation of the ATF presents particular challenges for BBA, and we describe here how we have deduced the offsets of the BPMs with respect to the quadrupoles. We also discuss a technique that allows for direct measurements of the beam-to-quad offsets

High anisotropy of flow-aligned bicellar membrane systems

KAUST Repository

Kogan, Maxim

2013-10-01

In recent years, multi-lipid bicellar systems have emerged as promising membrane models. The fast orientational diffusion and magnetic alignability made these systems very attractive for NMR investigations. However, their alignment was so far achieved with a strong magnetic field, which limited their use with other methods that require macroscopic orientation. Recently, it was shown that bicelles could be aligned also by shear flow in a Couette flow cell, making it applicable to structural and biophysical studies by polarized light spectroscopy. Considering the sensitivity of this lipid system to small variations in composition and physicochemical parameters, efficient use of such a flow-cell method with coupled techniques will critically depend on the detailed understanding of how the lipid systems behave under flow conditions. In the present study we have characterized the flow alignment behavior of the commonly used dimyristoyl phosphatidylcholine/dicaproyl phosphatidylcholine (DMPC/DHPC) bicelle system, for various temperatures, lipid compositions, and lipid concentrations. We conclude that at optimal flow conditions the selected bicellar systems can produce the most efficient flow alignment out of any lipid systems used so far. The highest degree of orientation of DMPC/DHPC samples is noticed in a narrow temperature interval, at a practical temperature around 25 C, most likely in the phase transition region characterized by maximum sample viscosity. The change of macroscopic orientation factor as function of the above conditions is now described in detail. The increase in macroscopic alignment observed for bicelles will most likely allow recording of higher resolution spectra on membrane systems, which provide deeper structural insight and analysis into properties of biomolecules interacting with solution phase lipid membranes. © 2013 Elsevier Ireland Ltd.

Confocal Microscope Alignment of Nanocrystals for Coherent Diffraction Imaging

International Nuclear Information System (INIS)

Beitra, Loren; Watari, Moyu; Matsuura, Takashi; Shimamoto, Naonobu; Harder, Ross; Robinson, Ian

2010-01-01

We have installed and tested an Olympus LEXT confocal microscope at the 34-ID-C beamline of the Advanced Photon Source (APS). The beamline is for Coherent X-ray Diffraction (CXD) experiments in which a nanometre-sized crystal is aligned inside a focussed X-ray beam. The microscope was required for three-dimensional (3D) sample alignment to get around sphere-of-confusion issues when locating Bragg peaks in reciprocal space. In this way, and by use of strategic sample preparations, we have succeeded in measuring six Bragg peaks from a single 200 nm gold crystal and obtained six projections of its internal displacement field. This enables the clear identification of stacking-fault bands within the crystal. The confocal alignment method will allow a full determination of the strain tensor provided three or more Bragg reflections from the same crystal are found.

Scintillation counter: photomultiplier tube alignment

International Nuclear Information System (INIS)

Olson, R.E.

1975-01-01

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

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...

ALIGNMENTS OF GROUP GALAXIES WITH NEIGHBORING GROUPS

International Nuclear Information System (INIS)

Wang Yougang; Chen Xuelei; Park, Changbom; Yang Xiaohu; Choi, Yun-Young

2009-01-01

Using a sample of galaxy groups found in the Sloan Digital Sky Survey Data Release 4, we measure the following four types of alignment signals: (1) the alignment between the distributions of the satellites of each group relative to the direction of the nearest neighbor group (NNG); (2) the alignment between the major axis direction of the central galaxy of the host group (HG) and the direction of the NNG; (3) the alignment between the major axes of the central galaxies of the HG and the NNG; and (4) the alignment between the major axes of the satellites of the HG and the direction of the NNG. We find strong signal of alignment between the satellite distribution and the orientation of central galaxy relative to the direction of the NNG, even when the NNG is located beyond 3r vir of the host group. The major axis of the central galaxy of the HG is aligned with the direction of the NNG. The alignment signals are more prominent for groups that are more massive and with early-type central galaxies. We also find that there is a preference for the two major axes of the central galaxies of the HG and NNG to be parallel for the system with both early central galaxies, however, not for the systems with both late-type central galaxies. For the orientation of satellite galaxies, we do not find any significant alignment signals relative to the direction of the NNG. From these four types of alignment measurements, we conclude that the large-scale environment traced by the nearby group affects primarily the shape of the host dark matter halo, and hence also affects the distribution of satellite galaxies and the orientation of central galaxies. In addition, the NNG directly affects the distribution of the satellite galaxies by inducing asymmetric alignment signals, and the NNG at very small separation may also contribute a second-order impact on the orientation of the central galaxy in the HG.

Measurements of linear attenuation coefficients of irregular shaped samples by two media method

International Nuclear Information System (INIS)

Singh, Sukhpal; Kumar, Ashok; Thind, Kulwant Singh; Mudahar, Gurmel S.

2008-01-01

The linear attenuation coefficient values of regular and irregular shaped flyash materials have been measured without knowing the thickness of a sample using a new technique namely 'two media method'. These values have also been measured with a standard gamma ray transmission method and obtained theoretically with winXCOM computer code. From the comparison it is reported that the two media method has given accurate results of attenuation coefficients of flyash materials

Alignment between galaxies and large-scale structure

International Nuclear Information System (INIS)

Faltenbacher, A.; Li Cheng; White, Simon D. M.; Jing, Yi-Peng; Mao Shude; Wang Jie

2009-01-01

Based on the Sloan Digital Sky Survey DR6 (SDSS) and the Millennium Simulation (MS), we investigate the alignment between galaxies and large-scale structure. For this purpose, we develop two new statistical tools, namely the alignment correlation function and the cos(2θ)-statistic. The former is a two-dimensional extension of the traditional two-point correlation function and the latter is related to the ellipticity correlation function used for cosmic shear measurements. Both are based on the cross correlation between a sample of galaxies with orientations and a reference sample which represents the large-scale structure. We apply the new statistics to the SDSS galaxy catalog. The alignment correlation function reveals an overabundance of reference galaxies along the major axes of red, luminous (L ∼ * ) galaxies out to projected separations of 60 h- 1 Mpc. The signal increases with central galaxy luminosity. No alignment signal is detected for blue galaxies. The cos(2θ)-statistic yields very similar results. Starting from a MS semi-analytic galaxy catalog, we assign an orientation to each red, luminous and central galaxy, based on that of the central region of the host halo (with size similar to that of the stellar galaxy). As an alternative, we use the orientation of the host halo itself. We find a mean projected misalignment between a halo and its central region of ∼ 25 deg. The misalignment decreases slightly with increasing luminosity of the central galaxy. Using the orientations and luminosities of the semi-analytic galaxies, we repeat our alignment analysis on mock surveys of the MS. Agreement with the SDSS results is good if the central orientations are used. Predictions using the halo orientations as proxies for central galaxy orientations overestimate the observed alignment by more than a factor of 2. Finally, the large volume of the MS allows us to generate a two-dimensional map of the alignment correlation function, which shows the reference

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.

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.

Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields

Energy Technology Data Exchange (ETDEWEB)

Armas-Pérez, Julio C.; Londono-Hurtado, Alejandro [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Guzmán, Orlando [Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, DF 09340, México (Mexico); Hernández-Ortiz, Juan P. [Departamento de Materiales y Minerales, Universidad Nacional de Colombia, Sede Medellín, Medellín (Colombia); Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Pablo, Juan J. de, E-mail: depablo@uchicago.edu [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637 (United States); Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

2015-07-28

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.

Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields.

Energy Technology Data Exchange (ETDEWEB)

Armas-Perez, Julio C.; Londono-Hurtado, Alejandro; Guzman, Orlando; Hernandez-Ortiz, Juan P.; de Pablo, Juan J.

2015-07-27

A theoretically informed coarse-grained Monte Carlo method is proposed for studying liquid crystals. The free energy functional of the system is described in the framework of the Landau-de Gennes formalism. The alignment field and its gradients are approximated by finite differences, and the free energy is minimized through a stochastic sampling technique. The validity of the proposed method is established by comparing the results of the proposed approach to those of traditional free energy minimization techniques. Its usefulness is illustrated in the context of three systems, namely, a nematic liquid crystal confined in a slit channel, a nematic liquid crystal droplet, and a chiral liquid crystal in the bulk. It is found that for systems that exhibit multiple metastable morphologies, the proposed Monte Carlo method is generally able to identify lower free energy states that are often missed by traditional approaches. Importantly, the Monte Carlo method identifies such states from random initial configurations, thereby obviating the need for educated initial guesses that can be difficult to formulate.

Observation of enhanced field-free molecular alignment by two laser pulses

DEFF Research Database (Denmark)

Bisgaard, Christer; Poulsen, Mikael Dahlerup; Peronne, Emmanuel

2004-01-01

We show experimentally that field-free alignment of iodobenzene molecules, induced by a single, intense, linearly polarized 1.4-ps-long laser pulse, can be strongly enhanced by dividing the pulse into two optimally synchronized pulses of the same duration. For a given total energy of the two...

Landmark matching based retinal image alignment by enforcing sparsity in correspondence matrix.

Science.gov (United States)

Zheng, Yuanjie; Daniel, Ebenezer; Hunter, Allan A; Xiao, Rui; Gao, Jianbin; Li, Hongsheng; Maguire, Maureen G; Brainard, David H; Gee, James C

2014-08-01

Retinal image alignment is fundamental to many applications in diagnosis of eye diseases. In this paper, we address the problem of landmark matching based retinal image alignment. We propose a novel landmark matching formulation by enforcing sparsity in the correspondence matrix and offer its solutions based on linear programming. The proposed formulation not only enables a joint estimation of the landmark correspondences and a predefined transformation model but also combines the benefits of the softassign strategy (Chui and Rangarajan, 2003) and the combinatorial optimization of linear programming. We also introduced a set of reinforced self-similarities descriptors which can better characterize local photometric and geometric properties of the retinal image. Theoretical analysis and experimental results with both fundus color images and angiogram images show the superior performances of our algorithms to several state-of-the-art techniques. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

Progress in ETA-II magnetic field alignment using stretched wire and low energy electron beam techniques

International Nuclear Information System (INIS)

Griffith, L.V.; Deadrick, F.J.

1991-01-01

Flux line alignment of the solenoidal focus magnets used on the ETA-II linear induction accelerator is a key element leading to a reduction of beam corkscrew motion. Two techniques have been used on the ETA-II accelerator to measure and establish magnet alignment. A low energy electron beam has been used to directly map magnetic field lines, and recent work has utilized a pulsed stretched wire technique to measure magnet tilts and offsets with respect to a reference axis. This paper reports on the techniques used in the ETA-II accelerator alignment, and presents results from those measurements which show that accelerator is magnetically aligned to within ∼ ± 200 microns

Stanford Linear Collider magnet positioning

International Nuclear Information System (INIS)

Wand, B.T.

1991-08-01

For the installation of the Stanford Linear Collider (SLC) the positioning and alignment of the beam line components was performed in several individual steps. In the following the general procedures for each step are outlined. The calculation of ideal coordinates for the magnets in the entire SLC will be discussed in detail. Special emphasis was given to the mathematical algorithms and geometry used in the programs to calculate these ideal positions. 35 refs., 21 figs

Segmented rail linear induction motor

Science.gov (United States)

Cowan, Jr., Maynard; Marder, Barry M.

1996-01-01

A segmented rail linear induction motor has a segmented rail consisting of a plurality of nonferrous electrically conductive segments aligned along a guideway. The motor further includes a carriage including at least one pair of opposed coils fastened to the carriage for moving the carriage. A power source applies an electric current to the coils to induce currents in the conductive surfaces to repel the coils from adjacent edges of the conductive surfaces.

Alignment verification in stereotactic radiosurgery with use of graphic arts film

International Nuclear Information System (INIS)

Sweet, J.; Lamba, M.

1990-01-01

This paper evaluates the use of graphic arts film for field alignment verification of linear accelerator-based stereotactic radiosurgery. The characteristic curve was generated for Fuji RO-100 graphic arts film in a standard leaded radiation therapy cassette at 6 MV. The linear portion of the curve and the film contrast are presented and their clinical advantages discussed. The high contrast of this graphic arts film improves visualization of the 5-mm ball bearing (simulated target) in small, circular treatment fields. Comparison with standard port film demonstrates the large linear range of the graphic arts film, which proved useful in visualization of the simulated target within the small, circular treatment field

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 ...

Development of a High Precision Edge Alignment System for Touch-Panel Glass Substrates

Directory of Open Access Journals (Sweden)

Hau-Wei Lee

2014-06-01

Full Text Available There are two kinds of alignment systems, marked and unmarked. The glass substrate for touch panels is categorized as an unmarked work piece. Vision based glass substrate alignment (GSA relies on the edge of the glass. Traditional GSA systems compensate first for angular and then for linear error. This reduces alignment accuracy and increases alignment time and edge detection usually takes longer than 10 ms. This study proposes an effortless edge detection method. This method is very simple and can significantly reduce the time taken to detect the edge to about 6 ms using a 1.3 megapixel image. In this study, a floating center idea is used to control the glass substrate on a high precision coplanar XXY alignment stage. According to the method, users can set the rotation center anywhere as long as it is on the working (xy plane. Tolerance prognosis is also considered in this study to help the operator decide if the substrate is usable or should be rejected. The experimental results show alignment repeatability of the x, y, and θ axes to be 1 μm, 1 μm, and 5 arcsec, respectively.

A new formulation of the linear sampling method: spatial resolution and post-processing

International Nuclear Information System (INIS)

Piana, M; Aramini, R; Brignone, M; Coyle, J

2008-01-01

A new formulation of the linear sampling method is described, which requires the regularized solution of a single functional equation set in a direct sum of L 2 spaces. This new approach presents the following notable advantages: it is computationally more effective than the traditional implementation, since time consuming samplings of the Tikhonov minimum problem and of the generalized discrepancy equation are avoided; it allows a quantitative estimate of the spatial resolution achievable by the method; it facilitates a post-processing procedure for the optimal selection of the scatterer profile by means of edge detection techniques. The formulation is described in a two-dimensional framework and in the case of obstacle scattering, although generalizations to three dimensions and penetrable inhomogeneities are straightforward

Near-optimal alternative generation using modified hit-and-run sampling for non-linear, non-convex problems

Science.gov (United States)

Rosenberg, D. E.; Alafifi, A.

2016-12-01

Water resources systems analysis often focuses on finding optimal solutions. Yet an optimal solution is optimal only for the modelled issues and managers often seek near-optimal alternatives that address un-modelled objectives, preferences, limits, uncertainties, and other issues. Early on, Modelling to Generate Alternatives (MGA) formalized near-optimal as the region comprising the original problem constraints plus a new constraint that allowed performance within a specified tolerance of the optimal objective function value. MGA identified a few maximally-different alternatives from the near-optimal region. Subsequent work applied Markov Chain Monte Carlo (MCMC) sampling to generate a larger number of alternatives that span the near-optimal region of linear problems or select portions for non-linear problems. We extend the MCMC Hit-And-Run method to generate alternatives that span the full extent of the near-optimal region for non-linear, non-convex problems. First, start at a feasible hit point within the near-optimal region, then run a random distance in a random direction to a new hit point. Next, repeat until generating the desired number of alternatives. The key step at each iterate is to run a random distance along the line in the specified direction to a new hit point. If linear equity constraints exist, we construct an orthogonal basis and use a null space transformation to confine hits and runs to a lower-dimensional space. Linear inequity constraints define the convex bounds on the line that runs through the current hit point in the specified direction. We then use slice sampling to identify a new hit point along the line within bounds defined by the non-linear inequity constraints. This technique is computationally efficient compared to prior near-optimal alternative generation techniques such MGA, MCMC Metropolis-Hastings, evolutionary, or firefly algorithms because search at each iteration is confined to the hit line, the algorithm can move in one

Alighment and Vibration Issues in TeV Linear Collider Design

Energy Technology Data Exchange (ETDEWEB)

Fischer, G.E.; /SLAC

2005-08-12

The next generation of linear colliders will require alignment accuracies and stabilities of component placement at least one, perhaps two, orders of magnitude better than can be achieved by the conventional methods and procedures in practice today. The magnitudes of these component-placement tolerances for current designs of various linear collider subsystems are tabulated. In the micron range, long-term ground motion is sufficiently rapid that on-line reference and mechanical correction systems are called for. Some recent experiences with the upgraded SLAC laser alignment systems and examples of some conceivable solutions for the future are described. The so called ''girder'' problem is discussed in the light of ambient and vibratory disturbances. The importance of the quality of the underlying geology is stressed. The necessity and limitations of particle-beam-derived placement information are mentioned.

Jackknife Variance Estimator for Two Sample Linear Rank Statistics

Science.gov (United States)

1988-11-01

Accesion For - - ,NTIS GPA&I "TIC TAB Unann c, nc .. [d Keywords: strong consistency; linear rank test’ influence function . i , at L By S- )Distribut...reverse if necessary and identify by block number) FIELD IGROUP SUB-GROUP Strong consistency; linear rank test; influence function . 19. ABSTRACT

Biological sample collector

Science.gov (United States)

Murphy, Gloria A [French Camp, CA

2010-09-07

A biological sample collector is adapted to a collect several biological samples in a plurality of filter wells. A biological sample collector may comprise a manifold plate for mounting a filter plate thereon, the filter plate having a plurality of filter wells therein; a hollow slider for engaging and positioning a tube that slides therethrough; and a slide case within which the hollow slider travels to allow the tube to be aligned with a selected filter well of the plurality of filter wells, wherein when the tube is aligned with the selected filter well, the tube is pushed through the hollow slider and into the selected filter well to sealingly engage the selected filter well and to allow the tube to deposit a biological sample onto a filter in the bottom of the selected filter well. The biological sample collector may be portable.

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 ...

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...

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

Directory of Open Access Journals (Sweden)

Kierzynka Michal

2011-05-01

Full Text Available Abstract Background Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. Results In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable. Conclusions The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.

Optical alignment control of polyimide molecules containing azobenzene in the backbone structure

International Nuclear Information System (INIS)

Sakamoto, Kenji; Usami, Kiyoaki; Sasaki, Toru; Kanayama, Takashi; Ushioda, Sukekatsu

2004-01-01

Using polarized infrared absorption spectroscopy, we have determined the orientation of the polyimide backbone structure in photo-alignment films for liquid crystals (LC). The polyimide used in this study contains azobenzene in the backbone structure. Photo-alignment treatment was performed on the corresponding polyamic acid film, using a light source of wavelength 340-500 nm. The polyamic acid film (∼16 nm thick) was first irradiated at normal incidence with linearly polarized light (LP-light) of 156 J/cm 2 , and then oblique angle irradiation of unpolarized light (UP-light) was performed in the plane of incidence perpendicular to the polarization direction of the LP-light. The UP-light exposure was varied up to 882 J/cm 2 . We found that the average inclination angle of the polyimide backbone structure, measured from the surface plane, increases almost linearly with UP-light exposure. On the other hand, the in-plane anisotropy induced by the first irradiation with LP-light decreases with the increase of UP-light exposure

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

Science.gov (United States)

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

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Linear Response of Field-Aligned Currents to the Interplanetary Electric Field

DEFF Research Database (Denmark)

Weimer, D. R.; R. Edwards, T.; Olsen, Nils

2017-01-01

Many studies that have shown that the ionospheric, polar cap electric potentials (PCEP) exhibit a “saturation” behavior in response to the level of the driving by the solar wind. As the magnitude of the interplanetary magnetic field (IMF) and electric field (IEF) increase, the PCEP response...... of the field-aligned currents (FAC) with the solar wind/magnetosphere/ionosphere system has a role. As the FAC are more difficult to measure, their behavior in response to the level of the IEF has not been investigated as thoroughly. In order to resolve the question of whether or not the FAC also exhibit...... saturation, we have processed the magnetic field measurements from the Ørsted, CHAMP, and Swarm missions, spanning more than a decade. As the amount of current in each region needs to be known, a new technique is used to separate and sum the current by region, widely known as R0, R1, and R2. These totals...

A Radial Measurement of the Galaxy Tidal Alignment Magnitude with BOSS Data

Science.gov (United States)

Martens, Daniel; Hirata, Christopher M.; Ross, Ashley J.; Fang, Xiao

2018-05-01

The anisotropy of galaxy clustering in redshift space has long been used to probe the rate of growth of cosmological perturbations. However, if galaxies are aligned by large-scale tidal fields, then a sample with an orientation-dependent selection effect has an additional anisotropy imprinted onto its correlation function. We use the LOWZ and CMASS catalogs of SDSS-III BOSS Data Release 12 to divide galaxies into two sub-samples based on their offset from the Fundamental Plane, which should be correlated with orientation. These sub-samples must trace the same underlying cosmology, but have opposite orientation-dependent selection effects. We measure the clustering parameters of each sub-sample and compare them in order to calculate the dimensionless parameter B, a measure of how strongly galaxies are aligned by gravitational tidal fields. We found that for CMASS (LOWZ), the measured B was -0.024 ± 0.015 (-0.030 ± 0.016). This result can be compared to the theoretical predictions of Hirata (2009), who argued that since galaxy formation physics does not depend on the direction of the "observer," the same intrinsic alignment parameters that describe galaxy-ellipticity correlations should also describe intrinsic alignments in the radial direction. We find that the ratio of observed to theoretical values is 0.51 ± 0.32 (0.77 ± 0.41) for CMASS (LOWZ). We combine the results to obtain a total Obs/Theory = 0.61 ± 0.26. This measurement constitutes evidence (between 2 and 3σ) for radial intrinsic alignments, and is consistent with theoretical expectations (<2σ difference).

Final focus systems for linear colliders

International Nuclear Information System (INIS)

Helm, R.; Irwin, J.

1992-08-01

Final focus systems for linear colliders present many exacting challenges in beam optics, component design, and beam quality. Efforts to resolve these problems as they relate to a new generation of linear colliders are under way at several laboratories around the world. We will outline criteria for final focus systems and discuss the current state of understanding and resolution of the outstanding problems. We will discuss tolerances on alignment, field quality and stability for optical elements, and the implications for beam parameters such as emittance, energy spread, bunch length, and stability in position and energy. Beam-based correction procedures, which in principle can alleviate many of the tolerances, will be described. Preliminary results from the Final Focus Test Beam (FFTB) under construction at SLAC will be given. Finally, we mention conclusions from operating experience at the Stanford Linear Collider (SLC)

Final focus systems for linear colliders

International Nuclear Information System (INIS)

Helm, R.; Irwing, J.

1992-01-01

Final focus systems for linear colliders present many exacting challenges in beam optics, component design, and beam quality. Efforts to resolve these problems as they relate to a new generation of linear colliders are under way at several laboratories around the world. We outline criteria for final focus systems and discuss the current state of understanding and resolution of the outstanding problems. We discuss tolerances on alignment, field quality and stability for optical elements, and the implications for beam parameters such as emittance, energy spread , bunch length, and stability in position and energy. Beam-based correction procedures, which in principle can alleviate many of the tolerances, are described. Preliminary results from the Final Focus Test Beam (FFTB) under construction at SLAC are given. Finally, we mention conclusions from operating experience at the Stanford Linear Collider (SLC). (Author) 16 refs., 4 tabs., 6 figs

Status and experiece with the alignment of Linac4

CERN Document Server

Fuchs, Jean-Frederic

2016-01-01

LINAC4 (L4) is an H- linear accelerator that will deliver, for the High Luminosity LHC (HL-LHC) project requirements, a beam of protons at 160 MeV energy to the PS complex and then to the LHC. Its connection to the PS booster will take place during the Long Shutdown 2 (LS2) in 2019-2020 or earlier if any major failure of the LINAC2. The Linac4 project requires the precise alignment with a tolerance of about +/- 0.2 mm in both the horizontal and vertical planes, of elements along approximately 150 m beam line. This paper will give a status, an overview of the challenges of the alignment, the issues solved by the survey section, the techniques and methodology used to realise the survey activities over the last five years.

Apical root resorption during orthodontic treatment with aligners? A retrospective radiometric study

OpenAIRE

Krieger, Elena; Drechsler, Thomas; Schmidtmann, Irene; Jacobs, Collin; Haag, Simeon; Wehrbein, Heinrich

2013-01-01

Introduction Objective of this study was to investigate the incidence and severity of apical root resorptions (ARR) during orthodontic treatment with aligners. Materials and methods The sample comprised 100 patients (17?75 years of age) with a class I occlusion and anterior crowding before treatment, treated exclusively with aligners (Invisalign?, Align Technologies, Santa Clara, CA, USA). The following teeth were assessed: upper and lower anterior teeth and first molars. Root and crown lengt...

Transient reflectivity on vertically aligned single-wall carbon nanotubes

NARCIS (Netherlands)

Galimberti, Gianluca; Ponzoni, Stefano; Ferrini, Gabriele; Hofmann, Stephan; Arshad, Muhammad; Cepek, Cinzia; Pagliara, Stefania

2013-01-01

One-color transient reflectivity measurements are carried out on two different samples of vertically aligned single-wall carbon nanotube bundles and compared with the response recently published on unaligned bundles. The negative sign of the optical response for both samples indicates that the free

Nanoparticle amount, and not size, determines chain alignment and nonlinear hardening in polymer nanocomposites

Science.gov (United States)

Varol, H. Samet; Meng, Fanlong; Hosseinkhani, Babak; Malm, Christian; Bonn, Daniel; Bonn, Mischa; Zaccone, Alessio

2017-01-01

Polymer nanocomposites—materials in which a polymer matrix is blended with nanoparticles (or fillers)—strengthen under sufficiently large strains. Such strain hardening is critical to their function, especially for materials that bear large cyclic loads such as car tires or bearing sealants. Although the reinforcement (i.e., the increase in the linear elasticity) by the addition of filler particles is phenomenologically understood, considerably less is known about strain hardening (the nonlinear elasticity). Here, we elucidate the molecular origin of strain hardening using uniaxial tensile loading, microspectroscopy of polymer chain alignment, and theory. The strain-hardening behavior and chain alignment are found to depend on the volume fraction, but not on the size of nanofillers. This contrasts with reinforcement, which depends on both volume fraction and size of nanofillers, potentially allowing linear and nonlinear elasticity of nanocomposites to be tuned independently. PMID:28377517

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...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

YAHA: fast and flexible long-read alignment with optimal breakpoint detection.

Science.gov (United States)

Faust, Gregory G; Hall, Ira M

2012-10-01

With improved short-read assembly algorithms and the recent development of long-read sequencers, split mapping will soon be the preferred method for structural variant (SV) detection. Yet, current alignment tools are not well suited for this. We present YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints. YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from http://faculty.virginia.edu/irahall/YAHA. imh4y@virginia.edu.

Emittance control in linear colliders

International Nuclear Information System (INIS)

Ruth, R.D.

1991-05-01

In this paper, we discuss the generation and control of the emittance in a next-generation linear collider. The beams are extracted from a damping ring and compressed in length by the first bunch compressor. They are then accelerated in a preaccelerator linac up to an energy appropriate for injection into a high gradient linac. In many designs this pre-acceleration is followed by another bunch compression to reach a short bunch. After acceleration in the linac, the bunches are finally focused transversely to a small spot. The proposed vertical beam sizes at the interaction point are the order of a few nanometers while the horizontal sizes are about a factor of 100 larger. This cross-sectional area is about a factor of 10 4 smaller than the SLC. However, the main question is: what are the tolerances to achieve such a small size, and how do they compare to present techniques for alignment and stability? These tolerances are very design dependent. Alignment tolerances in the linac can vary from 1 μm to 100 μm depending upon the basic approach. In this paper we discuss techniques of emittance generation and control which move alignment tolerances to the 100 μm range

Fiber optics frequency comb enabled linear optical sampling with operation wavelength range extension.

Science.gov (United States)

Liao, Ruolin; Wu, Zhichao; Fu, Songnian; Zhu, Shengnan; Yu, Zhe; Tang, Ming; Liu, Deming

2018-02-01

Although the linear optical sampling (LOS) technique is powerful enough to characterize various advanced modulation formats with high symbol rates, the central wavelength of a pulsed local oscillator (LO) needs to be carefully set according to that of the signal under test, due to the coherent mixing operation. Here, we experimentally demonstrate wideband LOS enabled by a fiber optics frequency comb (FOFC). Meanwhile, when the broadband FOFC acts as the pulsed LO, we propose a scheme to mitigate the enhanced sampling error arising in the non-ideal response of a balanced photodetector. Finally, precise characterizations of arbitrary 128 Gbps PDM-QPSK wavelength channels from 1550 to 1570 nm are successfully achieved, when a 101.3 MHz frequency spaced comb with a 3 dB spectral power ripple of 20 nm is used.

Characteristics of Philips SL-20 linear accelerator used for stereotactic radiosurgery/radiotherapy

International Nuclear Information System (INIS)

D'Souza, Harold; Ganesh, T.; Joshi, R.C.; Julka, P.K.; Rath, G.K.; Chander, Subhash; Pant, G.S.

2002-01-01

Commissioning of a stereotactic radiosurgery/stereotactic radiotherapy (SRS/SRT) facility on a modified linear accelerator requires validation of mechanical parameters and establishment of parameters, such as tissue maximum ratio (TMR), relative output factors (OF), and off axis ratios (OAR). The mechanical and beam characteristics of Philips SL-20 linear accelerator modified for SRS/SRT were evaluated and presented. The SRS/SRT procedure carried on Philips SL-20 linear accelerator with Brown-Robert-Wells (BRW) and relocatable Gill-Thomas-Cosman (GTC) head frames along with the Radionics planning system was evaluated. The tertiary collimator consists of the actual treatment cones and their sizes vary from 12.5 mm to 40 mm diameter. The alignment of the auxillary collimator axis with mechanical axes and stability of the isocenter of Philips SL-20 machine was evaluated using Iso-Align device and mechanical isocenter standard (MIS). All the mechanical errors of the linear accelerator were within 1 mm, except the stability of the isocenter while rotating the couch. Alignment of auxiliary collimator axis with the central axis, gantry and couch axes were achieved. The TMR, OF and OAR for 6 MV x-rays from Philips SL-20 linear accelerator for different cone sizes were deduced using a Multidata water phantom with 0.015 cc ion chamber. The difference between 50% width of profiles in two major axes (x and y) were within ± 0.4 mm. The cone dimensions were accurate up to 0.7 mm. The penumbra width for different cones varies from 3.1 mm to 3.5 mm. Dose linearity of the monitoring system was ≤ 1% above 5 MU. The mechanical and beam characteristics including dose linearity of the SL-20 machine are presented. The beam characteristics of this machine are comparable with the other modified linear accelerators for SRS/SRT. The shift of isocenter during rotation of couch can be nullified by fine adjusting laser target localizing frame to the laser position using micrometer screws

Study and application of micrometric alignment on the prototype girders of the CLIC Two-Beam Module

CERN Document Server

Gazis, Nikolaos; Mainaud-Durand, Hélène; Samochkine, Alexandre; Anastasopoulos, Michail

2011-01-01

The Compact LInear Collider (CLIC), currently under study at CERN, aims at the development of a Multi-TeV e+ e- collider. The micro-precision CLIC RF-structures will have an accelerating gradient of 100 MV/m and will be mounted and aligned on specially developed supporting girders. The girder fabrication constraints are dictated by stringent physics requirements. The micrometric pre-alignment over several kilometers of girders, allow for the CLIC structures to fulfill their acceleration and collision functionality. Study of such girders and their sophisticated alignment method, is a challenging case involving dedicated mechanical design as well as prototype production and experimental testing.

Advantages of axially aligned crystals used in positron production at future linear colliders

Directory of Open Access Journals (Sweden)

X. Artru

2003-09-01

Full Text Available The characteristics of the electron-photon showers initiated by 2 to 10 GeV electrons aligned along the ⟨111⟩ axis of tungsten crystals are compared with those for the amorphous tungsten. In this energy range, as known, the positron yield at the optimal target thicknesses is larger in a crystal case only by several percent. However, the amount of the energy deposition in a crystal turns out to be considerably (by 20%–50% lower than in an amorphous target providing the same positron yield, while the peak energy-deposition density is approximately of the same magnitude in both cases.

Multispectral linear array (MLA) focal plane mechanical and thermal design

Science.gov (United States)

Mitchell, A. S.; Kaminski, E. F.

1982-01-01

The mechanical and thermal design of an integrated focal plane subsystem of a Multispectral Linear Array (MLA) instrument is discussed in terms of focal-plane alignment, thermoelastic performance, and thermal requirements. The modular construction and thermal control of the focal plane array are discussed.

Magnetohydrodynamic Ekman layers with field-aligned flow

Energy Technology Data Exchange (ETDEWEB)

Nunez, Manuel, E-mail: mnjmhd@am.uva.es [Departamento de Analisis Matematico, Universidad de Valladolid, 47005 Valladolid (Spain)

2011-05-01

The Ekman layer in a conducting fluid with constant angular velocity, provided with a magnetic field aligned with the flow, is studied here. The existence of solutions to the magnetohydrodynamic linearized equations depends on the balance between viscosity and resistivity, on the one hand, and the angular and Alfven velocities, on the other. In most cases, exponentially decreasing solutions exist, although their longitudinal oscillations do not need to be periodic. One of the instances without a solution is explained by the presence of Alfven waves traveling backwards along the streamlines.

Comparison of LHC collimator beam-based alignment to BPM-Interpolated centers

CERN Document Server

Valentino, G; Assmann, R W; Bruce, R; Muller, G J; Redaelli, S; Rossi, A; Lari, L

2012-01-01

The beam centers at the Large Hadron Collider collimators are determined by beam-based alignment, where both jaws of a collimator are moved in separately until a loss spike is detected on a Beam LossMonitor downstream. Orbit drifts of more than a few hundred micrometers cannot be tolerated, as they would compromise the performance of the collimation system. Beam Position Monitors (BPMs) are installed at various locations around the LHC ring, and a linear interpolation of the orbit can be obtained at the collimator positions. In this paper, the results obtained from beam-based alignment are compared with the orbit interpolated from the BPM data throughout the 2011 and 2012 LHC proton runs.

The effects of alignments: examining group faultlines, organizational cultures, and performance.

Science.gov (United States)

Bezrukova, Katerina; Thatcher, Sherry M B; Jehn, Karen A; Spell, Chester S

2012-01-01

By integrating literature on group faultlines, organizational cultures, and value congruence, this research presents a framework that explains how cultural alignment across organizational levels may influence the relationship between faultlines and performance. The hypotheses were tested using representatively sampled multisource qualitative and quantitative data on 138 teams from a Fortune 500 company. The present findings demonstrate that although informational faultlines were detrimental for group performance, the negative relationship between faultlines and performance was reversed when cultures with a strong emphasis on results were aligned, was lessened when cultures with a weak emphasis on results were aligned, and remained negative when cultures were misaligned with respect to their results orientation. These findings show the importance of recognizing alignments not only within groups (group faultlines) but also outside groups (cultural alignments between the group and departments) when considering their implications for group performance.

Alignments of galaxies within cosmic filaments from SDSS DR7

Energy Technology Data Exchange (ETDEWEB)

Zhang, Youcai; Yang, Xiaohu [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Nandan Road 80, Shanghai 200030 (China); Wang, Huiyuan [Key Laboratory for Research in Galaxies and Cosmology, University of Science and Technology of China, Hefei, Anhui 230026 (China); Wang, Lei [Purple Mountain Observatory, the Partner Group of MPI für Astronomie, 2 West Beijing Road, Nanjing 210008 (China); Mo, H. J. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003-9305 (United States); Van den Bosch, Frank C., E-mail: yczhang@shao.ac.cn, E-mail: xyang@sjtu.edu.cn [Department of Astronomy, Yale University, P.O. Box 208101, New Haven, CT 06520-8101 (United States)

2013-12-20

Using a sample of galaxy groups selected from the Sloan Digital Sky Survey Data Release 7, we examine the alignment between the orientation of galaxies and their surrounding large-scale structure in the context of the cosmic web. The latter is quantified using the large-scale tidal field, reconstructed from the data using galaxy groups above a certain mass threshold. We find that the major axes of galaxies in filaments tend to be preferentially aligned with the directions of the filaments, while galaxies in sheets have their major axes preferentially aligned parallel to the plane of the sheets. The strength of this alignment signal is strongest for red, central galaxies, and in good agreement with that of dark matter halos in N-body simulations. This suggests that red, central galaxies are well aligned with their host halos, in quantitative agreement with previous studies based on the spatial distribution of satellite galaxies. There is a luminosity and mass dependence that brighter and more massive galaxies in filaments and sheets have stronger alignment signals. We also find that the orientation of galaxies is aligned with the eigenvector associated with the smallest eigenvalue of the tidal tensor. These observational results indicate that galaxy formation is affected by large-scale environments and strongly suggest that galaxies are aligned with each other over scales comparable to those of sheets and filaments in the cosmic web.

Alignments of galaxies within cosmic filaments from SDSS DR7

International Nuclear Information System (INIS)

Zhang, Youcai; Yang, Xiaohu; Wang, Huiyuan; Wang, Lei; Mo, H. J.; Van den Bosch, Frank C.

2013-01-01

Using a sample of galaxy groups selected from the Sloan Digital Sky Survey Data Release 7, we examine the alignment between the orientation of galaxies and their surrounding large-scale structure in the context of the cosmic web. The latter is quantified using the large-scale tidal field, reconstructed from the data using galaxy groups above a certain mass threshold. We find that the major axes of galaxies in filaments tend to be preferentially aligned with the directions of the filaments, while galaxies in sheets have their major axes preferentially aligned parallel to the plane of the sheets. The strength of this alignment signal is strongest for red, central galaxies, and in good agreement with that of dark matter halos in N-body simulations. This suggests that red, central galaxies are well aligned with their host halos, in quantitative agreement with previous studies based on the spatial distribution of satellite galaxies. There is a luminosity and mass dependence that brighter and more massive galaxies in filaments and sheets have stronger alignment signals. We also find that the orientation of galaxies is aligned with the eigenvector associated with the smallest eigenvalue of the tidal tensor. These observational results indicate that galaxy formation is affected by large-scale environments and strongly suggest that galaxies are aligned with each other over scales comparable to those of sheets and filaments in the cosmic web.

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...

2 GHz self-aligning tandem A/D converter for SAR

DEFF Research Database (Denmark)

Søbjærg, Sten Schmidl; Christensen, Erik Lintz

2001-01-01

digitizing, and the other is to digitize the signal before digital I/Q demodulation. In both cases the digitizing may be performed by a digital front end (DFE) with two parallel analog-to-digital-converters (ADCs) sampling at 1 GHz in phase or in anti-phase respectively, provided the analog bandwidth...... of the ADC is sufficient. In the first case each ADC has to digitize a 0-400 MHz signal, and in the second case both ADCs have to digitize a 100-900 MHz signal. In both cases the sampling time alignment is a critical parameter. The paper addresses some aspects of ADC alignment in the implementation of a DFE...

Introduction to generalized linear models

CERN Document Server

Dobson, Annette J

2008-01-01

Introduction Background Scope Notation Distributions Related to the Normal Distribution Quadratic Forms Estimation Model Fitting Introduction Examples Some Principles of Statistical Modeling Notation and Coding for Explanatory Variables Exponential Family and Generalized Linear Models Introduction Exponential Family of Distributions Properties of Distributions in the Exponential Family Generalized Linear Models Examples Estimation Introduction Example: Failure Times for Pressure Vessels Maximum Likelihood Estimation Poisson Regression Example Inference Introduction Sampling Distribution for Score Statistics Taylor Series Approximations Sampling Distribution for MLEs Log-Likelihood Ratio Statistic Sampling Distribution for the Deviance Hypothesis Testing Normal Linear Models Introduction Basic Results Multiple Linear Regression Analysis of Variance Analysis of Covariance General Linear Models Binary Variables and Logistic Regression Probability Distributions ...

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

Science.gov (United States)

Nielsen, Morten; Lundegaard, Claus; Lund, Ole

2007-07-04

Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making 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. 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 between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR), we demonstrate a consistent gain in predictive performance 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 amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. The SMM-align method was shown to outperform other

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

Directory of Open Access Journals (Sweden)

Lund Ole

2007-07-01

Full Text Available Abstract Background Antigen presenting cells (APCs sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making 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 between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR, we demonstrate a consistent gain in predictive performance 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 amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. Conclusion

Gyrokinetic linearized Landau collision operator

DEFF Research Database (Denmark)

Madsen, Jens

2013-01-01

, which is important in multiple ion-species plasmas. Second, the equilibrium operator describes drag and diffusion of the magnetic field aligned component of the vorticity associated with the E×B drift. Therefore, a correct description of collisional effects in turbulent plasmas requires the equilibrium......The full gyrokinetic electrostatic linearized Landau collision operator is calculated including the equilibrium operator, which represents the effect of collisions between gyrokinetic Maxwellian particles. First, the equilibrium operator describes energy exchange between different plasma species...... operator, even for like-particle collisions....

MaxAlign: maximizing usable data in an alignment

DEFF Research Database (Denmark)

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

2007-01-01

Align. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. CONCLUSION: We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also...

Three dimensional force prediction in a model linear brushless dc motor

Energy Technology Data Exchange (ETDEWEB)

Moghani, J.S.; Eastham, J.F.; Akmese, R.; Hill-Cottingham, R.J. (Univ. of Bath (United Kingdom). School of Electronic and Electric Engineering)

1994-11-01

Practical results are presented for the three axes forces produced on the primary of a linear brushless dc machine which is supplied from a three-phase delta-modulated inverter. Conditions of both lateral alignment and lateral displacement are considered. Finite element analysis using both two and three dimensional modeling is compared with the practical results. It is shown that a modified two dimensional model is adequate, where it can be used, in the aligned position and that the full three dimensional method gives good results when the machine is axially misaligned.

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.

Influence of filler alignment in the mechanical and electrical properties of carbon nanotubes/epoxy nanocomposites

Energy Technology Data Exchange (ETDEWEB)

Felisberto, M. [LPyMC, FCEyN-UBA and IFIBA-CONICET, Pab I Ciudad Universitaria, Buenos Aires 1428 (Argentina); INQUIMAE-CONICET-UBA, Pab II Ciudad Universitaria, Buenos Aires 1428 (Argentina); Arias-Duran, A. [LPyMC, FCEyN-UBA and IFIBA-CONICET, Pab I Ciudad Universitaria, Buenos Aires 1428 (Argentina); Ramos, J.A.; Mondragon, I. [Dep. Ingenieria Quimica y M. Ambiente. Esc. Politecnica. UPV/EHU, Pza. Europa 1, Donostia-San Sebastian 20018 (Spain); Candal, R. [INQUIMAE-CONICET-UBA, Pab II Ciudad Universitaria, Buenos Aires 1428 (Argentina); Escuela de Ciencia y Tecnologia-UNSAM, San Martin, Prov. De Buenos Aires (Argentina); Goyanes, S. [LPyMC, FCEyN-UBA and IFIBA-CONICET, Pab I Ciudad Universitaria, Buenos Aires 1428 (Argentina); Rubiolo, G.H., E-mail: rubiolo@cnea.gov.ar [LPyMC, FCEyN-UBA and IFIBA-CONICET, Pab I Ciudad Universitaria, Buenos Aires 1428 (Argentina); Dep. Materiales, Comision Nacional de Energia Atomica (CNEA-CAC), Avda Gral Paz 1499, B1650KNA San Martin (Argentina)

2012-08-15

In this work, we report the mechanical and electrical properties of carbon nanotubes/epoxy composites prepared with aligned and randomly oriented nanotubes as filler. The samples are disks of 30 mm in diameter and 3 mm in thickness. To obtain the carbon nanotubes alignment, an external electric field (250 VAC; 50 Hz) was applied through the thickness of the sample during all the cure process. The AC electrical current was measured, during the cure, as a strategy to determine the optimum time in which the alignment reaches the maximum value. DC conductivity measured after the cure shows a percolation threshold in the filler content one order of magnitude smaller for composites with aligned nanotubes than for composites with randomly oriented filler (from 0.06 to 0.5 wt%). In the percolation threshold, the achieved conductivity was 1.4 Multiplication-Sign 10{sup -5} Sm{sup -1}. In both cases, aligned and randomly distributed carbon nanotube composites, the wear resistance increases with the addition of the filler while the Rockwell hardness decreases independently of the nanotubes alignment.

Evaluation of Multiple Linear Regression-Based Limited Sampling Strategies for Enteric-Coated Mycophenolate Sodium in Adult Kidney Transplant Recipients.

Science.gov (United States)

Brooks, Emily K; Tett, Susan E; Isbel, Nicole M; McWhinney, Brett; Staatz, Christine E

2018-04-01

Although multiple linear regression-based limited sampling strategies (LSSs) have been published for enteric-coated mycophenolate sodium, none have been evaluated for the prediction of subsequent mycophenolic acid (MPA) exposure. This study aimed to examine the predictive performance of the published LSS for the estimation of future MPA area under the concentration-time curve from 0 to 12 hours (AUC0-12) in renal transplant recipients. Total MPA plasma concentrations were measured in 20 adult renal transplant patients on 2 occasions a week apart. All subjects received concomitant tacrolimus and were approximately 1 month after transplant. Samples were taken at 0, 0.33, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 6, and 8 hours and 0, 0.25, 0.5, 0.75, 1, 1.25, 1.5, 2, 3, 4, 6, 9, and 12 hours after dose on the first and second sampling occasion, respectively. Predicted MPA AUC0-12 was calculated using 19 published LSSs and data from the first or second sampling occasion for each patient and compared with the second occasion full MPA AUC0-12 calculated using the linear trapezoidal rule. Bias (median percentage prediction error) and imprecision (median absolute prediction error) were determined. Median percentage prediction error and median absolute prediction error for the prediction of full MPA AUC0-12 were multiple linear regression-based LSS was not possible without concentrations up to at least 8 hours after the dose.

Precisely Assembled Nanofiber Arrays as a Platform to Engineer Aligned Cell Sheets for Biofabrication

Directory of Open Access Journals (Sweden)

Vince Beachley

2014-08-01

Full Text Available A hybrid cell sheet engineering approach was developed using ultra-thin nanofiber arrays to host the formation of composite nanofiber/cell sheets. It was found that confluent aligned cell sheets could grow on uniaxially-aligned and crisscrossed nanofiber arrays with extremely low fiber densities. The porosity of the nanofiber sheets was sufficient to allow aligned linear myotube formation from differentiated myoblasts on both sides of the nanofiber sheets, in spite of single-side cell seeding. The nanofiber content of the composite cell sheets is minimized to reduce the hindrance to cell migration, cell-cell contacts, mass transport, as well as the foreign body response or inflammatory response associated with the biomaterial. Even at extremely low densities, the nanofiber component significantly enhanced the stability and mechanical properties of the composite cell sheets. In addition, the aligned nanofiber arrays imparted excellent handling properties to the composite cell sheets, which allowed easy processing into more complex, thick 3D structures of higher hierarchy. Aligned nanofiber array-based composite cell sheet engineering combines several advantages of material-free cell sheet engineering and polymer scaffold-based cell sheet engineering; and it represents a new direction in aligned cell sheet engineering for a multitude of tissue engineering applications.

Using Set Covering with Item Sampling to Analyze the Infeasibility of Linear Programming Test Assembly Models

Science.gov (United States)

Huitzing, Hiddo A.

2004-01-01

This article shows how set covering with item sampling (SCIS) methods can be used in the analysis and preanalysis of linear programming models for test assembly (LPTA). LPTA models can construct tests, fulfilling a set of constraints set by the test assembler. Sometimes, no solution to the LPTA model exists. The model is then said to be…

Protein alignment using cellulose nanocrystals: practical considerations and range of application

International Nuclear Information System (INIS)

Denisov, Alexey Y.; Kloser, Elisabeth; Gray, Derek G.; Mittermaier, Anthony K.

2010-01-01

Cellulose nanocrystals (CNCs) form liquid crystals in aqueous solution that confer alignment to macromolecules and permit the measurement of residual dipolar couplings. CNCs possess many attractive features as an alignment medium. They are inexpensive, non-toxic, chemically inert, and robust to denaturants and temperature. Despite these advantages, CNCs are seldom employed as an alignment medium and the range of their applicability has not yet been explored. We have re-examined the use of CNCs in biomolecular NMR by analyzing the effects concentration, ionic strength, and temperature on molecular alignment. Stable alignment was obtained over wide ranges of temperature (10-70 o C) and pH (2.5-8.0), which makes CNCs potentially very useful in studies of thermophilic proteins and acid-stabilized molecules. Notably, we find that CNC suspensions are very sensitive to the concentrations of biological buffers, which must be taken into account when they are used in NMR analyses. These results have led us to develop a general procedure for preparing aligned samples with CNCs. Using the SH3 domain from the Fyn tyrosine kinase as a model system, we find that CNCs produce an alignment frame collinear with that of the commonly used Pf1 bacteriophage alignment medium, but of opposite magnitude.

Magnetic Alignment of Block Copolymer Microdomains by Intrinsic Chain Anisotropy.

Science.gov (United States)

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

2015-12-18

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

Control rod housing alignment

International Nuclear Information System (INIS)

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

1990-01-01

This patent describes a process for measuring the vertical alignment between a hole in a core plate and the top of a corresponding control rod drive housing within a boiling water reactor. It comprises: providing an alignment apparatus. The alignment apparatus including a lower end for fitting to the top of the control rod drive housing; an upper end for fitting to the aperture in the core plate, and a leveling means attached to the alignment apparatus to read out the difference in angularity with respect to gravity, and alignment pin registering means for registering to the alignment pin on the core plate; lowering the alignment device on a depending support through a lattice position in the top guide through the hole in the core plate down into registered contact with the top of the control rod drive housing; registering the upper end to the sides of the hole in the core plate; registering the alignment pin registering means to an alignment pin on the core plate to impart to the alignment device the required angularity; and reading out the angle of the control rod drive housing with respect to the hole in the core plate through the leveling devices whereby the angularity of the top of the control rod drive housing with respect to the hole in the core plate can be determined

Improving the performance of the actinic inspection tool with an optimized alignment procedure

International Nuclear Information System (INIS)

Mochi, I.; Goldberg, K.A.; Naulleau, P.; Huh, Sungmin

2009-01-01

Extreme ultraviolet (EUV) microscopy is an important tool for the investigation of the performance of EUV masks, for detecting the presence and the characteristics of defects, and for evaluating the effectiveness of defect repair techniques. Aerial image measurement bypasses the difficulties inherent to photoresist imaging and enables high data collection speed and flexibility. It provides reliable and quick feedback for the development of masks and lithography system modeling methods. We operate the SEMATECH Berkeley Actinic Inspection Tool (AIT), a EUV microscope installed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The AIT is equipped with several high-magnification Fresnel zoneplate lenses, with various numerical aperture values, that enable it image the reflective mask surface with various resolution and magnification settings. Although the AIT has undergone significant recent improvements in terms of imaging resolution and illumination uniformity, there is still room for improvement. In the AIT, an off-axis zoneplate lens collects the light coming from the sample and an image of the sample is projected onto an EUV-sensitive CCD camera. The simplicity of the optical system is particularly helpful considering that the AIT alignment has to be performed every time that a sample or a zoneplate is replaced. The alignment is sensitive to several parameters such as the lens position and orientation, the illumination direction and the sample characteristics. Since the AIT works in high vacuum, there is no direct access to the optics or to the sample during the alignment and the measurements. For all these reasons the alignment procedures and feedback can be complex, and in some cases can reduce the overall data throughput of the system. In this paper we review the main strategies and procedures that have been developed for quick and reliable alignments, and we describe the performance improvements we have achieved, in terms of aberration

Improving the performance of the actinic inspection tool with an optimized alignment procedure

Energy Technology Data Exchange (ETDEWEB)

Mochi, I.; Goldberg, K.A.; Naulleau, P.; Huh, Sungmin

2009-03-04

Extreme ultraviolet (EUV) microscopy is an important tool for the investigation of the performance of EUV masks, for detecting the presence and the characteristics of defects, and for evaluating the effectiveness of defect repair techniques. Aerial image measurement bypasses the difficulties inherent to photoresist imaging and enables high data collection speed and flexibility. It provides reliable and quick feedback for the development of masks and lithography system modeling methods. We operate the SEMATECH Berkeley Actinic Inspection Tool (AIT), a EUV microscope installed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The AIT is equipped with several high-magnification Fresnel zoneplate lenses, with various numerical aperture values, that enable it image the reflective mask surface with various resolution and magnification settings. Although the AIT has undergone significant recent improvements in terms of imaging resolution and illumination uniformity, there is still room for improvement. In the AIT, an off-axis zoneplate lens collects the light coming from the sample and an image of the sample is projected onto an EUV-sensitive CCD camera. The simplicity of the optical system is particularly helpful considering that the AIT alignment has to be performed every time that a sample or a zoneplate is replaced. The alignment is sensitive to several parameters such as the lens position and orientation, the illumination direction and the sample characteristics. Since the AIT works in high vacuum, there is no direct access to the optics or to the sample during the alignment and the measurements. For all these reasons the alignment procedures and feedback can be complex, and in some cases can reduce the overall data throughput of the system. In this paper we review the main strategies and procedures that have been developed for quick and reliable alignments, and we describe the performance improvements we have achieved, in terms of aberration

Self-adapting denoising, alignment and reconstruction in electron tomography in materials science

Energy Technology Data Exchange (ETDEWEB)

Printemps, Tony, E-mail: tony.printemps@cea.fr [Université Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France); Mula, Guido [Dipartimento di Fisica, Università di Cagliari, Cittadella Universitaria, S.P. 8km 0.700, 09042 Monserrato (Italy); Sette, Daniele; Bleuet, Pierre; Delaye, Vincent; Bernier, Nicolas; Grenier, Adeline; Audoit, Guillaume; Gambacorti, Narciso; Hervé, Lionel [Université Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France)

2016-01-15

An automatic procedure for electron tomography is presented. This procedure is adapted for specimens that can be fashioned into a needle-shaped sample and has been evaluated on inorganic samples. It consists of self-adapting denoising, automatic and accurate alignment including detection and correction of tilt axis, and 3D reconstruction. We propose the exploitation of a large amount of information of an electron tomography acquisition to achieve robust and automatic mixed Poisson–Gaussian noise parameter estimation and denoising using undecimated wavelet transforms. The alignment is made by mixing three techniques, namely (i) cross-correlations between neighboring projections, (ii) common line algorithm to get a precise shift correction in the direction of the tilt axis and (iii) intermediate reconstructions to precisely determine the tilt axis and shift correction in the direction perpendicular to that axis. Mixing alignment techniques turns out to be very efficient and fast. Significant improvements are highlighted in both simulations and real data reconstructions of porous silicon in high angle annular dark field mode and agglomerated silver nanoparticles in incoherent bright field mode. 3D reconstructions obtained with minimal user-intervention present fewer artefacts and less noise, which permits easier and more reliable segmentation and quantitative analysis. After careful sample preparation and data acquisition, the denoising procedure, alignment and reconstruction can be achieved within an hour for a 3D volume of about a hundred million voxels, which is a step toward a more routine use of electron tomography. - Highlights: • Goal: perform a reliable and user-independent 3D electron tomography reconstruction. • Proposed method: self-adapting denoising and alignment prior to 3D reconstruction. • Noise estimation and denoising are performed using wavelet transform. • Tilt axis determination is done automatically as well as projection alignment. �

Simulation of beamline alignment operations

International Nuclear Information System (INIS)

Annese, C; Miller, M G.

1999-01-01

The CORBA-based Simulator was a Laboratory Directed Research and Development (LDRD) project that applied simulation techniques to explore critical questions about distributed control systems. The simulator project used a three-prong approach that studied object-oriented distribution tools, computer network modeling, and simulation of key control system scenarios. The National Ignition Facility's (NIF) optical alignment system was modeled to study control system operations. The alignment of NIF's 192 beamlines is a large complex operation involving more than 100 computer systems and 8000 mechanized devices. The alignment process is defined by a detailed set of procedures; however, many of the steps are deterministic. The alignment steps for a poorly aligned component are similar to that of a nearly aligned component; however, additional operations/iterations are required to complete the process. Thus, the same alignment operations will require variable amounts of time to perform depending on the current alignment condition as well as other factors. Simulation of the alignment process is necessary to understand beamline alignment time requirements and how shared resources such as the Output Sensor and Target Alignment Sensor effect alignment efficiency. The simulation has provided alignment time estimates and other results based on documented alignment procedures and alignment experience gained in the laboratory. Computer communication time, mechanical hardware actuation times, image processing algorithm execution times, etc. have been experimentally determined and incorporated into the model. Previous analysis of alignment operations utilized average implementation times for all alignment operations. Resource sharing becomes rather simple to model when only average values are used. The time required to actually implement the many individual alignment operations will be quite dynamic. The simulation model estimates the time to complete an operation using

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

Directory of Open Access Journals (Sweden)

Genki Terashi

Full Text Available 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

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

BinAligner: a heuristic method to align biological networks.

Science.gov (United States)

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

2013-01-01

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

Prediction of molecular alignment of nucleic acids in aligned media

International Nuclear Information System (INIS)

Wu Bin; Petersen, Michael; Girard, Frederic; Tessari, Marco; Wijmenga, Sybren S.

2006-01-01

We demonstrate - using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined - that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye-Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye-Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye-Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it's functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request

Temporal alignment of electrocorticographic recordings for upper limb movement.

Science.gov (United States)

Talakoub, Omid; Popovic, Milos R; Navaro, Jessie; Hamani, Clement; Fonoff, Erich T; Wong, Willy

2014-01-01

The detection of movement-related components of the brain activity is useful in the design of brain-machine interfaces. A common approach is to classify the brain activity into a number of templates or states. To find these templates, the neural responses are averaged over each movement task. For averaging to be effective, one must assume that the neural components occur at identical times over repeated trials. However, complex arm movements such as reaching and grasping are prone to cross-trial variability due to the way movements are performed. Typically initiation time, duration of movement and movement speed are variable even as a subject tries to reproduce the same task identically across trials. Therefore, movement-related neural activity will tend to occur at different times across the trials. Due to this mismatch, the averaging of neural activity will not bring into salience movement-related components. To address this problem, we present a method of alignment that accounts for the variabilities in the way the movements are conducted. In this study, arm speed was used to align neural activity. Four subjects had electrocorticographic (ECoG) electrodes implanted over their primary motor cortex and were asked to perform reaching and retrieving tasks using the upper limb contralateral to the site of electrode implantation. The arm speeds were aligned using a non-linear transformation of the temporal axes resulting in average spectrograms with superior visualization of movement-related neural activity when compared to averaging without alignment.

A new prosthetic alignment device to read and record prosthesis alignment data.

Science.gov (United States)

Pirouzi, Gholamhossein; Abu Osman, Noor Azuan; Ali, Sadeeq; Davoodi Makinejad, Majid

2017-12-01

Prosthetic alignment is an essential process to rehabilitate patients with amputations. This study presents, for the first time, an invented device to read and record prosthesis alignment data. The digital device consists of seven main parts: the trigger, internal shaft, shell, sensor adjustment button, digital display, sliding shell, and tip. The alignment data were read and recorded by the user or a computer to replicate prosthesis adjustment for future use or examine the sequence of changes in alignment and its effect on the posture of the patient. Alignment data were recorded at the anterior/posterior and medial/lateral positions for five patients. Results show the high level of confidence to record alignment data and replicate adjustments. Therefore, the device helps patients readjust their prosthesis by themselves, or prosthetists to perform adjustment for patients and analyze the effects of malalignment.

Percolation modelling for highly aligned polycrystalline superconducting tapes

Energy Technology Data Exchange (ETDEWEB)

Rutter, N A; Glowacki, B A; Evetts, J E [Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ (United Kingdom); IRC in Superconductivity, Madingley Road, Cambridge CB3 0HE (United Kingdom)

2000-11-01

Surface and bulk texture measurements have been carried out on highly aligned NiFe tapes, suitable for use as coated conductor substrates. Data from small-area electron backscatter diffraction measurements are compared with those from bulk x-ray analysis in the development of a two-dimensional percolation model, and the two are shown to give very similar results. No evidence of grain-to-grain correlation is found. The model is then developed to assess how the properties of a superconducting layer grown epitaxially on buffered tapes will depend on parameters such as sample size, grain size and the extent of grain alignment. (author)

SymPix: A Spherical Grid for Efficient Sampling of Rotationally Invariant Operators

Science.gov (United States)

Seljebotn, D. S.; Eriksen, H. K.

2016-02-01

We present SymPix, a special-purpose spherical grid optimized for efficiently sampling rotationally invariant linear operators. This grid is conceptually similar to the Gauss-Legendre (GL) grid, aligning sample points with iso-latitude rings located on Legendre polynomial zeros. Unlike the GL grid, however, the number of grid points per ring varies as a function of latitude, avoiding expensive oversampling near the poles and ensuring nearly equal sky area per grid point. The ratio between the number of grid points in two neighboring rings is required to be a low-order rational number (3, 2, 1, 4/3, 5/4, or 6/5) to maintain a high degree of symmetries. Our main motivation for this grid is to solve linear systems using multi-grid methods, and to construct efficient preconditioners through pixel-space sampling of the linear operator in question. As a benchmark and representative example, we compute a preconditioner for a linear system that involves the operator \\widehat{{\\boldsymbol{D}}}+{\\widehat{{\\boldsymbol{B}}}}T{{\\boldsymbol{N}}}-1\\widehat{{\\boldsymbol{B}}}, where \\widehat{{\\boldsymbol{B}}} and \\widehat{{\\boldsymbol{D}}} may be described as both local and rotationally invariant operators, and {\\boldsymbol{N}} is diagonal in the pixel domain. For a bandwidth limit of {{\\ell }}{max} = 3000, we find that our new SymPix implementation yields average speed-ups of 360 and 23 for {\\widehat{{\\boldsymbol{B}}}}T{{\\boldsymbol{N}}}-1\\widehat{{\\boldsymbol{B}}} and \\widehat{{\\boldsymbol{D}}}, respectively, compared with the previous state-of-the-art implementation.

Comparative Analysis of Mass Spectral Similarity Measures on Peak Alignment for Comprehensive Two-Dimensional Gas Chromatography Mass Spectrometry

Science.gov (United States)

2013-01-01

Peak alignment is a critical procedure in mass spectrometry-based biomarker discovery in metabolomics. One of peak alignment approaches to comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) data is peak matching-based alignment. A key to the peak matching-based alignment is the calculation of mass spectral similarity scores. Various mass spectral similarity measures have been developed mainly for compound identification, but the effect of these spectral similarity measures on the performance of peak matching-based alignment still remains unknown. Therefore, we selected five mass spectral similarity measures, cosine correlation, Pearson's correlation, Spearman's correlation, partial correlation, and part correlation, and examined their effects on peak alignment using two sets of experimental GC×GC-MS data. The results show that the spectral similarity measure does not affect the alignment accuracy significantly in analysis of data from less complex samples, while the partial correlation performs much better than other spectral similarity measures when analyzing experimental data acquired from complex biological samples. PMID:24151524

Aligning the CMS Muon Endcap Detector with a System of Optical Sensors

CERN Document Server

Hohlmann, Marcus; Guragain, Samir; Andreev, Valery; Yang, Xiaofeng; Bellinger, James; Carlsmith, Duncan; Feyzi, Farshid; Loveless, Richard J; Northacker, David; Eartly, David P; Prokofiev, Oleg; Sknar, Vladimir

2008-01-01

The positions and orientations of one sixth of 468 large cathode strip chambers in the endcaps of the CMS muon detector are directly monitored by several hundred sensors including 2-D optical sensors with linear CCDs illuminated by cross-hair lasers. Position measurements obtained by photogrammetry and survey under field-off conditions show that chambers in the +Z endcap have been placed on the yoke disks with an average accuracy of $\\approx 1$ mm in all 3 dimensions. We reconstruct absolute Z$_{CMS}$ positions and orientations of chambers at B=0T and B=4T using data from the optical alignment system. The measured position resolution and sensitivity to relative motion is about 60 $\\mu m$. The precision for measuring chamber positions taking into account mechanical tolerances is \\mbox{$\\approx 270 \\mu m$}. Comparing reconstruction of optical alignment data and photogrammetry measurements at B=0T indicates an accuracy of $\\approx$ 680 $\\mu m$ currently achieved with the hardware alignment system. Optical positi...

Object oriented software for simulation and reconstruction of big alignment systems

International Nuclear Information System (INIS)

Arce, P.

2003-01-01

Modern high-energy physics experiments require tracking detectors to provide high precision under difficult working conditions (high magnetic field, gravity loads and temperature gradients). This is the reason why several of them are deciding to implement optical alignment systems to monitor the displacement of tracking elements in operation. To simulate and reconstruct optical alignment systems a general purpose software, named COCOA, has been developed, using the object oriented paradigm and software engineering techniques. Thanks to the big flexibility in its design, COCOA is able to reconstruct any optical system made of a combination of the following objects: laser, x-hair laser, incoherent source--pinhole, lens, mirror, plate splitter, cube splitter, optical square, rhomboid prism, 2D sensor, 1D sensor, distance-meter, tilt-meter, user-defined. COCOA was designed to satisfy the requirements of the CMS alignment system, which has several thousands of components. Sparse matrix techniques had been investigated for solving non-linear least squares fits with such a big number of parameters. The soundness of COCOA has already been stressed in the reconstruction of the data of a full simulation of a quarter plane of the CMS muon alignment system, which implied solving a system of 900 equations with 850 unknown parameters. Full simulation of the whole CMS alignment system, with over 30,000 parameters, is quite advanced. The integration of COCOA in the CMS software framework is also under progress

Linear models for airborne-laser-scanning-based operational forest inventory with small field sample size and highly correlated LiDAR data

Science.gov (United States)

Junttila, Virpi; Kauranne, Tuomo; Finley, Andrew O.; Bradford, John B.

2015-01-01

Modern operational forest inventory often uses remotely sensed data that cover the whole inventory area to produce spatially explicit estimates of forest properties through statistical models. The data obtained by airborne light detection and ranging (LiDAR) correlate well with many forest inventory variables, such as the tree height, the timber volume, and the biomass. To construct an accurate model over thousands of hectares, LiDAR data must be supplemented with several hundred field sample measurements of forest inventory variables. This can be costly and time consuming. Different LiDAR-data-based and spatial-data-based sampling designs can reduce the number of field sample plots needed. However, problems arising from the features of the LiDAR data, such as a large number of predictors compared with the sample size (overfitting) or a strong correlation among predictors (multicollinearity), may decrease the accuracy and precision of the estimates and predictions. To overcome these problems, a Bayesian linear model with the singular value decomposition of predictors, combined with regularization, is proposed. The model performance in predicting different forest inventory variables is verified in ten inventory areas from two continents, where the number of field sample plots is reduced using different sampling designs. The results show that, with an appropriate field plot selection strategy and the proposed linear model, the total relative error of the predicted forest inventory variables is only 5%–15% larger using 50 field sample plots than the error of a linear model estimated with several hundred field sample plots when we sum up the error due to both the model noise variance and the model’s lack of fit.

Resonant optical alignment and orientation of Mn2+ spins in CdMnTe crystals

Science.gov (United States)

Baryshnikov, K. A.; Langer, L.; Akimov, I. A.; Korenev, V. L.; Kusrayev, Yu. G.; Averkiev, N. S.; Yakovlev, D. R.; Bayer, M.

2015-11-01

We report on spin orientation and alignment of Mn2 + ions in (Cd,Mn)Te diluted magnetic semiconductor crystals using resonant intracenter excitation with circular- and linear-polarized light. The resulting polarized emission of the magnetic ions is observed at low temperatures when the spin relaxation time of the Mn2 + ions is in the order of 1 ms , which considerably exceeds the photoluminescence decay time of 23 μ s . We demonstrate that the experimental data on optical orientation and alignment of Mn2 + ions can be explained using a phenomenological model that is based on the approximation of isolated centers.

Alignment of E-Business with SMEs’ strategies in Northeast of Mexico

Directory of Open Access Journals (Sweden)

Norma Pedraza

2011-11-01

Full Text Available The alignment of e-business with business strategy is a theme that has gained interest among managers and researchers in the area. In this sense, the objectives of the present study are: (i to identify the existing perspective of the strategic alignment in the SMEs; (ii to find out the perception that the SMEs’ managers have about the criteria that determine the maturity level of the e-business alignment with the business strategy; and (iii to identify the existing relationship between the perspective of the e-business alignment with the criteria that promotes its alignment with the business strategy.  This study adopted the models developed by Henderson and Venkatraman (1993, 1999, Luftman (2000 and Sledgianoswki et al. (2006. Methodologically, a 52 item questionnaire was administered to a sample of 82 managers of enterprises located in the northeast of Mexico. The results present relevant implications for the strategic management of private organizations.

Shear Alignment of Diblock Copolymers for Patterning Nanowire Meshes

Energy Technology Data Exchange (ETDEWEB)

Gustafson, Kyle T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2016-09-08

Metallic nanowire meshes are useful as cheap, flexible alternatives to indium tin oxide – an expensive, brittle material used in transparent conductive electrodes. We have fabricated nanowire meshes over areas up to 2.5 cm² by: 1) mechanically aligning parallel rows of diblock copolymer (diBCP) microdomains; 2) selectively infiltrating those domains with metallic ions; 3) etching away the diBCP template; 4) sintering to reduce ions to metal nanowires; and, 5) repeating steps 1 – 4 on the same sample at a 90° offset. We aligned parallel rows of polystyrene-b-poly(2-vinylpyridine) [PS(48.5 kDa)-b-P2VP(14.5 kDa)] microdomains by heating above its glass transition temperature (T_g ≈ 100°C), applying mechanical shear pressure (33 kPa) and normal force (13.7 N), and cooling below T_g. DiBCP samples were submerged in aqueous solutions of metallic ions (15 – 40 mM ions; 0.1 – 0.5 M HCl) for 30 – 90 minutes, which coordinate to nitrogen in P2VP. Subsequent ozone-etching and sintering steps yielded parallel nanowires. We aimed to optimize alignment parameters (e.g. shear and normal pressures, alignment duration, and PDMS thickness) to improve the quality, reproducibility, and scalability of meshes. We also investigated metals other than Pt and Au that may be patterned using this technique (Cu, Ag).

Field-free molecular alignment probed by the free electron laser in Hamburg (FLASH)

Energy Technology Data Exchange (ETDEWEB)

Johnsson, P; Rouzee, A; Siu, W; Huismans, Y; Vrakking, M J J [FOM Institute for Atomic and Molecular Physics (AMOLF), Science Park 113, 1098 XG Amsterdam (Netherlands); Lepine, F [Universite Lyon 1, CNRS, LASIM, UMR 5579, 43 bvd. du 11 novembre 1918, F-69622 Villeurbanne (France); Marchenko, T [Laboratoire d' Optique Applique, ENSTA/Ecole Polytechnique, Chemin de la Huniere, 91761 Palaiseau (France); Duesterer, S; Tavella, F; Stojanovic, N; Azima, A; Treusch, R [Hamburger Synchrotronstrahlungslabor (HASYLAB) at Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85, D-22607 Hamburg (Germany); Kling, M F [Max-Planck Institut fuer Quantenoptik, Hans-Kopfermann Strasse 1, D-85748 Garching (Germany)], E-mail: per.johnsson@fysik.lth.se

2009-07-14

High flux extreme ultraviolet (XUV) sources like the free electron laser (FEL) in Hamburg (FLASH) offer the possibility of diffractive imaging of small objects. Irrespective of whether the diffraction is based on the detection of photons or photoelectrons, it is required that the measurement is done in the reference frame of the molecule meaning that, for a sample of several molecules, it is necessary to pre-align the molecules in the sample. As a step towards performing molecular frame diffraction experiments, we report experiments on field-free molecular alignment performed at FLASH. The impulsive alignment induced by a 100 fs near-infrared laser pulse in a rotationally cold CO{sub 2} sample is characterized by ionizing and dissociating the molecules with a time-delayed XUV-FEL pulse. The time-dependent angular distributions of ionic fragments measured by a velocity map imaging spectrometer exhibit rapid changes associated with the induced rotational dynamics. The experimental results show hints of a dissociation process that depends nonlinearly on the XUV intensity.

DNA Translator and Aligner: HyperCard utilities to aid phylogenetic analysis of molecules.

Science.gov (United States)

Eernisse, D J

1992-04-01

DNA Translator and Aligner are molecular phylogenetics HyperCard stacks for Macintosh computers. They manipulate sequence data to provide graphical gene mapping, conversions, translations and manual multiple-sequence alignment editing. DNA Translator is able to convert documented GenBank or EMBL documented sequences into linearized, rescalable gene maps whose gene sequences are extractable by clicking on the corresponding map button or by selection from a scrolling list. Provided gene maps, complete with extractable sequences, consist of nine metazoan, one yeast, and one ciliate mitochondrial DNAs and three green plant chloroplast DNAs. Single or multiple sequences can be manipulated to aid in phylogenetic analysis. Sequences can be translated between nucleic acids and proteins in either direction with flexible support of alternate genetic codes and ambiguous nucleotide symbols. Multiple aligned sequence output from diverse sources can be converted to Nexus, Hennig86 or PHYLIP format for subsequent phylogenetic analysis. Input or output alignments can be examined with Aligner, a convenient accessory stack included in the DNA Translator package. Aligner is an editor for the manual alignment of up to 100 sequences that toggles between display of matched characters and normal unmatched sequences. DNA Translator also generates graphic displays of amino acid coding and codon usage frequency relative to all other, or only synonymous, codons for approximately 70 select organism-organelle combinations. Codon usage data is compatible with spreadsheet or UWGCG formats for incorporation of additional molecules of interest. The complete package is available via anonymous ftp and is free for non-commercial uses.

Mask alignment system for semiconductor processing

Science.gov (United States)

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.

On the Alignment of Shapes Represented by Fourier Descriptors

DEFF Research Database (Denmark)

Sjöstrand, Karl; Ericsson, Anders; Larsen, Rasmus

2006-01-01

The representation of shapes by Fourier descriptors is a time-honored technique that has received relatively little attention lately. Nevertheless, it has many benefits and is applicable for describing a range of medical structures in two dimensions. Delineations in medical applications often...... consist of continuous outlines of structures, where no information of correspondence between samples exist. In this article, we discuss an alignment method that works directly with the functional representation of Fourier descriptors, and that is optimal in a least-squares sense. With corresponding...... represented by common landmarks can be constructed in an automatic fashion. If the aligned Fourier descriptors are inverse transformed from the frequency domain to the spatial domain, a set of roughly aligned landmarks are obtained. The positions of these are then adjusted along the contour of the objects...

Cryo-EM image alignment based on nonuniform fast Fourier transform

International Nuclear Information System (INIS)

Yang Zhengfan; Penczek, Pawel A.

2008-01-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis

Cryo-EM image alignment based on nonuniform fast Fourier transform.

Science.gov (United States)

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.

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...

A Novel Marker Based Method to Teeth Alignment in MRI

Science.gov (United States)

Luukinen, Jean-Marc; Aalto, Daniel; Malinen, Jarmo; Niikuni, Naoko; Saunavaara, Jani; Jääsaari, Päivi; Ojalammi, Antti; Parkkola, Riitta; Soukka, Tero; Happonen, Risto-Pekka

2018-04-01

Magnetic resonance imaging (MRI) can precisely capture the anatomy of the vocal tract. However, the crowns of teeth are not visible in standard MRI scans. In this study, a marker-based teeth alignment method is presented and evaluated. Ten patients undergoing orthognathic surgery were enrolled. Supraglottal airways were imaged preoperatively using structural MRI. MRI visible markers were developed, and they were attached to maxillary teeth and corresponding locations on the dental casts. Repeated measurements of intermarker distances in MRI and in a replica model was compared using linear regression analysis. Dental cast MRI and corresponding caliper measurements did not differ significantly. In contrast, the marker locations in vivo differed somewhat from the dental cast measurements likely due to marker placement inaccuracies. The markers were clearly visible in MRI and allowed for dental models to be aligned to head and neck MRI scans.

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

Fast global sequence alignment technique

KAUST Repository

Bonny, Mohamed Talal; Salama, Khaled N.

2011-01-01

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

Low-sensitivity H ∞ filter design for linear delta operator systems with sampling time jitter

Science.gov (United States)

Guo, Xiang-Gui; Yang, Guang-Hong

2012-04-01

This article is concerned with the problem of designing H ∞ filters for a class of linear discrete-time systems with low-sensitivity to sampling time jitter via delta operator approach. Delta-domain model is used to avoid the inherent numerical ill-condition resulting from the use of the standard shift-domain model at high sampling rates. Based on projection lemma in combination with the descriptor system approach often used to solve problems related to delay, a novel bounded real lemma with three slack variables for delta operator systems is presented. A sensitivity approach based on this novel lemma is proposed to mitigate the effects of sampling time jitter on system performance. Then, the problem of designing a low-sensitivity filter can be reduced to a convex optimisation problem. An important consideration in the design of correlation filters is the optimal trade-off between the standard H ∞ criterion and the sensitivity of the transfer function with respect to sampling time jitter. Finally, a numerical example demonstrating the validity of the proposed design method is given.

Alignment statistics of clusters with their brightest members at bright and faint isophotes

International Nuclear Information System (INIS)

Struble, M.F.

1987-01-01

For a sample of 21 first-ranked cluster galaxies with published isophotal photometry and position angles of these isophotes, it is found that the major axes of both the bright and faint isophotal contours tend to be aligned within about 30 deg of the major axis of the parent cluster. This supports the hypothesis that first-ranked galaxies are formed already aligned with their parent clusters rather than the hypothesis that only outer envelopes which accreted after formation are aligned with the cluster. 21 references

Dipole Alignment at the Carbon Nanotube and Methyl Ammonium Lead Iodide Perovskite Interface

Energy Technology Data Exchange (ETDEWEB)

Przepioski, Joshua [SLAC National Accelerator Lab., Menlo Park, CA (United States)

2015-08-28

This work correlates resonant peaks from first principles calculation on ammonia (NH₃) Nitrogen 1s x-ray absorption spectroscopy (XAS) within the methyl ammonium lead iodide perovskite (CH₃NH₃PbI₃), and proposes a curve to determine the alignment of the methyl ammonium dipole if there exists angular dependence. The Nitrogen 1s XAS was performed at varying incident angles on the perovskite with and without a carbon nanotube (CNT) interface produced from an ultrasonic spray deposition. We investigated the peak contribution from PbI₂ and the poly(9,9-dioctylfluorene- 2,7-diyl) with bipyridine (PFO-BPy) wrapped around the CNT, and used normalization techniques to better identify the dipole alignment. There was angular dependence on samples containing the CNT interface suggesting an existing dipole alignment, but there was no angular dependence on the perovskite samples alone; however, more normalization techniques and experimental work must be performed in order to ensure its validity and to better describe its alignment, and possible controlling factors.

DNA motif alignment by evolving a population of Markov chains.

Science.gov (United States)

Bi, Chengpeng

2009-01-30

Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

Ancestral sequence alignment under optimal conditions

Directory of Open Access Journals (Sweden)

Brown Daniel G

2005-11-01

Full Text Available Abstract Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree. In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences. Results We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth. We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang. Conclusion We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the

Orthopedic complications of linear morphea: Implications for early interdisciplinary care.

Science.gov (United States)

Schoch, Jennifer J; Schoch, Bradley S; Werthel, Jean David; McIntosh, Amy L; Davis, Dawn M R

2018-01-01

Linear morphea of the limb primarily affects children, and extracutaneous manifestations are common. Orthopedic surgeons are often essential in the care of patients with linear morphea, yet there are few reports outlining specific orthopedic complications in this population. We sought to improve the understanding of orthopedic complications in linear morphea of the limb. Between 1999 and 2014, 51 children were evaluated for linear morphea of an extremity. Twenty-six (51%) had documented orthopedic manifestations. Outcome measures included limb length discrepancy, angular malalignment, limb atrophy, and orthopedic surgical intervention. Joint contractures were most common, affecting 88% of patients, followed by limb atrophy, angular deformity, and limb length discrepancy; 14% required surgical intervention. Despite the use of systemic immunosuppressive therapy in many patients, approximately half of patients with linear morphea of an extremity have orthopedic disease. Early orthopedist involvement is crucial to improve limb alignment and preserve function. © 2017 Wiley Periodicals, Inc.

Measuring and aligning accelerator components to the nanometre scale

CERN Document Server

Catalán Lasheras, N; Modena, M

2014-01-01

First tests have shown that the precision and accuracy required for linear colliders and other future accelerators of 10 micrometers is costly and lengthy with a process based on independent fiducializations of single components. Indeed, the systematic and random errors at each step add up during the process with the final accuracy of each component center well above the target. A new EC-funded training network named PACMAN (a study on Particle Accelerator Components Metrology and Alignment to the Nanometer scale) will propose and develop an alternative solution integrating all the alignment steps and a large number of technologies at the same time and location, in order to gain the required precision and accuracy. The network composed of seven industrial partners and nine universities and research centers will be based at CERN where ten doctoral students will explore the technology limitations of metrology. They will develop new techniques to measure magnetic and microwave fields, optical and non-contact sen...

Aligned deposition and electrical measurements on single DNA molecules

International Nuclear Information System (INIS)

Eidelshtein, Gennady; Kotlyar, Alexander; Hashemi, Mohtadin; Gurevich, Leonid

2015-01-01

A reliable method of deposition of aligned individual dsDNA molecules on mica, silicon, and micro/nanofabricated circuits is presented. Complexes of biotinylated double stranded poly(dG)–poly(dC) DNA with avidin were prepared and deposited on mica and silicon surfaces in the absence of Mg 2+ ions. Due to its positive charge, the avidin attached to one end of the DNA anchors the complex to negatively charged substrates. Subsequent drying with a directional gas flow yields DNA molecules perfectly aligned on the surface. In the avidin–DNA complex only the avidin moiety is strongly and irreversibly bound to the surface, while the DNA counterpart interacts with the substrates much more weakly and can be lifted from the surface and realigned in any direction. Using this technique, avidin–DNA complexes were deposited across platinum electrodes on a silicon substrate. Electrical measurements on the deposited DNA molecules revealed linear IV-characteristics and exponential dependence on relative humidity. (paper)

Matrix effect study in the determination of linear alkylbenzene sulfonates in sewage sludge samples.

Science.gov (United States)

Cantarero, Samuel; Zafra-Gómez, Alberto; Ballesteros, Oscar; Navalón, Alberto; Vílchez, José L; Verge, Coral; De Ferrer, Juan A

2011-04-01

We propose a study of the matrix effect in the determination of linear alkylbenzene sulfonates (LAS) in sewage sludge samples. First, a rapid, selective and sensitive method is proposed. The method involves two stages: the extraction of the compound from the samples and analysis by liquid chromatography with fluorescence detection (LC-FLD). Three different techniques of extraction (microwave-assisted extraction, Soxhlet, and ultrasounds) were compared, and microwave-assisted extraction was selected as the best suited for our purpose. Microwave-assisted extraction allows reducing the extraction time (25 min compared with 12 h for conventional Soxhlet extraction) and solvent waste (25 ml of methanol compared with 200 ml for Soxhlet or more than 50 ml for the ultrasonic procedure). Absence of matrix effect was evaluated with two standards (2ØC(8:0) and 2ØC(16:0) ) that are not commercial; therefore, neither of them was detected in sewage sludge samples and they showed similar environmental behavior (adsorption and precipitation) to LAS (C(11:0) -C(13.0) ), which allow us to evaluate the matrix effect. Validation was carried out by a recovery assay, and the method was applied to samples from different sources; therefore, they had different compositions. Copyright © 2011 SETAC.

Clear aligners in orthodontic treatment.

Science.gov (United States)

Weir, T

2017-03-01

Since the introduction of the Tooth Positioner (TP Orthodontics) in 1944, removable appliances analogous to clear aligners have been employed for mild to moderate orthodontic tooth movements. Clear aligner therapy has been a part of orthodontic practice for decades, but has, particularly since the introduction of Invisalign appliances (Align Technology) in 1998, become an increasingly common addition to the orthodontic armamentarium. An internet search reveals at least 27 different clear aligner products currently on offer for orthodontic treatment. The present paper will highlight the increasing popularity of clear aligner appliances, as well as the clinical scope and the limitations of aligner therapy in general. Further, the paper will outline the differences between the various types of clear aligner products currently available. © 2017 Australian Dental Association.

The influence of conductivities consistent with field-aligned currents on high-latitude convection patterns

International Nuclear Information System (INIS)

Blomberg, L.G.; Marklund, G.T.

1988-02-01

The influence on the high-latitude ionospheric convection of conductivities associated with upward field-aligned currents is investigated. Potential patterns are calculated from a given distribution of field-aligned currents and a conductivity model. The resulting patterns are shown to be modified considerably by including a coupling term between the conductivity and the field-aligned current in the conductivity model. The clockwise rotation of the entire potential pattern is reduced when the conductivity enhancement coincides with the regions of upward field-aligned current. Also, the electric field within these regions turns out to be rather insensitive to change in the magnitude of the current. In regions of downward current or when the current-dependent conductivity is excluded there is on the other hand an almost linear relationship between current and electric field. Although the particles producing the conductivity enhancement may not be the same as those carrying the major part of the field-aligned current it is clear from observations that there is a positive correlation between upward current conductivity. Therefore, the simple relationship used in this study is believed to reflect rather well the principal features of the current-conductivity coupling, which is of im- portance to the modelling of ionospheric electrodynamics. (With 26 refs.) (authors)

Field emission from vertically aligned few-layer graphene

International Nuclear Information System (INIS)

Malesevic, Alexander; Kemps, Raymond; Vanhulsel, Annick; Chowdhury, Manish Pal; Volodin, Alexander; Van Haesendonck, Chris

2008-01-01

The electric field emission behavior of vertically aligned few-layer graphene was studied in a parallel plate-type setup. Few-layer graphene was synthesized in the absence of any metallic catalyst by microwave plasma enhanced chemical vapor deposition with gas mixtures of methane and hydrogen. The deposit consists of nanostructures that are several micrometers wide, highly crystalline stacks of four to six atomic layers of graphene, aligned vertically to the substrate surface in a high density network. The few-layer graphene is found to be a good field emitter, characterized by turn-on fields as low as 1 V/μm and field amplification factors up to several thousands. We observe a clear dependence of the few-layer graphene field emission behavior on the synthesis parameters: Hydrogen is identified as an efficient etchant to improve field emission, and samples grown on titanium show lower turn-on field values and higher amplification factors when compared to samples grown on silicon

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...

High performance electronics for alignment regulation on the CLIC 30GHz modules

International Nuclear Information System (INIS)

Carrica, D.; Coosemans, W.; Pittin, R.

1999-01-01

CERN is studying a linear collider (CLIC) to obtain electron-positron collisions with centre-of-mass energies in the TeV range. To demonstrate the feasibility of CLIC, a test facility (CTF2) is being constructed. CTF2 consists of 4 identical modules, each 1.4 m long module consists of 2 linac with a girder and a doublet or a triplet quadrupole. Girders are elements that support mechanically the cavities of the accelerator while the main objective of the quadrupole is to focus particle beams. The alignment system has 2 principal utilities. The first is to pre-align the elements to make the beam pass through the aperture and produce signals in beam position monitors. In respect to these signals the girders and the quadrupoles are moved for making the definitive alignment. The second utility is to maintain the elements in this position. The alignment control system of CTF2 must regulate the position of the girders and quadrupoles with a precision < 10 μm. In fact an accuracy of 1 μ has been obtained on CTF2. Thanks to its flexibility and its simplicity, the system is expected to adapt easily to CLIC even if it means to control modules that involve up to a maximum of 384 motors and 896 sensors

Intradomain phase transitions in flexible block copolymers with self-aligning segments

Science.gov (United States)

Burke, Christopher J.; Grason, Gregory M.

2018-05-01

We study a model of flexible block copolymers (BCPs) in which there is an enlthalpic preference for orientational order, or local alignment, among like-block segments. We describe a generalization of the self-consistent field theory of flexible BCPs to include inter-segment orientational interactions via a Landau-de Gennes free energy associated with a polar or nematic order parameter for segments of one component of a diblock copolymer. We study the equilibrium states of this model numerically, using a pseudo-spectral approach to solve for chain conformation statistics in the presence of a self-consistent torque generated by inter-segment alignment forces. Applying this theory to the structure of lamellar domains composed of symmetric diblocks possessing a single block of "self-aligning" polar segments, we show the emergence of spatially complex segment order parameters (segment director fields) within a given lamellar domain. Because BCP phase separation gives rise to spatially inhomogeneous orientation order of segments even in the absence of explicit intra-segment aligning forces, the director fields of BCPs, as well as thermodynamics of lamellar domain formation, exhibit a highly non-linear dependence on both the inter-block segregation (χN) and the enthalpy of alignment (ɛ). Specifically, we predict the stability of new phases of lamellar order in which distinct regions of alignment coexist within the single mesodomain and spontaneously break the symmetries of the lamella (or smectic) pattern of composition in the melt via in-plane tilt of the director in the centers of the like-composition domains. We further show that, in analogy to Freedericksz transition confined nematics, the elastic costs to reorient segments within the domain, as described by the Frank elasticity of the director, increase the threshold value ɛ needed to induce this intra-domain phase transition.

How accurate is anatomic limb alignment in predicting mechanical limb alignment after total knee arthroplasty?

Science.gov (United States)

Lee, Seung Ah; Choi, Sang-Hee; Chang, Moon Jong

2015-10-27

Anatomic limb alignment often differs from mechanical limb alignment after total knee arthroplasty (TKA). We sought to assess the accuracy, specificity, and sensitivity for each of three commonly used ranges for anatomic limb alignment (3-9°, 5-10° and 2-10°) in predicting an acceptable range (neutral ± 3°) for mechanical limb alignment after TKA. We also assessed whether the accuracy of anatomic limb alignment was affected by anatomic variation. This retrospective study included 314 primary TKAs. The alignment of the limb was measured with both anatomic and mechanical methods of measurement. We also measured anatomic variation, including the femoral bowing angle, tibial bowing angle, and neck-shaft angle of the femur. All angles were measured on the same full-length standing anteroposterior radiographs. The accuracy, specificity, and sensitivity for each range of anatomic limb alignment were calculated and compared using mechanical limb alignment as the reference standard. The associations between the accuracy of anatomic limb alignment and anatomic variation were also determined. The range of 2-10° for anatomic limb alignment showed the highest accuracy, but it was only 73 % (3-9°, 65 %; 5-10°, 67 %). The specificity of the 2-10° range was 81 %, which was higher than that of the other ranges (3-9°, 69 %; 5-10°, 67 %). However, the sensitivity of the 2-10° range to predict varus malalignment was only 16 % (3-9°, 35 %; 5-10°, 68 %). In addition, the sensitivity of the 2-10° range to predict valgus malalignment was only 43 % (3-9°, 71 %; 5-10°, 43 %). The accuracy of anatomical limb alignment was lower for knees with greater femoral (odds ratio = 1.2) and tibial (odds ratio = 1.2) bowing. Anatomic limb alignment did not accurately predict mechanical limb alignment after TKA, and its accuracy was affected by anatomic variation. Thus, alignment after TKA should be assessed by measuring mechanical alignment rather than anatomic

Vision Servo Motion Control and Error Analysis of a Coplanar XXY Stage for Image Alignment Motion

Directory of Open Access Journals (Sweden)

Hau-Wei Lee

2013-01-01

Full Text Available In recent years, as there is demand for smart mobile phones with touch panels, the alignment/compensation system of alignment stage with vision servo control has also increased. Due to the fact that the traditional stacked-type XYθ stage has cumulative errors of assembly and it is heavy, it has been gradually replaced by the coplanar stage characterized by three actuators on the same plane with three degrees of freedom. The simplest image alignment mode uses two cameras as the equipments for feedback control, and the work piece is placed on the working stage. The work piece is usually engraved/marked. After the cameras capture images and when the position of the mark in the camera is obtained by image processing, the mark can be moved to the designated position in the camera by moving the stage and using alignment algorithm. This study used a coplanar XXY stage with 1 μm positioning resolution. Due to the fact that the resolution of the camera is about 3.75 μm per pixel, thus a subpixel technology is used, and the linear and angular alignment repeatability of the alignment system can achieve 1 μm and 5 arcsec, respectively. The visual servo motion control for alignment motion is completed within 1 second using the coplanar XXY stage.

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...... of NPD performance indicators. Strategic planning and innovativeness appear to affect technological, market, and NPD-marketing alignment positively. Environmental munificence is negatively associated with NPD-marketing alignment, but has no effect on the two other forms of alignment. Technological change...... has a positive effect on technological alignment, a negative effect on NPD-marketing alignment, but no effect on market alignment. These findings suggest that internal capabilities are more likely to be associated with the development of strategic alignment than environmental factors are. Furthermore...

Resolution and systematic limitations in beam based alignment

Energy Technology Data Exchange (ETDEWEB)

Tenenbaum, P.G.

2000-03-15

Beam based alignment of quadrupoles by variation of quadrupole strength is a widely-used technique in accelerators today. The authors describe the dominant systematic limitation of this technique, which arises from the change in the center position of the quadrupole as the strength is varied, and derive expressions for the resulting error. In addition, the authors derive an expression for the statistical resolution of such techniques in a periodic transport line, given knowledge of the line's transport matrices, the resolution of the beam position monitor system, and the details of the strength variation procedure. These results are applied to the Next Linear Collider main linear accelerator, an 11 kilometer accelerator containing 750 quadrupoles and 5,000 accelerator structures. The authors find that in principle a statistical resolution of 1 micron is easily achievable but the systematic error due to variation of the magnetic centers could be several times larger.

ABS: Sequence alignment by scanning

KAUST Repository

Bonny, Mohamed Talal; Salama, Khaled N.

2011-01-01

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.

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.

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.

Angular momentum-large-scale structure alignments in ΛCDM models and the SDSS

Science.gov (United States)

Paz, Dante J.; Stasyszyn, Federico; Padilla, Nelson D.

2008-09-01

We study the alignments between the angular momentum of individual objects and the large-scale structure in cosmological numerical simulations and real data from the Sloan Digital Sky Survey, Data Release 6 (SDSS-DR6). To this end, we measure anisotropies in the two point cross-correlation function around simulated haloes and observed galaxies, studying separately the one- and two-halo regimes. The alignment of the angular momentum of dark-matter haloes in Λ cold dark matter (ΛCDM) simulations is found to be dependent on scale and halo mass. At large distances (two-halo regime), the spins of high-mass haloes are preferentially oriented in the direction perpendicular to the distribution of matter; lower mass systems show a weaker trend that may even reverse to show an angular momentum in the plane of the matter distribution. In the one-halo term regime, the angular momentum is aligned in the direction perpendicular to the matter distribution; the effect is stronger than for the one-halo term and increases for higher mass systems. On the observational side, we focus our study on galaxies in the SDSS-DR6 with elongated apparent shapes, and study alignments with respect to the major semi-axis. We study five samples of edge-on galaxies; the full SDSS-DR6 edge-on sample, bright galaxies, faint galaxies, red galaxies and blue galaxies (the latter two consisting mainly of ellipticals and spirals, respectively). Using the two-halo term of the projected correlation function, we find an excess of structure in the direction of the major semi-axis for all samples; the red sample shows the highest alignment (2.7 +/- 0.8per cent) and indicates that the angular momentum of flattened spheroidals tends to be perpendicular to the large-scale structure. These results are in qualitative agreement with the numerical simulation results indicating that the angular momentum of galaxies could be built up as in the Tidal Torque scenario. The one-halo term only shows a significant alignment

Automated angular and translational tomographic alignment and application to phase-contrast imaging

DEFF Research Database (Denmark)

Cunha Ramos, Tiago Joao; Jørgensen, Jakob Sauer; Andreasen, Jens Wenzel

2017-01-01

X-ray computerized tomography (CT) is a 3D imaging technique that makes use of x-ray illumination and image reconstruction techniques to reproduce the internal cross-sections of a sample. Tomographic projection data usually require an initial relative alignment or knowledge of the exact object po...... improvement in the reconstruction resolution. A MATLAB implementation is made publicly available and will allow robust analysis of large volumes of phase-contrast tomography data.......X-ray computerized tomography (CT) is a 3D imaging technique that makes use of x-ray illumination and image reconstruction techniques to reproduce the internal cross-sections of a sample. Tomographic projection data usually require an initial relative alignment or knowledge of the exact object...... reconstruction artifacts and limit the attained resolution in the final tomographic reconstruction. Alignment algorithms that require manual interaction impede data analysis with ever-increasing data acquisition rates, supplied by more brilliant sources. We present in this paper an iterative reconstruction...

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.

Association of professional identity, gender, team understanding, anxiety and workplace learning alignment with burnout in junior doctors: a longitudinal cohort study.

Science.gov (United States)

Monrouxe, Lynn V; Bullock, Alison; Tseng, Hsu-Min; Wells, Stephanie E

2017-12-27

To examine how burnout across medical student to junior doctor transition relates to: measures of professional identity, team understanding, anxiety, gender, age and workplace learning (assistantship) alignment to first post. A longitudinal 1-year cohort design. Two groups of final-year medical students: (1) those undertaking end-of-year assistantships aligned in location and specialty with their first post and (2) those undertaking assistantships non-aligned. An online questionnaire included: Professional Identity Scale, Team Understanding Scale, modified Hamilton Anxiety Rating Scale and modified Copenhagen Burnout Inventory. Data were collected on four occasions: (T1) prior to graduation; (T2) 1 month post-transition; (T3) 6 months post-transition and (T4) 10 months post-transition. Questionnaires were analysed individually and using linear mixed-effect models. Medical schools and postgraduate training in one UK country. All aligned assistantship (n=182) and non-aligned assistantship students (n=319) were contacted; n=281 (56%) responded: 68% (n=183) females, 73% (n=206) 22-30 years, 46% aligned (n=129). Completion rates: aligned 72% (93/129) and non-aligned 64% (98/152). Analyses of individual scales revealed that self-reported anxiety, professional identity and patient-related burnout were stable, while team understanding, personal and work-related burnout increased, all irrespective of alignment. Three linear mixed-effect models (personal, patient-related and work-related burnout as outcome measures; age and gender as confounding variables) found that males self-reported significantly lower personal, but higher patient-related burnout, than females. Age and team understanding had no effect. Anxiety was significantly positively related and professional identity was significantly negatively related to burnout. Participants experiencing non-aligned assistantships reported higher personal and work-related burnout over time. Implications for practice

Association of professional identity, gender, team understanding, anxiety and workplace learning alignment with burnout in junior doctors: a longitudinal cohort study

Science.gov (United States)

Bullock, Alison; Tseng, Hsu-Min; Wells, Stephanie E

2017-01-01

Objectives To examine how burnout across medical student to junior doctor transition relates to: measures of professional identity, team understanding, anxiety, gender, age and workplace learning (assistantship) alignment to first post. Design A longitudinal 1-year cohort design. Two groups of final-year medical students: (1) those undertaking end-of-year assistantships aligned in location and specialty with their first post and (2) those undertaking assistantships non-aligned. An online questionnaire included: Professional Identity Scale, Team Understanding Scale, modified Hamilton Anxiety Rating Scale and modified Copenhagen Burnout Inventory. Data were collected on four occasions: (T1) prior to graduation; (T2) 1 month post-transition; (T3) 6 months post-transition and (T4) 10 months post-transition. Questionnaires were analysed individually and using linear mixed-effect models. Setting Medical schools and postgraduate training in one UK country. Participants All aligned assistantship (n=182) and non-aligned assistantship students (n=319) were contacted; n=281 (56%) responded: 68% (n=183) females, 73% (n=206) 22–30 years, 46% aligned (n=129). Completion rates: aligned 72% (93/129) and non-aligned 64% (98/152). Results Analyses of individual scales revealed that self-reported anxiety, professional identity and patient-related burnout were stable, while team understanding, personal and work-related burnout increased, all irrespective of alignment. Three linear mixed-effect models (personal, patient-related and work-related burnout as outcome measures; age and gender as confounding variables) found that males self-reported significantly lower personal, but higher patient-related burnout, than females. Age and team understanding had no effect. Anxiety was significantly positively related and professional identity was significantly negatively related to burnout. Participants experiencing non-aligned assistantships reported higher personal and work

Alignment for CSR

International Nuclear Information System (INIS)

Wang Shoujin; Man Kaidi; Guo Yizhen; Cai Guozhu; Guo Yuhui

2002-01-01

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

A generalized global alignment algorithm.

Science.gov (United States)

Huang, Xiaoqiu; Chao, Kun-Mao

2003-01-22

Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.

Strategic alignment of the South African retail sector with the national development plan

Directory of Open Access Journals (Sweden)

Roger B Mason

2014-12-01

Full Text Available This paper provides an evaluation of the strategy alignment of the South African retail sector with the National Development Plan (NDP governance values and objectives. The paper considers the commercial realities which form the framework for retail decision-makers when they address the challenges in aligning their business growth strategies with the regulatory framework of a capable, developmental state. Within that context, the outcomes of a retail stakeholder alignment study of the NDP strategy themes are analysed. The method involved a policy survey of a purposive sample of retail business and governance stakeholders. The survey findings reflect retailer alignment with many NDP regulatory and ‘active citizenry’ strategies, but with strong beliefs that others are not the retail business sector’s governance responsibility.

Pairwise Sequence Alignment Library

Energy Technology Data Exchange (ETDEWEB)

2015-05-20

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

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.

Belt Aligning Revisited

Directory of Open Access Journals (Sweden)

Yurchenko Vadim

2017-01-01

parts of the conveyor, the sides of the belt wear intensively. This results in reducing the life of the belt. The reasons for this phenomenon are well investigated, but the difficulty lies in the fact that they all act simultaneously. The belt misalignment prevention can be carried out in two ways: by minimizing the effect of causes and by aligning the belt. The construction of aligning devices and errors encountered in practice are considered in this paper. Self-aligning roller supports rotational in plan view are recommended as a means of combating the belt misalignment.

The Alignment of easyCBM[R] Math Measures to Curriculum Standards. Technical Report #1002

Science.gov (United States)

Nese, Joseph F. T.; Lai, Cheng-Fei; Anderson, Daniel; Park, Bitnara Jasmine; Tindal, Gerald; Alonzo, Julie

2010-01-01

The purpose of this study was to examine the alignment of the easyCBM[R] mathematics benchmark and progress monitoring measures to the National Council of Teachers of Mathematics "Curriculum Focal Points" (NCTM, 2006). Based on Webb's alignment model (1997, 2002), we collected expert judgments on individual math items across a sampling of forms…

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

Directory of Open Access Journals (Sweden)

Shunichi Kosugi

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

Antares beam-alignment-system performance

International Nuclear Information System (INIS)

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

1983-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Hoang, Thiem [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Lazarian, A. [Department of Astronomy, University of Wisconsin-Madison (United States)

2016-11-10

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

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...

Movement of anterior teeth using clear aligners: a three-dimensional, retrospective evaluation.

Science.gov (United States)

Tepedino, Michele; Paoloni, Valeria; Cozza, Paola; Chimenti, Claudio

2018-04-02

Clear aligner treatment offers several advantages, but the available literature shows that some kind of tooth movements are unpredictable. In addition, the majority of the studies are focused on one clear aligner system, while different characteristics of various systems can provide different treatment outcomes. The aim of the present retrospective cohort study was to evaluate the predictability of Nuvola® aligner system in achieving torque movements of anterior teeth. Thirty-nine adult patients, who were consecutively treated with clear aligners, were retrospectively selected, and digital models pre-treatment (T0), post-treatment (T1) and the digital setup models (TS) were collected. Only the first phase of treatment made of 12 aligners was considered for the present study. Torque of anterior teeth was measured as labiolingual inclination on digital models at T0, T1, and TS using VAM software. Any difference between the predicted and achieved torque movements was evaluated using Wilcoxon signed-rank test or paired sample t test. First-type error was set as p clear aligner system was able to produce clinical outcomes comparable to the planning of the digital setup relative to torque movements of the anterior teeth.

Short-term magnetic field alignment variations of equatorial ionospheric irregularities

International Nuclear Information System (INIS)

Johnson, A.L.

1988-01-01

The ionospheric irregularities that cause equatorial scintillation are elongated along the north-south magnetic field lines. During a 1981 field campaign at Ascension Island, 250-MHz receivers were spaced from 300 m to 1.6 km along the field lines, and the signals received from the Marisat satellite were cross correlated. Data collected during eight nights of fading showed a linear relationship between fading rate and cross correlation. The alignment of the antennas was adjusted to give a zero time lag between the widely spaced receivers with a measurement accuracy of 0.03 s. Since the average irregularity velocity was 125 m/s, this time accuracy translated to an angular measurement accuracy of 0.1 deg. During a 4-hour period of nightly fading, occasional differences in time of arrival were noted that corresponded to a tilt in the north-south alignment of + or - 1 deg. Data from several nights of fading were analyzed, and each night exhibited the same variance in the north-south irregularity alignment. It is postulated that the shift in the measured peak correlation may have been caused by patches of irregularities at different altitudes where the magnetic field lines have a slightly different direction. 13 references

Parental alignments and rejection: an empirical study of alienation in children of divorce.

Science.gov (United States)

Johnston, Janet R

2003-01-01

This study of family relationships after divorce examined the frequency and extent of child-parent alignments and correlates of children's rejection of a parent, these being basic components of the controversial idea of "parental alienation syndrome." The sample consisted of 215 children from the family courts and general community two to three years after parental separation. The findings indicate that children's attitudes toward their parents range from positive to negative, with relatively few being extremely aligned or rejecting. Rejection of a parent has multiple determinants, with both the aligned and rejected parents contributing to the problem, in addition to vulnerabilities within children themselves.

Galaxy Alignments: Theory, Modelling & Simulations

Science.gov (United States)

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

2015-11-01

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 the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta 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 field, providing a solid basis for future work.

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...

Relation between film character and wafer alignment: critical alignment issues on HV device for VLSI manufacturing

Science.gov (United States)

Lo, Yi-Chuan; Lee, Chih-Hsiung; Lin, Hsun-Peng; Peng, Chiou-Shian

1998-06-01

Several continuous splits for wafer alignment target topography conditions to improve epitaxy film alignment were applied. The alignment evaluation among former layer pad oxide thickness (250 angstrom - 500 angstrom), drive oxide thickness (6000 angstrom - 10000 angstrom), nitride film thickness (600 angstrom - 1500 angstrom), initial oxide etch (fully wet etch, fully dry etch and dry plus wet etch) will be split to this experiment. Also various epitaxy deposition recipe such as: epitaxy source (SiHCl2 or SiCHCl3) and growth rate (1.3 micrometer/min approximately 2.0 micrometer/min) will be used to optimize the process window for alignment issue. All the reflectance signal and cross section photography of alignment target during NIKON stepper alignment process will be examined. Experimental results show epitaxy recipe plays an important role to wafer alignment. Low growth rate with good performance conformity epitaxy lead to alignment target avoid washout, pattern shift and distortion. All the results (signal monitor and film character) combined with NIKON's stepper standard laser scanning alignment system will be discussed in this paper.

Consistent Alignment of World Embedding Models

Science.gov (United States)

2017-03-02

propose a solution that aligns variations of the same model (or different models) in a joint low-dimensional la- tent space leveraging carefully...representations of linguistic enti- ties, most often referred to as embeddings. This includes techniques that rely on matrix factoriza- tion (Levy & Goldberg ...higher, the variation is much higher as well. As we increase the size of the neighborhood, or improve the quality of our sample by only picking the most

Analysis of the collagen birefringence and the relative attenuation coefficient of health and burned skin irradiated with linearly polarized He-Ne laser

International Nuclear Information System (INIS)

Silva, Daniela de Fatima Teixeira da

2002-01-01

Low-intensity laser therapy is characterized by its ability to induce athermic effects and nondestructive photobiological processes. Although it has been in use for more than 40 years, this phototherapy is still not an established therapeutic modality. The objectives of this study were: to quantify the collagen fibers organization by polarized light microscopy in normal and burned skin samples at day 17 post-injury considering preferential axis as the animal's spinal column and aligning the linear laser polarization in two directions of polarization, parallel or perpendicular to this axis; to determine the relative attenuation coefficient for the intensity light by the technique of imaging the light distribution in normal and burned skin during wound healing process taking only parallel direction of polarization. To reach the objectives, burns about 6 mm in diameter were created with liquid N 2 on the back of the rats and the lesions were irradiated on days 3, 7, 10 and 14 post-wounding, D= 1 J/cm 2 , to investigate the effects of low-intensity linearly polarized He-Ne laser beam on skin wounds healing. Control lesions were not irradiated. The results have demonstrated that: the skin samples irradiated with linearly parallel polarized He-Ne laser beam showed collagen fibers more organized; burned skin samples presents a higher attenuation coefficient than normal skin samples. These results are important to optimize low intensity laser therapy dosimetry on acceleration wound healing. (author)

Nova laser alignment control system

International Nuclear Information System (INIS)

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

1984-01-01

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

Method validation using weighted linear regression models for quantification of UV filters in water samples.

Science.gov (United States)

da Silva, Claudia Pereira; Emídio, Elissandro Soares; de Marchi, Mary Rosa Rodrigues

2015-01-01

This paper describes the validation of a method consisting of solid-phase extraction followed by gas chromatography-tandem mass spectrometry for the analysis of the ultraviolet (UV) filters benzophenone-3, ethylhexyl salicylate, ethylhexyl methoxycinnamate and octocrylene. The method validation criteria included evaluation of selectivity, analytical curve, trueness, precision, limits of detection and limits of quantification. The non-weighted linear regression model has traditionally been used for calibration, but it is not necessarily the optimal model in all cases. Because the assumption of homoscedasticity was not met for the analytical data in this work, a weighted least squares linear regression was used for the calibration method. The evaluated analytical parameters were satisfactory for the analytes and showed recoveries at four fortification levels between 62% and 107%, with relative standard deviations less than 14%. The detection limits ranged from 7.6 to 24.1 ng L(-1). The proposed method was used to determine the amount of UV filters in water samples from water treatment plants in Araraquara and Jau in São Paulo, Brazil. Copyright © 2014 Elsevier B.V. All rights reserved.

Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography

International Nuclear Information System (INIS)

Winkler, Hanspeter; Taylor, Kenneth A.

2006-01-01

An image alignment method for electron tomography is presented which is based on cross-correlation techniques and which includes a simultaneous refinement of the tilt geometry. A coarsely aligned tilt series is iteratively refined with a procedure consisting of two steps for each cycle: area matching and subsequent geometry correction. The first step, area matching, brings into register equivalent specimen regions in all images of the tilt series. It determines four parameters of a linear two-dimensional transformation, not just translation and rotation as is done during the preceding coarse alignment with conventional methods. The refinement procedure also differs from earlier methods in that the alignment references are now computed from already aligned images by reprojection of a backprojected volume. The second step, geometry correction, refines the initially inaccurate estimates of the geometrical parameters, including the direction of the tilt axis, a tilt angle offset, and the inclination of the specimen with respect to the support film or specimen holder. The correction values serve as an indicator for the progress of the refinement. For each new iteration, the correction values are used to compute an updated set of geometry parameters by a least squares fit. Model calculations show that it is essential to refine the geometrical parameters as well as the accurate alignment of the images to obtain a faithful map of the original structure

Energy level alignment at interfaces in organic photovoltaic devices

International Nuclear Information System (INIS)

Opitz, Andreas; Frisch, Johannes; Schlesinger, Raphael; Wilke, Andreas; Koch, Norbert

2013-01-01

Highlights: ► Energy level alignment is crucial for organic solar cell efficiency. ► Photoelectron spectroscopy can reliably determine energy levels of organic material interfaces. ► Care must be taken to avoid even subtle sample damage. -- Abstract: The alignment of energy levels at interfaces in organic photovoltaic devices is crucial for their energy conversion efficiency. Photoelectron spectroscopy (PES) is a well-established and widely used technique for determining the electronic structure of materials; at the same time PES measurements of conjugated organic materials often pose significant challenges, such as obtaining sufficiently defined sample structures and radiation-induced damage of the organic layers. Here we report how these challenges can be tackled to unravel the energy levels at interfaces in organic photovoltaic devices, i.e., electrode/organic and organic/organic interfaces. The electronic structure across entire photovoltaic multilayer devices can thus be reconciled. Finally, general considerations for correlating the electronic structure and the photovoltaic performance of devices will be discussed

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

Science.gov (United States)

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

2013-07-01

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

An improved image alignment procedure for high-resolution transmission electron microscopy.

Science.gov (United States)

Lin, Fang; Liu, Yan; Zhong, Xiaoyan; Chen, Jianghua

2010-06-01

Image alignment is essential for image processing methods such as through-focus exit-wavefunction reconstruction and image averaging in high-resolution transmission electron microscopy. Relative image displacements exist in any experimentally recorded image series due to the specimen drifts and image shifts, hence image alignment for correcting the image displacements has to be done prior to any further image processing. The image displacement between two successive images is determined by the correlation function of the two relatively shifted images. Here it is shown that more accurate image alignment can be achieved by using an appropriate aperture to filter the high-frequency components of the images being aligned, especially for a crystalline specimen with little non-periodic information. For the image series of crystalline specimens with little amorphous, the radius of the filter aperture should be as small as possible, so long as it covers the innermost lattice reflections. Testing with an experimental through-focus series of Si[110] images, the accuracies of image alignment with different correlation functions are compared with respect to the error functions in through-focus exit-wavefunction reconstruction based on the maximum-likelihood method. Testing with image averaging over noisy experimental images from graphene and carbon-nanotube samples, clear and sharp crystal lattice fringes are recovered after applying optimal image alignment. Copyright 2010 Elsevier Ltd. All rights reserved.

Alignment of CEBAF cryomodules

International Nuclear Information System (INIS)

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

1993-06-01

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

Aligning experimental design with bioinformatics analysis to meet discovery research objectives.

Science.gov (United States)

Kane, Michael D

2002-01-01

The utility of genomic technology and bioinformatic analytical support to provide new and needed insight into the molecular basis of disease, development, and diversity continues to grow as more research model systems and populations are investigated. Yet deriving results that meet a specific set of research objectives requires aligning or coordinating the design of the experiment, the laboratory techniques, and the data analysis. The following paragraphs describe several important interdependent factors that need to be considered to generate high quality data from the microarray platform. These factors include aligning oligonucleotide probe design with the sample labeling strategy if oligonucleotide probes are employed, recognizing that compromises are inherent in different sample procurement methods, normalizing 2-color microarray raw data, and distinguishing the difference between gene clustering and sample clustering. These factors do not represent an exhaustive list of technical variables in microarray-based research, but this list highlights those variables that span both experimental execution and data analysis. Copyright 2001 Wiley-Liss, Inc.

Angular dependence of coercivity in isotropically aligned Nd-Fe-B sintered magnets

Science.gov (United States)

Matsuura, Yutaka; Nakamura, Tetsuya; Sumitani, Kazushi; Kajiwara, Kentaro; Tamura, Ryuji; Osamura, Kozo

2018-05-01

In order to understand the coercivity mechanism in Nd-Fe-B sintered magnets, the angular dependence of the coercivity of an isotropically aligned Nd15Co1.0B6Febal. sintered magnet was investigated through magnetization measurements using a vibrating sample magnetometer. These results are compared with the angular dependence calculated under the assumption that the magnetization reversal of each grain follows the Kondorskii law or, in other words, the 1/cos θ law for isotropic alignment distributions. The calculated angular dependence of the coercivity agrees very well with the experiment for magnetic fields applied between angles of 0 and 60°, and it is expected that the magnetization reversal occurs in each grain individually followed the 1/cos θ law. In contrast, this agreement between calculation and experiment is not found for anisotropic Nd-Fe-B samples. This implies that the coercivity of the aligned magnets depends upon the de-pinning of the domain walls from pinning sites. When the de-pinning occurs, it is expected that the domain walls are displaced through several grains at once.

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. Copyright 2015, SLACK Incorporated.

Using sampled-data feedback control and linear feedback synchronization in a new hyperchaotic system

International Nuclear Information System (INIS)

Zhao Junchan; Lu Junan

2008-01-01

This paper investigates control and synchronization of a new hyperchaotic system which was proposed by [Chen A, Lu J-A, Lue J, Yu S. Generating hyperchaotic Lue attractor via state feedback control. Physica A 2006;364:103-10]. Firstly, we give different sampled-data feedback control schemes with the variation of system parameter d. Specifically, we only use one controller to drive the system to the origin when d element of (-0.35, 0), and use two controllers if d element of [0, 1.3]. Next, we combine PC method with linear feedback approach to realize synchronization, and derive similar conclusions with varying d. Numerical simulations are also given to validate the proposed approaches

Flexible and Lightweight Pressure Sensor Based on Carbon Nanotube/Thermoplastic Polyurethane-Aligned Conductive Foam with Superior Compressibility and Stability.

Science.gov (United States)

Huang, Wenju; Dai, Kun; Zhai, Yue; Liu, Hu; Zhan, Pengfei; Gao, Jiachen; Zheng, Guoqiang; Liu, Chuntai; Shen, Changyu

2017-12-06

Flexible and lightweight carbon nanotube (CNT)/thermoplastic polyurethane (TPU) conductive foam with a novel aligned porous structure was fabricated. The density of the aligned porous material was as low as 0.123 g·cm -3 . Homogeneous dispersion of CNTs was achieved through the skeleton of the foam, and an ultralow percolation threshold of 0.0023 vol % was obtained. Compared with the disordered foam, mechanical properties of the aligned foam were enhanced and the piezoresistive stability of the flexible foam was improved significantly. The compression strength of the aligned TPU foam increases by 30.7% at the strain of 50%, and the stress of the aligned foam is 22 times that of the disordered foam at the strain of 90%. Importantly, the resistance variation of the aligned foam shows a fascinating linear characteristic under the applied strain until 77%, which would benefit the application of the foam as a desired pressure sensor. During multiple cyclic compression-release measurements, the aligned conductive CNT/TPU foam represents excellent reversibility and reproducibility in terms of resistance. This nice capability benefits from the aligned porous structure composed of ladderlike cells along the orientation direction. Simultaneously, the human motion detections, such as walk, jump, squat, etc. were demonstrated by using our flexible pressure sensor. Because of the lightweight, flexibility, high compressibility, excellent reversibility, and reproducibility of the conductive aligned foam, the present study is capable of providing new insights into the fabrication of a high-performance pressure sensor.

Factors influencing the alignment of accounting information systems of accepted manufacturing firms in Tehran Stock Exchange

Directory of Open Access Journals (Sweden)

Fazel Tamoradi

2014-03-01

Full Text Available The primary objective of this paper is to detect factors influencing the alignment of accounting information systems for firms in manufacturing sector listed on Tehran Stock Exchange. The concept of alignment has been investigated for many years, and strategic alignment plays essential role in increasing company performance. This paper investigates different levels of alignment and studies the factors, which influence alignment. More specifically, the work concentrates on the alignment between the requirements for accounting information (AIS requirements and the capacity of accounting systems (AIS capacity to build the information, in the specific context of manufacturing in Iran. The research sample consists of 216 companies over the period 2011-2007. The fit between these two sets was explored based on the moderation method and evidences indicate that AIS alignment in some firms was high. In addition, the relationship between the dependent variable and independent variables through multiple regressions yields a positive relationship between these variables.

Correlation between Auroral kilometric radiation and field-aligned currents

International Nuclear Information System (INIS)

Green, J.L.; Saflekos, N.A.; Gurnett, D.A.; Potemra, T.A.

1982-01-01

Simultaneous observations of field-aligned currents (FAC) and auroral kilometric radiation (AKR) are compared from the polar-orbiting satellites Triad and Hawkeye. The Triad observations were restricted to the evening-to-midnight local time sector (1900 to 0100 hours magnetic local time) in the northern hemisphere. This is the region in which the most intense storms of AKR are believed to originate. The Hawkeye observations were restricted to when the satellite was in the AKR emission cone in the northern hemisphere and at radial distances > or =7R/sub E/ (earth radii) to avoid local propagation cutoff effects. A(R/7R/sub E/) 2 normalization to the power flux measurements of the kilometric radiation from Hawkeye is used to take into account the radial dependence of this radiation and to scale all intensity measurements so that they are independent of Hawkeye's position in the emission cone. Integrated field-aligned current intensities from Triad are determined from the observed transverse magnetic field disturbances. There appears to be a weak correlation between AKR intensity and the integrated current sheet intensity of field-aligned currents. In general, as the intensity of auroral kilometric radiation increases so does the integrated auroral zone current sheet intensity increase. Statistically, the linear correlation coefficient between the log of the AKR power flux and the log of the current sheet intensity is 0.57. During weak AKR bursts ( - 18 W m - 2 Hz - 1 ), Triad always observed weak FAC'S ( - 1 ), and when Triad observed large FAC's (> or =0.6 A m - 1 ), the AKR intensity from Hawkeye was moderately intense (10 - 5 to 10 - 14 W m - 2 Hz - 1 ) to intense (>10 - 14 W m - 2 Hz - 1 ). It is not clear from these preliminary results what the exact role is that auroral zone field-aligned currents play in the generation or amplification of auroral kilometric radiation

Optimization of bicelle lipid composition and temperature for EPR spectroscopy of aligned membranes.

Science.gov (United States)

McCaffrey, Jesse E; James, Zachary M; Thomas, David D

2015-01-01

We have optimized the magnetic alignment of phospholipid bilayered micelles (bicelles) for EPR spectroscopy, by varying lipid composition and temperature. Bicelles have been extensively used in NMR spectroscopy for several decades, in order to obtain aligned samples in a near-native membrane environment and take advantage of the intrinsic sensitivity of magnetic resonance to molecular orientation. Recently, bicelles have also seen increasing use in EPR, which offers superior sensitivity and orientational resolution. However, the low magnetic field strength (less than 1 T) of most conventional EPR spectrometers results in homogeneously oriented bicelles only at a temperature well above physiological. To optimize bicelle composition for magnetic alignment at reduced temperature, we prepared bicelles containing varying ratios of saturated (DMPC) and unsaturated (POPC) phospholipids, using EPR spectra of a spin-labeled fatty acid to assess alignment as a function of lipid composition and temperature. Spectral analysis showed that bicelles containing an equimolar mixture of DMPC and POPC homogeneously align at 298 K, 20 K lower than conventional DMPC-only bicelles. It is now possible to perform EPR studies of membrane protein structure and dynamics in well-aligned bicelles at physiological temperatures and below. Copyright © 2014 Elsevier Inc. All rights reserved.

Unraveling the growth of vertically aligned multi-walled carbon nanotubes by chemical vapor deposition

International Nuclear Information System (INIS)

Ramirez, A; Royo, C; Latorre, N; Mallada, R; Monzón, A; Tiggelaar, R M

2014-01-01

The interaction between the main operational variables during the growth of vertically aligned multiwalled carbon nanotubes (VA-MWCNTs) by catalytic chemical vapor deposition is studied. In this contribution, we report the influence of the carbon source (i.e. acetylene, ethylene and propylene), the reaction/activation temperature, the rate of heating, the reaction time, the metal loading, and the metallic nanoparticle size and distribution on the growth and alignment of carbon nanotubes. Fe/Al thin films deposited onto silicon samples by electron-beam evaporation are used as catalyst. A phenomenological growth mechanism is proposed to explain the interaction between these multiple factors. Three different outcomes of the synthesis process are found: i) formation of forests of non-aligned, randomly oriented multi-walled carbon nanotubes, ii) growth of vertically aligned tubes with a thin and homogeneous carbonaceous layer on the top, and iii) formation of vertically aligned carbon nanotubes. This carbonaceous layer (ii) has not been reported before. The main requirements to promote vertically aligned carbon nanotube growth are determined. (paper)

Flow-alignment of bicellar lipid mixtures: orientations of probe molecules and membrane-associated biomacromolecules in lipid membranes studied with polarized light

KAUST Repository

Kogan, Maxim; Beke-Somfai, Tamá s; Nordé n, Bengt

2011-01-01

Bicelles are excellent membrane-mimicking hosts for a dynamic and structural study of solutes with NMR, but the magnetic fields required for their alignment are hard to apply to optical conditions. Here we demonstrate that bicellar mixtures can be aligned by shear forces in a Couette flow cell, to provide orientation of membrane-bound retinoic acid, pyrene and cytochrome c (cyt c) protein, conveniently studied with linear dichroism spectroscopy. © 2011 The Royal Society of Chemistry.

A 30 GHz 5-TeV Linear Collider

International Nuclear Information System (INIS)

Wilson, Perry B

2003-01-01

We present parameters for a linear collider with a 3 to 5 TeV center-of-mass energy that utilizes conventional rf technology operating at a frequency around 30 GHz. We discuss the scaling laws and assumed limitations that lead to the parameters described and we compare the merits and liabilities of different technological options including rf power source, accelerator structure, and final focus system design. Finally, we outline the components of the collider while specifying the required alignment and construction tolerances

Surveying and optical tooling technologies combined to align a skewed beamline at the LAMPF accelerator

International Nuclear Information System (INIS)

Bauke, W.; Clark, D.A.; Trujillo, P.B.

1985-01-01

Optical Tooling evolved from traditional surveying, and both technologies are sometimes used interchangeably in large industrial installations, since the instruments and their specialized adapters and supports complement each other well. A unique marriage of both technologies was accomplished in a novel application at LAMPF, the Los Alamos Meson Physics Facility. LAMPF consists of a linear accelerator with multiple target systems, one of which had to be altered to accommodate a new beamline for a neutrino experiment. The new line was to be installed into a crowded beam tunnel and had to be skewed and tilted in compound angles to avoid existing equipment. In this paper we describe how Optical Tooling was used in conjunction with simple alignment and reference fixtures to set fiducials on the magnets and other mechanical components of the beamline, and how theodolites and sight levels were then adapted to align these components along the calculated skew planes. Design tolerances are compared with measured alignment results

Unified Alignment of Protein-Protein Interaction Networks.

Science.gov (United States)

Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

2017-04-19

Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

Non-Linear Approximation of Bayesian Update

KAUST Repository

Litvinenko, Alexander

2016-01-01

We develop a non-linear approximation of expensive Bayesian formula. This non-linear approximation is applied directly to Polynomial Chaos Coefficients. In this way, we avoid Monte Carlo sampling and sampling error. We can show that the famous Kalman Update formula is a particular case of this update.

Non-Linear Approximation of Bayesian Update

KAUST Repository

Litvinenko, Alexander

2016-06-23

We develop a non-linear approximation of expensive Bayesian formula. This non-linear approximation is applied directly to Polynomial Chaos Coefficients. In this way, we avoid Monte Carlo sampling and sampling error. We can show that the famous Kalman Update formula is a particular case of this update.

Precision alignment device

Science.gov (United States)

Jones, N.E.

1988-03-10

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

Curricular Alignment: A Re-examination.

Science.gov (United States)

Anderson, Lorin W.

2002-01-01

Examines key differences among content coverage, opportunity to learn, and curriculum alignment, suggesting that the revised Taxonomy provides a framework for analyzing curriculum alignment and illustrating how the Taxonomy Table can be used to estimate curriculum alignment. The paper notes that the revised Taxonomy enables educators to probe…

Amplitude differences least squares method applied to temporal cardiac beat alignment

International Nuclear Information System (INIS)

Correa, R O; Laciar, E; Valentinuzzi, M E

2007-01-01

High resolution averaged ECG is an important diagnostic technique in post-infarcted and/or chagasic patients with high risk of ventricular tachycardia (VT). It calls for precise determination of the synchronism point (fiducial point) in each beat to be averaged. Cross-correlation (CC) between each detected beat and a reference beat is, by and large, the standard alignment procedure. However, the fiducial point determination is not precise in records contaminated with high levels of noise. Herein, we propose an alignment procedure based on the least squares calculation of the amplitude differences (LSAD) between the ECG samples and a reference or template beat. Both techniques, CC and LSAD, were tested in high resolution ECG's corrupted with white noise and 50 Hz line interference of varying amplitudes (RMS range: 0-100μV). Results point out that LSDA produced a lower alignment error in all contaminated records while in those blurred by power line interference better results were found only within the 0-40 μV range. It is concluded that the proposed method represents a valid alignment alternative

Defining Spino-Pelvic Alignment Thresholds: Should Operative Goals in Adult Spinal Deformity Surgery Account for Age?

Science.gov (United States)

Lafage, Renaud; Schwab, Frank; Challier, Vincent; Henry, Jensen K; Gum, Jeffrey; Smith, Justin; Hostin, Richard; Shaffrey, Christopher; Kim, Han J; Ames, Christopher; Scheer, Justin; Klineberg, Eric; Bess, Shay; Burton, Douglas; Lafage, Virginie

2016-01-01

Retrospective review of prospective, multicenter database. The aim of the study was to determine age-specific spino-pelvic parameters, to extrapolate age-specific Oswestry Disability Index (ODI) values from published Short Form (SF)-36 Physical Component Score (PCS) data, and to propose age-specific realignment thresholds for adult spinal deformity (ASD). The Scoliosis Research Society-Schwab classification offers a framework for defining alignment in patients with ASD. Although age-specific changes in spinal alignment and patient-reported outcomes have been established in the literature, their relationship in the setting of ASD operative realignment has not been reported. ASD patients who received operative or nonoperative treatment were consecutively enrolled. Patients were stratified by age, consistent with published US-normative values (Norms) of the SF-36 PCS (75  y old). At baseline, relationships between between radiographic spino-pelvic parameters (lumbar-pelvic mismatch [PI-LL], pelvic tilt [PT], sagittal vertical axis [SVA], and T1 pelvic angle [TPA]), age, and PCS were established using linear regression analysis; normative PCS values were then used to establish age-specific targets. Correlation analysis with ODI and PCS was used to determine age-specific ideal alignment. Baseline analysis included 773 patients (53.7 y old, 54% operative, 83% female). There was a strong correlation between ODI and PCS (r = 0.814, P US-normative ODI by age group. Linear regression analysis (all with r > 0.510, P US-normative PCS values demonstrated that ideal spino-pelvic values increased with age, ranging from PT = 10.9 degrees, PI-LL = -10.5 degrees, and SVA = 4.1 mm for patients under 35 years to PT = 28.5 degrees, PI-LL = 16.7 degrees, and SVA = 78.1 mm for patients over 75 years. Clinically, older patients had greater compensation, more degenerative loss of lordosis, and were more pitched forward. This study demonstrated that

libgapmis: extending short-read alignments.

Science.gov (United States)

Alachiotis, Nikolaos; Berger, Simon; Flouri, Tomáš; Pissis, Solon P; Stamatakis, Alexandros

2013-01-01

A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. We present libgapmis, a library for extending pairwise short-read alignments. We

A Glucose Biosensor Using CMOS Potentiostat and Vertically Aligned Carbon Nanofibers.

Science.gov (United States)

Al Mamun, Khandaker A; Islam, Syed K; Hensley, Dale K; McFarlane, Nicole

2016-08-01

This paper reports a linear, low power, and compact CMOS based potentiostat for vertically aligned carbon nanofibers (VACNF) based amperometric glucose sensors. The CMOS based potentiostat consists of a single-ended potential control unit, a low noise common gate difference-differential pair transimpedance amplifier and a low power VCO. The potentiostat current measuring unit can detect electrochemical current ranging from 500 nA to 7 [Formula: see text] from the VACNF working electrodes with high degree of linearity. This current corresponds to a range of glucose, which depends on the fiber forest density. The potentiostat consumes 71.7 [Formula: see text] of power from a 1.8 V supply and occupies 0.017 [Formula: see text] of chip area realized in a 0.18 [Formula: see text] standard CMOS process.

Geodetic alignment of laser power installations

International Nuclear Information System (INIS)

Shtorm, V.V.; Gostev, A.M.; Drobikov, A.V.

1989-01-01

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

Intrinsic alignment of redMaPPer clusters: cluster shape-matter density correlation

Science.gov (United States)

van Uitert, Edo; Joachimi, Benjamin

2017-07-01

We measure the alignment of the shapes of galaxy clusters, as traced by their satellite distributions, with the matter density field using the public redMaPPer catalogue based on Sloan Digital Sky Survey-Data Release 8 (SDSS-DR8), which contains 26 111 clusters up to z ˜ 0.6. The clusters are split into nine redshift and richness samples; in each of them, we detect a positive alignment, showing that clusters point towards density peaks. We interpret the measurements within the tidal alignment paradigm, allowing for a richness and redshift dependence. The intrinsic alignment (IA) amplitude at the pivot redshift z = 0.3 and pivot richness λ = 30 is A_IA^gen=12.6_{-1.2}^{+1.5}. We obtain tentative evidence that the signal increases towards higher richness and lower redshift. Our measurements agree well with results of maxBCG clusters and with dark-matter-only simulations. Comparing our results to the IA measurements of luminous red galaxies, we find that the IA amplitude of galaxy clusters forms a smooth extension towards higher mass. This suggests that these systems share a common alignment mechanism, which can be exploited to improve our physical understanding of IA.

Determination of tartrazine in beverage samples by stopped-flow analysis and three-way multivariate calibration of non-linear kinetic-spectrophotometric data.

Science.gov (United States)

Schenone, Agustina V; Culzoni, María J; Marsili, Nilda R; Goicoechea, Héctor C

2013-06-01

The performance of MCR-ALS was studied in the modeling of non-linear kinetic-spectrophotometric data acquired by a stopped-flow system for the quantitation of tartrazine in the presence of brilliant blue and sunset yellow FCF as possible interferents. In the present work, MCR-ALS and U-PCA/RBL were firstly applied to remove the contribution of unexpected components not included in the calibration set. Secondly, a polynomial function was used to model the non-linear data obtained by the implementation of the algorithms. MCR-ALS was the only strategy that allowed the determination of tartrazine in test samples accurately. Therefore, it was applied for the analysis of tartrazine in beverage samples with minimum sample preparation and short analysis time. The proposed method was validated by comparison with a chromatographic procedure published in the literature. Mean recovery values between 98% and 100% and relative errors of prediction values between 4% and 9% were indicative of the good performance of the method. Copyright © 2012 Elsevier Ltd. All rights reserved.

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

Science.gov (United States)

Richmond, Nicola J.; Abrams, Charlene A.; Wolohan, Philippa R. N.; Abrahamian, Edmond; Willett, Peter; Clark, Robert D.

2006-09-01

Alignment of multiple ligands based on shared pharmacophoric and pharmacosteric features is a long-recognized challenge in drug discovery and development. This is particularly true when the spatial overlap between structures is incomplete, in which case no good template molecule is likely to exist. Pair-wise rigid ligand alignment based on linear assignment (the LAMDA algorithm) has the potential to address this problem (Richmond et al. in J Mol Graph Model 23:199-209, 2004). Here we present the version of LAMDA embodied in the GALAHAD program, which carries out multi-way alignments by iterative construction of hypermolecules that retain the aggregate as well as the individual attributes of the ligands. We have also generalized the cost function from being purely atom-based to being one that operates on ionic, hydrogen bonding, hydrophobic and steric features. Finally, we have added the ability to generate useful partial-match 3D search queries from the hypermolecules obtained. By running frozen conformations through the GALAHAD program, one can utilize the extended version of LAMDA to generate pharmacophores and pharmacosteres that agree well with crystal structure alignments for a range of literature datasets, with minor adjustments of the default parameters generating even better models. Allowing for inclusion of partial match constraints in the queries yields pharmacophores that are consistently a superset of full-match pharmacophores identified in previous analyses, with the additional features representing points of potentially beneficial interaction with the target.

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

Directory of Open Access Journals (Sweden)

Giovanni Ciriello

Full Text Available 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.

FMIT alignment cart

International Nuclear Information System (INIS)

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

1981-01-01

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

Aligned and Electrospun Piezoelectric Polymer Fiber Assembly and Scaffold

Science.gov (United States)

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

2015-01-01

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

A beam-based alignment technique for correction of accelerator structure misalignments

International Nuclear Information System (INIS)

Kubo, K.; Raubenheimer, T.O.

1994-08-01

This paper describes a method of reducing the transverse emittance dilution in linear colliders due to transverse wakefields arising-from misaligned accelerator structures. The technique is a generalization of the Wake-Free correction algorithm. The structure alignment errors are measured locally by varying the bunch charge and/or bunch length and measuring the change in the beam trajectory. The misalignments can then be corrected by varying the beam trajectory or moving structures. The results of simulations are presented demonstrating the viability of the technique

Alignment method for parabolic trough solar concentrators

Science.gov (United States)

Diver, Richard B [Albuquerque, NM

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.

Extrinsic Factors as Component Positions to Bone and Intrinsic Factors Affecting Postoperative Rotational Limb Alignment in Total Knee Arthroplasty.

Science.gov (United States)

Mochizuki, Tomoharu; Sato, Takashi; Tanifuji, Osamu; Watanabe, Satoshi; Kobayashi, Koichi; Endo, Naoto

2018-02-13

This study aimed to identify the factors affecting postoperative rotational limb alignment of the tibia relative to the femur. We hypothesized that not only component positions but also several intrinsic factors were associated with postoperative rotational limb alignment. This study included 99 knees (90 women and 9 men) with a mean age of 77 ± 6 years. A three-dimensional (3D) assessment system was applied under weight-bearing conditions to biplanar long-leg radiographs using 3D-to-2D image registration technique. The evaluation parameters were (1) component position; (2) preoperative and postoperative coronal, sagittal, and rotational limb alignment; (3) preoperative bony deformity, including femoral torsion, condylar twist angle, and tibial torsion; and (4) preoperative and postoperative range of motion (ROM). In multiple linear regression analysis using a stepwise procedure, postoperative rotational limb alignment was associated with the following: (1) rotation of the component position (tibia: β = 0.371, P intrinsic factors, such as preoperative rotational limb alignment, ROM, and tibial torsion, affected postoperative rotational limb alignment. On a premise of correct component positions, the intrinsic factors that can be controlled by surgeons should be taken care. In particular, ROM is necessary to be improved within the possible range to acquire better postoperative rotational limb alignment. Copyright © 2018 Elsevier Inc. All rights reserved.

Probabilistic biological network alignment.

Science.gov (United States)

Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

Fabrication of Vertically Aligned CNT Composite for Membrane Applications Using Chemical Vapor Deposition through In Situ Polymerization

Directory of Open Access Journals (Sweden)

Munir Mohammad

2013-01-01

Full Text Available We report the fabrication of vertically aligned carbon nanotubes (CNT composite using thermal chemical vapor deposition (CVD. A forest of vertically aligned CNTs was grown using catalytic CVD. Fluorocarbon polymer, films were deposited in the spaces between vertically aligned MWCNTs using thermal CVD apparatus developed in-house. The excessive polymer top layer was etched by exposing the sample to water plasma. Infrared spectroscopy confirmed the attachment of functional groups to CNTs. Alignment of CNTs, deposition of polymer and postetched specimens were analyzed by field emission scanning electron microscope (FE-SEM. Uniform distribution of monomodel vertically aligned CNTs embedded in the deposited polymer matrix was observed in the micrograph. Observed uniform distribution otherwise is not possible using conventional techniques such as spin coating.

A primer on linear models

CERN Document Server

Monahan, John F

2008-01-01

Preface Examples of the General Linear Model Introduction One-Sample Problem Simple Linear Regression Multiple Regression One-Way ANOVA First Discussion The Two-Way Nested Model Two-Way Crossed Model Analysis of Covariance Autoregression Discussion The Linear Least Squares Problem The Normal Equations The Geometry of Least Squares Reparameterization Gram-Schmidt Orthonormalization Estimability and Least Squares Estimators Assumptions for the Linear Mean Model Confounding, Identifiability, and Estimability Estimability and Least Squares Estimators F

Hybrid vehicle motor alignment

Science.gov (United States)

Levin, Michael Benjamin

2001-07-03

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

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

International Nuclear Information System (INIS)

Potter, J.D.

1995-01-01

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

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.

Tasting soil fungal diversity with earth tongues: phylogenetic test of SATe alignments for environmental ITS data.

Directory of Open Access Journals (Sweden)

Zheng Wang

Full Text Available An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes, a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with Geoglossum but not with Trichoglossum earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit.

Beam-based alignment and tuning procedures for e+e- collider final focus systems

International Nuclear Information System (INIS)

Bulos, F.; Burke, D.; Helm, R.; Irwin, J.; Odian, A.; Roy, G.; Ruth, R.; Yamamoto

1991-01-01

For future linear colliders, with very small emittances and beam sizes and demanding tolerances on final focus system alignment and magnet errors, it becomes increasingly important to use the beam as a diagnostic tool. The authors report here procedures they have identified and will be implemented in the Final Focus Test Beam at SLAC incorporating (1) quadrupole strength changes, (2) central orbit modifications, (3) spot size measurements, and (4) beam stability monitoring

Effects of collisions on linear and non-linear spectroscopic line shapes

International Nuclear Information System (INIS)

Berman, P.R.

1978-01-01

A fundamental physical problem is the determination of atom-atom, atom-molecule and molecule-molecule differential and total scattering cross sections. In this work, a technique for studying atomic and molecular collisions using spectroscopic line shape analysis is discussed. Collisions occurring within an atomic or molecular sample influence the sample's absorptive or emissive properties. Consequently the line shapes associated with the linear or non-linear absorption of external fields by an atomic system reflect the collisional processes occurring in the gas. Explicit line shape expressions are derived characterizing linear or saturated absorption by two-or three-level 'active' atoms which are undergoing collisions with perturber atoms. The line shapes may be broadened, shifted, narrowed, or distorted as a result of collisions which may be 'phase-interrupting' or 'velocity-changing' in nature. Systematic line shape studies can be used to obtain information on both the differential and total active atom-perturber scattering cross sections. (Auth.)

Feasibility study of multipoint based laser alignment system for CLIC

CERN Document Server

Stern, G; Mainaud-Durand, H; Piedigrossi, D; Geiger, A

2012-01-01

CLIC (Compact LInear Collider) is a study for a future electron-positron collider that would allow physicists to explore a new energy region beyond the capabilities oftoday’s particle accelerators. Alignment is one of the major challenges within the CLIC study in order to achieve the high requirement of a multi-TeV center of mass colliding beam energy range (nominal 3 TeV). To reach this energy in a realistic and cost efficient scenario all accelerator components have to be aligned with an accuracy of 10 μm over a sliding window of 200 m. The demand for a straight line reference is so far based on stretched wires coupled with Wire Positioning Sensors (WPS). These solutions are currently further developed inorder to reduce the drawbacks which are mainly given by their costs and difficult implementation. However, it should be validated through inter-comparison with a solution ideally based on a different physical principle. Therefore, a new metrological approach is proposed using a laser beam as straight lin...

Modified alignment CGHs for aspheric surface test

Science.gov (United States)

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

2009-08-01

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

Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

Science.gov (United States)

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

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.

Dual-Mode SERS-Fluorescence Immunoassay Using Graphene Quantum Dot Labeling on One-Dimensional Aligned Magnetoplasmonic Nanoparticles.

Science.gov (United States)

Zou, Fengming; Zhou, Hongjian; Tan, Tran Van; Kim, Jeonghyo; Koh, Kwangnak; Lee, Jaebeom

2015-06-10

A novel dual-mode immunoassay based on surface-enhanced Raman scattering (SERS) and fluorescence was designed using graphene quantum dot (GQD) labels to detect a tuberculosis (TB) antigen, CFP-10, via a newly developed sensing platform of linearly aligned magnetoplasmonic (MagPlas) nanoparticles (NPs). The GQDs were excellent bilabeling materials for simultaneous Raman scattering and photoluminescence (PL). The one-dimensional (1D) alignment of MagPlas NPs simplified the immunoassay process and enabled fast, enhanced signal transduction. With a sandwich-type immunoassay using dual-mode nanoprobes, both SERS signals and fluorescence images were recognized in a highly sensitive and selective manner with a detection limit of 0.0511 pg mL(-1).

Application of probabilistic modelling for the uncertainty evaluation of alignment measurements of large accelerator magnets assemblies

Science.gov (United States)

Doytchinov, I.; Tonnellier, X.; Shore, P.; Nicquevert, B.; Modena, M.; Mainaud Durand, H.

2018-05-01

Micrometric assembly and alignment requirements for future particle accelerators, and especially large assemblies, create the need for accurate uncertainty budgeting of alignment measurements. Measurements and uncertainties have to be accurately stated and traceable, to international standards, for metre-long sized assemblies, in the range of tens of µm. Indeed, these hundreds of assemblies will be produced and measured by several suppliers around the world, and will have to be integrated into a single machine. As part of the PACMAN project at CERN, we proposed and studied a practical application of probabilistic modelling of task-specific alignment uncertainty by applying a simulation by constraints calibration method. Using this method, we calibrated our measurement model using available data from ISO standardised tests (10360 series) for the metrology equipment. We combined this model with reference measurements and analysis of the measured data to quantify the actual specific uncertainty of each alignment measurement procedure. Our methodology was successfully validated against a calibrated and traceable 3D artefact as part of an international inter-laboratory study. The validated models were used to study the expected alignment uncertainty and important sensitivity factors in measuring the shortest and longest of the compact linear collider study assemblies, 0.54 m and 2.1 m respectively. In both cases, the laboratory alignment uncertainty was within the targeted uncertainty budget of 12 µm (68% confidence level). It was found that the remaining uncertainty budget for any additional alignment error compensations, such as the thermal drift error due to variation in machine operation heat load conditions, must be within 8.9 µm and 9.8 µm (68% confidence level) respectively.

Using Linear and Non-Linear Temporal Adjustments to Align Multiple Phenology Curves, Making Vegetation Status and Health Directly Comparable

Science.gov (United States)

Hargrove, W. W.; Norman, S. P.; Kumar, J.; Hoffman, F. M.

2017-12-01

National-scale polar analysis of MODIS NDVI allows quantification of degree of seasonality expressed by local vegetation, and also selects the most optimum start/end of a local "phenological year" that is empirically customized for the vegetation that is growing at each location. Interannual differences in timing of phenology make direct comparisons of vegetation health and performance between years difficult, whether at the same or different locations. By "sliding" the two phenologies in time using a Procrustean linear time shift, any particular phenological event or "completion milestone" can be synchronized, allowing direct comparison of differences in timing of other remaining milestones. Going beyond a simple linear translation, time can be "rubber-sheeted," compressed or dilated. Considering one phenology curve to be a reference, the second phenology can be "rubber-sheeted" to fit that baseline as well as possible by stretching or shrinking time to match multiple control points, which can be any recognizable phenological events. Similar to "rubber sheeting" to georectify a map inside a GIS, rubber sheeting a phenology curve also yields a warping signature that shows at every time and every location how many days the adjusted phenology is ahead or behind the phenological development of the reference vegetation. Using such temporal methods to "adjust" phenologies may help to quantify vegetation impacts from frost, drought, wildfire, insects and diseases by permitting the most commensurate quantitative comparisons with unaffected vegetation.

Definition of a reference metrology network for the positioning of a large linear accelerator

International Nuclear Information System (INIS)

Becker, F.

2003-12-01

This thesis is a study of the Compact Linear Collider (CLIC) alignment system, a project of linear accelerator of about 30 km long of the European Organization for Nuclear Research (CERN). The pre-alignment tolerance on the transverse positions of the components of the CLIC linacs is typically ten microns over distances of 200 m. This research is a consequence of 10 years work, where several sets of special sensors dedicated to metrology have been adapted for the CLIC project. Most of these sensors deliver measurements linked to geometric references sensitive to gravity fluctuation. An important part of this work is therefore dedicated to study the gravity disruptions as a high level of accuracy is required. The parameters to take into account in the use of the hydrostatic leveling have thus been highlighted. A proposal of configuration of the system alignment based on a selection of sensors has also been given in this research. Computer models of different possible configurations have been presented. As the existing computing software was inappropriate, a new object oriented software package has been developed, to ensure future upgrades. An optimized configuration of the network has been defined from a set of simulations. Finally, due to problems in the use of hydrostatic leveling systems, a solution based on the use of a long laser beam as an alternative solution is discussed. (author)

Chromatic bifocus alignment system for SR stepper

International Nuclear Information System (INIS)

Miyatake, Tsutomu

1991-01-01

A new alignment system developed for synchrotron radiation (SR) X-ray stepper is described. The alignment system has three key elements as follows. The first is a chromatic bifocus optics which observe high contrast bright images of alignment marks printed on a mask and a wafer. The second is broad band light illumination to observe the wafer alignment mark images which is unaffected by resist film coated on a wafer. The third is a new correlation function which is used in measuring of displacement between a mask and a wafer. The alignment system has achieved alignment accuracy on the order of 0.01 μm. The experimental results of this alignment system are discussed in this paper. (author)

Tracing magnetic fields with aligned grains

International Nuclear Information System (INIS)

Lazarian, A.

2007-01-01

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

DNAAlignEditor: DNA alignment editor tool

Directory of Open Access Journals (Sweden)

Guill Katherine E

2008-03-01

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

Status report on the alignment activities at SLAC

International Nuclear Information System (INIS)

Le Cocq, Catherine; Fuss, Brian; Ruland, Robert

2003-01-01

This report mainly focuses on the Alignment Engineering Group, which deals with all aspects of activities involving surveying and alignment at SLAC (Stanford Linear Accelerator Center). These activities are field work, ongoing studies and mapping effort. The majority of fieldwork at SLAC is initiated by the various current physics experiments. As PEP-II switched into operational mode, another major project was fully ramping up: SPEAR. The Stanford Synchrotron Radiation Laboratory (SSRL) had been preparing the upgrade SPEAR3 (3 GeV, 200 mA). Currently the effort has been to remap the entire SPEAR2 ring including existing magnets but also to map and tie in the connected booster ring. Laser trackers, total stations, and digital levels were used and substantial post processing was necessary to tie everything together. In parallel with field works, several instrumentation studies are in progress on laser tracker and total station, leveling instrumentation and gyro theodolites. Further enhancements have been included in the core network analysis package used at SLAC (LEGO). To keep up with the new installation, SLAC is undergoing an update of its site map. Overall this is a very interesting and dynamic time at SLAC, which celebrated its 40th anniversary on October 2nd 2002. (Y. Tanaka)

MEMS Integrated Submount Alignment for Optoelectronics

Science.gov (United States)

Shakespeare, W. Jeffrey; Pearson, Raymond A.; Grenestedt, Joachim L.; Hutapea, Parsaoran; Gupta, Vikas

2005-02-01

One of the most expensive and time-consuming production processes for single-mode fiber-optic components is the alignment of the photonic chip or waveguide to the fiber. The alignment equipment is capital intensive and usually requires trained technicians to achieve desired results. Current technology requires active alignment since tolerances are only ~0.2 μ m or less for a typical laser diode. This is accomplished using piezoelectric actuated stages and active optical feedback. Joining technologies such as soldering, epoxy bonding, or laser welding may contribute significant postbond shift, and final coupling efficiencies are often less than 80%. This paper presents a method of adaptive optical alignment to freeze in place directly on an optical submount using a microelectromechanical system (MEMS) shape memory alloy (SMA) actuation technology. Postbond shift is eliminated since the phase change is the alignment actuation. This technology is not limited to optical alignment but can be applied to a variety of MEMS actuations, including nano-actuation and nano-alignment for biomedical applications. Experimental proof-of-concept results are discussed, and a simple analytical model is proposed to predict the stress strain behavior of the optical submount. Optical coupling efficiencies and alignment times are compared with traditional processes. The feasibility of this technique in high-volume production is discussed.

Simulations of the Static Tuning for the TESLA Linear Collider

CERN Document Server

Schulte, Daniel

2003-01-01

At the heart of the TESLA linear collider are the two 10 km long superconducting linacs. A linac is constructed from 858 cryomodules each containing 12 nine-cell 1.3 GHz superconducting cavities. 355 quadrupoles provide the necessary beam focusing. The advantages of low-frequency superconducting RF in terms of wakefield behaviour are well known, and the TESLA alignment tolerances are relatively loose. However, the effects of cavity tilts and their impact of the linac beam-based alignment algorithms have until recently not been fully investigated. In addition, the strong sensitivity to correlated emittance growth due to the high beam-beam disruption parameter makes it desirable to control the linac emittance down to a few percent. In this report we discuss various static tuning algorithms and present new simulation results. Discussions of the relative merits and applicability of the methods is also discussed.

A cross-species alignment tool (CAT)

DEFF Research Database (Denmark)

Li, Heng; Guan, Liang; Liu, Tao

2007-01-01

BACKGROUND: The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more...... sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web...... at http://xat.sourceforge.net/. CONCLUSIONS: Examined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT...

Methods in ALFA Alignment

CERN Document Server

Melendez, Jordan

2014-01-01

This note presents two model-independent methods for use in the alignment of the ALFA forward detectors. Using a Monte Carlo simulated LHC run at \\beta = 90m and \\sqrt{s} = 7 TeV, the Kinematic Peak alignment method is utilized to reconstruct the Mandelstam momentum transfer variable t for single-diractive protons. The Hot Spot method uses fluctuations in the hitmap density to pinpoint particular regions in the detector that could signal a misalignment. Another method uses an error function fit to find the detector edge. With this information, the vertical alignment can be determined.

Gratitude facilitates private conformity: A test of the social alignment hypothesis.

Science.gov (United States)

Ng, Jomel W X; Tong, Eddie M W; Sim, Dael L Y; Teo, Samantha W Y; Loy, Xingqi; Giesbrecht, Timo

2017-03-01

Past research has established clear support for the prosocial function of gratitude in improving the well-being of others. The present research provides evidence for another hypothesized function of gratitude: the social alignment function, which enhances the tendency of grateful individuals to follow social norms. We tested the social alignment hypothesis of gratitude in 2 studies with large samples. Using 2 different conformity paradigms, participants were subjected to a color judgment task (Experiment 1) and a material consumption task (Experiment 2). They were provided with information showing choices allegedly made by others, but were allowed to state their responses in private. Supporting the social alignment hypothesis, the results showed that induced gratitude increased private conformity. Specifically, participants induced to feel gratitude were more likely to conform to the purportedly popular choice, even if the option was factually incorrect (Experiment 1). This effect appears to be specific to gratitude; induction of joy produced significantly less conformity than gratitude (Experiment 2). We discuss whether the social alignment function provides a behavioral pathway in the role of gratitude in building social relationships. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

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.

On the use of small integrating spheres to improve the linearity range of RASNIKS systems

International Nuclear Information System (INIS)

Alberdi, J.; Burgos, C.; Ferrando, A.; Molinero, A.; Schvachkin, V.; Figueroa, C.F.; Matorras, F.; Rodrigo, T.; Ruiz, A.; Vila, I.

1997-10-01

Rasniks elements will be used in the CMS alignment system. The large displacements of the different sub detectors expected in the CMS experiment demands large linearity response of this system. By the use of a small integrating sphere we have optimized the source definition such that a factor three improvement in the linearity range with respect to conventional Rasniks configurations is obtained. The response range reached coincides with the maximum one can get with the components used in the test

Alignment system for SGII-Up laser facility

Science.gov (United States)

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

2018-03-01

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

Improving the quality of biomarker candidates in untargeted metabolomics via peak table-based alignment of comprehensive two-dimensional gas chromatography-mass spectrometry data

Science.gov (United States)

Bean, Heather D.; Hill, Jane E.; Dimandja, Jean-Marie D.

2015-01-01

The potential of high-resolution analytical technologies like GC×GC/TOF MS in untargeted metabolomics and biomarker discovery has been limited by the development of fully automated software that can efficiently align and extract information from multiple chromatographic data sets. In this work we report the first investigation on a peak-by-peak basis of the chromatographic factors that impact GC×GC data alignment. A representative set of 16 compounds of different chromatographic characteristics were followed through the alignment of 63 GC×GC chromatograms. We found that varying the mass spectral match parameter had a significant influence on the alignment for poorly- resolved peaks, especially those at the extremes of the detector linear range, and no influence on well- chromatographed peaks. Therefore, optimized chromatography is required for proper GC×GC data alignment. Based on these observations, a workflow is presented for the conservative selection of biomarker candidates from untargeted metabolomics analyses. PMID:25857541

Improving the quality of biomarker candidates in untargeted metabolomics via peak table-based alignment of comprehensive two-dimensional gas chromatography-mass spectrometry data.

Science.gov (United States)

Bean, Heather D; Hill, Jane E; Dimandja, Jean-Marie D

2015-05-15

The potential of high-resolution analytical technologies like GC×GC/TOF MS in untargeted metabolomics and biomarker discovery has been limited by the development of fully automated software that can efficiently align and extract information from multiple chromatographic data sets. In this work we report the first investigation on a peak-by-peak basis of the chromatographic factors that impact GC×GC data alignment. A representative set of 16 compounds of different chromatographic characteristics were followed through the alignment of 63 GC×GC chromatograms. We found that varying the mass spectral match parameter had a significant influence on the alignment for poorly-resolved peaks, especially those at the extremes of the detector linear range, and no influence on well-chromatographed peaks. Therefore, optimized chromatography is required for proper GC×GC data alignment. Based on these observations, a workflow is presented for the conservative selection of biomarker candidates from untargeted metabolomics analyses. Copyright © 2015 Elsevier B.V. All rights reserved.

The stonehenge technique: a new method of crystal alignment for coherent bremsstrahlung experiments

Science.gov (United States)

Livingston, Kenneth

2005-08-01

In the coherent bremsstrahlung technique a thin diamond crystal oriented correctly in an electron beam can produce photons with a high degree of linear polarization.1 The crystal is mounted on a goniometer to control its orientation and it is necessary to measure the angular offsets a) between the crystal axes and the goniometer axes and b) between the goniometer and the electron beam axis. A method for measuring these offsets and aligning the crystal was developed by Lohman et al, and has been used successfully in Mainz.2 However, recent attempts to investigate new crystals have shown that this approach has limitations which become more serious at higher beam energies where more accurate setting of the crystal angles, which scale with l/Ebeam, is required. (Eg. the recent installation of coherent bremsstrahlung facility at Jlab, with Ebeam = 6 GeV ) This paper describes a new, more general alignment technique, which overcomes these limitations. The technique is based on scans where the horizontal and vertical rotation axes of the goniometer are adjusted in a series of steps to make the normal to the crystal describe a cone of a given angle. For each step in the scan, the photon energy spectrum is measured using a tagging spectrometer, and the offsets between the electron beam and the crystal lattice are inferred from the resulting 2D plot. Using this method, it is possible to align the crystal with the beam quickly, and hence to set any desired orientation of the crystal relative to the beam. This is essential for any experiment requiring linearly polarized photons produced via coherent bremsstrahlung, and is also required for a systematic study of the channeling radiation produced by the electron beam incident on the crystal.

Heuristics for multiobjective multiple sequence alignment.

Science.gov (United States)

Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B

2016-07-15

Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity. Choosing only one parameter setting may provide an undesirable bias in further steps of the analysis and give too simplistic interpretations. In this work, we reformulate multiple sequence alignment from a multiobjective point of view. The goal is to generate several sequence alignments that represent a trade-off between maximizing the substitution score and minimizing the number of indels/gaps in the sum-of-pairs score function. This trade-off gives to the practitioner further information about the similarity of the sequences, from which she could analyse and choose the most plausible alignment. We introduce several heuristic approaches, based on local search procedures, that compute a set of sequence alignments, which are representative of the trade-off between the two objectives (substitution score and indels). Several algorithm design options are discussed and analysed, with particular emphasis on the influence of the starting alignment and neighborhood search definitions on the overall performance. A perturbation technique is proposed to improve the local search, which provides a wide range of high-quality alignments. The proposed approach is tested experimentally on a wide range of instances. We performed several experiments with sequences obtained from the benchmark database BAliBASE 3.0. To evaluate the quality of the results, we calculate the hypervolume indicator of the set of score vectors returned by the algorithms. The results obtained allow us to identify reasonably good choices of parameters for our approach. Further, we compared our method in terms of correctly aligned pairs ratio and columns correctly aligned ratio with respect to reference alignments. Experimental results show

Crab cavities for linear colliders

CERN Document Server

Burt, G; Carter, R; Dexter, A; Tahir, I; Beard, C; Dykes, M; Goudket, P; Kalinin, A; Ma, L; McIntosh, P; Shulte, D; Jones, Roger M; Bellantoni, L; Chase, B; Church, M; Khabouline, T; Latina, A; Adolphsen, C; Li, Z; Seryi, Andrei; Xiao, L

2008-01-01

Crab cavities have been proposed for a wide number of accelerators and interest in crab cavities has recently increased after the successful operation of a pair of crab cavities in KEK-B. In particular crab cavities are required for both the ILC and CLIC linear colliders for bunch alignment. Consideration of bunch structure and size constraints favour a 3.9 GHz superconducting, multi-cell cavity as the solution for ILC, whilst bunch structure and beam-loading considerations suggest an X-band copper travelling wave structure for CLIC. These two cavity solutions are very different in design but share complex design issues. Phase stabilisation, beam loading, wakefields and mode damping are fundamental issues for these crab cavities. Requirements and potential design solutions will be discussed for both colliders.

Magnetic field-aligned particle precipitation

International Nuclear Information System (INIS)

Carlson, W.

1985-01-01

Magnetic field-aligned particle fluxes are a common auroral phenomenon. Precipitating field-aligned electrons are seen in the vicinity of auroral arcs as suprathermal bursts, as well as superimposed on the more isotropic inverted V electron precipitation. Electron distribution functions reveal two distinct source populations for the inverted V and field-aligned electron components, and also suggest possible acceleration mechanisms. The inverted V electrons are a hot, boundary plasma sheet population that gains the full parallel acceleration. The field-aligned component appears to originate from cold ionospheric electrons that may be distributed throughout the acceleration region. A turbulent parallel field might explain the apparent lifetime of cold electrons in the acceleration region

Sales Territory Alignment: A Review and Model

OpenAIRE

Andris A. Zoltners; Prabhakant Sinha

1983-01-01

The sales territory alignment problem may be viewed as the problem of grouping small geographic sales coverage units into larger geographic clusters called sales territories in a way that the sales territories are acceptable according to managerially relevant alignment criteria. This paper first reviews sales territory alignment models which have appeared in the marketing literature. A framework for sales territory alignment and several properties of a good sales territory alignment are devel...

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.

Beam-based alignment and tuning procedures for e+e- collider final focus systems

International Nuclear Information System (INIS)

Bulos, F.; Burke, D.; Helm, R.; Irwin, J.; Odian, A.; Roy, G.; Ruth, R.; Yamamoto, N.

1991-05-01

For future linear colliders, with very small emittances and beam sizes and demanding tolerances on final focus system alignment and magnet errors, it becomes increasingly important to use the beam as a diagnostic tool. We report here procedures we have identified and will be implemented in the Final Focus Test Beam at SLAC incorporating (1) quadrupole strength changes, (2) central orbit modifications, (3) spot size measurements, and (4) beam stability monitoring. 3 refs., 4 figs., 3 tabs

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

Science.gov (United States)

Löytynoja, Ari

2012-01-01

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

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel

Directory of Open Access Journals (Sweden)

Alachiotis Nikolaos

2012-08-01

Full Text Available Abstract Background Aligning short DNA reads to a reference sequence alignment is a prerequisite for detecting their biological origin and analyzing them in a phylogenetic context. With the PaPaRa tool we introduced a dedicated dynamic programming algorithm for simultaneously aligning short reads to reference alignments and corresponding evolutionary reference trees. The algorithm aligns short reads to phylogenetic profiles that correspond to the branches of such a reference tree. The algorithm needs to perform an immense number of pairwise alignments. Therefore, we explore vector intrinsics and GPUs to accelerate the PaPaRa alignment kernel. Results We optimized and parallelized PaPaRa on CPUs and GPUs. Via SSE 4.1 SIMD (Single Instruction, Multiple Data intrinsics for x86 SIMD architectures and multi-threading, we obtained a 9-fold acceleration on a single core as well as linear speedups with respect to the number of cores. The peak CPU performance amounts to 18.1 GCUPS (Giga Cell Updates per Second using all four physical cores on an Intel i7 2600 CPU running at 3.4 GHz. The average CPU performance (averaged over all test runs is 12.33 GCUPS. We also used OpenCL to execute PaPaRa on a GPU SIMT (Single Instruction, Multiple Threads architecture. A NVIDIA GeForce 560 GPU delivered peak and average performance of 22.1 and 18.4 GCUPS respectively. Finally, we combined the SIMD and SIMT implementations into a hybrid CPU-GPU system that achieved an accumulated peak performance of 33.8 GCUPS. Conclusions This accelerated version of PaPaRa (available at http://www.exelixis-lab.org/software.html provides a significant performance improvement that allows for analyzing larger datasets in less time. We observe that state-of-the-art SIMD and SIMT architectures deliver comparable performance for this dynamic programming kernel when the “competing programmer approach” is deployed. Finally, we show that overall performance can be substantially increased

Field-aligned current density versus electric potential characteristics for magnetospheric flux tubes

International Nuclear Information System (INIS)

Lemaire, J.; Scherer, M.

1983-01-01

The field-aligned current density (Jsub(tot)) is a non-linear function of the applied potential difference (phi) between the ionosphere and the magnetosphere. This nonlinear function has been calculated for plasma boundary conditions typical in a dayside cusp magnetic flux tube. The J-characteristic of such a flux tube changes when the temperatures of the warm magnetospheric electrons and of the cold ionospheric electrons are modified; it changes also when the relative density of the warm plasma is modified; the presence of trapped secondary electrons changes also the J-characteristic. The partial currents contributed by the warm and cold electrons, and by warm and cold ions are illustrated. The dynamic characteristic of an electric circuit depends on the static characteristic of each component of the sytem: i.e. the resistive ionosphere, the return current region, and the region of particle precipitation whose field-aligned current/voltage characteristics have been studied in this article

Alignment of galaxy spins in the vicinity of voids

International Nuclear Information System (INIS)

Slosar, Anže; White, Martin

2009-01-01

We provide limits on the alignment of galaxy orientations with the direction to the void center for galaxies lying near the edges of voids. We locate spherical voids in volume limited samples of galaxies from the Sloan Digital Sky Survey using the HB inspired void finder and investigate the orientation of (color selected) spiral galaxies that are nearly edge-on or face-on. In contrast with previous literature, we find no statistical evidence for departure from random orientations. Expressed in terms of the parameter c, introduced by Lee and Pen to describe the strength of such an alignment, we find that c0.11(0.13) at 95% (99.7%) confidence limit within a context of a toy model that assumes a perfectly spherical voids with sharp boundaries

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].

High precision mirror alignment mechanism for use in synchrotron radiation beamlines

International Nuclear Information System (INIS)

Verma, Adu; Srivastava, P.K.; Das, Suraj; Nookaraju, Mogali

2009-01-01

The performance of a synchrotron radiation beamline is highly depends on parameters, crucially on the manufacturing accuracies of the optical elements and very good alignment of optical elements in the beam path. To develop a synchrotron beamline the misalignment effects have to be estimated and the mechanical components that hold optical elements have to be designed and developed within the specified tolerance limits. The translational inaccuracies result in shifting the image spot, which affect the flux throughput. The misorientation errors i.e. the rotation of optical elements about their mean position affects the image quality. The horizontal misorientation i.e. the rotation of an optical element about an axis passing through its centre and perpendicular to the plane containing the mirror has the most sever effect on the spectral resolution of the beamline, because of an increase in the dispersive spot size at the image plane. The design development and testing of a high precision mirror alignment mechanism is reported in this abstract. Though this mirror alignment mechanism is developed for the X-ray diffraction beamline on synchrotron radiation source Indus-2, 2.5 GeV, 300 mA, the design is general purpose and can be adapted for any other synchrotron facility or a similar ultra high vacuum environment. The mirror alignment mechanism is based on a constrained kinematic chain which provides the angular motions about three co-ordinate axes in the range of 0 to ±1° with the backlash free resolution of 1 arc second. The linear motions in three orthogonal directions are performed by other kinematic mounts in the range of 0 to ± 10 mm with a fine adjustment of 10 μm. The motions are transferred from air to ultra high vacuum through bellows. The ultra high vacuum chamber has been designed, fabricated and tested as per the ASME code. The rotational motions of the mirror alignment mechanism has been tested using a laser interferometer. (author)

Development of an Eccentric CAM Based Active Pre-Alignment System for the CLIC Main Beam Quadrupole Magnet

CERN Document Server

Lackner, F; Collette, C; Mainaud Durand, H; Hauviller, C; Kemppinen, J; Leuxe, R

2010-01-01

CLIC (Compact Linear Collider) is a study for a future electron-positron collider that would allow physicists to explore a new energy region beyond the capabilities of today's particle accelerators. The demanding transverse and vertical beam sizes and emittance specifications are resulting in stringent alignment and a nanometre stability requirement. In the current feasibility study, the main beam quadrupole magnets have to be actively pre-aligned with a precision of 1 µm in 5 degrees of freedom (d.o.f.) before being mechanically stabilized to the nm scale above 1 Hz. This contribution describes the approach of performing this active pre-alignment based on an eccentric cam system. In order to limit the amplification of the vibration sources at resonant frequencies a sufficiently high Eigenfrequency is required. Therefore the contact region between cam and support was optimized for adequate stiffness based on the Hertzian theory. Furthermore, practical tests performed on a single degree of freedom mock-up wil...

Fitting boxes to Manhattan scenes using linear integer programming

KAUST Repository

Li, Minglei

2016-02-19

We propose an approach for automatic generation of building models by assembling a set of boxes using a Manhattan-world assumption. The method first aligns the point cloud with a per-building local coordinate system, and then fits axis-aligned planes to the point cloud through an iterative regularization process. The refined planes partition the space of the data into a series of compact cubic cells (candidate boxes) spanning the entire 3D space of the input data. We then choose to approximate the target building by the assembly of a subset of these candidate boxes using a binary linear programming formulation. The objective function is designed to maximize the point cloud coverage and the compactness of the final model. Finally, all selected boxes are merged into a lightweight polygonal mesh model, which is suitable for interactive visualization of large scale urban scenes. Experimental results and a comparison with state-of-the-art methods demonstrate the effectiveness of the proposed framework.

Robustness of average Stokes polarimetry characterization of digitally addressed parallel-aligned LCoS displays

OpenAIRE

Martínez Guardiola, Francisco Javier; Márquez Ruiz, Andrés; Gallego Rico, Sergi; Ortuño Sánchez, Manuel; Francés Monllor, Jorge; Beléndez Vázquez, Augusto; Pascual Villalobos, Inmaculada

2014-01-01

Parallel-aligned liquid crystal on silicon (PA-LCoS) displays have become the most attractive spatial light modulator device for a wide range of applications, due to their superior resolution and light efficiency, added to their phase-only capability. Recently we proposed a novel polarimetric method, based on Stokes polarimetry, enabling the characterization of their linear retardance and the magnitude of their associated phase fluctuations, if existent, as it happens in most of digital backp...

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 aligns...... is so high that it took more than a decade before the first implementation of a Sankoff style algorithm was published. However, with the faster computers available today and the improved heuristics used in the implementations the Sankoff-based methods have become practical. This chapter describes...... 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....

Fixture for aligning motor assembly

Science.gov (United States)

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

2009-12-08

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

Proposition d'une méthode d'alignement de l'accélérateur linéaire CLIC

CERN Document Server

Touzé, Thomas; Mainaud-Durand, H

2011-01-01

The compact linear collider (CLIC) is the particles accelerator project proposed by the european organization for nuclear research (CERN) for high energy physics after the large hadron collider (LHC). Because of the nanometric scale of the CLIC leptons beams, the emittance growth budget is very tight. It induces alignment tolerances on the positions of the CLIC components that have never been achieved. The last step of the CLIC alignment will be done according to the beam itself. It falls within the competence of the physicists. However, in order to implement the beam-based feedback, a challenging pre-alignment is required : 10 μm at 3σ along a 200 m sliding window. For such a precision, the proposed solution must be compatible with a feedback between the measurement and repositioning systems. The CLIC pre-alignment will have to be active. This thesis does not demonstrate the feasibility of the CLIC active prealignment but shows the way to the last developments that have to be done for that purpose. A metho...

Flow-induced endothelial cell alignment requires the RhoGEF Trio as a scaffold protein to polarize active Rac1 distribution

NARCIS (Netherlands)

Kroon, Jeffrey; Heemskerk, Niels; Kalsbeek, Martin J. T.; de Waard, Vivian; van Rijssel, Jos; van Buul, Jaap D.

2017-01-01

Endothelial cells line the lumen of the vessel wall and are exposed to flow. In linear parts of the vessel, the endothelial cells experience laminar flow, resulting in endothelial cell alignment in the direction of flow, thereby protecting the vessel wall from inflammation and permeability. In order

Flexible SiO2 cantilevers for torsional self-aligning micro scale four-point probes

DEFF Research Database (Denmark)

Kjær, Daniel; Gammelgaard, Lauge; Bøggild, Peter

2007-01-01

In order to successfully measure the conductivity of a sample with a four- point probe, good alignment of the electrodes to the sample is important to establish even contact pressure and contact areas of the electrodes. By incorporating a hinge in a microfabricated SiO2 mono- cantilever the ability...

Interaction of low-intensity linearly polarized laser radiation with living tissues: effects on tissular acceleration of skin wound healing

International Nuclear Information System (INIS)

Ribeiro, Martha Simoes

2000-01-01

According to the Maxwell's equations to optical properties of surfaces, the energy deposition efficiency in a microroughness interface depends on the electrical field polarization component. Considering a linearly polarized beam, this efficiency will depend on the roughness parameters to p-polarized light and it will not depend on such parameters to s-polarized light. In this work it was investigated the effects of low-intensity, linearly polarized He-Ne laser beam on skin wounds healing, considering two orthogonal directions of polarization. We have considered a preferential axis as the animals' spinal column and we aligned the linear laser polarization first parallel, then perpendicular to this direction. Burns about 6 mm in diameter were created with liquid N 2 on the back of the animals and the lesions were irradiated on days 3, 7, 10 and 14 post-wounding, D= 1,0 J/cm 2 . Control lesions were not irradiated. The theoretical model consisted in describing linearly polarized light propagation in biological tissues using transport theory. The degree of polarization was measured in normal and pathological skin samples. It was verified that linearly polarized light can survive in the superficial layers of skin and it can be more preserved in skin under pathological condition when compared with health skin. The analysis of skin wound healing process has demonstrated that the relative direction of the laser polarization plays an important role on the wound healing process by light microscopy, transmission electron microscopy and radioautography. (author)

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.

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.

Alignment of dipole magnet in micro-beam line of HIRFL

International Nuclear Information System (INIS)

Wang Shaoming; Chen Wenjun; Yang Shengli; Cai Guozhu; Guo Yizhen; Zhou Guangming; Man Kaidi; Song Mingtao

2010-01-01

Microbeam irradiation facility is an experiment platform, which can reduce the beam-spot on the irradiated sample to micrometer level, and can accurately locate and count the radioactive particles. It is a powerful research tool for the irradiation material science, irradiation biology, irradiation biomedicine and micro mechanical machining. The microbeam irradiation facility requires the precise work for installation and alignment. These conditions make magnet's change for directions and positions because the location space of dipole magnets in micro-beam line of HIRFL (Heavy Ion Research Facility in Lanzhou) is very small. It is a challenge for the installation and alignment work of magnets. It was solved by transforming coordinates of benchmarks of magnets, which controlled the error of magnet setup within error tolerance range. (authors)

Structural anisotropy of magnetically aligned single wall carbon nanotube films

International Nuclear Information System (INIS)

Smith, B. W.; Benes, Z.; Luzzi, D. E.; Fischer, J. E.; Walters, D. A.; Casavant, M. J.; Schmidt, J.; Smalley, R. E.

2000-01-01

Thick films of aligned single wall carbon nanotubes and ropes have been produced by filtration/deposition from suspension in strong magnetic fields. We measured mosaic distributions of rope orientations in the film plane, for samples of different thicknesses. For an ∼1 μm film the full width at half maximum (FWHM) derived from electron diffraction is 25 degree sign -28 degree sign . The FWHM of a thicker film (∼7 μm) measured by x-ray diffraction is slightly broader, 35±3 degree sign . Aligned films are denser than ordinary filter-deposited ones, and much denser than as-grown material. Optimization of the process is expected to yield smaller FWHMs and higher densities. (c) 2000 American Institute of Physics

Electronic properties of field aligned CrO2 powders

International Nuclear Information System (INIS)

Tripathy, D.; Adeyeye, A.O.

2005-01-01

We have investigated in detail the electronic transport properties of half metallic CrO 2 powder-based devices, fabricated using optical lithography and field alignment technique. A transition in the conduction mechanism from spin-dependent intergranular tunneling to inelastic hopping was observed at 215 K. This transition temperature shifts to 230 K in the presence of 10 kOe field cooling due to reduction of the spin-independent hopping conductance channel. I-V characteristics exhibit strong temperature dependence and are non-linear even at room temperature. Our experimental results are in good agreement with a simple theoretical model. A novel 'double switching' phenomenon was observed in the I-V curves below the transition temperature

Aligning with New Digital Strategy

DEFF Research Database (Denmark)

Yeow, Adrian; Soh, Christina; Hansen, Rina

2018-01-01

Prior IS research has not fully addressed the aligning process in the highly dynamic context of digital strategy. To address this gap, we conduct a longitudinal analysis of a B2B company's journey to enact its B2C digital strategy, using the dynamic capabilities approach. We found...... that as an organization shifts towards a digital strategy, misalignments between the emergent strategy and resources give rise to tension. Our study resulted in the development of an aligning process model that is comprised of three phases (exploratory, building, and extending) and generalizable organizational aligning...... actions that form the organization's sensing, seizing, and transforming capacities. These aligning actions iteratively reconfigured organizational resources and refined strategy in order to respond to both changes in the environment and internal tensions. We also recognized that there are challenges...

Antares automatic beam alignment system

International Nuclear Information System (INIS)

Appert, Q.; Swann, T.; Sweatt, W.; Saxman, A.

1980-01-01

Antares is a 24-beam-line CO 2 laser system for controlled fusion research, under construction at Los Alamos Scientific Laboratory (LASL). Rapid automatic alignment of this system is required prior to each experiment shot. The alignment requirements, operational constraints, and a developed prototype system are discussed. A visible-wavelength alignment technique is employed that uses a telescope/TV system to view point light sources appropriately located down the beamline. Auto-alignment is accomplished by means of a video centroid tracker, which determines the off-axis error of the point sources. The error is nulled by computer-driven, movable mirrors in a closed-loop system. The light sources are fiber-optic terminations located at key points in the optics path, primarily at the center of large copper mirrors, and remotely illuminated to reduce heating effects

Bi axially textured YBCO coated tape prepared using dynamic magnetic grain alignment

International Nuclear Information System (INIS)

Genoud, Jean-Yves; Quinton, William

1999-01-01

A new magnetic grain alignment technique has been applied to produce bi axially aligned YBCO coated tapes. A bi axially aligned dispersion of orthorhombic Y 2 Ba 4 Cu 7 O 15 (Y-247) powder was settled on un textured silver substrates. The Y-247 tapes were then melt processed to achieve high critical current YBa 2 Cu 3 O 7 (Y-123) tapes with CuO as a secondary phase. The biaxial alignment is preserved after the densification process and a clear enhancement of J c relative to identically prepared un textured or uniaxially textured samples is obtained. Critical current densities of up to 5000 A cm -2 at 77 K in self-field and 1500 A cm -2 in 0.5 T magnetic field at 65 K were obtained in films from 20 to 40 μm thick. Problems were experienced in achieving fully densified thick films while retaining biaxial texture. The initial grain size distribution was found to have a major influence on the final microstructure. Provided significant improvements in J c can be obtained this method offers an alternative to coated tape processes based on epitaxial growth which has the advantage that it does not require textured substrates. The biaxial alignment technique described here intrinsically acts on the bulk material rather than at surfaces. This offers the possibility of texturing without thickness limitations. (author)

FACT. Bokeh alignment for Cherenkov telescopes

Energy Technology Data Exchange (ETDEWEB)

Mueller, Sebastian Achim [ETH Zurich (Switzerland); Buss, Jens [TU Dortmund (Germany)

2016-07-01

Imaging Atmospheric Cherenkov Telescopes (IACTs) need fast and large imaging optics to map the faint Cherenkov light emitted in cosmic ray air showers onto their image sensors. Segmented reflectors are inexpensive, lightweight and offer good image quality. However, alignment of the mirror facets remains a challenge. A good alignment is crucial in IACT observations to separate gamma rays from hadronic cosmic rays. We present a simple, yet extendable method, to align segmented reflectors using their Bokeh. Bokeh alignment does not need a star or good weather nights but can be done anytime, even during the day. Bokeh alignment optimizes the facet orientations by comparing the segmented reflector's Bokeh to a predefined template. The Bokeh is observed using the out of focus image of a nearby point like light source in a distance of about ten times the focal lengths. We introduce Bokeh alignment on segmented reflectors and present its use on the First Geiger-mode Avalanche Cherenkov Telescope (FACT) on Canary Island La Palma, as well as on the Cherenkov Telescope Array (CTA) Medium Size Telescope (MST) prototype in Berlin Adlershof.

Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

Directory of Open Access Journals (Sweden)

Inês Soares

2012-01-01

Full Text Available The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions. In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L—L-words—in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

Balanced sampling